[phenixbb] Resolution Limits in the transition from AutoMR to AutoBuild

17 Dec 2007

      The structure factors that I downloaded from the PDB for my
little MR project contains both reflections behind the beam stop
and reflections of higher resolution than even the original authors
would use.  When setting up the MR I entered the more restrictive
resolution limits into the Wizard and Phaser appears to have obeyed.

    As near as I can tell from the log files, however, Resolve is
using all the data in the rebuild.  I am including a copy of the
log file from the "best" refinement.  I would prefer that only
data between 30 and 2.2A were used but it is clear that the
refinement is, at least, monitoring the fit to all the data. I
am presuming that the program is refining against the same data
it is monitoring.

    I would like to suggest that either the log file be clearer
about the resolution limits it is actually refining to, or the
plumbing that passes the resolution limits from the AutoMR wizard
to the AutoBuild wizard be checked.

Dale Tronrud

P.S. That's all my problems... For now.  The project I'm working
on is cursed and brings out the worst in all the software I have
used.

AutoBuild_run_3_/TEMP0/LIG_EDITED_EDITED_edit_model.pdb
  Monomer Library directory:
    "/usr/local/phenix-1.3b-rc6/ext_ref_files/mon_lib"
  Total number of atoms: 6255
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 6255
      Number of chains: 4
        Number of residues, atoms: 352, 2697
          Classifications: {'peptide': 352}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 16, 'TRANS': 333, 'PCIS': 2}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLN:plan2': 2, 'GLN%COO:plan2': 1, 'GLN%COO:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 26
        Number of residues, atoms: 352, 2694
          Classifications: {'peptide': 352}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 17, 'TRANS': 333, 'PCIS': 1}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLN:plan2': 2, 'GLN%COO:plan2': 1, 'GLN%COO:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 34
        Number of residues, atoms: 7, 432
          Unusual residues: {'BCL': 7}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 146
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 12
        Number of residues, atoms: 7, 432
          Unusual residues: {'BCL': 7}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 146
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 12
  Time building chain proxies: 8.94, per 1000 atoms: 1.43

================================== X-ray data =================================

F-obs:
  AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz:FP,SIGFP

R-free flags:
  AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz:FreeR_flag

Miller array info: AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz:FP,SIGFP
Observation type: xray.amplitude
Type of data: double, size=38159
Type of sigmas: double, size=38159
Number of Miller indices: 38159
Anomalous flag: False
Unit cell: (169.1, 169.1, 169.1, 90, 90, 90)
Space group: P 43 3 2 (No. 212)
Systematic absences: 0
Centric reflections: 4505
Resolution range: 75.6238 2.14896
Completeness in resolution range: 0.839637
Completeness with d_max=infinity: 0.8396

Number of F-obs in resolution range:                   38159
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  75.6238
                             d_min =   2.1490

Miller array info: AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz:FreeR_flag
Observation type: None
Type of data: int, size=38159
Type of sigmas: None
Number of Miller indices: 38159
Anomalous flag: False
Unit cell: (169.1, 169.1, 169.1, 90, 90, 90)
Space group: P 43 3 2 (No. 212)
Systematic absences: 0
Centric reflections: 4505
Resolution range: 75.6238 2.14896
Completeness in resolution range: 0.839637
Completeness with d_max=infinity: 0.8396

Test (R-free flags) flag value: 0

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 75.6707 -  4.6295 [4755/4893]  4536   219   4.6%
  bin  2:  4.6295 -  3.6746 [4493/4607]  4248   245   5.5%
  bin  3:  3.6746 -  3.2101 [4414/4577]  4178   236   5.3%
  bin  4:  3.2101 -  2.9166 [4232/4498]  4007   225   5.3%
  bin  5:  2.9166 -  2.7075 [4221/4533]  4026   195   4.6%
  bin  6:  2.7075 -  2.5479 [4005/4483]  3792   213   5.3%
  bin  7:  2.5479 -  2.4203 [3811/4480]  3637   174   4.6%
  bin  8:  2.4203 -  2.3149 [3223/4472]  3066   157   4.9%
  bin  9:  2.3149 -  2.2258 [2846/4459]  2702   144   5.1%
  bin 10:  2.2258 -  2.1490 [2159/4445]  2042   117   5.4%
                                overall 36234  1925   5.0%

No array of experimental phases found.

========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.40 seconds
  Histogram of bond lengths:
        1.12 -     1.26: 957
        1.26 -     1.40: 1621
        1.40 -     1.55: 3702
        1.55 -     1.69: 131
        1.69 -     1.83: 23
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " O1A BCL B   6 " - " CGA BCL B   6 " 1.212  1.117  0.095 2.50e+03 2.25e+01
  " O1A BCL D   6 " - " CGA BCL D   6 " 1.212  1.118  0.094 2.50e+03 2.22e+01
  " C15 BCL D   6 " - " C16 BCL D   6 " 1.540  1.459  0.081 2.50e+03 1.63e+01
  " C15 BCL B   6 " - " C16 BCL B   6 " 1.540  1.460  0.080 2.50e+03 1.60e+01
  " N   PRO A 188 " - " CD  PRO A 188 " 1.473  1.418  0.055 5.10e+03 1.56e+01
  ... (remaining 6429 not shown)
  Histogram of nonbonded interaction distances:
        1.49 -     2.17: 9
        2.17 -     2.85: 1981
        2.85 -     3.53: 8408
        3.53 -     4.22: 16251
        4.22 -     4.90: 27426
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OG  SER A  24 " - " C   GLY C  23 "  1.486 3.270
  " OG  SER A  24 " - " N   SER C  24 "  1.747 3.120
  " OH  TYR A 330 " - " OE1 GLN C 333 "  1.870 3.040 x-1/4,-z-1/4,y+1/4
  " C   ASN A 121 " - " N   LEU A 122 "  1.941 3.350 x+1,y+1,z+1
  " OG  SER A  24 " - " O   GLY C  23 "  1.956 3.040
  ... (remaining 54070 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.73: 1959
       22.73 -    45.46: 198
       45.46 -    68.20: 68
       68.20 -    90.93: 27
       90.93 -   113.66: 1
  Dihedral angle restraints sorted by residual:
  " CA  ALA C 327 "
  " C   ALA C 327 "
  " N   PRO C 328 "
  " CA  PRO C 328 "
      ideal   model   delta periodicty    weight residual
     180.00  -66.34 -113.66     1       4.00e-02 5.17e+02
  " C2B BCL D   7 "
  " C3B BCL D   7 "
  " CAB BCL D   7 "
  " OBB BCL D   7 "
      ideal   model   delta periodicty    weight residual
       0.00  147.16   32.84     2       4.00e-02 4.31e+01
  " C2B BCL B   7 "
  " C3B BCL B   7 "
  " CAB BCL B   7 "
  " OBB BCL B   7 "
      ideal   model   delta periodicty    weight residual
       0.00  147.20   32.80     2       4.00e-02 4.30e+01
  ... (remaining 2250 not shown)

==================== Fixing bad ADP in input model (if any) ===================

============================== Scattering factors =============================

                ----------X-ray scattering dictionary----------                

Number of scattering types: 4
  Type Number    sf(0)   Gaussians
   S      14     15.96       2
   O    1076      7.97       2
   N    1007      6.97       2
   C    4158      5.97       2
  sf(0) = scattering factor at diffraction angle 0.

====================== Modifying start model if requested =====================

atom_attributes_list is modified in-place to define missing element types when possible.

==================== Fixing bad ADP in input model (if any) ===================

================== Extract refinement strategy and selections =================

individual_sites       = True
rigid_body             = False
individual_adp         = True
group_adp              = False
tls                    = False
individual_occupancies = False
group_occupancies      = False
group_anomalous        = False
size = 6255

n_use            =  6255
n_use_u_iso      =  6255
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  6255

==================== Process input NCS or/and find new NCS ====================

NCS groups found in parameter file: 0

Automatic NCS search:
Chains in this PDB file:  ['A', 'C']
GROUPS BASED ON QUICK COMPARISON: []
Looking for invariant domains for ...: ['A', 'C'] [[[9, 366]], [[9, 366]]]

Updated/new NCS groups: 
refinement.ncs.restraint_group {
  reference = chain A and (resseq 9:118 or resseq 128:207 or resseq 215:366 )
  selection = chain C and (resseq 9:118 or resseq 128:207 or resseq 215:366 )
}

                  ----------Building NCS restraints----------                  

NCS restraint group 1:
  NCS operator 1:
    Reference selection: "chain A and (resseq 9:118 or resseq 128:207 or resseq 215:366 )"
        Other selection: "chain C and (resseq 9:118 or resseq 128:207 or resseq 215:366 )"
    Number of atom pairs: 2603
    Rotation={{-0.999509, -0.0190423, 0.0248896},
              {0.0243783, 0.0266261, 0.999348},
              {-0.0196926, 0.999464, -0.0261488}}
    Translation={{38.5072}, {-44.0643}, {42.3394}}
    Histogram of differences:
      0.001760 - 0.701888: 2552
      0.701888 - 1.402017: 14
      1.402017 - 2.102145: 22
      2.102145 - 2.802274: 6
      2.802274 - 3.502402: 4
      3.502402 - 4.202531: 5
    RMS difference with respect to the reference: 0.312576

=================== Write initial parameters into .eff file ===================

============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  input {
    pdb {
      file_name = "/usr/users/dale/structure/fmo-ct/tronrud_2007/AutoBuild_run_3_/TEMP0/LIG_EDITED_EDITED_edit_model.pdb"
    }
    xray_data {
      file_name = "AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz"
      labels = "FP,SIGFP"
      high_resolution = 2.2
      r_free_flags {
        file_name = "AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz"
        label = "FreeR_flag"
        test_flag_value = 0
      }
    }
    monomers {
      file_name = "/usr/users/dale/geometry/chromophores/bcl_tnt.cif"
    }
  }
  output {
    prefix = "AutoBuild_run_3_/TEMP0/Build_composite_refined_side_3"
    serial = 1
    write_eff_file = False
    write_geo_file = False
    write_def_file = False
    export_final_f_model = *mtz cns
    write_maps = False
  }
  main {
    ordered_solvent = True
    ncs = True
    use_experimental_phases = False
    random_seed = 516344
  }
  ncs {
    special_position_warnings_only = True
    restraint_group {
      reference = "chain A and (resseq 9:118 or resseq 128:207 or resseq 215:366 )"
      selection = "chain C and (resseq 9:118 or resseq 128:207 or resseq 215:366 )"
    }
  }
  ordered_solvent {
    low_resolution = 3
  }
  mask {
    ignore_zero_occupancy_atoms = False
  }
}
#phil __OFF__

============================= ml refinement start =============================

   ----------structure factors based statistics (before refinement)----------  

                         ----------X-ray data----------                        

|--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------|
|                                                                             |
| r_work= 0.3243   r_free= 0.3131   ksol= 0.00   Bsol= 0.00   scale= 1.698    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 7.754289                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 75.6707 -  5.1788 0.97   3272  159 0.4168 0.3905      8.6988      8.5536|
|  2:  5.1788 -  4.1106 0.98   3112  155 0.2200 0.2341      8.4215      8.4968|
|  3:  4.1106 -  3.5910 0.97   3000  188 0.2279 0.2321      8.1284      8.1202|
|  4:  3.5910 -  3.2627 0.97   2977  168 0.2388 0.2465      7.9459      8.0053|
|  5:  3.2627 -  3.0288 0.95   2930  152 0.2747 0.2878      7.8061      7.8021|
|  6:  3.0288 -  2.8502 0.93   2844  159 0.2741 0.2804      7.6418      7.6974|
|  7:  2.8502 -  2.7075 0.93   2860  139 0.2757 0.3123      7.5349      7.6274|
|  8:  2.7075 -  2.5896 0.89   2705  156 0.2878 0.3340       7.453      7.4977|
|  9:  2.5896 -  2.4899 0.89   2715  135 0.2982 0.3356      7.3586      7.5621|
| 10:  2.4899 -  2.4040 0.81   2488  115 0.3089 0.3543      7.3181      7.3706|
| 11:  2.4040 -  2.3288 0.72   2176  109 0.3142 0.3613      7.3041      7.3373|
| 12:  2.3288 -  2.2623 0.67   2018  110 0.3096 0.3293      7.3086      7.3357|
| 13:  2.2623 -  2.2027 0.58   1742  104 0.3370 0.3823      7.3303       7.508|
| 14:  2.2027 -  2.1490 0.46   1395   76 0.3749 0.3710      7.4161      7.4587|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 75.6707 -  5.1788  3272   159  0.64  39.15   1.16     1.12    4689001.73|
|  2:  5.1788 -  4.1106  3112   155  0.79  26.44   2.03     1.66    3059064.97|
|  3:  4.1106 -  3.5910  3000   188  0.82  24.63   2.13     1.94    1936112.07|
|  4:  3.5910 -  3.2627  2977   168  0.81  25.88   2.18     2.02    1377840.11|
|  5:  3.2627 -  3.0288  2930   152  0.78  28.52   2.16     2.01    1065329.57|
|  6:  3.0288 -  2.8502  2844   159  0.76  30.45   2.06     1.97     856549.95|
|  7:  2.8502 -  2.7075  2860   139  0.77  30.05   2.04     1.88     690049.30|
|  8:  2.7075 -  2.5896  2705   156  0.75  31.56   1.99     1.78     594991.98|
|  9:  2.5896 -  2.4899  2715   135  0.72  34.01   1.90     1.74     528160.82|
| 10:  2.4899 -  2.4040  2488   115  0.71  35.26   1.94     1.68     488836.19|
| 11:  2.4040 -  2.3288  2176   109  0.72  34.25   1.95     1.68     443633.67|
| 12:  2.3288 -  2.2623  2018   110  0.73  33.21   1.92     1.64     434086.87|
| 13:  2.2623 -  2.2027  1742   104  0.67  39.14   2.01     1.62     524747.84|
| 14:  2.2027 -  2.1490  1395    76  0.56  47.31   2.05     1.54     720558.54|
|alpha:            min =        1.12 max =            2.02 mean =         1.74|
|beta:             min =   434086.87 max =      4689001.73 mean =   1388851.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.74|
|phase err.(work): min =        0.00 max =           89.94 mean =        31.97|
|phase err.(test): min =        0.00 max =           89.63 mean =        32.13|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 2
beamstop_shadow_outliers = 6
total                    = 8

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.037420             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.336   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.231372              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.656   (deg)                 |
|-----------------------------------------------------------------------------|

        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.009:  4797 |   0.000 -   2.504:  7924 |  1.486 -  1.828:        2 |
| 0.009 - 0.019:  1097 |   2.504 -   5.009:   655 |  1.828 -  2.169:        7 |
| 0.019 - 0.028:   284 |   5.009 -   7.513:   145 |  2.169 -  2.511:       30 |
| 0.028 - 0.038:   144 |   7.513 -  10.018:    40 |  2.511 -  2.852:     1951 |
| 0.038 - 0.047:    61 |  10.018 -  12.522:     8 |  2.852 -  3.193:     3550 |
| 0.047 - 0.057:    31 |  12.522 -  15.026:     4 |  3.193 -  3.535:     4858 |
| 0.057 - 0.066:    13 |  15.026 -  17.531:     2 |  3.535 -  3.876:     8239 |
| 0.066 - 0.076:     3 |  17.531 -  20.035:     0 |  3.876 -  4.217:     8012 |
| 0.076 - 0.085:     2 |  20.035 -  22.539:     0 |  4.217 -  4.559:    11917 |
| 0.085 - 0.095:     2 |  22.539 -  25.044:     1 |  4.559 -  4.900:    15509 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     6434 |   0.012    0.095  0.000 |       0.323 |              |
|     angle |     8779 |   1.693   25.044  0.000 |       0.420 |              |
| chirality |      905 |   0.089    0.406  0.000 |       0.199 |        0.156 |
| planarity |      977 |   0.007    0.154  0.000 |       0.242 |              |
|  dihedral |     2253 |  17.723  113.659  0.001 |       1.614 |              |
| nonbonded |     6434 |   4.142    4.900  1.486 |       0.255 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 25.121)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 6255   0      7.67    118.66  27.52    None  None   None       |
|    all(noH): 6255   0      7.67    118.66  27.52    None  None   None       |
|    Sol.    : 0      0      None    None    None     None  None   None       |
|    Mac.    : 6255   0      7.67    118.66  27.52    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     7.670 -  18.769: 1649   |   5:    63.165 -  74.264:  119        |
|      1:    18.769 -  29.868: 2973   |   6:    74.264 -  85.363:   80        |
|      2:    29.868 -  40.967:  840   |   7:    85.363 -  96.462:   50        |
|      3:    40.967 -  52.066:  296   |   8:    96.462 - 107.561:   28        |
|      4:    52.066 -  63.165:  198   |   9:   107.561 - 118.660:   22        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.47   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 3 *************************

|--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------|
|                                                                             |
| r_work= 0.3243   r_free= 0.3131   ksol= 0.00   Bsol= 0.00   scale= 1.698    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 7.754289                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------|
|                                                                             |
| r_work= 0.2582   r_free= 0.2742   ksol= 0.35   Bsol= 50.00   scale= 2.164   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.32,2.32,2.32,0.00,0.00,-0.00); trace/3= 2.32                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 7.690252                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.750300             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.207   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.205411              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.015   (deg)                 |
|-----------------------------------------------------------------------------|

================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2582      final r-factor (work) = 0.2348          |
| start r-factor (free) = 0.2742      final r-factor (free) = 0.2713          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.5209 = 10.75 * 0.50 * 7.7632 + 1.00 * 0.7926                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.1803 = 10.75 * 0.50 * 7.6326 + 1.00 * 0.1541                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================

                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2348      final r-factor (work) = 0.2216          |
| start r-factor (free) = 0.2713      final r-factor (free) = 0.2676          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5745 = 0.21 * 1.00 * 7.6326 + 1.00 * 0.0067                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5631 = 0.21 * 1.00 * 7.5874 + 1.00 * 0.0045                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 25.121)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 6255   0      0.00    117.10  26.33    None  None   None       |
|    all(noH): 6255   0      0.00    117.10  26.33    None  None   None       |
|    Sol.    : 0      0      None    None    None     None  None   None       |
|    Mac.    : 6255   0      0.00    117.10  26.33    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.710:  203   |   5:    58.550 -  70.260:  136        |
|      1:    11.710 -  23.420: 3284   |   6:    70.260 -  81.969:   72        |
|      2:    23.420 -  35.130: 1811   |   7:    81.969 -  93.679:   42        |
|      3:    35.130 -  46.840:  395   |   8:    93.679 - 105.389:   25        |
|      4:    46.840 -  58.550:  266   |   9:   105.389 - 117.099:   21        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 2 OF 3 *************************

|--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------|
|                                                                             |
| r_work= 0.2216   r_free= 0.2676   ksol= 0.35   Bsol= 50.00   scale= 2.155   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.32,2.32,2.32,0.00,0.00,-0.00); trace/3= 2.32                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 7.578854                   |
|-----------------------------------------------------------------------------|

================== ordered solvent: location/analysis/update ==================

Start model:
  number           = 0      
  b_iso_min        =    None (limit = 1.00)
  b_iso_max        =    None (limit = 50.00)
  b_iso_mean       =    None             
  occupancy_min    =    None (limit = 0.10)
  occupancy_max    =    None (limit = 1.20)
  dist_sol_mol_min =    None (limit = 1.80)
  dist_sol_mol_max =    None (limit = 6.00)
Peak search:
   maximum allowed number of peaks:           6250
   number of peaks from mFobs-DFmodel map:  449
   number of peaks from 2mFobs-DFmodel map: 2500
   number of peaks after clustering:          392
Filter by distance & map next to the model:
   mapped sites are within: 0.520 - 5.987 
   number of sites selected in [dist_min= 1.80, dist_max= 6.00]: 291 from: 392
   mapped sites are within: 1.816 - 5.987 
Peak filtering (peak - peak close contact elimination):
   peaks rejected:                  0
   total number of peaks selected:  291
Final model:
  number           = 291    
  b_iso_min        = 26.33   (limit = 1.00)
  b_iso_max        = 26.33   (limit = 50.00)
  b_iso_mean       = 26.33               
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.20)
  dist_sol_mol_min = 1.82    (limit = 1.80)
  dist_sol_mol_max = 5.99    (limit = 6.00)

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------|
|                                                                             |
| r_work= 0.2037   r_free= 0.2379   ksol= 0.34   Bsol= 50.00   scale= 2.123   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.43,2.43,2.43,0.00,0.00,-0.00); trace/3= 2.43                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 7.486761                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.888030              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.803  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.171233              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.753  (deg)                 |
|-----------------------------------------------------------------------------|

================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2037      final r-factor (work) = 0.1944          |
| start r-factor (free) = 0.2379      final r-factor (free) = 0.2423          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.1593 = 6.89 * 0.50 * 7.5465 + 1.00 * 0.1690                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.8504 = 6.89 * 0.50 * 7.4673 + 1.00 * 0.1330                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================

                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1944      final r-factor (work) = 0.1882          |
| start r-factor (free) = 0.2423      final r-factor (free) = 0.2396          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2834 = 0.17 * 1.00 * 7.4673 + 1.00 * 0.0047                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2813 = 0.17 * 1.00 * 7.4563 + 1.00 * 0.0045                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 25.121)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 6546   0      2.33    119.19  25.98    None  None   None       |
|    all(noH): 6546   0      2.33    119.19  25.98    None  None   None       |
|    Sol.    : 291    0      3.23    59.44   29.93    None  None   None       |
|    Mac.    : 6255   0      2.33    119.19  25.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.330 -  14.016:  627   |   5:    60.762 -  72.449:  124        |
|      1:    14.016 -  25.703: 3737   |   6:    72.449 -  84.135:   75        |
|      2:    25.703 -  37.389: 1297   |   7:    84.135 -  95.822:   35        |
|      3:    37.389 -  49.076:  396   |   8:    95.822 - 107.508:   18        |
|      4:    49.076 -  60.762:  219   |   9:   107.508 - 119.195:   18        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 3 OF 3 *************************

|--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------|
|                                                                             |
| r_work= 0.1882   r_free= 0.2396   ksol= 0.34   Bsol= 50.00   scale= 2.114   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.43,2.43,2.43,0.00,0.00,-0.00); trace/3= 2.43                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 7.449879                   |
|-----------------------------------------------------------------------------|

================== ordered solvent: location/analysis/update ==================

Start model:
  number           = 291    
  b_iso_min        = 3.23    (limit = 1.00)
  b_iso_max        = 59.44   (limit = 50.00)
  b_iso_mean       = 29.93               
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.20)
  dist_sol_mol_min = 2.06    (limit = 1.80)
  dist_sol_mol_max = 5.96    (limit = 6.00)
Peak search:
   maximum allowed number of peaks:           6250
   number of peaks from mFobs-DFmodel map:  420
   number of peaks from 2mFobs-DFmodel map: 2405
   number of peaks after clustering:          300
Filter by distance & map next to the model:
   mapped sites are within: 0.214 - 5.940 
   number of sites selected in [dist_min= 1.80, dist_max= 6.00]: 118 from: 300
   mapped sites are within: 1.802 - 5.940 
Peak filtering (peak - peak close contact elimination):
   peaks rejected:                  0
   total number of peaks selected:  118
Final model:
  number           = 398    
  b_iso_min        = 3.23    (limit = 1.00)
  b_iso_max        = 49.81   (limit = 50.00)
  b_iso_mean       = 28.22               
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.20)
  dist_sol_mol_min = 1.80    (limit = 1.80)
  dist_sol_mol_max = 5.96    (limit = 6.00)

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------|
|                                                                             |
| r_work= 0.1875   r_free= 0.2312   ksol= 0.33   Bsol= 50.00   scale= 2.126   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.18,3.18,3.18,0.00,0.00,-0.00); trace/3= 3.18                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 7.433926                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.792070              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 137.678  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.173077              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.742  (deg)                 |
|-----------------------------------------------------------------------------|

================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1875      final r-factor (work) = 0.1857          |
| start r-factor (free) = 0.2312      final r-factor (free) = 0.2341          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.0062 = 4.79 * 0.50 * 7.4550 + 1.00 * 0.1437                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.9146 = 4.79 * 0.50 * 7.4304 + 1.00 * 0.1110                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================

                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1857      final r-factor (work) = 0.1818          |
| start r-factor (free) = 0.2341      final r-factor (free) = 0.2331          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2906 = 0.17 * 1.00 * 7.4304 + 1.00 * 0.0046                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2897 = 0.17 * 1.00 * 7.4228 + 1.00 * 0.0050                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 25.121)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 6653   0      0.00    118.91  25.71    None  None   None       |
|    all(noH): 6653   0      0.00    118.91  25.71    None  None   None       |
|    Sol.    : 398    0      0.00    55.54   31.76    None  None   None       |
|    Mac.    : 6255   0      2.01    118.91  25.32    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.891:  364   |   5:    59.455 -  71.345:  131        |
|      1:    11.891 -  23.782: 3643   |   6:    71.345 -  83.236:   75        |
|      2:    23.782 -  35.673: 1625   |   7:    83.236 -  95.127:   43        |
|      3:    35.673 -  47.564:  492   |   8:    95.127 - 107.018:   20        |
|      4:    47.564 -  59.455:  243   |   9:   107.018 - 118.909:   17        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

======================= ordered solvent: final clean up =======================

Start model:
  number           = 398    
  b_iso_min        = 0.00    (limit = 1.00)
  b_iso_max        = 55.54   (limit = 50.00)
  b_iso_mean       = 31.76               
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.20)
  dist_sol_mol_min = 2.05    (limit = 1.80)
  dist_sol_mol_max = 5.96    (limit = 6.00)
Final model:
  number           = 388    
  b_iso_min        = 3.51    (limit = 1.00)
  b_iso_max        = 49.97   (limit = 50.00)
  b_iso_mean       = 31.36               
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.20)
  dist_sol_mol_min = 2.05    (limit = 1.80)
  dist_sol_mol_max = 5.96    (limit = 6.00)

                         ----------X-ray data----------                        

|--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------|
|                                                                             |
| r_work= 0.1831   r_free= 0.2329   ksol= 0.33   Bsol= 50.00   scale= 2.114   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.18,3.18,3.18,0.00,0.00,-0.00); trace/3= 3.18                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 7.422958                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 75.6707 -  5.1788 0.97   3272  159 0.2130 0.2552      8.1276       8.228|
|  2:  5.1788 -  4.1106 0.98   3112  155 0.1356 0.1644      7.8761      8.0672|
|  3:  4.1106 -  3.5910 0.97   3000  188 0.1468 0.1750      7.7387      7.8215|
|  4:  3.5910 -  3.2627 0.97   2977  168 0.1558 0.1979      7.5865      7.8088|
|  5:  3.2627 -  3.0288 0.95   2930  152 0.1709 0.2266      7.4557      7.5858|
|  6:  3.0288 -  2.8502 0.93   2844  159 0.1755 0.2362      7.2991      7.4461|
|  7:  2.8502 -  2.7075 0.93   2860  139 0.1762 0.2620      7.2285      7.4876|
|  8:  2.7075 -  2.5896 0.89   2705  156 0.1910 0.2717      7.1596      7.3038|
|  9:  2.5896 -  2.4899 0.89   2715  135 0.2060 0.2556      7.0999      7.3902|
| 10:  2.4899 -  2.4040 0.81   2488  115 0.2115 0.3023      7.0774      7.2784|
| 11:  2.4040 -  2.3288 0.72   2176  109 0.2299 0.3153      7.0902      7.1912|
| 12:  2.3288 -  2.2623 0.67   2018  110 0.2312 0.2806      7.1132      7.2823|
| 13:  2.2623 -  2.2027 0.58   1742  104 0.2705 0.3734       7.181       7.532|
| 14:  2.2027 -  2.1490 0.46   1395   76 0.3164 0.3752       7.339       7.432|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 75.6707 -  5.1788  3272   159  0.84  21.52   2.03     1.91    1706271.76|
|  2:  5.1788 -  4.1106  3112   155  0.92  13.72   2.19     2.12    1119490.86|
|  3:  4.1106 -  3.5910  3000   188  0.90  16.33   2.16     2.10     948218.23|
|  4:  3.5910 -  3.2627  2977   168  0.88  18.25   2.15     2.06     723060.91|
|  5:  3.2627 -  3.0288  2930   152  0.86  20.64   2.12     2.04     602696.08|
|  6:  3.0288 -  2.8502  2844   159  0.85  21.95   2.09     2.03     469088.14|
|  7:  2.8502 -  2.7075  2860   139  0.84  22.75   2.07     2.01     423879.11|
|  8:  2.7075 -  2.5896  2705   156  0.83  23.91   2.02     1.89     364459.47|
|  9:  2.5896 -  2.4899  2715   135  0.80  26.95   1.96     1.80     333699.76|
| 10:  2.4899 -  2.4040  2488   115  0.80  26.92   1.99     1.83     318772.98|
| 11:  2.4040 -  2.3288  2176   109  0.80  27.04   2.01     1.79     305463.63|
| 12:  2.3288 -  2.2623  2018   110  0.81  26.41   2.04     1.78     298736.36|
| 13:  2.2623 -  2.2027  1742   104  0.76  30.75   2.14     1.86     366985.74|
| 14:  2.2027 -  2.1490  1395    76  0.63  41.90   2.25     1.80     624233.56|
|alpha:            min =        1.78 max =            2.12 mean =         1.95|
|beta:             min =   298736.36 max =      1706271.76 mean =    657914.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.84|
|phase err.(work): min =        0.00 max =           90.00 mean =        23.00|
|phase err.(test): min =        0.00 max =           89.39 mean =        23.30|
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------|
|                                                                             |
| r_work= 0.1826   r_free= 0.2324   ksol= 0.34   Bsol= 65.65   scale= 2.111   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,-0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 7.421608                   |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------|
|                                                                             |
| r_work= 0.1826   r_free= 0.2324   ksol= 0.34   Bsol= 65.65   scale= 2.111   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,-0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 7.421608                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 75.6707 -  5.1788 0.97   3272  159 0.2125 0.2562      8.1276        8.23|
|  2:  5.1788 -  4.1106 0.98   3112  155 0.1356 0.1646      7.8765      8.0679|
|  3:  4.1106 -  3.5910 0.97   3000  188 0.1471 0.1753      7.7395      7.8223|
|  4:  3.5910 -  3.2627 0.97   2977  168 0.1557 0.1975      7.5862      7.8097|
|  5:  3.2627 -  3.0288 0.95   2930  152 0.1700 0.2270      7.4544      7.5859|
|  6:  3.0288 -  2.8502 0.93   2844  159 0.1744 0.2359      7.2964      7.4451|
|  7:  2.8502 -  2.7075 0.93   2860  139 0.1754 0.2619       7.227      7.4839|
|  8:  2.7075 -  2.5896 0.89   2705  156 0.1902 0.2712      7.1561      7.3014|
|  9:  2.5896 -  2.4899 0.89   2715  135 0.2054 0.2548      7.0962      7.3838|
| 10:  2.4899 -  2.4040 0.81   2488  115 0.2109 0.3026      7.0744      7.2786|
| 11:  2.4040 -  2.3288 0.72   2176  109 0.2295 0.3132       7.088      7.1878|
| 12:  2.3288 -  2.2623 0.67   2018  110 0.2309 0.2813       7.112      7.2824|
| 13:  2.2623 -  2.2027 0.58   1742  104 0.2704 0.3724      7.1801      7.5313|
| 14:  2.2027 -  2.1490 0.46   1395   76 0.3163 0.3749      7.3386       7.432|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 75.6707 -  5.1788  3272   159  0.83  21.68   2.02     1.90    1729678.56|
|  2:  5.1788 -  4.1106  3112   155  0.92  13.76   2.19     2.11    1122862.76|
|  3:  4.1106 -  3.5910  3000   188  0.90  16.38   2.16     2.10     950321.91|
|  4:  3.5910 -  3.2627  2977   168  0.88  18.29   2.16     2.07     725331.21|
|  5:  3.2627 -  3.0288  2930   152  0.86  20.71   2.13     2.04     606450.12|
|  6:  3.0288 -  2.8502  2844   159  0.85  22.01   2.10     2.04     469766.50|
|  7:  2.8502 -  2.7075  2860   139  0.84  22.78   2.08     2.02     424394.38|
|  8:  2.7075 -  2.5896  2705   156  0.83  23.83   2.03     1.89     361907.39|
|  9:  2.5896 -  2.4899  2715   135  0.80  26.81   1.97     1.81     330530.78|
| 10:  2.4899 -  2.4040  2488   115  0.80  26.80   1.99     1.84     316100.00|
| 11:  2.4040 -  2.3288  2176   109  0.80  26.93   2.01     1.80     303267.90|
| 12:  2.3288 -  2.2623  2018   110  0.81  26.36   2.05     1.79     297871.94|
| 13:  2.2623 -  2.2027  1742   104  0.76  30.68   2.15     1.87     365788.30|
| 14:  2.2027 -  2.1490  1395    76  0.63  41.83   2.25     1.81     622797.66|
|alpha:            min =        1.79 max =            2.11 mean =         1.95|
|beta:             min =   297871.94 max =      1729678.56 mean =    660171.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.84|
|phase err.(work): min =        0.00 max =           89.91 mean =        23.00|
|phase err.(test): min =        0.00 max =           89.92 mean =        23.31|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 25.121)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 6643   0      5.23    122.12  28.89    None  None   None       |
|    all(noH): 6643   0      5.23    122.12  28.89    None  None   None       |
|    Sol.    : 388    0      6.73    53.19   34.57    None  None   None       |
|    Mac.    : 6255   0      5.23    122.12  28.54    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.229 -  16.918:  693   |   5:    63.676 -  75.366:  120        |
|      1:    16.918 -  28.608: 3694   |   6:    75.366 -  87.055:   73        |
|      2:    28.608 -  40.297: 1313   |   7:    87.055 -  98.744:   43        |
|      3:    40.297 -  51.987:  450   |   8:    98.744 - 110.434:   19        |
|      4:    51.987 -  63.676:  221   |   9:   110.434 - 122.123:   17        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

================= overall refinement statistics: step by step =================

****************** REFINEMENT STATISTICS STEP BY STEP ******************
leading digit, like 1_, means number of macro-cycle                     
0    : statistics at the very beginning when nothing is done yet        
1_bss: bulk solvent correction and/or (anisotropic) scaling             
1_xyz: refinement of coordinates                                        
1_adp: refinement of ADPs (Atomic Displacement Parameters)              
1_wat: ordered solvent update (add / remove)                            
------------------------------------------------------------------------
 R-factors, x-ray target values and norm of gradient of x-ray target
 stage     r-work r-free  xray_target_w  xray_target_t
   0    :  0.3243 0.3131   7.754289e+00   7.797944e+00
   1_bss:  0.2582 0.2742   7.690252e+00   7.754360e+00
   1_xyz:  0.2348 0.2713   7.623999e+00   7.734510e+00
   1_adp:  0.2216 0.2676   7.578854e+00   7.714267e+00
   2_bss:  0.2037 0.2379   7.486761e+00   7.615026e+00
   2_xyz:  0.1944 0.2423   7.473436e+00   7.629683e+00
   2_adp:  0.1882 0.2396   7.449879e+00   7.620893e+00
   3_bss:  0.1875 0.2312   7.433926e+00   7.596287e+00
   3_xyz:  0.1857 0.2341   7.435421e+00   7.607941e+00
   3_adp:  0.1818 0.2331   7.418785e+00   7.599553e+00
   3_bss:  0.1826 0.2324   7.421608e+00   7.597030e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.347  50.000   2.318   2.318   2.318   0.000   0.000  -0.000
   1_xyz:  0.347  50.000   2.318   2.318   2.318   0.000   0.000  -0.000
   1_adp:  0.347  50.000   2.318   2.318   2.318   0.000   0.000  -0.000
   2_bss:  0.337  50.000   2.425   2.425   2.425   0.000   0.000  -0.000
   2_xyz:  0.337  50.000   2.425   2.425   2.425   0.000   0.000  -0.000
   2_adp:  0.337  50.000   2.425   2.425   2.425   0.000   0.000  -0.000
   3_bss:  0.335  50.000   3.181   3.181   3.181   0.000   0.000  -0.000
   3_xyz:  0.335  50.000   3.181   3.181   3.181   0.000   0.000  -0.000
   3_adp:  0.335  50.000   3.181   3.181   3.181   0.000   0.000  -0.000
   3_bss:  0.337  65.653   0.000   0.000   0.000   0.000   0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  31.982 0.7396  1.7443  1387840.945
   1_bss:  29.194 0.7699  1.9599   974799.679
   1_xyz:  28.118 0.7819  1.9866   928279.367
   1_adp:  27.348 0.7902  1.9633   892955.282
   2_bss:  24.199 0.8225  1.9720   689127.593
   2_xyz:  24.569 0.8186  1.9572   710017.017
   2_adp:  23.913 0.8260  1.9393   697946.465
   3_bss:  23.043 0.8347  1.9776   647848.901
   3_xyz:  23.264 0.8326  1.9689   664228.536
   3_adp:  22.951 0.8359  1.9502   655975.202
   3_bss:  23.013 0.8352  1.9517   659994.149
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.693  0.012  0.089 17.723  0.007  4.142   1.5608e-01
   1_bss:   1.693  0.012  0.089 17.723  0.007  4.142   1.5608e-01
   1_xyz:   1.635  0.010  0.087 18.407  0.008  4.141   1.4451e-01
   1_adp:   1.635  0.010  0.087 18.407  0.008  4.141   1.4451e-01
   2_bss:   1.635  0.010  0.087 18.407  0.008  4.135   1.6105e-01
   2_xyz:   1.421  0.009  0.083 18.369  0.007  4.141   1.2821e-01
   2_adp:   1.421  0.009  0.083 18.369  0.007  4.141   1.2821e-01
   3_bss:   1.421  0.009  0.083 18.369  0.007  4.136   1.3974e-01
   3_xyz:   1.283  0.007  0.075 17.946  0.007  4.138   1.0907e-01
   3_adp:   1.283  0.007  0.075 17.946  0.007  4.138   1.0907e-01
   3_bss:   1.283  0.007  0.075 17.946  0.007  4.138   1.0822e-01
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  25.044  0.095  0.406113.659  0.154  1.486   1.5120e-01
   1_bss:  25.044  0.095  0.406113.659  0.154  1.486   1.5120e-01
   1_xyz:  25.658  0.089  0.312115.970  0.157  1.921   6.5351e-02
   1_adp:  25.658  0.089  0.312115.970  0.157  1.921   6.5351e-02
   2_bss:  25.658  0.089  0.312115.970  0.157  1.816   6.3368e-02
   2_xyz:  23.516  0.082  0.391119.400  0.155  1.926   4.8056e-02
   2_adp:  23.516  0.082  0.391119.400  0.155  1.926   4.8056e-02
   3_bss:  23.516  0.082  0.391119.400  0.155  1.802   4.8972e-02
   3_xyz:  23.841  0.048  0.338113.663  0.152  1.976   3.4188e-02
   3_adp:  23.841  0.048  0.338113.663  0.152  1.976   3.4188e-02
   3_bss:  23.841  0.048  0.338113.663  0.152  1.976   3.4255e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    : 118.66   7.67  27.52 117.10   0.00  26.33  26.33  26.33  26.33
   1_bss: 118.66   7.67  27.52 117.10   0.00  26.33  26.33  26.33  26.33
   1_xyz: 118.66   7.67  27.52 119.19   2.33  25.79  59.44   3.23  29.93
   1_adp: 117.10   0.00  26.33 119.19   2.33  25.79  49.81   3.23  28.22
   2_bss: 117.10   0.00  26.33 119.19   2.33  25.79  49.81   3.23  28.22
   2_xyz: 117.10   0.00  26.33 118.91   2.01  25.32  55.54   0.00  31.76
   2_adp: 119.19   2.33  25.98 122.12   5.23  28.54  53.19   6.73  34.57
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    2.308    0.002    0.111
   1_adp:    2.308    0.002    0.111
   2_bss:    2.308    0.002    0.111
   2_xyz:    2.461    0.002    0.117
   2_adp:    2.461    0.002    0.117
   3_bss:    2.461    0.002    0.117
   3_xyz:    2.748    0.003    0.122
   3_adp:    2.748    0.003    0.122
   3_bss:    2.748    0.003    0.122
------------------------------------------------------------------------
 stage  number of ordered solvent
     0    :                0
     1_bss:                0
     1_xyz:                0
     1_adp:                0
     2_bss:              291
     2_xyz:              291
     2_adp:              291
     3_bss:              398
     3_xyz:              398
     3_adp:              398
     3_bss:              388
------------------------------------------------------------------------

===================== NCS restraints at end of refinement =====================

NCS restraint group 1:
  NCS operator 1:
    Reference selection: "chain A and (resseq 9:118 or resseq 128:207 or resseq 215:366 )"
        Other selection: "chain C and (resseq 9:118 or resseq 128:207 or resseq 215:366 )"
    Number of atom pairs: 2603
    Rotation={{-0.999497, -0.0191321, 0.0252909},
              {0.0247831, 0.0263321, 0.999346},
              {-0.0197855, 0.99947, -0.0258447}}
    Translation={{38.4881}, {-44.0747}, {42.34}}
    Histogram of differences:
      0.002570 - 0.054938: 2350
      0.054938 - 0.107305: 233
      0.107305 - 0.159673: 16
      0.159673 - 0.212040: 2
      0.212040 - 0.264408: 1
      0.264408 - 0.316775: 1
    RMS difference with respect to the reference: 0.037521
Writing refined structure to PDB file:
  AutoBuild_run_3_/TEMP0/Build_composite_refined_side_3.pdb
n_use            =  6643
n_use_u_iso      =  6643
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  6643
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  6643

Writing map coefficients to MTZ file:
  /usr/users/dale/structure/fmo-ct/tronrud_2007/AutoBuild_run_3_/TEMP0/Build_composite_refined_side_3_001_map_coeffs.mtz

Writing refined fmodel to MTZ file:
  /usr/users/dale/structure/fmo-ct/tronrud_2007/AutoBuild_run_3_/TEMP0/Build_composite_refined_side_3_001_f_model.mtz

# Date 2007/12/14 11:38:03
Final R(work) = 0.1826, R(free) = 0.2324