Starting phenix.real_space_refine
on Sun May 19 16:31:06 2024 by afonine
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7un3_26612.map
  Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7un3_26612.pdb

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    run=minimization_global
    c_beta_restraints=False
    ramachandran_plot_restraints.enabled=False
    secondary_structure.enabled=False
    resolution=3.5

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7un3_26612.map"
    default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7un3_26612.map"
    model {
      file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7un3_26612.pdb"
    }
    default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7un3_26612.pdb"
  }
  resolution = 3.5
  refinement {
    run = *minimization_global rigid_body local_grid_search morphing \
          simulated_annealing adp occupancy nqh_flips
  }
  pdb_interpretation {
    secondary_structure {
      enabled = False
    }
    c_beta_restraints = False
    ramachandran_plot_restraints {
      enabled = False
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.026 sd=   0.153
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      41      5.16       5
     C    6056      2.51       5
     N    1605      2.21       5
     O    1738      1.98       5
     H    9482      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE  292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE  574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE  584": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE 1256": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B TYR  106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B PHE  218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C TYR  110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C PHE  212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C PHE  300": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib"
  Total number of atoms: 18922
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "D"
      Number of atoms: 1193
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1193
          Classifications: {'peptide': 73}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "A"
      Number of atoms: 10424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 649, 10424
          Inner-chain residues flagged as termini: ['pdbres="HIS A  83 "', 'pdbres="VAL A 122 "', 'pdbres="TYR A 241 "', 'pdbres="PHE A 260 "', 'pdbres="PHE A 313 "', 'pdbres="VAL A 321 "', 'pdbres="LEU A 339 "', 'pdbres="ASP A 343 "', 'pdbres="PRO A 358 "', 'pdbres="ASP A 542 "', 'pdbres="GLY A 663 "', 'pdbres="GLU A 675 "', 'pdbres="ILE A 710 "', 'pdbres="VAL A 928 "', 'pdbres="THR A1046 "', 'pdbres="ARG A1054 "', 'pdbres="LEU A1152 "', 'pdbres="PRO A1252 "']
          Classifications: {'peptide': 649}
          Modifications used: {'COO': 10, 'NH2': 1, 'NH3': 9}
          Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 611}
          Chain breaks: 9
    Chain: "B"
      Number of atoms: 3686
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 3686
          Inner-chain residues flagged as termini: ['pdbres="ILE B 121 "', 'pdbres="PRO B 164 "', 'pdbres="VAL B 306 "', 'pdbres="ILE B 319 "']
          Classifications: {'peptide': 223}
          Modifications used: {'COO': 3, 'NH2': 1, 'NH3': 2}
          Link IDs: {'PTRANS': 12, 'TRANS': 210}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 3619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 3619
          Inner-chain residues flagged as termini: ['pdbres="ASN C 122 "', 'pdbres="GLY C 166 "', 'pdbres="VAL C 306 "', 'pdbres="ASP C 315 "']
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 3, 'NH3': 3}
          Link IDs: {'PTRANS': 11, 'TRANS': 207}
          Chain breaks: 2
  Time building chain proxies: 3.03, per 1000 atoms: 0.16
  Number of scatterers: 18922
  At special positions: 0
  Unit cell: (84.975, 114.675, 142.725, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      41     16.00
     O    1738      8.00
     N    1605      7.00
     C    6056      6.00
     H    9482      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 5.51
  Conformation dependent library (CDL) restraints added in 736.5 milliseconds
  
  Time building geometry restraints manager: 6.08 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.98 -     1.15: 9462
        1.15 -     1.31: 1597
        1.31 -     1.48: 3812
        1.48 -     1.65: 4200
        1.65 -     1.82: 62
  Bond restraints: 19133
  Sorted by residual:
  bond pdb=" N   CYS A1025 "
       pdb=" H   CYS A1025 "
    ideal  model  delta    sigma   weight residual
    0.860  1.027 -0.167 2.00e-02 2.50e+03 6.94e+01
  bond pdb=" N   ASP A 144 "
       pdb=" H   ASP A 144 "
    ideal  model  delta    sigma   weight residual
    0.860  1.025 -0.165 2.00e-02 2.50e+03 6.79e+01
  bond pdb=" N   ARG B 337 "
       pdb=" H   ARG B 337 "
    ideal  model  delta    sigma   weight residual
    0.860  1.024 -0.164 2.00e-02 2.50e+03 6.72e+01
  bond pdb=" N   GLU A1081 "
       pdb=" H   GLU A1081 "
    ideal  model  delta    sigma   weight residual
    0.860  1.024 -0.164 2.00e-02 2.50e+03 6.70e+01
  bond pdb=" N   ASP A 151 "
       pdb=" H   ASP A 151 "
    ideal  model  delta    sigma   weight residual
    0.860  1.023 -0.163 2.00e-02 2.50e+03 6.64e+01
  ... (remaining 19128 not shown)

  Histogram of bond angle deviations from ideal:
      100.23 -   106.99: 422
      106.99 -   113.74: 22868
      113.74 -   120.50: 6186
      120.50 -   127.25: 5082
      127.25 -   134.01: 112
  Bond angle restraints: 34670
  Sorted by residual:
  angle pdb=" C   ALA A 695 "
        pdb=" CA  ALA A 695 "
        pdb=" CB  ALA A 695 "
      ideal   model   delta    sigma   weight residual
     117.23  111.62    5.61 1.36e+00 5.41e-01 1.70e+01
  angle pdb=" CA  ALA A 695 "
        pdb=" C   ALA A 695 "
        pdb=" N   ASP A 696 "
      ideal   model   delta    sigma   weight residual
     119.98  117.43    2.55 8.50e-01 1.38e+00 9.00e+00
  angle pdb=" N   GLN B 111 "
        pdb=" CA  GLN B 111 "
        pdb=" C   GLN B 111 "
      ideal   model   delta    sigma   weight residual
     109.81  114.20   -4.39 2.21e+00 2.05e-01 3.95e+00
  angle pdb=" CA  GLN B 111 "
        pdb=" C   GLN B 111 "
        pdb=" N   PRO B 112 "
      ideal   model   delta    sigma   weight residual
     118.44  121.37   -2.93 1.59e+00 3.96e-01 3.39e+00
  angle pdb=" N   ASN A 581 "
        pdb=" CA  ASN A 581 "
        pdb=" CB  ASN A 581 "
      ideal   model   delta    sigma   weight residual
     114.27  111.25    3.02 1.64e+00 3.72e-01 3.39e+00
  ... (remaining 34665 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.29: 5958
       17.29 -    34.58: 571
       34.58 -    51.87: 172
       51.87 -    69.16: 46
       69.16 -    86.45: 8
  Dihedral angle restraints: 6755
    sinusoidal: 4897
      harmonic: 1858
  Sorted by residual:
  dihedral pdb=" CA  PHE B 224 "
           pdb=" C   PHE B 224 "
           pdb=" N   THR B 225 "
           pdb=" CA  THR B 225 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.31  -16.69     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CA  ARG B 333 "
           pdb=" C   ARG B 333 "
           pdb=" N   ILE B 334 "
           pdb=" CA  ILE B 334 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.32  -16.68     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CG  LYS A 217 "
           pdb=" CD  LYS A 217 "
           pdb=" CE  LYS A 217 "
           pdb=" NZ  LYS A 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  124.91   55.09     3      1.50e+01 4.44e-03 9.33e+00
  ... (remaining 6752 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 924
       0.031 -    0.061: 306
       0.061 -    0.092: 114
       0.092 -    0.123: 81
       0.123 -    0.154: 16
  Chirality restraints: 1441
  Sorted by residual:
  chirality pdb=" CA  ILE A1254 "
            pdb=" N   ILE A1254 "
            pdb=" C   ILE A1254 "
            pdb=" CB  ILE A1254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.90e-01
  chirality pdb=" CA  ILE A 660 "
            pdb=" N   ILE A 660 "
            pdb=" C   ILE A 660 "
            pdb=" CB  ILE A 660 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.44e-01
  chirality pdb=" CA  ILE B 199 "
            pdb=" N   ILE B 199 "
            pdb=" C   ILE B 199 "
            pdb=" CB  ILE B 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.05e-01
  ... (remaining 1438 not shown)

  Planarity restraints: 2768
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 111 "   -0.030 5.00e-02 4.00e+02   4.57e-02 3.35e+00
        pdb=" N   PRO B 112 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B 112 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 112 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A1256 "    0.029 5.00e-02 4.00e+02   4.43e-02 3.13e+00
        pdb=" N   PRO A1257 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A1257 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A1257 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 190 "    0.026 5.00e-02 4.00e+02   3.94e-02 2.48e+00
        pdb=" N   PRO B 191 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO B 191 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 191 "    0.022 5.00e-02 4.00e+02
  ... (remaining 2765 not shown)

  Histogram of nonbonded interaction distances:
        1.41 -     2.05: 1095
        2.05 -     2.69: 27749
        2.69 -     3.32: 56693
        3.32 -     3.96: 73935
        3.96 -     4.60: 108567
  Nonbonded interactions: 268039
  Sorted by model distance:
  nonbonded pdb=" HH  TYR A 643 "
            pdb=" OE1 GLU A1102 "
     model   vdw
     1.412 1.850
  nonbonded pdb=" O   TYR A 203 "
            pdb=" H   LEU A 339 "
     model   vdw
     1.413 1.850
  nonbonded pdb=" H   GLY A 263 "
            pdb=" O   VAL A 296 "
     model   vdw
     1.481 1.850
  nonbonded pdb=" OD1 ASN C 226 "
            pdb=" H   ASP C 261 "
     model   vdw
     1.487 1.850
  nonbonded pdb=" O   VAL B 178 "
            pdb=" H   SER B 182 "
     model   vdw
     1.502 1.850
  ... (remaining 268034 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 73 through 120 or (resid 121 and (name N or name CA or nam \ 
e C or name O or name CB or name CG1 or name CG2 or name CD1 or name H or name H \ 
A or name HB or name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or \ 
 name HD11 or name HD12 or name HD13)) or (resid 166 and (name N or name CA or n \ 
ame C or name O or name HA2 or name HA3)) or resid 167 through 187 or (resid 188 \ 
 and (name N or name CA or name C or name O or name CB or name CG or name ND1 or \ 
 name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 o \ 
r name HD1 or name HD2 or name HE1)) or resid 189 through 306 or (resid 319 and  \ 
(name N or name CA or name C or name O or name CB or name CG1 or name CG2 or nam \ 
e CD1 or name HA or name HB or name HG12 or name HG13 or name HG21 or name HG22  \ 
or name HG23 or name HD11 or name HD12 or name HD13)) or resid 320 through 342)) \ 

  selection = (chain 'C' and (resid 73 through 99 or (resid 100 and (name N or name CA or name \ 
 C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ 
E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name  \ 
HE2)) or resid 101 through 121 or (resid 166 and (name N or name CA or name C or \ 
 name O or name HA2 or name HA3)) or resid 167 through 306 or (resid 319 and (na \ 
me N or name CA or name C or name O or name CB or name CG1 or name CG2 or name C \ 
D1 or name HA or name HB or name HG12 or name HG13 or name HG21 or name HG22 or  \ 
name HG23 or name HD11 or name HD12 or name HD13)) or resid 320 through 341 or ( \ 
resid 342 and (name N or name CA or name C or name O or name CB or name CG or na \ 
me CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H or name HA or na \ 
me HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ )) \ 
))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 5
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.50
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will not be refined
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.100
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     18.710
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:20.570
  Internal consistency checks:             0.000
  Total:   40.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6102
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9651  Z= 0.113
  Angle     :  0.528   5.608  13050  Z= 0.283
  Chirality :  0.043   0.154   1441
  Planarity :  0.004   0.046   1682
  Dihedral  : 12.824  86.452   3630
  Min Nonbonded Distance : 1.791

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.89 %
    Favored  : 98.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.24), residues: 1130
  helix:  0.05 (0.28), residues: 308
  sheet: -0.86 (0.32), residues: 248
  loop : -1.51 (0.25), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  72 
 TYR   0.013   0.001   TYR A1100 
 PHE   0.011   0.001   PHE A 622 
 TRP   0.008   0.001   TRP B 171 
 HIS   0.004   0.001   HIS B 328 

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    6.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    7.9990
   chunk 100 optimal weight:    6.9990
   overall best weight:    6.5990

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6418
moved from start:          0.1507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   9651  Z= 0.234
  Angle     :  0.595   6.666  13050  Z= 0.311
  Chirality :  0.056   0.246   1441
  Planarity :  0.005   0.048   1682
  Dihedral  : 12.222  84.953   3630
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.62 %
    Allowed  : 10.09 %
    Favored  : 89.29 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  2.37 %
    Favored  : 97.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.66 (0.21), residues: 1130
  helix: -2.40 (0.22), residues: 291
  sheet: -1.95 (0.30), residues: 254
  loop : -2.68 (0.23), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 154 
 TYR   0.012   0.002   TYR B 233 
 PHE   0.026   0.002   PHE B 212 
 TRP   0.013   0.002   TRP A 278 
 HIS   0.008   0.001   HIS B 217 

*********************** REFINEMENT MACRO_CYCLE 2 OF 5 *************************

-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 106 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:   20.0000
   chunk 45 optimal weight:   20.0000
   chunk 74 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 64 optimal weight:   20.0000
   chunk 17 optimal weight:    8.9990
   chunk 36 optimal weight:   10.0000
   chunk 96 optimal weight:   10.0000
   chunk 12 optimal weight:    7.9990
   overall best weight:    9.3996

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6665
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.070   9651  Z= 0.290
  Angle     :  0.673   7.228  13050  Z= 0.358
  Chirality :  0.061   0.229   1441
  Planarity :  0.005   0.052   1682
  Dihedral  : 12.782  84.660   3630
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 27.18
  Ramachandran Plot:
    Outliers :  4.16 %
    Allowed  : 18.14 %
    Favored  : 77.70 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  :  5.02 %
    Favored  : 93.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.89 (0.19), residues: 1130
  helix: -4.39 (0.17), residues: 292
  sheet: -3.14 (0.30), residues: 218
  loop : -4.07 (0.19), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 150 
 TYR   0.017   0.002   TYR B 233 
 PHE   0.024   0.002   PHE B 212 
 TRP   0.021   0.002   TRP A 278 
 HIS   0.007   0.001   HIS A 155 

*********************** REFINEMENT MACRO_CYCLE 3 OF 5 *************************

-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 79 optimal weight:    8.9990
   chunk 102 optimal weight:   10.0000
   chunk 32 optimal weight:    7.9990
   chunk 68 optimal weight:   20.0000
   chunk 90 optimal weight:   10.0000
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    1.9990
   chunk 18 optimal weight:    8.9990
   chunk 39 optimal weight:   20.0000
   chunk 12 optimal weight:    5.9990
   chunk 93 optimal weight:   10.0000
   overall best weight:    6.7990

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6647
moved from start:          0.3531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9651  Z= 0.191
  Angle     :  0.545   5.476  13050  Z= 0.284
  Chirality :  0.055   0.200   1441
  Planarity :  0.004   0.044   1682
  Dihedral  : 12.241  80.962   3630
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 16.90
  Ramachandran Plot:
    Outliers :  2.30 %
    Allowed  : 14.16 %
    Favored  : 83.54 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  4.64 %
    Favored  : 93.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.55 (0.18), residues: 1130
  helix: -4.03 (0.17), residues: 298
  sheet: -3.01 (0.31), residues: 212
  loop : -3.86 (0.19), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 569 
 TYR   0.012   0.001   TYR B 233 
 PHE   0.020   0.002   PHE B 212 
 TRP   0.014   0.001   TRP A 278 
 HIS   0.005   0.001   HIS B 217 

*********************** REFINEMENT MACRO_CYCLE 4 OF 5 *************************

-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 108 optimal weight:   40.0000
   chunk 87 optimal weight:   80.0000
   chunk 42 optimal weight:    7.9990
   chunk 60 optimal weight:   20.0000
   chunk 71 optimal weight:   40.0000
   chunk 12 optimal weight:    7.9990
   chunk 45 optimal weight:   10.0000
   chunk 55 optimal weight:   30.0000
   chunk 40 optimal weight:   10.0000
   chunk 78 optimal weight:   10.0000
   overall best weight:    9.1996

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6772
moved from start:          0.4563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.064   9651  Z= 0.278
  Angle     :  0.663   6.436  13050  Z= 0.357
  Chirality :  0.061   0.220   1441
  Planarity :  0.006   0.063   1682
  Dihedral  : 12.900  77.725   3630
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 29.36
  Ramachandran Plot:
    Outliers :  5.66 %
    Allowed  : 21.77 %
    Favored  : 72.57 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  :  6.63 %
    Favored  : 90.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.48 (0.18), residues: 1130
  helix: -4.75 (0.14), residues: 288
  sheet: -3.83 (0.27), residues: 239
  loop : -4.38 (0.19), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1118 
 TYR   0.017   0.002   TYR B 233 
 PHE   0.023   0.002   PHE B 212 
 TRP   0.020   0.002   TRP A 278 
 HIS   0.007   0.001   HIS A 155 

*********************** REFINEMENT MACRO_CYCLE 5 OF 5 *************************

-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 81 optimal weight:   10.0000
   chunk 26 optimal weight:    7.9990
   chunk 70 optimal weight:   10.0000
   chunk 61 optimal weight:   20.0000
   chunk 56 optimal weight:   20.0000
   chunk 110 optimal weight:   50.0000
   chunk 66 optimal weight:   40.0000
   chunk 33 optimal weight:    8.9990
   chunk 7 optimal weight:   10.0000
   chunk 103 optimal weight:   20.0000
   chunk 1 optimal weight:   50.0000
   overall best weight:    9.3996

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6768
moved from start:          0.4915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064   9651  Z= 0.252
  Angle     :  0.595   5.417  13050  Z= 0.317
  Chirality :  0.058   0.196   1441
  Planarity :  0.005   0.053   1682
  Dihedral  : 12.980  76.355   3630
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 23.16
  Ramachandran Plot:
    Outliers :  4.07 %
    Allowed  : 19.29 %
    Favored  : 76.64 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  :  6.91 %
    Favored  : 90.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.40 (0.17), residues: 1130
  helix: -4.57 (0.14), residues: 294
  sheet: -4.02 (0.27), residues: 215
  loop : -4.29 (0.18), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 154 
 TYR   0.013   0.002   TYR B 233 
 PHE   0.022   0.002   PHE B 212 
 TRP   0.018   0.002   TRP A 278 
 HIS   0.006   0.001   HIS B 217 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 407.90 seconds
wall clock time: 8 minutes 2.26 seconds (482.26 seconds total)