Dear bb

I have encountered a quite significant difference between Rfree reported by phenix.maps, refine and reciprocal_space_arrays. I have used default values in the GUI, and don’t find differences in reflections statistics reported in the phenix.maps log that could explain the difference. I have another example also, but with a smaller difference between phenix.maps and phenix.refine. Both are quite large structures with maximum resolution between 3.5 and 4. Any explanation?

phenix.maps

-------------------------------------------------------------------------------

Bulk solvent correction and anisotropic scaling:

|--(resolution: 3.68 - 29.45 A, n_refl.=22769 (all), 10.16 % free)------------|

|                                                                             |

| r_work= 0.2550 r_free= 0.2823 coordinate error (max.-lik. estimate): 0.60 A |

|                                                                             |

| x-ray target function (ml) for work reflections: 6.433959                   |

|-----------------------------------------------------------------------------|

phenix.reciprocal_space_arrays

|--(resolution: 3.68 - 29.45 A, n_refl.=22769 (all), 10.16 % free)------------|

|                                                                             |

| r_work= 0.2741 r_free= 0.3045 coordinate error (max.-lik. estimate): 0.69 A |

|                                                                             |

| x-ray target function (ml) for work reflections: 6.492710                   |

|-----------------------------------------------------------------------------|

phenix.refine, strategy=none 1 macrocycle

|--(resolution: 3.68 - 29.45 A, n_refl.=22769 (all), 10.16 % free)------------|

|                                                                             |

| r_work= 0.2741 r_free= 0.3045 coordinate error (max.-lik. estimate): 0.69 A |

|                                                                             |

| x-ray target function (ml) for work reflections: 6.492702                   |

|-----------------------------------------------------------------------------|

gregers

Professor Gregers Rom Andersen

Department of Molecular Biology and Genetics

Aarhus University

Gustav Wiedsvej 10C DK8000 Aarhus C

phone +45 871 55507 fax +45 861 23178

email [email protected]

-------------extract of log files--------

phenix.maps log

Parameters to compute maps::

maps {

   input {

     pdb_file_name = "/u/gra/myproject/juli2014/mave/ref_01.pdb"

     reflection_data {

       file_name = "/u/gra/myproject/juli2014/mave/reflections.mtz"

       labels = "FP,SIGFP"

       high_resolution = None

       low_resolution = None

       outliers_rejection = True

       french_wilson_scale = True

       french_wilson {

max_bins = 60

         min_bin_size = 40

}

       sigma_fobs_rejection_criterion = None

       sigma_iobs_rejection_criterion = None

       r_free_flags {

         file_name = "/u/gra/myproject/juli2014/mave/reflections.mtz"

         label = "R-free-flags43"

         test_flag_value = 1

         ignore_r_free_flags = False

       }

     }

   }

=============================== Reflection data ===============================

F-obs:

  /u/gra/myproject/juli2014/mave/reflections.mtz:FP,SIGFP

Miller array info: /u/gra/myproject/juli2014/mave/reflections.mtz:FP,SIGFP

Observation type: xray.amplitude

Type of data: double, size=22776

Type of sigmas: double, size=22776

Number of Miller indices: 22776

Anomalous flag: False

Unit cell: (168.063, 154.031, 78.988, 90, 90, 90)

Space group: P 21 21 2 (No. 18)

Systematic absences: 0

Centric reflections: 2864

Resolution range: 29.4462 3.67631

Completeness in resolution range: 0.992029

Completeness with d_max=infinity: 0.989401

Wavelength: 0.0000

Number of F-obs in resolution range:                   22776

Number of F-obs<0 (these reflections will be rejected): 0

Number of F-obs=0 (these reflections will be used in refinement): 0

Refinement resolution range: d_max =  29.4462

d_min =   3.6763

R-free flags:

  /u/gra/myproject/juli2014/mave/reflections.mtz:R-free-flags43

Miller array info: /u/gra/myproject/juli2014/mave/reflections.mtz:R-free-flags43

Observation type: None

Type of data: int, size=22776

Type of sigmas: None

Number of Miller indices: 22776

Anomalous flag: False

Unit cell: (168.063, 154.031, 78.988, 90, 90, 90)

Space group: P 21 21 2 (No. 18)

Systematic absences: 0

Centric reflections: 2864

Resolution range: 29.4462 3.67631

Completeness in resolution range: 0.992029

Completeness with d_max=infinity: 0.989401

Wavelength: 0.0000

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:

                                         work  free  %free

  bin  1: 29.4471 -  7.8747 [2434/2441]  2190   244  10.0%

  bin  2:  7.8747 -  6.2702 [2347/2348]  2103   244  10.4%

bin  3:  6.2702 -  5.4834 [2297/2300]  2076   221   9.6%

  bin  4:  5.4834 -  4.9847 [2284/2286]  2053   231  10.1%

  bin  5:  4.9847 -  4.6289 [2272/2274]  2045   227  10.0%

  bin  6:  4.6289 -  4.3569 [2294/2295]  2066   228   9.9%

  bin  7:  4.3569 -  4.1393 [2240/2241]  1994   246  11.0%

bin  8:  4.1393 -  3.9595 [2254/2255]  2027   227  10.1%

  bin  9:  3.9595 -  3.8074 [2277/2278]  2055   222   9.7%

  bin 10:  3.8074 -  3.6763 [2077/2241]  1853   224  10.8%

                                overall 20462  2314  10.2%

-------------------------------------------------------------------------------

Input model file: /u/gra/myproject/juli2014/mave/ref_01.pdb

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

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

Number of scattering types: 6

  Type Number    sf(0)   Gaussians

   S      48     15.91       1

   P      28     14.91       1

   Mg      2     11.95       2

   O    2498      7.97       1

   N    2146      6.97       1

   C    7880      5.97       1

  sf(0) = scattering factor at diffraction angle 0.

  Number of scatterers: 12602

  At special positions: 0

  Unit cell: (168.063, 154.031, 78.988, 90, 90, 90)

  Space group: P 21 21 2 (No. 18)

-------------------------------------------------------------------------------

Bulk solvent correction and anisotropic scaling:

|--(resolution: 3.68 - 29.45 A, n_refl.=22769 (all), 10.16 % free)------------|

|                                                                             |

| r_work= 0.2550 r_free= 0.2823 coordinate error (max.-lik. estimate): 0.60 A |

|                                                                             |

| x-ray target function (ml) for work reflections: 6.433959                   |

|-----------------------------------------------------------------------------|

phenix.reciprocal_space_arrays

Default params::

  hkl_file = None

  pdb_file = None

  f_obs_label = None

  r_free_flags_label = None

  remove_f_obs_outliers = True

  bulk_solvent_and_scaling = True

  hendrickson_lattman_coefficients_label = None

  output_file_name = None

  space_group = None

  unit_cell = None

  job_title = None

|--(resolution: 3.68 - 29.45 A, n_refl.=22769 (all), 10.16 % free)------------|

|                                                                             |

| r_work= 0.2741 r_free= 0.3045 coordinate error (max.-lik. estimate): 0.69 A |

|                                                                             |

| x-ray target function (ml) for work reflections: 6.492710                   |

|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|

| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |

|number     range              work test   work   test        work        test|

|  1: 29.4471 -  9.3567 0.99   1316  144 0.1750 0.1935       7.111      7.2567|

|  2:  9.3567 -  7.4666 1.00   1244  147 0.1844 0.2442      6.8649      7.0955|

|  3:  7.4666 -  6.5345 1.00   1243  135 0.2403 0.3183      6.6514      6.7683|

|  4:  6.5345 -  5.9424 1.00   1221  136 0.2622 0.3386      6.5345       6.547|

|  5:  5.9424 -  5.5195 1.00   1230  131 0.2482 0.3091      6.3934      6.5161|

|  6:  5.5195 -  5.1959 1.00   1199  141 0.2741 0.2699      6.3987      6.4315|

|  7:  5.1959 -  4.9370 1.00   1196  129 0.2528 0.2600      6.3987      6.4955|

|  8:  4.9370 -  4.7230 1.00   1227  136 0.2747 0.3240      6.4448      6.5001|

|  9:  4.7230 -  4.5418 1.00   1178  151 0.2867 0.3278      6.4205      6.5232|

| 10:  4.5418 -  4.3856 1.00   1224  113 0.2871 0.2980      6.4246      6.5162|

| 11:  4.3856 -  4.2489 1.00   1201  151 0.3209 0.4007      6.4221      6.5583|

| 12:  4.2489 -  4.1278 1.00   1174  137 0.3552 0.3395      6.4274      6.4033|

| 13:  4.1278 -  4.0194 1.00   1190  129 0.3917 0.3944      6.4059       6.366|

| 14:  4.0194 -  3.9216 1.00   1184  149 0.3931 0.3915      6.3718        6.38|

| 15:  3.9216 -  3.8326 1.00   1221  116 0.3952 0.3998      6.3442      6.3031|

| 16:  3.8326 -  3.7512 1.00   1168  138 0.4077 0.3949       6.334      6.3252|

| 17:  3.7512 -  3.6763 0.88   1040  130 0.4322 0.4220      6.3237      6.2334|

|-----------------------------------------------------------------------------|

-------------------------------

phenix.refine

  refine {

    strategy = individual_sites individual_sites_real_space rigid_body \

               individual_adp group_adp tls occupancies group_anomalous

  main {

    number_of_macro_cycles = 1

============================= updating all scales =============================

start: r_work=0.3857 r_free=0.4073 n_reflections: 22776

start: r_work=0.3857 r_free=0.4073 (reset all scales to undefined)

    bulk-solvent and scaling: r_work=0.2758 r_free=0.3049

    remove outliers:          r_work=0.2758 r_free=0.3049

    correct solvent mask:     r_work=0.2741 r_free=0.3045

final: r_work=0.2741 r_free=0.3045 n_reflections: 22769

overall anisotropic scale matrix:

      V0: 0.0014,6.7700,1.3003,-6.1473,-1.1440,0.3484

      V1: -0.0036,-0.0045,-0.0442,0.0324,0.0082,0.0028

======================== Statistics in resolution bins ========================

Total model structure factor:

  F_model = k_total * (F_calc + k_mask * F_mask)

    k_total = k_isotropic * k_anisotropic

   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask

29.446-20.724   97.09    90    10 0.2436  1579.386  1497.822 1.000 2.341 0.338

20.553-17.465  100.00    91    10 0.2757  1238.791  1140.148 1.000 1.886 0.335

17.444-14.852   99.35   137    16 0.2182  1221.185  1176.515 1.000 1.685 0.327

14.833-12.617   98.73   210    23 0.1958  1278.964  1244.386 1.000 1.494 0.307

12.608-10.717   98.98   349    39 0.1500  1428.238  1389.811 1.000 1.395 0.300

10.715-9.108    99.84   547    62 0.1416  1410.502  1384.438 1.000 1.354 0.290

  9.104-7.738   100.00   883    99 0.1789  1027.723  1002.711 1.000 1.233 0.290

  7.736-6.574    99.94  1427   159 0.2385   682.594   646.245 1.000 1.076 0.290

  6.573-5.586    99.88  2288   254 0.2567   515.856   486.005 1.000 0.892 0.270

  5.586-4.747    99.90  3710   411 0.2654   489.477   455.553 1.000 0.818 0.220

  4.746-4.033    99.95  5973   671 0.3225   441.426   390.526 1.000 0.817 0.170

  4.033-3.676    96.99  4751   559 0.4048   366.235   296.284 1.000 0.848 0.170

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)

    k_overall=1.1939   b_overall=26.4160