# Date 2008-01-16 Time 04:26:53 PST -0800 (1200486413.64 s)
#phil __OFF__

Command line arguments: "../319.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18316
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 319

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 47.3993, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.30, per 1000 atoms: 1.17


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

F-obs:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA

R-free flags:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.3993, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.793 1.95141
Completeness in resolution range: 0.945461
Completeness with d_max=infinity: 0.942595

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7930
                             d_min =   1.9514

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.3993, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.793 1.95141
Completeness in resolution range: 0.945461
Completeness with d_max=infinity: 0.942595

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7934 -  4.1756 [2179/2208]  1961   218  10.0%
  bin  2:  4.1756 -  3.3267 [2086/2109]  1876   210  10.1%
  bin  3:  3.3267 -  2.9098 [2065/2090]  1856   209  10.1%
  bin  4:  2.9098 -  2.6454 [2040/2056]  1842   198   9.7%
  bin  5:  2.6454 -  2.4567 [2031/2075]  1821   210  10.3%
  bin  6:  2.4567 -  2.3125 [2022/2050]  1833   189   9.3%
  bin  7:  2.3125 -  2.1970 [1999/2035]  1792   207  10.4%
  bin  8:  2.1970 -  2.1017 [1989/2031]  1794   195   9.8%
  bin  9:  2.1017 -  2.0210 [2005/2051]  1809   196   9.8%
  bin 10:  2.0210 -  1.9514 [1173/2014]  1046   127  10.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_319/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.29 -     2.01: 23
        2.01 -     2.74: 259
        2.74 -     3.46: 4703
        3.46 -     4.18: 9526
        4.18 -     4.90: 14262
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.294 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.437 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.565 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.614 3.040 -x+1/2,-y+1,z+1/2
  " O   SER A  95 " - " O   HOH Z 404 "  1.721 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28768 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.19: 754
       17.19 -    34.36: 62
       34.36 -    51.54: 27
       51.54 -    68.71: 23
       68.71 -    85.89: 4
  Dihedral angle restraints sorted by residual:
  " CA  PHE A 192 "
  " CB  PHE A 192 "
  " CG  PHE A 192 "
  " CD1 PHE A 192 "
      ideal   model   delta periodicty    weight residual
      90.00    7.91   82.09     2       2.50e-03 1.68e+01
  " N   PRO A  54 "
  " CG  PRO A  54 "
  " CD  PRO A  54 "
  " CB  PRO A  54 "
      ideal   model   delta periodicty    weight residual
      30.00  -27.17   57.17     3       4.44e-03 1.45e+01
  " N   PRO A 280 "
  " CA  PRO A 280 "
  " CB  PRO A 280 "
  " CG  PRO A 280 "
      ideal   model   delta periodicty    weight residual
     -25.00   38.44   56.56     3       4.44e-03 1.42e+01
  ... (remaining 867 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      13     15.96       2
   O     902      7.97       2
   N     437      6.97       2
   C    1471      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


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


==================== 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 = True
group_occupancies      = False
group_anomalous        = False
size = 2823

n_use            =  2823
n_use_u_iso      =  2823
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 =  2823

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

Using existing and finding new NCS is disabled.
Use refinement.main.ncs=true to activate it.
Look at refinement.ncs for more NCS related parameters.

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

Writing effective parameters to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_319/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_319/model_refine_001.geo

CPU time processing inputs: 9.29


============================ 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 {
  crystal_symmetry {
    unit_cell = 69.19625 47.3993 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4393   r_free= 0.4324   ksol= 0.00   Bsol= 0.00   scale= 0.925    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.242044                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7934 -  4.6573 0.99   1410  157 0.3495 0.3612      6.5114      6.5251|
|  2:  4.6573 -  3.7159 0.99   1365  150 0.3691 0.3480      6.7227      6.7021|
|  3:  3.7159 -  3.2519 0.99   1330  152 0.3926 0.3954      6.5929      6.7095|
|  4:  3.2519 -  2.9572 0.99   1323  143 0.4154 0.4176      6.4524      6.4558|
|  5:  2.9572 -  2.7467 0.98   1325  148 0.4467 0.4156      6.3202      6.2722|
|  6:  2.7467 -  2.5856 0.99   1308  146 0.4646 0.4592      6.2251      6.1447|
|  7:  2.5856 -  2.4567 0.98   1295  149 0.4746 0.4004       6.218      6.1467|
|  8:  2.4567 -  2.3502 0.99   1295  140 0.4874 0.5095      6.1532      6.1711|
|  9:  2.3502 -  2.2601 0.99   1300  143 0.5008 0.4950      6.1039      6.1324|
| 10:  2.2601 -  2.1824 0.98   1294  142 0.4923 0.5362      6.0904      6.1392|
| 11:  2.1824 -  2.1143 0.97   1274  141 0.5241 0.5050      6.0258      6.0126|
| 12:  2.1143 -  2.0540 0.99   1277  148 0.4913 0.5239      5.9527      5.9881|
| 13:  2.0540 -  2.0001 0.94   1257  134 0.5194 0.5293      5.8703      5.8688|
| 14:  2.0001 -  1.9514 0.45    577   66 0.5367 0.4825      5.8468      5.7265|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7934 -  4.6573  1410   157  0.70  34.00   0.85     0.73      67105.62|
|  2:  4.6573 -  3.7159  1365   150  0.73  32.70   0.94     0.83      90661.54|
|  3:  3.7159 -  3.2519  1330   152  0.65  39.40   0.95     0.85      94332.82|
|  4:  3.2519 -  2.9572  1323   143  0.59  44.74   0.96     0.82      82202.64|
|  5:  2.9572 -  2.7467  1325   148  0.54  48.45   0.91     0.77      64888.00|
|  6:  2.7467 -  2.5856  1308   146  0.52  50.22   0.94     0.73      55026.96|
|  7:  2.5856 -  2.4567  1295   149  0.51  51.01   0.94     0.70      51910.42|
|  8:  2.4567 -  2.3502  1295   140  0.45  55.96   0.93     0.64      51255.55|
|  9:  2.3502 -  2.2601  1300   143  0.39  60.91   0.95     0.57      50904.26|
| 10:  2.2601 -  2.1824  1294   142  0.34  64.16   0.99     0.50      49763.64|
| 11:  2.1824 -  2.1143  1274   141  0.28  68.81   0.95     0.44      48567.88|
| 12:  2.1143 -  2.0540  1277   148  0.29  68.51   0.99     0.46      45625.04|
| 13:  2.0540 -  2.0001  1257   134  0.29  68.16   0.95     0.48      37944.91|
| 14:  2.0001 -  1.9514   577    66  0.38  61.50   0.93     0.55      28071.82|
|alpha:            min =        0.44 max =            0.85 mean =         0.65|
|beta:             min =    28071.82 max =        94332.82 mean =     60053.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           89.98 mean =        52.81|
|phase err.(test): min =        0.00 max =           89.42 mean =        52.67|
|-----------------------------------------------------------------------------|

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

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.263516             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.119   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.217270              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.823   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.294 -  1.654:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.654 -  2.015:       19 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.015 -  2.376:       27 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.376 -  2.736:      232 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.736 -  3.097:     2383 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.097 -  3.457:     2320 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.457 -  3.818:     4279 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.818 -  4.179:     5247 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.179 -  4.539:     6415 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.539 -  4.900:     7847 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.205 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.294 |       0.847 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    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:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4393   r_free= 0.4324   ksol= 0.00   Bsol= 0.00   scale= 0.925    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.242044                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4303   r_free= 0.4230   ksol= 0.32   Bsol= 21.98   scale= 0.953   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.82,-0.40,2.57,-0.00,0.00,0.00); trace/3= 0.12                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.234146                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.264364             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.995   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.018152              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.682   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4303      final r-factor (work) = 0.2773          |
| start r-factor (free) = 0.4230      final r-factor (free) = 0.3023          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.1994 = 10.26 * 0.50 * 6.2340 + 1.00 * 0.2054                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.2244 = 10.26 * 0.50 * 6.0598 + 1.00 * 0.1242                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2773      final r-factor (work) = 0.2509          |
| start r-factor (free) = 0.3023      final r-factor (free) = 0.3133          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1806 = 1.02 * 1.00 * 6.0598 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0535 = 1.02 * 1.00 * 5.8272 + 1.00 * 0.1205                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.68   18.76    None  None   None       |
|    all(noH): 2823   0      0.00    80.68   18.76    None  None   None       |
|    Sol.    : 438    0      3.67    80.68   41.64    None  None   None       |
|    Mac.    : 2385   0      0.00    80.25   14.56    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 -   8.068:  693   |   5:    40.340 -  48.409:  120        |
|      1:     8.068 -  16.136:  983   |   6:    48.409 -  56.477:   84        |
|      2:    16.136 -  24.204:  455   |   7:    56.477 -  64.545:   60        |
|      3:    24.204 -  32.272:  227   |   8:    64.545 -  72.613:   37        |
|      4:    32.272 -  40.340:  145   |   9:    72.613 -  80.681:   19        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2509 r_free = 0.3133             target_work(ml) = 5.840         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2508 r_free = 0.3136             target_work(ml) = 5.839         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2508   r_free= 0.3136   ksol= 0.32   Bsol= 21.98   scale= 1.043   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.82,-0.40,2.57,-0.00,0.00,0.00); trace/3= 0.12                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.838975                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2466   r_free= 0.3096   ksol= 0.33   Bsol= 50.00   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.72,-1.34,-0.19,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.831163                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.376097              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.874   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.705617              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.224   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2466      final r-factor (work) = 0.1857          |
| start r-factor (free) = 0.3096      final r-factor (free) = 0.2410          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9619 = 3.38 * 0.50 * 5.8279 + 1.00 * 0.1242                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7163 = 3.38 * 0.50 * 5.7198 + 1.00 * 0.0610                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1857      final r-factor (work) = 0.1696          |
| start r-factor (free) = 0.2410      final r-factor (free) = 0.2292          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.4969 = 2.71 * 1.00 * 5.7198 + 1.00 * 0.0213                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.0178 = 2.71 * 1.00 * 5.5453 + 1.00 * 0.0143                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.49  18.97    None  None   None       |
|    all(noH): 2823   0      0.00    104.49  18.97    None  None   None       |
|    Sol.    : 438    0      5.23    95.13   45.39    None  None   None       |
|    Mac.    : 2385   0      0.00    104.49  14.11    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 -  10.449: 1078   |   5:    52.246 -  62.695:  104        |
|      1:    10.449 -  20.898: 1011   |   6:    62.695 -  73.144:   65        |
|      2:    20.898 -  31.348:  257   |   7:    73.144 -  83.593:   27        |
|      3:    31.348 -  41.797:  141   |   8:    83.593 -  94.042:   13        |
|      4:    41.797 -  52.246:  123   |   9:    94.042 - 104.492:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1696 r_free = 0.2292             target_work(ml) = 5.512         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1694 r_free = 0.2292             target_work(ml) = 5.512         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1694   r_free= 0.2292   ksol= 0.33   Bsol= 50.00   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.72,-1.34,-0.19,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.511704                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1696   r_free= 0.2276   ksol= 0.32   Bsol= 41.19   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-1.34,-1.02,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.508115                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.051969              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.258  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.184360              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 113.037  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1696      final r-factor (work) = 0.1345          |
| start r-factor (free) = 0.2276      final r-factor (free) = 0.1876          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2952 = 4.05 * 0.50 * 5.5451 + 1.00 * 0.0610                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0292 = 4.05 * 0.50 * 5.4114 + 1.00 * 0.0659                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1345      final r-factor (work) = 0.1263          |
| start r-factor (free) = 0.1876      final r-factor (free) = 0.1726          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0119 = 0.18 * 1.00 * 5.4114 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9830 = 0.18 * 1.00 * 5.2861 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.67    101.20  17.54    None  None   None       |
|    all(noH): 2823   0      1.67    101.20  17.54    None  None   None       |
|    Sol.    : 438    0      5.49    82.61   41.17    None  None   None       |
|    Mac.    : 2385   0      1.67    101.20  13.20    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:     1.673 -  11.626: 1379   |   5:    51.439 -  61.392:   93        |
|      1:    11.626 -  21.579:  859   |   6:    61.392 -  71.345:   28        |
|      2:    21.579 -  31.532:  174   |   7:    71.345 -  81.298:   16        |
|      3:    31.532 -  41.485:  131   |   8:    81.298 -  91.251:   11        |
|      4:    41.485 -  51.439:  130   |   9:    91.251 - 101.205:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1263 r_free = 0.1726             target_work(ml) = 5.237         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1261 r_free = 0.1723             target_work(ml) = 5.236         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1261   r_free= 0.1723   ksol= 0.32   Bsol= 41.19   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-1.34,-1.02,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.236016                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1265   r_free= 0.1719   ksol= 0.32   Bsol= 41.14   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,-1.71,-1.67,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.237452                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.550561              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.971  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.391442              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.003  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1265      final r-factor (work) = 0.1200          |
| start r-factor (free) = 0.1719      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1664 = 1.55 * 0.50 * 5.2892 + 1.00 * 0.0659                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0964 = 1.55 * 0.50 * 5.2182 + 1.00 * 0.0508                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1200      final r-factor (work) = 0.1174          |
| start r-factor (free) = 0.1637      final r-factor (free) = 0.1639          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0511 = 0.39 * 1.00 * 5.2182 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0379 = 0.39 * 1.00 * 5.1838 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.73    103.34  17.40    None  None   None       |
|    all(noH): 2823   0      1.73    103.34  17.40    None  None   None       |
|    Sol.    : 438    0      5.84    87.80   41.13    None  None   None       |
|    Mac.    : 2385   0      1.73    103.34  13.04    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:     1.726 -  11.888: 1460   |   5:    52.535 -  62.697:   84        |
|      1:    11.888 -  22.050:  799   |   6:    62.697 -  72.859:   30        |
|      2:    22.050 -  32.211:  169   |   7:    72.859 -  83.021:   14        |
|      3:    32.211 -  42.373:  128   |   8:    83.021 -  93.183:    4        |
|      4:    42.373 -  52.535:  132   |   9:    93.183 - 103.345:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1174 r_free = 0.1639             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1174 r_free = 0.1638             target_work(ml) = 5.182         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1174   r_free= 0.1638   ksol= 0.32   Bsol= 41.14   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,-1.71,-1.67,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.182450                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1173   r_free= 0.1638   ksol= 0.32   Bsol= 41.14   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,-1.71,-1.67,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.182482                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.994254              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.645  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.205144              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.782  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1173      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1638      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2196 = 1.99 * 0.50 * 5.1836 + 1.00 * 0.0508                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2005 = 1.99 * 0.50 * 5.1567 + 1.00 * 0.0586                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1107      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1588      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0667 = 0.21 * 1.00 * 5.1567 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0622 = 0.21 * 1.00 * 5.1396 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.76    101.44  16.94    None  None   None       |
|    all(noH): 2823   0      1.76    101.44  16.94    None  None   None       |
|    Sol.    : 438    0      5.31    88.85   39.30    None  None   None       |
|    Mac.    : 2385   0      1.76    101.44  12.83    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:     1.763 -  11.731: 1455   |   5:    51.601 -  61.568:   82        |
|      1:    11.731 -  21.698:  813   |   6:    61.568 -  71.536:   21        |
|      2:    21.698 -  31.666:  176   |   7:    71.536 -  81.503:   13        |
|      3:    31.666 -  41.633:  128   |   8:    81.503 -  91.471:    4        |
|      4:    41.633 -  51.601:  128   |   9:    91.471 - 101.438:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1107 r_free = 0.1576             target_work(ml) = 5.136         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1107 r_free = 0.1575             target_work(ml) = 5.136         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1107   r_free= 0.1575   ksol= 0.32   Bsol= 41.14   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,-1.71,-1.67,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.136244                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7934 -  4.6573 0.99   1410  157 0.0978 0.1283      5.3718       5.536|
|  2:  4.6573 -  3.7159 0.99   1365  150 0.0834 0.1067      5.4117      5.6046|
|  3:  3.7159 -  3.2519 0.99   1330  152 0.1044 0.1557      5.4489      5.8447|
|  4:  3.2519 -  2.9572 0.99   1323  143 0.1227 0.1578      5.4546      5.6235|
|  5:  2.9572 -  2.7467 0.98   1325  148 0.1271 0.1697      5.3001      5.4701|
|  6:  2.7467 -  2.5856 0.99   1308  146 0.1230 0.1955      5.2056      5.4384|
|  7:  2.5856 -  2.4567 0.98   1295  149 0.1204 0.1630      5.1197      5.3665|
|  8:  2.4567 -  2.3502 0.99   1295  140 0.1163 0.1649      5.0624      5.2465|
|  9:  2.3502 -  2.2601 0.99   1300  143 0.1196 0.1792      5.0214      5.3037|
| 10:  2.2601 -  2.1824 0.98   1294  142 0.1143 0.1843      4.9812      5.2498|
| 11:  2.1824 -  2.1143 0.97   1274  141 0.1106 0.1769      4.8992      5.2033|
| 12:  2.1143 -  2.0540 0.99   1277  148 0.1093 0.1633      4.8421      5.0781|
| 13:  2.0540 -  2.0001 0.94   1257  134 0.1131 0.1875      4.7727       5.074|
| 14:  2.0001 -  1.9514 0.45    577   66 0.1128 0.1548         4.7      4.8486|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7934 -  4.6573  1410   157  0.94   8.88   0.99     0.97       6957.83|
|  2:  4.6573 -  3.7159  1365   150  0.95   7.83   1.02     1.01       8636.66|
|  3:  3.7159 -  3.2519  1330   152  0.94  11.12   1.03     1.03       9876.39|
|  4:  3.2519 -  2.9572  1323   143  0.92  13.95   1.01     1.00      10428.63|
|  5:  2.9572 -  2.7467  1325   148  0.90  15.49   1.00     0.97       7859.07|
|  6:  2.7467 -  2.5856  1308   146  0.90  15.60   0.99     0.96       6876.88|
|  7:  2.5856 -  2.4567  1295   149  0.91  14.61   0.99     0.97       5530.65|
|  8:  2.4567 -  2.3502  1295   140  0.91  15.21   1.01     0.99       5363.97|
|  9:  2.3502 -  2.2601  1300   143  0.91  15.36   1.01     0.98       4832.17|
| 10:  2.2601 -  2.1824  1294   142  0.90  15.59   1.00     0.97       4594.39|
| 11:  2.1824 -  2.1143  1274   141  0.90  16.08   1.01     0.98       4088.86|
| 12:  2.1143 -  2.0540  1277   148  0.92  14.21   1.01     0.99       3561.48|
| 13:  2.0540 -  2.0001  1257   134  0.91  15.70   1.01     1.02       3170.88|
| 14:  2.0001 -  1.9514   577    66  0.91  15.18   1.00     0.96       2621.95|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2621.95 max =        10428.63 mean =      6212.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.84 mean =        13.80|
|phase err.(test): min =        0.00 max =           89.80 mean =        13.47|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1107   r_free= 0.1576   ksol= 0.32   Bsol= 41.14   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.67,-1.65,-1.64,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.136284                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1107   r_free= 0.1576   ksol= 0.32   Bsol= 41.14   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.67,-1.65,-1.64,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.136284                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7934 -  4.6573 0.99   1410  157 0.0978 0.1286      5.3727      5.5371|
|  2:  4.6573 -  3.7159 0.99   1365  150 0.0834 0.1068      5.4119      5.6045|
|  3:  3.7159 -  3.2519 0.99   1330  152 0.1044 0.1558      5.4491      5.8451|
|  4:  3.2519 -  2.9572 0.99   1323  143 0.1227 0.1579      5.4546      5.6238|
|  5:  2.9572 -  2.7467 0.98   1325  148 0.1271 0.1697         5.3      5.4698|
|  6:  2.7467 -  2.5856 0.99   1308  146 0.1230 0.1956      5.2056      5.4389|
|  7:  2.5856 -  2.4567 0.98   1295  149 0.1204 0.1630        5.12      5.3667|
|  8:  2.4567 -  2.3502 0.99   1295  140 0.1163 0.1648      5.0625      5.2465|
|  9:  2.3502 -  2.2601 0.99   1300  143 0.1196 0.1792      5.0215      5.3039|
| 10:  2.2601 -  2.1824 0.98   1294  142 0.1143 0.1841      4.9811      5.2491|
| 11:  2.1824 -  2.1143 0.97   1274  141 0.1105 0.1769       4.899      5.2031|
| 12:  2.1143 -  2.0540 0.99   1277  148 0.1093 0.1632      4.8417      5.0777|
| 13:  2.0540 -  2.0001 0.94   1257  134 0.1131 0.1872      4.7723      5.0727|
| 14:  2.0001 -  1.9514 0.45    577   66 0.1127 0.1549         4.7      4.8496|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7934 -  4.6573  1410   157  0.94   8.89   0.99     0.97       6981.35|
|  2:  4.6573 -  3.7159  1365   150  0.95   7.84   1.02     1.01       8648.14|
|  3:  3.7159 -  3.2519  1330   152  0.94  11.12   1.03     1.03       9880.55|
|  4:  3.2519 -  2.9572  1323   143  0.92  13.95   1.01     1.00      10429.51|
|  5:  2.9572 -  2.7467  1325   148  0.90  15.50   1.00     0.97       7861.96|
|  6:  2.7467 -  2.5856  1308   146  0.90  15.60   0.99     0.96       6876.93|
|  7:  2.5856 -  2.4567  1295   149  0.91  14.62   0.99     0.97       5534.87|
|  8:  2.4567 -  2.3502  1295   140  0.91  15.22   1.01     0.99       5365.43|
|  9:  2.3502 -  2.2601  1300   143  0.91  15.36   1.01     0.98       4835.34|
| 10:  2.2601 -  2.1824  1294   142  0.90  15.59   1.00     0.97       4592.16|
| 11:  2.1824 -  2.1143  1274   141  0.90  16.07   1.01     0.98       4087.69|
| 12:  2.1143 -  2.0540  1277   148  0.92  14.20   1.01     0.99       3555.55|
| 13:  2.0540 -  2.0001  1257   134  0.91  15.69   1.01     1.02       3167.39|
| 14:  2.0001 -  1.9514   577    66  0.91  15.17   1.00     0.96       2621.10|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2621.10 max =        10429.51 mean =      6215.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.85 mean =        13.80|
|phase err.(test): min =        0.00 max =           89.80 mean =        13.47|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.70    101.37  16.88    None  None   None       |
|    all(noH): 2823   0      1.70    101.37  16.88    None  None   None       |
|    Sol.    : 438    0      5.24    88.79   39.24    None  None   None       |
|    Mac.    : 2385   0      1.70    101.37  12.77    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:     1.700 -  11.668: 1455   |   5:    51.538 -  61.505:   82        |
|      1:    11.668 -  21.635:  813   |   6:    61.505 -  71.472:   21        |
|      2:    21.635 -  31.603:  176   |   7:    71.472 -  81.440:   13        |
|      3:    31.603 -  41.570:  128   |   8:    81.440 -  91.407:    4        |
|      4:    41.570 -  51.538:  128   |   9:    91.407 - 101.375:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


========== residual map mFobs-DFmodel: highest peaks and deepst holes =========


                           ----------peaks----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 305         
Filter by distance & map next to the model:
   mapped sites are within: 0.538 - 5.915
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 302 from: 305
   mapped sites are within: 0.702 - 5.915

peak=    5.642 closest distance to " NH2 ARG A  56 " =    2.172
peak=    5.571 closest distance to " CB  SER A  63 " =    1.152
peak=    5.536 closest distance to " O   HOH Z 126 " =    1.937
peak=    5.173 closest distance to " CB  ARG A 275 " =    0.954
peak=    5.169 closest distance to " CG  PRO A  54 " =    1.209
peak=    5.135 closest distance to " O   HOH Z 124 " =    1.512
peak=    5.023 closest distance to " O   HOH Z 234 " =    3.699
peak=    5.015 closest distance to " O   HOH Z 142 " =    1.717
peak=    5.006 closest distance to " O   HOH Z 278 " =    1.234
peak=    4.878 closest distance to " O   HOH Z 132 " =    1.384
peak=    4.861 closest distance to " O   HOH Z 108 " =    1.410
peak=    4.746 closest distance to " CB  GLN A 223 " =    1.446
peak=    4.671 closest distance to " C   PRO A 198 " =    1.532
peak=    4.669 closest distance to " O   HOH Z 232 " =    2.311
peak=    4.627 closest distance to " O   HOH Z  78 " =    1.809
peak=    4.605 closest distance to " O   SER A  87 " =    2.188
peak=    4.569 closest distance to " CA  TYR A  30 " =    1.007
peak=    4.558 closest distance to " O   HOH Z 298 " =    1.855
peak=    4.547 closest distance to " CG  PRO A  90 " =    1.135
peak=    4.531 closest distance to " CB  GLN A 183 " =    1.305
peak=    4.530 closest distance to " O   HOH Z  97 " =    2.523
peak=    4.526 closest distance to " O   HOH Z 193 " =    1.766
peak=    4.525 closest distance to " CB  SER A   3 " =    1.295
peak=    4.520 closest distance to " NH2BARG A 145 " =    2.043
peak=    4.513 closest distance to " O   HOH Z 207 " =    1.873
peak=    4.511 closest distance to " O   HOH Z 326 " =    1.582
peak=    4.471 closest distance to " NE2 GLN A  11 " =    1.053
peak=    4.441 closest distance to " O   HOH Z  15 " =    2.055
peak=    4.437 closest distance to " O   HOH Z  59 " =    2.247
peak=    4.437 closest distance to " CA  ALA A  21 " =    1.162
peak=    4.429 closest distance to " O   HOH Z 272 " =    1.846
peak=    4.416 closest distance to " O   HOH Z 199 " =    1.005
peak=    4.415 closest distance to " O   HOH Z 102 " =    1.249
peak=    4.393 closest distance to " O   HOH Z  97 " =    1.850
peak=    4.391 closest distance to " O   HOH Z 134 " =    1.584
peak=    4.366 closest distance to " O   HOH Z 368 " =    2.023
peak=    4.300 closest distance to " O   HOH Z 128 " =    1.917
peak=    4.285 closest distance to " O   HOH Z 236 " =    1.969
peak=    4.284 closest distance to " O   HOH Z 403 " =    1.886
peak=    4.233 closest distance to " O   HOH Z 426 " =    1.465
peak=    4.222 closest distance to " O   HOH Z 260 " =    1.262
peak=    4.211 closest distance to " O   HOH Z  54 " =    1.660
peak=    4.199 closest distance to " CG1 ILE A  33 " =    1.264
peak=    4.194 closest distance to " CG  PRO A 198 " =    1.243
peak=    4.193 closest distance to " O   HOH Z 316 " =    2.840
peak=    4.193 closest distance to " CB  TYR A 169 " =    0.742
peak=    4.192 closest distance to " CB  ASN A 148 " =    1.599
peak=    4.192 closest distance to " O   HOH Z 427 " =    2.651
peak=    4.178 closest distance to " O   HOH Z 402 " =    1.414
peak=    4.172 closest distance to " CB  GLU A 152 " =    1.145
peak=    4.164 closest distance to " NZ  LYS A 117 " =    3.120
peak=    4.140 closest distance to " O   HOH Z 344 " =    2.710
peak=    4.124 closest distance to " NZ  LYS A 119 " =    1.931
peak=    4.114 closest distance to " O   HOH Z 389 " =    1.852
peak=    4.100 closest distance to " O   HOH Z 227 " =    1.673
peak=    4.095 closest distance to " CB  GLU A 128 " =    1.097
peak=    4.069 closest distance to " O   HOH Z 334 " =    1.432
peak=    4.063 closest distance to " CB  GLU A 277 " =    3.492
peak=    4.056 closest distance to " O   HOH Z   6 " =    2.157
peak=    4.042 closest distance to " NH2AARG A 145 " =    2.251
peak=    4.013 closest distance to " O   HOH Z  85 " =    1.750
peak=    4.000 closest distance to " OD2 ASP A 286 " =    2.677
peak=    3.993 closest distance to " O   HOH Z 203 " =    1.737
peak=    3.988 closest distance to " CB  ARG A  79 " =    1.365
peak=    3.969 closest distance to " O   HOH Z 423 " =    2.014
peak=    3.968 closest distance to " O   HOH Z 416 " =    2.745
peak=    3.949 closest distance to " ND2 ASN A 187 " =    1.591
peak=    3.935 closest distance to " O   HOH Z 374 " =    2.453
peak=    3.932 closest distance to " O   HOH Z 408 " =    1.547
peak=    3.925 closest distance to " N   ASN A  39 " =    1.239
peak=    3.919 closest distance to " O   HOH Z  49 " =    2.079
peak=    3.917 closest distance to " CG  ARG A  66 " =    2.716
peak=    3.917 closest distance to " O   HOH Z 369 " =    2.161
peak=    3.897 closest distance to " O   HOH Z 313 " =    1.711
peak=    3.881 closest distance to " O   HOH Z 118 " =    1.216
peak=    3.875 closest distance to " O   HOH Z 357 " =    1.871
peak=    3.874 closest distance to " CB  SER A 141 " =    1.080
peak=    3.855 closest distance to " CA  ASN A 176 " =    1.108
peak=    3.853 closest distance to " O   HOH Z 346 " =    1.496
peak=    3.848 closest distance to " O   HOH Z 279 " =    2.039
peak=    3.833 closest distance to " CG AARG A 275 " =    0.993
peak=    3.831 closest distance to " CA  THR A 221 " =    0.913
peak=    3.830 closest distance to " O   HOH Z  10 " =    1.779
peak=    3.823 closest distance to " OG BSER A 164 " =    2.496
peak=    3.816 closest distance to " O   HOH Z  40 " =    1.595
peak=    3.812 closest distance to " CB  PRO A  54 " =    0.909
peak=    3.811 closest distance to " O   HOH Z 345 " =    2.712
peak=    3.809 closest distance to " OD1 ASN A  69 " =    2.590
peak=    3.801 closest distance to " OD2 ASP A 298 " =    4.004
peak=    3.801 closest distance to " CB  LEU A 228 " =    1.155
peak=    3.799 closest distance to " CB  ARG A 139 " =    0.993
peak=    3.796 closest distance to " O   HOH Z  44 " =    2.105
peak=    3.795 closest distance to " CD  ARG A 269 " =    1.056
peak=    3.791 closest distance to " O   HOH Z 284 " =    2.818
peak=    3.790 closest distance to " O   HOH Z 411 " =    3.682
peak=    3.785 closest distance to " O   HOH Z 156 " =    3.373
peak=    3.773 closest distance to " O   HOH Z  80 " =    1.625
peak=    3.772 closest distance to " O   HOH Z  43 " =    2.272
peak=    3.761 closest distance to " CD2 LEU A 297 " =    0.954
peak=    3.751 closest distance to " O   HOH Z 380 " =    2.015
peak=    3.743 closest distance to " CB  TRP A 179 " =    1.204
peak=    3.743 closest distance to " CA  ASN A 215 " =    1.194
peak=    3.732 closest distance to " CG1BVAL A  72 " =    1.566
peak=    3.725 closest distance to " O   HOH Z  63 " =    1.934
peak=    3.724 closest distance to " O   HOH Z 173 " =    2.070
peak=    3.717 closest distance to " O   HOH Z  88 " =    3.089
peak=    3.712 closest distance to " O   HOH Z 209 " =    2.408
peak=    3.705 closest distance to " CG2 THR A 221 " =    1.160
peak=    3.695 closest distance to " O   HOH Z 163 " =    2.002
peak=    3.694 closest distance to " CG  ARG A  66 " =    1.034
peak=    3.680 closest distance to " O   HOH Z 214 " =    2.166
peak=    3.675 closest distance to " O   HOH Z 345 " =    1.711
peak=    3.673 closest distance to " O   HOH Z 132 " =    2.547
peak=    3.666 closest distance to " O   HOH Z  61 " =    1.587
peak=    3.655 closest distance to " O   HOH Z 327 " =    1.771
peak=    3.650 closest distance to " O   HOH Z 419 " =    1.497
peak=    3.649 closest distance to " O   HOH Z 194 " =    1.979
peak=    3.646 closest distance to " O   HOH Z 250 " =    1.353
peak=    3.645 closest distance to " NH2AARG A 190 " =    1.242
peak=    3.637 closest distance to " O   HOH Z  21 " =    1.812
peak=    3.636 closest distance to " CB  ASN A  39 " =    0.869
peak=    3.636 closest distance to " O   HOH Z 197 " =    2.647
peak=    3.633 closest distance to " CD2 TRP A 179 " =    1.346
peak=    3.628 closest distance to " CG  PRO A 243 " =    1.186
peak=    3.623 closest distance to " O   HOH Z 365 " =    2.831
peak=    3.613 closest distance to " O   HOH Z 281 " =    4.325
peak=    3.600 closest distance to " CB  ALA A 291 " =    1.268
peak=    3.598 closest distance to " CG  GLN A  77 " =    2.095
peak=    3.597 closest distance to " O   HOH Z 128 " =    2.160
peak=    3.597 closest distance to " O   HOH Z 193 " =    2.287
peak=    3.590 closest distance to " CB  TYR A 169 " =    0.779
peak=    3.580 closest distance to " O   HOH Z 427 " =    3.045
peak=    3.578 closest distance to " O   HOH Z 280 " =    2.337
peak=    3.577 closest distance to " O   HOH Z 247 " =    1.288
peak=    3.576 closest distance to " O   HOH Z 255 " =    1.614
peak=    3.572 closest distance to " O   HOH Z  11 " =    1.244
peak=    3.572 closest distance to " CB  SER A  26 " =    1.631
peak=    3.563 closest distance to " CB  VAL A 202 " =    1.597
peak=    3.559 closest distance to " O   HOH Z  71 " =    1.405
peak=    3.557 closest distance to " CB  ARG A 190 " =    1.686
peak=    3.550 closest distance to " CA  ARG A  36 " =    1.017
peak=    3.547 closest distance to " O   HOH Z 261 " =    1.651
peak=    3.540 closest distance to " CG2 ILE A 120 " =    1.212
peak=    3.539 closest distance to " NH2 ARG A 156 " =    1.153
peak=    3.539 closest distance to " CG2 ILE A  20 " =    1.469
peak=    3.537 closest distance to " O   HOH Z 147 " =    1.721
peak=    3.533 closest distance to " O   HOH Z 273 " =    2.728
peak=    3.525 closest distance to " CE  LYS A 119 " =    1.116
peak=    3.518 closest distance to " O   HOH Z  67 " =    1.765
peak=    3.517 closest distance to " CA  MET A  40 " =    1.031
peak=    3.516 closest distance to " O   HOH Z 144 " =    2.057
peak=    3.513 closest distance to " NZ  LYS A  76 " =    1.348
peak=    3.510 closest distance to " O   HOH Z  30 " =    2.037
peak=    3.504 closest distance to " O   SER A  26 " =    1.683
peak=    3.494 closest distance to " O   HOH Z  19 " =    1.715
peak=    3.493 closest distance to " C   ILE A 106 " =    1.900
peak=    3.490 closest distance to " CG2BVAL A  41 " =    0.869
peak=    3.489 closest distance to " O   HOH Z 336 " =    1.783
peak=    3.477 closest distance to " O   HOH Z 189 " =    1.464
peak=    3.476 closest distance to " CA  ALA A 248 " =    1.381
peak=    3.476 closest distance to " O   HOH Z 108 " =    2.005
peak=    3.475 closest distance to " CB  SER A  62 " =    1.223
peak=    3.473 closest distance to " CB  ASN A 148 " =    1.114
peak=    3.460 closest distance to " O   HOH Z 106 " =    2.217
peak=    3.454 closest distance to " O   HOH Z  47 " =    1.564
peak=    3.453 closest distance to " O   HOH Z 421 " =    1.547
peak=    3.452 closest distance to " CA  ASP A 140 " =    1.130
peak=    3.449 closest distance to " CA  ALA A 291 " =    0.913
peak=    3.434 closest distance to " CD  LYS A 166 " =    1.289
peak=    3.431 closest distance to " O   HOH Z  61 " =    1.484
peak=    3.428 closest distance to " CB  PRO A 198 " =    1.113
peak=    3.426 closest distance to " O   HOH Z 261 " =    1.910
peak=    3.424 closest distance to " O   HOH Z 132 " =    2.165
peak=    3.421 closest distance to " CA  ALA A  84 " =    1.277
peak=    3.417 closest distance to " CA  VAL A  41 " =    0.870
peak=    3.415 closest distance to " O   HOH Z 303 " =    1.945
peak=    3.413 closest distance to " O   HOH Z 291 " =    1.495
peak=    3.412 closest distance to " O   HOH Z 299 " =    4.318
peak=    3.411 closest distance to " O   HOH Z  66 " =    2.198
peak=    3.404 closest distance to " O   HOH Z 438 " =    2.086
peak=    3.400 closest distance to " O   HOH Z 358 " =    2.152
peak=    3.396 closest distance to " CA  ALA A  51 " =    0.866
peak=    3.390 closest distance to " O   HOH Z 126 " =    2.216
peak=    3.388 closest distance to " CA  ASP A 162 " =    1.113
peak=    3.373 closest distance to " OH  TYR A  30 " =    1.066
peak=    3.373 closest distance to " O   HOH Z 267 " =    2.044
peak=    3.368 closest distance to " OD1 ASP A 238 " =    0.941
peak=    3.360 closest distance to " O   HOH Z 263 " =    2.347
peak=    3.358 closest distance to " CB  VAL A 265 " =    1.236
peak=    3.358 closest distance to " CD  ARG A 159 " =    0.702
peak=    3.357 closest distance to " C   ALA A   1 " =    1.656
peak=    3.355 closest distance to " CA  LYS A 117 " =    1.258
peak=    3.349 closest distance to " CH2 TRP A 274 " =    1.928
peak=    3.348 closest distance to " CD2 LEU A 255 " =    1.139
peak=    3.348 closest distance to " O   HOH Z 192 " =    1.780
peak=    3.344 closest distance to " O   HOH Z 195 " =    1.907
peak=    3.343 closest distance to " CZ2 TRP A 179 " =    1.716
peak=    3.342 closest distance to " OE1 GLN A  58 " =    5.915
peak=    3.341 closest distance to " CB  MET A  47 " =    1.110
peak=    3.341 closest distance to " O   HOH Z 154 " =    1.327
peak=    3.341 closest distance to " OE1 GLN A  11 " =    1.848
peak=    3.340 closest distance to " O   HOH Z 250 " =    1.645
peak=    3.336 closest distance to " O   ALA A 165 " =    1.336
peak=    3.332 closest distance to " O   HOH Z 362 " =    3.586
peak=    3.323 closest distance to " O   HOH Z 276 " =    1.253
peak=    3.315 closest distance to " CA  GLY A  80 " =    0.823
peak=    3.315 closest distance to " OG BSER A 210 " =    1.263
peak=    3.312 closest distance to " O   HOH Z 185 " =    1.659
peak=    3.309 closest distance to " O   HOH Z 353 " =    2.721
peak=    3.308 closest distance to " C   PRO A 163 " =    1.678
peak=    3.307 closest distance to " O   HOH Z 265 " =    2.323
peak=    3.305 closest distance to " OG  SER A  62 " =    2.952
peak=    3.305 closest distance to " CA  ARG A  66 " =    1.196
peak=    3.301 closest distance to " NH1BARG A 145 " =    1.337
peak=    3.300 closest distance to " CG2AVAL A 121 " =    2.136
peak=    3.300 closest distance to " OG1 THR A 294 " =    2.296
peak=    3.298 closest distance to " O   TRP A 274 " =    1.805
peak=    3.298 closest distance to " OD1 ASP A 253 " =    1.931
peak=    3.297 closest distance to " CG  GLN A  58 " =    2.406
peak=    3.294 closest distance to " O   HOH Z  35 " =    2.483
peak=    3.292 closest distance to " O   HOH Z 425 " =    2.007
peak=    3.290 closest distance to " CD  ARG A 139 " =    1.340
peak=    3.286 closest distance to " C   ALA A 299 " =    0.940
peak=    3.283 closest distance to " O   HOH Z 183 " =    1.589
peak=    3.283 closest distance to " O   HOH Z 245 " =    1.369
peak=    3.280 closest distance to " CA  ALA A 233 " =    1.207
peak=    3.279 closest distance to " O   HOH Z 217 " =    1.945
peak=    3.276 closest distance to " O   HOH Z  71 " =    1.833
peak=    3.274 closest distance to " O   HOH Z 166 " =    3.581
peak=    3.274 closest distance to " NZ  LYS A 117 " =    1.080
peak=    3.273 closest distance to " O   HOH Z 157 " =    1.596
peak=    3.273 closest distance to " O   HOH Z 292 " =    1.594
peak=    3.267 closest distance to " O   HOH Z 214 " =    2.191
peak=    3.266 closest distance to " NH1AARG A 145 " =    1.142
peak=    3.264 closest distance to " CD  GLN A 194 " =    1.572
peak=    3.257 closest distance to " CB  SER A  62 " =    0.907
peak=    3.256 closest distance to " CG1 ILE A 120 " =    1.027
peak=    3.255 closest distance to " O   HOH Z 189 " =    1.494
peak=    3.254 closest distance to " O   HOH Z 163 " =    1.354
peak=    3.250 closest distance to " O   HOH Z  59 " =    2.241
peak=    3.247 closest distance to " CA  ALA A 158 " =    1.145
peak=    3.246 closest distance to " NE2 GLN A  58 " =    2.634
peak=    3.244 closest distance to " CB  ALA A   9 " =    1.495
peak=    3.243 closest distance to " O   HOH Z 155 " =    2.763
peak=    3.241 closest distance to " O   HOH Z 337 " =    3.536
peak=    3.240 closest distance to " CB  PRO A  90 " =    1.874
peak=    3.236 closest distance to " CD  PRO A  54 " =    1.072
peak=    3.235 closest distance to " CB  ASN A 127 " =    1.102
peak=    3.233 closest distance to " O   HOH Z 383 " =    1.863
peak=    3.233 closest distance to " O   HOH Z 155 " =    1.562
peak=    3.232 closest distance to " O   HOH Z 166 " =    1.272
peak=    3.228 closest distance to " CB  PRO A 163 " =    3.949
peak=    3.223 closest distance to " O   HOH Z 151 " =    1.884
peak=    3.207 closest distance to " CG2 VAL A 197 " =    1.031
peak=    3.207 closest distance to " OG BSER A 258 " =    3.367
peak=    3.198 closest distance to " O   HOH Z 144 " =    2.363
peak=    3.198 closest distance to " O   HOH Z   1 " =    2.212
peak=    3.197 closest distance to " CE1 TYR A 186 " =    1.189
peak=    3.192 closest distance to " CE  MET A 188 " =    2.232
peak=    3.190 closest distance to " N   SER A 135 " =    1.268
peak=    3.186 closest distance to " CB  TRP A 266 " =    1.049
peak=    3.186 closest distance to " CB  ALA A   1 " =    1.194
peak=    3.185 closest distance to " O   HOH Z 299 " =    2.262
peak=    3.184 closest distance to " CD  LYS A 119 " =    1.458
peak=    3.184 closest distance to " CG2 THR A 294 " =    1.539
peak=    3.183 closest distance to " O   HOH Z 325 " =    2.084
peak=    3.179 closest distance to " CD BLYS A 290 " =    1.169
peak=    3.178 closest distance to " O   HOH Z 211 " =    2.471
peak=    3.174 closest distance to " CA  ASP A 191 " =    0.809
peak=    3.166 closest distance to " O   HOH Z 215 " =    1.538
peak=    3.166 closest distance to " OD1 ASP A 286 " =    1.494
peak=    3.165 closest distance to " CG  GLN A  11 " =    1.310
peak=    3.161 closest distance to " CB  ALA A 295 " =    1.204
peak=    3.160 closest distance to " CB  ASP A 140 " =    0.746
peak=    3.155 closest distance to " O   HOH Z 261 " =    1.667
peak=    3.149 closest distance to " CD2 HIS A  81 " =    1.265
peak=    3.147 closest distance to " CB  THR A  31 " =    1.680
peak=    3.145 closest distance to " SD AMET A  47 " =    1.305
peak=    3.138 closest distance to " O   HOH Z 303 " =    1.638
peak=    3.137 closest distance to " O   HOH Z 368 " =    2.550
peak=    3.137 closest distance to " N   ASN A 127 " =    1.249
peak=    3.136 closest distance to " O   HOH Z  39 " =    2.533
peak=    3.134 closest distance to " CA  ILE A  33 " =    1.328
peak=    3.131 closest distance to " CG  MET A  93 " =    0.985
peak=    3.126 closest distance to " CB  SER A 216 " =    0.718
peak=    3.125 closest distance to " O   HOH Z 148 " =    3.038
peak=    3.122 closest distance to " CD1 ILE A 106 " =    0.937
peak=    3.120 closest distance to " O   HOH Z 234 " =    1.773
peak=    3.119 closest distance to " CA  ASN A 217 " =    1.294
peak=    3.115 closest distance to " CG  GLN A  89 " =    1.525
peak=    3.108 closest distance to " CG  ARG A 269 " =    1.020
peak=    3.102 closest distance to " O   HOH Z 394 " =    1.587
peak=    3.102 closest distance to " O   HOH Z 156 " =    2.786
peak=    3.099 closest distance to " CB  ARG A 102 " =    0.712
peak=    3.094 closest distance to " N   ARG A 156 " =    1.366
peak=    3.089 closest distance to " O   HOH Z 381 " =    1.735
peak=    3.084 closest distance to " CB  THR A  52 " =    1.197
peak=    3.072 closest distance to " OG  SER A 206 " =    1.512
peak=    3.065 closest distance to " CD1AILE A 234 " =    0.958
peak=    3.053 closest distance to " NE AARG A 275 " =    1.270
peak=    3.034 closest distance to " CA  THR A 264 " =    0.791
peak=    3.006 closest distance to " CB  PRO A  90 " =    1.258

                           ----------holes----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 208         
Filter by distance & map next to the model:
   mapped sites are within: 0.465 - 5.878
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 208
   mapped sites are within: 0.828 - 5.878

peak=   -4.711 closest distance to " O   HOH Z 266 " =    4.117
peak=   -4.371 closest distance to " OXT GLY A 302 " =    2.833
peak=   -4.286 closest distance to " C   HIS A 108 " =    1.107
peak=   -4.266 closest distance to " SG  CYS A 254 " =    3.261
peak=   -4.252 closest distance to " O   HOH Z  13 " =    1.457
peak=   -4.220 closest distance to " O   HOH Z 290 " =    0.851
peak=   -4.197 closest distance to " CD  ARG A 156 " =    2.012
peak=   -4.114 closest distance to " O   PRO A 163 " =    2.054
peak=   -4.036 closest distance to " O   HOH Z 407 " =    2.985
peak=   -4.016 closest distance to " CB  TYR A  15 " =    2.211
peak=   -4.010 closest distance to " N   GLN A  58 " =    1.662
peak=   -3.995 closest distance to " O   HOH Z 292 " =    4.398
peak=   -3.969 closest distance to " C   ALA A 158 " =    1.189
peak=   -3.958 closest distance to " O   VAL A  67 " =    2.811
peak=   -3.955 closest distance to " CD1 LEU A 101 " =    2.440
peak=   -3.953 closest distance to " CD  GLN A  58 " =    1.072
peak=   -3.942 closest distance to " ND2 ASN A 187 " =    1.455
peak=   -3.929 closest distance to " O   VAL A  67 " =    2.644
peak=   -3.887 closest distance to " N   ALA A 248 " =    1.716
peak=   -3.866 closest distance to " CD1 LEU A 228 " =    2.144
peak=   -3.857 closest distance to " O   HOH Z 234 " =    4.125
peak=   -3.848 closest distance to " OG ASER A 134 " =    1.310
peak=   -3.832 closest distance to " CG  LYS A 193 " =    2.225
peak=   -3.830 closest distance to " N   SER A 276 " =    1.255
peak=   -3.830 closest distance to " NH2 ARG A  79 " =    1.939
peak=   -3.827 closest distance to " CB  ALA A 291 " =    2.458
peak=   -3.826 closest distance to " OG  SER A  97 " =    2.061
peak=   -3.820 closest distance to " CD2 LEU A 300 " =    2.787
peak=   -3.814 closest distance to " OG BSER A 134 " =    1.717
peak=   -3.811 closest distance to " O   HOH Z  11 " =    1.776
peak=   -3.810 closest distance to " ND2 ASN A  45 " =    0.949
peak=   -3.798 closest distance to " O   SER A 210 " =    1.886
peak=   -3.787 closest distance to " O   HOH Z  92 " =    1.564
peak=   -3.775 closest distance to " OG BSER A 134 " =    1.298
peak=   -3.766 closest distance to " CE2 TYR A  30 " =    2.823
peak=   -3.760 closest distance to " O   HOH Z 118 " =    2.820
peak=   -3.735 closest distance to " O   PRO A 198 " =    1.295
peak=   -3.733 closest distance to " O   HOH Z 388 " =    1.989
peak=   -3.732 closest distance to " O   TRP A  92 " =    1.811
peak=   -3.726 closest distance to " O   HOH Z 166 " =    1.709
peak=   -3.719 closest distance to " N   THR A 220 " =    2.309
peak=   -3.714 closest distance to " O   HOH Z 377 " =    1.909
peak=   -3.690 closest distance to " CB  ALA A 161 " =    2.517
peak=   -3.689 closest distance to " O   VAL A 153 " =    2.326
peak=   -3.688 closest distance to " O   VAL A 174 " =    1.938
peak=   -3.682 closest distance to " O   ALA A 161 " =    1.572
peak=   -3.682 closest distance to " O   HOH Z   3 " =    1.861
peak=   -3.676 closest distance to " CA  GLY A 133 " =    1.783
peak=   -3.676 closest distance to " CG  ASP A 231 " =    0.828
peak=   -3.674 closest distance to " O   HOH Z  52 " =    1.605
peak=   -3.655 closest distance to " CH2 TRP A 179 " =    1.366
peak=   -3.638 closest distance to " O   HOH Z 165 " =    2.080
peak=   -3.638 closest distance to " NH1 ARG A 195 " =    2.544
peak=   -3.635 closest distance to " CB  ASN A  39 " =    2.286
peak=   -3.622 closest distance to " NH2 ARG A  66 " =    4.633
peak=   -3.620 closest distance to " OD2 ASP A 171 " =    2.334
peak=   -3.619 closest distance to " CZ  TYR A 169 " =    1.847
peak=   -3.597 closest distance to " O   HOH Z  43 " =    1.630
peak=   -3.588 closest distance to " O   HOH Z 395 " =    5.084
peak=   -3.584 closest distance to " C   GLY A  80 " =    2.327
peak=   -3.580 closest distance to " O   HOH Z 423 " =    2.276
peak=   -3.565 closest distance to " O   GLY A 196 " =    0.973
peak=   -3.559 closest distance to " CG  GLU A  53 " =    1.535
peak=   -3.550 closest distance to " C   THR A 279 " =    1.216
peak=   -3.550 closest distance to " O   HOH Z 126 " =    1.880
peak=   -3.547 closest distance to " CD1 PHE A 130 " =    2.227
peak=   -3.544 closest distance to " N   GLN A 122 " =    1.533
peak=   -3.536 closest distance to " CB  ALA A 244 " =    2.058
peak=   -3.528 closest distance to " CD  ARG A 139 " =    1.598
peak=   -3.524 closest distance to " O   HOH Z 198 " =    1.983
peak=   -3.524 closest distance to " O   SER A 273 " =    1.287
peak=   -3.520 closest distance to " O   HOH Z  11 " =    1.835
peak=   -3.510 closest distance to " CD  GLN A  58 " =    1.375
peak=   -3.497 closest distance to " O   HOH Z 435 " =    2.648
peak=   -3.488 closest distance to " OG  SER A  62 " =    1.434
peak=   -3.478 closest distance to " ND2 ASN A  39 " =    1.170
peak=   -3.473 closest distance to " CD1 PHE A  59 " =    1.950
peak=   -3.468 closest distance to " O   HOH Z 360 " =    2.472
peak=   -3.465 closest distance to " O   ALA A 160 " =    1.469
peak=   -3.464 closest distance to " O   HOH Z 362 " =    5.878
peak=   -3.447 closest distance to " O   ASN A  45 " =    1.822
peak=   -3.447 closest distance to " O   PRO A 198 " =    1.297
peak=   -3.444 closest distance to " OE1 GLN A 223 " =    2.263
peak=   -3.439 closest distance to " CD2 LEU A 237 " =    2.649
peak=   -3.438 closest distance to " O   PHE A 218 " =    1.550
peak=   -3.436 closest distance to " CB  CYS A 201 " =    2.554
peak=   -3.435 closest distance to " CB  PRO A 243 " =    2.565
peak=   -3.434 closest distance to " N   HIS A 115 " =    1.987
peak=   -3.431 closest distance to " O   HOH Z 427 " =    1.373
peak=   -3.431 closest distance to " C   ASN A 285 " =    2.180
peak=   -3.430 closest distance to " CD  LYS A 289 " =    2.532
peak=   -3.427 closest distance to " O   SER A 135 " =    1.620
peak=   -3.423 closest distance to " O   HOH Z 417 " =    2.509
peak=   -3.418 closest distance to " O   SER A 146 " =    0.851
peak=   -3.409 closest distance to " O   HOH Z 385 " =    2.006
peak=   -3.409 closest distance to " CD1 TYR A 247 " =    2.452
peak=   -3.408 closest distance to " O   LEU A 167 " =    1.582
peak=   -3.403 closest distance to " CG  ASP A 132 " =    2.262
peak=   -3.399 closest distance to " CE  MET A 105 " =    1.758
peak=   -3.399 closest distance to " CB  SER A 258 " =    1.986
peak=   -3.398 closest distance to " O   HOH Z  15 " =    1.611
peak=   -3.392 closest distance to " O   HOH Z 250 " =    1.365
peak=   -3.389 closest distance to " O   ALA A 256 " =    1.450
peak=   -3.387 closest distance to " O   ASN A 187 " =    1.439
peak=   -3.382 closest distance to " CB  PHE A 208 " =    2.231
peak=   -3.377 closest distance to " O   HOH Z 311 " =    3.469
peak=   -3.373 closest distance to " O   HOH Z  93 " =    1.386
peak=   -3.371 closest distance to " CD1 LEU A  83 " =    2.312
peak=   -3.370 closest distance to " O   ASP A 231 " =    2.502
peak=   -3.366 closest distance to " O   HOH Z  71 " =    1.344
peak=   -3.356 closest distance to " O   HOH Z 313 " =    1.027
peak=   -3.353 closest distance to " CB  PHE A 192 " =    1.878
peak=   -3.349 closest distance to " CA  ASP A 298 " =    1.100
peak=   -3.347 closest distance to " OD1 ASP A 200 " =    1.216
peak=   -3.342 closest distance to " O   HOH Z  10 " =    1.535
peak=   -3.340 closest distance to " OG  SER A   3 " =    1.688
peak=   -3.337 closest distance to " N   ALA A 248 " =    2.221
peak=   -3.309 closest distance to " CD  GLN A  88 " =    0.998
peak=   -3.301 closest distance to " N   GLN A  58 " =    1.354
peak=   -3.297 closest distance to " CE3 TRP A 274 " =    2.463
peak=   -3.296 closest distance to " O   MET A  40 " =    2.677
peak=   -3.294 closest distance to " O   HOH Z  97 " =    1.375
peak=   -3.289 closest distance to " CG  ASP A  50 " =    2.422
peak=   -3.289 closest distance to " O   HOH Z 265 " =    1.951
peak=   -3.287 closest distance to " OXT GLY A 302 " =    3.047
peak=   -3.284 closest distance to " O   VAL A 197 " =    1.094
peak=   -3.280 closest distance to " CZ3 TRP A 274 " =    1.090
peak=   -3.277 closest distance to " CG  ARG A 269 " =    2.221
peak=   -3.276 closest distance to " CG  ASN A 110 " =    1.183
peak=   -3.273 closest distance to " OG  SER A  63 " =    1.365
peak=   -3.272 closest distance to " O   HOH Z 310 " =    3.540
peak=   -3.272 closest distance to " O   HOH Z 185 " =    2.247
peak=   -3.269 closest distance to " O   HOH Z  17 " =    1.420
peak=   -3.269 closest distance to " O   HOH Z  52 " =    0.863
peak=   -3.268 closest distance to " O   HOH Z 351 " =    1.538
peak=   -3.262 closest distance to " O   TYR A 186 " =    1.447
peak=   -3.261 closest distance to " O   HOH Z 377 " =    1.377
peak=   -3.260 closest distance to " O   HOH Z 418 " =    1.417
peak=   -3.259 closest distance to " N   ALA A  43 " =    2.478
peak=   -3.256 closest distance to " ND2 ASN A  69 " =    1.415
peak=   -3.254 closest distance to " OG1 THR A 279 " =    1.351
peak=   -3.253 closest distance to " O   LEU A 228 " =    2.429
peak=   -3.251 closest distance to " N   SER A 206 " =    1.787
peak=   -3.251 closest distance to " CB  ALA A 248 " =    1.946
peak=   -3.250 closest distance to " O   HOH Z 222 " =    1.171
peak=   -3.247 closest distance to " O   HOH Z 100 " =    0.834
peak=   -3.246 closest distance to " CG2 THR A 178 " =    2.056
peak=   -3.241 closest distance to " ND2 ASN A 209 " =    1.561
peak=   -3.239 closest distance to " OG1 THR A 178 " =    1.238
peak=   -3.238 closest distance to " CE  MET A  93 " =    1.180
peak=   -3.237 closest distance to " O   HOH Z 196 " =    1.945
peak=   -3.234 closest distance to " OD1 ASP A 171 " =    1.624
peak=   -3.230 closest distance to " OD1 ASP A 191 " =    1.664
peak=   -3.225 closest distance to " CG  GLU A 277 " =    1.152
peak=   -3.222 closest distance to " CE3 TRP A 123 " =    1.264
peak=   -3.219 closest distance to " CG  PHE A 283 " =    2.618
peak=   -3.209 closest distance to " O   HOH Z 297 " =    2.796
peak=   -3.201 closest distance to " SG ACYS A 201 " =    2.216
peak=   -3.198 closest distance to " CG1 VAL A 112 " =    2.716
peak=   -3.197 closest distance to " CG  PRO A 243 " =    1.627
peak=   -3.196 closest distance to " OH  TYR A 214 " =    1.326
peak=   -3.195 closest distance to " O   HOH Z  41 " =    2.279
peak=   -3.191 closest distance to " CB  ASP A 286 " =    2.066
peak=   -3.188 closest distance to " CB  ASP A 124 " =    2.071
peak=   -3.183 closest distance to " O   HOH Z 116 " =    1.164
peak=   -3.179 closest distance to " O   GLY A 118 " =    2.266
peak=   -3.177 closest distance to " O   HOH Z 385 " =    3.415
peak=   -3.173 closest distance to " O   HOH Z 431 " =    1.872
peak=   -3.170 closest distance to " O   ALA A  34 " =    2.396
peak=   -3.168 closest distance to " O   HOH Z 148 " =    3.558
peak=   -3.164 closest distance to " O   HOH Z 361 " =    3.448
peak=   -3.158 closest distance to " O   HOH Z 424 " =    3.012
peak=   -3.153 closest distance to " CB  ALA A   1 " =    2.138
peak=   -3.153 closest distance to " NE2 GLN A 194 " =    1.583
peak=   -3.152 closest distance to " CA  TRP A 274 " =    1.643
peak=   -3.150 closest distance to " O   HOH Z 174 " =    4.101
peak=   -3.149 closest distance to " CG2 VAL A 189 " =    2.188
peak=   -3.148 closest distance to " N   ALA A 226 " =    1.912
peak=   -3.145 closest distance to " O   HOH Z 197 " =    5.002
peak=   -3.139 closest distance to " OD1 ASN A 249 " =    1.007
peak=   -3.138 closest distance to " CZ  PHE A 130 " =    0.829
peak=   -3.133 closest distance to " NH2 ARG A  66 " =    1.922
peak=   -3.133 closest distance to " O   HOH Z  90 " =    2.842
peak=   -3.133 closest distance to " CE3 TRP A 150 " =    1.914
peak=   -3.124 closest distance to " CG  LYS A 119 " =    2.892
peak=   -3.123 closest distance to " O   HOH Z 264 " =    1.813
peak=   -3.117 closest distance to " O   HOH Z  61 " =    1.661
peak=   -3.115 closest distance to " N   ARG A 159 " =    1.559
peak=   -3.114 closest distance to " N   VAL A 189 " =    1.640
peak=   -3.110 closest distance to " O   ALA A  51 " =    1.435
peak=   -3.109 closest distance to " O   HOH Z 263 " =    3.006
peak=   -3.103 closest distance to " CB  CYS A 254 " =    2.633
peak=   -3.094 closest distance to " OG  SER A 206 " =    1.584
peak=   -3.092 closest distance to " O   SER A 146 " =    0.931
peak=   -3.089 closest distance to " NH2 ARG A  66 " =    4.688
peak=   -3.089 closest distance to " OE1 GLN A  77 " =    1.672
peak=   -3.082 closest distance to " OG1 THR A  82 " =    1.400
peak=   -3.082 closest distance to " O   HOH Z 137 " =    1.470
peak=   -3.070 closest distance to " C   LEU A 143 " =    1.179
peak=   -3.067 closest distance to " O   HOH Z 422 " =    1.422
peak=   -3.064 closest distance to " O   HOH Z 298 " =    2.634
peak=   -3.063 closest distance to " O   HOH Z 384 " =    2.379
peak=   -3.061 closest distance to " OG  SER A 273 " =    2.128
peak=   -3.059 closest distance to " OG  SER A  87 " =    1.245
peak=   -3.055 closest distance to " O   GLU A 152 " =    1.623
peak=   -3.052 closest distance to " NE  ARG A 259 " =    1.213
peak=   -3.042 closest distance to " O   HOH Z 396 " =    1.617

================= 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_occ: refinement of individual occupancies                             
------------------------------------------------------------------------
 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    :  0.4393 0.4324   6.242044e+00   6.240473e+00
   1_bss:  0.4303 0.4230   6.234146e+00   6.222176e+00
   1_xyz:  0.2773 0.3023   5.894622e+00   5.970297e+00
   1_adp:  0.2509 0.3133   5.839718e+00   5.992590e+00
   1_occ:  0.2508 0.3136   5.838975e+00   5.991789e+00
   2_bss:  0.2466 0.3096   5.831163e+00   5.985660e+00
   2_xyz:  0.1857 0.2410   5.584710e+00   5.782638e+00
   2_adp:  0.1696 0.2292   5.511921e+00   5.725076e+00
   2_occ:  0.1694 0.2292   5.511704e+00   5.724808e+00
   3_bss:  0.1696 0.2276   5.508115e+00   5.719488e+00
   3_xyz:  0.1345 0.1876   5.307193e+00   5.546072e+00
   3_adp:  0.1263 0.1726   5.237066e+00   5.457355e+00
   3_occ:  0.1261 0.1723   5.236016e+00   5.456645e+00
   4_bss:  0.1265 0.1719   5.237452e+00   5.455583e+00
   4_xyz:  0.1200 0.1637   5.194122e+00   5.409897e+00
   4_adp:  0.1174 0.1639   5.182815e+00   5.407793e+00
   4_occ:  0.1174 0.1638   5.182450e+00   5.407723e+00
   5_bss:  0.1173 0.1638   5.182482e+00   5.407745e+00
   5_xyz:  0.1107 0.1588   5.140090e+00   5.380028e+00
   5_adp:  0.1107 0.1576   5.136448e+00   5.374567e+00
   5_occ:  0.1107 0.1575   5.136244e+00   5.374750e+00
   5_bss:  0.1107 0.1576   5.136284e+00   5.374789e+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:  0.322  21.975  -1.817  -0.396   2.572  -0.000   0.000   0.000
   1_xyz:  0.322  21.975  -1.817  -0.396   2.572  -0.000   0.000   0.000
   1_adp:  0.322  21.975  -1.817  -0.396   2.572  -0.000   0.000   0.000
   1_occ:  0.322  21.975  -1.817  -0.396   2.572  -0.000   0.000   0.000
   2_bss:  0.333  50.000  -2.720  -1.336  -0.191  -0.000  -0.000  -0.000
   2_xyz:  0.333  50.000  -2.720  -1.336  -0.191  -0.000  -0.000  -0.000
   2_adp:  0.333  50.000  -2.720  -1.336  -0.191  -0.000  -0.000  -0.000
   2_occ:  0.333  50.000  -2.720  -1.336  -0.191  -0.000  -0.000  -0.000
   3_bss:  0.318  41.186  -2.538  -1.341  -1.021  -0.000  -0.000  -0.000
   3_xyz:  0.318  41.186  -2.538  -1.341  -1.021  -0.000  -0.000  -0.000
   3_adp:  0.318  41.186  -2.538  -1.341  -1.021  -0.000  -0.000  -0.000
   3_occ:  0.318  41.186  -2.538  -1.341  -1.021  -0.000  -0.000  -0.000
   4_bss:  0.320  41.135  -2.785  -1.714  -1.666  -0.000  -0.000  -0.000
   4_xyz:  0.320  41.135  -2.785  -1.714  -1.666  -0.000  -0.000  -0.000
   4_adp:  0.320  41.135  -2.785  -1.714  -1.666  -0.000  -0.000  -0.000
   4_occ:  0.320  41.135  -2.785  -1.714  -1.666  -0.000  -0.000  -0.000
   5_bss:  0.320  41.135  -2.785  -1.714  -1.666  -0.000  -0.000  -0.000
   5_xyz:  0.320  41.135  -2.785  -1.714  -1.666  -0.000  -0.000  -0.000
   5_adp:  0.320  41.135  -2.785  -1.714  -1.666  -0.000  -0.000  -0.000
   5_occ:  0.320  41.135  -2.785  -1.714  -1.666  -0.000  -0.000  -0.000
   5_bss:  0.322  41.145  -2.672  -1.653  -1.638  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.799 0.4853  0.6549    60054.258
   1_bss:  51.379 0.5013  0.6813    55877.615
   1_xyz:  31.024 0.7470  0.9637    24261.607
   1_adp:  32.629 0.7277  0.9489    25929.826
   1_occ:  32.617 0.7278  0.9487    25882.990
   2_bss:  32.183 0.7322  0.9039    25238.702
   2_xyz:  24.091 0.8197  0.9777    14992.104
   2_adp:  21.896 0.8430  0.9824    13080.344
   2_occ:  21.892 0.8430  0.9823    13076.397
   3_bss:  21.716 0.8445  0.9753    12855.425
   3_xyz:  17.775 0.8814  0.9977     8782.313
   3_adp:  15.652 0.9010  1.0030     7410.895
   3_occ:  15.636 0.9012  1.0029     7396.124
   4_bss:  15.595 0.9016  0.9874     7387.947
   4_xyz:  14.538 0.9106  0.9912     6637.741
   4_adp:  14.422 0.9119  0.9889     6633.679
   4_occ:  14.413 0.9120  0.9888     6627.840
   5_bss:  14.414 0.9120  0.9888     6628.675
   5_xyz:  13.924 0.9156  0.9891     6259.342
   5_adp:  13.768 0.9170  0.9857     6213.647
   5_occ:  13.767 0.9170  0.9856     6212.640
   5_bss:  13.767 0.9170  0.9858     6215.707
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   2.0541e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   2.0541e-01
   1_xyz:   1.475  0.012  0.092 16.348  0.006  4.112   1.2423e-01
   1_adp:   1.475  0.012  0.092 16.348  0.006  4.112   1.2423e-01
   1_occ:   1.475  0.012  0.092 16.348  0.006  4.112   1.2423e-01
   2_bss:   1.475  0.012  0.092 16.348  0.006  4.112   1.2423e-01
   2_xyz:   1.062  0.006  0.068 14.694  0.004  4.109   6.1014e-02
   2_adp:   1.062  0.006  0.068 14.694  0.004  4.109   6.1014e-02
   2_occ:   1.062  0.006  0.068 14.694  0.004  4.109   6.1014e-02
   3_bss:   1.062  0.006  0.068 14.694  0.004  4.109   6.1014e-02
   3_xyz:   1.065  0.008  0.072 14.907  0.004  4.111   6.5871e-02
   3_adp:   1.065  0.008  0.072 14.907  0.004  4.111   6.5871e-02
   3_occ:   1.065  0.008  0.072 14.907  0.004  4.111   6.5871e-02
   4_bss:   1.065  0.008  0.072 14.907  0.004  4.111   6.5871e-02
   4_xyz:   0.915  0.005  0.065 14.607  0.004  4.113   5.0849e-02
   4_adp:   0.915  0.005  0.065 14.607  0.004  4.113   5.0849e-02
   4_occ:   0.915  0.005  0.065 14.607  0.004  4.113   5.0849e-02
   5_bss:   0.915  0.005  0.065 14.607  0.004  4.113   5.0849e-02
   5_xyz:   1.010  0.006  0.071 14.803  0.004  4.107   5.8632e-02
   5_adp:   1.010  0.006  0.071 14.803  0.004  4.107   5.8632e-02
   5_occ:   1.010  0.006  0.071 14.803  0.004  4.107   5.8632e-02
   5_bss:   1.010  0.006  0.071 14.803  0.004  4.107   5.8632e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.294   2.4050e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.294   2.4050e-01
   1_xyz:   8.498  0.094  0.303 87.253  0.032  2.096   1.1597e-01
   1_adp:   8.498  0.094  0.303 87.253  0.032  2.096   1.1597e-01
   1_occ:   8.498  0.094  0.303 87.253  0.032  2.096   1.1597e-01
   2_bss:   8.498  0.094  0.303 87.253  0.032  2.096   1.1597e-01
   2_xyz:   7.689  0.033  0.207 82.973  0.044  2.286   5.4109e-02
   2_adp:   7.689  0.033  0.207 82.973  0.044  2.286   5.4109e-02
   2_occ:   7.689  0.033  0.207 82.973  0.044  2.286   5.4109e-02
   3_bss:   7.689  0.033  0.207 82.973  0.044  2.286   5.4109e-02
   3_xyz:   7.009  0.046  0.324 80.922  0.038  2.332   7.3987e-02
   3_adp:   7.009  0.046  0.324 80.922  0.038  2.332   7.3987e-02
   3_occ:   7.009  0.046  0.324 80.922  0.038  2.332   7.3987e-02
   4_bss:   7.009  0.046  0.324 80.922  0.038  2.332   7.3987e-02
   4_xyz:   6.346  0.030  0.202 84.044  0.034  2.396   3.2366e-02
   4_adp:   6.346  0.030  0.202 84.044  0.034  2.396   3.2366e-02
   4_occ:   6.346  0.030  0.202 84.044  0.034  2.396   3.2366e-02
   5_bss:   6.346  0.030  0.202 84.044  0.034  2.396   3.2366e-02
   5_xyz:   6.834  0.036  0.232 82.231  0.036  2.319   3.9892e-02
   5_adp:   6.834  0.036  0.232 82.231  0.036  2.319   3.9892e-02
   5_occ:   6.834  0.036  0.232 82.231  0.036  2.319   3.9892e-02
   5_bss:   6.834  0.036  0.232 82.231  0.036  2.319   3.9892e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  80.68   0.00  18.76  80.25   0.00  14.56  80.68   3.67  41.64
   1_occ:  80.68   0.00  18.76  80.25   0.00  14.56  80.68   3.67  41.64
   2_bss:  80.68   0.00  18.76  80.25   0.00  14.56  80.68   3.67  41.64
   2_xyz:  80.68   0.00  18.76  80.25   0.00  14.56  80.68   3.67  41.64
   2_adp: 104.49   0.00  18.97 104.49   0.00  14.11  95.13   5.23  45.39
   2_occ: 104.49   0.00  18.97 104.49   0.00  14.11  95.13   5.23  45.39
   3_bss: 104.49   0.00  18.97 104.49   0.00  14.11  95.13   5.23  45.39
   3_xyz: 104.49   0.00  18.97 104.49   0.00  14.11  95.13   5.23  45.39
   3_adp: 101.20   1.67  17.54 101.20   1.67  13.20  82.61   5.49  41.17
   3_occ: 101.20   1.67  17.54 101.20   1.67  13.20  82.61   5.49  41.17
   4_bss: 101.20   1.67  17.54 101.20   1.67  13.20  82.61   5.49  41.17
   4_xyz: 101.20   1.67  17.54 101.20   1.67  13.20  82.61   5.49  41.17
   4_adp: 103.34   1.73  17.40 103.34   1.73  13.04  87.80   5.84  41.13
   4_occ: 103.34   1.73  17.40 103.34   1.73  13.04  87.80   5.84  41.13
   5_bss: 103.34   1.73  17.40 103.34   1.73  13.04  87.80   5.84  41.13
   5_xyz: 103.34   1.73  17.40 103.34   1.73  13.04  87.80   5.84  41.13
   5_adp: 101.44   1.76  16.94 101.44   1.76  12.83  88.85   5.31  39.30
   5_occ: 101.44   1.76  16.94 101.44   1.76  12.83  88.85   5.31  39.30
   5_bss: 101.37   1.70  16.88 101.37   1.70  12.77  88.79   5.24  39.24
------------------------------------------------------------------------
 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:    1.971    0.009    0.451
   1_adp:    1.971    0.009    0.451
   1_occ:    1.971    0.009    0.451
   2_bss:    1.971    0.009    0.451
   2_xyz:    1.643    0.030    0.530
   2_adp:    1.643    0.030    0.530
   2_occ:    1.643    0.030    0.530
   3_bss:    1.643    0.030    0.530
   3_xyz:    1.520    0.016    0.622
   3_adp:    1.520    0.016    0.622
   3_occ:    1.520    0.016    0.622
   4_bss:    1.520    0.016    0.622
   4_xyz:    1.610    0.029    0.639
   4_adp:    1.610    0.029    0.639
   4_occ:    1.610    0.029    0.639
   5_bss:    1.610    0.029    0.639
   5_xyz:    1.605    0.060    0.660
   5_adp:    1.605    0.060    0.660
   5_occ:    1.605    0.060    0.660
   5_bss:    1.605    0.060    0.660
------------------------------------------------------------------------

CPU time actual refinement: 333.31


============================== Exporting results ==============================

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_319/model_refine_001.pdb
n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  106
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

Writing 2mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_319/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_319/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_319/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_319/model_refine_002.def


=============================== Detailed timings ==============================

Pure refinement (no I/O, processing, etc)= 333.16 
  Macro-tasks:
    bulk solvent and scale       = 43.26  
    individual site refinement   = 134.16 
    weights calculation          = 29.63  
    collect and process          = 6.50   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 213.65 
  Micro-tasks:
    mask                            = 1.87   
    f_calc                          = 105.07 
    alpha_beta                      = 8.29   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 113.10 
    fmodel                         = 7.04   
    r_factors                      = 0.28   
    phase_errors                   = 10.53  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 247.60 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.784 micro seconds
Total CPU time: 5.78 minutes
from_scatterers_fft:    624 calls, 104.76 s
gradients_fft:          569 calls, 100.31 s

=========================== phenix.refine: finished ===========================

# Date 2008-01-16 Time 04:32:39 PST -0800 (1200486759.96 s)
Start R-work = 0.4393, R-free = 0.4324 (no bulk solvent and anisotropic scale)
Final R-work = 0.1358, R-free = 0.1790 (no bulk solvent and anisotropic scale)

Start R-work = 0.4303, R-free = 0.4230
Final R-work = 0.1107, R-free = 0.1576