# Date 2008-01-16 Time 03:31:55 PST -0800 (1200483115.70 s)
#phil __OFF__

Command line arguments: "../1272.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26461
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1272

-------------------------------------------------------------------------------
  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.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (72.0062, 46.93, 87.2539, 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: 3.26, per 1000 atoms: 1.15


================================== 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: (72.0062, 46.93, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3069 2.00276
Completeness in resolution range: 0.956588
Completeness with d_max=infinity: 0.953747

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3069
                             d_min =   2.0028

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: (72.0062, 46.93, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3069 2.00276
Completeness in resolution range: 0.956588
Completeness with d_max=infinity: 0.953747

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3073 -  4.2862 [2146/2172]  1933   213   9.9%
  bin  2:  4.2862 -  3.4145 [2067/2087]  1858   209  10.1%
  bin  3:  3.4145 -  2.9865 [2044/2063]  1842   202   9.9%
  bin  4:  2.9865 -  2.7151 [2019/2049]  1815   204  10.1%
  bin  5:  2.7151 -  2.5214 [2016/2035]  1820   196   9.7%
  bin  6:  2.5214 -  2.3734 [1989/2014]  1779   210  10.6%
  bin  7:  2.3734 -  2.2549 [1996/2024]  1801   195   9.8%
  bin  8:  2.2549 -  2.1570 [1981/2017]  1784   197   9.9%
  bin  9:  2.1570 -  2.0742 [1962/2004]  1763   199  10.1%
  bin 10:  2.0742 -  2.0028 [1369/2013]  1235   134   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1272/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: 0.13 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:
        1.76 -     2.39: 6
        2.39 -     3.02: 1997
        3.02 -     3.64: 4523
        3.64 -     4.27: 8969
        4.27 -     4.90: 12400
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.762 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.086 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.325 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27890 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 =====================

Setting all isotropic ADP = 10.000: selected atoms: all (2823)
Shaking sites (RMS = 0.500): selected atoms: all (2823)

==================== 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/trial/run_1272/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1272/model_refine_001.geo

CPU time processing inputs: 9.17


============================ 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 = 72.00625 46.93 87.2539 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
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4651   r_free= 0.4540   ksol= 0.00   Bsol= 0.00   scale= 0.791    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.267491                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3073 -  4.7810 0.99   1395  157 0.3841 0.3532      6.5779      6.5031|
|  2:  4.7810 -  3.8141 0.99   1343  148 0.3720 0.3942       6.754      6.7755|
|  3:  3.8141 -  3.3377 0.99   1326  144 0.4167 0.3728      6.6336      6.6462|
|  4:  3.3377 -  3.0351 0.99   1313  153 0.4454 0.4047      6.5048      6.4185|
|  5:  3.0351 -  2.8190 0.99   1296  143 0.4885 0.5093      6.3559      6.4014|
|  6:  2.8190 -  2.6537 0.99   1303  140 0.4846 0.5097      6.2617      6.2048|
|  7:  2.6537 -  2.5214 0.99   1292  139 0.5211 0.5268      6.2501      6.2494|
|  8:  2.5214 -  2.4121 0.98   1260  147 0.5267 0.4704      6.1647      6.1395|
|  9:  2.4121 -  2.3196 0.98   1272  148 0.4971 0.5520      6.1076      6.1942|
| 10:  2.3196 -  2.2398 1.00   1298  139 0.5210 0.4581      6.1089      6.0538|
| 11:  2.2398 -  2.1700 0.98   1286  137 0.5252 0.4724      6.0398      6.0198|
| 12:  2.1700 -  2.1081 0.98   1246  145 0.5123 0.5476      5.9687      6.0212|
| 13:  2.1081 -  2.0527 0.99   1283  137 0.5296 0.4846      5.8921      5.7991|
| 14:  2.0527 -  2.0028 0.55    717   82 0.5120 0.4465      5.8737      5.7421|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3073 -  4.7810  1395   157  0.72  32.25   0.79     0.76      64301.53|
|  2:  4.7810 -  3.8141  1343   148  0.74  31.96   0.88     0.79      89517.52|
|  3:  3.8141 -  3.3377  1326   144  0.65  39.51   0.83     0.74      96282.07|
|  4:  3.3377 -  3.0351  1313   153  0.57  46.08   0.80     0.66      88212.54|
|  5:  3.0351 -  2.8190  1296   143  0.47  54.40   0.73     0.55      75383.57|
|  6:  2.8190 -  2.6537  1303   140  0.43  57.84   0.74     0.48      68572.44|
|  7:  2.6537 -  2.5214  1292   139  0.37  61.94   0.72     0.41      64496.19|
|  8:  2.5214 -  2.4121  1260   147  0.35  64.05   0.70     0.40      59775.76|
|  9:  2.4121 -  2.3196  1272   148  0.37  61.94   0.73     0.41      52410.31|
| 10:  2.3196 -  2.2398  1298   139  0.39  60.88   0.74     0.45      46306.84|
| 11:  2.2398 -  2.1700  1286   137  0.38  61.50   0.76     0.45      43397.17|
| 12:  2.1700 -  2.1081  1246   145  0.38  61.28   0.75     0.46      40687.47|
| 13:  2.1081 -  2.0527  1283   137  0.41  59.52   0.70     0.49      32884.62|
| 14:  2.0527 -  2.0028   717    82  0.56  47.79   0.71     0.56      20329.28|
|alpha:            min =        0.40 max =            0.79 mean =         0.55|
|beta:             min =    20329.28 max =        96282.07 mean =     61778.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           89.99 mean =        52.82|
|phase err.(test): min =        0.00 max =           89.89 mean =        52.55|
|-----------------------------------------------------------------------------|

============================== 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 = 11.368679             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.380   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.967839              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.970   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      160 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      678 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1481 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2578 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3882 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4968 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6480 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7600 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.432 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.609 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.314)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    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:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 12.314)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     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:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4709   r_free= 0.4591   ksol= 0.00   Bsol= 0.00   scale= 0.762    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.267977                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4572   r_free= 0.4438   ksol= 0.30   Bsol= 20.00   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (10.22,6.93,8.80,0.00,0.00,0.00); trace/3= 8.65                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.260470                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.664501             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.683   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.913645              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.017   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4572      final r-factor (work) = 0.3626          |
| start r-factor (free) = 0.4438      final r-factor (free) = 0.3834          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 87.8603 = 10.66 * 0.50 * 6.2691 + 1.00 * 54.4319                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.9392 = 10.66 * 0.50 * 6.1519 + 1.00 * 0.1356                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3626      final r-factor (work) = 0.3132          |
| start r-factor (free) = 0.3834      final r-factor (free) = 0.3532          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6351 = 0.91 * 1.00 * 6.1519 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5359 = 0.91 * 1.00 * 6.0432 + 1.00 * 0.0146                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.314)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    64.78   11.69    None  None   None       |
|    all(noH): 2823   0      0.00    64.78   11.69    None  None   None       |
|    Sol.    : 438    0      0.00    64.78   26.73    None  None   None       |
|    Mac.    : 2385   0      0.00    59.83   8.93     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 -   6.478: 1175   |   5:    32.388 -  38.866:   80        |
|      1:     6.478 -  12.955:  725   |   6:    38.866 -  45.344:   51        |
|      2:    12.955 -  19.433:  371   |   7:    45.344 -  51.821:   42        |
|      3:    19.433 -  25.911:  232   |   8:    51.821 -  58.299:   14        |
|      4:    25.911 -  32.388:  127   |   9:    58.299 -  64.776:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3132 r_free = 0.3532             target_work(ml) = 6.013         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3126 r_free = 0.3544             target_work(ml) = 6.012         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3126   r_free= 0.3544   ksol= 0.30   Bsol= 20.00   scale= 1.075   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (10.22,6.93,8.80,0.00,0.00,0.00); trace/3= 8.65                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.012122                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3099   r_free= 0.3498   ksol= 0.32   Bsol= 50.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.83,3.99,5.78,0.00,0.00,0.00); trace/3= 5.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.011877                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.280455              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.645   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.489800              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.219  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3099      final r-factor (work) = 0.2293          |
| start r-factor (free) = 0.3498      final r-factor (free) = 0.2810          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.0605 = 4.28 * 0.50 * 6.0390 + 1.00 * 0.1356                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.6698 = 4.28 * 0.50 * 5.8835 + 1.00 * 0.0778                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2293      final r-factor (work) = 0.2116          |
| start r-factor (free) = 0.2810      final r-factor (free) = 0.2619          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9046 = 0.49 * 1.00 * 5.8835 + 1.00 * 0.0229                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8576 = 0.49 * 1.00 * 5.7216 + 1.00 * 0.0552                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 7      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.314)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.07   11.93    None  None   None       |
|    all(noH): 2823   0      0.00    98.07   11.93    None  None   None       |
|    Sol.    : 438    0      0.00    66.60   30.10    None  None   None       |
|    Mac.    : 2385   0      0.00    98.07   8.60     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 -   9.807: 1658   |   5:    49.034 -  58.841:   37        |
|      1:     9.807 -  19.614:  626   |   6:    58.841 -  68.647:    8        |
|      2:    19.614 -  29.420:  257   |   7:    68.647 -  78.454:    0        |
|      3:    29.420 -  39.227:  154   |   8:    78.454 -  88.261:    0        |
|      4:    39.227 -  49.034:   82   |   9:    88.261 -  98.068:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2116 r_free = 0.2619             target_work(ml) = 5.694         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2114 r_free = 0.2618             target_work(ml) = 5.694         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2114   r_free= 0.2618   ksol= 0.32   Bsol= 50.00   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.83,3.99,5.78,0.00,0.00,0.00); trace/3= 5.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.693663                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2100   r_free= 0.2603   ksol= 0.33   Bsol= 50.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.20,2.95,4.33,0.00,0.00,0.00); trace/3= 3.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.693975                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.817217              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.073   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.039565              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.732   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2100      final r-factor (work) = 0.1602          |
| start r-factor (free) = 0.2603      final r-factor (free) = 0.2083          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0031 = 3.82 * 0.50 * 5.7242 + 1.00 * 0.0778                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7219 = 3.82 * 0.50 * 5.5791 + 1.00 * 0.0735                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1602      final r-factor (work) = 0.1442          |
| start r-factor (free) = 0.2083      final r-factor (free) = 0.1962          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8171 = 1.04 * 1.00 * 5.5791 + 1.00 * 0.0172                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6263 = 1.04 * 1.00 * 5.3974 + 1.00 * 0.0153                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.314)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.91   13.13    None  None   None       |
|    all(noH): 2823   0      0.00    80.91   13.13    None  None   None       |
|    Sol.    : 438    0      0.40    80.91   37.84    None  None   None       |
|    Mac.    : 2385   0      0.00    77.19   8.59     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 -   8.091: 1508   |   5:    40.454 -  48.545:   84        |
|      1:     8.091 -  16.182:  668   |   6:    48.545 -  56.636:   76        |
|      2:    16.182 -  24.272:  201   |   7:    56.636 -  64.726:   49        |
|      3:    24.272 -  32.363:  100   |   8:    64.726 -  72.817:   20        |
|      4:    32.363 -  40.454:  105   |   9:    72.817 -  80.908:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1442 r_free = 0.1962             target_work(ml) = 5.372         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1441 r_free = 0.1962             target_work(ml) = 5.372         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1441   r_free= 0.1962   ksol= 0.33   Bsol= 50.00   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.20,2.95,4.33,0.00,0.00,0.00); trace/3= 3.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.371718                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1441   r_free= 0.1962   ksol= 0.34   Bsol= 68.36   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.08,2.39,3.77,0.00,0.00,0.00); trace/3= 3.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.371785                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.936600              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.569  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.554320              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.253  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1441      final r-factor (work) = 0.1338          |
| start r-factor (free) = 0.1962      final r-factor (free) = 0.1856          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3030 = 1.94 * 0.50 * 5.4008 + 1.00 * 0.0735                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2313 = 1.94 * 0.50 * 5.3403 + 1.00 * 0.0603                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1338      final r-factor (work) = 0.1315          |
| start r-factor (free) = 0.1856      final r-factor (free) = 0.1818          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9756 = 0.55 * 1.00 * 5.3403 + 1.00 * 0.0154                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1350 = 0.55 * 1.00 * 5.3058 + 1.00 * 0.1939                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.314)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.03   12.95    None  None   None       |
|    all(noH): 2823   0      0.00    82.03   12.95    None  None   None       |
|    Sol.    : 438    0      0.87    82.03   37.70    None  None   None       |
|    Mac.    : 2385   0      0.00    78.75   8.40     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 -   8.203: 1577   |   5:    41.014 -  49.216:   89        |
|      1:     8.203 -  16.406:  627   |   6:    49.216 -  57.419:   75        |
|      2:    16.406 -  24.608:  184   |   7:    57.419 -  65.622:   44        |
|      3:    24.608 -  32.811:  105   |   8:    65.622 -  73.824:   19        |
|      4:    32.811 -  41.014:   92   |   9:    73.824 -  82.027:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1315 r_free = 0.1818             target_work(ml) = 5.295         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1313 r_free = 0.1819             target_work(ml) = 5.295         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1313   r_free= 0.1819   ksol= 0.34   Bsol= 68.36   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.08,2.39,3.77,0.00,0.00,0.00); trace/3= 3.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.294953                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1313   r_free= 0.1819   ksol= 0.33   Bsol= 65.83   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.08,2.39,3.77,0.00,0.00,0.00); trace/3= 3.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.294855                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.288985              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.216  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.537458              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.185   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1313      final r-factor (work) = 0.1230          |
| start r-factor (free) = 0.1819      final r-factor (free) = 0.1734          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1321 = 2.29 * 0.50 * 5.3052 + 1.00 * 0.0603                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0991 = 2.29 * 0.50 * 5.2669 + 1.00 * 0.0712                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1230      final r-factor (work) = 0.1210          |
| start r-factor (free) = 0.1734      final r-factor (free) = 0.1720          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.6554 = 3.54 * 1.00 * 5.2669 + 1.00 * 0.0240                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.5194 = 3.54 * 1.00 * 5.2306 + 1.00 * 0.0164                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.314)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.98  13.14    None  None   None       |
|    all(noH): 2823   0      0.00    100.98  13.14    None  None   None       |
|    Sol.    : 438    0      0.89    100.98  38.89    None  None   None       |
|    Mac.    : 2385   0      0.00    90.74   8.41     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 -  10.098: 1818   |   5:    50.489 -  60.587:   91        |
|      1:    10.098 -  20.196:  490   |   6:    60.587 -  70.684:   42        |
|      2:    20.196 -  30.293:  144   |   7:    70.684 -  80.782:   16        |
|      3:    30.293 -  40.391:  122   |   8:    80.782 -  90.880:    8        |
|      4:    40.391 -  50.489:   87   |   9:    90.880 - 100.978:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1210 r_free = 0.1720             target_work(ml) = 5.229         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1209 r_free = 0.1719             target_work(ml) = 5.228         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1209   r_free= 0.1719   ksol= 0.33   Bsol= 65.83   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.08,2.39,3.77,0.00,0.00,0.00); trace/3= 3.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.228290                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3073 -  4.7810 0.99   1395  157 0.1013 0.1391      5.4109       5.583|
|  2:  4.7810 -  3.8141 0.99   1343  148 0.0873 0.1142      5.4637      5.6487|
|  3:  3.8141 -  3.3377 0.99   1326  144 0.1101 0.1544      5.5189      5.8727|
|  4:  3.3377 -  3.0351 0.99   1313  153 0.1270 0.1807      5.5098       5.704|
|  5:  3.0351 -  2.8190 0.99   1296  143 0.1483 0.1896      5.4188      5.6365|
|  6:  2.8190 -  2.6537 0.99   1303  140 0.1335 0.2141      5.3046      5.5764|
|  7:  2.6537 -  2.5214 0.99   1292  139 0.1368 0.1748      5.2536      5.4181|
|  8:  2.5214 -  2.4121 0.98   1260  147 0.1313 0.1868      5.1641      5.4147|
|  9:  2.4121 -  2.3196 0.98   1272  148 0.1292 0.2006       5.131      5.4305|
| 10:  2.3196 -  2.2398 1.00   1298  139 0.1282 0.1832      5.0652      5.2537|
| 11:  2.2398 -  2.1700 0.98   1286  137 0.1274 0.2031      5.0536      5.3717|
| 12:  2.1700 -  2.1081 0.98   1246  145 0.1235 0.1913      4.9722      5.2614|
| 13:  2.1081 -  2.0527 0.99   1283  137 0.1308 0.1867      4.9007      5.1382|
| 14:  2.0527 -  2.0028 0.55    717   82 0.1165 0.1805      4.7756      5.0393|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3073 -  4.7810  1395   157  0.94   9.47   0.97     0.94       7818.17|
|  2:  4.7810 -  3.8141  1343   148  0.95   8.47   1.00     0.98       9809.11|
|  3:  3.8141 -  3.3377  1326   144  0.93  11.89   1.02     1.02      11481.63|
|  4:  3.3377 -  3.0351  1313   153  0.91  14.93   1.01     0.99      11868.48|
|  5:  3.0351 -  2.8190  1296   143  0.88  17.80   1.00     0.98      10049.23|
|  6:  2.8190 -  2.6537  1303   140  0.88  17.96   0.98     0.95       8802.93|
|  7:  2.6537 -  2.5214  1292   139  0.89  17.34   0.99     0.96       7569.81|
|  8:  2.5214 -  2.4121  1260   147  0.89  17.55   0.98     0.95       6477.45|
|  9:  2.4121 -  2.3196  1272   148  0.89  17.38   0.99     0.95       6176.59|
| 10:  2.3196 -  2.2398  1298   139  0.88  17.82   0.99     0.94       5362.20|
| 11:  2.2398 -  2.1700  1286   137  0.89  17.96   0.99     0.93       5372.56|
| 12:  2.1700 -  2.1081  1246   145  0.90  17.13   0.99     0.98       4889.27|
| 13:  2.1081 -  2.0527  1283   137  0.88  19.08   0.98     0.95       4282.07|
| 14:  2.0527 -  2.0028   717    82  0.89  17.06   0.96     0.93       3329.72|
|alpha:            min =        0.93 max =            1.02 mean =         0.96|
|beta:             min =     3329.72 max =        11868.48 mean =      7545.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.64 mean =        15.73|
|phase err.(test): min =        0.00 max =           89.62 mean =        15.18|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1211   r_free= 0.1712   ksol= 0.33   Bsol= 68.92   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.10,-0.61,0.71,-0.00,0.00,0.00); trace/3= -0.00                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.227950                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1211   r_free= 0.1712   ksol= 0.33   Bsol= 68.92   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.10,-0.61,0.71,-0.00,0.00,0.00); trace/3= -0.00                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.227950                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3073 -  4.7810 0.99   1395  157 0.1021 0.1302      5.4044      5.5584|
|  2:  4.7810 -  3.8141 0.99   1343  148 0.0878 0.1129      5.4623      5.6439|
|  3:  3.8141 -  3.3377 0.99   1326  144 0.1100 0.1551      5.5188      5.8779|
|  4:  3.3377 -  3.0351 0.99   1313  153 0.1267 0.1814      5.5101      5.7077|
|  5:  3.0351 -  2.8190 0.99   1296  143 0.1481 0.1900      5.4199      5.6363|
|  6:  2.8190 -  2.6537 0.99   1303  140 0.1336 0.2138      5.3049      5.5763|
|  7:  2.6537 -  2.5214 0.99   1292  139 0.1368 0.1746       5.254      5.4174|
|  8:  2.5214 -  2.4121 0.98   1260  147 0.1313 0.1873      5.1644      5.4169|
|  9:  2.4121 -  2.3196 0.98   1272  148 0.1292 0.2005      5.1314      5.4302|
| 10:  2.3196 -  2.2398 1.00   1298  139 0.1282 0.1832      5.0653       5.253|
| 11:  2.2398 -  2.1700 0.98   1286  137 0.1274 0.2035      5.0536      5.3719|
| 12:  2.1700 -  2.1081 0.98   1246  145 0.1236 0.1915      4.9726      5.2621|
| 13:  2.1081 -  2.0527 0.99   1283  137 0.1307 0.1872      4.9011      5.1397|
| 14:  2.0527 -  2.0028 0.55    717   82 0.1165 0.1809      4.7767      5.0402|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3073 -  4.7810  1395   157  0.94   9.42   0.96     0.94       7475.81|
|  2:  4.7810 -  3.8141  1343   148  0.95   8.36   1.00     0.99       9581.84|
|  3:  3.8141 -  3.3377  1326   144  0.93  11.86   1.02     1.02      11443.56|
|  4:  3.3377 -  3.0351  1313   153  0.91  14.98   1.01     0.99      11921.95|
|  5:  3.0351 -  2.8190  1296   143  0.88  17.84   1.00     0.98      10100.08|
|  6:  2.8190 -  2.6537  1303   140  0.88  17.96   0.99     0.95       8809.10|
|  7:  2.6537 -  2.5214  1292   139  0.89  17.35   0.99     0.96       7579.03|
|  8:  2.5214 -  2.4121  1260   147  0.89  17.55   0.98     0.95       6487.25|
|  9:  2.4121 -  2.3196  1272   148  0.89  17.39   0.99     0.95       6176.96|
| 10:  2.3196 -  2.2398  1298   139  0.88  17.82   0.99     0.94       5365.29|
| 11:  2.2398 -  2.1700  1286   137  0.89  17.97   0.99     0.93       5373.07|
| 12:  2.1700 -  2.1081  1246   145  0.90  17.14   0.99     0.99       4895.23|
| 13:  2.1081 -  2.0527  1283   137  0.88  19.09   0.98     0.95       4288.20|
| 14:  2.0527 -  2.0028   717    82  0.89  17.10   0.96     0.93       3340.71|
|alpha:            min =        0.93 max =            1.02 mean =         0.96|
|beta:             min =     3340.71 max =        11921.95 mean =      7509.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.73|
|phase err.(test): min =        0.00 max =           89.63 mean =        15.17|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.314)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.09    104.07  16.24    None  None   None       |
|    all(noH): 2823   0      3.09    104.07  16.24    None  None   None       |
|    Sol.    : 438    0      3.98    104.07  41.98    None  None   None       |
|    Mac.    : 2385   0      3.09    93.83   11.51    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:     3.094 -  13.191: 1818   |   5:    53.582 -  63.680:   91        |
|      1:    13.191 -  23.289:  490   |   6:    63.680 -  73.778:   42        |
|      2:    23.289 -  33.387:  144   |   7:    73.778 -  83.876:   16        |
|      3:    33.387 -  43.485:  122   |   8:    83.876 -  93.974:    8        |
|      4:    43.485 -  53.582:   87   |   9:    93.974 - 104.071:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 338         
Filter by distance & map next to the model:
   mapped sites are within: 0.281 - 4.731
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 329 from: 338
   mapped sites are within: 0.720 - 4.731

peak=   10.256 closest distance to " CB  VAL A 230 " =    1.453
peak=    8.808 closest distance to " CG2 VAL A 296 " =    1.398
peak=    7.289 closest distance to " CG  ARG A 138 " =    1.236
peak=    5.815 closest distance to " CG  LEU A   5 " =    1.141
peak=    5.752 closest distance to " CB  GLN A 223 " =    1.429
peak=    5.662 closest distance to " CD2 LEU A   5 " =    1.092
peak=    5.353 closest distance to " CG  LEU A 228 " =    1.141
peak=    5.136 closest distance to " O   HOH Z 111 " =    1.929
peak=    5.091 closest distance to " O   HOH Z 232 " =    2.281
peak=    5.052 closest distance to " CD1AILE A 234 " =    1.065
peak=    5.043 closest distance to " NH1 ARG A 138 " =    1.038
peak=    4.910 closest distance to " NE2 GLN A  11 " =    1.097
peak=    4.872 closest distance to " O   HOH Z 369 " =    2.030
peak=    4.855 closest distance to " O   HOH Z 102 " =    1.383
peak=    4.796 closest distance to " CB  TRP A 266 " =    1.038
peak=    4.767 closest distance to " O   HOH Z 298 " =    2.094
peak=    4.736 closest distance to " CB  GLN A 183 " =    1.269
peak=    4.691 closest distance to " CB  SER A  63 " =    1.339
peak=    4.645 closest distance to " NH1AARG A 145 " =    1.200
peak=    4.614 closest distance to " CZ  PHE A 218 " =    1.094
peak=    4.587 closest distance to " CB  VAL A 230 " =    1.265
peak=    4.558 closest distance to " CG  PRO A 198 " =    1.225
peak=    4.479 closest distance to " CB  ASN A 148 " =    1.320
peak=    4.452 closest distance to " O   HOH Z 368 " =    2.147
peak=    4.422 closest distance to " O   HOH Z 427 " =    3.273
peak=    4.422 closest distance to " CG  PRO A 243 " =    1.137
peak=    4.404 closest distance to " O   HOH Z 144 " =    1.776
peak=    4.378 closest distance to " O   HOH Z  54 " =    2.248
peak=    4.358 closest distance to " O   HOH Z 303 " =    2.189
peak=    4.320 closest distance to " O   HOH Z 183 " =    1.311
peak=    4.319 closest distance to " CG2 THR A 221 " =    1.102
peak=    4.290 closest distance to " O   HOH Z 410 " =    1.398
peak=    4.286 closest distance to " CB  ASP A 124 " =    0.773
peak=    4.268 closest distance to " O   HOH Z 411 " =    3.441
peak=    4.268 closest distance to " O   HOH Z 261 " =    1.965
peak=    4.266 closest distance to " CG  PRO A 213 " =    1.291
peak=    4.241 closest distance to " CD  ARG A 138 " =    1.213
peak=    4.215 closest distance to " O   PRO A 198 " =    1.571
peak=    4.193 closest distance to " CE  LYS A  76 " =    0.834
peak=    4.173 closest distance to " O   HOH Z 425 " =    1.523
peak=    4.173 closest distance to " O   HOH Z 316 " =    3.133
peak=    4.168 closest distance to " O   HOH Z 290 " =    1.371
peak=    4.167 closest distance to " NH1 ARG A  56 " =    1.100
peak=    4.098 closest distance to " O   HOH Z 287 " =    2.063
peak=    4.084 closest distance to " CD2 LEU A 228 " =    1.184
peak=    4.024 closest distance to " O   HOH Z 193 " =    2.112
peak=    4.012 closest distance to " O   HOH Z 184 " =    1.666
peak=    3.992 closest distance to " CD1 LEU A 300 " =    1.199
peak=    3.951 closest distance to " CB  GLU A 128 " =    1.076
peak=    3.939 closest distance to " O   SER A  87 " =    2.358
peak=    3.939 closest distance to " CD ALYS A 290 " =    1.001
peak=    3.933 closest distance to " O   HOH Z  80 " =    1.781
peak=    3.926 closest distance to " CA  MET A  40 " =    1.178
peak=    3.925 closest distance to " CB  LEU A 228 " =    1.210
peak=    3.925 closest distance to " O   HOH Z 214 " =    2.074
peak=    3.919 closest distance to " CB  ARG A 275 " =    0.999
peak=    3.915 closest distance to " CB  LEU A 143 " =    1.317
peak=    3.909 closest distance to " O   HOH Z 112 " =    1.524
peak=    3.896 closest distance to " CB  GLU A 277 " =    3.736
peak=    3.894 closest distance to " CD  ARG A 159 " =    0.771
peak=    3.890 closest distance to " O   HOH Z 174 " =    1.311
peak=    3.872 closest distance to " O   HOH Z  88 " =    3.359
peak=    3.866 closest distance to " O   HOH Z 158 " =    3.026
peak=    3.864 closest distance to " CB  ASP A 140 " =    0.886
peak=    3.864 closest distance to " O   HOH Z  78 " =    1.748
peak=    3.826 closest distance to " O   HOH Z 193 " =    1.762
peak=    3.821 closest distance to " CG1 ILE A  33 " =    1.246
peak=    3.812 closest distance to " CB  SER A 216 " =    0.979
peak=    3.811 closest distance to " O   HOH Z   9 " =    2.099
peak=    3.810 closest distance to " CB  SER A   3 " =    1.590
peak=    3.805 closest distance to " CA  ALA A  51 " =    1.054
peak=    3.801 closest distance to " CG2 ILE A 234 " =    0.872
peak=    3.799 closest distance to " O   HOH Z 272 " =    1.902
peak=    3.798 closest distance to " CA  TYR A  30 " =    0.962
peak=    3.787 closest distance to " CD  ARG A 269 " =    0.889
peak=    3.781 closest distance to " OD1 ASN A 217 " =    1.534
peak=    3.765 closest distance to " CG  LEU A 167 " =    1.207
peak=    3.763 closest distance to " CB  SER A 212 " =    1.183
peak=    3.747 closest distance to " CB  VAL A 202 " =    1.603
peak=    3.741 closest distance to " O   HOH Z 156 " =    2.839
peak=    3.738 closest distance to " CB  ALA A 104 " =    0.916
peak=    3.730 closest distance to " CB  PRO A  54 " =    0.824
peak=    3.722 closest distance to " O   HOH Z 247 " =    1.362
peak=    3.711 closest distance to " CB  THR A  82 " =    1.279
peak=    3.709 closest distance to " O   HOH Z 359 " =    3.956
peak=    3.699 closest distance to " CB  ASN A 142 " =    1.010
peak=    3.698 closest distance to " CA  ALA A  21 " =    1.238
peak=    3.698 closest distance to " O   HOH Z 353 " =    2.707
peak=    3.697 closest distance to " O   HOH Z 346 " =    1.580
peak=    3.695 closest distance to " CG  MET A 185 " =    1.336
peak=    3.689 closest distance to " CZ  PHE A 192 " =    0.926
peak=    3.687 closest distance to " O   HOH Z 437 " =    1.507
peak=    3.668 closest distance to " CB  ARG A 190 " =    1.708
peak=    3.660 closest distance to " ND2 ASN A 187 " =    1.439
peak=    3.659 closest distance to " CB  VAL A 265 " =    1.244
peak=    3.657 closest distance to " CD1 ILE A  33 " =    1.773
peak=    3.656 closest distance to " CB  ASN A  39 " =    0.948
peak=    3.656 closest distance to " O   HOH Z 258 " =    2.002
peak=    3.656 closest distance to " CB  ASN A 187 " =    2.072
peak=    3.655 closest distance to " CG  LEU A   5 " =    0.757
peak=    3.650 closest distance to " CD  ARG A  66 " =    2.284
peak=    3.647 closest distance to " CG BARG A 102 " =    1.883
peak=    3.646 closest distance to " O   MET A 105 " =    1.851
peak=    3.646 closest distance to " CG1 VAL A 153 " =    0.985
peak=    3.631 closest distance to " O   HOH Z  53 " =    2.571
peak=    3.624 closest distance to " CA  ALA A 295 " =    1.219
peak=    3.624 closest distance to " CG  GLU A  37 " =    0.905
peak=    3.619 closest distance to " CE2 TYR A 186 " =    0.928
peak=    3.611 closest distance to " CA  VAL A 112 " =    1.154
peak=    3.596 closest distance to " CA  ASP A 124 " =    0.720
peak=    3.592 closest distance to " CA  ARG A 195 " =    1.286
peak=    3.589 closest distance to " CB  ALA A  34 " =    0.929
peak=    3.586 closest distance to " O   HOH Z   4 " =    1.713
peak=    3.584 closest distance to " N   ALA A 256 " =    1.092
peak=    3.571 closest distance to " CB  GLN A  89 " =    1.213
peak=    3.569 closest distance to " O   HOH Z 188 " =    3.008
peak=    3.568 closest distance to " CB  ARG A  79 " =    1.547
peak=    3.563 closest distance to " O   HOH Z 148 " =    2.100
peak=    3.561 closest distance to " O   HOH Z 180 " =    2.115
peak=    3.559 closest distance to " CG2BVAL A  41 " =    1.217
peak=    3.556 closest distance to " CA  ALA A 291 " =    0.905
peak=    3.553 closest distance to " CB  ALA A   9 " =    1.670
peak=    3.550 closest distance to " OE1 GLN A 278 " =    0.949
peak=    3.544 closest distance to " NZ  LYS A 117 " =    3.334
peak=    3.540 closest distance to " CB  TRP A 150 " =    1.352
peak=    3.529 closest distance to " O   HOH Z 234 " =    3.890
peak=    3.529 closest distance to " O   ASP A 124 " =    1.103
peak=    3.528 closest distance to " CA  ARG A  36 " =    1.183
peak=    3.526 closest distance to " O   HOH Z 302 " =    1.820
peak=    3.518 closest distance to " CD  GLU A 152 " =    0.828
peak=    3.516 closest distance to " CA  ALA A 160 " =    0.960
peak=    3.516 closest distance to " CA  ASN A 127 " =    1.091
peak=    3.515 closest distance to " CE1 TYR A 186 " =    1.293
peak=    3.508 closest distance to " CD2 LEU A 255 " =    1.692
peak=    3.507 closest distance to " CB  ALA A 242 " =    0.907
peak=    3.507 closest distance to " O   HOH Z 109 " =    2.671
peak=    3.506 closest distance to " CZ3 TRP A 266 " =    1.147
peak=    3.505 closest distance to " O   HOH Z   1 " =    1.853
peak=    3.501 closest distance to " CB  LYS A 117 " =    1.166
peak=    3.501 closest distance to " O   HOH Z 250 " =    1.302
peak=    3.493 closest distance to " OD1 ASN A  69 " =    2.658
peak=    3.491 closest distance to " CB  ALA A 161 " =    0.934
peak=    3.482 closest distance to " CB  MET A  40 " =    0.739
peak=    3.480 closest distance to " O   HOH Z 403 " =    1.745
peak=    3.479 closest distance to " OE1 GLN A  11 " =    1.835
peak=    3.475 closest distance to " CB  ALA A 227 " =    1.025
peak=    3.472 closest distance to " CB  GLU A 152 " =    1.276
peak=    3.471 closest distance to " O   HOH Z  88 " =    3.674
peak=    3.470 closest distance to " CA  LEU A 282 " =    1.027
peak=    3.469 closest distance to " CD  LYS A 166 " =    1.314
peak=    3.469 closest distance to " O   HOH Z 133 " =    2.496
peak=    3.458 closest distance to " O   HOH Z 126 " =    1.610
peak=    3.457 closest distance to " CB  ALA A 248 " =    1.321
peak=    3.457 closest distance to " O   HOH Z 147 " =    1.651
peak=    3.452 closest distance to " CZ3 TRP A  92 " =    1.364
peak=    3.451 closest distance to " CA  TYR A 116 " =    1.502
peak=    3.450 closest distance to " CB  GLN A  88 " =    1.279
peak=    3.446 closest distance to " NE2 HIS A 207 " =    1.251
peak=    3.439 closest distance to " N   PHE A 130 " =    1.275
peak=    3.438 closest distance to " O   HOH Z  57 " =    1.519
peak=    3.437 closest distance to " O   HOH Z 313 " =    1.748
peak=    3.436 closest distance to " OD2 ASP A 286 " =    2.861
peak=    3.435 closest distance to " CB  ASN A 187 " =    1.115
peak=    3.435 closest distance to " CG  ARG A 159 " =    1.047
peak=    3.428 closest distance to " O   HOH Z  98 " =    1.892
peak=    3.427 closest distance to " N   TYR A  15 " =    0.876
peak=    3.426 closest distance to " CA  ILE A 234 " =    0.998
peak=    3.422 closest distance to " O   HOH Z 175 " =    2.238
peak=    3.422 closest distance to " O   HOH Z 422 " =    2.623
peak=    3.422 closest distance to " CB  LEU A 237 " =    0.906
peak=    3.419 closest distance to " N   SER A 135 " =    1.330
peak=    3.418 closest distance to " CG  GLN A  88 " =    1.123
peak=    3.411 closest distance to " CD  GLN A 240 " =    1.612
peak=    3.410 closest distance to " CD1 LEU A   5 " =    1.330
peak=    3.403 closest distance to " CD  ARG A  14 " =    1.270
peak=    3.400 closest distance to " CB  TRP A 179 " =    1.413
peak=    3.387 closest distance to " CA  ASP A 162 " =    1.051
peak=    3.386 closest distance to " CG BARG A 275 " =    1.530
peak=    3.383 closest distance to " O   ALA A 165 " =    1.501
peak=    3.383 closest distance to " CG1 ILE A 151 " =    1.190
peak=    3.381 closest distance to " CA  ASN A  74 " =    1.351
peak=    3.380 closest distance to " CB  ASN A 110 " =    1.243
peak=    3.379 closest distance to " NH2 ARG A  79 " =    1.686
peak=    3.378 closest distance to " O   HOH Z  88 " =    2.668
peak=    3.377 closest distance to " OG  SER A  62 " =    3.111
peak=    3.375 closest distance to " CB  MET A  47 " =    1.101
peak=    3.364 closest distance to " O   HOH Z  68 " =    2.022
peak=    3.362 closest distance to " O   HOH Z 134 " =    2.581
peak=    3.361 closest distance to " O   HOH Z  64 " =    2.871
peak=    3.358 closest distance to " O   HOH Z 391 " =    3.003
peak=    3.349 closest distance to " O   HOH Z 227 " =    1.679
peak=    3.348 closest distance to " O   HOH Z 261 " =    1.578
peak=    3.347 closest distance to " O   HOH Z 135 " =    2.082
peak=    3.344 closest distance to " O   ALA A 291 " =    1.567
peak=    3.344 closest distance to " N   VAL A 126 " =    1.412
peak=    3.341 closest distance to " CB  SER A 141 " =    1.005
peak=    3.340 closest distance to " O   HOH Z 368 " =    4.118
peak=    3.337 closest distance to " CB  GLN A 103 " =    1.070
peak=    3.335 closest distance to " O   HOH Z 423 " =    1.555
peak=    3.334 closest distance to " CA  ASP A 140 " =    1.330
peak=    3.333 closest distance to " CB  GLU A  46 " =    1.007
peak=    3.333 closest distance to " CZ  PHE A  38 " =    1.286
peak=    3.332 closest distance to " CB  ARG A 138 " =    1.698
peak=    3.330 closest distance to " O   HOH Z 332 " =    1.616
peak=    3.329 closest distance to " CB  SER A 210 " =    0.957
peak=    3.327 closest distance to " CA  LYS A 290 " =    1.325
peak=    3.325 closest distance to " ND2 ASN A 249 " =    1.905
peak=    3.324 closest distance to " O   HOH Z 167 " =    1.732
peak=    3.320 closest distance to " N   ASN A 127 " =    1.283
peak=    3.313 closest distance to " CB  VAL A 268 " =    0.869
peak=    3.311 closest distance to " O   ASP A 200 " =    1.723
peak=    3.310 closest distance to " CA  ARG A 102 " =    1.164
peak=    3.310 closest distance to " CD1 LEU A 101 " =    1.224
peak=    3.308 closest distance to " OG1 THR A 279 " =    1.554
peak=    3.306 closest distance to " CB  ILE A 120 " =    1.372
peak=    3.305 closest distance to " ND1 HIS A  81 " =    1.715
peak=    3.305 closest distance to " NZ  LYS A  48 " =    1.455
peak=    3.305 closest distance to " CG2 VAL A 257 " =    0.946
peak=    3.305 closest distance to " CA  VAL A 125 " =    1.255
peak=    3.303 closest distance to " O   HOH Z 172 " =    3.644
peak=    3.299 closest distance to " CD1 TRP A 266 " =    1.172
peak=    3.298 closest distance to " CA  THR A 221 " =    0.957
peak=    3.296 closest distance to " CA  SER A  87 " =    0.936
peak=    3.296 closest distance to " CE3 TRP A  85 " =    1.155
peak=    3.295 closest distance to " CG  GLN A  89 " =    1.506
peak=    3.293 closest distance to " NE1 TRP A 274 " =    0.917
peak=    3.293 closest distance to " O   HOH Z 197 " =    2.987
peak=    3.289 closest distance to " O   HOH Z 213 " =    1.868
peak=    3.286 closest distance to " CG1 VAL A 174 " =    1.096
peak=    3.283 closest distance to " CB  ALA A   1 " =    4.731
peak=    3.278 closest distance to " OH  TYR A 247 " =    1.115
peak=    3.278 closest distance to " O   GLN A 278 " =    1.285
peak=    3.277 closest distance to " OH  TYR A 214 " =    1.333
peak=    3.277 closest distance to " O   HOH Z 132 " =    2.626
peak=    3.275 closest distance to " CB  ALA A 291 " =    1.343
peak=    3.271 closest distance to " O   HOH Z 371 " =    3.243
peak=    3.270 closest distance to " C   ALA A 299 " =    0.980
peak=    3.269 closest distance to " CA  ASN A 217 " =    1.490
peak=    3.269 closest distance to " O   HOH Z 128 " =    2.270
peak=    3.264 closest distance to " CA  ALA A 184 " =    1.137
peak=    3.264 closest distance to " CD2 TRP A 179 " =    1.326
peak=    3.263 closest distance to " CD  ARG A  66 " =    2.209
peak=    3.260 closest distance to " CA  LEU A 101 " =    1.537
peak=    3.260 closest distance to " O   HOH Z 280 " =    2.981
peak=    3.259 closest distance to " O   HOH Z 124 " =    1.884
peak=    3.259 closest distance to " O   HOH Z  10 " =    1.869
peak=    3.259 closest distance to " O   HOH Z 285 " =    2.791
peak=    3.257 closest distance to " O   HOH Z 392 " =    1.796
peak=    3.257 closest distance to " O   HOH Z  63 " =    1.805
peak=    3.254 closest distance to " CA  GLU A  46 " =    0.775
peak=    3.250 closest distance to " CA  ARG A 139 " =    1.169
peak=    3.249 closest distance to " O   HOH Z 352 " =    1.828
peak=    3.249 closest distance to " CA  ALA A 158 " =    1.190
peak=    3.248 closest distance to " ND2 ASN A 249 " =    0.798
peak=    3.246 closest distance to " O   HOH Z 340 " =    2.290
peak=    3.243 closest distance to " CG1BVAL A  72 " =    1.584
peak=    3.243 closest distance to " O   HOH Z 185 " =    2.320
peak=    3.242 closest distance to " OG1 THR A 264 " =    0.869
peak=    3.239 closest distance to " O   HOH Z 298 " =    2.526
peak=    3.239 closest distance to " OG BSER A 134 " =    2.880
peak=    3.235 closest distance to " CG1 ILE A 120 " =    1.125
peak=    3.234 closest distance to " CA  ILE A  33 " =    1.744
peak=    3.227 closest distance to " CG AARG A 275 " =    1.194
peak=    3.224 closest distance to " O   HOH Z 326 " =    2.209
peak=    3.223 closest distance to " CE3 TRP A 274 " =    1.321
peak=    3.223 closest distance to " CB  ALA A  43 " =    1.012
peak=    3.223 closest distance to " O   HOH Z 294 " =    1.535
peak=    3.222 closest distance to " NE2 GLN A  58 " =    3.783
peak=    3.220 closest distance to " CB  SER A 273 " =    0.915
peak=    3.219 closest distance to " CG1 ILE A  49 " =    1.607
peak=    3.215 closest distance to " CB  THR A  52 " =    0.807
peak=    3.209 closest distance to " N   ASN A  39 " =    1.364
peak=    3.207 closest distance to " CA  ASN A 215 " =    1.241
peak=    3.205 closest distance to " CA  MET A 105 " =    0.984
peak=    3.205 closest distance to " O   HOH Z 201 " =    2.828
peak=    3.204 closest distance to " O   HOH Z 197 " =    1.859
peak=    3.202 closest distance to " CB  ALA A  10 " =    1.079
peak=    3.197 closest distance to " O   HOH Z 359 " =    1.296
peak=    3.195 closest distance to " O   HOH Z  59 " =    2.288
peak=    3.193 closest distance to " O   PRO A  90 " =    1.413
peak=    3.191 closest distance to " O   HOH Z   7 " =    1.201
peak=    3.191 closest distance to " O   HOH Z 368 " =    3.617
peak=    3.191 closest distance to " O   HOH Z 313 " =    1.675
peak=    3.191 closest distance to " CA  TYR A 186 " =    1.525
peak=    3.191 closest distance to " O   ALA A 158 " =    1.431
peak=    3.188 closest distance to " O   HOH Z 116 " =    1.924
peak=    3.180 closest distance to " O   HOH Z 350 " =    1.649
peak=    3.179 closest distance to " O   HOH Z 435 " =    2.064
peak=    3.176 closest distance to " CB  THR A 235 " =    1.146
peak=    3.176 closest distance to " CG  LEU A  25 " =    1.917
peak=    3.176 closest distance to " O   HOH Z 215 " =    2.953
peak=    3.173 closest distance to " OD2 ASP A 200 " =    1.344
peak=    3.170 closest distance to " O   HOH Z 329 " =    3.975
peak=    3.169 closest distance to " CD2 LEU A 297 " =    0.884
peak=    3.168 closest distance to " O   HOH Z 166 " =    3.502
peak=    3.168 closest distance to " O   HOH Z   2 " =    1.493
peak=    3.163 closest distance to " CA  ALA A 154 " =    1.028
peak=    3.158 closest distance to " O   HOH Z 130 " =    3.870
peak=    3.157 closest distance to " OE1 GLN A  55 " =    1.328
peak=    3.155 closest distance to " CA  GLY A 211 " =    1.467
peak=    3.153 closest distance to " CB  LEU A  83 " =    0.894
peak=    3.152 closest distance to " CB  LEU A 261 " =    0.762
peak=    3.151 closest distance to " O   HOH Z 301 " =    1.819
peak=    3.148 closest distance to " CG2 ILE A  49 " =    1.358
peak=    3.129 closest distance to " O   THR A 182 " =    1.460
peak=    3.124 closest distance to " CB  SER A  62 " =    1.096
peak=    3.123 closest distance to " CA  ASP A 191 " =    1.053
peak=    3.118 closest distance to " OG BSER A 164 " =    2.257
peak=    3.117 closest distance to " O   HOH Z 383 " =    2.356
peak=    3.115 closest distance to " O   THR A 294 " =    1.189
peak=    3.111 closest distance to " CB  ALA A 100 " =    1.394
peak=    3.109 closest distance to " CA  GLY A 241 " =    0.872
peak=    3.106 closest distance to " N   GLU A  44 " =    1.031
peak=    3.104 closest distance to " O   THR A 251 " =    1.320
peak=    3.099 closest distance to " CD  LYS A  76 " =    2.054
peak=    3.099 closest distance to " O   HOH Z 423 " =    2.785
peak=    3.092 closest distance to " O   TYR A 116 " =    1.192
peak=    3.090 closest distance to " CD1 ILE A 106 " =    0.841
peak=    3.084 closest distance to " CB  GLU A 236 " =    1.120
peak=    3.083 closest distance to " CD1 LEU A  96 " =    0.744
peak=    3.082 closest distance to " O   HOH Z  43 " =    1.826
peak=    3.079 closest distance to " CG  ARG A 269 " =    1.708
peak=    3.076 closest distance to " O   HOH Z 271 " =    2.829
peak=    3.072 closest distance to " O   HOH Z 291 " =    1.646
peak=    3.061 closest distance to " O   HOH Z 271 " =    2.271
peak=    3.056 closest distance to " CE3 TRP A 150 " =    1.063
peak=    3.054 closest distance to " CB  TYR A 116 " =    0.882
peak=    3.030 closest distance to " OE2 GLU A   2 " =    1.743
peak=    3.004 closest distance to " O   HOH Z 359 " =    4.034

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.818 - 5.642
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 210 from: 210
   mapped sites are within: 0.818 - 5.642

peak=   -4.785 closest distance to " O   HOH Z 102 " =    1.152
peak=   -4.733 closest distance to " CD  ARG A 138 " =    1.204
peak=   -4.408 closest distance to " O   HOH Z 231 " =    1.776
peak=   -4.404 closest distance to " CZ2 TRP A  92 " =    2.899
peak=   -4.379 closest distance to " CG2 VAL A 230 " =    0.981
peak=   -4.225 closest distance to " CA  ASP A  27 " =    2.526
peak=   -4.198 closest distance to " CD  ARG A 156 " =    2.122
peak=   -4.081 closest distance to " CD  ARG A  14 " =    3.288
peak=   -4.063 closest distance to " CG  ARG A 138 " =    0.846
peak=   -4.042 closest distance to " CG1 VAL A 250 " =    2.618
peak=   -4.011 closest distance to " CG  GLN A 223 " =    2.337
peak=   -4.000 closest distance to " O   ILE A 109 " =    2.705
peak=   -3.996 closest distance to " OG  SER A  97 " =    2.263
peak=   -3.954 closest distance to " O   HOH Z 211 " =    1.173
peak=   -3.938 closest distance to " OG BSER A 134 " =    1.428
peak=   -3.935 closest distance to " O   HOH Z 411 " =    5.243
peak=   -3.930 closest distance to " CE2 TYR A  30 " =    2.789
peak=   -3.927 closest distance to " CG  TRP A 266 " =    1.826
peak=   -3.918 closest distance to " O   SER A 271 " =    2.228
peak=   -3.913 closest distance to " OE1 GLN A  88 " =    1.102
peak=   -3.899 closest distance to " CG1 VAL A 296 " =    1.496
peak=   -3.891 closest distance to " N   THR A  18 " =    1.246
peak=   -3.850 closest distance to " O   HOH Z  73 " =    2.050
peak=   -3.839 closest distance to " CA  ALA A 158 " =    1.271
peak=   -3.835 closest distance to " CD2 LEU A 167 " =    1.812
peak=   -3.834 closest distance to " O   HOH Z 377 " =    1.676
peak=   -3.828 closest distance to " O   HOH Z 394 " =    1.550
peak=   -3.820 closest distance to " O   HOH Z 198 " =    2.355
peak=   -3.817 closest distance to " O   PRO A 198 " =    1.257
peak=   -3.817 closest distance to " O   GLY A  80 " =    2.571
peak=   -3.799 closest distance to " O   HOH Z  43 " =    1.581
peak=   -3.783 closest distance to " CG1 VAL A 112 " =    2.605
peak=   -3.739 closest distance to " O   HOH Z 216 " =    1.467
peak=   -3.729 closest distance to " OG  SER A  87 " =    1.545
peak=   -3.724 closest distance to " CG2 VAL A 230 " =    2.748
peak=   -3.709 closest distance to " O   HOH Z 166 " =    1.859
peak=   -3.704 closest distance to " O   HOH Z 196 " =    2.387
peak=   -3.694 closest distance to " O   HOH Z  38 " =    1.166
peak=   -3.690 closest distance to " CB  PRO A 243 " =    2.669
peak=   -3.688 closest distance to " CD1 LEU A   5 " =    2.637
peak=   -3.673 closest distance to " CE3 TRP A 150 " =    2.330
peak=   -3.669 closest distance to " O   HOH Z 350 " =    1.763
peak=   -3.668 closest distance to " CG1 VAL A 112 " =    2.900
peak=   -3.667 closest distance to " CD1 LEU A 101 " =    2.561
peak=   -3.659 closest distance to " CG  GLN A  88 " =    0.843
peak=   -3.658 closest distance to " O   HOH Z  44 " =    2.197
peak=   -3.627 closest distance to " CA  ASP A 298 " =    1.027
peak=   -3.624 closest distance to " CB  ALA A   9 " =    2.631
peak=   -3.624 closest distance to " O   PRO A 163 " =    2.110
peak=   -3.624 closest distance to " CD  GLN A  58 " =    0.913
peak=   -3.622 closest distance to " CA  GLY A 241 " =    2.333
peak=   -3.611 closest distance to " N   ALA A  43 " =    2.509
peak=   -3.610 closest distance to " NE2 GLN A  55 " =    2.560
peak=   -3.599 closest distance to " NH2 ARG A  66 " =    2.230
peak=   -3.589 closest distance to " O   HOH Z 388 " =    1.999
peak=   -3.588 closest distance to " CA  ASN A 127 " =    1.019
peak=   -3.579 closest distance to " CB  ALA A  43 " =    2.634
peak=   -3.577 closest distance to " CZ2 TRP A 274 " =    0.934
peak=   -3.575 closest distance to " CA  GLY A 241 " =    3.103
peak=   -3.573 closest distance to " CD1 PHE A  59 " =    1.911
peak=   -3.561 closest distance to " CG  MET A 105 " =    1.029
peak=   -3.550 closest distance to " O   ASP A  27 " =    1.949
peak=   -3.542 closest distance to " CD2 PHE A  61 " =    1.948
peak=   -3.538 closest distance to " O   LEU A 101 " =    2.832
peak=   -3.519 closest distance to " CA  GLY A 203 " =    2.462
peak=   -3.517 closest distance to " CD1 LEU A 228 " =    2.471
peak=   -3.511 closest distance to " CG2BVAL A  41 " =    2.602
peak=   -3.510 closest distance to " O   HOH Z   9 " =    1.541
peak=   -3.501 closest distance to " O   HOH Z 185 " =    2.316
peak=   -3.500 closest distance to " CG  GLU A  53 " =    1.351
peak=   -3.500 closest distance to " O   HOH Z 183 " =    1.310
peak=   -3.497 closest distance to " CB  VAL A 230 " =    1.153
peak=   -3.495 closest distance to " CB  PRO A  54 " =    2.509
peak=   -3.482 closest distance to " O   HOH Z 407 " =    3.291
peak=   -3.479 closest distance to " O   VAL A 189 " =    2.569
peak=   -3.478 closest distance to " CE3 TRP A  70 " =    1.736
peak=   -3.477 closest distance to " OG ASER A 134 " =    1.208
peak=   -3.470 closest distance to " O   HOH Z 389 " =    2.071
peak=   -3.464 closest distance to " OD1 ASN A 148 " =    1.425
peak=   -3.463 closest distance to " O   HOH Z 113 " =    2.314
peak=   -3.455 closest distance to " O   HOH Z  11 " =    1.885
peak=   -3.450 closest distance to " CG2 VAL A 296 " =    1.899
peak=   -3.443 closest distance to " CD1 TYR A 247 " =    2.423
peak=   -3.438 closest distance to " O   GLY A 203 " =    2.367
peak=   -3.436 closest distance to " CD1 ILE A  33 " =    2.648
peak=   -3.435 closest distance to " N   ALA A 226 " =    2.190
peak=   -3.424 closest distance to " CD  LYS A 289 " =    2.437
peak=   -3.414 closest distance to " CG  PRO A 163 " =    2.224
peak=   -3.413 closest distance to " CB  TRP A  85 " =    2.443
peak=   -3.405 closest distance to " CG  HIS A  86 " =    1.042
peak=   -3.405 closest distance to " CG  GLU A 277 " =    1.299
peak=   -3.403 closest distance to " O   HOH Z 351 " =    1.484
peak=   -3.402 closest distance to " CB  SER A  63 " =    3.391
peak=   -3.398 closest distance to " CB  PRO A 163 " =    2.512
peak=   -3.390 closest distance to " O   HOH Z 275 " =    1.630
peak=   -3.387 closest distance to " CZ3 TRP A 179 " =    1.124
peak=   -3.385 closest distance to " O   HOH Z 111 " =    2.128
peak=   -3.383 closest distance to " SG ACYS A 201 " =    1.119
peak=   -3.383 closest distance to " O   HOH Z 184 " =    1.609
peak=   -3.376 closest distance to " OG  SER A 206 " =    1.717
peak=   -3.376 closest distance to " N   THR A 157 " =    1.524
peak=   -3.371 closest distance to " CG2AVAL A  41 " =    2.810
peak=   -3.368 closest distance to " NH2AARG A 275 " =    5.642
peak=   -3.367 closest distance to " ND2 ASN A  45 " =    2.247
peak=   -3.364 closest distance to " CG2 ILE A 263 " =    2.459
peak=   -3.364 closest distance to " O   HOH Z 359 " =    3.175
peak=   -3.361 closest distance to " N   ARG A  24 " =    1.432
peak=   -3.360 closest distance to " CE BMET A  47 " =    1.629
peak=   -3.357 closest distance to " OD2 ASP A  50 " =    2.211
peak=   -3.357 closest distance to " CB  PHE A 130 " =    1.267
peak=   -3.356 closest distance to " O   HOH Z 243 " =    1.666
peak=   -3.356 closest distance to " O   HOH Z  65 " =    1.225
peak=   -3.355 closest distance to " O   HOH Z 166 " =    1.628
peak=   -3.354 closest distance to " N   LYS A 166 " =    2.009
peak=   -3.351 closest distance to " O   TRP A  70 " =    1.499
peak=   -3.344 closest distance to " N   TYR A  68 " =    2.779
peak=   -3.338 closest distance to " ND2 ASN A  69 " =    1.748
peak=   -3.335 closest distance to " CG1 VAL A 112 " =    2.665
peak=   -3.335 closest distance to " NE2 GLN A 240 " =    1.574
peak=   -3.332 closest distance to " O   HOH Z  13 " =    1.613
peak=   -3.331 closest distance to " CB  PHE A 192 " =    1.806
peak=   -3.329 closest distance to " O   HOH Z 105 " =    2.059
peak=   -3.327 closest distance to " CG  PRO A 163 " =    2.276
peak=   -3.324 closest distance to " O   HOH Z 435 " =    2.700
peak=   -3.323 closest distance to " OH  TYR A 214 " =    1.144
peak=   -3.323 closest distance to " CE1 TYR A 169 " =    2.574
peak=   -3.322 closest distance to " O   HOH Z  60 " =    2.331
peak=   -3.320 closest distance to " O   GLY A 211 " =    1.394
peak=   -3.319 closest distance to " C   HIS A 108 " =    1.162
peak=   -3.317 closest distance to " O   HOH Z 236 " =    1.381
peak=   -3.316 closest distance to " O   HOH Z 118 " =    1.299
peak=   -3.315 closest distance to " CB  ALA A 227 " =    2.393
peak=   -3.315 closest distance to " O   HOH Z 353 " =    2.116
peak=   -3.311 closest distance to " OD2 ASP A 171 " =    1.911
peak=   -3.311 closest distance to " O   HOH Z  10 " =    1.564
peak=   -3.306 closest distance to " CG  ARG A 269 " =    2.333
peak=   -3.305 closest distance to " OXT GLY A 302 " =    3.196
peak=   -3.300 closest distance to " SD BMET A  47 " =    1.094
peak=   -3.299 closest distance to " O   HOH Z 292 " =    4.639
peak=   -3.295 closest distance to " CZ  PHE A 130 " =    1.124
peak=   -3.292 closest distance to " CA  GLY A 133 " =    2.221
peak=   -3.290 closest distance to " O   HOH Z 231 " =    0.998
peak=   -3.287 closest distance to " N   SER A 212 " =    1.960
peak=   -3.286 closest distance to " O   HOH Z  92 " =    1.243
peak=   -3.284 closest distance to " OD1 ASN A 173 " =    1.234
peak=   -3.284 closest distance to " CE  LYS A  76 " =    2.640
peak=   -3.273 closest distance to " O   GLU A  44 " =    1.522
peak=   -3.269 closest distance to " O   HOH Z 281 " =    2.322
peak=   -3.268 closest distance to " N   ALA A 248 " =    1.806
peak=   -3.265 closest distance to " CE  MET A 105 " =    2.334
peak=   -3.262 closest distance to " O   HOH Z 186 " =    0.956
peak=   -3.261 closest distance to " C   LEU A 222 " =    0.878
peak=   -3.261 closest distance to " ND2 ASN A 173 " =    1.912
peak=   -3.258 closest distance to " CG  TYR A 186 " =    2.324
peak=   -3.257 closest distance to " O   SER A 276 " =    1.606
peak=   -3.256 closest distance to " N   ASN A  60 " =    1.245
peak=   -3.252 closest distance to " OH  TYR A 247 " =    1.774
peak=   -3.247 closest distance to " O   HOH Z  52 " =    1.727
peak=   -3.240 closest distance to " ND2 ASN A  60 " =    1.752
peak=   -3.239 closest distance to " C   MET A 188 " =    1.443
peak=   -3.236 closest distance to " O   HOH Z 113 " =    2.118
peak=   -3.231 closest distance to " OG  SER A  28 " =    1.998
peak=   -3.227 closest distance to " CD2 TYR A 293 " =    1.900
peak=   -3.227 closest distance to " O   HOH Z 410 " =    1.816
peak=   -3.223 closest distance to " O   ASP A 270 " =    1.497
peak=   -3.221 closest distance to " O   HOH Z  32 " =    1.970
peak=   -3.220 closest distance to " O   HOH Z 251 " =    4.925
peak=   -3.220 closest distance to " OD1 ASN A  39 " =    2.198
peak=   -3.210 closest distance to " O   PHE A 218 " =    1.540
peak=   -3.204 closest distance to " OG BSER A 134 " =    1.921
peak=   -3.201 closest distance to " O   HOH Z 177 " =    1.794
peak=   -3.200 closest distance to " CG  GLU A 152 " =    2.052
peak=   -3.200 closest distance to " ND2 ASN A  45 " =    1.172
peak=   -3.199 closest distance to " CG2 VAL A 189 " =    2.003
peak=   -3.197 closest distance to " CG  ARG A 259 " =    2.541
peak=   -3.197 closest distance to " CB  ASN A  39 " =    2.265
peak=   -3.191 closest distance to " SG  CYS A 254 " =    2.890
peak=   -3.191 closest distance to " C   ASN A 187 " =    1.643
peak=   -3.190 closest distance to " CA  SER A  62 " =    2.705
peak=   -3.189 closest distance to " N   SER A 276 " =    1.416
peak=   -3.187 closest distance to " CD  PRO A 213 " =    2.192
peak=   -3.187 closest distance to " O   HOH Z 103 " =    1.771
peak=   -3.186 closest distance to " CG  ASP A 231 " =    0.818
peak=   -3.182 closest distance to " CE2 PHE A 218 " =    2.566
peak=   -3.173 closest distance to " CB  HIS A  81 " =    1.072
peak=   -3.172 closest distance to " OE1 GLN A 278 " =    1.153
peak=   -3.168 closest distance to " O   HOH Z 423 " =    1.160
peak=   -3.164 closest distance to " C   LEU A 143 " =    1.189
peak=   -3.164 closest distance to " CG  LEU A 101 " =    2.397
peak=   -3.158 closest distance to " O   HOH Z 345 " =    2.138
peak=   -3.154 closest distance to " OG  SER A  26 " =    1.370
peak=   -3.153 closest distance to " NH2 ARG A  79 " =    2.048
peak=   -3.147 closest distance to " OD1 ASN A  60 " =    0.980
peak=   -3.142 closest distance to " O   HOH Z 189 " =    2.728
peak=   -3.135 closest distance to " O   HOH Z 325 " =    1.672
peak=   -3.134 closest distance to " O   HOH Z 259 " =    4.120
peak=   -3.131 closest distance to " C   GLY A  13 " =    0.934
peak=   -3.130 closest distance to " O   HOH Z 118 " =    1.033
peak=   -3.129 closest distance to " CB  ALA A 291 " =    2.250
peak=   -3.104 closest distance to " O   HOH Z 357 " =    2.197
peak=   -3.101 closest distance to " O   HOH Z 109 " =    1.132
peak=   -3.100 closest distance to " O   THR A  31 " =    1.399
peak=   -3.098 closest distance to " O   HOH Z 396 " =    1.887
peak=   -3.094 closest distance to " O   HOH Z 250 " =    1.572
peak=   -3.079 closest distance to " CG2 VAL A 112 " =    2.536
peak=   -3.071 closest distance to " O   HOH Z 112 " =    1.444
peak=   -3.055 closest distance to " O   HOH Z 106 " =    2.003
peak=   -3.051 closest distance to " O   HOH Z 430 " =    1.951
peak=   -3.051 closest distance to " CD2 TYR A 169 " =    2.161
peak=   -3.041 closest distance to " N   ILE A 120 " =    1.102

================= 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    :  0.4651 0.4540   6.267491e+00   6.247795e+00
   1_bss:  0.4572 0.4438   6.260470e+00   6.239298e+00
   1_xyz:  0.3626 0.3834   6.116527e+00   6.156243e+00
   1_adp:  0.3132 0.3532   6.012819e+00   6.105509e+00
   1_occ:  0.3126 0.3544   6.012122e+00   6.106891e+00
   2_bss:  0.3099 0.3498   6.011877e+00   6.104765e+00
   2_xyz:  0.2293 0.2810   5.758859e+00   5.912915e+00
   2_adp:  0.2116 0.2619   5.694370e+00   5.862411e+00
   2_occ:  0.2114 0.2618   5.693663e+00   5.861446e+00
   3_bss:  0.2100 0.2603   5.693975e+00   5.860170e+00
   3_xyz:  0.1602 0.2083   5.445998e+00   5.645024e+00
   3_adp:  0.1442 0.1962   5.371786e+00   5.595195e+00
   3_occ:  0.1441 0.1962   5.371718e+00   5.595652e+00
   4_bss:  0.1441 0.1962   5.371785e+00   5.594728e+00
   4_xyz:  0.1338 0.1856   5.311306e+00   5.543438e+00
   4_adp:  0.1315 0.1818   5.294922e+00   5.524396e+00
   4_occ:  0.1313 0.1819   5.294953e+00   5.524760e+00
   5_bss:  0.1313 0.1819   5.294855e+00   5.524724e+00
   5_xyz:  0.1230 0.1734   5.237767e+00   5.476422e+00
   5_adp:  0.1210 0.1720   5.228508e+00   5.470655e+00
   5_occ:  0.1209 0.1719   5.228290e+00   5.470474e+00
   5_bss:  0.1211 0.1712   5.227950e+00   5.469037e+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:  0.300  20.000  10.216   6.930   8.796   0.000   0.000   0.000
   1_xyz:  0.300  20.000  10.216   6.930   8.796   0.000   0.000   0.000
   1_adp:  0.300  20.000  10.216   6.930   8.796   0.000   0.000   0.000
   1_occ:  0.300  20.000  10.216   6.930   8.796   0.000   0.000   0.000
   2_bss:  0.317  50.001   6.833   3.990   5.780   0.000   0.000   0.000
   2_xyz:  0.317  50.001   6.833   3.990   5.780   0.000   0.000   0.000
   2_adp:  0.317  50.001   6.833   3.990   5.780   0.000   0.000   0.000
   2_occ:  0.317  50.001   6.833   3.990   5.780   0.000   0.000   0.000
   3_bss:  0.326  50.001   4.205   2.945   4.327   0.000   0.000   0.000
   3_xyz:  0.326  50.001   4.205   2.945   4.327   0.000   0.000   0.000
   3_adp:  0.326  50.001   4.205   2.945   4.327   0.000   0.000   0.000
   3_occ:  0.326  50.001   4.205   2.945   4.327   0.000   0.000   0.000
   4_bss:  0.336  68.362   3.082   2.386   3.767   0.000   0.000   0.000
   4_xyz:  0.336  68.362   3.082   2.386   3.767   0.000   0.000   0.000
   4_adp:  0.336  68.362   3.082   2.386   3.767   0.000   0.000   0.000
   4_occ:  0.336  68.362   3.082   2.386   3.767   0.000   0.000   0.000
   5_bss:  0.330  65.829   3.082   2.386   3.767   0.000   0.000   0.000
   5_xyz:  0.330  65.829   3.082   2.386   3.767   0.000   0.000   0.000
   5_adp:  0.330  65.829   3.082   2.386   3.767   0.000   0.000   0.000
   5_occ:  0.330  65.829   3.082   2.386   3.767   0.000   0.000   0.000
   5_bss:  0.330  68.923  -0.103  -0.610   0.714  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.797 0.4860  0.5476    61779.652
   1_bss:  52.902 0.4835  0.7040    60457.669
   1_xyz:  44.202 0.5906  0.8333    43211.157
   1_adp:  39.207 0.6519  0.9302    36508.042
   1_occ:  39.296 0.6508  0.9280    36619.681
   2_bss:  39.095 0.6531  0.8360    36272.525
   2_xyz:  28.901 0.7694  0.9593    21125.906
   2_adp:  26.503 0.7961  0.9876    18547.124
   2_occ:  26.481 0.7963  0.9873    18500.244
   3_bss:  26.432 0.7969  0.9294    18464.947
   3_xyz:  19.888 0.8627  0.9800    11072.751
   3_adp:  18.676 0.8742  0.9836     9854.507
   3_occ:  18.682 0.8742  0.9833     9858.033
   4_bss:  18.656 0.8744  0.9574     9839.050
   4_xyz:  17.371 0.8863  0.9630     8764.603
   4_adp:  16.876 0.8911  0.9621     8462.010
   4_occ:  16.888 0.8909  0.9617     8463.303
   5_bss:  16.887 0.8909  0.9616     8461.035
   5_xyz:  15.817 0.9002  0.9673     7634.821
   5_adp:  15.680 0.9015  0.9626     7548.872
   5_occ:  15.675 0.9016  0.9626     7545.531
   5_bss:  15.672 0.9015  0.9629     7509.425
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4432e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4432e+01
   1_xyz:   1.645  0.013  0.107 18.244  0.006  4.113   1.3562e-01
   1_adp:   1.645  0.013  0.107 18.244  0.006  4.113   1.3562e-01
   1_occ:   1.645  0.013  0.107 18.244  0.006  4.113   1.3562e-01
   2_bss:   1.645  0.013  0.107 18.244  0.006  4.113   1.3562e-01
   2_xyz:   1.073  0.009  0.073 16.471  0.005  4.133   7.7829e-02
   2_adp:   1.073  0.009  0.073 16.471  0.005  4.133   7.7829e-02
   2_occ:   1.073  0.009  0.073 16.471  0.005  4.133   7.7829e-02
   3_bss:   1.073  0.009  0.073 16.471  0.005  4.133   7.7829e-02
   3_xyz:   1.124  0.008  0.083 16.212  0.004  4.117   7.3457e-02
   3_adp:   1.124  0.008  0.083 16.212  0.004  4.117   7.3457e-02
   3_occ:   1.124  0.008  0.083 16.212  0.004  4.117   7.3457e-02
   4_bss:   1.124  0.008  0.083 16.212  0.004  4.117   7.3457e-02
   4_xyz:   0.959  0.007  0.073 15.816  0.003  4.124   6.0327e-02
   4_adp:   0.959  0.007  0.073 15.816  0.003  4.124   6.0327e-02
   4_occ:   0.959  0.007  0.073 15.816  0.003  4.124   6.0327e-02
   5_bss:   0.959  0.007  0.073 15.816  0.003  4.124   6.0327e-02
   5_xyz:   1.081  0.009  0.083 15.784  0.004  4.131   7.1182e-02
   5_adp:   1.081  0.009  0.083 15.784  0.004  4.131   7.1182e-02
   5_occ:   1.081  0.009  0.083 15.784  0.004  4.131   7.1182e-02
   5_bss:   1.081  0.009  0.083 15.784  0.004  4.131   7.1182e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0581e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0581e+00
   1_xyz:  13.469  0.156  0.418 85.646  0.040  2.212   1.0182e-01
   1_adp:  13.469  0.156  0.418 85.646  0.040  2.212   1.0182e-01
   1_occ:  13.469  0.156  0.418 85.646  0.040  2.212   1.0182e-01
   2_bss:  13.469  0.156  0.418 85.646  0.040  2.212   1.0182e-01
   2_xyz:   6.898  0.091  0.274 82.940  0.042  2.301   1.4997e-01
   2_adp:   6.898  0.091  0.274 82.940  0.042  2.301   1.4997e-01
   2_occ:   6.898  0.091  0.274 82.940  0.042  2.301   1.4997e-01
   3_bss:   6.898  0.091  0.274 82.940  0.042  2.301   1.4997e-01
   3_xyz:   9.170  0.069  0.377 87.836  0.037  2.405   5.2975e-02
   3_adp:   9.170  0.069  0.377 87.836  0.037  2.405   5.2975e-02
   3_occ:   9.170  0.069  0.377 87.836  0.037  2.405   5.2975e-02
   4_bss:   9.170  0.069  0.377 87.836  0.037  2.405   5.2975e-02
   4_xyz:   8.183  0.050  0.298 80.671  0.038  2.394   3.5340e-02
   4_adp:   8.183  0.050  0.298 80.671  0.038  2.394   3.5340e-02
   4_occ:   8.183  0.050  0.298 80.671  0.038  2.394   3.5340e-02
   5_bss:   8.183  0.050  0.298 80.671  0.038  2.394   3.5340e-02
   5_xyz:   8.709  0.066  0.382 82.806  0.040  2.354   5.4702e-02
   5_adp:   8.709  0.066  0.382 82.806  0.040  2.354   5.4702e-02
   5_occ:   8.709  0.066  0.382 82.806  0.040  2.354   5.4702e-02
   5_bss:   8.709  0.066  0.382 82.806  0.040  2.354   5.4702e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  64.78   0.00  11.69  59.83   0.00   8.93  64.78   0.00  26.73
   1_occ:  64.78   0.00  11.69  59.83   0.00   8.93  64.78   0.00  26.73
   2_bss:  64.78   0.00  11.69  59.83   0.00   8.93  64.78   0.00  26.73
   2_xyz:  64.78   0.00  11.69  59.83   0.00   8.93  64.78   0.00  26.73
   2_adp:  98.07   0.00  11.93  98.07   0.00   8.60  66.60   0.00  30.10
   2_occ:  98.07   0.00  11.93  98.07   0.00   8.60  66.60   0.00  30.10
   3_bss:  98.07   0.00  11.93  98.07   0.00   8.60  66.60   0.00  30.10
   3_xyz:  98.07   0.00  11.93  98.07   0.00   8.60  66.60   0.00  30.10
   3_adp:  80.91   0.00  13.13  77.19   0.00   8.59  80.91   0.40  37.84
   3_occ:  80.91   0.00  13.13  77.19   0.00   8.59  80.91   0.40  37.84
   4_bss:  80.91   0.00  13.13  77.19   0.00   8.59  80.91   0.40  37.84
   4_xyz:  80.91   0.00  13.13  77.19   0.00   8.59  80.91   0.40  37.84
   4_adp:  82.03   0.00  12.95  78.75   0.00   8.40  82.03   0.87  37.70
   4_occ:  82.03   0.00  12.95  78.75   0.00   8.40  82.03   0.87  37.70
   5_bss:  82.03   0.00  12.95  78.75   0.00   8.40  82.03   0.87  37.70
   5_xyz:  82.03   0.00  12.95  78.75   0.00   8.40  82.03   0.87  37.70
   5_adp: 100.98   0.00  13.14  90.74   0.00   8.41 100.98   0.89  38.89
   5_occ: 100.98   0.00  13.14  90.74   0.00   8.41 100.98   0.89  38.89
   5_bss: 104.07   3.09  16.24  93.83   3.09  11.51 104.07   3.98  41.98
------------------------------------------------------------------------
 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:    1.228    0.015    0.409
   1_adp:    1.228    0.015    0.409
   1_occ:    1.228    0.015    0.409
   2_bss:    1.228    0.015    0.409
   2_xyz:    1.596    0.026    0.544
   2_adp:    1.596    0.026    0.544
   2_occ:    1.596    0.026    0.544
   3_bss:    1.596    0.026    0.544
   3_xyz:    1.544    0.058    0.613
   3_adp:    1.544    0.058    0.613
   3_occ:    1.544    0.058    0.613
   4_bss:    1.544    0.058    0.613
   4_xyz:    1.631    0.040    0.641
   4_adp:    1.631    0.040    0.641
   4_occ:    1.631    0.040    0.641
   5_bss:    1.631    0.040    0.641
   5_xyz:    1.693    0.065    0.662
   5_adp:    1.693    0.065    0.662
   5_occ:    1.693    0.065    0.662
   5_bss:    1.693    0.065    0.662
------------------------------------------------------------------------

CPU time actual refinement: 328.04


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1272/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/trial/run_1272/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1272/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1272/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1272/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 327.89 
  Macro-tasks:
    bulk solvent and scale       = 40.43  
    individual site refinement   = 131.84 
    weights calculation          = 31.20  
    collect and process          = 6.63   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 210.22 
  Micro-tasks:
    mask                            = 2.37   
    f_calc                          = 100.53 
    alpha_beta                      = 8.28   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 110.77 
    fmodel                         = 7.19   
    r_factors                      = 0.24   
    phase_errors                   = 10.82  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 241.59 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.632 micro seconds
Total CPU time: 5.69 minutes
from_scatterers_fft:    655 calls, 100.19 s
gradients_fft:          599 calls,  97.64 s

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

# Date 2008-01-16 Time 03:37:38 PST -0800 (1200483458.25 s)
Start R-work = 0.4651, R-free = 0.4540 (no bulk solvent and anisotropic scale)
Final R-work = 0.1370, R-free = 0.1874 (no bulk solvent and anisotropic scale)

Start R-work = 0.4572, R-free = 0.4438
Final R-work = 0.1211, R-free = 0.1712