# Date 2008-01-16 Time 02:44:33 PST -0800 (1200480273.35 s)
#phil __OFF__

Command line arguments: "../956.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15170
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 956

-------------------------------------------------------------------------------
  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: (70.9525, 47.8686, 88.5498, 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: 3.28, per 1000 atoms: 1.16


================================== 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: (70.9525, 47.8686, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 2.02065
Completeness in resolution range: 0.963314
Completeness with d_max=infinity: 0.960292

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2039
                             d_min =   2.0206

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: (70.9525, 47.8686, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 2.02065
Completeness in resolution range: 0.963314
Completeness with d_max=infinity: 0.960292

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2043 -  4.3231 [2145/2172]  1929   216  10.1%
  bin  2:  4.3231 -  3.4445 [2038/2054]  1837   201   9.9%
  bin  3:  3.4445 -  3.0130 [2036/2055]  1831   205  10.1%
  bin  4:  3.0130 -  2.7392 [1996/2026]  1794   202  10.1%
  bin  5:  2.7392 -  2.5439 [1997/2016]  1796   201  10.1%
  bin  6:  2.5439 -  2.3945 [1982/2007]  1789   193   9.7%
  bin  7:  2.3945 -  2.2750 [1971/2004]  1776   195   9.9%
  bin  8:  2.2750 -  2.1762 [1975/2006]  1775   200  10.1%
  bin  9:  2.1762 -  2.0927 [1940/1982]  1744   196  10.1%
  bin 10:  2.0927 -  2.0206 [1509/2013]  1359   150   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_956/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.74 -     2.37: 14
        2.37 -     3.01: 1901
        3.01 -     3.64: 4483
        3.64 -     4.27: 8835
        4.27 -     4.90: 12361
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.742 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.851 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.851 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.887 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27589 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_956/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_956/model_refine_001.geo

CPU time processing inputs: 9.18


============================ 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 = 70.9525 47.8686 88.54975 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: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5164   r_free= 0.5067   ksol= 0.00   Bsol= 0.00   scale= 0.749    |
|                                                                             |
| 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:   0.98 A                  |
| x-ray target function (ml) for work reflections: 6.307723                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.8215 0.99   1390  153 0.4242 0.4119       6.644      6.6075|
|  2:  4.8215 -  3.8474 0.99   1325  151 0.4587 0.5062       6.882      7.0031|
|  3:  3.8474 -  3.3671 0.99   1318  146 0.4970 0.4656      6.7426       6.708|
|  4:  3.3671 -  3.0620 0.99   1296  137 0.5112 0.4551      6.5823      6.4926|
|  5:  3.0620 -  2.8440 0.99   1293  144 0.5403 0.4977       6.405      6.4294|
|  6:  2.8440 -  2.6773 0.99   1283  148 0.5386 0.5747      6.2998      6.2333|
|  7:  2.6773 -  2.5439 0.99   1282  146 0.5518 0.4833      6.2659      6.1713|
|  8:  2.5439 -  2.4336 0.98   1290  135 0.5437 0.4843      6.2052      6.1881|
|  9:  2.4336 -  2.3403 0.98   1257  146 0.5418 0.6633      6.1138      6.1895|
| 10:  2.3403 -  2.2598 0.99   1268  140 0.5684 0.5104       6.136      6.1387|
| 11:  2.2598 -  2.1893 0.99   1270  141 0.5412 0.5398      6.0424      6.0872|
| 12:  2.1893 -  2.1269 0.97   1259  138 0.5551 0.5519      5.9835      6.0457|
| 13:  2.1269 -  2.0711 0.99   1268  139 0.5565 0.5133      5.9053      5.8331|
| 14:  2.0711 -  2.0206 0.65    831   95 0.5662 0.5832      5.8622      5.7772|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2043 -  4.8215  1390   153  0.65  38.54   0.77     0.68      86640.04|
|  2:  4.8215 -  3.8474  1325   151  0.63  40.91   0.83     0.68     134714.17|
|  3:  3.8474 -  3.3671  1318   146  0.52  50.69   0.77     0.62     141554.67|
|  4:  3.3671 -  3.0620  1296   137  0.41  58.87   0.75     0.49     123024.01|
|  5:  3.0620 -  2.8440  1293   144  0.33  64.83   0.70     0.39      93569.71|
|  6:  2.8440 -  2.6773  1283   148  0.31  66.77   0.68     0.35      80758.35|
|  7:  2.6773 -  2.5439  1282   146  0.30  67.33   0.69     0.34      71213.83|
|  8:  2.5439 -  2.4336  1290   135  0.27  70.00   0.71     0.31      66343.85|
|  9:  2.4336 -  2.3403  1257   146  0.18  76.63   0.67     0.21      64847.50|
| 10:  2.3403 -  2.2598  1268   140  0.13  80.17   0.69     0.15      60318.72|
| 11:  2.2598 -  2.1893  1270   141  0.13  80.59   0.71     0.15      56659.60|
| 12:  2.1893 -  2.1269  1259   138  0.16  78.00   0.71     0.20      49856.02|
| 13:  2.1269 -  2.0711  1268   139  0.12  81.06   0.69     0.14      43438.96|
| 14:  2.0711 -  2.0206   831    95  0.13  80.42   0.69     0.14      36098.58|
|alpha:            min =        0.14 max =            0.68 mean =         0.36|
|beta:             min =    36098.58 max =       141554.67 mean =     80783.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.31|
|phase err.(work): min =        0.00 max =           89.99 mean =        66.09|
|phase err.(test): min =        0.00 max =           89.93 mean =        66.26|
|-----------------------------------------------------------------------------|

============================== 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 = 23.567986             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.584   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.643731              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 85.363   (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:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       26 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      159 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      668 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1471 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2550 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3805 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4941 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6417 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7542 |
|-----------------------------------------------------------------------------|
|-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 |       54.857 |
| 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 |       1.764 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.502)------------------------------------------|
|    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 = 12.502)------------------------------------------|
|    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: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5204   r_free= 0.5118   ksol= 0.00   Bsol= 0.00   scale= 0.722    |
|                                                                             |
| 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:   0.98 A                  |
| x-ray target function (ml) for work reflections: 6.308492                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5103   r_free= 0.5012   ksol= 0.30   Bsol= 50.00   scale= 0.925   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.47,9.32,10.18,0.00,0.00,0.00); trace/3= 8.32                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.96 A                  |
| x-ray target function (ml) for work reflections: 6.304036                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 20.103354             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.222   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.143684              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.173   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5103      final r-factor (work) = 0.4526          |
| start r-factor (free) = 0.5012      final r-factor (free) = 0.4696          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 118.2430 = 20.10 * 0.50 * 6.3060 + 1.00 * 54.8567                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 63.0607 = 20.10 * 0.50 * 6.2582 + 1.00 * 0.1550                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4526      final r-factor (work) = 0.4086          |
| start r-factor (free) = 0.4696      final r-factor (free) = 0.4601          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.4301 = 2.14 * 1.00 * 6.2582 + 1.00 * 0.0145                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.3350 = 2.14 * 1.00 * 6.2065 + 1.00 * 0.0303                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.502)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    128.15  18.99    None  None   None       |
|    all(noH): 2823   0      0.00    128.15  18.99    None  None   None       |
|    Sol.    : 438    0      0.00    128.15  31.01    None  None   None       |
|    Mac.    : 2385   0      0.00    96.92   16.78    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 -  12.815: 1249   |   5:    64.076 -  76.891:   41        |
|      1:    12.815 -  25.630:  830   |   6:    76.891 -  89.706:   15        |
|      2:    25.630 -  38.446:  380   |   7:    89.706 - 102.521:    4        |
|      3:    38.446 -  51.261:  204   |   8:   102.521 - 115.337:    1        |
|      4:    51.261 -  64.076:   96   |   9:   115.337 - 128.152:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4086 r_free = 0.4601             target_work(ml) = 6.196         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4079 r_free = 0.4599             target_work(ml) = 6.195         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4079   r_free= 0.4599   ksol= 0.30   Bsol= 50.00   scale= 1.090   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.47,9.32,10.18,0.00,0.00,0.00); trace/3= 8.32                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.195254                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4068   r_free= 0.4566   ksol= 0.30   Bsol= 50.00   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,5.80,6.67,0.00,0.00,0.00); trace/3= 5.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.197098                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.275607             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.462  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.648403              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.732  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4068      final r-factor (work) = 0.3326          |
| start r-factor (free) = 0.4566      final r-factor (free) = 0.4029          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 59.9205 = 19.28 * 0.50 * 6.2012 + 1.00 * 0.1550                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 59.1008 = 19.28 * 0.50 * 6.1183 + 1.00 * 0.1341                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3326      final r-factor (work) = 0.3119          |
| start r-factor (free) = 0.4029      final r-factor (free) = 0.3760          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9997 = 0.65 * 1.00 * 6.1183 + 1.00 * 0.0326                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9231 = 0.65 * 1.00 * 6.0306 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.502)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    128.46  16.18    None  None   None       |
|    all(noH): 2823   0      0.00    128.46  16.18    None  None   None       |
|    Sol.    : 438    0      0.00    128.46  32.66    None  None   None       |
|    Mac.    : 2385   0      0.00    74.60   13.16    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 -  12.846: 1488   |   5:    64.232 -  77.078:   26        |
|      1:    12.846 -  25.693:  807   |   6:    77.078 -  89.925:    3        |
|      2:    25.693 -  38.539:  310   |   7:    89.925 - 102.771:    1        |
|      3:    38.539 -  51.385:  124   |   8:   102.771 - 115.617:    2        |
|      4:    51.385 -  64.232:   61   |   9:   115.617 - 128.464:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3119 r_free = 0.3760             target_work(ml) = 6.005         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3116 r_free = 0.3758             target_work(ml) = 6.005         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3116   r_free= 0.3758   ksol= 0.30   Bsol= 50.00   scale= 1.050   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,5.80,6.67,0.00,0.00,0.00); trace/3= 5.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.004767                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3103   r_free= 0.3748   ksol= 0.30   Bsol= 70.58   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.69,3.22,3.91,0.00,0.00,0.00); trace/3= 2.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.005822                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.609081              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.019  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.434778              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.218  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3103      final r-factor (work) = 0.2536          |
| start r-factor (free) = 0.3748      final r-factor (free) = 0.3042          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.0462 = 5.61 * 0.50 * 6.0302 + 1.00 * 0.1341                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.7164 = 5.61 * 0.50 * 5.9292 + 1.00 * 0.0877                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2536      final r-factor (work) = 0.2351          |
| start r-factor (free) = 0.3042      final r-factor (free) = 0.2881          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5908 = 0.43 * 1.00 * 5.9292 + 1.00 * 0.0129                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5330 = 0.43 * 1.00 * 5.7975 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.502)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    126.59  15.62    None  None   None       |
|    all(noH): 2823   0      0.00    126.59  15.62    None  None   None       |
|    Sol.    : 438    0      0.00    126.59  36.50    None  None   None       |
|    Mac.    : 2385   0      0.00    69.28   11.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.659: 1616   |   5:    63.296 -  75.956:   25        |
|      1:    12.659 -  25.319:  663   |   6:    75.956 -  88.615:    4        |
|      2:    25.319 -  37.978:  290   |   7:    88.615 - 101.274:    2        |
|      3:    37.978 -  50.637:  159   |   8:   101.274 - 113.933:    1        |
|      4:    50.637 -  63.296:   62   |   9:   113.933 - 126.593:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2351 r_free = 0.2881             target_work(ml) = 5.777         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2347 r_free = 0.2882             target_work(ml) = 5.777         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2347   r_free= 0.2882   ksol= 0.30   Bsol= 70.58   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.69,3.22,3.91,0.00,0.00,0.00); trace/3= 2.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.777162                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2339   r_free= 0.2873   ksol= 0.32   Bsol= 70.58   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.40,1.77,2.62,0.00,0.00,0.00); trace/3= 1.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.775940                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.176018              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.011   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.249214              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.271  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2339      final r-factor (work) = 0.1792          |
| start r-factor (free) = 0.2873      final r-factor (free) = 0.2292          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.0960 = 5.18 * 0.50 * 5.7992 + 1.00 * 0.0877                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.7560 = 5.18 * 0.50 * 5.6666 + 1.00 * 0.0907                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1792      final r-factor (work) = 0.1598          |
| start r-factor (free) = 0.2292      final r-factor (free) = 0.2164          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.7578 = 2.25 * 1.00 * 5.6666 + 1.00 * 0.0123                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.3574 = 2.25 * 1.00 * 5.4857 + 1.00 * 0.0188                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.502)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.14  16.45    None  None   None       |
|    all(noH): 2823   0      0.00    115.14  16.45    None  None   None       |
|    Sol.    : 438    0      1.67    115.14  45.87    None  None   None       |
|    Mac.    : 2385   0      0.00    91.94   11.05    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.514: 1634   |   5:    57.570 -  69.084:   86        |
|      1:    11.514 -  23.028:  632   |   6:    69.084 -  80.598:   50        |
|      2:    23.028 -  34.542:  175   |   7:    80.598 -  92.112:   24        |
|      3:    34.542 -  46.056:  113   |   8:    92.112 - 103.626:    9        |
|      4:    46.056 -  57.570:   99   |   9:   103.626 - 115.139:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1598 r_free = 0.2164             target_work(ml) = 5.456         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1597 r_free = 0.2165             target_work(ml) = 5.456         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1597   r_free= 0.2165   ksol= 0.32   Bsol= 70.58   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.40,1.77,2.62,0.00,0.00,0.00); trace/3= 1.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.455839                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1598   r_free= 0.2169   ksol= 0.34   Bsol= 88.09   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.44,1.44,2.49,0.00,0.00,0.00); trace/3= 1.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.457400                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.542176              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.329  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.390384              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.173   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1598      final r-factor (work) = 0.1410          |
| start r-factor (free) = 0.2169      final r-factor (free) = 0.1937          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8077 = 3.54 * 0.50 * 5.4860 + 1.00 * 0.0915                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6574 = 3.54 * 0.50 * 5.4081 + 1.00 * 0.0792                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1410      final r-factor (work) = 0.1383          |
| start r-factor (free) = 0.1937      final r-factor (free) = 0.1906          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1296 = 0.39 * 1.00 * 5.4081 + 1.00 * 0.0184                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1138 = 0.39 * 1.00 * 5.3438 + 1.00 * 0.0277                               |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 4      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.502)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.68  16.26    None  None   None       |
|    all(noH): 2823   0      0.00    114.68  16.26    None  None   None       |
|    Sol.    : 438    0      1.75    114.68  45.58    None  None   None       |
|    Mac.    : 2385   0      0.00    91.47   10.87    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.468: 1672   |   5:    57.338 -  68.806:   85        |
|      1:    11.468 -  22.935:  604   |   6:    68.806 -  80.274:   50        |
|      2:    22.935 -  34.403:  167   |   7:    80.274 -  91.741:   25        |
|      3:    34.403 -  45.871:  110   |   8:    91.741 - 103.209:    9        |
|      4:    45.871 -  57.338:  100   |   9:   103.209 - 114.677:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1383 r_free = 0.1906             target_work(ml) = 5.334         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1381 r_free = 0.1905             target_work(ml) = 5.333         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1381   r_free= 0.1905   ksol= 0.34   Bsol= 88.09   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.44,1.44,2.49,0.00,0.00,0.00); trace/3= 1.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.333198                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.8215 0.99   1390  153 0.1057 0.1460      5.4625      5.6236|
|  2:  4.8215 -  3.8474 0.99   1325  151 0.0947 0.1202      5.5421      5.7792|
|  3:  3.8474 -  3.3671 0.99   1318  146 0.1273 0.1748      5.6465      5.9934|
|  4:  3.3671 -  3.0620 0.99   1296  137 0.1450 0.1823      5.6222      5.7665|
|  5:  3.0620 -  2.8440 0.99   1293  144 0.1705 0.2095      5.5617      5.7243|
|  6:  2.8440 -  2.6773 0.99   1283  148 0.1550 0.2674      5.4328      5.7246|
|  7:  2.6773 -  2.5439 0.99   1282  146 0.1607 0.2058      5.3943      5.5591|
|  8:  2.5439 -  2.4336 0.98   1290  135 0.1561 0.2020      5.3255       5.551|
|  9:  2.4336 -  2.3403 0.98   1257  146 0.1590 0.2242      5.2537      5.5003|
| 10:  2.3403 -  2.2598 0.99   1268  140 0.1453 0.1986      5.1842      5.3672|
| 11:  2.2598 -  2.1893 0.99   1270  141 0.1469 0.2366      5.1367      5.4716|
| 12:  2.1893 -  2.1269 0.97   1259  138 0.1362 0.1996      5.0456      5.3507|
| 13:  2.1269 -  2.0711 0.99   1268  139 0.1410 0.1937      4.9798      5.1567|
| 14:  2.0711 -  2.0206 0.65    831   95 0.1358 0.2019      4.8676      5.1643|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2043 -  4.8215  1390   153  0.93  10.81   0.95     0.93       9131.59|
|  2:  4.8215 -  3.8474  1325   151  0.94   9.95   1.00     0.98      11506.33|
|  3:  3.8474 -  3.3671  1318   146  0.92  13.75   1.03     1.02      14257.97|
|  4:  3.3671 -  3.0620  1296   137  0.90  16.64   1.01     0.99      14489.09|
|  5:  3.0620 -  2.8440  1293   144  0.85  21.02   1.01     0.99      13679.56|
|  6:  2.8440 -  2.6773  1283   148  0.85  21.17   0.98     0.93      11390.74|
|  7:  2.6773 -  2.5439  1282   146  0.86  20.66   0.99     0.95      10153.97|
|  8:  2.5439 -  2.4336  1290   135  0.86  20.49   0.98     0.94       8876.22|
|  9:  2.4336 -  2.3403  1257   146  0.86  20.47   1.00     0.94       7851.12|
| 10:  2.3403 -  2.2598  1268   140  0.86  20.33   0.99     0.94       6888.11|
| 11:  2.2598 -  2.1893  1270   141  0.86  20.55   0.98     0.92       6371.78|
| 12:  2.1893 -  2.1269  1259   138  0.87  19.42   1.00     0.97       5754.91|
| 13:  2.1269 -  2.0711  1268   139  0.87  19.58   0.97     0.94       4843.86|
| 14:  2.0711 -  2.0206   831    95  0.88  18.53   0.94     0.89       3731.38|
|alpha:            min =        0.89 max =            1.02 mean =         0.95|
|beta:             min =     3731.38 max =        14489.09 mean =      9385.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           90.00 mean =        18.01|
|phase err.(test): min =        0.00 max =           89.44 mean =        17.08|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1383   r_free= 0.1904   ksol= 0.33   Bsol= 82.49   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.93,-0.16,1.09,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.333663                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1383   r_free= 0.1904   ksol= 0.33   Bsol= 82.49   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.93,-0.16,1.09,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.333663                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.8215 0.99   1390  153 0.1064 0.1442       5.464      5.6241|
|  2:  4.8215 -  3.8474 0.99   1325  151 0.0954 0.1191      5.5454      5.7697|
|  3:  3.8474 -  3.3671 0.99   1318  146 0.1273 0.1749      5.6454      5.9939|
|  4:  3.3671 -  3.0620 0.99   1296  137 0.1454 0.1825       5.624        5.77|
|  5:  3.0620 -  2.8440 0.99   1293  144 0.1706 0.2092      5.5634      5.7255|
|  6:  2.8440 -  2.6773 0.99   1283  148 0.1551 0.2678      5.4332      5.7247|
|  7:  2.6773 -  2.5439 0.99   1282  146 0.1607 0.2059      5.3945      5.5593|
|  8:  2.5439 -  2.4336 0.98   1290  135 0.1560 0.2021      5.3252      5.5512|
|  9:  2.4336 -  2.3403 0.98   1257  146 0.1589 0.2243      5.2534      5.5002|
| 10:  2.3403 -  2.2598 0.99   1268  140 0.1451 0.1988       5.184      5.3678|
| 11:  2.2598 -  2.1893 0.99   1270  141 0.1468 0.2365      5.1366      5.4713|
| 12:  2.1893 -  2.1269 0.97   1259  138 0.1361 0.1995      5.0454      5.3507|
| 13:  2.1269 -  2.0711 0.99   1268  139 0.1411 0.1934      4.9793      5.1557|
| 14:  2.0711 -  2.0206 0.65    831   95 0.1360 0.2015      4.8672      5.1631|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2043 -  4.8215  1390   153  0.93  10.91   0.95     0.93       9179.94|
|  2:  4.8215 -  3.8474  1325   151  0.94   9.93   1.00     0.98      11461.17|
|  3:  3.8474 -  3.3671  1318   146  0.92  13.71   1.03     1.02      14181.28|
|  4:  3.3671 -  3.0620  1296   137  0.89  16.68   1.01     0.99      14531.00|
|  5:  3.0620 -  2.8440  1293   144  0.85  21.04   1.01     0.99      13722.75|
|  6:  2.8440 -  2.6773  1283   148  0.85  21.17   0.98     0.93      11400.12|
|  7:  2.6773 -  2.5439  1282   146  0.86  20.66   0.99     0.95      10161.88|
|  8:  2.5439 -  2.4336  1290   135  0.86  20.48   0.98     0.94       8872.68|
|  9:  2.4336 -  2.3403  1257   146  0.86  20.47   1.00     0.95       7851.99|
| 10:  2.3403 -  2.2598  1268   140  0.86  20.33   1.00     0.95       6888.18|
| 11:  2.2598 -  2.1893  1270   141  0.86  20.55   0.99     0.92       6377.94|
| 12:  2.1893 -  2.1269  1259   138  0.87  19.42   1.00     0.97       5753.18|
| 13:  2.1269 -  2.0711  1268   139  0.87  19.56   0.97     0.94       4834.73|
| 14:  2.0711 -  2.0206   831    95  0.88  18.50   0.94     0.90       3718.58|
|alpha:            min =        0.90 max =            1.02 mean =         0.96|
|beta:             min =     3718.58 max =        14531.00 mean =      9386.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.98 mean =        18.01|
|phase err.(test): min =        0.00 max =           88.05 mean =        17.13|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.502)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.52    116.20  17.78    None  None   None       |
|    all(noH): 2823   0      1.52    116.20  17.78    None  None   None       |
|    Sol.    : 438    0      3.27    116.20  47.10    None  None   None       |
|    Mac.    : 2385   0      1.52    92.98   12.39    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.520 -  12.988: 1672   |   5:    58.858 -  70.326:   85        |
|      1:    12.988 -  24.455:  604   |   6:    70.326 -  81.793:   50        |
|      2:    24.455 -  35.923:  167   |   7:    81.793 -  93.261:   25        |
|      3:    35.923 -  47.391:  110   |   8:    93.261 - 104.729:    9        |
|      4:    47.391 -  58.858:  100   |   9:   104.729 - 116.196:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 342         
Filter by distance & map next to the model:
   mapped sites are within: 0.324 - 5.663
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 329 from: 342
   mapped sites are within: 0.709 - 5.663

peak=    8.370 closest distance to " CB  VAL A 230 " =    1.390
peak=    6.245 closest distance to " CD1AILE A 234 " =    1.345
peak=    6.224 closest distance to " O   HOH Z 120 " =    1.258
peak=    5.812 closest distance to " O   HOH Z 210 " =    1.560
peak=    5.684 closest distance to " O   HOH Z  32 " =    1.126
peak=    5.622 closest distance to " O   HOH Z 400 " =    0.709
peak=    5.532 closest distance to " O   HOH Z 117 " =    1.523
peak=    5.174 closest distance to " O   HOH Z 431 " =    1.533
peak=    5.075 closest distance to " CG  LEU A   5 " =    1.150
peak=    4.960 closest distance to " CZ  PHE A 218 " =    1.122
peak=    4.943 closest distance to " O   HOH Z 425 " =    1.761
peak=    4.915 closest distance to " O   HOH Z 128 " =    1.753
peak=    4.898 closest distance to " O   HOH Z 248 " =    1.389
peak=    4.883 closest distance to " O   HOH Z 411 " =    3.854
peak=    4.863 closest distance to " O   HOH Z 102 " =    1.486
peak=    4.839 closest distance to " NH1 ARG A 138 " =    1.001
peak=    4.699 closest distance to " O   HOH Z 107 " =    1.119
peak=    4.658 closest distance to " CG1 VAL A 296 " =    1.214
peak=    4.627 closest distance to " CA  TYR A  30 " =    0.995
peak=    4.624 closest distance to " CB  SER A  63 " =    1.330
peak=    4.602 closest distance to " CB  GLN A 223 " =    1.488
peak=    4.599 closest distance to " O   PRO A 198 " =    1.666
peak=    4.592 closest distance to " O   HOH Z  54 " =    1.161
peak=    4.520 closest distance to " CG1 ILE A 120 " =    0.877
peak=    4.488 closest distance to " CG  GLN A  77 " =    0.866
peak=    4.424 closest distance to " O  BHOH Z 338 " =    1.138
peak=    4.420 closest distance to " CA  VAL A 230 " =    1.203
peak=    4.418 closest distance to " OE1 GLN A  88 " =    1.000
peak=    4.368 closest distance to " O   HOH Z  49 " =    1.660
peak=    4.366 closest distance to " O   HOH Z 279 " =    0.870
peak=    4.345 closest distance to " NE2 GLN A  11 " =    1.174
peak=    4.330 closest distance to " CD2 LEU A   5 " =    1.167
peak=    4.328 closest distance to " O   HOH Z 394 " =    1.524
peak=    4.327 closest distance to " CA  ALA A 295 " =    0.928
peak=    4.316 closest distance to " CA  ASP A 191 " =    1.202
peak=    4.307 closest distance to " NH1BARG A 102 " =    1.004
peak=    4.298 closest distance to " NH2 ARG A  56 " =    2.205
peak=    4.276 closest distance to " N   SER A 164 " =    0.891
peak=    4.273 closest distance to " O   HOH Z 130 " =    1.199
peak=    4.255 closest distance to " O   HOH Z 126 " =    1.665
peak=    4.254 closest distance to " CD2 TRP A 179 " =    1.253
peak=    4.246 closest distance to " O   HOH Z 369 " =    1.967
peak=    4.240 closest distance to " CG2 VAL A 197 " =    1.230
peak=    4.232 closest distance to " CG AARG A 275 " =    1.197
peak=    4.227 closest distance to " CG  PRO A  54 " =    1.357
peak=    4.203 closest distance to " CG2 ILE A 234 " =    1.229
peak=    4.190 closest distance to " CB  TRP A 179 " =    1.262
peak=    4.178 closest distance to " CB  VAL A 296 " =    1.078
peak=    4.154 closest distance to " O   HOH Z 246 " =    1.606
peak=    4.152 closest distance to " CA  ARG A 195 " =    1.227
peak=    4.133 closest distance to " CB  GLN A 183 " =    1.236
peak=    4.126 closest distance to " CG  LEU A 228 " =    1.411
peak=    4.125 closest distance to " O   HOH Z 359 " =    1.793
peak=    4.074 closest distance to " CG2 THR A 221 " =    1.128
peak=    4.071 closest distance to " CD  LYS A 166 " =    1.696
peak=    4.059 closest distance to " O   GLN A  11 " =    0.838
peak=    4.047 closest distance to " CB  VAL A 202 " =    1.409
peak=    4.045 closest distance to " CA  GLY A 267 " =    1.094
peak=    4.040 closest distance to " CD2 LEU A 228 " =    1.326
peak=    4.033 closest distance to " CB  GLN A  89 " =    1.210
peak=    4.026 closest distance to " O   HOH Z  54 " =    1.329
peak=    4.018 closest distance to " O   HOH Z 151 " =    2.047
peak=    4.009 closest distance to " CA  ALA A 100 " =    1.016
peak=    4.000 closest distance to " O   HOH Z 193 " =    1.518
peak=    3.987 closest distance to " O   HOH Z  67 " =    1.125
peak=    3.978 closest distance to " CB  ARG A 275 " =    1.041
peak=    3.955 closest distance to " CB AVAL A  41 " =    1.272
peak=    3.948 closest distance to " O   HOH Z 154 " =    1.614
peak=    3.943 closest distance to " O   HOH Z 251 " =    1.736
peak=    3.940 closest distance to " CB  MET A  40 " =    0.842
peak=    3.939 closest distance to " CG2 VAL A 296 " =    1.012
peak=    3.934 closest distance to " O   HOH Z 142 " =    1.837
peak=    3.920 closest distance to " CB  ASN A  39 " =    0.804
peak=    3.919 closest distance to " CA  ARG A 156 " =    1.104
peak=    3.917 closest distance to " O   HOH Z 417 " =    3.296
peak=    3.914 closest distance to " CB  ASP A 124 " =    0.828
peak=    3.907 closest distance to " O   HOH Z 144 " =    1.945
peak=    3.904 closest distance to " O   SER A  87 " =    2.360
peak=    3.903 closest distance to " O   HOH Z  56 " =    2.126
peak=    3.896 closest distance to " O   HOH Z  80 " =    2.100
peak=    3.895 closest distance to " O   HOH Z 422 " =    0.854
peak=    3.892 closest distance to " CG  PRO A 198 " =    1.395
peak=    3.882 closest distance to " O   HOH Z 261 " =    1.285
peak=    3.868 closest distance to " CB  SER A  62 " =    0.984
peak=    3.865 closest distance to " CD  PRO A  54 " =    1.180
peak=    3.860 closest distance to " N   LYS A 119 " =    0.786
peak=    3.858 closest distance to " O   HOH Z  40 " =    1.900
peak=    3.856 closest distance to " O   HOH Z 214 " =    1.635
peak=    3.853 closest distance to " CB  PRO A 280 " =    1.372
peak=    3.846 closest distance to " O   HOH Z 261 " =    2.196
peak=    3.842 closest distance to " O   HOH Z 207 " =    1.495
peak=    3.839 closest distance to " O   HOH Z 277 " =    1.265
peak=    3.824 closest distance to " O   HOH Z 133 " =    1.529
peak=    3.823 closest distance to " O   HOH Z 393 " =    3.520
peak=    3.819 closest distance to " OG  SER A 245 " =    1.626
peak=    3.815 closest distance to " O   HOH Z 426 " =    1.034
peak=    3.812 closest distance to " O   HOH Z 402 " =    1.546
peak=    3.804 closest distance to " O   HOH Z 234 " =    3.602
peak=    3.800 closest distance to " O   HOH Z 433 " =    1.820
peak=    3.788 closest distance to " O   HOH Z 199 " =    1.551
peak=    3.769 closest distance to " O   HOH Z 265 " =    2.160
peak=    3.767 closest distance to " CB  ASN A 142 " =    1.131
peak=    3.756 closest distance to " CB  ARG A  79 " =    1.275
peak=    3.752 closest distance to " O   HOH Z   4 " =    1.738
peak=    3.747 closest distance to " NH2AARG A 145 " =    0.898
peak=    3.745 closest distance to " C   ASN A 209 " =    1.456
peak=    3.742 closest distance to " CA  ALA A  51 " =    0.988
peak=    3.735 closest distance to " O   HOH Z 403 " =    1.893
peak=    3.731 closest distance to " CG  PRO A 243 " =    1.246
peak=    3.714 closest distance to " O   HOH Z 343 " =    2.544
peak=    3.713 closest distance to " CG1 VAL A 153 " =    1.085
peak=    3.713 closest distance to " OE1 GLU A   2 " =    1.313
peak=    3.710 closest distance to " CA  ALA A 154 " =    0.986
peak=    3.702 closest distance to " O   HOH Z  63 " =    1.297
peak=    3.695 closest distance to " O   HOH Z 193 " =    2.065
peak=    3.692 closest distance to " CA  ASP A 162 " =    0.955
peak=    3.684 closest distance to " NE2 HIS A 115 " =    1.053
peak=    3.678 closest distance to " CE3 TRP A  85 " =    1.125
peak=    3.678 closest distance to " CA  ALA A  21 " =    1.325
peak=    3.677 closest distance to " O   HOH Z 130 " =    2.580
peak=    3.669 closest distance to " O   HOH Z 176 " =    1.830
peak=    3.644 closest distance to " OE1 GLN A  55 " =    1.334
peak=    3.639 closest distance to " O   HOH Z 377 " =    1.428
peak=    3.635 closest distance to " NH2 ARG A 156 " =    1.064
peak=    3.627 closest distance to " C   VAL A 265 " =    1.124
peak=    3.625 closest distance to " N   SER A 271 " =    1.059
peak=    3.622 closest distance to " O   HOH Z 232 " =    2.114
peak=    3.620 closest distance to " O   HOH Z 124 " =    1.039
peak=    3.610 closest distance to " CB  GLN A  88 " =    1.261
peak=    3.599 closest distance to " CB  GLU A 128 " =    1.056
peak=    3.586 closest distance to " CB  GLU A 277 " =    3.789
peak=    3.584 closest distance to " CB  VAL A 296 " =    1.365
peak=    3.576 closest distance to " O   HOH Z  57 " =    2.077
peak=    3.575 closest distance to " CD1 ILE A 199 " =    1.184
peak=    3.575 closest distance to " O   GLU A   2 " =    1.722
peak=    3.573 closest distance to " CD  ARG A 159 " =    0.787
peak=    3.569 closest distance to " ND2 ASN A 249 " =    2.134
peak=    3.567 closest distance to " OE1 GLN A  11 " =    2.131
peak=    3.564 closest distance to " O   HOH Z  48 " =    1.680
peak=    3.564 closest distance to " OE2 GLU A   2 " =    2.142
peak=    3.560 closest distance to " CB  SER A 288 " =    1.624
peak=    3.555 closest distance to " O   HOH Z 146 " =    1.727
peak=    3.553 closest distance to " CB  ASN A 215 " =    1.248
peak=    3.541 closest distance to " O   HOH Z 155 " =    3.189
peak=    3.539 closest distance to " CB  VAL A 265 " =    1.325
peak=    3.535 closest distance to " O   HOH Z  85 " =    2.227
peak=    3.534 closest distance to " O   ASP A 200 " =    1.655
peak=    3.532 closest distance to " O   HOH Z  59 " =    2.382
peak=    3.531 closest distance to " O   HOH Z  26 " =    1.081
peak=    3.526 closest distance to " CB  THR A 235 " =    1.365
peak=    3.525 closest distance to " CZ3 TRP A  85 " =    0.817
peak=    3.524 closest distance to " CZ3 TRP A 266 " =    1.139
peak=    3.523 closest distance to " CD  ARG A 195 " =    1.181
peak=    3.523 closest distance to " CA  TYR A 116 " =    1.403
peak=    3.523 closest distance to " CB  PHE A 283 " =    0.829
peak=    3.523 closest distance to " CG2AVAL A 121 " =    1.869
peak=    3.514 closest distance to " CG1 VAL A 296 " =    1.718
peak=    3.514 closest distance to " O   HOH Z 368 " =    2.356
peak=    3.509 closest distance to " CB  SER A  26 " =    1.685
peak=    3.508 closest distance to " O   HOH Z 213 " =    1.673
peak=    3.499 closest distance to " CB  ASN A 148 " =    1.437
peak=    3.496 closest distance to " O   HOH Z 182 " =    1.053
peak=    3.482 closest distance to " CB  ALA A 248 " =    1.434
peak=    3.478 closest distance to " O   HOH Z 316 " =    3.107
peak=    3.476 closest distance to " O  BHOH Z 338 " =    2.081
peak=    3.475 closest distance to " CB  ASP A 140 " =    0.809
peak=    3.473 closest distance to " CA  ASP A 140 " =    1.428
peak=    3.471 closest distance to " O   HOH Z 388 " =    1.149
peak=    3.470 closest distance to " CD  LYS A 119 " =    1.782
peak=    3.468 closest distance to " O   THR A 251 " =    1.174
peak=    3.467 closest distance to " O   HOH Z 420 " =    5.663
peak=    3.463 closest distance to " CB  GLU A  37 " =    0.922
peak=    3.463 closest distance to " CB  PHE A  16 " =    1.172
peak=    3.459 closest distance to " CE  LYS A  76 " =    0.886
peak=    3.457 closest distance to " O   HOH Z 422 " =    2.461
peak=    3.457 closest distance to " CB  ASN A 285 " =    0.897
peak=    3.454 closest distance to " CA  PRO A 198 " =    0.916
peak=    3.451 closest distance to " CZ3 TRP A 274 " =    4.577
peak=    3.446 closest distance to " O   HOH Z 188 " =    3.364
peak=    3.443 closest distance to " O   HOH Z 303 " =    2.314
peak=    3.441 closest distance to " CB  ASN A 187 " =    1.033
peak=    3.439 closest distance to " N   TYR A  15 " =    0.932
peak=    3.434 closest distance to " CB  TRP A 150 " =    1.344
peak=    3.433 closest distance to " CA  SER A  87 " =    0.983
peak=    3.432 closest distance to " O   HOH Z  63 " =    2.013
peak=    3.430 closest distance to " N   TYR A 247 " =    1.202
peak=    3.428 closest distance to " CB  SER A  95 " =    0.875
peak=    3.428 closest distance to " CB  TYR A  30 " =    1.005
peak=    3.425 closest distance to " O   HOH Z 346 " =    1.678
peak=    3.422 closest distance to " CB  TRP A 266 " =    1.027
peak=    3.420 closest distance to " O   HOH Z 406 " =    1.585
peak=    3.418 closest distance to " OD1 ASN A 301 " =    1.070
peak=    3.409 closest distance to " CD1 LEU A  96 " =    1.089
peak=    3.408 closest distance to " O   HOH Z   9 " =    1.257
peak=    3.407 closest distance to " CA  ALA A 291 " =    0.920
peak=    3.406 closest distance to " O   HOH Z  32 " =    2.228
peak=    3.398 closest distance to " O   HOH Z 134 " =    1.598
peak=    3.397 closest distance to " CG1 ILE A  20 " =    1.294
peak=    3.392 closest distance to " O   HOH Z 291 " =    1.438
peak=    3.386 closest distance to " CD1 LEU A 300 " =    1.123
peak=    3.384 closest distance to " CB  GLU A 152 " =    1.166
peak=    3.382 closest distance to " N   ALA A 256 " =    1.126
peak=    3.374 closest distance to " CA  ALA A 160 " =    0.969
peak=    3.373 closest distance to " NE1 TRP A  92 " =    1.817
peak=    3.372 closest distance to " CG  PRO A 213 " =    1.275
peak=    3.369 closest distance to " O   HOH Z 250 " =    1.235
peak=    3.366 closest distance to " CB  SER A 210 " =    1.050
peak=    3.364 closest distance to " CB  PRO A  54 " =    0.843
peak=    3.362 closest distance to " O   THR A 220 " =    1.193
peak=    3.360 closest distance to " CA  THR A 246 " =    1.050
peak=    3.355 closest distance to " O   HOH Z 272 " =    1.379
peak=    3.353 closest distance to " O   ASP A 124 " =    1.193
peak=    3.346 closest distance to " CB  THR A  52 " =    0.935
peak=    3.345 closest distance to " NH2 ARG A  56 " =    1.125
peak=    3.341 closest distance to " CZ  PHE A  38 " =    1.200
peak=    3.337 closest distance to " CG  MET A 188 " =    0.936
peak=    3.336 closest distance to " CA  ILE A 106 " =    0.840
peak=    3.335 closest distance to " CG  LEU A 167 " =    1.006
peak=    3.326 closest distance to " CA  VAL A 125 " =    1.107
peak=    3.326 closest distance to " O   HOH Z 174 " =    1.955
peak=    3.321 closest distance to " CA  GLY A 196 " =    0.849
peak=    3.320 closest distance to " N   THR A  52 " =    1.217
peak=    3.319 closest distance to " O   HOH Z 427 " =    2.933
peak=    3.313 closest distance to " NH1AARG A 145 " =    1.300
peak=    3.312 closest distance to " CA  LEU A   5 " =    0.971
peak=    3.311 closest distance to " O   HOH Z 437 " =    1.713
peak=    3.308 closest distance to " O   HOH Z 313 " =    1.908
peak=    3.308 closest distance to " O   HOH Z 250 " =    1.119
peak=    3.308 closest distance to " CB  SER A  97 " =    0.968
peak=    3.303 closest distance to " CA  CYS A 260 " =    1.151
peak=    3.301 closest distance to " CD  ARG A 269 " =    0.888
peak=    3.298 closest distance to " CG  GLU A  37 " =    0.898
peak=    3.297 closest distance to " O   HOH Z 131 " =    0.829
peak=    3.297 closest distance to " CB  ALA A 100 " =    1.555
peak=    3.296 closest distance to " O   ASN A  74 " =    1.975
peak=    3.293 closest distance to " CD ALYS A 290 " =    1.056
peak=    3.287 closest distance to " O   HOH Z  76 " =    1.264
peak=    3.285 closest distance to " O   PRO A 213 " =    1.402
peak=    3.281 closest distance to " CD2 LEU A 255 " =    1.560
peak=    3.279 closest distance to " O   THR A 182 " =    1.498
peak=    3.278 closest distance to " OG BSER A 164 " =    1.923
peak=    3.277 closest distance to " CB  PRO A 243 " =    1.220
peak=    3.277 closest distance to " O   HOH Z 395 " =    1.516
peak=    3.275 closest distance to " O   HOH Z 171 " =    3.802
peak=    3.274 closest distance to " CB  MET A 105 " =    1.237
peak=    3.274 closest distance to " O   HOH Z 139 " =    1.222
peak=    3.266 closest distance to " CA  ASP A 124 " =    0.913
peak=    3.260 closest distance to " O   HOH Z 132 " =    2.987
peak=    3.258 closest distance to " O   HOH Z  27 " =    1.059
peak=    3.257 closest distance to " CD1 LEU A 101 " =    1.097
peak=    3.257 closest distance to " N   GLN A 278 " =    1.402
peak=    3.256 closest distance to " CE1 TYR A  30 " =    0.988
peak=    3.255 closest distance to " CZ3 TRP A  92 " =    1.194
peak=    3.254 closest distance to " ND1 HIS A  81 " =    1.509
peak=    3.252 closest distance to " O   HOH Z 435 " =    2.078
peak=    3.251 closest distance to " OG  SER A  62 " =    2.747
peak=    3.247 closest distance to " CA  ARG A 102 " =    1.266
peak=    3.246 closest distance to " O   HOH Z 280 " =    2.945
peak=    3.242 closest distance to " CA  GLY A   6 " =    0.815
peak=    3.242 closest distance to " CE1 HIS A 108 " =    1.065
peak=    3.240 closest distance to " CB  TRP A 179 " =    1.422
peak=    3.237 closest distance to " O   HOH Z 253 " =    1.894
peak=    3.235 closest distance to " O   HOH Z 238 " =    1.082
peak=    3.234 closest distance to " O   HOH Z 247 " =    1.143
peak=    3.224 closest distance to " CA  GLN A  11 " =    0.943
peak=    3.220 closest distance to " CG1BVAL A  72 " =    0.862
peak=    3.217 closest distance to " CA  ARG A 139 " =    1.501
peak=    3.215 closest distance to " O   ALA A 165 " =    1.344
peak=    3.212 closest distance to " O   HOH Z  88 " =    2.419
peak=    3.210 closest distance to " CZ  PHE A 192 " =    1.003
peak=    3.209 closest distance to " O   HOH Z 391 " =    3.084
peak=    3.209 closest distance to " CG1 VAL A 174 " =    1.482
peak=    3.207 closest distance to " CD2 PHE A 204 " =    0.988
peak=    3.207 closest distance to " O   HOH Z 357 " =    2.205
peak=    3.207 closest distance to " O   HOH Z 158 " =    1.084
peak=    3.206 closest distance to " CB  SER A   3 " =    1.668
peak=    3.205 closest distance to " CB  LEU A 281 " =    0.879
peak=    3.203 closest distance to " O   HOH Z 293 " =    1.938
peak=    3.203 closest distance to " O   HOH Z 141 " =    1.432
peak=    3.202 closest distance to " NZ  LYS A 181 " =    0.807
peak=    3.194 closest distance to " O   PRO A  90 " =    1.543
peak=    3.185 closest distance to " CD1 LEU A   5 " =    1.335
peak=    3.183 closest distance to " CA  ALA A 131 " =    1.261
peak=    3.180 closest distance to " N   ALA A 180 " =    0.797
peak=    3.179 closest distance to " OH  TYR A 293 " =    1.293
peak=    3.177 closest distance to " O   HOH Z 258 " =    2.063
peak=    3.173 closest distance to " O   HOH Z   9 " =    2.082
peak=    3.165 closest distance to " CZ3 TRP A  85 " =    1.077
peak=    3.165 closest distance to " CB  ALA A  21 " =    0.858
peak=    3.164 closest distance to " CG2 THR A  42 " =    0.997
peak=    3.159 closest distance to " O   MET A 105 " =    1.687
peak=    3.158 closest distance to " CD2 TYR A  15 " =    0.968
peak=    3.157 closest distance to " O   HOH Z 147 " =    1.342
peak=    3.154 closest distance to " CG  ASP A 253 " =    1.223
peak=    3.154 closest distance to " O   HOH Z 337 " =    1.818
peak=    3.152 closest distance to " O   HOH Z 201 " =    2.763
peak=    3.151 closest distance to " O  BHOH Z  74 " =    1.241
peak=    3.148 closest distance to " CD1 ILE A  33 " =    1.755
peak=    3.148 closest distance to " ND2 ASN A 249 " =    0.901
peak=    3.144 closest distance to " O   HOH Z 193 " =    1.583
peak=    3.140 closest distance to " CB  ASP A 107 " =    1.113
peak=    3.139 closest distance to " CB  ASP A 140 " =    0.709
peak=    3.127 closest distance to " CA  GLU A  46 " =    0.814
peak=    3.122 closest distance to " O   LYS A 290 " =    1.767
peak=    3.120 closest distance to " O   HOH Z  59 " =    2.386
peak=    3.119 closest distance to " CE1 PHE A 225 " =    1.094
peak=    3.116 closest distance to " CA  GLY A 287 " =    1.258
peak=    3.114 closest distance to " O   THR A 294 " =    1.798
peak=    3.113 closest distance to " CB  LEU A 101 " =    1.356
peak=    3.110 closest distance to " N   ALA A 292 " =    1.066
peak=    3.109 closest distance to " CA  ALA A 129 " =    0.819
peak=    3.106 closest distance to " O   HOH Z 327 " =    2.270
peak=    3.104 closest distance to " O   ALA A 158 " =    1.285
peak=    3.103 closest distance to " CG ALYS A 290 " =    1.121
peak=    3.102 closest distance to " O   HOH Z 301 " =    1.847
peak=    3.100 closest distance to " CB  LEU A 255 " =    1.957
peak=    3.096 closest distance to " N   ASN A  39 " =    1.209
peak=    3.089 closest distance to " O   HOH Z 238 " =    3.583
peak=    3.084 closest distance to " CB  PRO A 163 " =    0.975
peak=    3.083 closest distance to " CB  ARG A 259 " =    1.986
peak=    3.080 closest distance to " O   HOH Z  55 " =    2.557
peak=    3.068 closest distance to " CE1 PHE A  16 " =    1.157
peak=    3.067 closest distance to " O   ASN A 284 " =    1.912
peak=    3.064 closest distance to " O   HOH Z 211 " =    1.488
peak=    3.062 closest distance to " O   HOH Z 150 " =    2.052
peak=    3.034 closest distance to " O   HOH Z 106 " =    3.778
peak=    3.026 closest distance to " CB  ARG A 219 " =    1.633
peak=    3.021 closest distance to " CB  GLN A 103 " =    0.944
peak=    3.016 closest distance to " CG1 VAL A 257 " =    1.163

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 227         
Filter by distance & map next to the model:
   mapped sites are within: 0.689 - 5.487
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 225 from: 227
   mapped sites are within: 0.729 - 5.487

peak=   -4.450 closest distance to " CG1 VAL A 296 " =    1.083
peak=   -4.443 closest distance to " CD1 PHE A  59 " =    2.019
peak=   -4.362 closest distance to " O   HOH Z 166 " =    1.376
peak=   -4.359 closest distance to " O   HOH Z 216 " =    0.888
peak=   -4.306 closest distance to " CA  ASP A 298 " =    1.198
peak=   -4.250 closest distance to " O   HOH Z 411 " =    5.487
peak=   -4.208 closest distance to " CD  GLN A  58 " =    0.945
peak=   -4.203 closest distance to " CG  GLN A 103 " =    2.456
peak=   -4.182 closest distance to " O   PRO A 198 " =    1.230
peak=   -4.172 closest distance to " CD2 TYR A 293 " =    1.816
peak=   -4.090 closest distance to " CG1 VAL A 250 " =    2.599
peak=   -4.051 closest distance to " CG  ARG A 269 " =    2.430
peak=   -4.003 closest distance to " N   ARG A 275 " =    1.359
peak=   -3.954 closest distance to " CB  ALA A 291 " =    2.578
peak=   -3.933 closest distance to " CD  GLN A  88 " =    1.078
peak=   -3.920 closest distance to " NH1 ARG A 195 " =    0.992
peak=   -3.914 closest distance to " CG  PRO A 243 " =    1.766
peak=   -3.903 closest distance to " CD  ARG A  14 " =    3.149
peak=   -3.895 closest distance to " CG2 VAL A 189 " =    2.114
peak=   -3.890 closest distance to " NE2 HIS A  86 " =    0.964
peak=   -3.889 closest distance to " CZ2 TRP A  92 " =    2.948
peak=   -3.851 closest distance to " O   HOH Z 150 " =    1.491
peak=   -3.840 closest distance to " OE1 GLN A  88 " =    1.002
peak=   -3.822 closest distance to " CA  SER A 164 " =    2.128
peak=   -3.802 closest distance to " O   SER A 276 " =    1.676
peak=   -3.797 closest distance to " CG1 VAL A 112 " =    2.640
peak=   -3.777 closest distance to " C   VAL A 265 " =    0.956
peak=   -3.777 closest distance to " O   HOH Z 351 " =    1.862
peak=   -3.775 closest distance to " OD2 ASP A 171 " =    1.986
peak=   -3.766 closest distance to " CD2 TYR A  15 " =    2.356
peak=   -3.755 closest distance to " CD  GLN A 223 " =    1.383
peak=   -3.750 closest distance to " CG  ARG A 259 " =    2.513
peak=   -3.738 closest distance to " O   HOH Z 155 " =    1.746
peak=   -3.737 closest distance to " CA  SER A 271 " =    2.213
peak=   -3.732 closest distance to " O   HOH Z 231 " =    1.782
peak=   -3.726 closest distance to " O   HOH Z  10 " =    1.541
peak=   -3.708 closest distance to " O   VAL A  67 " =    2.907
peak=   -3.690 closest distance to " O   HOH Z  19 " =    2.162
peak=   -3.685 closest distance to " CE2 TYR A  30 " =    2.624
peak=   -3.679 closest distance to " O   HOH Z 166 " =    1.491
peak=   -3.675 closest distance to " CE3 TRP A  70 " =    1.940
peak=   -3.668 closest distance to " O   HOH Z 136 " =    1.340
peak=   -3.663 closest distance to " O   HOH Z  53 " =    1.647
peak=   -3.662 closest distance to " O   HOH Z  54 " =    1.302
peak=   -3.654 closest distance to " CE  MET A 105 " =    2.397
peak=   -3.629 closest distance to " O   HOH Z 400 " =    1.477
peak=   -3.626 closest distance to " CB  ALA A   9 " =    2.409
peak=   -3.622 closest distance to " CG2 VAL A 202 " =    2.755
peak=   -3.606 closest distance to " O   HOH Z 257 " =    1.274
peak=   -3.596 closest distance to " CE2 PHE A  61 " =    2.625
peak=   -3.593 closest distance to " NE2 GLN A 194 " =    2.106
peak=   -3.591 closest distance to " CG  GLN A  11 " =    1.412
peak=   -3.578 closest distance to " OXT GLY A 302 " =    3.069
peak=   -3.562 closest distance to " O   HOH Z  52 " =    2.068
peak=   -3.559 closest distance to " O   HOH Z 196 " =    1.829
peak=   -3.558 closest distance to " CH2 TRP A 179 " =    1.158
peak=   -3.553 closest distance to " ND2BASN A 224 " =    2.092
peak=   -3.552 closest distance to " CB  ALA A  10 " =    2.222
peak=   -3.548 closest distance to " O   HOH Z 103 " =    2.060
peak=   -3.544 closest distance to " OG  SER A  97 " =    2.210
peak=   -3.542 closest distance to " CG  ASN A  45 " =    0.834
peak=   -3.541 closest distance to " CD1 ILE A 263 " =    2.311
peak=   -3.533 closest distance to " O   HOH Z  73 " =    2.607
peak=   -3.528 closest distance to " OG1 THR A  82 " =    1.912
peak=   -3.517 closest distance to " O   HOH Z 250 " =    1.691
peak=   -3.512 closest distance to " CD1 LEU A   5 " =    2.405
peak=   -3.511 closest distance to " CE3 TRP A 150 " =    2.425
peak=   -3.500 closest distance to " O   HOH Z 156 " =    3.218
peak=   -3.496 closest distance to " CG  GLN A  58 " =    1.454
peak=   -3.495 closest distance to " O   HOH Z 407 " =    1.404
peak=   -3.491 closest distance to " CG  GLU A  53 " =    1.539
peak=   -3.491 closest distance to " OD1 ASN A 148 " =    1.605
peak=   -3.483 closest distance to " O   HOH Z  37 " =    1.536
peak=   -3.480 closest distance to " NE2 GLN A 103 " =    1.793
peak=   -3.479 closest distance to " O   HOH Z 407 " =    3.491
peak=   -3.478 closest distance to " O   HOH Z 352 " =    1.619
peak=   -3.477 closest distance to " CG  PRO A 163 " =    1.994
peak=   -3.474 closest distance to " O   HOH Z  11 " =    1.866
peak=   -3.474 closest distance to " O   HOH Z 200 " =    1.453
peak=   -3.466 closest distance to " CD1 TYR A 247 " =    2.407
peak=   -3.463 closest distance to " O   HOH Z 251 " =    4.503
peak=   -3.456 closest distance to " O   HOH Z 340 " =    1.602
peak=   -3.456 closest distance to " CB  ALA A 161 " =    2.658
peak=   -3.450 closest distance to " OE1 GLU A  44 " =    0.867
peak=   -3.435 closest distance to " CD2 PHE A  61 " =    2.003
peak=   -3.432 closest distance to " OD1 ASP A 298 " =    2.126
peak=   -3.432 closest distance to " NE2 GLN A  55 " =    2.262
peak=   -3.429 closest distance to " CA  GLY A  98 " =    2.217
peak=   -3.423 closest distance to " CG  LEU A   5 " =    1.682
peak=   -3.420 closest distance to " OG1 THR A  82 " =    1.365
peak=   -3.416 closest distance to " O   HOH Z 388 " =    1.929
peak=   -3.413 closest distance to " O   HOH Z 193 " =    1.442
peak=   -3.412 closest distance to " O   HOH Z 215 " =    1.324
peak=   -3.404 closest distance to " NE  ARG A  79 " =    1.221
peak=   -3.402 closest distance to " N   SER A 134 " =    1.168
peak=   -3.401 closest distance to " O   HOH Z 150 " =    1.659
peak=   -3.401 closest distance to " O   HOH Z 183 " =    1.426
peak=   -3.400 closest distance to " CB  ALA A 160 " =    2.112
peak=   -3.397 closest distance to " O   SER A 210 " =    1.914
peak=   -3.396 closest distance to " CG2 THR A 182 " =    2.359
peak=   -3.394 closest distance to " O   SER A 135 " =    1.898
peak=   -3.392 closest distance to " O   HOH Z  43 " =    1.709
peak=   -3.375 closest distance to " O   HOH Z 424 " =    3.062
peak=   -3.366 closest distance to " O   HOH Z 431 " =    2.480
peak=   -3.365 closest distance to " OG BSER A 134 " =    1.504
peak=   -3.360 closest distance to " O   GLY A 262 " =    2.476
peak=   -3.360 closest distance to " O   HOH Z  64 " =    1.483
peak=   -3.359 closest distance to " SG  CYS A 254 " =    2.822
peak=   -3.359 closest distance to " O   HOH Z 189 " =    2.257
peak=   -3.351 closest distance to " O   GLY A  17 " =    1.184
peak=   -3.350 closest distance to " CD1 PHE A  59 " =    2.036
peak=   -3.346 closest distance to " OE1 GLN A  89 " =    2.023
peak=   -3.344 closest distance to " CG  ARG A 259 " =    1.522
peak=   -3.333 closest distance to " CA  TYR A  68 " =    2.941
peak=   -3.329 closest distance to " ND2 ASN A 249 " =    1.051
peak=   -3.327 closest distance to " O   HOH Z 396 " =    1.915
peak=   -3.325 closest distance to " CZ  PHE A  38 " =    2.565
peak=   -3.324 closest distance to " CB  SER A 146 " =    2.217
peak=   -3.324 closest distance to " O   HOH Z   6 " =    1.672
peak=   -3.323 closest distance to " N   ALA A 226 " =    2.290
peak=   -3.323 closest distance to " CB  PRO A 243 " =    2.968
peak=   -3.319 closest distance to " CE2 PHE A 283 " =    2.606
peak=   -3.319 closest distance to " O   HOH Z 285 " =    1.987
peak=   -3.312 closest distance to " O   HOH Z 424 " =    1.424
peak=   -3.311 closest distance to " N   ALA A 242 " =    1.843
peak=   -3.311 closest distance to " O   HOH Z 371 " =    1.013
peak=   -3.307 closest distance to " O   ALA A 160 " =    1.476
peak=   -3.305 closest distance to " O   HOH Z 377 " =    0.965
peak=   -3.304 closest distance to " CB  SER A 276 " =    1.136
peak=   -3.299 closest distance to " ND2 ASN A  39 " =    1.571
peak=   -3.298 closest distance to " ND2 ASN A  60 " =    1.717
peak=   -3.295 closest distance to " OH  TYR A 169 " =    0.892
peak=   -3.295 closest distance to " N   ILE A 120 " =    1.199
peak=   -3.291 closest distance to " CZ  TYR A 169 " =    1.841
peak=   -3.287 closest distance to " CD2 HIS A 115 " =    1.217
peak=   -3.284 closest distance to " O   HOH Z 369 " =    2.485
peak=   -3.280 closest distance to " O   HOH Z 151 " =    1.294
peak=   -3.279 closest distance to " C   LEU A 101 " =    1.151
peak=   -3.278 closest distance to " OE1 GLN A 223 " =    2.464
peak=   -3.277 closest distance to " O   HOH Z 211 " =    1.547
peak=   -3.272 closest distance to " O   TYR A 186 " =    1.942
peak=   -3.272 closest distance to " O   HOH Z 329 " =    1.101
peak=   -3.271 closest distance to " CG  TRP A 266 " =    1.716
peak=   -3.266 closest distance to " CA  GLY A 241 " =    3.289
peak=   -3.263 closest distance to " SD  MET A 105 " =    1.012
peak=   -3.258 closest distance to " O   HOH Z 325 " =    1.904
peak=   -3.257 closest distance to " O   HOH Z  82 " =    1.437
peak=   -3.255 closest distance to " CD2 LEU A 228 " =    2.387
peak=   -3.255 closest distance to " CA  VAL A 121 " =    1.516
peak=   -3.253 closest distance to " NH2 ARG A  79 " =    2.257
peak=   -3.253 closest distance to " O   VAL A  67 " =    2.422
peak=   -3.252 closest distance to " O   HOH Z 231 " =    2.201
peak=   -3.244 closest distance to " NE  ARG A  66 " =    4.330
peak=   -3.242 closest distance to " CA  VAL A  67 " =    2.937
peak=   -3.242 closest distance to " O   HOH Z 361 " =    4.534
peak=   -3.242 closest distance to " O   HOH Z 418 " =    1.486
peak=   -3.237 closest distance to " O   HOH Z  32 " =    2.072
peak=   -3.237 closest distance to " O   HOH Z 120 " =    4.616
peak=   -3.234 closest distance to " CB  PHE A  16 " =    2.280
peak=   -3.233 closest distance to " CE  LYS A  76 " =    0.876
peak=   -3.227 closest distance to " CE3 TRP A 274 " =    2.173
peak=   -3.226 closest distance to " O   ASP A 298 " =    1.986
peak=   -3.225 closest distance to " O   HOH Z 435 " =    1.984
peak=   -3.223 closest distance to " O   HOH Z 287 " =    2.115
peak=   -3.222 closest distance to " O   HOH Z 428 " =    1.318
peak=   -3.218 closest distance to " CG1 VAL A 112 " =    2.689
peak=   -3.214 closest distance to " O   HOH Z 118 " =    4.956
peak=   -3.211 closest distance to " O   HOH Z 275 " =    1.644
peak=   -3.211 closest distance to " O   HOH Z 128 " =    2.681
peak=   -3.209 closest distance to " O   HOH Z 137 " =    1.815
peak=   -3.205 closest distance to " CD1 ILE A 151 " =    2.494
peak=   -3.204 closest distance to " O   HOH Z 171 " =    2.468
peak=   -3.203 closest distance to " N   VAL A  41 " =    2.145
peak=   -3.198 closest distance to " CG  ASP A 286 " =    1.496
peak=   -3.198 closest distance to " CA  PRO A 198 " =    1.215
peak=   -3.197 closest distance to " CA  TRP A 274 " =    1.025
peak=   -3.197 closest distance to " O   HOH Z 140 " =    1.964
peak=   -3.196 closest distance to " CG1 VAL A 189 " =    2.666
peak=   -3.195 closest distance to " ND2 ASN A  45 " =    2.438
peak=   -3.193 closest distance to " O   LYS A 117 " =    2.059
peak=   -3.190 closest distance to " CD  GLN A 223 " =    0.729
peak=   -3.189 closest distance to " N   ALA A  43 " =    2.752
peak=   -3.185 closest distance to " O   HOH Z 336 " =    5.130
peak=   -3.182 closest distance to " O   HOH Z 411 " =    1.708
peak=   -3.180 closest distance to " CB  ALA A 248 " =    2.140
peak=   -3.179 closest distance to " C   MET A 188 " =    1.276
peak=   -3.178 closest distance to " CA  ASN A 110 " =    1.038
peak=   -3.178 closest distance to " O  BHOH Z 338 " =    1.924
peak=   -3.170 closest distance to " CG1BVAL A  72 " =    2.600
peak=   -3.164 closest distance to " O   HOH Z 154 " =    0.996
peak=   -3.161 closest distance to " O   HOH Z 185 " =    2.486
peak=   -3.157 closest distance to " O   ASP A 253 " =    2.008
peak=   -3.155 closest distance to " N   ALA A 295 " =    1.016
peak=   -3.150 closest distance to " OE2 GLU A 277 " =    2.853
peak=   -3.149 closest distance to " O   HOH Z 414 " =    1.924
peak=   -3.143 closest distance to " O   HOH Z 109 " =    1.040
peak=   -3.133 closest distance to " O   TYR A  15 " =    1.729
peak=   -3.133 closest distance to " OD2 ASP A 270 " =    1.526
peak=   -3.125 closest distance to " CB  PRO A 163 " =    2.523
peak=   -3.125 closest distance to " OD2 ASP A 270 " =    1.075
peak=   -3.121 closest distance to " CA  ASN A 127 " =    1.085
peak=   -3.118 closest distance to " O   HOH Z 175 " =    3.491
peak=   -3.112 closest distance to " O   HOH Z 128 " =    3.230
peak=   -3.109 closest distance to " O   HOH Z 111 " =    1.496
peak=   -3.109 closest distance to " O   HOH Z 304 " =    1.390
peak=   -3.105 closest distance to " CE  LYS A  76 " =    2.694
peak=   -3.100 closest distance to " O   HOH Z 177 " =    1.832
peak=   -3.098 closest distance to " C   HIS A 108 " =    1.265
peak=   -3.097 closest distance to " O   HOH Z   9 " =    2.514
peak=   -3.093 closest distance to " CG  LEU A   5 " =    1.015
peak=   -3.090 closest distance to " CA  GLY A 133 " =    2.180
peak=   -3.089 closest distance to " CD  ARG A 156 " =    1.914
peak=   -3.087 closest distance to " NH2 ARG A  66 " =    1.902
peak=   -3.085 closest distance to " CZ2 TRP A 179 " =    2.200
peak=   -3.082 closest distance to " CB  ASP A 286 " =    1.906
peak=   -3.078 closest distance to " O   HOH Z  29 " =    1.516
peak=   -3.075 closest distance to " O   HOH Z  83 " =    1.330
peak=   -3.070 closest distance to " O   HOH Z 120 " =    1.181
peak=   -3.066 closest distance to " O   HOH Z 133 " =    1.129
peak=   -3.059 closest distance to " O   HOH Z  64 " =    2.255
peak=   -3.059 closest distance to " O   HOH Z 115 " =    1.241
peak=   -3.055 closest distance to " O   HOH Z  91 " =    2.186
peak=   -3.050 closest distance to " CD  LYS A 289 " =    2.241
peak=   -3.042 closest distance to " CB  TRP A  85 " =    2.551
peak=   -3.042 closest distance to " CG2BVAL A  41 " =    1.881

================= 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    :  0.5164 0.5067   6.307723e+00   6.297777e+00
   1_bss:  0.5103 0.5012   6.304036e+00   6.293369e+00
   1_xyz:  0.4526 0.4696   6.248161e+00   6.259882e+00
   1_adp:  0.4086 0.4601   6.195509e+00   6.248429e+00
   1_occ:  0.4079 0.4599   6.195254e+00   6.249212e+00
   2_bss:  0.4068 0.4566   6.197098e+00   6.249651e+00
   2_xyz:  0.3326 0.4029   6.051722e+00   6.169627e+00
   2_adp:  0.3119 0.3760   6.005365e+00   6.129324e+00
   2_occ:  0.3116 0.3758   6.004767e+00   6.129006e+00
   3_bss:  0.3103 0.3748   6.005822e+00   6.129150e+00
   3_xyz:  0.2536 0.3042   5.831888e+00   5.976925e+00
   3_adp:  0.2351 0.2881   5.777337e+00   5.936279e+00
   3_occ:  0.2347 0.2882   5.777162e+00   5.936748e+00
   4_bss:  0.2339 0.2873   5.775940e+00   5.935842e+00
   4_xyz:  0.1792 0.2292   5.540323e+00   5.736017e+00
   4_adp:  0.1598 0.2164   5.456077e+00   5.677716e+00
   4_occ:  0.1597 0.2165   5.455839e+00   5.677630e+00
   5_bss:  0.1598 0.2169   5.457400e+00   5.678572e+00
   5_xyz:  0.1410 0.1937   5.351520e+00   5.583504e+00
   5_adp:  0.1383 0.1906   5.333615e+00   5.565177e+00
   5_occ:  0.1381 0.1905   5.333198e+00   5.565287e+00
   5_bss:  0.1383 0.1904   5.333663e+00   5.564883e+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  50.000   5.467   9.321  10.176   0.000   0.000   0.000
   1_xyz:  0.300  50.000   5.467   9.321  10.176   0.000   0.000   0.000
   1_adp:  0.300  50.000   5.467   9.321  10.176   0.000   0.000   0.000
   1_occ:  0.300  50.000   5.467   9.321  10.176   0.000   0.000   0.000
   2_bss:  0.299  50.000   2.984   5.802   6.671   0.000   0.000   0.000
   2_xyz:  0.299  50.000   2.984   5.802   6.671   0.000   0.000   0.000
   2_adp:  0.299  50.000   2.984   5.802   6.671   0.000   0.000   0.000
   2_occ:  0.299  50.000   2.984   5.802   6.671   0.000   0.000   0.000
   3_bss:  0.296  70.579   1.692   3.216   3.909   0.000   0.000   0.000
   3_xyz:  0.296  70.579   1.692   3.216   3.909   0.000   0.000   0.000
   3_adp:  0.296  70.579   1.692   3.216   3.909   0.000   0.000   0.000
   3_occ:  0.296  70.579   1.692   3.216   3.909   0.000   0.000   0.000
   4_bss:  0.316  70.579   0.399   1.768   2.618   0.000   0.000   0.000
   4_xyz:  0.316  70.579   0.399   1.768   2.618   0.000   0.000   0.000
   4_adp:  0.316  70.579   0.399   1.768   2.618   0.000   0.000   0.000
   4_occ:  0.316  70.579   0.399   1.768   2.618   0.000   0.000   0.000
   5_bss:  0.339  88.086   0.443   1.440   2.488   0.000   0.000   0.000
   5_xyz:  0.339  88.086   0.443   1.440   2.488   0.000   0.000   0.000
   5_adp:  0.339  88.086   0.443   1.440   2.488   0.000   0.000   0.000
   5_occ:  0.339  88.086   0.443   1.440   2.488   0.000   0.000   0.000
   5_bss:  0.330  82.494  -0.930  -0.155   1.085   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  66.106 0.3136  0.3573    80778.120
   1_bss:  64.734 0.3312  0.4759    79805.694
   1_xyz:  56.519 0.4368  0.6183    65152.776
   1_adp:  54.783 0.4591  0.7288    62680.687
   1_occ:  54.937 0.4572  0.7241    62931.215
   2_bss:  54.902 0.4576  0.6554    62948.131
   2_xyz:  45.597 0.5738  0.8284    46373.144
   2_adp:  41.346 0.6263  0.8784    40116.672
   2_occ:  41.345 0.6263  0.8776    40041.140
   3_bss:  41.235 0.6277  0.8160    40035.579
   3_xyz:  31.777 0.7384  0.9282    25362.690
   3_adp:  29.514 0.7641  0.9399    22592.846
   3_occ:  29.536 0.7639  0.9390    22601.401
   4_bss:  29.443 0.7648  0.8967    22416.197
   4_xyz:  22.610 0.8357  0.9525    13605.896
   4_adp:  20.842 0.8533  0.9485    11973.112
   4_occ:  20.836 0.8534  0.9485    11973.139
   5_bss:  20.867 0.8532  0.9436    12029.230
   5_xyz:  18.445 0.8763  0.9558     9724.393
   5_adp:  17.910 0.8815  0.9533     9389.425
   5_occ:  17.914 0.8815  0.9530     9384.371
   5_bss:  17.921 0.8814  0.9553     9385.411
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4857e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4857e+01
   1_xyz:   1.772  0.014  0.110 18.419  0.007  4.111   1.5503e-01
   1_adp:   1.772  0.014  0.110 18.419  0.007  4.111   1.5503e-01
   1_occ:   1.772  0.014  0.110 18.419  0.007  4.111   1.5503e-01
   2_bss:   1.772  0.014  0.110 18.419  0.007  4.111   1.5503e-01
   2_xyz:   1.555  0.013  0.100 17.482  0.006  4.115   1.3413e-01
   2_adp:   1.555  0.013  0.100 17.482  0.006  4.115   1.3413e-01
   2_occ:   1.555  0.013  0.100 17.482  0.006  4.115   1.3413e-01
   3_bss:   1.555  0.013  0.100 17.482  0.006  4.115   1.3413e-01
   3_xyz:   1.127  0.009  0.077 16.140  0.004  4.117   8.7677e-02
   3_adp:   1.127  0.009  0.077 16.140  0.004  4.117   8.7677e-02
   3_occ:   1.127  0.009  0.077 16.140  0.004  4.117   8.7677e-02
   4_bss:   1.127  0.009  0.077 16.140  0.004  4.117   8.7677e-02
   4_xyz:   1.241  0.011  0.088 16.074  0.004  4.142   9.0686e-02
   4_adp:   1.241  0.011  0.088 16.074  0.004  4.142   9.0686e-02
   4_occ:   1.241  0.011  0.088 16.074  0.004  4.142   9.0686e-02
   5_bss:   1.241  0.011  0.088 16.074  0.004  4.142   9.0686e-02
   5_xyz:   1.159  0.010  0.088 15.594  0.004  4.137   7.9232e-02
   5_adp:   1.159  0.010  0.088 15.594  0.004  4.137   7.9232e-02
   5_occ:   1.159  0.010  0.088 15.594  0.004  4.137   7.9232e-02
   5_bss:   1.159  0.010  0.088 15.594  0.004  4.137   7.9232e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.1119e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.1119e+00
   1_xyz:  14.831  0.169  0.463 88.094  0.049  2.214   1.0938e-01
   1_adp:  14.831  0.169  0.463 88.094  0.049  2.214   1.0938e-01
   1_occ:  14.831  0.169  0.463 88.094  0.049  2.214   1.0938e-01
   2_bss:  14.831  0.169  0.463 88.094  0.049  2.214   1.0938e-01
   2_xyz:   9.673  0.127  0.340 88.477  0.034  2.043   9.0165e-02
   2_adp:   9.673  0.127  0.340 88.477  0.034  2.043   9.0165e-02
   2_occ:   9.673  0.127  0.340 88.477  0.034  2.043   9.0165e-02
   3_bss:   9.673  0.127  0.340 88.477  0.034  2.043   9.0165e-02
   3_xyz:   7.822  0.065  0.230 83.124  0.040  2.249   2.1638e-01
   3_adp:   7.822  0.065  0.230 83.124  0.040  2.249   2.1638e-01
   3_occ:   7.822  0.065  0.230 83.124  0.040  2.249   2.1638e-01
   4_bss:   7.822  0.065  0.230 83.124  0.040  2.249   2.1638e-01
   4_xyz:   9.600  0.059  0.313 87.983  0.035  2.202   8.8799e-02
   4_adp:   9.600  0.059  0.313 87.983  0.035  2.202   8.8799e-02
   4_occ:   9.600  0.059  0.313 87.983  0.035  2.202   8.8799e-02
   5_bss:   9.600  0.059  0.313 87.983  0.035  2.202   8.8799e-02
   5_xyz:   7.472  0.052  0.434 82.758  0.047  2.255   4.8713e-02
   5_adp:   7.472  0.052  0.434 82.758  0.047  2.255   4.8713e-02
   5_occ:   7.472  0.052  0.434 82.758  0.047  2.255   4.8713e-02
   5_bss:   7.472  0.052  0.434 82.758  0.047  2.255   4.8713e-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: 128.15   0.00  18.99  96.92   0.00  16.78 128.15   0.00  31.01
   1_occ: 128.15   0.00  18.99  96.92   0.00  16.78 128.15   0.00  31.01
   2_bss: 128.15   0.00  18.99  96.92   0.00  16.78 128.15   0.00  31.01
   2_xyz: 128.15   0.00  18.99  96.92   0.00  16.78 128.15   0.00  31.01
   2_adp: 128.46   0.00  16.18  74.60   0.00  13.16 128.46   0.00  32.66
   2_occ: 128.46   0.00  16.18  74.60   0.00  13.16 128.46   0.00  32.66
   3_bss: 128.46   0.00  16.18  74.60   0.00  13.16 128.46   0.00  32.66
   3_xyz: 128.46   0.00  16.18  74.60   0.00  13.16 128.46   0.00  32.66
   3_adp: 126.59   0.00  15.62  69.28   0.00  11.79 126.59   0.00  36.50
   3_occ: 126.59   0.00  15.62  69.28   0.00  11.79 126.59   0.00  36.50
   4_bss: 126.59   0.00  15.62  69.28   0.00  11.79 126.59   0.00  36.50
   4_xyz: 126.59   0.00  15.62  69.28   0.00  11.79 126.59   0.00  36.50
   4_adp: 115.14   0.00  16.45  91.94   0.00  11.05 115.14   1.67  45.87
   4_occ: 115.14   0.00  16.45  91.94   0.00  11.05 115.14   1.67  45.87
   5_bss: 115.14   0.00  16.45  91.94   0.00  11.05 115.14   1.67  45.87
   5_xyz: 115.14   0.00  16.45  91.94   0.00  11.05 115.14   1.67  45.87
   5_adp: 114.68   0.00  16.26  91.47   0.00  10.87 114.68   1.75  45.58
   5_occ: 114.68   0.00  16.26  91.47   0.00  10.87 114.68   1.75  45.58
   5_bss: 116.20   1.52  17.78  92.98   1.52  12.39 116.20   3.27  47.10
------------------------------------------------------------------------
 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:    1.249    0.016    0.411
   1_adp:    1.249    0.016    0.411
   1_occ:    1.249    0.016    0.411
   2_bss:    1.249    0.016    0.411
   2_xyz:    1.742    0.042    0.640
   2_adp:    1.742    0.042    0.640
   2_occ:    1.742    0.042    0.640
   3_bss:    1.742    0.042    0.640
   3_xyz:    1.782    0.028    0.743
   3_adp:    1.782    0.028    0.743
   3_occ:    1.782    0.028    0.743
   4_bss:    1.782    0.028    0.743
   4_xyz:    1.862    0.066    0.869
   4_adp:    1.862    0.066    0.869
   4_occ:    1.862    0.066    0.869
   5_bss:    1.862    0.066    0.869
   5_xyz:    2.120    0.034    0.906
   5_adp:    2.120    0.034    0.906
   5_occ:    2.120    0.034    0.906
   5_bss:    2.120    0.034    0.906
------------------------------------------------------------------------

CPU time actual refinement: 341.94


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_956/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_956/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_956/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_956/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_956/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 341.79 
  Macro-tasks:
    bulk solvent and scale       = 43.42  
    individual site refinement   = 137.34 
    weights calculation          = 32.76  
    collect and process          = 6.49   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 220.15 
  Micro-tasks:
    mask                            = 2.97   
    f_calc                          = 104.78 
    alpha_beta                      = 8.51   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 114.86 
    fmodel                         = 7.58   
    r_factors                      = 0.22   
    phase_errors                   = 10.16  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 250.50 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.866 micro seconds
Total CPU time: 5.92 minutes
from_scatterers_fft:    640 calls, 104.47 s
gradients_fft:          586 calls, 102.06 s

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

# Date 2008-01-16 Time 02:50:27 PST -0800 (1200480627.65 s)
Start R-work = 0.5164, R-free = 0.5067 (no bulk solvent and anisotropic scale)
Final R-work = 0.1539, R-free = 0.2047 (no bulk solvent and anisotropic scale)

Start R-work = 0.5103, R-free = 0.5012
Final R-work = 0.1383, R-free = 0.1904