# Date 2008-01-16 Time 03:02:53 PST -0800 (1200481373.71 s)
#phil __OFF__

Command line arguments: "../1082.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21289
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1082

-------------------------------------------------------------------------------
  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: (71.3037, 48.1033, 85.9581, 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: (71.3037, 48.1033, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1358 1.99138
Completeness in resolution range: 0.941236
Completeness with d_max=infinity: 0.938395

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1358
                             d_min =   1.9914

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: (71.3037, 48.1033, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1358 1.99138
Completeness in resolution range: 0.941236
Completeness with d_max=infinity: 0.938395

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1362 -  4.2614 [2192/2221]  1973   219  10.0%
  bin  2:  4.2614 -  3.3949 [2087/2110]  1880   207   9.9%
  bin  3:  3.3949 -  2.9695 [2068/2093]  1855   213  10.3%
  bin  4:  2.9695 -  2.6996 [2065/2081]  1867   198   9.6%
  bin  5:  2.6996 -  2.5071 [2034/2071]  1824   210  10.3%
  bin  6:  2.5071 -  2.3598 [2037/2071]  1839   198   9.7%
  bin  7:  2.3598 -  2.2421 [2007/2044]  1804   203  10.1%
  bin  8:  2.2421 -  2.1447 [1997/2039]  1796   201  10.1%
  bin  9:  2.1447 -  2.0624 [2010/2045]  1807   203  10.1%
  bin 10:  2.0624 -  1.9914 [1092/2037]   985   107   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1082/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:
        1.39 -     2.09: 7
        2.09 -     2.80: 679
        2.80 -     3.50: 4401
        3.50 -     4.20: 9181
        4.20 -     4.90: 13597
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.393 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.507 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.643 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.760 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 27860 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_1082/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1082/model_refine_001.geo

CPU time processing inputs: 9.27


============================ 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 = 71.30375 48.10325 85.95805 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: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4987   r_free= 0.4806   ksol= 0.00   Bsol= 0.00   scale= 0.768    |
|                                                                             |
| 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:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.301493                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7531 0.99   1417  161 0.4156 0.4256      6.6344      6.6376|
|  2:  4.7531 -  3.7922 0.99   1368  145 0.4286 0.4618       6.863      6.8923|
|  3:  3.7922 -  3.3186 0.99   1334  154 0.4746 0.3999      6.7204      6.6491|
|  4:  3.3186 -  3.0178 0.99   1339  149 0.4997 0.4509      6.5564      6.5115|
|  5:  3.0178 -  2.8029 0.98   1314  145 0.5311 0.5373        6.39      6.3926|
|  6:  2.8029 -  2.6386 0.99   1313  143 0.5289 0.4589      6.2988      6.1524|
|  7:  2.6386 -  2.5071 0.99   1314  150 0.5178 0.4904      6.2525      6.2194|
|  8:  2.5071 -  2.3984 0.99   1302  145 0.5288 0.5263      6.1587      6.1866|
|  9:  2.3984 -  2.3064 0.99   1304  145 0.5375 0.5412       6.134      6.1395|
| 10:  2.3064 -  2.2271 0.98   1297  141 0.5270 0.5076      6.1089      6.1156|
| 11:  2.2271 -  2.1576 0.98   1285  139 0.5360 0.5386      6.0358      6.0453|
| 12:  2.1576 -  2.0961 0.99   1272  147 0.5388 0.5050      5.9704       5.991|
| 13:  2.0961 -  2.0411 0.96   1282  146 0.5383 0.5246      5.8689      5.8438|
| 14:  2.0411 -  1.9914 0.37    489   49 0.5648 0.4747      5.8572      5.7264|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7531  1417   161  0.65  38.81   0.78     0.68      88838.85|
|  2:  4.7531 -  3.7922  1368   145  0.66  38.33   0.86     0.71     118867.13|
|  3:  3.7922 -  3.3186  1334   154  0.57  46.53   0.79     0.67     123067.83|
|  4:  3.3186 -  3.0178  1339   149  0.48  53.54   0.77     0.57     106378.39|
|  5:  3.0178 -  2.8029  1314   145  0.41  58.75   0.71     0.50      84747.21|
|  6:  2.8029 -  2.6386  1313   143  0.40  59.61   0.72     0.46      69342.35|
|  7:  2.6386 -  2.5071  1314   150  0.40  59.72   0.73     0.44      61904.35|
|  8:  2.5071 -  2.3984  1302   145  0.33  65.26   0.69     0.39      61138.56|
|  9:  2.3984 -  2.3064  1304   145  0.26  70.58   0.70     0.31      60873.98|
| 10:  2.3064 -  2.2271  1297   141  0.25  71.59   0.74     0.29      57179.11|
| 11:  2.2271 -  2.1576  1285   139  0.27  70.21   0.73     0.32      49944.39|
| 12:  2.1576 -  2.0961  1272   147  0.30  67.90   0.74     0.38      44538.11|
| 13:  2.0961 -  2.0411  1282   146  0.27  69.86   0.70     0.34      38709.01|
| 14:  2.0411 -  1.9914   489    49  0.20  75.39   0.72     0.24      35052.94|
|alpha:            min =        0.24 max =            0.71 mean =         0.46|
|beta:             min =    35052.94 max =       123067.83 mean =     73714.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           90.00 mean =        59.44|
|phase err.(test): min =        0.00 max =           90.00 mean =        59.45|
|-----------------------------------------------------------------------------|

============================== 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 = 17.692874             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.855   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.426958              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.012   (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:        6 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      163 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      679 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1483 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2581 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3852 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5007 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6447 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7641 |
|-----------------------------------------------------------------------------|
|-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 |       54.404 |
| 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 |       1.925 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.298)------------------------------------------|
|    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 = 12.298)------------------------------------------|
|    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: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5033   r_free= 0.4887   ksol= 0.00   Bsol= 0.00   scale= 0.740    |
|                                                                             |
| 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:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.302088                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4919   r_free= 0.4740   ksol= 0.30   Bsol= 20.00   scale= 0.951   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.80,11.74,6.45,0.00,0.00,0.00); trace/3= 8.33                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.298308                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.456419             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.284   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.280887              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.262   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4919      final r-factor (work) = 0.4265          |
| start r-factor (free) = 0.4740      final r-factor (free) = 0.4380          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 106.2249 = 16.46 * 0.50 * 6.2979 + 1.00 * 54.4044                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 51.4517 = 16.46 * 0.50 * 6.2342 + 1.00 * 0.1550                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4265      final r-factor (work) = 0.3850          |
| start r-factor (free) = 0.4380      final r-factor (free) = 0.4228          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0001 = 1.28 * 1.00 * 6.2342 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9319 = 1.28 * 1.00 * 6.1778 + 1.00 * 0.0188                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.298)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    120.49  14.78    None  None   None       |
|    all(noH): 2823   0      0.00    120.49  14.78    None  None   None       |
|    Sol.    : 438    0      0.00    120.49  26.05    None  None   None       |
|    Mac.    : 2385   0      0.00    69.91   12.71    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 -  12.049: 1494   |   5:    60.243 -  72.291:   18        |
|      1:    12.049 -  24.097:  824   |   6:    72.291 -  84.340:   10        |
|      2:    24.097 -  36.146:  299   |   7:    84.340 -  96.388:    2        |
|      3:    36.146 -  48.194:  126   |   8:    96.388 - 108.437:    1        |
|      4:    48.194 -  60.243:   48   |   9:   108.437 - 120.485:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3850 r_free = 0.4228             target_work(ml) = 6.165         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3845 r_free = 0.4224             target_work(ml) = 6.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3845   r_free= 0.4224   ksol= 0.30   Bsol= 20.00   scale= 1.073   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.80,11.74,6.45,0.00,0.00,0.00); trace/3= 8.33                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.164193                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3828   r_free= 0.4192   ksol= 0.31   Bsol= 44.71   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.57,7.11,3.94,0.00,0.00,0.00); trace/3= 4.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.166291                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.023639             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.100  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.616640              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.703  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3828      final r-factor (work) = 0.3208          |
| start r-factor (free) = 0.4192      final r-factor (free) = 0.3921          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.2716 = 12.02 * 0.50 * 6.1740 + 1.00 * 0.1546                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.6690 = 12.02 * 0.50 * 6.0803 + 1.00 * 0.1155                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3208      final r-factor (work) = 0.3093          |
| start r-factor (free) = 0.3921      final r-factor (free) = 0.3832          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7707 = 0.62 * 1.00 * 6.0803 + 1.00 * 0.0214                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7432 = 0.62 * 1.00 * 6.0352 + 1.00 * 0.0216                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.298)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.41  14.00    None  None   None       |
|    all(noH): 2823   0      0.00    113.41  14.00    None  None   None       |
|    Sol.    : 438    0      0.00    113.41  27.46    None  None   None       |
|    Mac.    : 2385   0      0.00    67.28   11.53    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 -  11.341: 1497   |   5:    56.705 -  68.046:   22        |
|      1:    11.341 -  22.682:  816   |   6:    68.046 -  79.387:    4        |
|      2:    22.682 -  34.023:  312   |   7:    79.387 -  90.728:    2        |
|      3:    34.023 -  45.364:  121   |   8:    90.728 - 102.068:    0        |
|      4:    45.364 -  56.705:   47   |   9:   102.068 - 113.409:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3093 r_free = 0.3832             target_work(ml) = 6.026         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3088 r_free = 0.3832             target_work(ml) = 6.026         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3088   r_free= 0.3832   ksol= 0.31   Bsol= 44.71   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.57,7.11,3.94,0.00,0.00,0.00); trace/3= 4.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.025763                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3089   r_free= 0.3823   ksol= 0.32   Bsol= 62.76   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.76,5.24,3.10,0.00,0.00,0.00); trace/3= 3.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.026300                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.323617              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.634  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.976939              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.247   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3089      final r-factor (work) = 0.2633          |
| start r-factor (free) = 0.3823      final r-factor (free) = 0.3219          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.1964 = 6.32 * 0.50 * 6.0348 + 1.00 * 0.1155                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.9385 = 6.32 * 0.50 * 5.9655 + 1.00 * 0.0768                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2633      final r-factor (work) = 0.2440          |
| start r-factor (free) = 0.3219      final r-factor (free) = 0.3092          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8485 = 0.98 * 1.00 * 5.9655 + 1.00 * 0.0206                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7318 = 0.98 * 1.00 * 5.8495 + 1.00 * 0.0171                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.298)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.95  15.20    None  None   None       |
|    all(noH): 2823   0      0.00    113.95  15.20    None  None   None       |
|    Sol.    : 438    0      0.00    113.95  35.61    None  None   None       |
|    Mac.    : 2385   0      0.00    83.15   11.45    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 -  11.395: 1577   |   5:    56.975 -  68.370:   57        |
|      1:    11.395 -  22.790:  641   |   6:    68.370 -  79.765:   18        |
|      2:    22.790 -  34.185:  270   |   7:    79.765 -  91.160:    7        |
|      3:    34.185 -  45.580:  155   |   8:    91.160 - 102.555:    1        |
|      4:    45.580 -  56.975:   96   |   9:   102.555 - 113.950:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2440 r_free = 0.3092             target_work(ml) = 5.837         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2439 r_free = 0.3095             target_work(ml) = 5.837         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2439   r_free= 0.3095   ksol= 0.32   Bsol= 62.76   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.76,5.24,3.10,0.00,0.00,0.00); trace/3= 3.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.837126                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2437   r_free= 0.3089   ksol= 0.32   Bsol= 62.76   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,4.05,2.38,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.837265                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.300654              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.168  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.552033              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.338  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2437      final r-factor (work) = 0.1879          |
| start r-factor (free) = 0.3089      final r-factor (free) = 0.2436          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.5035 = 6.30 * 0.50 * 5.8491 + 1.00 * 0.0768                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.1599 = 6.30 * 0.50 * 5.7339 + 1.00 * 0.0963                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1879      final r-factor (work) = 0.1701          |
| start r-factor (free) = 0.2436      final r-factor (free) = 0.2187          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1826 = 0.55 * 1.00 * 5.7339 + 1.00 * 0.0173                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0760 = 0.55 * 1.00 * 5.5470 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.298)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.84  14.79    None  None   None       |
|    all(noH): 2823   0      0.00    104.84  14.79    None  None   None       |
|    Sol.    : 438    0      1.10    104.84  39.77    None  None   None       |
|    Mac.    : 2385   0      0.00    87.77   10.21    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.484: 1633   |   5:    52.422 -  62.906:   67        |
|      1:    10.484 -  20.969:  623   |   6:    62.906 -  73.391:   41        |
|      2:    20.969 -  31.453:  177   |   7:    73.391 -  83.875:   18        |
|      3:    31.453 -  41.938:  142   |   8:    83.875 -  94.360:    8        |
|      4:    41.938 -  52.422:  112   |   9:    94.360 - 104.844:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1701 r_free = 0.2187             target_work(ml) = 5.500         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1699 r_free = 0.2186             target_work(ml) = 5.500         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1699   r_free= 0.2186   ksol= 0.32   Bsol= 62.76   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,4.05,2.38,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.499841                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1697   r_free= 0.2192   ksol= 0.33   Bsol= 65.81   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.41,2.73,2.19,0.00,0.00,0.00); trace/3= 2.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.500988                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.351570              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.104   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.196535              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.448  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1697      final r-factor (work) = 0.1489          |
| start r-factor (free) = 0.2192      final r-factor (free) = 0.1972          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6199 = 2.35 * 0.50 * 5.5483 + 1.00 * 0.0963                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4666 = 2.35 * 0.50 * 5.4448 + 1.00 * 0.0647                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1489      final r-factor (work) = 0.1460          |
| start r-factor (free) = 0.1972      final r-factor (free) = 0.1941          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0839 = 0.20 * 1.00 * 5.4448 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0694 = 0.20 * 1.00 * 5.3870 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.298)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.33  14.26    None  None   None       |
|    all(noH): 2823   0      0.00    101.33  14.26    None  None   None       |
|    Sol.    : 438    0      2.18    101.33  38.49    None  None   None       |
|    Mac.    : 2385   0      0.00    86.16   9.81     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.133: 1655   |   5:    50.665 -  60.797:   70        |
|      1:    10.133 -  20.266:  637   |   6:    60.797 -  70.930:   36        |
|      2:    20.266 -  30.399:  150   |   7:    70.930 -  81.063:   16        |
|      3:    30.399 -  40.532:  140   |   8:    81.063 -  91.196:    8        |
|      4:    40.532 -  50.665:  109   |   9:    91.196 - 101.329:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1460 r_free = 0.1941             target_work(ml) = 5.376         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1459 r_free = 0.1938             target_work(ml) = 5.375         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1459   r_free= 0.1938   ksol= 0.33   Bsol= 65.81   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.41,2.73,2.19,0.00,0.00,0.00); trace/3= 2.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.375126                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7531 0.99   1417  161 0.1076 0.1437        5.48      5.6558|
|  2:  4.7531 -  3.7922 0.99   1368  145 0.1000 0.1332      5.5829      5.8113|
|  3:  3.7922 -  3.3186 0.99   1334  154 0.1341 0.1854      5.6847       5.968|
|  4:  3.3186 -  3.0178 0.99   1339  149 0.1608 0.1981      5.6688      5.8288|
|  5:  3.0178 -  2.8029 0.98   1314  145 0.1780 0.1999      5.5689      5.6723|
|  6:  2.8029 -  2.6386 0.99   1313  143 0.1681 0.2368      5.4491       5.628|
|  7:  2.6386 -  2.5071 0.99   1314  150 0.1632 0.2096      5.3859      5.6053|
|  8:  2.5071 -  2.3984 0.99   1302  145 0.1616 0.2098      5.3005      5.4789|
|  9:  2.3984 -  2.3064 0.99   1304  145 0.1639 0.2310      5.2764      5.4908|
| 10:  2.3064 -  2.2271 0.98   1297  141 0.1602 0.2309      5.2509      5.4739|
| 11:  2.2271 -  2.1576 0.98   1285  139 0.1580 0.2267      5.1885      5.4761|
| 12:  2.1576 -  2.0961 0.99   1272  147 0.1494 0.2058      5.1007      5.2804|
| 13:  2.0961 -  2.0411 0.96   1282  146 0.1643 0.2206      5.0464      5.2455|
| 14:  2.0411 -  1.9914 0.37    489   49 0.1516 0.2253      4.9508      5.2216|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7531  1417   161  0.93  10.91   0.96     0.93       9343.20|
|  2:  4.7531 -  3.7922  1368   145  0.94  10.41   1.01     0.99      12336.94|
|  3:  3.7922 -  3.3186  1334   154  0.91  14.94   1.02     1.01      15557.39|
|  4:  3.3186 -  3.0178  1339   149  0.89  17.36   1.00     0.97      14432.37|
|  5:  3.0178 -  2.8029  1314   145  0.86  20.58   1.01     1.00      12977.36|
|  6:  2.8029 -  2.6386  1313   143  0.87  19.91   0.99     0.95      10305.76|
|  7:  2.6386 -  2.5071  1314   150  0.87  19.39   1.00     0.97       9098.23|
|  8:  2.5071 -  2.3984  1302   145  0.87  19.48   1.01     0.97       8059.64|
|  9:  2.3984 -  2.3064  1304   145  0.86  20.64   1.01     0.96       7887.38|
| 10:  2.3064 -  2.2271  1297   141  0.86  20.64   1.00     0.95       7495.70|
| 11:  2.2271 -  2.1576  1285   139  0.85  21.34   1.00     0.94       6926.22|
| 12:  2.1576 -  2.0961  1272   147  0.87  19.99   1.00     0.97       6082.99|
| 13:  2.0961 -  2.0411  1282   146  0.85  21.75   1.00     0.99       5419.62|
| 14:  2.0411 -  1.9914   489    49  0.85  21.30   0.99     0.95       4532.94|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     4532.94 max =        15557.39 mean =      9588.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.94 mean =        18.25|
|phase err.(test): min =        0.00 max =           89.60 mean =        17.52|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1463   r_free= 0.1944   ksol= 0.33   Bsol= 67.46   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.64,0.42,0.22,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.376374                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1463   r_free= 0.1944   ksol= 0.33   Bsol= 67.46   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.64,0.42,0.22,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.376374                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7531 0.99   1417  161 0.1105 0.1448      5.4897      5.6499|
|  2:  4.7531 -  3.7922 0.99   1368  145 0.1010 0.1341       5.586      5.8116|
|  3:  3.7922 -  3.3186 0.99   1334  154 0.1345 0.1856      5.6874      5.9679|
|  4:  3.3186 -  3.0178 0.99   1339  149 0.1614 0.1990      5.6699      5.8312|
|  5:  3.0178 -  2.8029 0.98   1314  145 0.1778 0.1997      5.5693      5.6722|
|  6:  2.8029 -  2.6386 0.99   1313  143 0.1682 0.2365       5.449      5.6277|
|  7:  2.6386 -  2.5071 0.99   1314  150 0.1631 0.2098      5.3863      5.6061|
|  8:  2.5071 -  2.3984 0.99   1302  145 0.1612 0.2096      5.3004      5.4784|
|  9:  2.3984 -  2.3064 0.99   1304  145 0.1635 0.2315      5.2757      5.4908|
| 10:  2.3064 -  2.2271 0.98   1297  141 0.1601 0.2315      5.2505      5.4749|
| 11:  2.2271 -  2.1576 0.98   1285  139 0.1579 0.2269      5.1878      5.4755|
| 12:  2.1576 -  2.0961 0.99   1272  147 0.1493 0.2061      5.1007      5.2809|
| 13:  2.0961 -  2.0411 0.96   1282  146 0.1642 0.2210      5.0469      5.2474|
| 14:  2.0411 -  1.9914 0.37    489   49 0.1515 0.2242        4.95      5.2178|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7531  1417   161  0.93  10.78   0.96     0.93       9109.14|
|  2:  4.7531 -  3.7922  1368   145  0.94  10.28   1.00     0.98      12211.59|
|  3:  3.7922 -  3.3186  1334   154  0.91  14.93   1.01     1.01      15592.06|
|  4:  3.3186 -  3.0178  1339   149  0.89  17.32   0.99     0.96      14387.33|
|  5:  3.0178 -  2.8029  1314   145  0.86  20.58   0.99     0.99      12992.28|
|  6:  2.8029 -  2.6386  1313   143  0.87  19.91   0.98     0.94      10319.95|
|  7:  2.6386 -  2.5071  1314   150  0.87  19.41   0.98     0.95       9123.12|
|  8:  2.5071 -  2.3984  1302   145  0.87  19.50   0.99     0.95       8076.24|
|  9:  2.3984 -  2.3064  1304   145  0.86  20.63   0.99     0.94       7896.07|
| 10:  2.3064 -  2.2271  1297   141  0.86  20.63   0.98     0.93       7500.82|
| 11:  2.2271 -  2.1576  1285   139  0.85  21.33   0.98     0.92       6925.66|
| 12:  2.1576 -  2.0961  1272   147  0.87  20.00   0.98     0.95       6093.68|
| 13:  2.0961 -  2.0411  1282   146  0.85  21.74   0.97     0.97       5418.95|
| 14:  2.0411 -  1.9914   489    49  0.85  21.30   0.97     0.93       4520.93|
|alpha:            min =        0.92 max =            1.01 mean =         0.95|
|beta:             min =     4520.93 max =        15592.06 mean =      9565.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.98 mean =        18.22|
|phase err.(test): min =        0.00 max =           89.43 mean =        17.47|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.298)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.65    102.97  15.90    None  None   None       |
|    all(noH): 2823   0      1.65    102.97  15.90    None  None   None       |
|    Sol.    : 438    0      3.83    102.97  40.14    None  None   None       |
|    Mac.    : 2385   0      1.65    87.80   11.45    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:     1.646 -  11.779: 1655   |   5:    52.310 -  62.443:   70        |
|      1:    11.779 -  21.912:  637   |   6:    62.443 -  72.576:   36        |
|      2:    21.912 -  32.044:  150   |   7:    72.576 -  82.709:   16        |
|      3:    32.044 -  42.177:  140   |   8:    82.709 -  92.842:    8        |
|      4:    42.177 -  52.310:  109   |   9:    92.842 - 102.975:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 341         
Filter by distance & map next to the model:
   mapped sites are within: 0.611 - 5.330
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 339 from: 341
   mapped sites are within: 0.716 - 5.330

peak=    7.614 closest distance to " O   HOH Z 120 " =    1.625
peak=    6.868 closest distance to " CG2 VAL A 296 " =    1.289
peak=    6.823 closest distance to " O   HOH Z 426 " =    1.279
peak=    6.281 closest distance to " CG1 ILE A 234 " =    1.492
peak=    6.175 closest distance to " OD1 ASN A 301 " =    1.147
peak=    5.766 closest distance to " O   HOH Z  57 " =    1.132
peak=    5.659 closest distance to " CG2 VAL A 230 " =    1.164
peak=    5.560 closest distance to " CG  LEU A   5 " =    1.449
peak=    5.510 closest distance to " NH1BARG A 275 " =    1.214
peak=    5.480 closest distance to " CG  ARG A 138 " =    1.212
peak=    5.458 closest distance to " N   ASP A 298 " =    0.985
peak=    5.305 closest distance to " CG  PRO A 280 " =    1.027
peak=    5.219 closest distance to " O   HOH Z 210 " =    1.640
peak=    5.155 closest distance to " NH1 ARG A 138 " =    0.966
peak=    5.094 closest distance to " O   HOH Z  54 " =    1.337
peak=    5.083 closest distance to " O   HOH Z  37 " =    1.272
peak=    5.081 closest distance to " O   ASP A 298 " =    0.920
peak=    5.020 closest distance to " O   GLN A  11 " =    1.027
peak=    4.994 closest distance to " CB  SER A  63 " =    1.258
peak=    4.955 closest distance to " O   HOH Z 422 " =    1.242
peak=    4.882 closest distance to " CG  PRO A  54 " =    1.280
peak=    4.865 closest distance to " O   HOH Z 111 " =    1.964
peak=    4.741 closest distance to " CG  GLN A  77 " =    0.923
peak=    4.737 closest distance to " CB  VAL A 230 " =    1.288
peak=    4.669 closest distance to " O   HOH Z 102 " =    1.563
peak=    4.544 closest distance to " CD2 LEU A 228 " =    1.263
peak=    4.443 closest distance to " O   HOH Z 126 " =    1.625
peak=    4.381 closest distance to " CB  PRO A  54 " =    0.979
peak=    4.345 closest distance to " O   HOH Z 303 " =    2.528
peak=    4.340 closest distance to " CB  GLN A  73 " =    1.056
peak=    4.311 closest distance to " CB  ARG A 275 " =    0.866
peak=    4.295 closest distance to " O   HOH Z 130 " =    1.177
peak=    4.286 closest distance to " O   HOH Z 404 " =    1.491
peak=    4.284 closest distance to " O   HOH Z 117 " =    1.117
peak=    4.279 closest distance to " O   HOH Z 395 " =    1.553
peak=    4.262 closest distance to " O   HOH Z 154 " =    1.546
peak=    4.257 closest distance to " CB  GLN A  88 " =    1.173
peak=    4.228 closest distance to " O   HOH Z 425 " =    1.778
peak=    4.224 closest distance to " O   HOH Z 411 " =    3.247
peak=    4.219 closest distance to " CD  ARG A 269 " =    0.913
peak=    4.219 closest distance to " CD  ARG A 138 " =    1.196
peak=    4.211 closest distance to " O   HOH Z 431 " =    1.923
peak=    4.191 closest distance to " CG1 ILE A 120 " =    1.145
peak=    4.179 closest distance to " O   HOH Z 246 " =    1.540
peak=    4.178 closest distance to " O   HOH Z 272 " =    2.035
peak=    4.163 closest distance to " CB  GLN A 223 " =    1.421
peak=    4.160 closest distance to " CG  PRO A 198 " =    1.399
peak=    4.157 closest distance to " N   SER A 164 " =    0.974
peak=    4.144 closest distance to " O   HOH Z  80 " =    2.233
peak=    4.141 closest distance to " O   HOH Z 134 " =    2.294
peak=    4.125 closest distance to " CB  ASN A 285 " =    0.967
peak=    4.110 closest distance to " O   HOH Z 174 " =    1.749
peak=    4.101 closest distance to " O   HOH Z 234 " =    3.456
peak=    4.099 closest distance to " O   LYS A 289 " =    0.998
peak=    4.081 closest distance to " CB  TRP A 179 " =    1.353
peak=    4.078 closest distance to " CB  PRO A 198 " =    1.004
peak=    4.073 closest distance to " OE1 GLN A  11 " =    2.091
peak=    4.064 closest distance to " CD  LYS A 166 " =    1.746
peak=    4.051 closest distance to " CB  SER A  26 " =    0.969
peak=    4.042 closest distance to " NE2 HIS A 115 " =    1.104
peak=    4.023 closest distance to " CA  GLU A 277 " =    0.981
peak=    4.015 closest distance to " ND2 ASN A 301 " =    1.074
peak=    4.012 closest distance to " CA  GLY A 196 " =    0.809
peak=    4.009 closest distance to " O   HOH Z 416 " =    1.578
peak=    4.000 closest distance to " O   HOH Z  20 " =    2.085
peak=    3.988 closest distance to " NH2BARG A 102 " =    1.071
peak=    3.981 closest distance to " O   HOH Z 133 " =    2.089
peak=    3.980 closest distance to " O   HOH Z 418 " =    1.803
peak=    3.971 closest distance to " CG AARG A 275 " =    1.089
peak=    3.934 closest distance to " C   ALA A 299 " =    0.848
peak=    3.925 closest distance to " CD  ARG A  36 " =    0.986
peak=    3.920 closest distance to " O   HOH Z 434 " =    2.281
peak=    3.915 closest distance to " O   HOH Z 209 " =    2.450
peak=    3.908 closest distance to " OE1 GLU A   2 " =    1.857
peak=    3.906 closest distance to " CB  VAL A 296 " =    1.140
peak=    3.905 closest distance to " CB  TRP A 266 " =    0.851
peak=    3.905 closest distance to " O   HOH Z 214 " =    1.351
peak=    3.904 closest distance to " O   HOH Z  63 " =    2.101
peak=    3.900 closest distance to " O   ARG A 275 " =    0.756
peak=    3.900 closest distance to " O   HOH Z 377 " =    1.675
peak=    3.896 closest distance to " O   HOH Z 394 " =    1.864
peak=    3.895 closest distance to " CG1 ILE A  33 " =    1.408
peak=    3.879 closest distance to " O   HOH Z  15 " =    2.088
peak=    3.877 closest distance to " OE1 GLN A  88 " =    0.986
peak=    3.868 closest distance to " O   HOH Z 209 " =    1.962
peak=    3.865 closest distance to " O   HOH Z 184 " =    1.641
peak=    3.858 closest distance to " CB  SER A  62 " =    1.023
peak=    3.845 closest distance to " O   HOH Z 410 " =    1.108
peak=    3.836 closest distance to " O   HOH Z  67 " =    2.017
peak=    3.834 closest distance to " CB  ALA A   1 " =    1.422
peak=    3.833 closest distance to " CD BLYS A 290 " =    1.103
peak=    3.830 closest distance to " OD2 ASP A 298 " =    1.003
peak=    3.818 closest distance to " CA  ALA A  21 " =    1.409
peak=    3.816 closest distance to " CG1 VAL A 153 " =    1.203
peak=    3.813 closest distance to " N   TYR A  15 " =    0.924
peak=    3.807 closest distance to " CB  VAL A 296 " =    1.296
peak=    3.803 closest distance to " O   HOH Z  47 " =    1.621
peak=    3.799 closest distance to " O   HOH Z 159 " =    1.264
peak=    3.791 closest distance to " CB  ILE A 199 " =    1.009
peak=    3.790 closest distance to " O   HOH Z  52 " =    1.564
peak=    3.782 closest distance to " O   HOH Z  88 " =    3.358
peak=    3.779 closest distance to " CG1BVAL A 121 " =    1.456
peak=    3.776 closest distance to " CZ  PHE A 218 " =    1.072
peak=    3.776 closest distance to " CA  THR A 246 " =    1.220
peak=    3.773 closest distance to " O   HOH Z 350 " =    1.284
peak=    3.768 closest distance to " O   HOH Z   1 " =    3.041
peak=    3.760 closest distance to " CA  ARG A 195 " =    1.058
peak=    3.758 closest distance to " CB  SER A 141 " =    1.002
peak=    3.753 closest distance to " CB  MET A  47 " =    1.044
peak=    3.752 closest distance to " O   HOH Z 124 " =    1.402
peak=    3.750 closest distance to " O   HOH Z 277 " =    2.764
peak=    3.749 closest distance to " O   HOH Z 420 " =    5.330
peak=    3.734 closest distance to " CD1 LEU A 222 " =    0.874
peak=    3.728 closest distance to " NH1AARG A 145 " =    1.169
peak=    3.709 closest distance to " CE BMET A  47 " =    1.404
peak=    3.701 closest distance to " O   HOH Z  44 " =    1.728
peak=    3.701 closest distance to " C   SER A  32 " =    1.093
peak=    3.695 closest distance to " NH2 ARG A 156 " =    1.204
peak=    3.695 closest distance to " C   VAL A 265 " =    1.074
peak=    3.693 closest distance to " O   HOH Z 149 " =    1.999
peak=    3.692 closest distance to " NH1 ARG A 269 " =    0.935
peak=    3.689 closest distance to " O   ALA A 292 " =    1.430
peak=    3.686 closest distance to " CB  MET A  40 " =    0.772
peak=    3.679 closest distance to " CG2 THR A 221 " =    1.084
peak=    3.655 closest distance to " ND2 ASN A  45 " =    1.396
peak=    3.651 closest distance to " O   HOH Z 389 " =    2.066
peak=    3.651 closest distance to " CE  LYS A 119 " =    1.443
peak=    3.642 closest distance to " CB  TYR A  30 " =    0.991
peak=    3.639 closest distance to " N   LYS A 166 " =    0.894
peak=    3.632 closest distance to " O   HOH Z 417 " =    1.385
peak=    3.632 closest distance to " CD1 TRP A 274 " =    1.089
peak=    3.624 closest distance to " O   GLY A  91 " =    1.216
peak=    3.624 closest distance to " CD  ARG A  36 " =    1.056
peak=    3.623 closest distance to " O   HOH Z 335 " =    1.067
peak=    3.615 closest distance to " CA  SER A  12 " =    1.298
peak=    3.608 closest distance to " CA  ALA A 248 " =    1.145
peak=    3.605 closest distance to " O   VAL A 121 " =    0.952
peak=    3.600 closest distance to " O   HOH Z 149 " =    1.411
peak=    3.598 closest distance to " O   HOH Z  78 " =    2.398
peak=    3.597 closest distance to " CB  ALA A 299 " =    0.946
peak=    3.595 closest distance to " CD  ARG A 159 " =    0.784
peak=    3.593 closest distance to " O   HOH Z 369 " =    1.848
peak=    3.589 closest distance to " O   HOH Z 155 " =    1.671
peak=    3.585 closest distance to " O   HOH Z 415 " =    1.801
peak=    3.573 closest distance to " CB  ASN A 187 " =    1.147
peak=    3.573 closest distance to " O   HOH Z 295 " =    1.101
peak=    3.573 closest distance to " CD AARG A 275 " =    1.505
peak=    3.572 closest distance to " CA  SER A  87 " =    0.716
peak=    3.567 closest distance to " N   ASN A  39 " =    1.186
peak=    3.555 closest distance to " O   HOH Z 139 " =    4.856
peak=    3.551 closest distance to " OE1 GLN A  73 " =    1.477
peak=    3.550 closest distance to " CB  GLU A 277 " =    0.857
peak=    3.548 closest distance to " OD1 ASP A 298 " =    0.854
peak=    3.542 closest distance to " CA  TYR A  30 " =    0.952
peak=    3.537 closest distance to " CG2 THR A 220 " =    0.752
peak=    3.537 closest distance to " CB  GLN A  58 " =    1.174
peak=    3.532 closest distance to " OE1 GLN A 223 " =    2.146
peak=    3.527 closest distance to " O   HOH Z 271 " =    2.292
peak=    3.522 closest distance to " CB  PRO A 243 " =    1.213
peak=    3.522 closest distance to " CE1 HIS A 108 " =    1.139
peak=    3.520 closest distance to " CD  GLN A  73 " =    1.027
peak=    3.513 closest distance to " O   HOH Z  57 " =    2.288
peak=    3.507 closest distance to " O   HOH Z 128 " =    1.512
peak=    3.506 closest distance to " O   HOH Z   5 " =    1.916
peak=    3.506 closest distance to " O   HOH Z  43 " =    2.059
peak=    3.505 closest distance to " CB  GLU A   2 " =    1.254
peak=    3.504 closest distance to " CB  ALA A 100 " =    1.520
peak=    3.498 closest distance to " CG  GLN A  11 " =    1.154
peak=    3.497 closest distance to " O   HOH Z 272 " =    1.364
peak=    3.486 closest distance to " OG  SER A 245 " =    1.652
peak=    3.486 closest distance to " NZ  LYS A 181 " =    0.754
peak=    3.482 closest distance to " O   HOH Z 327 " =    2.737
peak=    3.481 closest distance to " O   HOH Z  40 " =    2.194
peak=    3.465 closest distance to " CB  GLU A 236 " =    1.176
peak=    3.464 closest distance to " O   HOH Z  47 " =    1.744
peak=    3.462 closest distance to " O   HOH Z 133 " =    1.683
peak=    3.458 closest distance to " O   HOH Z  85 " =    2.220
peak=    3.454 closest distance to " O   HOH Z 403 " =    1.820
peak=    3.453 closest distance to " CD2 LEU A 255 " =    1.349
peak=    3.450 closest distance to " CA  ARG A  66 " =    0.950
peak=    3.449 closest distance to " CB  ASN A 148 " =    1.364
peak=    3.448 closest distance to " ND1 HIS A  81 " =    1.422
peak=    3.442 closest distance to " CB  ALA A 256 " =    1.345
peak=    3.442 closest distance to " N   ALA A 256 " =    1.180
peak=    3.439 closest distance to " CG  MET A 185 " =    1.287
peak=    3.439 closest distance to " O   HOH Z 146 " =    1.786
peak=    3.437 closest distance to " O   HOH Z 368 " =    3.109
peak=    3.436 closest distance to " CG  ASP A 231 " =    1.237
peak=    3.430 closest distance to " O   HOH Z 418 " =    3.274
peak=    3.423 closest distance to " CA  GLU A 152 " =    0.930
peak=    3.418 closest distance to " CB  PHE A 283 " =    0.963
peak=    3.416 closest distance to " O   HOH Z 388 " =    1.161
peak=    3.415 closest distance to " O   HOH Z  97 " =    2.060
peak=    3.414 closest distance to " CA  MET A  40 " =    1.262
peak=    3.410 closest distance to " O   HOH Z 185 " =    2.320
peak=    3.409 closest distance to " O   HOH Z 128 " =    2.132
peak=    3.409 closest distance to " OD1 ASP A 238 " =    0.918
peak=    3.407 closest distance to " O   HOH Z 427 " =    3.068
peak=    3.399 closest distance to " CG  PRO A 213 " =    1.323
peak=    3.398 closest distance to " O   HOH Z   4 " =    1.542
peak=    3.397 closest distance to " O   HOH Z 234 " =    1.932
peak=    3.394 closest distance to " O   HOH Z 104 " =    2.911
peak=    3.390 closest distance to " O   HOH Z 359 " =    1.558
peak=    3.388 closest distance to " N   GLY A  75 " =    0.958
peak=    3.388 closest distance to " O   HOH Z 130 " =    2.555
peak=    3.387 closest distance to " O   PRO A 198 " =    1.623
peak=    3.386 closest distance to " O   HOH Z 146 " =    1.714
peak=    3.386 closest distance to " CB AVAL A  41 " =    1.318
peak=    3.384 closest distance to " NZ  LYS A 166 " =    3.305
peak=    3.383 closest distance to " O   HOH Z 258 " =    2.610
peak=    3.375 closest distance to " O   HOH Z 265 " =    1.859
peak=    3.375 closest distance to " CB  LYS A  76 " =    0.942
peak=    3.375 closest distance to " CG2 ILE A 106 " =    1.047
peak=    3.374 closest distance to " OD2 ASP A 286 " =    3.010
peak=    3.373 closest distance to " NH1 ARG A  14 " =    1.164
peak=    3.372 closest distance to " CB  PHE A  16 " =    1.312
peak=    3.371 closest distance to " CA  THR A 294 " =    1.809
peak=    3.369 closest distance to " O   HOH Z 387 " =    2.601
peak=    3.369 closest distance to " CG  GLN A 205 " =    1.181
peak=    3.368 closest distance to " O   HOH Z  91 " =    2.520
peak=    3.363 closest distance to " CB  ARG A 269 " =    1.327
peak=    3.363 closest distance to " O   HOH Z 332 " =    1.664
peak=    3.363 closest distance to " CE1 TYR A 186 " =    1.432
peak=    3.360 closest distance to " CB  ASN A 301 " =    0.827
peak=    3.354 closest distance to " ND1 HIS A  81 " =    1.460
peak=    3.352 closest distance to " O   HOH Z 437 " =    2.560
peak=    3.352 closest distance to " CA  HIS A 115 " =    1.019
peak=    3.347 closest distance to " O   HOH Z 193 " =    1.824
peak=    3.344 closest distance to " CD  LYS A 289 " =    1.117
peak=    3.344 closest distance to " OG1 THR A 279 " =    1.620
peak=    3.340 closest distance to " CB  VAL A 202 " =    1.349
peak=    3.333 closest distance to " O   HOH Z 287 " =    2.081
peak=    3.329 closest distance to " CG  GLU A 277 " =    3.111
peak=    3.325 closest distance to " CB  GLN A 183 " =    1.200
peak=    3.324 closest distance to " CB  LEU A 255 " =    1.289
peak=    3.324 closest distance to " N   THR A  52 " =    1.099
peak=    3.322 closest distance to " OG  SER A  62 " =    3.247
peak=    3.320 closest distance to " O   HOH Z 393 " =    3.833
peak=    3.320 closest distance to " N   TYR A 247 " =    1.335
peak=    3.318 closest distance to " O   THR A 251 " =    1.286
peak=    3.317 closest distance to " NH1 ARG A  56 " =    1.318
peak=    3.315 closest distance to " O   HOH Z 119 " =    2.139
peak=    3.314 closest distance to " CA  ILE A  33 " =    1.531
peak=    3.308 closest distance to " O   HOH Z 162 " =    1.910
peak=    3.299 closest distance to " CB  SER A 273 " =    0.790
peak=    3.298 closest distance to " CB  SER A  28 " =    1.058
peak=    3.295 closest distance to " CA  VAL A  41 " =    0.799
peak=    3.295 closest distance to " O   HOH Z 232 " =    2.175
peak=    3.293 closest distance to " O   HOH Z 415 " =    1.298
peak=    3.292 closest distance to " CZ  PHE A 192 " =    0.927
peak=    3.291 closest distance to " CG  LEU A 228 " =    1.454
peak=    3.282 closest distance to " O   ARG A  56 " =    1.619
peak=    3.280 closest distance to " O   GLY A  23 " =    2.538
peak=    3.273 closest distance to " O   ASP A 124 " =    1.383
peak=    3.272 closest distance to " O   HOH Z  89 " =    3.724
peak=    3.271 closest distance to " NZ  LYS A  76 " =    0.965
peak=    3.270 closest distance to " N   ALA A 299 " =    0.944
peak=    3.268 closest distance to " O   GLU A   2 " =    1.080
peak=    3.268 closest distance to " CG2 ILE A 109 " =    1.145
peak=    3.267 closest distance to " OG  SER A  62 " =    2.914
peak=    3.266 closest distance to " O   HOH Z  35 " =    1.957
peak=    3.266 closest distance to " O   HOH Z 327 " =    1.805
peak=    3.263 closest distance to " O   HOH Z 339 " =    1.240
peak=    3.263 closest distance to " O   SER A 276 " =    1.288
peak=    3.259 closest distance to " CD  ARG A  24 " =    1.438
peak=    3.256 closest distance to " CG AARG A 190 " =    0.987
peak=    3.254 closest distance to " O   VAL A  72 " =    1.129
peak=    3.253 closest distance to " CB  GLN A 103 " =    0.940
peak=    3.252 closest distance to " CG2 THR A  42 " =    0.898
peak=    3.250 closest distance to " CA  GLY A  23 " =    0.907
peak=    3.247 closest distance to " OD2 ASP A  50 " =    1.250
peak=    3.246 closest distance to " CG  MET A 185 " =    1.017
peak=    3.244 closest distance to " O   HOH Z 245 " =    1.495
peak=    3.240 closest distance to " O   HOH Z 193 " =    1.531
peak=    3.236 closest distance to " CB  VAL A 265 " =    1.314
peak=    3.236 closest distance to " CB  GLU A 128 " =    1.110
peak=    3.232 closest distance to " N   CYS A 260 " =    0.787
peak=    3.232 closest distance to " N   TYR A 116 " =    1.802
peak=    3.229 closest distance to " NE2 HIS A  86 " =    1.365
peak=    3.226 closest distance to " O   HOH Z 404 " =    2.215
peak=    3.226 closest distance to " CB  ALA A 137 " =    1.253
peak=    3.224 closest distance to " CG2 VAL A 197 " =    1.248
peak=    3.224 closest distance to " CA  VAL A  78 " =    1.236
peak=    3.223 closest distance to " CA  ASP A 191 " =    0.746
peak=    3.223 closest distance to " O   HOH Z 193 " =    1.190
peak=    3.223 closest distance to " N   SER A 271 " =    1.115
peak=    3.221 closest distance to " CA  THR A  42 " =    0.982
peak=    3.220 closest distance to " CD2 LEU A 297 " =    1.155
peak=    3.217 closest distance to " O   HOH Z 406 " =    1.473
peak=    3.215 closest distance to " N   VAL A 121 " =    0.833
peak=    3.214 closest distance to " CA  ALA A 295 " =    1.049
peak=    3.207 closest distance to " O   SER A 273 " =    1.212
peak=    3.204 closest distance to " OG1 THR A 294 " =    4.007
peak=    3.198 closest distance to " CB  GLU A 175 " =    1.216
peak=    3.197 closest distance to " O   HOH Z 426 " =    3.476
peak=    3.195 closest distance to " CB  ARG A 190 " =    1.801
peak=    3.194 closest distance to " O   HOH Z  48 " =    2.120
peak=    3.192 closest distance to " CB  SER A  97 " =    1.869
peak=    3.182 closest distance to " O   HOH Z 222 " =    2.869
peak=    3.178 closest distance to " O   HOH Z 435 " =    2.107
peak=    3.177 closest distance to " O   HOH Z 425 " =    3.125
peak=    3.166 closest distance to " O   HOH Z  35 " =    1.691
peak=    3.166 closest distance to " CA  ALA A 100 " =    1.265
peak=    3.165 closest distance to " O   HOH Z  49 " =    1.369
peak=    3.165 closest distance to " C   GLY A  80 " =    1.259
peak=    3.163 closest distance to " O   HOH Z 409 " =    4.080
peak=    3.159 closest distance to " OG1 THR A 294 " =    2.259
peak=    3.150 closest distance to " O   HOH Z 155 " =    2.689
peak=    3.150 closest distance to " CG2 ILE A 234 " =    0.948
peak=    3.149 closest distance to " CA  ARG A 139 " =    1.376
peak=    3.143 closest distance to " N   GLU A  44 " =    1.062
peak=    3.141 closest distance to " O   HOH Z 167 " =    1.503
peak=    3.140 closest distance to " CB  TRP A 179 " =    1.967
peak=    3.138 closest distance to " CA  THR A 264 " =    0.968
peak=    3.136 closest distance to " O   HOH Z 370 " =    1.164
peak=    3.136 closest distance to " CA  GLN A 223 " =    0.767
peak=    3.132 closest distance to " CD2 TRP A 179 " =    1.170
peak=    3.130 closest distance to " NE2 GLN A  11 " =    0.956
peak=    3.128 closest distance to " O   HOH Z 261 " =    1.896
peak=    3.125 closest distance to " CD2 TYR A  68 " =    1.144
peak=    3.124 closest distance to " O   HOH Z 191 " =    1.502
peak=    3.121 closest distance to " N   ARG A 275 " =    0.920
peak=    3.119 closest distance to " O   HOH Z  39 " =    1.566
peak=    3.101 closest distance to " O   HOH Z 203 " =    1.813
peak=    3.101 closest distance to " O   LYS A 117 " =    0.957
peak=    3.100 closest distance to " NH2AARG A 190 " =    1.124
peak=    3.100 closest distance to " O   HOH Z 248 " =    2.030
peak=    3.093 closest distance to " CG  ASN A 173 " =    1.097
peak=    3.086 closest distance to " O   HOH Z 353 " =    2.946
peak=    3.078 closest distance to " O   HOH Z 311 " =    4.681
peak=    3.077 closest distance to " CE1 PHE A 208 " =    1.139
peak=    3.076 closest distance to " CB  GLN A 194 " =    0.789
peak=    3.074 closest distance to " CB  MET A 105 " =    1.274
peak=    3.067 closest distance to " OD2 ASP A 171 " =    1.581
peak=    3.065 closest distance to " OG  SER A  22 " =    2.874
peak=    3.061 closest distance to " CB  ASN A 142 " =    1.214
peak=    3.035 closest distance to " N   VAL A 121 " =    1.094
peak=    3.032 closest distance to " CA  ALA A  51 " =    1.157
peak=    3.029 closest distance to " OG  SER A  62 " =    3.924

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 222         
Filter by distance & map next to the model:
   mapped sites are within: 0.431 - 4.862
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 216 from: 222
   mapped sites are within: 0.701 - 4.862

peak=   -4.965 closest distance to " OD1 ASN A 301 " =    0.769
peak=   -4.665 closest distance to " CG  ARG A 138 " =    0.930
peak=   -4.436 closest distance to " N   ARG A 275 " =    0.887
peak=   -4.421 closest distance to " O   HOH Z 166 " =    1.421
peak=   -4.411 closest distance to " O   HOH Z 426 " =    0.816
peak=   -4.387 closest distance to " O   HOH Z  52 " =    2.123
peak=   -4.373 closest distance to " CB  ALA A 291 " =    2.454
peak=   -4.329 closest distance to " CD  GLN A  77 " =    0.858
peak=   -4.329 closest distance to " CG2 VAL A 230 " =    1.000
peak=   -4.323 closest distance to " O   VAL A 121 " =    0.899
peak=   -4.256 closest distance to " C   ASN A 285 " =    2.481
peak=   -4.219 closest distance to " NE  ARG A 138 " =    1.254
peak=   -4.215 closest distance to " C   TRP A 274 " =    0.977
peak=   -4.179 closest distance to " O   HOH Z 151 " =    1.193
peak=   -4.166 closest distance to " CD1 PHE A  59 " =    1.896
peak=   -4.121 closest distance to " CA  SER A 164 " =    1.813
peak=   -4.108 closest distance to " CG2BVAL A  41 " =    2.260
peak=   -4.076 closest distance to " O   HOH Z  37 " =    1.294
peak=   -4.072 closest distance to " CG  ASP A 231 " =    0.729
peak=   -4.071 closest distance to " CA  ASP A 298 " =    1.178
peak=   -4.049 closest distance to " O   ASP A 298 " =    0.734
peak=   -4.040 closest distance to " O   HOH Z 400 " =    0.877
peak=   -4.040 closest distance to " SG  CYS A 168 " =    1.227
peak=   -4.039 closest distance to " O   GLN A  11 " =    0.798
peak=   -4.027 closest distance to " CA  ASN A 127 " =    0.948
peak=   -4.023 closest distance to " O   HOH Z 184 " =    0.826
peak=   -4.022 closest distance to " CA  GLU A 277 " =    1.158
peak=   -4.006 closest distance to " CG  TRP A 266 " =    1.999
peak=   -4.001 closest distance to " CG  GLU A   2 " =    1.424
peak=   -3.974 closest distance to " NH2 ARG A  66 " =    1.110
peak=   -3.956 closest distance to " O   HOH Z  13 " =    1.464
peak=   -3.908 closest distance to " O   HOH Z 411 " =    4.862
peak=   -3.886 closest distance to " CD1 LEU A   5 " =    1.375
peak=   -3.876 closest distance to " O   HOH Z 231 " =    1.196
peak=   -3.857 closest distance to " N   ASP A 272 " =    1.221
peak=   -3.854 closest distance to " O   HOH Z 369 " =    2.376
peak=   -3.852 closest distance to " O   HOH Z 103 " =    2.299
peak=   -3.849 closest distance to " O   ASP A 298 " =    1.196
peak=   -3.849 closest distance to " NH2 ARG A  36 " =    1.113
peak=   -3.807 closest distance to " O   HOH Z 423 " =    1.049
peak=   -3.801 closest distance to " O   HOH Z 222 " =    1.267
peak=   -3.795 closest distance to " CG1 VAL A 296 " =    1.285
peak=   -3.793 closest distance to " CG  ASP A  50 " =    2.219
peak=   -3.776 closest distance to " O   TYR A  15 " =    1.544
peak=   -3.772 closest distance to " O   HOH Z 290 " =    1.034
peak=   -3.764 closest distance to " CD  GLN A 223 " =    1.405
peak=   -3.763 closest distance to " CD2 PHE A  59 " =    2.422
peak=   -3.760 closest distance to " O   SER A 135 " =    1.955
peak=   -3.757 closest distance to " O   HOH Z   5 " =    1.669
peak=   -3.755 closest distance to " O   HOH Z 132 " =    1.265
peak=   -3.747 closest distance to " C   ALA A 299 " =    0.938
peak=   -3.735 closest distance to " O   TYR A 186 " =    2.560
peak=   -3.730 closest distance to " O   HOH Z  92 " =    1.342
peak=   -3.724 closest distance to " O   SER A  95 " =    1.981
peak=   -3.723 closest distance to " CB  LEU A 167 " =    2.098
peak=   -3.712 closest distance to " O   HOH Z 288 " =    0.903
peak=   -3.708 closest distance to " OXT GLY A 302 " =    3.006
peak=   -3.690 closest distance to " CG  PRO A 243 " =    1.681
peak=   -3.677 closest distance to " OH  TYR A 169 " =    0.944
peak=   -3.675 closest distance to " O   HOH Z 407 " =    1.153
peak=   -3.669 closest distance to " O   HOH Z 422 " =    1.081
peak=   -3.669 closest distance to " CG1 VAL A 112 " =    2.418
peak=   -3.667 closest distance to " O   HOH Z 246 " =    0.850
peak=   -3.667 closest distance to " CD  ARG A  14 " =    3.033
peak=   -3.664 closest distance to " CD  GLN A  88 " =    0.941
peak=   -3.655 closest distance to " CA  VAL A 197 " =    0.996
peak=   -3.647 closest distance to " O   HOH Z 414 " =    1.829
peak=   -3.641 closest distance to " O   HOH Z 174 " =    2.045
peak=   -3.637 closest distance to " CA  ALA A 137 " =    2.704
peak=   -3.637 closest distance to " N   ARG A 275 " =    1.261
peak=   -3.628 closest distance to " O   HOH Z 351 " =    1.696
peak=   -3.628 closest distance to " CD  GLU A 236 " =    1.045
peak=   -3.627 closest distance to " O   HOH Z 210 " =    0.997
peak=   -3.612 closest distance to " CA  GLY A 203 " =    2.490
peak=   -3.586 closest distance to " CD  GLN A 223 " =    0.701
peak=   -3.585 closest distance to " CE  MET A 105 " =    2.151
peak=   -3.575 closest distance to " O   VAL A 174 " =    1.892
peak=   -3.563 closest distance to " O   HOH Z  60 " =    1.391
peak=   -3.562 closest distance to " O   HOH Z   7 " =    1.416
peak=   -3.558 closest distance to " OE2 GLU A 277 " =    2.681
peak=   -3.550 closest distance to " CB  SER A 271 " =    2.254
peak=   -3.543 closest distance to " CD2 LEU A 237 " =    2.491
peak=   -3.542 closest distance to " OD1 ASN A 148 " =    1.307
peak=   -3.539 closest distance to " O  BHOH Z  74 " =    1.530
peak=   -3.528 closest distance to " O   HOH Z 388 " =    1.764
peak=   -3.525 closest distance to " CB  ALA A 161 " =    2.602
peak=   -3.522 closest distance to " C   THR A 279 " =    1.093
peak=   -3.518 closest distance to " N   SER A   3 " =    2.593
peak=   -3.517 closest distance to " NE1 TRP A 150 " =    2.276
peak=   -3.514 closest distance to " CA  TYR A  68 " =    2.630
peak=   -3.511 closest distance to " O   ALA A 256 " =    1.918
peak=   -3.510 closest distance to " O   HOH Z 418 " =    1.376
peak=   -3.506 closest distance to " CD  LYS A 289 " =    2.351
peak=   -3.505 closest distance to " O   HOH Z 196 " =    2.353
peak=   -3.504 closest distance to " O   HOH Z  38 " =    1.147
peak=   -3.503 closest distance to " CA  GLY A  98 " =    2.181
peak=   -3.499 closest distance to " O   HOH Z 401 " =    1.427
peak=   -3.498 closest distance to " CA  LEU A 143 " =    0.905
peak=   -3.490 closest distance to " CE2 PHE A 283 " =    2.652
peak=   -3.489 closest distance to " O   HOH Z  50 " =    1.376
peak=   -3.477 closest distance to " CE2 TRP A  85 " =    1.131
peak=   -3.475 closest distance to " O   HOH Z 402 " =    1.164
peak=   -3.475 closest distance to " OG  SER A  32 " =    1.362
peak=   -3.459 closest distance to " CG2 THR A 221 " =    2.502
peak=   -3.455 closest distance to " O   HOH Z 118 " =    1.652
peak=   -3.441 closest distance to " O   HOH Z  64 " =    1.756
peak=   -3.441 closest distance to " CB  PHE A 130 " =    1.252
peak=   -3.439 closest distance to " N   THR A 235 " =    1.226
peak=   -3.417 closest distance to " O   HOH Z 414 " =    2.452
peak=   -3.413 closest distance to " OD2 ASP A 298 " =    0.826
peak=   -3.409 closest distance to " N   GLN A  58 " =    1.529
peak=   -3.409 closest distance to " O   GLY A 118 " =    2.058
peak=   -3.397 closest distance to " O   HOH Z 183 " =    1.229
peak=   -3.397 closest distance to " O   HOH Z 185 " =    2.496
peak=   -3.391 closest distance to " O   HOH Z 113 " =    2.226
peak=   -3.382 closest distance to " N   ASP A 191 " =    1.400
peak=   -3.381 closest distance to " O   HOH Z  91 " =    2.204
peak=   -3.374 closest distance to " CD1 TRP A 179 " =    0.938
peak=   -3.370 closest distance to " CB  ALA A 291 " =    2.391
peak=   -3.366 closest distance to " CD2 LEU A 237 " =    2.753
peak=   -3.364 closest distance to " O   HOH Z 119 " =    2.084
peak=   -3.358 closest distance to " N   VAL A 230 " =    1.073
peak=   -3.356 closest distance to " OD2 ASP A 171 " =    1.834
peak=   -3.352 closest distance to " CD  GLN A 223 " =    0.790
peak=   -3.349 closest distance to " CG  ARG A 269 " =    2.385
peak=   -3.349 closest distance to " O   ASN A 301 " =    1.067
peak=   -3.345 closest distance to " OG1 THR A  82 " =    1.973
peak=   -3.340 closest distance to " O   ASP A  27 " =    1.471
peak=   -3.339 closest distance to " N   THR A 264 " =    1.401
peak=   -3.338 closest distance to " O   HOH Z 275 " =    1.489
peak=   -3.335 closest distance to " N   SER A 134 " =    1.208
peak=   -3.332 closest distance to " O   HOH Z  54 " =    1.306
peak=   -3.323 closest distance to " CG2 VAL A 296 " =    1.005
peak=   -3.323 closest distance to " O   LYS A 289 " =    0.869
peak=   -3.321 closest distance to " O   HOH Z  15 " =    1.635
peak=   -3.319 closest distance to " CD1 TYR A 247 " =    2.584
peak=   -3.318 closest distance to " O   HOH Z 250 " =    1.570
peak=   -3.316 closest distance to " OG1 THR A   4 " =    1.865
peak=   -3.315 closest distance to " NE2 GLN A  58 " =    3.857
peak=   -3.306 closest distance to " O   HOH Z 335 " =    0.946
peak=   -3.286 closest distance to " O   HOH Z 124 " =    1.388
peak=   -3.285 closest distance to " O   HOH Z 156 " =    1.383
peak=   -3.284 closest distance to " O   HOH Z 174 " =    1.537
peak=   -3.278 closest distance to " CB  ALA A  43 " =    2.732
peak=   -3.276 closest distance to " OD2 ASP A 231 " =    1.687
peak=   -3.274 closest distance to " CA  GLY A 241 " =    3.381
peak=   -3.272 closest distance to " O   HOH Z 198 " =    1.294
peak=   -3.265 closest distance to " O   HOH Z 407 " =    1.715
peak=   -3.265 closest distance to " CZ  ARG A 259 " =    0.833
peak=   -3.263 closest distance to " O   HOH Z 231 " =    1.140
peak=   -3.256 closest distance to " CG BARG A 145 " =    2.195
peak=   -3.255 closest distance to " O   HOH Z 252 " =    1.081
peak=   -3.254 closest distance to " N   THR A  52 " =    1.506
peak=   -3.249 closest distance to " CB  ALA A 114 " =    2.542
peak=   -3.248 closest distance to " O   HOH Z 263 " =    3.632
peak=   -3.242 closest distance to " CG2AVAL A  41 " =    2.660
peak=   -3.240 closest distance to " O   HOH Z 120 " =    0.821
peak=   -3.236 closest distance to " O   HOH Z 272 " =    0.974
peak=   -3.235 closest distance to " OD1 ASP A 298 " =    2.560
peak=   -3.233 closest distance to " OE1 GLN A  88 " =    1.436
peak=   -3.228 closest distance to " O   SER A 164 " =    2.015
peak=   -3.227 closest distance to " OD1 ASP A 107 " =    2.006
peak=   -3.226 closest distance to " O   HOH Z  17 " =    1.326
peak=   -3.225 closest distance to " O   HOH Z 348 " =    2.346
peak=   -3.221 closest distance to " N   GLY A  17 " =    1.675
peak=   -3.209 closest distance to " CG2 THR A 178 " =    1.927
peak=   -3.206 closest distance to " CD2 LEU A 237 " =    2.491
peak=   -3.205 closest distance to " O   HOH Z  43 " =    1.834
peak=   -3.203 closest distance to " CA  SER A 276 " =    1.460
peak=   -3.201 closest distance to " O   HOH Z 175 " =    4.772
peak=   -3.199 closest distance to " CG2 VAL A 232 " =    2.138
peak=   -3.198 closest distance to " CB  TRP A 150 " =    1.558
peak=   -3.197 closest distance to " O   HOH Z 311 " =    3.315
peak=   -3.195 closest distance to " NH1 ARG A 195 " =    0.952
peak=   -3.194 closest distance to " O   MET A  47 " =    2.578
peak=   -3.192 closest distance to " O   HOH Z  93 " =    2.107
peak=   -3.189 closest distance to " O   HOH Z 130 " =    2.582
peak=   -3.189 closest distance to " N   GLU A   2 " =    1.191
peak=   -3.187 closest distance to " O   HOH Z 137 " =    1.337
peak=   -3.186 closest distance to " OG ASER A 134 " =    1.208
peak=   -3.182 closest distance to " O   HOH Z 109 " =    3.399
peak=   -3.180 closest distance to " O   HOH Z 111 " =    1.034
peak=   -3.176 closest distance to " O   PHE A  59 " =    2.358
peak=   -3.169 closest distance to " O   HOH Z 120 " =    0.867
peak=   -3.163 closest distance to " O   PRO A 198 " =    1.297
peak=   -3.161 closest distance to " OG1 THR A  82 " =    1.213
peak=   -3.159 closest distance to " O   ALA A  43 " =    1.921
peak=   -3.158 closest distance to " O   HOH Z 384 " =    1.750
peak=   -3.154 closest distance to " CD  GLU A 128 " =    2.049
peak=   -3.152 closest distance to " N   GLY A 262 " =    2.073
peak=   -3.145 closest distance to " ND2 ASN A  60 " =    2.271
peak=   -3.142 closest distance to " O   HOH Z  71 " =    1.210
peak=   -3.141 closest distance to " O   HOH Z  90 " =    1.654
peak=   -3.133 closest distance to " O   HOH Z 134 " =    1.600
peak=   -3.132 closest distance to " O   HOH Z 325 " =    0.859
peak=   -3.121 closest distance to " CD  PRO A 243 " =    1.701
peak=   -3.118 closest distance to " OD2 ASP A 171 " =    2.336
peak=   -3.117 closest distance to " O   HOH Z 295 " =    1.236
peak=   -3.116 closest distance to " CG  TYR A 169 " =    2.303
peak=   -3.114 closest distance to " OD2 ASP A 286 " =    2.804
peak=   -3.111 closest distance to " CD2 TYR A  30 " =    2.694
peak=   -3.104 closest distance to " SD  MET A 105 " =    0.907
peak=   -3.099 closest distance to " O   ASN A 170 " =    1.088
peak=   -3.099 closest distance to " CD2 TYR A 293 " =    1.563
peak=   -3.098 closest distance to " O   HOH Z 177 " =    1.922
peak=   -3.098 closest distance to " NH1 ARG A 219 " =    1.988
peak=   -3.096 closest distance to " O   HOH Z 423 " =    2.496
peak=   -3.092 closest distance to " O   HOH Z 351 " =    1.356
peak=   -3.085 closest distance to " OD1 ASP A 238 " =    1.356
peak=   -3.083 closest distance to " O   HOH Z   7 " =    0.883
peak=   -3.081 closest distance to " O   ARG A 275 " =    0.884
peak=   -3.069 closest distance to " O   HOH Z 105 " =    3.172
peak=   -3.053 closest distance to " O   HOH Z  19 " =    2.165
peak=   -3.041 closest distance to " NE2 GLN A 278 " =    2.643
peak=   -3.038 closest distance to " OG  SER A  87 " =    1.715
peak=   -3.032 closest distance to " O   HOH Z 368 " =    1.070

================= 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    :  0.4987 0.4806   6.301493e+00   6.281866e+00
   1_bss:  0.4919 0.4740   6.298308e+00   6.278689e+00
   1_xyz:  0.4265 0.4380   6.223170e+00   6.240746e+00
   1_adp:  0.3850 0.4228   6.165023e+00   6.224136e+00
   1_occ:  0.3845 0.4224   6.164193e+00   6.224168e+00
   2_bss:  0.3828 0.4192   6.166291e+00   6.224514e+00
   2_xyz:  0.3208 0.3921   6.046523e+00   6.168020e+00
   2_adp:  0.3093 0.3832   6.026446e+00   6.153451e+00
   2_occ:  0.3088 0.3832   6.025763e+00   6.153378e+00
   3_bss:  0.3089 0.3823   6.026300e+00   6.153694e+00
   3_xyz:  0.2633 0.3219   5.882657e+00   6.028768e+00
   3_adp:  0.2440 0.3092   5.837165e+00   6.000972e+00
   3_occ:  0.2439 0.3095   5.837126e+00   6.001038e+00
   4_bss:  0.2437 0.3089   5.837265e+00   6.000193e+00
   4_xyz:  0.1879 0.2436   5.593860e+00   5.789388e+00
   4_adp:  0.1701 0.2187   5.500441e+00   5.696263e+00
   4_occ:  0.1699 0.2186   5.499841e+00   5.695659e+00
   5_bss:  0.1697 0.2192   5.500988e+00   5.696425e+00
   5_xyz:  0.1489 0.1972   5.392398e+00   5.600596e+00
   5_adp:  0.1460 0.1941   5.375821e+00   5.580304e+00
   5_occ:  0.1459 0.1938   5.375126e+00   5.579575e+00
   5_bss:  0.1463 0.1944   5.376374e+00   5.579401e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000   6.796  11.742   6.453   0.000   0.000   0.000
   1_xyz:  0.300  20.000   6.796  11.742   6.453   0.000   0.000   0.000
   1_adp:  0.300  20.000   6.796  11.742   6.453   0.000   0.000   0.000
   1_occ:  0.300  20.000   6.796  11.742   6.453   0.000   0.000   0.000
   2_bss:  0.310  44.711   3.567   7.109   3.945   0.000   0.000   0.000
   2_xyz:  0.310  44.711   3.567   7.109   3.945   0.000   0.000   0.000
   2_adp:  0.310  44.711   3.567   7.109   3.945   0.000   0.000   0.000
   2_occ:  0.310  44.711   3.567   7.109   3.945   0.000   0.000   0.000
   3_bss:  0.321  62.756   2.755   5.239   3.103   0.000   0.000   0.000
   3_xyz:  0.321  62.756   2.755   5.239   3.103   0.000   0.000   0.000
   3_adp:  0.321  62.756   2.755   5.239   3.103   0.000   0.000   0.000
   3_occ:  0.321  62.756   2.755   5.239   3.103   0.000   0.000   0.000
   4_bss:  0.320  62.756   1.990   4.053   2.384   0.000   0.000   0.000
   4_xyz:  0.320  62.756   1.990   4.053   2.384   0.000   0.000   0.000
   4_adp:  0.320  62.756   1.990   4.053   2.384   0.000   0.000   0.000
   4_occ:  0.320  62.756   1.990   4.053   2.384   0.000   0.000   0.000
   5_bss:  0.328  65.810   1.408   2.728   2.191   0.000   0.000   0.000
   5_xyz:  0.328  65.810   1.408   2.728   2.191   0.000   0.000   0.000
   5_adp:  0.328  65.810   1.408   2.728   2.191   0.000   0.000   0.000
   5_occ:  0.328  65.810   1.408   2.728   2.191   0.000   0.000   0.000
   5_bss:  0.331  67.455  -0.643   0.423   0.220   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.444 0.4014  0.4636    73716.833
   1_bss:  59.673 0.3968  0.5777    71932.226
   1_xyz:  52.278 0.4911  0.7034    58919.861
   1_adp:  49.294 0.5286  0.8145    53928.152
   1_occ:  49.254 0.5291  0.8148    53912.384
   2_bss:  49.008 0.5321  0.7320    53672.938
   2_xyz:  44.675 0.5847  0.8051    44868.182
   2_adp:  43.081 0.6045  0.8232    42478.940
   2_occ:  42.986 0.6057  0.8239    42397.887
   3_bss:  42.863 0.6071  0.7943    42218.909
   3_xyz:  34.266 0.7092  0.9030    28576.364
   3_adp:  32.726 0.7271  0.9124    26529.096
   3_occ:  32.735 0.7270  0.9119    26534.715
   4_bss:  32.663 0.7277  0.8850    26417.689
   4_xyz:  24.426 0.8166  0.9617    15246.099
   4_adp:  21.480 0.8469  0.9731    12372.012
   4_occ:  21.457 0.8472  0.9732    12364.678
   5_bss:  21.454 0.8473  0.9502    12379.171
   5_xyz:  18.814 0.8731  0.9663     9941.644
   5_adp:  18.196 0.8794  0.9687     9597.848
   5_occ:  18.175 0.8796  0.9689     9588.833
   5_bss:  18.150 0.8798  0.9537     9566.135
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4404e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4404e+01
   1_xyz:   1.774  0.014  0.110 18.155  0.007  4.125   1.5500e-01
   1_adp:   1.774  0.014  0.110 18.155  0.007  4.125   1.5500e-01
   1_occ:   1.774  0.014  0.110 18.155  0.007  4.125   1.5500e-01
   2_bss:   1.774  0.014  0.110 18.155  0.007  4.125   1.5500e-01
   2_xyz:   1.393  0.011  0.091 17.072  0.005  4.112   1.1546e-01
   2_adp:   1.393  0.011  0.091 17.072  0.005  4.112   1.1546e-01
   2_occ:   1.393  0.011  0.091 17.072  0.005  4.112   1.1546e-01
   3_bss:   1.393  0.011  0.091 17.072  0.005  4.112   1.1546e-01
   3_xyz:   1.122  0.008  0.084 15.377  0.004  4.112   7.6830e-02
   3_adp:   1.122  0.008  0.084 15.377  0.004  4.112   7.6830e-02
   3_occ:   1.122  0.008  0.084 15.377  0.004  4.112   7.6830e-02
   4_bss:   1.122  0.008  0.084 15.377  0.004  4.112   7.6830e-02
   4_xyz:   1.249  0.011  0.084 15.861  0.005  4.134   9.6320e-02
   4_adp:   1.249  0.011  0.084 15.861  0.005  4.134   9.6320e-02
   4_occ:   1.249  0.011  0.084 15.861  0.005  4.134   9.6320e-02
   5_bss:   1.249  0.011  0.084 15.861  0.005  4.134   9.6320e-02
   5_xyz:   1.023  0.007  0.079 15.491  0.003  4.116   6.4657e-02
   5_adp:   1.023  0.007  0.079 15.491  0.003  4.116   6.4657e-02
   5_occ:   1.023  0.007  0.079 15.491  0.003  4.116   6.4657e-02
   5_bss:   1.023  0.007  0.079 15.491  0.003  4.116   6.4657e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0521e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0521e+00
   1_xyz:  15.744  0.127  0.521 87.976  0.054  2.172   1.0778e-01
   1_adp:  15.744  0.127  0.521 87.976  0.054  2.172   1.0778e-01
   1_occ:  15.744  0.127  0.521 87.976  0.054  2.172   1.0778e-01
   2_bss:  15.744  0.127  0.521 87.976  0.054  2.172   1.0778e-01
   2_xyz:   8.743  0.098  0.290 84.881  0.038  2.007   7.8388e-02
   2_adp:   8.743  0.098  0.290 84.881  0.038  2.007   7.8388e-02
   2_occ:   8.743  0.098  0.290 84.881  0.038  2.007   7.8388e-02
   3_bss:   8.743  0.098  0.290 84.881  0.038  2.007   7.8388e-02
   3_xyz:   7.150  0.074  0.314 80.320  0.034  2.249   8.8818e-02
   3_adp:   7.150  0.074  0.314 80.320  0.034  2.249   8.8818e-02
   3_occ:   7.150  0.074  0.314 80.320  0.034  2.249   8.8818e-02
   4_bss:   7.150  0.074  0.314 80.320  0.034  2.249   8.8818e-02
   4_xyz:   8.754  0.071  0.304 82.640  0.047  2.215   1.6668e-01
   4_adp:   8.754  0.071  0.304 82.640  0.047  2.215   1.6668e-01
   4_occ:   8.754  0.071  0.304 82.640  0.047  2.215   1.6668e-01
   5_bss:   8.754  0.071  0.304 82.640  0.047  2.215   1.6668e-01
   5_xyz:   7.717  0.049  0.400 86.900  0.040  2.259   3.7478e-02
   5_adp:   7.717  0.049  0.400 86.900  0.040  2.259   3.7478e-02
   5_occ:   7.717  0.049  0.400 86.900  0.040  2.259   3.7478e-02
   5_bss:   7.717  0.049  0.400 86.900  0.040  2.259   3.7478e-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: 120.49   0.00  14.78  69.91   0.00  12.71 120.49   0.00  26.05
   1_occ: 120.49   0.00  14.78  69.91   0.00  12.71 120.49   0.00  26.05
   2_bss: 120.49   0.00  14.78  69.91   0.00  12.71 120.49   0.00  26.05
   2_xyz: 120.49   0.00  14.78  69.91   0.00  12.71 120.49   0.00  26.05
   2_adp: 113.41   0.00  14.00  67.28   0.00  11.53 113.41   0.00  27.46
   2_occ: 113.41   0.00  14.00  67.28   0.00  11.53 113.41   0.00  27.46
   3_bss: 113.41   0.00  14.00  67.28   0.00  11.53 113.41   0.00  27.46
   3_xyz: 113.41   0.00  14.00  67.28   0.00  11.53 113.41   0.00  27.46
   3_adp: 113.95   0.00  15.20  83.15   0.00  11.45 113.95   0.00  35.61
   3_occ: 113.95   0.00  15.20  83.15   0.00  11.45 113.95   0.00  35.61
   4_bss: 113.95   0.00  15.20  83.15   0.00  11.45 113.95   0.00  35.61
   4_xyz: 113.95   0.00  15.20  83.15   0.00  11.45 113.95   0.00  35.61
   4_adp: 104.84   0.00  14.79  87.77   0.00  10.21 104.84   1.10  39.77
   4_occ: 104.84   0.00  14.79  87.77   0.00  10.21 104.84   1.10  39.77
   5_bss: 104.84   0.00  14.79  87.77   0.00  10.21 104.84   1.10  39.77
   5_xyz: 104.84   0.00  14.79  87.77   0.00  10.21 104.84   1.10  39.77
   5_adp: 101.33   0.00  14.26  86.16   0.00   9.81 101.33   2.18  38.49
   5_occ: 101.33   0.00  14.26  86.16   0.00   9.81 101.33   2.18  38.49
   5_bss: 102.97   1.65  15.90  87.80   1.65  11.45 102.97   3.83  40.14
------------------------------------------------------------------------
 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:    1.105    0.027    0.415
   1_adp:    1.105    0.027    0.415
   1_occ:    1.105    0.027    0.415
   2_bss:    1.105    0.027    0.415
   2_xyz:    1.679    0.030    0.601
   2_adp:    1.679    0.030    0.601
   2_occ:    1.679    0.030    0.601
   3_bss:    1.679    0.030    0.601
   3_xyz:    1.608    0.027    0.696
   3_adp:    1.608    0.027    0.696
   3_occ:    1.608    0.027    0.696
   4_bss:    1.608    0.027    0.696
   4_xyz:    1.910    0.064    0.850
   4_adp:    1.910    0.064    0.850
   4_occ:    1.910    0.064    0.850
   5_bss:    1.910    0.064    0.850
   5_xyz:    2.090    0.056    0.882
   5_adp:    2.090    0.056    0.882
   5_occ:    2.090    0.056    0.882
   5_bss:    2.090    0.056    0.882
------------------------------------------------------------------------

CPU time actual refinement: 336.83


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1082/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_1082/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1082/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1082/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1082/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.68 
  Macro-tasks:
    bulk solvent and scale       = 42.22  
    individual site refinement   = 134.45 
    weights calculation          = 32.43  
    collect and process          = 6.34   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 215.57 
  Micro-tasks:
    mask                            = 2.98   
    f_calc                          = 104.20 
    alpha_beta                      = 8.18   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 113.11 
    fmodel                         = 7.27   
    r_factors                      = 0.18   
    phase_errors                   = 10.04  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 247.37 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.806 micro seconds
Total CPU time: 5.84 minutes
from_scatterers_fft:    635 calls, 103.86 s
gradients_fft:          580 calls, 100.70 s

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

# Date 2008-01-16 Time 03:08:44 PST -0800 (1200481724.06 s)
Start R-work = 0.4987, R-free = 0.4806 (no bulk solvent and anisotropic scale)
Final R-work = 0.1611, R-free = 0.2091 (no bulk solvent and anisotropic scale)

Start R-work = 0.4919, R-free = 0.4740
Final R-work = 0.1463, R-free = 0.1944