# Date 2008-01-16 Time 02:32:05 PST -0800 (1200479525.81 s)
#phil __OFF__

Command line arguments: "../869.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26890
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 869

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 46.2261, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.76, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.2261, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9961 1.95111
Completeness in resolution range: 0.943912
Completeness with d_max=infinity: 0.9411

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9961
                             d_min =   1.9511

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.2261, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9961 1.95111
Completeness in resolution range: 0.943912
Completeness with d_max=infinity: 0.9411

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9965 -  4.1761 [2170/2199]  1957   213   9.8%
  bin  2:  4.1761 -  3.3266 [2101/2117]  1888   213  10.1%
  bin  3:  3.3266 -  2.9096 [2051/2070]  1842   209  10.2%
  bin  4:  2.9096 -  2.6451 [2054/2084]  1858   196   9.5%
  bin  5:  2.6451 -  2.4564 [2044/2063]  1837   207  10.1%
  bin  6:  2.4564 -  2.3122 [2032/2057]  1821   211  10.4%
  bin  7:  2.3122 -  2.1967 [2006/2040]  1808   198   9.9%
  bin  8:  2.1967 -  2.1014 [2004/2034]  1804   200  10.0%
  bin  9:  2.1014 -  2.0207 [2004/2046]  1808   196   9.8%
  bin 10:  2.0207 -  1.9511 [1123/2043]  1007   116  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_869/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: 0.12 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:
        1.65 -     2.30: 29
        2.30 -     2.95: 1701
        2.95 -     3.60: 4611
        3.60 -     4.25: 9339
        4.25 -     4.90: 13053
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.649 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.667 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.708 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.782 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28728 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_869/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_869/model_refine_001.geo

CPU time processing inputs: 7.72


============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 46.22605 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  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: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5022   r_free= 0.4909   ksol= 0.00   Bsol= 0.00   scale= 0.786    |
|                                                                             |
| 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:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.298675                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6584 0.99   1410  159 0.4203 0.4403      6.6245      6.6755|
|  2:  4.6584 -  3.7160 0.99   1364  145 0.4381 0.4148      6.8482      6.8458|
|  3:  3.7160 -  3.2518 0.99   1327  151 0.4711 0.4295      6.7111      6.7556|
|  4:  3.2518 -  2.9569 0.99   1338  151 0.4932 0.4466      6.5606      6.5047|
|  5:  2.9569 -  2.7464 0.99   1316  146 0.5292 0.5108       6.382      6.3629|
|  6:  2.7464 -  2.5853 0.99   1312  149 0.5307 0.5517      6.2911      6.2886|
|  7:  2.5853 -  2.4564 0.99   1315  137 0.5347 0.4656      6.2676      6.1837|
|  8:  2.4564 -  2.3499 0.98   1293  150 0.5432 0.5244      6.1731      6.2002|
|  9:  2.3499 -  2.2598 0.98   1298  146 0.5283 0.5134      6.1321      6.1065|
| 10:  2.2598 -  2.1820 0.99   1291  141 0.5495 0.5811      6.0967        6.12|
| 11:  2.1820 -  2.1140 0.99   1299  139 0.5294 0.5368      6.0491      6.0483|
| 12:  2.1140 -  2.0537 0.97   1266  146 0.5387 0.5587      5.9565      6.0006|
| 13:  2.0537 -  1.9998 0.95   1236  141 0.5562 0.5256      5.8909      5.8175|
| 14:  1.9998 -  1.9511 0.43    565   58 0.5641 0.5866      5.8298      5.8519|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9965 -  4.6584  1410   159  0.62  40.78   0.79     0.68      94279.47|
|  2:  4.6584 -  3.7160  1364   145  0.65  39.51   0.85     0.75     130805.70|
|  3:  3.7160 -  3.2518  1327   151  0.54  48.76   0.82     0.69     136943.21|
|  4:  3.2518 -  2.9569  1338   151  0.46  55.08   0.80     0.59     118064.70|
|  5:  2.9569 -  2.7464  1316   146  0.36  63.18   0.73     0.45      92838.80|
|  6:  2.7464 -  2.5853  1312   149  0.35  63.64   0.71     0.42      77905.75|
|  7:  2.5853 -  2.4564  1315   137  0.33  65.55   0.74     0.37      67493.51|
|  8:  2.4564 -  2.3499  1293   150  0.32  65.69   0.71     0.39      61988.39|
|  9:  2.3499 -  2.2598  1298   146  0.28  68.71   0.74     0.34      58350.96|
| 10:  2.2598 -  2.1820  1291   141  0.24  71.77   0.74     0.31      56160.85|
| 11:  2.1820 -  2.1140  1299   139  0.21  74.58   0.78     0.26      53719.33|
| 12:  2.1140 -  2.0537  1266   146  0.19  75.78   0.75     0.25      48595.45|
| 13:  2.0537 -  1.9998  1236   141  0.18  76.81   0.74     0.24      42184.56|
| 14:  1.9998 -  1.9511   565    58  0.18  77.02   0.69     0.21      35430.16|
|alpha:            min =        0.21 max =            0.75 mean =         0.44|
|beta:             min =    35430.16 max =       136943.21 mean =     79185.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.36|
|phase err.(work): min =        0.00 max =           89.99 mean =        62.43|
|phase err.(test): min =        0.00 max =           89.96 mean =        62.49|
|-----------------------------------------------------------------------------|

============================== 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 = 20.039863             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.364   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.889850              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.150   (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:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       31 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      187 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      710 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1553 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2681 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3976 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5154 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6655 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7801 |
|-----------------------------------------------------------------------------|
|-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 |       53.109 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.087    4.900  1.196 |       2.113 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.548)------------------------------------------|
|    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 = 11.548)------------------------------------------|
|    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: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5055   r_free= 0.4956   ksol= 0.00   Bsol= 0.00   scale= 0.756    |
|                                                                             |
| 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:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.300062                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4930   r_free= 0.4804   ksol= 0.36   Bsol= 0.00   scale= 0.980    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.16,8.71,9.04,0.00,0.00,0.00); trace/3= 8.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.90 A                  |
| x-ray target function (ml) for work reflections: 6.293777                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.344792             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.425   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.605801              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.403   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4930      final r-factor (work) = 0.4311          |
| start r-factor (free) = 0.4804      final r-factor (free) = 0.4563          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 101.3996 = 15.34 * 0.50 * 6.2941 + 1.00 * 53.1090                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 48.0122 = 15.34 * 0.50 * 6.2389 + 1.00 * 0.1447                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4311      final r-factor (work) = 0.3959          |
| start r-factor (free) = 0.4563      final r-factor (free) = 0.4549          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0328 = 1.61 * 1.00 * 6.2389 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.9528 = 1.61 * 1.00 * 6.1863 + 1.00 * 0.0188                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.548)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.63  15.11    None  None   None       |
|    all(noH): 2823   0      0.00    102.63  15.11    None  None   None       |
|    Sol.    : 438    0      0.00    95.36   24.03    None  None   None       |
|    Mac.    : 2385   0      0.00    102.63  13.47    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 -  10.263: 1235   |   5:    51.316 -  61.579:   34        |
|      1:    10.263 -  20.526:  864   |   6:    61.579 -  71.842:   17        |
|      2:    20.526 -  30.790:  402   |   7:    71.842 -  82.105:    2        |
|      3:    30.790 -  41.053:  179   |   8:    82.105 -  92.368:    2        |
|      4:    41.053 -  51.316:   85   |   9:    92.368 - 102.632:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3959 r_free = 0.4549             target_work(ml) = 6.182         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3957 r_free = 0.4555             target_work(ml) = 6.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3957   r_free= 0.4555   ksol= 0.36   Bsol= 0.00   scale= 1.111    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.16,8.71,9.04,0.00,0.00,0.00); trace/3= 8.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.181353                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3933   r_free= 0.4490   ksol= 0.38   Bsol= 50.00   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.52,4.34,5.62,0.00,0.00,0.00); trace/3= 4.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.181715                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.096178              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.247  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.675144              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.310  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3933      final r-factor (work) = 0.3278          |
| start r-factor (free) = 0.4490      final r-factor (free) = 0.3882          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.1764 = 8.10 * 0.50 * 6.1836 + 1.00 * 0.1447                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.8427 = 8.10 * 0.50 * 6.1147 + 1.00 * 0.0900                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3278      final r-factor (work) = 0.3094          |
| start r-factor (free) = 0.3882      final r-factor (free) = 0.3712          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1471 = 0.68 * 1.00 * 6.1147 + 1.00 * 0.0188                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0788 = 0.68 * 1.00 * 6.0232 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.548)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.97  15.28    None  None   None       |
|    all(noH): 2823   0      0.00    100.97  15.28    None  None   None       |
|    Sol.    : 438    0      0.00    90.44   29.48    None  None   None       |
|    Mac.    : 2385   0      0.00    100.97  12.68    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 -  10.097: 1201   |   5:    50.483 -  60.579:   31        |
|      1:    10.097 -  20.193:  900   |   6:    60.579 -  70.676:   11        |
|      2:    20.193 -  30.290:  384   |   7:    70.676 -  80.773:    3        |
|      3:    30.290 -  40.386:  200   |   8:    80.773 -  90.869:    2        |
|      4:    40.386 -  50.483:   88   |   9:    90.869 - 100.966:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3094 r_free = 0.3712             target_work(ml) = 6.006         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3092 r_free = 0.3710             target_work(ml) = 6.006         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3092   r_free= 0.3710   ksol= 0.38   Bsol= 50.00   scale= 1.076   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.52,4.34,5.62,0.00,0.00,0.00); trace/3= 4.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.005933                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3076   r_free= 0.3698   ksol= 0.35   Bsol= 50.00   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.87,2.01,3.29,0.00,0.00,0.00); trace/3= 2.39                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.005965                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.755677              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.698   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.139302              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.573  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3076      final r-factor (work) = 0.2313          |
| start r-factor (free) = 0.3698      final r-factor (free) = 0.2955          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.4205 = 5.76 * 0.50 * 6.0221 + 1.00 * 0.0900                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.0691 = 5.76 * 0.50 * 5.9003 + 1.00 * 0.0891                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2313      final r-factor (work) = 0.2047          |
| start r-factor (free) = 0.2955      final r-factor (free) = 0.2756          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7346 = 1.14 * 1.00 * 5.9003 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5335 = 1.14 * 1.00 * 5.7211 + 1.00 * 0.0154                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.548)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.30  16.01    None  None   None       |
|    all(noH): 2823   0      0.00    103.30  16.01    None  None   None       |
|    Sol.    : 438    0      1.52    94.32   40.21    None  None   None       |
|    Mac.    : 2385   0      0.00    103.30  11.56    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.330: 1421   |   5:    51.649 -  61.979:   81        |
|      1:    10.330 -  20.660:  722   |   6:    61.979 -  72.309:   35        |
|      2:    20.660 -  30.990:  253   |   7:    72.309 -  82.639:   19        |
|      3:    30.990 -  41.319:  157   |   8:    82.639 -  92.969:    1        |
|      4:    41.319 -  51.649:  130   |   9:    92.969 - 103.298:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2047 r_free = 0.2756             target_work(ml) = 5.685         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2045 r_free = 0.2754             target_work(ml) = 5.684         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2045   r_free= 0.2754   ksol= 0.35   Bsol= 50.00   scale= 1.054   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.87,2.01,3.29,0.00,0.00,0.00); trace/3= 2.39                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.683700                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2038   r_free= 0.2733   ksol= 0.34   Bsol= 46.15   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.91,0.66,1.64,0.00,0.00,0.00); trace/3= 1.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.680595                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.190662              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.522   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.403900              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.554  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2038      final r-factor (work) = 0.1606          |
| start r-factor (free) = 0.2733      final r-factor (free) = 0.2191          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0867 = 4.19 * 0.50 * 5.7259 + 1.00 * 0.0891                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7795 = 4.19 * 0.50 * 5.5919 + 1.00 * 0.0627                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1606      final r-factor (work) = 0.1483          |
| start r-factor (free) = 0.2191      final r-factor (free) = 0.2006          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2737 = 0.40 * 1.00 * 5.5919 + 1.00 * 0.0151                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2075 = 0.40 * 1.00 * 5.4388 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.548)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.92  15.35    None  None   None       |
|    all(noH): 2823   0      0.00    100.92  15.35    None  None   None       |
|    Sol.    : 438    0      3.76    90.84   40.65    None  None   None       |
|    Mac.    : 2385   0      0.00    100.92  10.70    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 -  10.092: 1540   |   5:    50.462 -  60.555:   92        |
|      1:    10.092 -  20.185:  695   |   6:    60.555 -  70.647:   49        |
|      2:    20.185 -  30.277:  176   |   7:    70.647 -  80.739:    9        |
|      3:    30.277 -  40.370:  142   |   8:    80.739 -  90.832:    5        |
|      4:    40.370 -  50.462:  111   |   9:    90.832 - 100.924:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1483 r_free = 0.2006             target_work(ml) = 5.390         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1480 r_free = 0.2002             target_work(ml) = 5.389         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1480   r_free= 0.2002   ksol= 0.34   Bsol= 46.15   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.91,0.66,1.64,0.00,0.00,0.00); trace/3= 1.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.389188                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1482   r_free= 0.2004   ksol= 0.32   Bsol= 41.16   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.44,0.09,0.94,0.00,0.00,0.00); trace/3= 0.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.388888                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.180411              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.932  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.858820              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.916  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1482      final r-factor (work) = 0.1277          |
| start r-factor (free) = 0.2004      final r-factor (free) = 0.1738          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7148 = 3.18 * 0.50 * 5.4408 + 1.00 * 0.0627                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5396 = 3.18 * 0.50 * 5.3294 + 1.00 * 0.0647                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1277      final r-factor (work) = 0.1225          |
| start r-factor (free) = 0.1738      final r-factor (free) = 0.1696          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5877 = 0.86 * 1.00 * 5.3294 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5047 = 0.86 * 1.00 * 5.2319 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.548)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.15  15.35    None  None   None       |
|    all(noH): 2823   0      0.00    106.15  15.35    None  None   None       |
|    Sol.    : 438    0      4.01    96.30   41.35    None  None   None       |
|    Mac.    : 2385   0      0.00    106.15  10.58    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 -  10.615: 1634   |   5:    53.075 -  63.689:   83        |
|      1:    10.615 -  21.230:  654   |   6:    63.689 -  74.304:   44        |
|      2:    21.230 -  31.845:  161   |   7:    74.304 -  84.919:   13        |
|      3:    31.845 -  42.460:  125   |   8:    84.919 -  95.534:    4        |
|      4:    42.460 -  53.075:  100   |   9:    95.534 - 106.149:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1225 r_free = 0.1696             target_work(ml) = 5.219         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1224 r_free = 0.1695             target_work(ml) = 5.218         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1224   r_free= 0.1695   ksol= 0.32   Bsol= 41.16   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.44,0.09,0.94,0.00,0.00,0.00); trace/3= 0.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.218426                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6584 0.99   1410  159 0.1040 0.1324       5.413      5.5755|
|  2:  4.6584 -  3.7160 0.99   1364  145 0.0914 0.1249      5.4967      5.7535|
|  3:  3.7160 -  3.2518 0.99   1327  151 0.1174 0.1601      5.5562      5.8869|
|  4:  3.2518 -  2.9569 0.99   1338  151 0.1391 0.1706      5.5561      5.6774|
|  5:  2.9569 -  2.7464 0.99   1316  146 0.1443 0.1737       5.383      5.5467|
|  6:  2.7464 -  2.5853 0.99   1312  149 0.1326 0.1993       5.273      5.5464|
|  7:  2.5853 -  2.4564 0.99   1315  137 0.1387 0.1823      5.2572      5.4458|
|  8:  2.4564 -  2.3499 0.98   1293  150 0.1252 0.1823      5.1046      5.4078|
|  9:  2.3499 -  2.2598 0.98   1298  146 0.1255 0.1978      5.0792      5.3625|
| 10:  2.2598 -  2.1820 0.99   1291  141 0.1219 0.1903      5.0042      5.2632|
| 11:  2.1820 -  2.1140 0.99   1299  139 0.1253 0.2029      5.0268      5.3954|
| 12:  2.1140 -  2.0537 0.97   1266  146 0.1197 0.1711       4.952      5.1478|
| 13:  2.0537 -  1.9998 0.95   1236  141 0.1280 0.1953      4.8743      5.1116|
| 14:  1.9998 -  1.9511 0.43    565   58 0.1171 0.1701      4.7279      5.0332|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9965 -  4.6584  1410   159  0.94   9.34   0.98     0.96       7420.69|
|  2:  4.6584 -  3.7160  1364   145  0.95   8.84   1.03     1.01      10145.21|
|  3:  3.7160 -  3.2518  1327   151  0.92  12.83   1.05     1.04      12129.69|
|  4:  3.2518 -  2.9569  1338   151  0.91  15.27   1.02     1.01      12152.51|
|  5:  2.9569 -  2.7464  1316   146  0.89  17.01   1.01     0.97       8980.78|
|  6:  2.7464 -  2.5853  1312   149  0.89  17.59   1.00     0.97       8186.43|
|  7:  2.5853 -  2.4564  1315   137  0.89  17.21   1.00     0.98       7437.69|
|  8:  2.4564 -  2.3499  1293   150  0.90  16.40   0.99     0.95       5592.67|
|  9:  2.3499 -  2.2598  1298   146  0.90  16.21   1.02     1.01       5447.44|
| 10:  2.2598 -  2.1820  1291   141  0.90  16.45   1.01     0.98       4827.90|
| 11:  2.1820 -  2.1140  1299   139  0.88  18.59   1.01     0.97       5345.44|
| 12:  2.1140 -  2.0537  1266   146  0.89  17.54   1.02     1.01       4810.09|
| 13:  2.0537 -  1.9998  1236   141  0.89  17.87   1.01     1.00       3935.08|
| 14:  1.9998 -  1.9511   565    58  0.89  16.94   1.00     0.98       3000.95|
|alpha:            min =        0.95 max =            1.04 mean =         0.99|
|beta:             min =     3000.95 max =        12152.51 mean =      7324.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.44|
|phase err.(test): min =        0.00 max =           89.80 mean =        14.77|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1228   r_free= 0.1704   ksol= 0.32   Bsol= 41.65   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.05,-0.40,0.45,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.220599                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1228   r_free= 0.1704   ksol= 0.32   Bsol= 41.65   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.05,-0.40,0.45,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.220599                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6584 0.99   1410  159 0.1036 0.1371      5.4201      5.5981|
|  2:  4.6584 -  3.7160 0.99   1364  145 0.0930 0.1254      5.5111       5.761|
|  3:  3.7160 -  3.2518 0.99   1327  151 0.1179 0.1606      5.5614      5.8863|
|  4:  3.2518 -  2.9569 0.99   1338  151 0.1395 0.1709      5.5593      5.6798|
|  5:  2.9569 -  2.7464 0.99   1316  146 0.1443 0.1738      5.3846       5.548|
|  6:  2.7464 -  2.5853 0.99   1312  149 0.1331 0.1999      5.2746      5.5479|
|  7:  2.5853 -  2.4564 0.99   1315  137 0.1384 0.1823      5.2577      5.4474|
|  8:  2.4564 -  2.3499 0.98   1293  150 0.1250 0.1828      5.1046      5.4096|
|  9:  2.3499 -  2.2598 0.98   1298  146 0.1253 0.1966      5.0782      5.3597|
| 10:  2.2598 -  2.1820 0.99   1291  141 0.1215 0.1901      5.0027      5.2628|
| 11:  2.1820 -  2.1140 0.99   1299  139 0.1251 0.2027      5.0256      5.3948|
| 12:  2.1140 -  2.0537 0.97   1266  146 0.1197 0.1708      4.9514      5.1476|
| 13:  2.0537 -  1.9998 0.95   1236  141 0.1281 0.1949      4.8736      5.1106|
| 14:  1.9998 -  1.9511 0.43    565   58 0.1173 0.1693      4.7266      5.0292|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9965 -  4.6584  1410   159  0.94   9.55   0.98     0.96       7802.04|
|  2:  4.6584 -  3.7160  1364   145  0.95   9.05   1.03     1.01      10490.01|
|  3:  3.7160 -  3.2518  1327   151  0.92  12.98   1.05     1.04      12336.43|
|  4:  3.2518 -  2.9569  1338   151  0.91  15.35   1.02     1.01      12239.14|
|  5:  2.9569 -  2.7464  1316   146  0.89  17.05   1.01     0.97       9016.15|
|  6:  2.7464 -  2.5853  1312   149  0.89  17.64   1.00     0.97       8214.77|
|  7:  2.5853 -  2.4564  1315   137  0.89  17.24   1.00     0.98       7467.81|
|  8:  2.4564 -  2.3499  1293   150  0.90  16.45   0.99     0.95       5618.09|
|  9:  2.3499 -  2.2598  1298   146  0.90  16.22   1.02     1.01       5446.68|
| 10:  2.2598 -  2.1820  1291   141  0.90  16.45   1.01     0.98       4822.95|
| 11:  2.1820 -  2.1140  1299   139  0.88  18.56   1.01     0.97       5330.81|
| 12:  2.1140 -  2.0537  1266   146  0.89  17.53   1.02     1.01       4804.17|
| 13:  2.0537 -  1.9998  1236   141  0.89  17.84   1.01     1.00       3923.49|
| 14:  1.9998 -  1.9511   565    58  0.89  16.91   1.00     0.98       2984.29|
|alpha:            min =        0.95 max =            1.04 mean =         0.99|
|beta:             min =     2984.29 max =        12336.43 mean =      7409.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.50|
|phase err.(test): min =        0.00 max =           89.84 mean =        14.86|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.548)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.49    106.64  15.84    None  None   None       |
|    all(noH): 2823   0      0.49    106.64  15.84    None  None   None       |
|    Sol.    : 438    0      4.50    96.79   41.84    None  None   None       |
|    Mac.    : 2385   0      0.49    106.64  11.07    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:     0.489 -  11.104: 1634   |   5:    53.564 -  64.179:   83        |
|      1:    11.104 -  21.719:  654   |   6:    64.179 -  74.793:   44        |
|      2:    21.719 -  32.334:  161   |   7:    74.793 -  85.408:   13        |
|      3:    32.334 -  42.949:  125   |   8:    85.408 -  96.023:    4        |
|      4:    42.949 -  53.564:  100   |   9:    96.023 - 106.638:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 329         
Filter by distance & map next to the model:
   mapped sites are within: 0.711 - 5.593
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 329 from: 329
   mapped sites are within: 0.711 - 5.593

peak=    9.993 closest distance to " CB  VAL A 230 " =    1.400
peak=    8.195 closest distance to " CG2 VAL A 296 " =    1.286
peak=    7.274 closest distance to " CG  ARG A 138 " =    1.174
peak=    6.603 closest distance to " CD1AILE A 234 " =    1.203
peak=    6.475 closest distance to " O   HOH Z 278 " =    2.077
peak=    6.309 closest distance to " O   HOH Z 205 " =    1.266
peak=    6.248 closest distance to " O   HOH Z  37 " =    1.665
peak=    6.198 closest distance to " O   HOH Z   7 " =    1.792
peak=    6.096 closest distance to " O   HOH Z 130 " =    0.960
peak=    5.768 closest distance to " O   HOH Z 124 " =    1.694
peak=    5.686 closest distance to " CD2 LEU A   5 " =    1.256
peak=    5.638 closest distance to " O   HOH Z 214 " =    1.668
peak=    5.594 closest distance to " O   HOH Z  65 " =    1.063
peak=    5.545 closest distance to " NH2 ARG A  56 " =    2.095
peak=    5.524 closest distance to " NE2 GLN A  11 " =    1.286
peak=    5.523 closest distance to " O   HOH Z  97 " =    1.427
peak=    5.495 closest distance to " O   HOH Z 132 " =    1.726
peak=    5.116 closest distance to " CG  PRO A 213 " =    1.269
peak=    5.090 closest distance to " O   HOH Z 344 " =    1.358
peak=    5.051 closest distance to " CB  ASN A 148 " =    1.315
peak=    5.025 closest distance to " O   HOH Z 427 " =    2.688
peak=    4.969 closest distance to " O   HOH Z 142 " =    1.963
peak=    4.922 closest distance to " CG  LEU A   5 " =    1.202
peak=    4.901 closest distance to " O   HOH Z 134 " =    1.508
peak=    4.892 closest distance to " O   HOH Z 202 " =    1.467
peak=    4.882 closest distance to " CG  PRO A 198 " =    1.359
peak=    4.853 closest distance to " CG  PRO A  54 " =    1.261
peak=    4.852 closest distance to " O   HOH Z 117 " =    1.565
peak=    4.835 closest distance to " O   HOH Z 374 " =    1.158
peak=    4.832 closest distance to " O   HOH Z 199 " =    1.159
peak=    4.803 closest distance to " O   HOH Z 183 " =    1.389
peak=    4.787 closest distance to " O   HOH Z 411 " =    3.666
peak=    4.728 closest distance to " O   HOH Z 373 " =    2.262
peak=    4.658 closest distance to " CB  VAL A 230 " =    1.103
peak=    4.650 closest distance to " O   HOH Z 143 " =    1.529
peak=    4.594 closest distance to " O   HOH Z 193 " =    1.730
peak=    4.532 closest distance to " O   HOH Z 186 " =    1.240
peak=    4.514 closest distance to " CD2 LEU A 228 " =    1.205
peak=    4.485 closest distance to " CB  PRO A  54 " =    0.966
peak=    4.474 closest distance to " O   HOH Z 260 " =    1.489
peak=    4.466 closest distance to " O   HOH Z 403 " =    1.343
peak=    4.426 closest distance to " O   HOH Z 316 " =    2.700
peak=    4.416 closest distance to " O   HOH Z 133 " =    1.639
peak=    4.409 closest distance to " O   HOH Z 326 " =    1.601
peak=    4.406 closest distance to " O   HOH Z   2 " =    2.045
peak=    4.400 closest distance to " O   HOH Z 193 " =    1.704
peak=    4.398 closest distance to " CB  SER A   3 " =    1.441
peak=    4.387 closest distance to " CB  GLN A 223 " =    1.428
peak=    4.370 closest distance to " CG  LEU A 167 " =    1.168
peak=    4.342 closest distance to " O   HOH Z 236 " =    1.637
peak=    4.329 closest distance to " O   HOH Z  97 " =    2.084
peak=    4.319 closest distance to " O   HOH Z 138 " =    1.009
peak=    4.293 closest distance to " CG  LEU A 228 " =    1.214
peak=    4.276 closest distance to " O   HOH Z 126 " =    1.587
peak=    4.249 closest distance to " CB  SER A  63 " =    1.310
peak=    4.248 closest distance to " O   HOH Z 126 " =    1.810
peak=    4.202 closest distance to " O   HOH Z 371 " =    2.801
peak=    4.178 closest distance to " O   HOH Z 147 " =    1.349
peak=    4.172 closest distance to " O   HOH Z 350 " =    1.342
peak=    4.168 closest distance to " O   HOH Z 116 " =    1.255
peak=    4.144 closest distance to " O   HOH Z 357 " =    1.363
peak=    4.140 closest distance to " O   HOH Z 184 " =    1.360
peak=    4.131 closest distance to " O   PRO A 198 " =    1.291
peak=    4.125 closest distance to " O   HOH Z  64 " =    1.924
peak=    4.121 closest distance to " CG2 THR A 221 " =    1.253
peak=    4.121 closest distance to " O   HOH Z 108 " =    1.628
peak=    4.118 closest distance to " O   HOH Z 232 " =    2.205
peak=    4.116 closest distance to " O   HOH Z  48 " =    1.696
peak=    4.102 closest distance to " O   HOH Z 334 " =    3.005
peak=    4.093 closest distance to " CD2 TRP A 179 " =    2.289
peak=    4.091 closest distance to " O   HOH Z 425 " =    1.456
peak=    4.091 closest distance to " O   HOH Z 287 " =    1.930
peak=    4.073 closest distance to " O   HOH Z  63 " =    1.418
peak=    4.056 closest distance to " O   HOH Z 148 " =    1.839
peak=    4.053 closest distance to " O   HOH Z 247 " =    1.353
peak=    4.048 closest distance to " O   HOH Z 112 " =    1.137
peak=    4.040 closest distance to " O   HOH Z  39 " =    1.232
peak=    4.014 closest distance to " OD1 ASN A  69 " =    2.664
peak=    4.000 closest distance to " O   HOH Z  92 " =    0.917
peak=    3.976 closest distance to " CB  VAL A 202 " =    1.588
peak=    3.973 closest distance to " CB  GLN A 183 " =    1.224
peak=    3.957 closest distance to " O   HOH Z 217 " =    1.504
peak=    3.940 closest distance to " O   HOH Z 227 " =    1.834
peak=    3.931 closest distance to " O   HOH Z 220 " =    1.406
peak=    3.915 closest distance to " CB  ARG A 275 " =    0.887
peak=    3.912 closest distance to " CB  GLU A 277 " =    3.536
peak=    3.910 closest distance to " O   HOH Z  11 " =    1.412
peak=    3.906 closest distance to " CB  TRP A 179 " =    1.387
peak=    3.895 closest distance to " NH2BARG A 190 " =    1.597
peak=    3.885 closest distance to " O   HOH Z 272 " =    1.865
peak=    3.881 closest distance to " NH1 ARG A  56 " =    1.063
peak=    3.872 closest distance to " OD2 ASP A 286 " =    2.617
peak=    3.860 closest distance to " CG  LYS A  76 " =    1.525
peak=    3.857 closest distance to " O   HOH Z  58 " =    1.644
peak=    3.857 closest distance to " O   HOH Z 298 " =    1.897
peak=    3.819 closest distance to " CB  VAL A 296 " =    1.049
peak=    3.819 closest distance to " O   HOH Z 369 " =    2.157
peak=    3.813 closest distance to " CB  TYR A 169 " =    0.827
peak=    3.813 closest distance to " CG  PRO A 280 " =    0.896
peak=    3.810 closest distance to " O   HOH Z  78 " =    1.683
peak=    3.809 closest distance to " O   HOH Z 145 " =    2.053
peak=    3.808 closest distance to " O   HOH Z 171 " =    2.909
peak=    3.805 closest distance to " O   HOH Z  68 " =    1.670
peak=    3.803 closest distance to " O   HOH Z  61 " =    1.485
peak=    3.789 closest distance to " O   HOH Z 204 " =    1.720
peak=    3.786 closest distance to " O   HOH Z 282 " =    1.567
peak=    3.776 closest distance to " O   SER A  87 " =    2.406
peak=    3.775 closest distance to " O   HOH Z 284 " =    1.690
peak=    3.767 closest distance to " CG2 VAL A 257 " =    0.937
peak=    3.760 closest distance to " O   HOH Z 180 " =    2.104
peak=    3.758 closest distance to " O   HOH Z  59 " =    1.574
peak=    3.738 closest distance to " CA  TYR A  30 " =    1.064
peak=    3.735 closest distance to " CB  VAL A 265 " =    1.220
peak=    3.731 closest distance to " CG  GLN A  88 " =    1.035
peak=    3.730 closest distance to " O   HOH Z 423 " =    1.589
peak=    3.729 closest distance to " O   HOH Z  89 " =    1.483
peak=    3.729 closest distance to " NZ  LYS A 117 " =    3.356
peak=    3.728 closest distance to " N   PHE A 130 " =    1.282
peak=    3.724 closest distance to " O   ALA A 165 " =    1.193
peak=    3.717 closest distance to " CA  LEU A 282 " =    1.144
peak=    3.715 closest distance to " NE2 GLN A  58 " =    5.469
peak=    3.704 closest distance to " NH1 ARG A 138 " =    1.071
peak=    3.701 closest distance to " OD1 ASN A 217 " =    1.684
peak=    3.671 closest distance to " O   HOH Z 181 " =    2.344
peak=    3.663 closest distance to " CG1 VAL A 153 " =    0.827
peak=    3.662 closest distance to " O   HOH Z   9 " =    2.173
peak=    3.658 closest distance to " O   HOH Z  88 " =    2.917
peak=    3.656 closest distance to " CB  LEU A 255 " =    0.867
peak=    3.654 closest distance to " CZ AARG A 102 " =    1.950
peak=    3.650 closest distance to " O   HOH Z 189 " =    2.071
peak=    3.649 closest distance to " NZ  LYS A 117 " =    1.078
peak=    3.647 closest distance to " CD1 LEU A 300 " =    1.189
peak=    3.644 closest distance to " O   HOH Z 419 " =    2.001
peak=    3.644 closest distance to " CA  ILE A 234 " =    0.905
peak=    3.638 closest distance to " O   HOH Z 414 " =    1.247
peak=    3.636 closest distance to " O   HOH Z 193 " =    1.946
peak=    3.633 closest distance to " OG  SER A  62 " =    3.323
peak=    3.626 closest distance to " O   HOH Z 120 " =    1.060
peak=    3.623 closest distance to " CA  ALA A  21 " =    1.180
peak=    3.620 closest distance to " CB  GLU A 152 " =    1.273
peak=    3.615 closest distance to " O   HOH Z 192 " =    1.229
peak=    3.611 closest distance to " NE AARG A 275 " =    1.401
peak=    3.606 closest distance to " CB  ALA A   1 " =    4.551
peak=    3.601 closest distance to " O   HOH Z 273 " =    0.985
peak=    3.600 closest distance to " CG1BVAL A 121 " =    1.124
peak=    3.589 closest distance to " O   HOH Z 234 " =    3.686
peak=    3.588 closest distance to " O   HOH Z 249 " =    1.218
peak=    3.583 closest distance to " O   HOH Z 123 " =    1.129
peak=    3.579 closest distance to " O   HOH Z 345 " =    3.242
peak=    3.578 closest distance to " O   HOH Z 227 " =    2.116
peak=    3.571 closest distance to " O   HOH Z 285 " =    1.800
peak=    3.563 closest distance to " CG  ASN A  60 " =    1.143
peak=    3.561 closest distance to " CA  VAL A  41 " =    0.959
peak=    3.557 closest distance to " O   HOH Z 280 " =    1.565
peak=    3.540 closest distance to " O   HOH Z 410 " =    1.492
peak=    3.537 closest distance to " O   HOH Z  78 " =    1.858
peak=    3.533 closest distance to " O   HOH Z 412 " =    3.438
peak=    3.528 closest distance to " O   HOH Z 209 " =    2.140
peak=    3.520 closest distance to " CB  ALA A 291 " =    1.486
peak=    3.519 closest distance to " CA  VAL A 126 " =    1.267
peak=    3.516 closest distance to " O   HOH Z 313 " =    1.772
peak=    3.514 closest distance to " O   HOH Z 211 " =    1.178
peak=    3.508 closest distance to " CB  ARG A 138 " =    1.791
peak=    3.506 closest distance to " O   HOH Z 361 " =    1.647
peak=    3.498 closest distance to " O   HOH Z 426 " =    3.173
peak=    3.495 closest distance to " O   HOH Z 302 " =    1.377
peak=    3.493 closest distance to " NH1 ARG A  14 " =    1.061
peak=    3.493 closest distance to " CA  LEU A 101 " =    1.623
peak=    3.492 closest distance to " CB  LEU A 228 " =    1.318
peak=    3.482 closest distance to " O   PRO A 198 " =    1.541
peak=    3.481 closest distance to " O   HOH Z 368 " =    2.065
peak=    3.479 closest distance to " O   GLY A 302 " =    1.595
peak=    3.478 closest distance to " O   HOH Z 271 " =    1.851
peak=    3.475 closest distance to " CD  ARG A 269 " =    0.940
peak=    3.470 closest distance to " O   HOH Z 392 " =    1.166
peak=    3.470 closest distance to " C   ALA A 299 " =    0.880
peak=    3.436 closest distance to " O   HOH Z 189 " =    2.996
peak=    3.435 closest distance to " O   HOH Z  59 " =    2.011
peak=    3.431 closest distance to " CA  ASN A  74 " =    1.268
peak=    3.430 closest distance to " CB  GLU A 128 " =    1.107
peak=    3.430 closest distance to " CA  GLY A 267 " =    1.232
peak=    3.421 closest distance to " O   HOH Z 151 " =    1.783
peak=    3.416 closest distance to " OE2 GLU A  53 " =    2.056
peak=    3.414 closest distance to " O   HOH Z 424 " =    1.098
peak=    3.414 closest distance to " O   HOH Z 130 " =    2.157
peak=    3.410 closest distance to " NH2 ARG A 219 " =    1.770
peak=    3.408 closest distance to " O   HOH Z 261 " =    1.758
peak=    3.405 closest distance to " CA  ASN A 127 " =    1.068
peak=    3.403 closest distance to " O   HOH Z 380 " =    1.657
peak=    3.396 closest distance to " CA  ASN A 217 " =    1.169
peak=    3.393 closest distance to " CA  PHE A 283 " =    1.399
peak=    3.387 closest distance to " CG  ARG A  66 " =    2.774
peak=    3.385 closest distance to " CD1 ILE A  33 " =    1.557
peak=    3.383 closest distance to " O   HOH Z 276 " =    1.457
peak=    3.379 closest distance to " O   HOH Z 371 " =    1.691
peak=    3.376 closest distance to " CB  MET A  40 " =    0.935
peak=    3.372 closest distance to " CG2 ILE A 234 " =    0.877
peak=    3.369 closest distance to " CA  ALA A 160 " =    0.769
peak=    3.364 closest distance to " O   HOH Z 353 " =    2.085
peak=    3.364 closest distance to " O   HOH Z 265 " =    2.056
peak=    3.358 closest distance to " O   HOH Z 222 " =    2.219
peak=    3.356 closest distance to " O   HOH Z 148 " =    3.603
peak=    3.355 closest distance to " CB  ARG A 102 " =    0.814
peak=    3.351 closest distance to " CD  ARG A 159 " =    0.816
peak=    3.343 closest distance to " OG ASER A 134 " =    1.364
peak=    3.339 closest distance to " O   HOH Z 385 " =    0.992
peak=    3.337 closest distance to " NE2 GLN A  58 " =    2.940
peak=    3.337 closest distance to " ND1 HIS A  86 " =    1.896
peak=    3.337 closest distance to " O   HOH Z 213 " =    1.926
peak=    3.335 closest distance to " O   HOH Z  93 " =    2.381
peak=    3.330 closest distance to " CB  ARG A 139 " =    1.055
peak=    3.328 closest distance to " O   HOH Z  44 " =    1.769
peak=    3.327 closest distance to " CG2 THR A 220 " =    0.999
peak=    3.324 closest distance to " OE2 GLU A   2 " =    1.668
peak=    3.323 closest distance to " CA  THR A 264 " =    0.711
peak=    3.323 closest distance to " O   HOH Z 346 " =    1.395
peak=    3.319 closest distance to " CB  ARG A  79 " =    1.609
peak=    3.317 closest distance to " CG1 ILE A 151 " =    1.142
peak=    3.309 closest distance to " O   HOH Z   1 " =    1.832
peak=    3.308 closest distance to " CB  ASN A 142 " =    0.951
peak=    3.308 closest distance to " CE1 TYR A 186 " =    1.218
peak=    3.302 closest distance to " O   HOH Z  64 " =    2.374
peak=    3.302 closest distance to " O   HOH Z  30 " =    2.206
peak=    3.301 closest distance to " O   HOH Z 359 " =    3.632
peak=    3.299 closest distance to " O   HOH Z 371 " =    2.390
peak=    3.299 closest distance to " NH2BARG A 145 " =    2.053
peak=    3.296 closest distance to " O   HOH Z 222 " =    2.287
peak=    3.296 closest distance to " CE AMET A  47 " =    1.378
peak=    3.296 closest distance to " CG  MET A 188 " =    1.295
peak=    3.292 closest distance to " O   HOH Z  22 " =    2.078
peak=    3.292 closest distance to " O   HOH Z 209 " =    1.133
peak=    3.291 closest distance to " O   HOH Z 189 " =    2.091
peak=    3.291 closest distance to " CG1BVAL A  72 " =    1.333
peak=    3.287 closest distance to " O   HOH Z 195 " =    1.455
peak=    3.285 closest distance to " O   HOH Z 427 " =    1.345
peak=    3.285 closest distance to " O   SER A  26 " =    1.509
peak=    3.284 closest distance to " O   MET A 105 " =    1.686
peak=    3.283 closest distance to " CD  ARG A 138 " =    0.946
peak=    3.283 closest distance to " CA  ALA A 295 " =    1.046
peak=    3.276 closest distance to " CA  TYR A 116 " =    1.585
peak=    3.270 closest distance to " O   HOH Z  49 " =    1.694
peak=    3.269 closest distance to " O   HOH Z 207 " =    2.173
peak=    3.266 closest distance to " CB  SER A 216 " =    0.910
peak=    3.265 closest distance to " CB  LEU A 237 " =    0.922
peak=    3.259 closest distance to " O   HOH Z 405 " =    1.555
peak=    3.256 closest distance to " O   HOH Z 194 " =    2.293
peak=    3.256 closest distance to " O   HOH Z 114 " =    1.538
peak=    3.256 closest distance to " CE  MET A  93 " =    1.506
peak=    3.255 closest distance to " CA  ALA A 154 " =    1.109
peak=    3.253 closest distance to " O   HOH Z  10 " =    1.814
peak=    3.251 closest distance to " O   HOH Z 411 " =    1.993
peak=    3.247 closest distance to " CB  ASN A  60 " =    0.840
peak=    3.246 closest distance to " CA  ALA A 114 " =    1.638
peak=    3.245 closest distance to " O   HOH Z 344 " =    2.782
peak=    3.244 closest distance to " SD  MET A 185 " =    1.486
peak=    3.243 closest distance to " CB  LEU A 300 " =    0.960
peak=    3.240 closest distance to " CA  ASP A  50 " =    1.025
peak=    3.239 closest distance to " O   HOH Z  61 " =    1.676
peak=    3.237 closest distance to " O   HOH Z 116 " =    5.593
peak=    3.233 closest distance to " CZ3 TRP A  92 " =    0.980
peak=    3.232 closest distance to " CD1 ILE A 263 " =    1.090
peak=    3.231 closest distance to " O   HOH Z 158 " =    2.543
peak=    3.229 closest distance to " CD1 LEU A 228 " =    1.522
peak=    3.228 closest distance to " O   HOH Z 134 " =    2.046
peak=    3.227 closest distance to " CB  ALA A  43 " =    1.147
peak=    3.225 closest distance to " O   HOH Z 389 " =    1.696
peak=    3.225 closest distance to " O   HOH Z 110 " =    1.906
peak=    3.223 closest distance to " CA  SER A  87 " =    0.957
peak=    3.223 closest distance to " CB  GLN A  88 " =    1.392
peak=    3.220 closest distance to " CB  THR A 157 " =    0.989
peak=    3.219 closest distance to " O   HOH Z 234 " =    2.137
peak=    3.217 closest distance to " O   HOH Z  80 " =    1.599
peak=    3.216 closest distance to " O   ALA A 158 " =    1.276
peak=    3.216 closest distance to " O   ALA A  10 " =    1.508
peak=    3.214 closest distance to " CB  LYS A 117 " =    1.178
peak=    3.213 closest distance to " O   HOH Z 422 " =    2.641
peak=    3.209 closest distance to " CA  SER A  99 " =    0.761
peak=    3.205 closest distance to " CB  SER A 273 " =    0.830
peak=    3.202 closest distance to " CB  PHE A 225 " =    1.358
peak=    3.199 closest distance to " O   HOH Z  33 " =    1.496
peak=    3.194 closest distance to " NH2AARG A 190 " =    1.546
peak=    3.192 closest distance to " O   HOH Z  15 " =    1.426
peak=    3.189 closest distance to " O   HOH Z 109 " =    2.510
peak=    3.187 closest distance to " O   HOH Z  43 " =    1.808
peak=    3.186 closest distance to " O   HOH Z 248 " =    1.555
peak=    3.185 closest distance to " CH2 TRP A 274 " =    2.391
peak=    3.184 closest distance to " O   HOH Z 116 " =    3.109
peak=    3.184 closest distance to " O   HOH Z  76 " =    1.339
peak=    3.184 closest distance to " CE3 TRP A  85 " =    1.017
peak=    3.183 closest distance to " O   HOH Z  69 " =    2.489
peak=    3.183 closest distance to " O   HOH Z 128 " =    1.892
peak=    3.180 closest distance to " CB  MET A  47 " =    1.419
peak=    3.179 closest distance to " O   HOH Z 214 " =    1.482
peak=    3.173 closest distance to " O   HOH Z 373 " =    1.244
peak=    3.171 closest distance to " CA  ASN A 215 " =    1.281
peak=    3.167 closest distance to " O   HOH Z  40 " =    2.350
peak=    3.165 closest distance to " CB  TRP A 150 " =    1.340
peak=    3.164 closest distance to " CA  LYS A  48 " =    1.428
peak=    3.162 closest distance to " O   HOH Z 253 " =    1.816
peak=    3.159 closest distance to " O   HOH Z 303 " =    1.664
peak=    3.157 closest distance to " O   HOH Z  59 " =    2.266
peak=    3.153 closest distance to " O   HOH Z 153 " =    3.537
peak=    3.153 closest distance to " OG  SER A  62 " =    2.840
peak=    3.140 closest distance to " O   HOH Z 425 " =    2.050
peak=    3.133 closest distance to " OE1 GLN A 240 " =    1.515
peak=    3.132 closest distance to " O   HOH Z 389 " =    1.279
peak=    3.132 closest distance to " O   HOH Z  30 " =    1.343
peak=    3.124 closest distance to " O   HOH Z 222 " =    1.017
peak=    3.122 closest distance to " CA  ASN A 284 " =    1.161
peak=    3.121 closest distance to " O   GLY A  57 " =    2.523
peak=    3.117 closest distance to " O   HOH Z 423 " =    1.762
peak=    3.116 closest distance to " O   HOH Z  99 " =    3.007
peak=    3.100 closest distance to " O   HOH Z 108 " =    1.577
peak=    3.098 closest distance to " CB  ALA A 161 " =    0.931
peak=    3.096 closest distance to " O   HOH Z 172 " =    3.318
peak=    3.096 closest distance to " O   HOH Z 132 " =    2.458
peak=    3.092 closest distance to " O   HOH Z 426 " =    1.126
peak=    3.091 closest distance to " O   HOH Z 329 " =    3.166
peak=    3.089 closest distance to " CA  ALA A 248 " =    1.196
peak=    3.089 closest distance to " O   HOH Z 423 " =    1.076
peak=    3.086 closest distance to " OD1 ASN A  45 " =    1.435
peak=    3.078 closest distance to " N   GLN A 278 " =    1.018
peak=    3.073 closest distance to " CD2 HIS A  81 " =    1.222
peak=    3.072 closest distance to " CA  THR A 221 " =    0.991
peak=    3.069 closest distance to " O   HOH Z 102 " =    1.907
peak=    3.064 closest distance to " CB  ASN A 187 " =    1.106
peak=    3.060 closest distance to " O   HOH Z 116 " =    1.225
peak=    3.060 closest distance to " CB  TYR A 116 " =    0.925
peak=    3.059 closest distance to " NZ  LYS A  76 " =    1.506

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 184         
Filter by distance & map next to the model:
   mapped sites are within: 0.521 - 5.422
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 181 from: 184
   mapped sites are within: 0.716 - 5.422

peak=   -4.795 closest distance to " CG2 VAL A 230 " =    0.934
peak=   -4.725 closest distance to " CD  ARG A 138 " =    1.269
peak=   -4.543 closest distance to " O   PRO A 198 " =    1.322
peak=   -4.494 closest distance to " CD  ARG A  14 " =    3.159
peak=   -4.474 closest distance to " CD  ARG A 156 " =    1.926
peak=   -4.407 closest distance to " O   HOH Z 198 " =    2.223
peak=   -4.291 closest distance to " OG ASER A 134 " =    1.116
peak=   -4.248 closest distance to " NH2 ARG A  79 " =    1.843
peak=   -4.223 closest distance to " O   HOH Z 377 " =    1.838
peak=   -4.208 closest distance to " O   HOH Z 266 " =    4.399
peak=   -4.157 closest distance to " O   HOH Z  43 " =    1.859
peak=   -4.130 closest distance to " O   HOH Z 388 " =    1.722
peak=   -4.104 closest distance to " O   HOH Z 231 " =    1.498
peak=   -4.040 closest distance to " CB  PRO A 243 " =    2.628
peak=   -3.973 closest distance to " CE2 TYR A  30 " =    2.823
peak=   -3.972 closest distance to " CD  GLN A  88 " =    0.900
peak=   -3.957 closest distance to " OG BSER A 134 " =    1.236
peak=   -3.952 closest distance to " O   HOH Z 298 " =    1.415
peak=   -3.945 closest distance to " O   HOH Z 407 " =    3.160
peak=   -3.933 closest distance to " O   SER A 135 " =    1.559
peak=   -3.909 closest distance to " CB  PRO A 163 " =    2.512
peak=   -3.899 closest distance to " O   HOH Z  98 " =    1.696
peak=   -3.853 closest distance to " CG  ARG A 138 " =    0.893
peak=   -3.840 closest distance to " CB  ASP A  27 " =    2.465
peak=   -3.836 closest distance to " O   HOH Z 166 " =    1.405
peak=   -3.825 closest distance to " O   HOH Z 385 " =    0.844
peak=   -3.814 closest distance to " O   HOH Z 350 " =    1.992
peak=   -3.810 closest distance to " O   HOH Z 365 " =    1.112
peak=   -3.805 closest distance to " NH2AARG A 275 " =    5.364
peak=   -3.793 closest distance to " CA  GLY A  35 " =    2.001
peak=   -3.761 closest distance to " CG  MET A 105 " =    0.915
peak=   -3.759 closest distance to " CD  LYS A 289 " =    2.503
peak=   -3.750 closest distance to " O   HOH Z 111 " =    0.970
peak=   -3.747 closest distance to " CB  ALA A 227 " =    2.389
peak=   -3.721 closest distance to " CD1 LEU A 101 " =    2.279
peak=   -3.716 closest distance to " CG2 THR A   4 " =    1.903
peak=   -3.714 closest distance to " OD1 ASN A  39 " =    2.068
peak=   -3.703 closest distance to " CA  GLY A 133 " =    1.935
peak=   -3.703 closest distance to " O   HOH Z  92 " =    1.592
peak=   -3.699 closest distance to " O   GLY A  98 " =    1.923
peak=   -3.675 closest distance to " O   GLY A  80 " =    2.427
peak=   -3.658 closest distance to " O   HOH Z 134 " =    2.315
peak=   -3.656 closest distance to " C   ASN A 187 " =    1.791
peak=   -3.652 closest distance to " O   PRO A 163 " =    1.947
peak=   -3.650 closest distance to " O   HOH Z 292 " =    4.488
peak=   -3.629 closest distance to " OD2 ASP A  50 " =    1.432
peak=   -3.623 closest distance to " O   HOH Z 410 " =    2.199
peak=   -3.617 closest distance to " O   HOH Z  63 " =    1.081
peak=   -3.616 closest distance to " N   HIS A 115 " =    1.885
peak=   -3.601 closest distance to " O   HOH Z 435 " =    1.712
peak=   -3.598 closest distance to " O   HOH Z 290 " =    1.106
peak=   -3.592 closest distance to " C   ASN A 285 " =    2.238
peak=   -3.591 closest distance to " O   HOH Z  93 " =    2.157
peak=   -3.588 closest distance to " O   HOH Z 111 " =    4.568
peak=   -3.580 closest distance to " CZ  PHE A  59 " =    1.523
peak=   -3.572 closest distance to " O   ALA A  51 " =    1.548
peak=   -3.559 closest distance to " O   VAL A 197 " =    1.405
peak=   -3.546 closest distance to " O   HOH Z 427 " =    1.580
peak=   -3.543 closest distance to " CE2 PHE A 218 " =    2.488
peak=   -3.533 closest distance to " N   GLN A  58 " =    1.856
peak=   -3.529 closest distance to " N   ALA A 248 " =    1.653
peak=   -3.519 closest distance to " CB  ASN A 301 " =    2.058
peak=   -3.485 closest distance to " O   HOH Z  88 " =    2.362
peak=   -3.483 closest distance to " O   HOH Z 231 " =    1.235
peak=   -3.481 closest distance to " N   GLN A  77 " =    1.556
peak=   -3.481 closest distance to " O   ALA A 158 " =    0.939
peak=   -3.479 closest distance to " CB  ALA A   7 " =    2.075
peak=   -3.469 closest distance to " O   ILE A  49 " =    1.689
peak=   -3.460 closest distance to " CB  VAL A 230 " =    1.138
peak=   -3.456 closest distance to " O   TYR A  30 " =    2.851
peak=   -3.448 closest distance to " OG  SER A  87 " =    1.639
peak=   -3.447 closest distance to " O   HOH Z 207 " =    1.907
peak=   -3.443 closest distance to " O   HOH Z 138 " =    0.783
peak=   -3.443 closest distance to " CB  CYS A 201 " =    2.481
peak=   -3.429 closest distance to " CD1 LEU A 255 " =    2.899
peak=   -3.429 closest distance to " CG2 VAL A 257 " =    2.916
peak=   -3.429 closest distance to " OE1 GLN A  88 " =    1.104
peak=   -3.428 closest distance to " O   HOH Z 166 " =    1.981
peak=   -3.426 closest distance to " O   HOH Z  40 " =    4.064
peak=   -3.422 closest distance to " NH1AARG A 102 " =    2.199
peak=   -3.401 closest distance to " CB  ALA A 227 " =    2.267
peak=   -3.400 closest distance to " O   HOH Z  44 " =    1.934
peak=   -3.397 closest distance to " CD1 ILE A 151 " =    2.320
peak=   -3.379 closest distance to " OG  SER A  87 " =    1.287
peak=   -3.374 closest distance to " OG  SER A 245 " =    1.315
peak=   -3.373 closest distance to " CB  PHE A 283 " =    2.528
peak=   -3.368 closest distance to " OG  SER A   3 " =    1.571
peak=   -3.367 closest distance to " CG  LYS A 193 " =    2.434
peak=   -3.366 closest distance to " CG  ASP A  50 " =    0.872
peak=   -3.365 closest distance to " CG  PRO A 163 " =    2.524
peak=   -3.361 closest distance to " O   HOH Z  98 " =    1.493
peak=   -3.353 closest distance to " CG  ASP A 231 " =    0.802
peak=   -3.352 closest distance to " O   HOH Z  13 " =    1.293
peak=   -3.350 closest distance to " O   HOH Z 250 " =    1.376
peak=   -3.350 closest distance to " CG  GLU A 277 " =    1.233
peak=   -3.349 closest distance to " O   ALA A   1 " =    1.195
peak=   -3.348 closest distance to " N   PHE A 283 " =    1.794
peak=   -3.345 closest distance to " O   VAL A  67 " =    2.790
peak=   -3.343 closest distance to " O   HOH Z 165 " =    2.196
peak=   -3.343 closest distance to " O   HOH Z 234 " =    4.226
peak=   -3.336 closest distance to " N   ALA A  84 " =    1.704
peak=   -3.334 closest distance to " O   HOH Z 221 " =    1.269
peak=   -3.327 closest distance to " O   VAL A  67 " =    2.737
peak=   -3.325 closest distance to " O   GLY A  57 " =    1.281
peak=   -3.323 closest distance to " CD  PRO A 198 " =    1.408
peak=   -3.322 closest distance to " O   HOH Z 392 " =    0.716
peak=   -3.321 closest distance to " O   HOH Z 438 " =    0.780
peak=   -3.319 closest distance to " O   HOH Z 275 " =    1.693
peak=   -3.310 closest distance to " N   SER A 276 " =    1.152
peak=   -3.308 closest distance to " O   VAL A 197 " =    1.070
peak=   -3.308 closest distance to " OH  TYR A 214 " =    1.246
peak=   -3.307 closest distance to " ND2 ASN A  60 " =    1.285
peak=   -3.305 closest distance to " C   LEU A 143 " =    1.363
peak=   -3.303 closest distance to " OH  TYR A 169 " =    0.985
peak=   -3.301 closest distance to " CD1 ILE A 239 " =    2.407
peak=   -3.299 closest distance to " NE2 GLN A 194 " =    2.828
peak=   -3.299 closest distance to " ND2 ASN A  45 " =    1.030
peak=   -3.294 closest distance to " O   HOH Z 138 " =    0.938
peak=   -3.293 closest distance to " OG  SER A 206 " =    1.913
peak=   -3.291 closest distance to " CB  ALA A 248 " =    1.887
peak=   -3.291 closest distance to " O   ALA A 161 " =    1.737
peak=   -3.287 closest distance to " O   HOH Z 256 " =    1.586
peak=   -3.286 closest distance to " O   HOH Z 117 " =    0.771
peak=   -3.284 closest distance to " OG1 THR A 178 " =    1.065
peak=   -3.283 closest distance to " CB  SER A 134 " =    1.726
peak=   -3.283 closest distance to " CB  ASN A  39 " =    2.199
peak=   -3.278 closest distance to " NH2 ARG A  66 " =    2.896
peak=   -3.278 closest distance to " OD1 ASP A 200 " =    1.138
peak=   -3.276 closest distance to " CG  ARG A 219 " =    2.327
peak=   -3.276 closest distance to " O   HOH Z 189 " =    2.499
peak=   -3.260 closest distance to " CB  ALA A 100 " =    2.452
peak=   -3.260 closest distance to " O   SER A 146 " =    0.998
peak=   -3.255 closest distance to " O   HOH Z 339 " =    1.666
peak=   -3.252 closest distance to " C   GLN A 240 " =    2.378
peak=   -3.252 closest distance to " CE  MET A  93 " =    1.177
peak=   -3.244 closest distance to " O   HOH Z 359 " =    1.761
peak=   -3.243 closest distance to " CB  ALA A  51 " =    1.827
peak=   -3.242 closest distance to " OE2 GLU A 152 " =    0.992
peak=   -3.239 closest distance to " C   ARG A 190 " =    1.052
peak=   -3.233 closest distance to " CB  TRP A  85 " =    2.418
peak=   -3.231 closest distance to " O   TRP A  70 " =    1.414
peak=   -3.229 closest distance to " O   HOH Z 130 " =    0.953
peak=   -3.225 closest distance to " CD1 TRP A 274 " =    1.550
peak=   -3.221 closest distance to " CE3 TRP A 150 " =    1.971
peak=   -3.219 closest distance to " OD2 ASP A 171 " =    1.731
peak=   -3.210 closest distance to " O   HOH Z 385 " =    1.131
peak=   -3.209 closest distance to " CB  TYR A 172 " =    2.112
peak=   -3.208 closest distance to " OG  SER A  97 " =    2.151
peak=   -3.206 closest distance to " CE  LYS A  76 " =    2.902
peak=   -3.205 closest distance to " O   HOH Z  37 " =    1.415
peak=   -3.202 closest distance to " O   HOH Z 211 " =    1.180
peak=   -3.195 closest distance to " CG  LEU A 228 " =    1.003
peak=   -3.194 closest distance to " OD1 ASN A 301 " =    2.138
peak=   -3.193 closest distance to " O   HOH Z 103 " =    1.813
peak=   -3.183 closest distance to " C   ASP A 124 " =    1.064
peak=   -3.181 closest distance to " NH1 ARG A 195 " =    2.319
peak=   -3.178 closest distance to " O   HOH Z 317 " =    2.985
peak=   -3.177 closest distance to " C   ARG A 102 " =    1.531
peak=   -3.170 closest distance to " CD2 LEU A   5 " =    1.072
peak=   -3.161 closest distance to " C   HIS A 108 " =    1.166
peak=   -3.159 closest distance to " O   HOH Z 158 " =    2.047
peak=   -3.157 closest distance to " O   PRO A 163 " =    1.140
peak=   -3.153 closest distance to " OD1 ASP A 191 " =    1.917
peak=   -3.150 closest distance to " C   VAL A 265 " =    0.910
peak=   -3.148 closest distance to " CG  LEU A 281 " =    1.691
peak=   -3.138 closest distance to " O   HOH Z  91 " =    1.497
peak=   -3.136 closest distance to " O   HOH Z 193 " =    1.827
peak=   -3.125 closest distance to " O   SER A  22 " =    1.403
peak=   -3.124 closest distance to " O   HOH Z 191 " =    5.422
peak=   -3.123 closest distance to " CD  ARG A 139 " =    1.662
peak=   -3.123 closest distance to " O   HOH Z 155 " =    1.227
peak=   -3.121 closest distance to " CD  GLU A 152 " =    2.467
peak=   -3.120 closest distance to " CG  TRP A 266 " =    1.420
peak=   -3.112 closest distance to " O   HOH Z 137 " =    1.577
peak=   -3.099 closest distance to " CA  ALA A 114 " =    2.287
peak=   -3.094 closest distance to " C   ALA A 158 " =    1.238
peak=   -3.089 closest distance to " O   HOH Z 424 " =    1.420
peak=   -3.079 closest distance to " CZ  PHE A  16 " =    1.430
peak=   -3.055 closest distance to " O   HOH Z 274 " =    2.774
peak=   -3.037 closest distance to " O   SER A  62 " =    1.591
peak=   -3.016 closest distance to " O   HOH Z 179 " =    1.676

================= 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    :  0.5022 0.4909   6.298675e+00   6.294275e+00
   1_bss:  0.4930 0.4804   6.293777e+00   6.286955e+00
   1_xyz:  0.4311 0.4563   6.224019e+00   6.251394e+00
   1_adp:  0.3959 0.4549   6.181658e+00   6.249264e+00
   1_occ:  0.3957 0.4555   6.181353e+00   6.249142e+00
   2_bss:  0.3933 0.4490   6.181715e+00   6.246761e+00
   2_xyz:  0.3278 0.3882   6.043837e+00   6.159839e+00
   2_adp:  0.3094 0.3712   6.005991e+00   6.135407e+00
   2_occ:  0.3092 0.3710   6.005933e+00   6.135521e+00
   3_bss:  0.3076 0.3698   6.005965e+00   6.135519e+00
   3_xyz:  0.2313 0.2955   5.775940e+00   5.954410e+00
   3_adp:  0.2047 0.2756   5.684812e+00   5.894641e+00
   3_occ:  0.2045 0.2754   5.683700e+00   5.893481e+00
   4_bss:  0.2038 0.2733   5.680595e+00   5.889337e+00
   4_xyz:  0.1606 0.2191   5.469805e+00   5.700091e+00
   4_adp:  0.1483 0.2006   5.390344e+00   5.616113e+00
   4_occ:  0.1480 0.2002   5.389188e+00   5.614976e+00
   5_bss:  0.1482 0.2004   5.388888e+00   5.613529e+00
   5_xyz:  0.1277 0.1738   5.250085e+00   5.486990e+00
   5_adp:  0.1225 0.1696   5.219167e+00   5.462808e+00
   5_occ:  0.1224 0.1695   5.218426e+00   5.461819e+00
   5_bss:  0.1228 0.1704   5.220599e+00   5.464307e+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:  0.357   0.000   7.157   8.705   9.044   0.000   0.000   0.000
   1_xyz:  0.357   0.000   7.157   8.705   9.044   0.000   0.000   0.000
   1_adp:  0.357   0.000   7.157   8.705   9.044   0.000   0.000   0.000
   1_occ:  0.357   0.000   7.157   8.705   9.044   0.000   0.000   0.000
   2_bss:  0.382  50.000   3.517   4.337   5.622   0.000   0.000   0.000
   2_xyz:  0.382  50.000   3.517   4.337   5.622   0.000   0.000   0.000
   2_adp:  0.382  50.000   3.517   4.337   5.622   0.000   0.000   0.000
   2_occ:  0.382  50.000   3.517   4.337   5.622   0.000   0.000   0.000
   3_bss:  0.353  50.000   1.867   2.010   3.290   0.000   0.000   0.000
   3_xyz:  0.353  50.000   1.867   2.010   3.290   0.000   0.000   0.000
   3_adp:  0.353  50.000   1.867   2.010   3.290   0.000   0.000   0.000
   3_occ:  0.353  50.000   1.867   2.010   3.290   0.000   0.000   0.000
   4_bss:  0.336  46.151   0.912   0.661   1.642   0.000   0.000   0.000
   4_xyz:  0.336  46.151   0.912   0.661   1.642   0.000   0.000   0.000
   4_adp:  0.336  46.151   0.912   0.661   1.642   0.000   0.000   0.000
   4_occ:  0.336  46.151   0.912   0.661   1.642   0.000   0.000   0.000
   5_bss:  0.321  41.156   0.438   0.086   0.943   0.000   0.000   0.000
   5_xyz:  0.321  41.156   0.438   0.086   0.943   0.000   0.000   0.000
   5_adp:  0.321  41.156   0.438   0.086   0.943   0.000   0.000   0.000
   5_occ:  0.321  41.156   0.438   0.086   0.943   0.000   0.000   0.000
   5_bss:  0.317  41.646  -0.051  -0.403   0.454   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  62.439 0.3622  0.4393    79188.247
   1_bss:  62.520 0.3595  0.5424    76245.513
   1_xyz:  55.630 0.4475  0.6664    63488.513
   1_adp:  54.807 0.4581  0.7455    62963.574
   1_occ:  54.910 0.4568  0.7431    63133.885
   2_bss:  54.368 0.4636  0.6710    62497.598
   2_xyz:  43.611 0.5975  0.8553    43399.780
   2_adp:  40.953 0.6301  0.9121    39591.810
   2_occ:  40.989 0.6296  0.9110    39623.987
   3_bss:  40.845 0.6312  0.8474    39460.773
   3_xyz:  30.453 0.7524  0.9778    23277.942
   3_adp:  27.642 0.7837  0.9967    20053.059
   3_occ:  27.590 0.7843  0.9968    19984.107
   4_bss:  27.400 0.7860  0.9511    19683.263
   4_xyz:  21.566 0.8461  0.9898    12566.233
   4_adp:  19.149 0.8702  0.9971    10576.956
   4_occ:  19.112 0.8706  0.9969    10525.653
   5_bss:  19.069 0.8709  0.9755    10480.894
   5_xyz:  15.993 0.8981  0.9906     7698.783
   5_adp:  15.402 0.9035  0.9894     7340.329
   5_occ:  15.377 0.9037  0.9894     7324.592
   5_bss:  15.437 0.9033  0.9888     7409.478
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.3109e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.3109e+01
   1_xyz:   1.696  0.013  0.106 18.460  0.007  4.106   1.4471e-01
   1_adp:   1.696  0.013  0.106 18.460  0.007  4.106   1.4471e-01
   1_occ:   1.696  0.013  0.106 18.460  0.007  4.106   1.4471e-01
   2_bss:   1.696  0.013  0.106 18.460  0.007  4.106   1.4471e-01
   2_xyz:   1.161  0.009  0.079 16.232  0.005  4.106   8.9955e-02
   2_adp:   1.161  0.009  0.079 16.232  0.005  4.106   8.9955e-02
   2_occ:   1.161  0.009  0.079 16.232  0.005  4.106   8.9955e-02
   3_bss:   1.161  0.009  0.079 16.232  0.005  4.106   8.9955e-02
   3_xyz:   1.201  0.009  0.082 15.894  0.005  4.123   8.9077e-02
   3_adp:   1.201  0.009  0.082 15.894  0.005  4.123   8.9077e-02
   3_occ:   1.201  0.009  0.082 15.894  0.005  4.123   8.9077e-02
   4_bss:   1.201  0.009  0.082 15.894  0.005  4.123   8.9077e-02
   4_xyz:   1.013  0.006  0.074 15.460  0.003  4.108   6.2725e-02
   4_adp:   1.013  0.006  0.074 15.460  0.003  4.108   6.2725e-02
   4_occ:   1.013  0.006  0.074 15.460  0.003  4.108   6.2725e-02
   5_bss:   1.013  0.006  0.074 15.460  0.003  4.108   6.2725e-02
   5_xyz:   1.047  0.007  0.077 15.489  0.004  4.112   6.4723e-02
   5_adp:   1.047  0.007  0.077 15.489  0.004  4.112   6.4723e-02
   5_occ:   1.047  0.007  0.077 15.489  0.004  4.112   6.4723e-02
   5_bss:   1.047  0.007  0.077 15.489  0.004  4.112   6.4723e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8828e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8828e+00
   1_xyz:  13.292  0.167  0.450 84.476  0.049  2.115   9.6977e-02
   1_adp:  13.292  0.167  0.450 84.476  0.049  2.115   9.6977e-02
   1_occ:  13.292  0.167  0.450 84.476  0.049  2.115   9.6977e-02
   2_bss:  13.292  0.167  0.450 84.476  0.049  2.115   9.6977e-02
   2_xyz:   6.760  0.093  0.264 78.645  0.042  2.249   1.1925e-01
   2_adp:   6.760  0.093  0.264 78.645  0.042  2.249   1.1925e-01
   2_occ:   6.760  0.093  0.264 78.645  0.042  2.249   1.1925e-01
   3_bss:   6.760  0.093  0.264 78.645  0.042  2.249   1.1925e-01
   3_xyz:   8.685  0.055  0.294 84.672  0.039  2.278   1.7895e-01
   3_adp:   8.685  0.055  0.294 84.672  0.039  2.278   1.7895e-01
   3_occ:   8.685  0.055  0.294 84.672  0.039  2.278   1.7895e-01
   4_bss:   8.685  0.055  0.294 84.672  0.039  2.278   1.7895e-01
   4_xyz:   6.853  0.046  0.378 84.750  0.020  2.375   4.1525e-02
   4_adp:   6.853  0.046  0.378 84.750  0.020  2.375   4.1525e-02
   4_occ:   6.853  0.046  0.378 84.750  0.020  2.375   4.1525e-02
   5_bss:   6.853  0.046  0.378 84.750  0.020  2.375   4.1525e-02
   5_xyz:   7.584  0.054  0.446 82.602  0.030  2.273   4.6394e-02
   5_adp:   7.584  0.054  0.446 82.602  0.030  2.273   4.6394e-02
   5_occ:   7.584  0.054  0.446 82.602  0.030  2.273   4.6394e-02
   5_bss:   7.584  0.054  0.446 82.602  0.030  2.273   4.6394e-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: 102.63   0.00  15.11 102.63   0.00  13.47  95.36   0.00  24.03
   1_occ: 102.63   0.00  15.11 102.63   0.00  13.47  95.36   0.00  24.03
   2_bss: 102.63   0.00  15.11 102.63   0.00  13.47  95.36   0.00  24.03
   2_xyz: 102.63   0.00  15.11 102.63   0.00  13.47  95.36   0.00  24.03
   2_adp: 100.97   0.00  15.28 100.97   0.00  12.68  90.44   0.00  29.48
   2_occ: 100.97   0.00  15.28 100.97   0.00  12.68  90.44   0.00  29.48
   3_bss: 100.97   0.00  15.28 100.97   0.00  12.68  90.44   0.00  29.48
   3_xyz: 100.97   0.00  15.28 100.97   0.00  12.68  90.44   0.00  29.48
   3_adp: 103.30   0.00  16.01 103.30   0.00  11.56  94.32   1.52  40.21
   3_occ: 103.30   0.00  16.01 103.30   0.00  11.56  94.32   1.52  40.21
   4_bss: 103.30   0.00  16.01 103.30   0.00  11.56  94.32   1.52  40.21
   4_xyz: 103.30   0.00  16.01 103.30   0.00  11.56  94.32   1.52  40.21
   4_adp: 100.92   0.00  15.35 100.92   0.00  10.70  90.84   3.76  40.65
   4_occ: 100.92   0.00  15.35 100.92   0.00  10.70  90.84   3.76  40.65
   5_bss: 100.92   0.00  15.35 100.92   0.00  10.70  90.84   3.76  40.65
   5_xyz: 100.92   0.00  15.35 100.92   0.00  10.70  90.84   3.76  40.65
   5_adp: 106.15   0.00  15.35 106.15   0.00  10.58  96.30   4.01  41.35
   5_occ: 106.15   0.00  15.35 106.15   0.00  10.58  96.30   4.01  41.35
   5_bss: 106.64   0.49  15.84 106.64   0.49  11.07  96.79   4.50  41.84
------------------------------------------------------------------------
 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:    1.255    0.019    0.408
   1_adp:    1.255    0.019    0.408
   1_occ:    1.255    0.019    0.408
   2_bss:    1.255    0.019    0.408
   2_xyz:    1.680    0.053    0.563
   2_adp:    1.680    0.053    0.563
   2_occ:    1.680    0.053    0.563
   3_bss:    1.680    0.053    0.563
   3_xyz:    1.638    0.052    0.706
   3_adp:    1.638    0.052    0.706
   3_occ:    1.638    0.052    0.706
   4_bss:    1.638    0.052    0.706
   4_xyz:    1.941    0.034    0.795
   4_adp:    1.941    0.034    0.795
   4_occ:    1.941    0.034    0.795
   5_bss:    1.941    0.034    0.795
   5_xyz:    2.072    0.094    0.828
   5_adp:    2.072    0.094    0.828
   5_occ:    2.072    0.094    0.828
   5_bss:    2.072    0.094    0.828
------------------------------------------------------------------------

CPU time actual refinement: 305.90


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_869/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_869/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_869/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_869/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_869/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 305.77 
  Macro-tasks:
    bulk solvent and scale       = 35.14  
    individual site refinement   = 130.54 
    weights calculation          = 27.23  
    collect and process          = 5.34   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 198.35 
  Micro-tasks:
    mask                            = 2.60   
    f_calc                          = 98.89  
    alpha_beta                      = 6.67   
    target                          = 0.92   
    gradients_wrt_atomic_parameters = 107.19 
    fmodel                         = 6.10   
    r_factors                      = 0.13   
    phase_errors                   = 8.29   
    foms                           = 0.23   
    TOTAL for micro-tasks          = 231.02 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.259 micro seconds
Total CPU time: 5.29 minutes
from_scatterers_fft:    660 calls, 98.55 s
gradients_fft:          604 calls, 95.50 s

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

# Date 2008-01-16 Time 02:37:22 PST -0800 (1200479842.54 s)
Start R-work = 0.5022, R-free = 0.4909 (no bulk solvent and anisotropic scale)
Final R-work = 0.1385, R-free = 0.1859 (no bulk solvent and anisotropic scale)

Start R-work = 0.4930, R-free = 0.4804
Final R-work = 0.1228, R-free = 0.1704