# Date 2008-01-16 Time 02:14:14 PST -0800 (1200478454.77 s)
#phil __OFF__

Command line arguments: "../747.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 19782
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 747

-------------------------------------------------------------------------------
  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: (70.6012, 45.9914, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 45.9914, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1485 1.96359
Completeness in resolution range: 0.925363
Completeness with d_max=infinity: 0.922704

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1485
                             d_min =   1.9636

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: (70.6012, 45.9914, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1485 1.96359
Completeness in resolution range: 0.925363
Completeness with d_max=infinity: 0.922704

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1489 -  4.2031 [2220/2246]  1997   223  10.0%
  bin  2:  4.2031 -  3.3480 [2141/2161]  1930   211   9.9%
  bin  3:  3.3480 -  2.9283 [2101/2120]  1892   209   9.9%
  bin  4:  2.9283 -  2.6621 [2102/2132]  1881   221  10.5%
  bin  5:  2.6621 -  2.4722 [2075/2094]  1871   204   9.8%
  bin  6:  2.4722 -  2.3270 [2072/2097]  1864   208  10.0%
  bin  7:  2.3270 -  2.2108 [2046/2074]  1842   204  10.0%
  bin  8:  2.2108 -  2.1148 [2065/2101]  1854   211  10.2%
  bin  9:  2.1148 -  2.0336 [2005/2078]  1817   188   9.4%
  bin 10:  2.0336 -  1.9636 [ 762/2066]   682    80  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_747/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.69 -     2.33: 28
        2.33 -     2.97: 1772
        2.97 -     3.62: 4565
        3.62 -     4.26: 9115
        4.26 -     4.90: 12711
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.688 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.700 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.800 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.828 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28186 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_747/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_747/model_refine_001.geo

CPU time processing inputs: 9.14


============================ 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 = 70.60125 45.9914 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5120   r_free= 0.5023   ksol= 0.00   Bsol= 0.00   scale= 0.765    |
|                                                                             |
| 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:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.311265                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.6887 0.99   1438  158 0.4380 0.4148      6.6727      6.6529|
|  2:  4.6887 -  3.7400 0.99   1391  158 0.4528 0.4358      6.8735      6.8524|
|  3:  3.7400 -  3.2727 0.99   1368  149 0.4801 0.4396      6.7131      6.6772|
|  4:  3.2727 -  2.9759 0.99   1351  153 0.5174 0.4897      6.5644      6.5086|
|  5:  2.9759 -  2.7640 0.99   1351  149 0.5483 0.5409      6.3805      6.4226|
|  6:  2.7640 -  2.6019 0.99   1340  146 0.5452 0.5665      6.2844      6.2179|
|  7:  2.6019 -  2.4722 0.99   1332  155 0.5413 0.4949       6.254      6.1933|
|  8:  2.4722 -  2.3650 0.98   1325  151 0.5591 0.5436      6.1813      6.1727|
|  9:  2.3650 -  2.2742 0.98   1313  140 0.5376 0.5638      6.1334      6.2325|
| 10:  2.2742 -  2.1960 1.00   1354  147 0.5358 0.5716      6.0854      6.0896|
| 11:  2.1960 -  2.1275 0.98   1318  147 0.5223 0.5434      6.0327      6.0471|
| 12:  2.1275 -  2.0669 0.98   1306  141 0.5525 0.5574      5.9375       5.941|
| 13:  2.0669 -  2.0126 0.87   1145  131 0.5569 0.5632      5.9034      5.7992|
| 14:  2.0126 -  1.9636 0.23    298   34 0.5206 0.4571      5.8383       5.854|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1489 -  4.6887  1438   158  0.66  37.49   0.77     0.71      84370.85|
|  2:  4.6887 -  3.7400  1391   158  0.66  38.46   0.83     0.74     126416.26|
|  3:  3.7400 -  3.2727  1368   149  0.53  49.66   0.82     0.67     135081.57|
|  4:  3.2727 -  2.9759  1351   153  0.42  57.76   0.74     0.53     120648.22|
|  5:  2.9759 -  2.7640  1351   149  0.32  65.86   0.70     0.41      95440.67|
|  6:  2.7640 -  2.6019  1340   146  0.28  68.90   0.69     0.34      82956.59|
|  7:  2.6019 -  2.4722  1332   155  0.23  72.82   0.72     0.27      75913.35|
|  8:  2.4722 -  2.3650  1325   151  0.21  74.34   0.70     0.26      69626.63|
|  9:  2.3650 -  2.2742  1313   140  0.17  77.55   0.71     0.20      65815.17|
| 10:  2.2742 -  2.1960  1354   147  0.16  77.76   0.73     0.20      58321.06|
| 11:  2.1960 -  2.1275  1318   147  0.13  80.01   0.75     0.17      56916.76|
| 12:  2.1275 -  2.0669  1306   141  0.16  77.79   0.71     0.22      49658.74|
| 13:  2.0669 -  2.0126  1145   131  0.20  75.13   0.71     0.27      42816.33|
| 14:  2.0126 -  1.9636   298    34  0.32  66.31   0.74     0.36      31787.24|
|alpha:            min =        0.17 max =            0.74 mean =         0.39|
|beta:             min =    31787.24 max =       135081.57 mean =     81802.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.32|
|phase err.(work): min =        0.00 max =           90.00 mean =        65.24|
|phase err.(test): min =        0.00 max =           89.91 mean =        65.50|
|-----------------------------------------------------------------------------|

============================== 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 = 24.300457             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.721   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.273397              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.770   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       35 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      172 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      693 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1501 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2641 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3911 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5054 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6526 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7679 |
|-----------------------------------------------------------------------------|
|-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 |       53.908 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       2.079 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.915)------------------------------------------|
|    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 = 11.915)------------------------------------------|
|    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: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5167   r_free= 0.5020   ksol= 0.00   Bsol= 0.00   scale= 0.737    |
|                                                                             |
| 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: 6.311681                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5043   r_free= 0.4912   ksol= 0.34   Bsol= 0.78   scale= 0.962    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.39,8.37,11.22,0.00,0.00,0.00); trace/3= 8.66                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.306676                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.626395             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.465   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.773384              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.719   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5043      final r-factor (work) = 0.4392          |
| start r-factor (free) = 0.4912      final r-factor (free) = 0.4681          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 115.7642 = 19.63 * 0.50 * 6.3034 + 1.00 * 53.9076                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 61.5205 = 19.63 * 0.50 * 6.2520 + 1.00 * 0.1680                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4392      final r-factor (work) = 0.4053          |
| start r-factor (free) = 0.4681      final r-factor (free) = 0.4702          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.1018 = 1.77 * 1.00 * 6.2520 + 1.00 * 0.0145                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.0276 = 1.77 * 1.00 * 6.2068 + 1.00 * 0.0207                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.915)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.24   17.27    None  None   None       |
|    all(noH): 2823   0      0.00    80.24   17.27    None  None   None       |
|    Sol.    : 438    0      0.00    80.24   24.50    None  None   None       |
|    Mac.    : 2385   0      0.00    79.44   15.94    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.024:  746   |   5:    40.119 -  48.142:   93        |
|      1:     8.024 -  16.048:  788   |   6:    48.142 -  56.166:   52        |
|      2:    16.048 -  24.071:  593   |   7:    56.166 -  64.190:   19        |
|      3:    24.071 -  32.095:  330   |   8:    64.190 -  72.214:   10        |
|      4:    32.095 -  40.119:  183   |   9:    72.214 -  80.237:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4053 r_free = 0.4702             target_work(ml) = 6.200         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4052 r_free = 0.4700             target_work(ml) = 6.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4052   r_free= 0.4700   ksol= 0.34   Bsol= 0.78   scale= 1.135    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.39,8.37,11.22,0.00,0.00,0.00); trace/3= 8.66                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.199895                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4024   r_free= 0.4664   ksol= 0.34   Bsol= 35.78   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.04,4.42,6.84,0.00,0.00,0.00); trace/3= 4.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.201896                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.759144              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.200  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.785878              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.051  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4024      final r-factor (work) = 0.3496          |
| start r-factor (free) = 0.4664      final r-factor (free) = 0.4255          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.4411 = 9.76 * 0.50 * 6.2040 + 1.00 * 0.1680                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.1108 = 9.76 * 0.50 * 6.1494 + 1.00 * 0.1045                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3496      final r-factor (work) = 0.3353          |
| start r-factor (free) = 0.4255      final r-factor (free) = 0.4179          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8537 = 0.79 * 1.00 * 6.1494 + 1.00 * 0.0210                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7963 = 0.79 * 1.00 * 6.0858 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.915)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.57   16.96    None  None   None       |
|    all(noH): 2823   0      0.00    83.57   16.96    None  None   None       |
|    Sol.    : 438    0      0.00    83.57   28.74    None  None   None       |
|    Mac.    : 2385   0      0.00    76.98   14.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.357:  793   |   5:    41.783 -  50.139:   87        |
|      1:     8.357 -  16.713:  832   |   6:    50.139 -  58.496:   34        |
|      2:    16.713 -  25.070:  613   |   7:    58.496 -  66.852:   16        |
|      3:    25.070 -  33.426:  300   |   8:    66.852 -  75.209:    5        |
|      4:    33.426 -  41.783:  139   |   9:    75.209 -  83.566:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3353 r_free = 0.4179             target_work(ml) = 6.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3351 r_free = 0.4184             target_work(ml) = 6.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3351   r_free= 0.4184   ksol= 0.34   Bsol= 35.78   scale= 1.085   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.04,4.42,6.84,0.00,0.00,0.00); trace/3= 4.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.077838                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3340   r_free= 0.4162   ksol= 0.34   Bsol= 55.50   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.13,1.83,4.13,0.00,0.00,0.00); trace/3= 2.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.078981                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.223183             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.491   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.597779              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.764  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3340      final r-factor (work) = 0.2598          |
| start r-factor (free) = 0.4162      final r-factor (free) = 0.3338          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.3469 = 13.22 * 0.50 * 6.0866 + 1.00 * 0.1046                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.7280 = 13.22 * 0.50 * 5.9914 + 1.00 * 0.1153                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2598      final r-factor (work) = 0.2337          |
| start r-factor (free) = 0.3338      final r-factor (free) = 0.3134          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5951 = 0.60 * 1.00 * 5.9914 + 1.00 * 0.0136                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5201 = 0.60 * 1.00 * 5.8314 + 1.00 * 0.0342                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.915)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    134.30  16.72    None  None   None       |
|    all(noH): 2823   0      0.00    134.30  16.72    None  None   None       |
|    Sol.    : 438    0      0.00    81.28   33.58    None  None   None       |
|    Mac.    : 2385   0      0.00    134.30  13.62    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 -  13.430: 1429   |   5:    67.152 -  80.582:    8        |
|      1:    13.430 -  26.861:  869   |   6:    80.582 -  94.012:    2        |
|      2:    26.861 -  40.291:  363   |   7:    94.012 - 107.443:    0        |
|      3:    40.291 -  53.721:  115   |   8:   107.443 - 120.873:    0        |
|      4:    53.721 -  67.152:   36   |   9:   120.873 - 134.303:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2337 r_free = 0.3134             target_work(ml) = 5.799         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2335 r_free = 0.3133             target_work(ml) = 5.798         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2335   r_free= 0.3133   ksol= 0.34   Bsol= 55.50   scale= 1.057   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.13,1.83,4.13,0.00,0.00,0.00); trace/3= 2.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.797671                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2332   r_free= 0.3120   ksol= 0.33   Bsol= 55.50   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.21,0.36,2.36,0.00,0.00,0.00); trace/3= 0.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.797499                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.007122              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.350  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.393457              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.671   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2332      final r-factor (work) = 0.1911          |
| start r-factor (free) = 0.3120      final r-factor (free) = 0.2586          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.6367 = 6.01 * 0.50 * 5.8336 + 1.00 * 0.1151                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.2725 = 6.01 * 0.50 * 5.7258 + 1.00 * 0.0746                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1911      final r-factor (work) = 0.1659          |
| start r-factor (free) = 0.2586      final r-factor (free) = 0.2276          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0060 = 1.39 * 1.00 * 5.7258 + 1.00 * 0.0273                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7716 = 1.39 * 1.00 * 5.5666 + 1.00 * 0.0148                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.915)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.64   16.64    None  None   None       |
|    all(noH): 2823   0      0.00    87.64   16.64    None  None   None       |
|    Sol.    : 438    0      3.19    87.64   42.52    None  None   None       |
|    Mac.    : 2385   0      0.00    83.05   11.89    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.764: 1107   |   5:    43.820 -  52.584:   97        |
|      1:     8.764 -  17.528:  924   |   6:    52.584 -  61.348:   98        |
|      2:    17.528 -  26.292:  265   |   7:    61.348 -  70.112:   39        |
|      3:    26.292 -  35.056:  148   |   8:    70.112 -  78.876:   19        |
|      4:    35.056 -  43.820:  120   |   9:    78.876 -  87.639:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1659 r_free = 0.2276             target_work(ml) = 5.501         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1657 r_free = 0.2272             target_work(ml) = 5.500         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1657   r_free= 0.2272   ksol= 0.33   Bsol= 55.50   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.21,0.36,2.36,0.00,0.00,0.00); trace/3= 0.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.500246                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1657   r_free= 0.2269   ksol= 0.32   Bsol= 55.50   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.26,-0.43,1.84,-0.00,0.00,0.00); trace/3= 0.38                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.497483                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.320010              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.596  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.526157              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.947  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1657      final r-factor (work) = 0.1482          |
| start r-factor (free) = 0.2269      final r-factor (free) = 0.2047          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5330 = 2.32 * 0.50 * 5.5675 + 1.00 * 0.0746                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3871 = 2.32 * 0.50 * 5.4566 + 1.00 * 0.0574                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1482      final r-factor (work) = 0.1420          |
| start r-factor (free) = 0.2047      final r-factor (free) = 0.1985          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.7989 = 2.53 * 1.00 * 5.4566 + 1.00 * 0.0147                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.6126 = 2.53 * 1.00 * 5.3822 + 1.00 * 0.0162                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.915)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.37  17.15    None  None   None       |
|    all(noH): 2823   0      0.00    108.37  17.15    None  None   None       |
|    Sol.    : 438    0      4.08    108.37  47.13    None  None   None       |
|    Mac.    : 2385   0      0.00    90.52   11.65    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 -  10.837: 1506   |   5:    54.184 -  65.020:   72        |
|      1:    10.837 -  21.674:  713   |   6:    65.020 -  75.857:   65        |
|      2:    21.674 -  32.510:  192   |   7:    75.857 -  86.694:   30        |
|      3:    32.510 -  43.347:  114   |   8:    86.694 -  97.531:   19        |
|      4:    43.347 -  54.184:  107   |   9:    97.531 - 108.367:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1420 r_free = 0.1985             target_work(ml) = 5.366         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1419 r_free = 0.1983             target_work(ml) = 5.365         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1419   r_free= 0.1983   ksol= 0.32   Bsol= 55.50   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.26,-0.43,1.84,-0.00,0.00,0.00); trace/3= 0.38                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.365227                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.6887 0.99   1438  158 0.1020 0.1341      5.4304      5.6193|
|  2:  4.6887 -  3.7400 0.99   1391  158 0.0945 0.1296      5.5415      5.7771|
|  3:  3.7400 -  3.2727 0.99   1368  149 0.1309 0.1879      5.6535      6.0009|
|  4:  3.2727 -  2.9759 0.99   1351  153 0.1593 0.2190      5.6764      5.8425|
|  5:  2.9759 -  2.7640 0.99   1351  149 0.1723 0.2234      5.5733      5.8041|
|  6:  2.7640 -  2.6019 0.99   1340  146 0.1663 0.2686      5.4628      5.7384|
|  7:  2.6019 -  2.4722 0.99   1332  155 0.1625 0.2032      5.3986      5.5305|
|  8:  2.4722 -  2.3650 0.98   1325  151 0.1618 0.2322      5.3374      5.5706|
|  9:  2.3650 -  2.2742 0.98   1313  140 0.1609 0.2277      5.2843      5.5413|
| 10:  2.2742 -  2.1960 1.00   1354  147 0.1508 0.2125      5.1861      5.3974|
| 11:  2.1960 -  2.1275 0.98   1318  147 0.1498 0.2288      5.1721      5.5234|
| 12:  2.1275 -  2.0669 0.98   1306  141 0.1508 0.2331      5.0866      5.3513|
| 13:  2.0669 -  2.0126 0.87   1145  131 0.1377 0.1840      4.9708      5.1135|
| 14:  2.0126 -  1.9636 0.23    298   34 0.1243 0.2320       4.847      5.2481|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1489 -  4.6887  1438   158  0.93  10.24   0.97     0.94       8388.83|
|  2:  4.6887 -  3.7400  1391   158  0.94   9.85   1.03     1.01      11597.78|
|  3:  3.7400 -  3.2727  1368   149  0.90  15.09   1.05     1.05      15155.12|
|  4:  3.2727 -  2.9759  1351   153  0.87  19.07   1.03     1.00      16952.44|
|  5:  2.9759 -  2.7640  1351   149  0.85  21.83   1.00     0.98      14702.74|
|  6:  2.7640 -  2.6019  1340   146  0.84  22.85   0.98     0.92      12413.36|
|  7:  2.6019 -  2.4722  1332   155  0.85  21.79   1.00     0.95      10728.57|
|  8:  2.4722 -  2.3650  1325   151  0.85  22.04   1.00     0.95       9467.35|
|  9:  2.3650 -  2.2742  1313   140  0.85  21.86   1.00     0.94       8518.37|
| 10:  2.2742 -  2.1960  1354   147  0.85  21.11   1.00     0.96       7238.99|
| 11:  2.1960 -  2.1275  1318   147  0.85  21.82   1.00     0.93       7201.81|
| 12:  2.1275 -  2.0669  1306   141  0.86  21.02   1.00     0.99       6218.28|
| 13:  2.0669 -  2.0126  1145   131  0.85  21.74   0.99     0.95       5109.89|
| 14:  2.0126 -  1.9636   298    34  0.90  16.90   0.99     0.96       3828.00|
|alpha:            min =        0.92 max =            1.05 mean =         0.97|
|beta:             min =     3828.00 max =        16952.44 mean =     10252.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           90.00 mean =        19.09|
|phase err.(test): min =        0.00 max =           89.48 mean =        18.36|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1419   r_free= 0.1984   ksol= 0.31   Bsol= 55.88   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.64,-0.81,1.46,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.365279                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1419   r_free= 0.1984   ksol= 0.31   Bsol= 55.88   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.64,-0.81,1.46,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.365279                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.6887 0.99   1438  158 0.1018 0.1347      5.4302      5.6239|
|  2:  4.6887 -  3.7400 0.99   1391  158 0.0946 0.1297      5.5427      5.7779|
|  3:  3.7400 -  3.2727 0.99   1368  149 0.1310 0.1880      5.6537      6.0012|
|  4:  3.2727 -  2.9759 0.99   1351  153 0.1593 0.2189      5.6763      5.8424|
|  5:  2.9759 -  2.7640 0.99   1351  149 0.1722 0.2234      5.5732      5.8039|
|  6:  2.7640 -  2.6019 0.99   1340  146 0.1663 0.2685      5.4627      5.7383|
|  7:  2.6019 -  2.4722 0.99   1332  155 0.1625 0.2033      5.3985      5.5305|
|  8:  2.4722 -  2.3650 0.98   1325  151 0.1618 0.2322      5.3374      5.5705|
|  9:  2.3650 -  2.2742 0.98   1313  140 0.1609 0.2277      5.2843      5.5413|
| 10:  2.2742 -  2.1960 1.00   1354  147 0.1508 0.2125      5.1861      5.3974|
| 11:  2.1960 -  2.1275 0.98   1318  147 0.1498 0.2288      5.1721      5.5234|
| 12:  2.1275 -  2.0669 0.98   1306  141 0.1508 0.2331      5.0866      5.3513|
| 13:  2.0669 -  2.0126 0.87   1145  131 0.1377 0.1840      4.9708      5.1135|
| 14:  2.0126 -  1.9636 0.23    298   34 0.1243 0.2320       4.847      5.2481|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1489 -  4.6887  1438   158  0.93  10.30   0.96     0.94       8461.16|
|  2:  4.6887 -  3.7400  1391   158  0.94   9.88   1.03     1.01      11652.09|
|  3:  3.7400 -  3.2727  1368   149  0.90  15.10   1.05     1.05      15168.15|
|  4:  3.2727 -  2.9759  1351   153  0.87  19.08   1.03     1.00      16957.50|
|  5:  2.9759 -  2.7640  1351   149  0.85  21.82   1.00     0.98      14699.55|
|  6:  2.7640 -  2.6019  1340   146  0.84  22.84   0.98     0.92      12408.33|
|  7:  2.6019 -  2.4722  1332   155  0.85  21.79   1.00     0.95      10725.70|
|  8:  2.4722 -  2.3650  1325   151  0.85  22.04   1.00     0.95       9466.00|
|  9:  2.3650 -  2.2742  1313   140  0.85  21.86   1.00     0.94       8517.71|
| 10:  2.2742 -  2.1960  1354   147  0.85  21.11   1.00     0.96       7238.25|
| 11:  2.1960 -  2.1275  1318   147  0.85  21.82   1.00     0.93       7201.08|
| 12:  2.1275 -  2.0669  1306   141  0.86  21.02   1.00     0.99       6218.01|
| 13:  2.0669 -  2.0126  1145   131  0.85  21.74   0.99     0.95       5109.76|
| 14:  2.0126 -  1.9636   298    34  0.90  16.90   0.99     0.96       3827.79|
|alpha:            min =        0.92 max =            1.05 mean =         0.97|
|beta:             min =     3827.79 max =        16957.50 mean =     10263.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.98 mean =        19.10|
|phase err.(test): min =        0.00 max =           89.19 mean =        18.36|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.915)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.38    108.75  17.54    None  None   None       |
|    all(noH): 2823   0      0.38    108.75  17.54    None  None   None       |
|    Sol.    : 438    0      4.47    108.75  47.51    None  None   None       |
|    Mac.    : 2385   0      0.38    90.91   12.03    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:     0.383 -  11.219: 1506   |   5:    54.566 -  65.403:   72        |
|      1:    11.219 -  22.056:  713   |   6:    65.403 -  76.240:   65        |
|      2:    22.056 -  32.893:  192   |   7:    76.240 -  87.076:   30        |
|      3:    32.893 -  43.730:  114   |   8:    87.076 -  97.913:   19        |
|      4:    43.730 -  54.566:  107   |   9:    97.913 - 108.750:    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)= 350         
Filter by distance & map next to the model:
   mapped sites are within: 0.436 - 4.948
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 345 from: 350
   mapped sites are within: 0.722 - 4.948

peak=    8.380 closest distance to " CB  VAL A 230 " =    1.405
peak=    7.506 closest distance to " O   HOH Z 103 " =    1.267
peak=    7.489 closest distance to " O   HOH Z 130 " =    1.766
peak=    7.373 closest distance to " CB  VAL A 296 " =    1.558
peak=    6.599 closest distance to " CD2 LEU A   5 " =    1.420
peak=    6.183 closest distance to " CG  ARG A 138 " =    1.220
peak=    5.734 closest distance to " O   HOH Z 246 " =    1.747
peak=    5.535 closest distance to " NH1 ARG A 138 " =    1.098
peak=    5.525 closest distance to " CD1AILE A 234 " =    1.046
peak=    5.450 closest distance to " CB  VAL A 230 " =    1.354
peak=    5.300 closest distance to " O   HOH Z  63 " =    1.687
peak=    5.195 closest distance to " O  BHOH Z  74 " =    1.032
peak=    5.164 closest distance to " CG  PRO A  54 " =    1.523
peak=    5.163 closest distance to " O   HOH Z 268 " =    1.075
peak=    5.057 closest distance to " O   HOH Z 385 " =    1.146
peak=    5.003 closest distance to " O   HOH Z 425 " =    1.768
peak=    4.986 closest distance to " O   PRO A 198 " =    1.458
peak=    4.986 closest distance to " CB  SER A  63 " =    1.409
peak=    4.973 closest distance to " CB  SER A 216 " =    1.138
peak=    4.908 closest distance to " CG  ARG A 138 " =    1.193
peak=    4.843 closest distance to " O   HOH Z 331 " =    1.265
peak=    4.827 closest distance to " O   HOH Z 427 " =    2.306
peak=    4.826 closest distance to " O   HOH Z  46 " =    1.214
peak=    4.821 closest distance to " OD1 ASN A  69 " =    1.145
peak=    4.816 closest distance to " O   HOH Z 127 " =    1.242
peak=    4.782 closest distance to " O   HOH Z 417 " =    2.024
peak=    4.769 closest distance to " O   HOH Z 330 " =    1.089
peak=    4.747 closest distance to " O   HOH Z  70 " =    1.080
peak=    4.740 closest distance to " O   HOH Z  65 " =    1.944
peak=    4.635 closest distance to " NE2 GLN A  11 " =    1.113
peak=    4.623 closest distance to " C   GLN A  73 " =    1.128
peak=    4.615 closest distance to " O   HOH Z 105 " =    1.241
peak=    4.594 closest distance to " O   HOH Z 255 " =    1.082
peak=    4.572 closest distance to " O   HOH Z 222 " =    1.718
peak=    4.561 closest distance to " O   HOH Z 258 " =    1.259
peak=    4.550 closest distance to " O   HOH Z  69 " =    1.591
peak=    4.460 closest distance to " O   HOH Z 245 " =    1.123
peak=    4.434 closest distance to " NH2 ARG A  56 " =    2.148
peak=    4.422 closest distance to " O   HOH Z 287 " =    1.841
peak=    4.401 closest distance to " CG  LEU A 228 " =    1.198
peak=    4.393 closest distance to " O   HOH Z 424 " =    2.200
peak=    4.370 closest distance to " CB  PRO A  54 " =    1.194
peak=    4.366 closest distance to " O   HOH Z 232 " =    2.254
peak=    4.361 closest distance to " O   HOH Z 427 " =    1.269
peak=    4.351 closest distance to " O   HOH Z 143 " =    2.043
peak=    4.326 closest distance to " CG  PRO A 243 " =    1.159
peak=    4.310 closest distance to " CZ3 TRP A 266 " =    1.293
peak=    4.303 closest distance to " CG  PRO A 198 " =    1.316
peak=    4.293 closest distance to " O   HOH Z 207 " =    1.092
peak=    4.222 closest distance to " CE3 TRP A 274 " =    1.260
peak=    4.219 closest distance to " N   TYR A  15 " =    1.092
peak=    4.179 closest distance to " CB  ASN A  39 " =    0.956
peak=    4.142 closest distance to " CD  ARG A 138 " =    1.155
peak=    4.136 closest distance to " CB  MET A  40 " =    1.001
peak=    4.126 closest distance to " CD2 LEU A 228 " =    1.344
peak=    4.118 closest distance to " O   HOH Z 437 " =    2.212
peak=    4.115 closest distance to " O   HOH Z  66 " =    1.000
peak=    4.083 closest distance to " O   HOH Z 403 " =    1.538
peak=    4.082 closest distance to " ND2BASN A 224 " =    1.040
peak=    4.069 closest distance to " O   HOH Z 298 " =    1.821
peak=    4.039 closest distance to " CB  ASN A 148 " =    1.472
peak=    4.038 closest distance to " O   HOH Z  39 " =    1.495
peak=    4.036 closest distance to " CD1 LEU A   5 " =    1.369
peak=    4.036 closest distance to " O   HOH Z 414 " =    1.511
peak=    4.026 closest distance to " O   HOH Z 350 " =    1.549
peak=    4.021 closest distance to " O   HOH Z  59 " =    1.887
peak=    4.007 closest distance to " O   HOH Z 225 " =    1.831
peak=    3.990 closest distance to " O   HOH Z 360 " =    1.307
peak=    3.978 closest distance to " O   HOH Z 411 " =    3.221
peak=    3.975 closest distance to " CB  ALA A  10 " =    1.024
peak=    3.968 closest distance to " O   HOH Z 369 " =    2.020
peak=    3.955 closest distance to " C   VAL A  72 " =    0.999
peak=    3.939 closest distance to " O   HOH Z 303 " =    2.101
peak=    3.938 closest distance to " O   HOH Z 236 " =    1.532
peak=    3.937 closest distance to " O   HOH Z  80 " =    1.916
peak=    3.932 closest distance to " O   HOH Z 359 " =    1.471
peak=    3.931 closest distance to " CZ  PHE A 218 " =    1.206
peak=    3.929 closest distance to " O   HOH Z 110 " =    0.891
peak=    3.928 closest distance to " CB  GLN A 223 " =    1.451
peak=    3.924 closest distance to " O   HOH Z  26 " =    1.613
peak=    3.911 closest distance to " O   HOH Z 316 " =    3.008
peak=    3.904 closest distance to " O   HOH Z 380 " =    1.924
peak=    3.902 closest distance to " O   HOH Z 126 " =    2.072
peak=    3.895 closest distance to " O   HOH Z 124 " =    1.349
peak=    3.883 closest distance to " NH1AARG A 145 " =    1.038
peak=    3.882 closest distance to " O   HOH Z 361 " =    1.480
peak=    3.881 closest distance to " CB  ARG A 138 " =    1.053
peak=    3.877 closest distance to " CG  LEU A   5 " =    1.083
peak=    3.875 closest distance to " O   HOH Z  49 " =    1.320
peak=    3.874 closest distance to " O   HOH Z 424 " =    1.163
peak=    3.873 closest distance to " CD  LYS A  76 " =    1.792
peak=    3.869 closest distance to " CG1 VAL A 296 " =    1.173
peak=    3.846 closest distance to " O   HOH Z  52 " =    1.040
peak=    3.839 closest distance to " O   HOH Z 392 " =    1.109
peak=    3.837 closest distance to " O   HOH Z  24 " =    1.951
peak=    3.835 closest distance to " O   HOH Z 389 " =    1.756
peak=    3.815 closest distance to " CG2 ILE A 234 " =    0.873
peak=    3.812 closest distance to " CA  ILE A 234 " =    1.047
peak=    3.794 closest distance to " CG  LEU A 167 " =    1.363
peak=    3.787 closest distance to " CB  SER A   3 " =    1.585
peak=    3.781 closest distance to " NE1 TRP A 266 " =    1.792
peak=    3.777 closest distance to " CD  GLN A 240 " =    1.725
peak=    3.774 closest distance to " O   HOH Z 143 " =    1.651
peak=    3.773 closest distance to " CB  MET A  47 " =    1.134
peak=    3.773 closest distance to " CG2 THR A 221 " =    1.165
peak=    3.770 closest distance to " O   HOH Z 148 " =    1.615
peak=    3.770 closest distance to " O   HOH Z 180 " =    2.248
peak=    3.756 closest distance to " O   HOH Z  61 " =    1.607
peak=    3.751 closest distance to " O   HOH Z  15 " =    0.908
peak=    3.750 closest distance to " O   HOH Z   4 " =    2.262
peak=    3.722 closest distance to " O   HOH Z  92 " =    1.235
peak=    3.720 closest distance to " C   ASN A 209 " =    1.683
peak=    3.710 closest distance to " O   HOH Z 418 " =    1.048
peak=    3.707 closest distance to " CG  GLN A  58 " =    1.336
peak=    3.706 closest distance to " CB  ALA A  43 " =    0.871
peak=    3.703 closest distance to " CG2 ILE A  20 " =    1.624
peak=    3.700 closest distance to " O   HOH Z 147 " =    1.413
peak=    3.696 closest distance to " O   HOH Z  49 " =    2.802
peak=    3.693 closest distance to " CB  ASN A 142 " =    0.956
peak=    3.687 closest distance to " O   HOH Z 112 " =    1.051
peak=    3.678 closest distance to " OE2 GLU A  53 " =    1.120
peak=    3.673 closest distance to " CE3 TRP A 150 " =    1.128
peak=    3.667 closest distance to " O   HOH Z 272 " =    1.902
peak=    3.666 closest distance to " NH2AARG A 190 " =    1.828
peak=    3.665 closest distance to " O   HOH Z 423 " =    1.791
peak=    3.659 closest distance to " CA  TYR A  30 " =    1.152
peak=    3.653 closest distance to " O   HOH Z 374 " =    1.241
peak=    3.643 closest distance to " O   HOH Z 153 " =    3.621
peak=    3.639 closest distance to " CA  ALA A 160 " =    1.071
peak=    3.627 closest distance to " N   TRP A  70 " =    0.913
peak=    3.626 closest distance to " O   HOH Z  97 " =    1.440
peak=    3.625 closest distance to " O   HOH Z  66 " =    2.427
peak=    3.620 closest distance to " N   ARG A 156 " =    1.295
peak=    3.620 closest distance to " O   HOH Z 257 " =    1.196
peak=    3.612 closest distance to " O   HOH Z 410 " =    1.487
peak=    3.611 closest distance to " O   HOH Z 329 " =    4.290
peak=    3.606 closest distance to " CB  LYS A 117 " =    1.276
peak=    3.605 closest distance to " CB  THR A  52 " =    1.108
peak=    3.600 closest distance to " CA  ARG A  36 " =    0.980
peak=    3.594 closest distance to " O   HOH Z  21 " =    1.403
peak=    3.592 closest distance to " NH2 ARG A 269 " =    1.090
peak=    3.591 closest distance to " NZ  LYS A 119 " =    3.005
peak=    3.587 closest distance to " CE  LYS A  76 " =    0.958
peak=    3.583 closest distance to " O   HOH Z  88 " =    3.502
peak=    3.564 closest distance to " O   HOH Z 368 " =    1.054
peak=    3.564 closest distance to " OG BSER A  12 " =    0.951
peak=    3.561 closest distance to " O   HOH Z 373 " =    1.553
peak=    3.558 closest distance to " O   HOH Z 240 " =    2.204
peak=    3.551 closest distance to " CB  ALA A 114 " =    0.833
peak=    3.546 closest distance to " O   HOH Z 216 " =    3.880
peak=    3.544 closest distance to " NE1 TRP A 274 " =    0.961
peak=    3.539 closest distance to " O   HOH Z  71 " =    1.429
peak=    3.537 closest distance to " C   HIS A 115 " =    0.976
peak=    3.533 closest distance to " O   HOH Z   9 " =    2.775
peak=    3.533 closest distance to " O   HOH Z 193 " =    1.705
peak=    3.529 closest distance to " CB  THR A  31 " =    1.594
peak=    3.528 closest distance to " CD  ARG A 159 " =    0.758
peak=    3.526 closest distance to " N   GLN A 122 " =    0.736
peak=    3.524 closest distance to " O   HOH Z 362 " =    1.982
peak=    3.523 closest distance to " CA  ARG A 195 " =    1.355
peak=    3.520 closest distance to " O   HOH Z 293 " =    1.419
peak=    3.519 closest distance to " CB  LEU A 237 " =    0.947
peak=    3.518 closest distance to " CB  ASP A 107 " =    1.103
peak=    3.517 closest distance to " O   HOH Z 296 " =    1.117
peak=    3.511 closest distance to " O   HOH Z 201 " =    1.454
peak=    3.508 closest distance to " O   HOH Z  91 " =    2.501
peak=    3.507 closest distance to " O   HOH Z 353 " =    2.319
peak=    3.503 closest distance to " O   TYR A 116 " =    1.097
peak=    3.502 closest distance to " CA  THR A 221 " =    0.877
peak=    3.502 closest distance to " CZ  PHE A  38 " =    1.258
peak=    3.500 closest distance to " CB  GLU A 128 " =    1.034
peak=    3.496 closest distance to " CD  LYS A 119 " =    1.749
peak=    3.492 closest distance to " O   HOH Z  20 " =    1.711
peak=    3.487 closest distance to " O   HOH Z 375 " =    1.040
peak=    3.485 closest distance to " CA  ALA A  51 " =    1.083
peak=    3.483 closest distance to " N   GLN A 278 " =    1.346
peak=    3.483 closest distance to " O   HOH Z 422 " =    2.579
peak=    3.482 closest distance to " CB  TRP A 179 " =    1.418
peak=    3.479 closest distance to " CB  ASN A 215 " =    1.251
peak=    3.474 closest distance to " O   HOH Z 422 " =    1.073
peak=    3.472 closest distance to " O   HOH Z 409 " =    4.948
peak=    3.472 closest distance to " CG BARG A 275 " =    1.334
peak=    3.467 closest distance to " O   HOH Z 328 " =    1.642
peak=    3.464 closest distance to " CB  GLU A 277 " =    3.622
peak=    3.464 closest distance to " O   HOH Z 415 " =    1.035
peak=    3.459 closest distance to " CB  PRO A  90 " =    1.058
peak=    3.458 closest distance to " CG BARG A 102 " =    2.057
peak=    3.457 closest distance to " NH2AARG A 190 " =    1.949
peak=    3.455 closest distance to " O   HOH Z 172 " =    2.274
peak=    3.452 closest distance to " CE  LYS A 119 " =    1.052
peak=    3.450 closest distance to " NE2 HIS A 207 " =    0.986
peak=    3.443 closest distance to " CG  GLN A  89 " =    1.583
peak=    3.440 closest distance to " CB  SER A 276 " =    1.128
peak=    3.437 closest distance to " CD  ARG A  66 " =    2.223
peak=    3.436 closest distance to " O   HOH Z 139 " =    1.097
peak=    3.435 closest distance to " CG2 VAL A 257 " =    0.830
peak=    3.434 closest distance to " CB  ALA A 233 " =    0.977
peak=    3.428 closest distance to " O   ASP A 200 " =    1.595
peak=    3.424 closest distance to " O   HOH Z 368 " =    3.161
peak=    3.418 closest distance to " O   HOH Z 167 " =    1.801
peak=    3.416 closest distance to " O   HOH Z  30 " =    1.315
peak=    3.416 closest distance to " C   PRO A  54 " =    0.854
peak=    3.413 closest distance to " O   HOH Z 357 " =    2.250
peak=    3.408 closest distance to " O   HOH Z 390 " =    1.275
peak=    3.408 closest distance to " ND2 ASN A 249 " =    0.777
peak=    3.407 closest distance to " CG  LEU A 281 " =    0.979
peak=    3.407 closest distance to " CG2 ILE A 120 " =    1.202
peak=    3.407 closest distance to " O   HOH Z 365 " =    3.145
peak=    3.406 closest distance to " CB  VAL A 265 " =    1.340
peak=    3.404 closest distance to " CB  ARG A 275 " =    1.104
peak=    3.403 closest distance to " O   HOH Z 389 " =    2.522
peak=    3.397 closest distance to " O   HOH Z 343 " =    2.768
peak=    3.396 closest distance to " N   GLY A 136 " =    1.095
peak=    3.396 closest distance to " CA  CYS A 260 " =    1.099
peak=    3.392 closest distance to " O   HOH Z  53 " =    2.273
peak=    3.391 closest distance to " O   HOH Z 101 " =    0.882
peak=    3.391 closest distance to " O   HOH Z 238 " =    1.188
peak=    3.391 closest distance to " O   HOH Z 145 " =    2.015
peak=    3.390 closest distance to " CA  ARG A 156 " =    1.172
peak=    3.383 closest distance to " CA  GLY A  80 " =    0.927
peak=    3.383 closest distance to " CB  SER A 141 " =    1.134
peak=    3.382 closest distance to " NH2AARG A 145 " =    1.175
peak=    3.379 closest distance to " CD  GLN A  77 " =    1.237
peak=    3.377 closest distance to " CB  ASP A 124 " =    0.831
peak=    3.374 closest distance to " CD1 LEU A 300 " =    1.138
peak=    3.371 closest distance to " O   HOH Z 425 " =    1.891
peak=    3.371 closest distance to " CB  ARG A 139 " =    1.317
peak=    3.366 closest distance to " N   PHE A  59 " =    0.788
peak=    3.364 closest distance to " CB  ASN A 110 " =    1.110
peak=    3.360 closest distance to " O   HOH Z  28 " =    1.208
peak=    3.360 closest distance to " O   HOH Z 392 " =    1.402
peak=    3.360 closest distance to " CG  PRO A 213 " =    1.258
peak=    3.359 closest distance to " CD ALYS A 290 " =    1.005
peak=    3.352 closest distance to " O   HOH Z 123 " =    1.061
peak=    3.347 closest distance to " O   HOH Z 220 " =    1.513
peak=    3.339 closest distance to " CB  ARG A  79 " =    0.891
peak=    3.330 closest distance to " O   HOH Z 104 " =    1.848
peak=    3.329 closest distance to " CG  GLN A  11 " =    2.217
peak=    3.329 closest distance to " CA  ALA A 129 " =    1.293
peak=    3.327 closest distance to " CE2 PHE A  16 " =    0.876
peak=    3.326 closest distance to " CE  MET A  93 " =    1.547
peak=    3.325 closest distance to " N   VAL A 296 " =    1.799
peak=    3.325 closest distance to " N   SER A 271 " =    0.951
peak=    3.323 closest distance to " CB  GLN A 183 " =    1.167
peak=    3.322 closest distance to " CB  VAL A 202 " =    1.663
peak=    3.319 closest distance to " O   HOH Z 263 " =    1.188
peak=    3.318 closest distance to " O   HOH Z 368 " =    4.144
peak=    3.314 closest distance to " OG  SER A 135 " =    1.235
peak=    3.313 closest distance to " O   HOH Z 213 " =    1.817
peak=    3.311 closest distance to " CD  GLU A   2 " =    2.089
peak=    3.309 closest distance to " CB  ASN A 142 " =    1.487
peak=    3.307 closest distance to " N   PHE A 130 " =    1.351
peak=    3.304 closest distance to " OG  SER A  62 " =    2.551
peak=    3.303 closest distance to " O   HOH Z   6 " =    1.574
peak=    3.301 closest distance to " N   GLN A  73 " =    0.957
peak=    3.300 closest distance to " O   HOH Z 181 " =    2.404
peak=    3.298 closest distance to " CA  ARG A 102 " =    1.099
peak=    3.298 closest distance to " O   HOH Z 358 " =    1.290
peak=    3.294 closest distance to " CB  TYR A 169 " =    0.722
peak=    3.293 closest distance to " CA  ASP A 124 " =    0.748
peak=    3.289 closest distance to " O   HOH Z 193 " =    1.336
peak=    3.288 closest distance to " CB  TRP A 266 " =    1.018
peak=    3.286 closest distance to " O   HOH Z 248 " =    2.011
peak=    3.284 closest distance to " O   HOH Z  58 " =    1.955
peak=    3.275 closest distance to " CG1 ILE A 151 " =    1.157
peak=    3.270 closest distance to " OE2 GLU A  53 " =    1.601
peak=    3.263 closest distance to " CB  PHE A 225 " =    1.508
peak=    3.257 closest distance to " OD1 ASN A 301 " =    1.517
peak=    3.257 closest distance to " O   PRO A 213 " =    1.277
peak=    3.253 closest distance to " O   GLY A 211 " =    1.031
peak=    3.253 closest distance to " N   SER A  97 " =    0.755
peak=    3.252 closest distance to " CA  LEU A 222 " =    1.159
peak=    3.250 closest distance to " O   HOH Z 158 " =    2.732
peak=    3.249 closest distance to " O   HOH Z  22 " =    2.700
peak=    3.249 closest distance to " O   HOH Z 119 " =    1.624
peak=    3.247 closest distance to " O   HOH Z 162 " =    1.164
peak=    3.246 closest distance to " OG  SER A 276 " =    1.048
peak=    3.246 closest distance to " CE3 TRP A  85 " =    1.253
peak=    3.245 closest distance to " O   HOH Z 342 " =    0.993
peak=    3.239 closest distance to " CB  GLU A 175 " =    1.096
peak=    3.234 closest distance to " O   HOH Z  16 " =    0.842
peak=    3.233 closest distance to " O   HOH Z  27 " =    1.102
peak=    3.230 closest distance to " OG BSER A 212 " =    2.594
peak=    3.229 closest distance to " O   HOH Z 265 " =    1.709
peak=    3.227 closest distance to " O   HOH Z 193 " =    1.605
peak=    3.226 closest distance to " CG  PRO A  90 " =    1.779
peak=    3.226 closest distance to " CD1 ILE A 120 " =    0.943
peak=    3.223 closest distance to " CG1AVAL A 121 " =    0.800
peak=    3.223 closest distance to " O   HOH Z 368 " =    1.543
peak=    3.223 closest distance to " NZ  LYS A 117 " =    3.160
peak=    3.217 closest distance to " CD  ARG A 269 " =    0.927
peak=    3.216 closest distance to " O   HOH Z 214 " =    2.752
peak=    3.215 closest distance to " O   HOH Z 211 " =    1.426
peak=    3.214 closest distance to " CD  ARG A 195 " =    3.568
peak=    3.209 closest distance to " O   HOH Z 325 " =    1.919
peak=    3.208 closest distance to " CA  VAL A 112 " =    1.274
peak=    3.201 closest distance to " CA  VAL A 125 " =    1.131
peak=    3.200 closest distance to " O   HOH Z 419 " =    1.735
peak=    3.200 closest distance to " CA  ARG A 159 " =    1.345
peak=    3.197 closest distance to " CA  ASN A 284 " =    0.856
peak=    3.192 closest distance to " CA  CYS A 201 " =    1.088
peak=    3.191 closest distance to " OD1 ASP A 200 " =    1.578
peak=    3.191 closest distance to " NZ BLYS A 290 " =    1.006
peak=    3.190 closest distance to " OG ASER A 212 " =    1.535
peak=    3.187 closest distance to " O   HOH Z 154 " =    2.374
peak=    3.183 closest distance to " CD1 ILE A  33 " =    1.879
peak=    3.180 closest distance to " CG2 VAL A 202 " =    1.304
peak=    3.179 closest distance to " N   ALA A   1 " =    1.571
peak=    3.179 closest distance to " O   HOH Z 182 " =    1.175
peak=    3.177 closest distance to " N   PHE A 208 " =    0.940
peak=    3.173 closest distance to " ND2 ASN A 176 " =    0.907
peak=    3.169 closest distance to " O   HOH Z  42 " =    1.396
peak=    3.169 closest distance to " O   GLN A  55 " =    1.033
peak=    3.166 closest distance to " C   VAL A  72 " =    0.931
peak=    3.165 closest distance to " CA  ASP A 253 " =    1.935
peak=    3.165 closest distance to " O   HOH Z 371 " =    3.093
peak=    3.164 closest distance to " CB  SER A  62 " =    1.148
peak=    3.164 closest distance to " O   MET A 105 " =    1.806
peak=    3.163 closest distance to " O   HOH Z 274 " =    2.551
peak=    3.162 closest distance to " O   HOH Z 146 " =    1.374
peak=    3.162 closest distance to " NH2BARG A 190 " =    1.163
peak=    3.154 closest distance to " O   HOH Z 389 " =    1.517
peak=    3.147 closest distance to " OH  TYR A 116 " =    1.888
peak=    3.146 closest distance to " O   HOH Z  40 " =    1.711
peak=    3.144 closest distance to " O   HOH Z  11 " =    1.085
peak=    3.144 closest distance to " N   PHE A 218 " =    0.815
peak=    3.141 closest distance to " O   HOH Z 261 " =    1.849
peak=    3.141 closest distance to " O   HOH Z 426 " =    0.925
peak=    3.137 closest distance to " CA  ILE A 106 " =    0.741
peak=    3.132 closest distance to " CB  TRP A 150 " =    1.201
peak=    3.132 closest distance to " C   ASN A 301 " =    1.027
peak=    3.113 closest distance to " CB  LEU A 143 " =    1.119
peak=    3.107 closest distance to " CB  ASP A 191 " =    1.294
peak=    3.107 closest distance to " O   ASN A 187 " =    1.419
peak=    3.096 closest distance to " CB  TYR A  30 " =    1.412
peak=    3.092 closest distance to " O   HOH Z  55 " =    1.711
peak=    3.087 closest distance to " NE AARG A 275 " =    1.829
peak=    3.083 closest distance to " CB  ALA A 248 " =    1.430
peak=    3.072 closest distance to " NH1AARG A 102 " =    0.994
peak=    3.071 closest distance to " O   HOH Z   7 " =    2.851
peak=    3.071 closest distance to " CA  ASP A  50 " =    1.225
peak=    3.063 closest distance to " O   HOH Z 389 " =    1.879
peak=    3.049 closest distance to " OD1 ASN A 148 " =    1.981
peak=    3.036 closest distance to " O   HOH Z  77 " =    1.261
peak=    3.021 closest distance to " O   HOH Z  88 " =    3.511

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.586 - 5.723
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 212
   mapped sites are within: 0.728 - 5.723

peak=   -5.601 closest distance to " CD  ARG A 138 " =    1.254
peak=   -4.840 closest distance to " O   PRO A 198 " =    1.205
peak=   -4.701 closest distance to " CB  GLN A  55 " =    1.130
peak=   -4.497 closest distance to " CB  VAL A 230 " =    0.989
peak=   -4.420 closest distance to " O   HOH Z 415 " =    0.953
peak=   -4.281 closest distance to " O   HOH Z 147 " =    2.039
peak=   -4.269 closest distance to " O   HOH Z  69 " =    2.093
peak=   -4.251 closest distance to " CA  ASP A  27 " =    2.498
peak=   -4.145 closest distance to " CG  ARG A 219 " =    2.384
peak=   -4.112 closest distance to " OE1 GLU A 277 " =    2.257
peak=   -4.086 closest distance to " CD  PRO A 213 " =    2.205
peak=   -4.086 closest distance to " CZ2 TRP A  92 " =    2.811
peak=   -4.067 closest distance to " CA  HIS A 207 " =    1.099
peak=   -4.040 closest distance to " CG2 VAL A 230 " =    0.854
peak=   -4.036 closest distance to " NE2 GLN A 223 " =    1.685
peak=   -4.020 closest distance to " CG  MET A 105 " =    0.981
peak=   -3.979 closest distance to " CB  ALA A 160 " =    2.278
peak=   -3.977 closest distance to " CG  ARG A 259 " =    2.436
peak=   -3.909 closest distance to " CD2 TYR A 293 " =    1.841
peak=   -3.900 closest distance to " O   HOH Z 165 " =    2.290
peak=   -3.898 closest distance to " N   THR A 157 " =    1.534
peak=   -3.865 closest distance to " CD  ARG A  14 " =    3.047
peak=   -3.838 closest distance to " O   HOH Z 131 " =    3.902
peak=   -3.833 closest distance to " O   HOH Z 177 " =    2.466
peak=   -3.828 closest distance to " CG1 VAL A 125 " =    2.354
peak=   -3.823 closest distance to " CD  LYS A 166 " =    2.475
peak=   -3.819 closest distance to " OG BSER A 134 " =    1.552
peak=   -3.796 closest distance to " O   HOH Z  39 " =    0.772
peak=   -3.796 closest distance to " N   PRO A  54 " =    1.047
peak=   -3.778 closest distance to " OG  SER A  97 " =    2.086
peak=   -3.778 closest distance to " CD2 TYR A 116 " =    2.278
peak=   -3.761 closest distance to " O   HOH Z 216 " =    1.538
peak=   -3.750 closest distance to " O   HOH Z 352 " =    1.464
peak=   -3.749 closest distance to " CE2 TYR A  30 " =    2.525
peak=   -3.744 closest distance to " OG  SER A  87 " =    1.825
peak=   -3.742 closest distance to " CA  GLY A 241 " =    2.317
peak=   -3.719 closest distance to " O   SER A 135 " =    1.528
peak=   -3.715 closest distance to " O   SER A  22 " =    2.584
peak=   -3.715 closest distance to " CG2AVAL A  41 " =    2.754
peak=   -3.713 closest distance to " O   HOH Z 276 " =    1.257
peak=   -3.706 closest distance to " N   ALA A  84 " =    1.718
peak=   -3.705 closest distance to " CG  LEU A 281 " =    1.801
peak=   -3.698 closest distance to " O   HOH Z 275 " =    1.826
peak=   -3.697 closest distance to " O  BHOH Z  74 " =    0.930
peak=   -3.687 closest distance to " O   HOH Z 128 " =    2.457
peak=   -3.671 closest distance to " O   HOH Z  60 " =    1.536
peak=   -3.665 closest distance to " CG  ARG A 138 " =    1.311
peak=   -3.664 closest distance to " CB  ALA A   9 " =    2.557
peak=   -3.652 closest distance to " OG  SER A  28 " =    1.985
peak=   -3.651 closest distance to " C   GLU A   2 " =    1.977
peak=   -3.647 closest distance to " O   HOH Z 292 " =    1.638
peak=   -3.647 closest distance to " CB  ALA A 129 " =    2.598
peak=   -3.643 closest distance to " CB  ASP A 132 " =    2.684
peak=   -3.634 closest distance to " CA  GLY A  91 " =    2.255
peak=   -3.617 closest distance to " OD2 ASP A 171 " =    1.778
peak=   -3.586 closest distance to " O   ALA A  10 " =    1.556
peak=   -3.581 closest distance to " CB  ALA A 248 " =    2.076
peak=   -3.578 closest distance to " CB  ALA A   7 " =    2.068
peak=   -3.568 closest distance to " O   HOH Z 257 " =    1.323
peak=   -3.564 closest distance to " CB  PHE A 130 " =    1.155
peak=   -3.558 closest distance to " CB  VAL A  67 " =    2.710
peak=   -3.550 closest distance to " O   ALA A  51 " =    1.322
peak=   -3.547 closest distance to " O   HOH Z 111 " =    1.817
peak=   -3.542 closest distance to " O   HOH Z 163 " =    1.690
peak=   -3.542 closest distance to " OE2 GLU A 152 " =    1.238
peak=   -3.533 closest distance to " O   HOH Z 411 " =    5.135
peak=   -3.530 closest distance to " O   HOH Z 155 " =    1.046
peak=   -3.527 closest distance to " CG  GLN A  88 " =    1.210
peak=   -3.523 closest distance to " CG2 VAL A 202 " =    2.803
peak=   -3.522 closest distance to " CE  MET A 188 " =    2.313
peak=   -3.516 closest distance to " O   HOH Z 166 " =    1.165
peak=   -3.512 closest distance to " CG2 THR A 178 " =    2.263
peak=   -3.500 closest distance to " O   HOH Z 300 " =    1.113
peak=   -3.495 closest distance to " CA  GLY A 133 " =    2.008
peak=   -3.492 closest distance to " O   HOH Z 368 " =    1.258
peak=   -3.492 closest distance to " ND2 ASN A 285 " =    2.157
peak=   -3.492 closest distance to " O   HOH Z  64 " =    1.239
peak=   -3.490 closest distance to " O   GLY A  80 " =    2.602
peak=   -3.487 closest distance to " O   HOH Z 202 " =    1.698
peak=   -3.484 closest distance to " OH  TYR A 247 " =    1.410
peak=   -3.482 closest distance to " O   HOH Z 134 " =    4.320
peak=   -3.479 closest distance to " O   HOH Z 231 " =    0.728
peak=   -3.479 closest distance to " O   THR A 178 " =    1.024
peak=   -3.470 closest distance to " O   HOH Z 255 " =    1.104
peak=   -3.469 closest distance to " NE2 GLN A 194 " =    1.950
peak=   -3.466 closest distance to " CG1 VAL A 265 " =    2.499
peak=   -3.462 closest distance to " O   HOH Z 144 " =    0.934
peak=   -3.461 closest distance to " CG2 ILE A  20 " =    2.604
peak=   -3.450 closest distance to " CG1AVAL A  72 " =    2.396
peak=   -3.440 closest distance to " O   HOH Z  22 " =    2.771
peak=   -3.438 closest distance to " O   HOH Z 117 " =    0.936
peak=   -3.434 closest distance to " O   HOH Z 165 " =    1.636
peak=   -3.433 closest distance to " O   SER A 245 " =    1.349
peak=   -3.427 closest distance to " O   ARG A 145 " =    0.805
peak=   -3.423 closest distance to " CB  ALA A 114 " =    2.533
peak=   -3.416 closest distance to " CB  ALA A 131 " =    1.869
peak=   -3.410 closest distance to " O   ILE A  49 " =    1.602
peak=   -3.405 closest distance to " O   GLY A 203 " =    2.355
peak=   -3.396 closest distance to " CA  ASN A 127 " =    1.267
peak=   -3.392 closest distance to " O   HOH Z 407 " =    2.881
peak=   -3.390 closest distance to " O   HOH Z 245 " =    0.918
peak=   -3.389 closest distance to " O   HOH Z  24 " =    1.202
peak=   -3.389 closest distance to " CD1 ILE A  33 " =    2.007
peak=   -3.389 closest distance to " NH2AARG A 275 " =    5.367
peak=   -3.388 closest distance to " N   GLN A 223 " =    2.022
peak=   -3.386 closest distance to " O   HOH Z 368 " =    1.995
peak=   -3.381 closest distance to " CD1 TYR A 247 " =    2.722
peak=   -3.381 closest distance to " O   HOH Z 435 " =    2.308
peak=   -3.380 closest distance to " O   SER A 206 " =    1.871
peak=   -3.379 closest distance to " O   HOH Z 389 " =    2.631
peak=   -3.377 closest distance to " C   ILE A 239 " =    2.019
peak=   -3.371 closest distance to " O   HOH Z 149 " =    1.427
peak=   -3.368 closest distance to " OD1 ASN A  69 " =    0.814
peak=   -3.366 closest distance to " CA  HIS A  86 " =    2.086
peak=   -3.365 closest distance to " O   HOH Z 268 " =    0.960
peak=   -3.360 closest distance to " O   TYR A 172 " =    1.630
peak=   -3.353 closest distance to " CG1BVAL A  72 " =    5.319
peak=   -3.343 closest distance to " CB  HIS A  86 " =    1.101
peak=   -3.337 closest distance to " CZ  PHE A  38 " =    2.381
peak=   -3.332 closest distance to " CZ  ARG A 259 " =    0.896
peak=   -3.331 closest distance to " O   HOH Z 278 " =    1.150
peak=   -3.331 closest distance to " CZ  PHE A 130 " =    1.189
peak=   -3.324 closest distance to " O   HOH Z  67 " =    1.436
peak=   -3.323 closest distance to " O   PRO A 163 " =    1.814
peak=   -3.322 closest distance to " O   HOH Z 193 " =    1.043
peak=   -3.320 closest distance to " O   HOH Z  53 " =    1.636
peak=   -3.319 closest distance to " O   HOH Z 438 " =    1.314
peak=   -3.317 closest distance to " OD1 ASP A 191 " =    1.855
peak=   -3.316 closest distance to " CG1 VAL A 125 " =    2.059
peak=   -3.316 closest distance to " CD1 TRP A 179 " =    1.222
peak=   -3.312 closest distance to " OE1 GLU A  44 " =    1.086
peak=   -3.311 closest distance to " CA  GLY A 203 " =    2.501
peak=   -3.309 closest distance to " O   HOH Z 389 " =    1.198
peak=   -3.309 closest distance to " O   HOH Z 350 " =    1.908
peak=   -3.306 closest distance to " O   HOH Z 286 " =    1.746
peak=   -3.305 closest distance to " C   VAL A  72 " =    0.815
peak=   -3.299 closest distance to " O   HOH Z 427 " =    1.977
peak=   -3.294 closest distance to " C   HIS A 108 " =    1.361
peak=   -3.283 closest distance to " C   SER A 276 " =    1.670
peak=   -3.281 closest distance to " CD  ARG A 156 " =    1.905
peak=   -3.280 closest distance to " ND2 ASN A  39 " =    1.508
peak=   -3.276 closest distance to " O   HOH Z   1 " =    3.556
peak=   -3.271 closest distance to " O   HOH Z  68 " =    1.660
peak=   -3.271 closest distance to " C   ARG A 269 " =    1.304
peak=   -3.270 closest distance to " CD1 TRP A  85 " =    1.076
peak=   -3.270 closest distance to " CB  SER A  62 " =    5.723
peak=   -3.267 closest distance to " NH2 ARG A  79 " =    2.311
peak=   -3.256 closest distance to " NE1 TRP A 177 " =    1.854
peak=   -3.251 closest distance to " CE3 TRP A 150 " =    2.479
peak=   -3.250 closest distance to " OE1 GLN A  88 " =    1.127
peak=   -3.248 closest distance to " O   HOH Z 108 " =    1.342
peak=   -3.247 closest distance to " O   HOH Z  44 " =    0.908
peak=   -3.242 closest distance to " C   ASN A 285 " =    2.209
peak=   -3.241 closest distance to " NH1AARG A 275 " =    2.238
peak=   -3.240 closest distance to " O   HOH Z 100 " =    0.948
peak=   -3.239 closest distance to " N   MET A 188 " =    2.038
peak=   -3.230 closest distance to " O   GLN A 240 " =    3.232
peak=   -3.229 closest distance to " CG1 ILE A 234 " =    1.355
peak=   -3.224 closest distance to " CD1 LEU A 282 " =    2.602
peak=   -3.223 closest distance to " CD2 HIS A 207 " =    2.251
peak=   -3.219 closest distance to " O   HOH Z 110 " =    1.481
peak=   -3.213 closest distance to " CG2 ILE A 120 " =    1.386
peak=   -3.211 closest distance to " O   HOH Z 394 " =    1.920
peak=   -3.210 closest distance to " O   HOH Z 139 " =    0.878
peak=   -3.209 closest distance to " CB  TYR A  68 " =    1.137
peak=   -3.203 closest distance to " O   HOH Z 359 " =    3.232
peak=   -3.200 closest distance to " O   HOH Z 385 " =    1.568
peak=   -3.197 closest distance to " CG2 ILE A 151 " =    2.652
peak=   -3.196 closest distance to " CA  ASN A 110 " =    0.967
peak=   -3.196 closest distance to " O   HOH Z 339 " =    1.736
peak=   -3.194 closest distance to " O   HOH Z 181 " =    2.075
peak=   -3.191 closest distance to " CG1 VAL A 197 " =    2.521
peak=   -3.186 closest distance to " O   ARG A 138 " =    1.805
peak=   -3.183 closest distance to " O   HOH Z  66 " =    1.168
peak=   -3.180 closest distance to " O   HOH Z 371 " =    1.218
peak=   -3.179 closest distance to " CB  TRP A  85 " =    2.236
peak=   -3.174 closest distance to " C   ARG A  79 " =    2.523
peak=   -3.174 closest distance to " O   THR A  52 " =    1.173
peak=   -3.174 closest distance to " O   HOH Z 275 " =    1.621
peak=   -3.171 closest distance to " O   HOH Z 268 " =    0.825
peak=   -3.170 closest distance to " O   HOH Z 281 " =    2.467
peak=   -3.159 closest distance to " CD1BILE A 234 " =    2.539
peak=   -3.153 closest distance to " CA  TYR A  68 " =    1.009
peak=   -3.149 closest distance to " O   HOH Z 355 " =    1.984
peak=   -3.132 closest distance to " O   LYS A 117 " =    1.896
peak=   -3.129 closest distance to " O   HOH Z 244 " =    1.566
peak=   -3.128 closest distance to " CB  HIS A  81 " =    1.106
peak=   -3.123 closest distance to " NH2BARG A 102 " =    0.920
peak=   -3.120 closest distance to " O   HOH Z 332 " =    1.164
peak=   -3.111 closest distance to " OG  SER A 141 " =    1.688
peak=   -3.109 closest distance to " O   SER A 271 " =    1.650
peak=   -3.107 closest distance to " CA  GLY A  98 " =    2.051
peak=   -3.106 closest distance to " C   GLN A 205 " =    2.013
peak=   -3.105 closest distance to " CB  PRO A  54 " =    2.303
peak=   -3.102 closest distance to " CE BMET A  47 " =    1.326
peak=   -3.099 closest distance to " OD2 ASP A 171 " =    2.502
peak=   -3.094 closest distance to " CG1 VAL A 257 " =    2.047
peak=   -3.094 closest distance to " N   ALA A  43 " =    2.721
peak=   -3.086 closest distance to " CG2 THR A 178 " =    2.318
peak=   -3.081 closest distance to " O   HOH Z 364 " =    2.389
peak=   -3.066 closest distance to " O   HOH Z 298 " =    2.786
peak=   -3.066 closest distance to " CB  ASN A  39 " =    2.331
peak=   -3.053 closest distance to " OD2 ASP A 272 " =    1.468
peak=   -3.050 closest distance to " O   HOH Z  15 " =    1.354
peak=   -3.044 closest distance to " CG2 ILE A 263 " =    2.202
peak=   -3.025 closest distance to " CA  GLY A  57 " =    2.111
peak=   -3.020 closest distance to " CB  PHE A  61 " =    1.398
peak=   -3.013 closest distance to " O   VAL A  67 " =    2.655
peak=   -3.008 closest distance to " CA  GLY A 133 " =    2.230

================= 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    :  0.5120 0.5023   6.311265e+00   6.296269e+00
   1_bss:  0.5043 0.4912   6.306676e+00   6.290408e+00
   1_xyz:  0.4392 0.4681   6.240018e+00   6.265475e+00
   1_adp:  0.4053 0.4702   6.200051e+00   6.264630e+00
   1_occ:  0.4052 0.4700   6.199895e+00   6.264879e+00
   2_bss:  0.4024 0.4664   6.201896e+00   6.264888e+00
   2_xyz:  0.3496 0.4255   6.097641e+00   6.202298e+00
   2_adp:  0.3353 0.4179   6.077637e+00   6.189624e+00
   2_occ:  0.3351 0.4184   6.077838e+00   6.190408e+00
   3_bss:  0.3340 0.4162   6.078981e+00   6.190777e+00
   3_xyz:  0.2598 0.3338   5.871523e+00   6.041636e+00
   3_adp:  0.2337 0.3134   5.798822e+00   5.991462e+00
   3_occ:  0.2335 0.3133   5.797671e+00   5.990746e+00
   4_bss:  0.2332 0.3120   5.797499e+00   5.989897e+00
   4_xyz:  0.1911 0.2586   5.623415e+00   5.838769e+00
   4_adp:  0.1659 0.2276   5.501218e+00   5.732422e+00
   4_occ:  0.1657 0.2272   5.500246e+00   5.731629e+00
   5_bss:  0.1657 0.2269   5.497483e+00   5.729200e+00
   5_xyz:  0.1482 0.2047   5.398607e+00   5.633586e+00
   5_adp:  0.1420 0.1985   5.366012e+00   5.602561e+00
   5_occ:  0.1419 0.1983   5.365227e+00   5.601662e+00
   5_bss:  0.1419 0.1984   5.365279e+00   5.602071e+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:  0.336   0.778   6.388   8.375  11.222   0.000   0.000   0.000
   1_xyz:  0.336   0.778   6.388   8.375  11.222   0.000   0.000   0.000
   1_adp:  0.336   0.778   6.388   8.375  11.222   0.000   0.000   0.000
   1_occ:  0.336   0.778   6.388   8.375  11.222   0.000   0.000   0.000
   2_bss:  0.344  35.777   3.040   4.423   6.838   0.000   0.000   0.000
   2_xyz:  0.344  35.777   3.040   4.423   6.838   0.000   0.000   0.000
   2_adp:  0.344  35.777   3.040   4.423   6.838   0.000   0.000   0.000
   2_occ:  0.344  35.777   3.040   4.423   6.838   0.000   0.000   0.000
   3_bss:  0.343  55.501   1.132   1.827   4.131   0.000   0.000   0.000
   3_xyz:  0.343  55.501   1.132   1.827   4.131   0.000   0.000   0.000
   3_adp:  0.343  55.501   1.132   1.827   4.131   0.000   0.000   0.000
   3_occ:  0.343  55.501   1.132   1.827   4.131   0.000   0.000   0.000
   4_bss:  0.334  55.501   0.205   0.361   2.359   0.000   0.000   0.000
   4_xyz:  0.334  55.501   0.205   0.361   2.359   0.000   0.000   0.000
   4_adp:  0.334  55.501   0.205   0.361   2.359   0.000   0.000   0.000
   4_occ:  0.334  55.501   0.205   0.361   2.359   0.000   0.000   0.000
   5_bss:  0.319  55.501  -0.262  -0.431   1.841  -0.000   0.000   0.000
   5_xyz:  0.319  55.501  -0.262  -0.431   1.841  -0.000   0.000   0.000
   5_adp:  0.319  55.501  -0.262  -0.431   1.841  -0.000   0.000   0.000
   5_occ:  0.319  55.501  -0.262  -0.431   1.841  -0.000   0.000   0.000
   5_bss:  0.312  55.883  -0.645  -0.814   1.459  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  65.263 0.3244  0.3911    81807.672
   1_bss:  63.379 0.3489  0.5378    80219.807
   1_xyz:  58.188 0.4148  0.6244    69289.762
   1_adp:  57.021 0.4299  0.7361    68724.861
   1_occ:  57.135 0.4285  0.7330    68941.433
   2_bss:  56.902 0.4314  0.6534    68542.784
   2_xyz:  48.240 0.5406  0.8120    52375.123
   2_adp:  46.830 0.5585  0.8465    50256.271
   2_occ:  46.930 0.5572  0.8440    50373.861
   3_bss:  46.751 0.5594  0.7800    50150.267
   3_xyz:  35.799 0.6904  0.9404    30544.384
   3_adp:  32.655 0.7271  0.9647    26532.375
   3_occ:  32.624 0.7274  0.9642    26437.609
   4_bss:  32.544 0.7282  0.9194    26358.153
   4_xyz:  26.237 0.7974  0.9700    17650.266
   4_adp:  22.743 0.8339  0.9768    13713.369
   4_occ:  22.710 0.8342  0.9768    13665.181
   5_bss:  22.619 0.8348  0.9568    13542.091
   5_xyz:  19.941 0.8614  0.9724    10958.735
   5_adp:  19.045 0.8704  0.9672    10282.040
   5_occ:  19.019 0.8706  0.9673    10253.226
   5_bss:  19.026 0.8706  0.9672    10263.671
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3908e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3908e+01
   1_xyz:   1.862  0.015  0.114 18.746  0.007  4.106   1.6804e-01
   1_adp:   1.862  0.015  0.114 18.746  0.007  4.106   1.6804e-01
   1_occ:   1.862  0.015  0.114 18.746  0.007  4.106   1.6804e-01
   2_bss:   1.862  0.015  0.114 18.746  0.007  4.106   1.6804e-01
   2_xyz:   1.225  0.010  0.079 16.881  0.005  4.125   1.0455e-01
   2_adp:   1.225  0.010  0.079 16.881  0.005  4.125   1.0455e-01
   2_occ:   1.225  0.010  0.079 16.881  0.005  4.125   1.0455e-01
   3_bss:   1.225  0.010  0.079 16.881  0.005  4.125   1.0455e-01
   3_xyz:   1.398  0.011  0.102 16.634  0.007  4.111   1.1526e-01
   3_adp:   1.398  0.011  0.102 16.634  0.007  4.111   1.1526e-01
   3_occ:   1.398  0.011  0.102 16.634  0.007  4.111   1.1526e-01
   4_bss:   1.398  0.011  0.102 16.634  0.007  4.111   1.1526e-01
   4_xyz:   1.120  0.008  0.081 16.059  0.004  4.124   7.4620e-02
   4_adp:   1.120  0.008  0.081 16.059  0.004  4.124   7.4620e-02
   4_occ:   1.120  0.008  0.081 16.059  0.004  4.124   7.4620e-02
   5_bss:   1.120  0.008  0.081 16.059  0.004  4.124   7.4620e-02
   5_xyz:   0.948  0.006  0.072 15.564  0.003  4.130   5.7364e-02
   5_adp:   0.948  0.006  0.072 15.564  0.003  4.130   5.7364e-02
   5_occ:   0.948  0.006  0.072 15.564  0.003  4.130   5.7364e-02
   5_bss:   0.948  0.006  0.072 15.564  0.003  4.130   5.7364e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9866e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9866e+00
   1_xyz:  14.658  0.206  0.456 85.197  0.034  2.051   1.1251e-01
   1_adp:  14.658  0.206  0.456 85.197  0.034  2.051   1.1251e-01
   1_occ:  14.658  0.206  0.456 85.197  0.034  2.051   1.1251e-01
   2_bss:  14.658  0.206  0.456 85.197  0.034  2.051   1.1251e-01
   2_xyz:   7.579  0.099  0.268 81.707  0.043  2.078   2.1379e-01
   2_adp:   7.579  0.099  0.268 81.707  0.043  2.078   2.1379e-01
   2_occ:   7.579  0.099  0.268 81.707  0.043  2.078   2.1379e-01
   3_bss:   7.579  0.099  0.268 81.707  0.043  2.078   2.1379e-01
   3_xyz:   9.443  0.078  0.364 86.417  0.060  2.101   9.0953e-02
   3_adp:   9.443  0.078  0.364 86.417  0.060  2.101   9.0953e-02
   3_occ:   9.443  0.078  0.364 86.417  0.060  2.101   9.0953e-02
   4_bss:   9.443  0.078  0.364 86.417  0.060  2.101   9.0953e-02
   4_xyz:   7.742  0.059  0.300 82.183  0.045  2.308   5.5814e-02
   4_adp:   7.742  0.059  0.300 82.183  0.045  2.308   5.5814e-02
   4_occ:   7.742  0.059  0.300 82.183  0.045  2.308   5.5814e-02
   5_bss:   7.742  0.059  0.300 82.183  0.045  2.308   5.5814e-02
   5_xyz:   7.053  0.042  0.228 79.703  0.039  2.327   3.4325e-02
   5_adp:   7.053  0.042  0.228 79.703  0.039  2.327   3.4325e-02
   5_occ:   7.053  0.042  0.228 79.703  0.039  2.327   3.4325e-02
   5_bss:   7.053  0.042  0.228 79.703  0.039  2.327   3.4325e-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:  80.24   0.00  17.27  79.44   0.00  15.94  80.24   0.00  24.50
   1_occ:  80.24   0.00  17.27  79.44   0.00  15.94  80.24   0.00  24.50
   2_bss:  80.24   0.00  17.27  79.44   0.00  15.94  80.24   0.00  24.50
   2_xyz:  80.24   0.00  17.27  79.44   0.00  15.94  80.24   0.00  24.50
   2_adp:  83.57   0.00  16.96  76.98   0.00  14.80  83.57   0.00  28.74
   2_occ:  83.57   0.00  16.96  76.98   0.00  14.80  83.57   0.00  28.74
   3_bss:  83.57   0.00  16.96  76.98   0.00  14.80  83.57   0.00  28.74
   3_xyz:  83.57   0.00  16.96  76.98   0.00  14.80  83.57   0.00  28.74
   3_adp: 134.30   0.00  16.72 134.30   0.00  13.62  81.28   0.00  33.58
   3_occ: 134.30   0.00  16.72 134.30   0.00  13.62  81.28   0.00  33.58
   4_bss: 134.30   0.00  16.72 134.30   0.00  13.62  81.28   0.00  33.58
   4_xyz: 134.30   0.00  16.72 134.30   0.00  13.62  81.28   0.00  33.58
   4_adp:  87.64   0.00  16.64  83.05   0.00  11.89  87.64   3.19  42.52
   4_occ:  87.64   0.00  16.64  83.05   0.00  11.89  87.64   3.19  42.52
   5_bss:  87.64   0.00  16.64  83.05   0.00  11.89  87.64   3.19  42.52
   5_xyz:  87.64   0.00  16.64  83.05   0.00  11.89  87.64   3.19  42.52
   5_adp: 108.37   0.00  17.15  90.52   0.00  11.65 108.37   4.08  47.13
   5_occ: 108.37   0.00  17.15  90.52   0.00  11.65 108.37   4.08  47.13
   5_bss: 108.75   0.38  17.54  90.91   0.38  12.03 108.75   4.47  47.51
------------------------------------------------------------------------
 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:    1.327    0.016    0.421
   1_adp:    1.327    0.016    0.421
   1_occ:    1.327    0.016    0.421
   2_bss:    1.327    0.016    0.421
   2_xyz:    1.790    0.024    0.564
   2_adp:    1.790    0.024    0.564
   2_occ:    1.790    0.024    0.564
   3_bss:    1.790    0.024    0.564
   3_xyz:    1.957    0.016    0.770
   3_adp:    1.957    0.016    0.770
   3_occ:    1.957    0.016    0.770
   4_bss:    1.957    0.016    0.770
   4_xyz:    1.755    0.039    0.850
   4_adp:    1.755    0.039    0.850
   4_occ:    1.755    0.039    0.850
   5_bss:    1.755    0.039    0.850
   5_xyz:    1.807    0.046    0.881
   5_adp:    1.807    0.046    0.881
   5_occ:    1.807    0.046    0.881
   5_bss:    1.807    0.046    0.881
------------------------------------------------------------------------

CPU time actual refinement: 346.47


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_747/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_747/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_747/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_747/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_747/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 346.31 
  Macro-tasks:
    bulk solvent and scale       = 41.73  
    individual site refinement   = 145.13 
    weights calculation          = 32.98  
    collect and process          = 6.34   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 226.33 
  Micro-tasks:
    mask                            = 2.39   
    f_calc                          = 108.51 
    alpha_beta                      = 8.23   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 118.59 
    fmodel                         = 7.26   
    r_factors                      = 0.23   
    phase_errors                   = 10.00  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 256.59 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.884 micro seconds
Total CPU time: 6.00 minutes
from_scatterers_fft:    645 calls, 108.19 s
gradients_fft:          590 calls, 105.44 s

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

# Date 2008-01-16 Time 02:20:15 PST -0800 (1200478815.69 s)
Start R-work = 0.5120, R-free = 0.5023 (no bulk solvent and anisotropic scale)
Final R-work = 0.1579, R-free = 0.2145 (no bulk solvent and anisotropic scale)

Start R-work = 0.5043, R-free = 0.4912
Final R-work = 0.1419, R-free = 0.1984