# Date 2008-01-16 Time 00:32:11 PST -0800 (1200472331.52 s)
#phil __OFF__

Command line arguments: "../42.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21041
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 42

-------------------------------------------------------------------------------
  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: (68.4938, 46.4607, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.75, per 1000 atoms: 0.97


================================== 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: (68.4938, 46.4607, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8486 1.95091
Completeness in resolution range: 0.931036
Completeness with d_max=infinity: 0.928213

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8486
                             d_min =   1.9509

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: (68.4938, 46.4607, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8486 1.95091
Completeness in resolution range: 0.931036
Completeness with d_max=infinity: 0.928213

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8490 -  4.1749 [2213/2240]  1988   225  10.2%
  bin  2:  4.1749 -  3.3260 [2129/2145]  1916   213  10.0%
  bin  3:  3.3260 -  2.9092 [2096/2115]  1894   202   9.6%
  bin  4:  2.9092 -  2.6448 [2072/2102]  1858   214  10.3%
  bin  5:  2.6448 -  2.4561 [2052/2071]  1844   208  10.1%
  bin  6:  2.4561 -  2.3119 [2061/2097]  1858   203   9.8%
  bin  7:  2.3119 -  2.1965 [2048/2082]  1846   202   9.9%
  bin  8:  2.1965 -  2.1012 [2041/2076]  1832   209  10.2%
  bin  9:  2.1012 -  2.0205 [1981/2049]  1790   191   9.6%
  bin 10:  2.0205 -  1.9509 [ 896/2063]   804    92  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_42/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: 0.11 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:
        1.04 -     1.81: 11
        1.81 -     2.59: 100
        2.59 -     3.36: 4124
        3.36 -     4.13: 9523
        4.13 -     4.90: 14958
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.043 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.073 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.320 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.372 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.528 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28711 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_42/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_42/model_refine_001.geo

CPU time processing inputs: 8.47


============================ 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 = 68.49375 46.4607 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5027   r_free= 0.4962   ksol= 0.00   Bsol= 0.00   scale= 0.783    |
|                                                                             |
| 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:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.299172                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8490 -  4.6567 0.99   1437  159 0.4106 0.3989      6.6203      6.6273|
|  2:  4.6567 -  3.7152 0.99   1388  154 0.4166 0.4602      6.7974      6.8796|
|  3:  3.7152 -  3.2512 0.99   1347  153 0.4834 0.4348      6.7038      6.6902|
|  4:  3.2512 -  2.9565 0.99   1346  143 0.5022 0.5175       6.547      6.5189|
|  5:  2.9565 -  2.7460 0.99   1328  153 0.5229 0.5159      6.3777      6.4503|
|  6:  2.7460 -  2.5850 0.99   1343  149 0.5416 0.5066      6.2919      6.1923|
|  7:  2.5850 -  2.4561 0.99   1311  151 0.5362 0.5299      6.2472      6.1631|
|  8:  2.4561 -  2.3497 0.98   1332  145 0.5422 0.5333      6.1815       6.208|
|  9:  2.3497 -  2.2595 0.98   1317  144 0.5474 0.5402      6.1369      6.1892|
| 10:  2.2595 -  2.1818 0.98   1320  141 0.5564 0.5330      6.0976      6.0946|
| 11:  2.1818 -  2.1138 1.00   1306  155 0.5421 0.5230      6.0203      6.0458|
| 12:  2.1138 -  2.0535 0.97   1314  138 0.5412 0.5284      5.9652      5.9651|
| 13:  2.0535 -  1.9996 0.86   1146  126 0.5559 0.4973      5.8979      5.8344|
| 14:  1.9996 -  1.9509 0.31    395   48 0.5345 0.5976      5.8976      5.7949|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8490 -  4.6567  1437   159  0.67  36.94   0.79     0.71      81304.74|
|  2:  4.6567 -  3.7152  1388   154  0.65  39.65   0.88     0.72     127131.29|
|  3:  3.7152 -  3.2512  1347   153  0.52  50.35   0.82     0.65     137560.58|
|  4:  3.2512 -  2.9565  1346   143  0.39  60.32   0.77     0.49     126666.19|
|  5:  2.9565 -  2.7460  1328   153  0.28  69.15   0.73     0.35     101405.24|
|  6:  2.7460 -  2.5850  1343   149  0.21  74.31   0.70     0.26      89357.88|
|  7:  2.5850 -  2.4561  1311   151  0.22  73.40   0.73     0.26      76582.46|
|  8:  2.4561 -  2.3497  1332   145  0.26  70.94   0.72     0.31      66667.51|
|  9:  2.3497 -  2.2595  1317   144  0.29  67.99   0.72     0.37      59533.45|
| 10:  2.2595 -  2.1818  1320   141  0.30  67.76   0.72     0.36      51402.77|
| 11:  2.1818 -  2.1138  1306   155  0.27  70.23   0.73     0.35      52165.79|
| 12:  2.1138 -  2.0535  1314   138  0.24  71.85   0.75     0.33      46819.69|
| 13:  2.0535 -  1.9996  1146   126  0.24  71.97   0.71     0.33      41394.67|
| 14:  1.9996 -  1.9509   395    48  0.30  67.23   0.77     0.33      30868.67|
|alpha:            min =        0.26 max =            0.72 mean =         0.42|
|beta:             min =    30868.67 max =       137560.58 mean =     81026.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.35|
|phase err.(work): min =        0.00 max =           90.00 mean =        63.17|
|phase err.(test): min =        0.00 max =           89.93 mean =        63.64|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 20.064292             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.058   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.829673              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.465   (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 |  1.113 -  1.492:       10 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.492 -  1.870:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.870 -  2.249:      161 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.249 -  2.628:      618 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.628 -  3.006:     1449 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.006 -  3.385:     2579 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.385 -  3.764:     3998 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.764 -  4.143:     5180 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.143 -  4.521:     6770 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.521 -  4.900:     7937 |
|-----------------------------------------------------------------------------|
|-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 |       53.222 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.086    4.900  1.113 |       3.170 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.554)------------------------------------------|
|    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 = 11.554)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5082   r_free= 0.4995   ksol= 0.00   Bsol= 0.00   scale= 0.753    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.299567                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4941   r_free= 0.4865   ksol= 0.36   Bsol= 20.00   scale= 0.971   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.98,7.35,9.74,0.00,0.00,0.00); trace/3= 8.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.292548                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.112717             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.710   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.768062              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.592   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4941      final r-factor (work) = 0.4283          |
| start r-factor (free) = 0.4865      final r-factor (free) = 0.4481          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 103.9348 = 16.11 * 0.50 * 6.2948 + 1.00 * 53.2216                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 50.4178 = 16.11 * 0.50 * 6.2396 + 1.00 * 0.1498                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4283      final r-factor (work) = 0.3840          |
| start r-factor (free) = 0.4481      final r-factor (free) = 0.4445          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.0463 = 1.77 * 1.00 * 6.2396 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.9322 = 1.77 * 1.00 * 6.1711 + 1.00 * 0.0212                              |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.554)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.01   15.28    None  None   None       |
|    all(noH): 2823   0      0.00    66.01   15.28    None  None   None       |
|    Sol.    : 438    0      0.00    66.01   24.68    None  None   None       |
|    Mac.    : 2385   0      0.00    60.04   13.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.601:  745   |   5:    33.004 -  39.604:  116        |
|      1:     6.601 -  13.201:  715   |   6:    39.604 -  46.205:   77        |
|      2:    13.201 -  19.802:  533   |   7:    46.205 -  52.806:   41        |
|      3:    19.802 -  26.403:  358   |   8:    52.806 -  59.406:   18        |
|      4:    26.403 -  33.004:  213   |   9:    59.406 -  66.007:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3840 r_free = 0.4445             target_work(ml) = 6.160         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3842 r_free = 0.4451             target_work(ml) = 6.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3842   r_free= 0.4451   ksol= 0.36   Bsol= 20.00   scale= 1.113   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.98,7.35,9.74,0.00,0.00,0.00); trace/3= 8.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.158975                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3821   r_free= 0.4437   ksol= 0.34   Bsol= 39.01   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.64,3.71,6.39,0.00,0.00,0.00); trace/3= 4.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.161153                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.814543              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.707   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.664555              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.375  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3821      final r-factor (work) = 0.3096          |
| start r-factor (free) = 0.4437      final r-factor (free) = 0.3715          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.3288 = 8.81 * 0.50 * 6.1669 + 1.00 * 0.1498                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.8909 = 8.81 * 0.50 * 6.0798 + 1.00 * 0.0958                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3096      final r-factor (work) = 0.2850          |
| start r-factor (free) = 0.3715      final r-factor (free) = 0.3527          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0617 = 0.66 * 1.00 * 6.0798 + 1.00 * 0.0213                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9845 = 0.66 * 1.00 * 5.9620 + 1.00 * 0.0224                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.554)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.91   15.00    None  None   None       |
|    all(noH): 2823   0      0.00    69.91   15.00    None  None   None       |
|    Sol.    : 438    0      0.00    69.91   31.57    None  None   None       |
|    Mac.    : 2385   0      0.00    65.72   11.96    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.991:  883   |   5:    34.954 -  41.944:  106        |
|      1:     6.991 -  13.982:  785   |   6:    41.944 -  48.935:   63        |
|      2:    13.982 -  20.972:  477   |   7:    48.935 -  55.926:   44        |
|      3:    20.972 -  27.963:  265   |   8:    55.926 -  62.917:   18        |
|      4:    27.963 -  34.954:  170   |   9:    62.917 -  69.907:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2850 r_free = 0.3527             target_work(ml) = 5.934         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2848 r_free = 0.3522             target_work(ml) = 5.934         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2848   r_free= 0.3522   ksol= 0.34   Bsol= 39.01   scale= 1.071   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.64,3.71,6.39,0.00,0.00,0.00); trace/3= 4.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.934085                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2833   r_free= 0.3499   ksol= 0.35   Bsol= 51.88   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.57,2.04,4.15,0.00,0.00,0.00); trace/3= 2.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.932850                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.945139              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.734   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.819173              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.483   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2833      final r-factor (work) = 0.2086          |
| start r-factor (free) = 0.3499      final r-factor (free) = 0.2659          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.8193 = 5.95 * 0.50 * 5.9624 + 1.00 * 0.0958                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.3761 = 5.95 * 0.50 * 5.8202 + 1.00 * 0.0751                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2086      final r-factor (work) = 0.1844          |
| start r-factor (free) = 0.2659      final r-factor (free) = 0.2478          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7825 = 0.82 * 1.00 * 5.8202 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6180 = 0.82 * 1.00 * 5.6200 + 1.00 * 0.0142                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.554)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.68   15.58    None  None   None       |
|    all(noH): 2823   0      0.00    87.68   15.58    None  None   None       |
|    Sol.    : 438    0      0.00    87.68   40.45    None  None   None       |
|    Mac.    : 2385   0      0.00    80.17   11.01    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 -   8.768: 1278   |   5:    43.840 -  52.608:   87        |
|      1:     8.768 -  17.536:  787   |   6:    52.608 -  61.376:   87        |
|      2:    17.536 -  26.304:  268   |   7:    61.376 -  70.144:   35        |
|      3:    26.304 -  35.072:  134   |   8:    70.144 -  78.912:   16        |
|      4:    35.072 -  43.840:  125   |   9:    78.912 -  87.680:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1844 r_free = 0.2478             target_work(ml) = 5.583         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1841 r_free = 0.2473             target_work(ml) = 5.582         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1841   r_free= 0.2473   ksol= 0.35   Bsol= 51.88   scale= 1.050   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.57,2.04,4.15,0.00,0.00,0.00); trace/3= 2.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.582059                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1828   r_free= 0.2479   ksol= 0.32   Bsol= 46.36   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.15,0.89,2.84,0.00,0.00,0.00); trace/3= 1.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.580562                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.723393              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.722  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.356688              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 107.748  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1828      final r-factor (work) = 0.1468          |
| start r-factor (free) = 0.2479      final r-factor (free) = 0.2026          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5491 = 3.72 * 0.50 * 5.6261 + 1.00 * 0.0750                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3031 = 3.72 * 0.50 * 5.4992 + 1.00 * 0.0654                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1468      final r-factor (work) = 0.1387          |
| start r-factor (free) = 0.2026      final r-factor (free) = 0.1889          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9765 = 0.36 * 1.00 * 5.4992 + 1.00 * 0.0150                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9346 = 0.36 * 1.00 * 5.3621 + 1.00 * 0.0220                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.554)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.22   15.02    None  None   None       |
|    all(noH): 2823   0      0.00    91.22   15.02    None  None   None       |
|    Sol.    : 438    0      2.33    89.67   40.12    None  None   None       |
|    Mac.    : 2385   0      0.00    91.22   10.42    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.122: 1395   |   5:    45.611 -  54.733:   92        |
|      1:     9.122 -  18.244:  787   |   6:    54.733 -  63.855:   63        |
|      2:    18.244 -  27.366:  208   |   7:    63.855 -  72.977:   32        |
|      3:    27.366 -  36.488:  116   |   8:    72.977 -  82.099:   14        |
|      4:    36.488 -  45.611:  113   |   9:    82.099 -  91.221:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1387 r_free = 0.1889             target_work(ml) = 5.326         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1385 r_free = 0.1887             target_work(ml) = 5.325         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1385   r_free= 0.1887   ksol= 0.32   Bsol= 46.36   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.15,0.89,2.84,0.00,0.00,0.00); trace/3= 1.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.324981                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1386   r_free= 0.1890   ksol= 0.32   Bsol= 46.36   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.36,0.48,2.33,0.00,0.00,0.00); trace/3= 0.81                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.324830                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.512562              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.777  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.165631              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.446   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1386      final r-factor (work) = 0.1222          |
| start r-factor (free) = 0.1890      final r-factor (free) = 0.1718          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4852 = 3.51 * 0.50 * 5.3635 + 1.00 * 0.0654                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3378 = 3.51 * 0.50 * 5.2760 + 1.00 * 0.0716                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1222      final r-factor (work) = 0.1206          |
| start r-factor (free) = 0.1718      final r-factor (free) = 0.1665          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8930 = 0.17 * 1.00 * 5.2760 + 1.00 * 0.0191                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8744 = 0.17 * 1.00 * 5.2245 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.554)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.61    91.29   14.51    None  None   None       |
|    all(noH): 2823   0      0.61    91.29   14.51    None  None   None       |
|    Sol.    : 438    0      3.13    85.67   38.13    None  None   None       |
|    Mac.    : 2385   0      0.61    91.29   10.17    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:     0.605 -   9.673: 1535   |   5:    45.947 -  55.015:   79        |
|      1:     9.673 -  18.742:  711   |   6:    55.015 -  64.083:   55        |
|      2:    18.742 -  27.810:  173   |   7:    64.083 -  73.152:   21        |
|      3:    27.810 -  36.878:  127   |   8:    73.152 -  82.220:   10        |
|      4:    36.878 -  45.947:  109   |   9:    82.220 -  91.288:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1206 r_free = 0.1665             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1204 r_free = 0.1664             target_work(ml) = 5.209         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1204   r_free= 0.1664   ksol= 0.32   Bsol= 46.36   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.36,0.48,2.33,0.00,0.00,0.00); trace/3= 0.81                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.208575                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8490 -  4.6567 0.99   1437  159 0.1016 0.1372      5.4259      5.6313|
|  2:  4.6567 -  3.7152 0.99   1388  154 0.0890 0.1187      5.4858      5.6868|
|  3:  3.7152 -  3.2512 0.99   1347  153 0.1162 0.1595      5.5483      5.8727|
|  4:  3.2512 -  2.9565 0.99   1346  143 0.1335 0.1804       5.504      5.7013|
|  5:  2.9565 -  2.7460 0.99   1328  153 0.1407 0.1565      5.3968      5.5241|
|  6:  2.7460 -  2.5850 0.99   1343  149 0.1332 0.2221      5.2589      5.5719|
|  7:  2.5850 -  2.4561 0.99   1311  151 0.1365 0.1807      5.2334       5.404|
|  8:  2.4561 -  2.3497 0.98   1332  145 0.1289 0.1742      5.1412      5.3518|
|  9:  2.3497 -  2.2595 0.98   1317  144 0.1295 0.1952      5.0911      5.3939|
| 10:  2.2595 -  2.1818 0.98   1320  141 0.1223 0.1687      5.0046       5.178|
| 11:  2.1818 -  2.1138 1.00   1306  155 0.1240 0.1942       4.971      5.3373|
| 12:  2.1138 -  2.0535 0.97   1314  138 0.1258 0.1696      4.9398      5.1497|
| 13:  2.0535 -  1.9996 0.86   1146  126 0.1121 0.1655      4.7763      4.9658|
| 14:  1.9996 -  1.9509 0.31    395   48 0.0960 0.1599      4.6265      4.9563|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8490 -  4.6567  1437   159  0.93  10.04   0.98     0.95       8267.26|
|  2:  4.6567 -  3.7152  1388   154  0.95   8.78   1.02     1.01      10137.09|
|  3:  3.7152 -  3.2512  1347   153  0.92  12.71   1.03     1.03      11911.98|
|  4:  3.2512 -  2.9565  1346   143  0.91  14.75   1.02     1.02      11252.74|
|  5:  2.9565 -  2.7460  1328   153  0.89  17.47   1.00     0.97       9888.43|
|  6:  2.7460 -  2.5850  1343   149  0.89  17.35   0.98     0.94       7524.89|
|  7:  2.5850 -  2.4561  1311   151  0.89  17.34   0.99     0.95       7010.01|
|  8:  2.4561 -  2.3497  1332   145  0.90  16.16   1.01     0.98       5969.71|
|  9:  2.3497 -  2.2595  1317   144  0.89  17.26   1.01     0.98       5626.54|
| 10:  2.2595 -  2.1818  1320   141  0.89  16.79   1.01     0.98       4786.96|
| 11:  2.1818 -  2.1138  1306   155  0.89  17.73   1.01     0.97       4827.97|
| 12:  2.1138 -  2.0535  1314   138  0.89  17.53   1.02     1.02       4445.67|
| 13:  2.0535 -  1.9996  1146   126  0.90  16.17   0.99     0.97       3280.59|
| 14:  1.9996 -  1.9509   395    48  0.93  12.03   1.00     0.97       2203.62|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2203.62 max =        11911.98 mean =      7261.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.24|
|phase err.(test): min =        0.00 max =           88.67 mean =        14.60|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1204   r_free= 0.1664   ksol= 0.32   Bsol= 47.18   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.18,-0.34,1.51,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.208575                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1204   r_free= 0.1664   ksol= 0.32   Bsol= 47.18   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.18,-0.34,1.51,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.208575                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8490 -  4.6567 0.99   1437  159 0.1016 0.1372      5.4259      5.6313|
|  2:  4.6567 -  3.7152 0.99   1388  154 0.0890 0.1187      5.4858      5.6868|
|  3:  3.7152 -  3.2512 0.99   1347  153 0.1162 0.1595      5.5483      5.8727|
|  4:  3.2512 -  2.9565 0.99   1346  143 0.1335 0.1804       5.504      5.7013|
|  5:  2.9565 -  2.7460 0.99   1328  153 0.1407 0.1565      5.3968      5.5241|
|  6:  2.7460 -  2.5850 0.99   1343  149 0.1332 0.2221      5.2589      5.5719|
|  7:  2.5850 -  2.4561 0.99   1311  151 0.1365 0.1807      5.2334       5.404|
|  8:  2.4561 -  2.3497 0.98   1332  145 0.1289 0.1742      5.1412      5.3518|
|  9:  2.3497 -  2.2595 0.98   1317  144 0.1295 0.1952      5.0911      5.3939|
| 10:  2.2595 -  2.1818 0.98   1320  141 0.1223 0.1687      5.0046       5.178|
| 11:  2.1818 -  2.1138 1.00   1306  155 0.1240 0.1942       4.971      5.3373|
| 12:  2.1138 -  2.0535 0.97   1314  138 0.1258 0.1696      4.9398      5.1497|
| 13:  2.0535 -  1.9996 0.86   1146  126 0.1121 0.1655      4.7763      4.9658|
| 14:  1.9996 -  1.9509 0.31    395   48 0.0960 0.1599      4.6265      4.9563|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8490 -  4.6567  1437   159  0.93  10.04   0.98     0.95       8267.26|
|  2:  4.6567 -  3.7152  1388   154  0.95   8.78   1.02     1.01      10137.09|
|  3:  3.7152 -  3.2512  1347   153  0.92  12.71   1.03     1.03      11911.98|
|  4:  3.2512 -  2.9565  1346   143  0.91  14.75   1.02     1.02      11252.74|
|  5:  2.9565 -  2.7460  1328   153  0.89  17.47   1.00     0.97       9888.43|
|  6:  2.7460 -  2.5850  1343   149  0.89  17.35   0.98     0.94       7524.89|
|  7:  2.5850 -  2.4561  1311   151  0.89  17.34   0.99     0.95       7010.01|
|  8:  2.4561 -  2.3497  1332   145  0.90  16.16   1.01     0.98       5969.71|
|  9:  2.3497 -  2.2595  1317   144  0.89  17.26   1.01     0.98       5626.54|
| 10:  2.2595 -  2.1818  1320   141  0.89  16.79   1.01     0.98       4786.96|
| 11:  2.1818 -  2.1138  1306   155  0.89  17.73   1.01     0.97       4827.97|
| 12:  2.1138 -  2.0535  1314   138  0.89  17.53   1.02     1.02       4445.67|
| 13:  2.0535 -  1.9996  1146   126  0.90  16.17   0.99     0.97       3280.59|
| 14:  1.9996 -  1.9509   395    48  0.93  12.03   1.00     0.97       2203.62|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2203.62 max =        11911.98 mean =      7261.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.24|
|phase err.(test): min =        0.00 max =           88.67 mean =        14.60|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.554)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.42    92.10   15.32    None  None   None       |
|    all(noH): 2823   0      1.42    92.10   15.32    None  None   None       |
|    Sol.    : 438    0      3.94    86.48   38.94    None  None   None       |
|    Mac.    : 2385   0      1.42    92.10   10.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.418 -  10.486: 1535   |   5:    46.760 -  55.828:   79        |
|      1:    10.486 -  19.555:  711   |   6:    55.828 -  64.896:   55        |
|      2:    19.555 -  28.623:  173   |   7:    64.896 -  73.965:   21        |
|      3:    28.623 -  37.691:  127   |   8:    73.965 -  83.033:   10        |
|      4:    37.691 -  46.760:  109   |   9:    83.033 -  92.101:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 320         
Filter by distance & map next to the model:
   mapped sites are within: 0.640 - 4.204
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 315 from: 320
   mapped sites are within: 0.705 - 4.204

peak=   10.766 closest distance to " CB  VAL A 230 " =    1.487
peak=    9.727 closest distance to " CB  VAL A 296 " =    1.552
peak=    7.626 closest distance to " O   HOH Z 130 " =    1.550
peak=    6.055 closest distance to " CD2 LEU A   5 " =    1.273
peak=    5.760 closest distance to " CG  PRO A  54 " =    1.376
peak=    5.740 closest distance to " O   HOH Z   9 " =    1.769
peak=    5.651 closest distance to " O   HOH Z 255 " =    1.017
peak=    5.586 closest distance to " NE2 GLN A  11 " =    1.169
peak=    5.553 closest distance to " O   HOH Z 188 " =    1.706
peak=    5.485 closest distance to " O   HOH Z 375 " =    1.311
peak=    5.415 closest distance to " CG  LEU A   5 " =    1.232
peak=    5.392 closest distance to " CB  ARG A 275 " =    0.934
peak=    5.279 closest distance to " CB  GLN A 223 " =    1.566
peak=    5.041 closest distance to " O   HOH Z 232 " =    2.319
peak=    4.987 closest distance to " O   HOH Z 403 " =    1.686
peak=    4.965 closest distance to " CD1AILE A 234 " =    0.957
peak=    4.961 closest distance to " O   HOH Z  43 " =    1.467
peak=    4.843 closest distance to " O   HOH Z 143 " =    1.681
peak=    4.791 closest distance to " CG  LEU A 228 " =    1.249
peak=    4.741 closest distance to " O   HOH Z 142 " =    1.707
peak=    4.690 closest distance to " NH2 ARG A  56 " =    2.029
peak=    4.676 closest distance to " NH2AARG A 145 " =    1.038
peak=    4.628 closest distance to " O   HOH Z 272 " =    1.874
peak=    4.573 closest distance to " O   HOH Z 238 " =    1.435
peak=    4.551 closest distance to " CG  GLN A  58 " =    1.127
peak=    4.550 closest distance to " O   HOH Z 248 " =    1.358
peak=    4.488 closest distance to " O   HOH Z 369 " =    2.334
peak=    4.473 closest distance to " CB  VAL A 265 " =    1.404
peak=    4.465 closest distance to " O   HOH Z 236 " =    1.443
peak=    4.448 closest distance to " O   HOH Z 402 " =    1.435
peak=    4.420 closest distance to " O   HOH Z 126 " =    1.915
peak=    4.416 closest distance to " O   SER A  87 " =    2.204
peak=    4.409 closest distance to " O   HOH Z  85 " =    1.593
peak=    4.395 closest distance to " O   HOH Z 107 " =    0.839
peak=    4.392 closest distance to " CG2 ILE A 234 " =    1.007
peak=    4.389 closest distance to " O   HOH Z  78 " =    1.662
peak=    4.362 closest distance to " CB  GLN A 183 " =    1.200
peak=    4.358 closest distance to " CA  VAL A 230 " =    1.248
peak=    4.342 closest distance to " O   HOH Z 124 " =    1.293
peak=    4.341 closest distance to " O   HOH Z   3 " =    2.260
peak=    4.338 closest distance to " O   HOH Z 425 " =    1.519
peak=    4.334 closest distance to " CD2 TRP A 179 " =    1.366
peak=    4.330 closest distance to " NH2AARG A 190 " =    1.942
peak=    4.296 closest distance to " CB  ASN A 148 " =    1.394
peak=    4.286 closest distance to " CB  PRO A  54 " =    0.945
peak=    4.253 closest distance to " CB  ASN A 142 " =    1.046
peak=    4.244 closest distance to " CB  ARG A  79 " =    1.500
peak=    4.228 closest distance to " CB  GLU A 152 " =    1.198
peak=    4.213 closest distance to " O   HOH Z 417 " =    1.319
peak=    4.201 closest distance to " O   HOH Z 112 " =    1.169
peak=    4.200 closest distance to " O   HOH Z 126 " =    1.621
peak=    4.196 closest distance to " O   HOH Z  49 " =    1.155
peak=    4.179 closest distance to " O   HOH Z 182 " =    1.048
peak=    4.177 closest distance to " O   HOH Z 251 " =    1.684
peak=    4.174 closest distance to " O   HOH Z 287 " =    1.948
peak=    4.174 closest distance to " CB  ALA A   9 " =    1.655
peak=    4.173 closest distance to " O   HOH Z 193 " =    1.884
peak=    4.134 closest distance to " O   HOH Z 178 " =    1.226
peak=    4.121 closest distance to " CG  LYS A  76 " =    1.525
peak=    4.104 closest distance to " O   HOH Z 359 " =    1.583
peak=    4.101 closest distance to " O   HOH Z 427 " =    2.822
peak=    4.095 closest distance to " O   HOH Z 234 " =    3.623
peak=    4.088 closest distance to " NH1 ARG A 138 " =    1.061
peak=    4.083 closest distance to " CG  PRO A 243 " =    1.123
peak=    4.075 closest distance to " CB AVAL A  41 " =    1.093
peak=    4.070 closest distance to " OG ASER A 258 " =    3.003
peak=    4.070 closest distance to " O   HOH Z  69 " =    1.034
peak=    4.069 closest distance to " N   ASP A 162 " =    1.165
peak=    4.039 closest distance to " O   HOH Z  69 " =    1.933
peak=    4.013 closest distance to " O   HOH Z  97 " =    1.436
peak=    4.001 closest distance to " CD  ARG A 269 " =    1.001
peak=    3.988 closest distance to " O   HOH Z  30 " =    1.704
peak=    3.988 closest distance to " O   HOH Z 261 " =    2.207
peak=    3.987 closest distance to " O   HOH Z 346 " =    1.581
peak=    3.969 closest distance to " CB  SER A  26 " =    1.759
peak=    3.945 closest distance to " O   HOH Z 406 " =    1.370
peak=    3.935 closest distance to " O   HOH Z 193 " =    1.490
peak=    3.933 closest distance to " O   HOH Z 188 " =    2.174
peak=    3.930 closest distance to " O   HOH Z 380 " =    1.772
peak=    3.909 closest distance to " N   ASN A  39 " =    1.222
peak=    3.909 closest distance to " O   HOH Z  22 " =    2.028
peak=    3.904 closest distance to " O   HOH Z  63 " =    1.847
peak=    3.899 closest distance to " CG AARG A 275 " =    1.285
peak=    3.892 closest distance to " CZ  PHE A 218 " =    1.202
peak=    3.878 closest distance to " NZ  LYS A 117 " =    2.817
peak=    3.877 closest distance to " CB  GLN A  88 " =    1.222
peak=    3.872 closest distance to " O   HOH Z 423 " =    1.793
peak=    3.872 closest distance to " CA  ALA A  51 " =    0.948
peak=    3.870 closest distance to " O   HOH Z  95 " =    1.258
peak=    3.855 closest distance to " CB  VAL A 202 " =    1.605
peak=    3.850 closest distance to " O   HOH Z  10 " =    1.788
peak=    3.847 closest distance to " O   HOH Z  40 " =    1.601
peak=    3.845 closest distance to " O   HOH Z  61 " =    1.770
peak=    3.842 closest distance to " O   HOH Z 128 " =    2.037
peak=    3.842 closest distance to " CB  GLU A 277 " =    3.555
peak=    3.835 closest distance to " O   HOH Z 246 " =    1.093
peak=    3.832 closest distance to " ND2 ASN A 187 " =    1.622
peak=    3.820 closest distance to " O   HOH Z 123 " =    1.320
peak=    3.819 closest distance to " O   HOH Z 303 " =    2.208
peak=    3.818 closest distance to " CA  PHE A 283 " =    1.113
peak=    3.813 closest distance to " O   HOH Z 422 " =    2.277
peak=    3.803 closest distance to " CB  ARG A  79 " =    1.013
peak=    3.783 closest distance to " O   PRO A 198 " =    1.585
peak=    3.781 closest distance to " CG2 VAL A 257 " =    0.889
peak=    3.771 closest distance to " CB  SER A  63 " =    1.234
peak=    3.763 closest distance to " CG  LEU A 167 " =    1.278
peak=    3.762 closest distance to " O   HOH Z 258 " =    2.130
peak=    3.751 closest distance to " O   HOH Z 213 " =    1.943
peak=    3.730 closest distance to " N   PHE A 130 " =    1.345
peak=    3.723 closest distance to " CD2 LEU A 228 " =    1.300
peak=    3.715 closest distance to " O   HOH Z 389 " =    1.581
peak=    3.711 closest distance to " O   HOH Z  80 " =    1.636
peak=    3.700 closest distance to " O   HOH Z  88 " =    2.681
peak=    3.688 closest distance to " CD2 TYR A 186 " =    1.094
peak=    3.684 closest distance to " CB  THR A  31 " =    1.547
peak=    3.659 closest distance to " CD1 ILE A 199 " =    1.365
peak=    3.658 closest distance to " CG  MET A 185 " =    1.173
peak=    3.653 closest distance to " CG  PRO A 280 " =    0.869
peak=    3.650 closest distance to " O   HOH Z 353 " =    2.464
peak=    3.641 closest distance to " CB  THR A  52 " =    1.012
peak=    3.640 closest distance to " ND2 ASN A 249 " =    0.954
peak=    3.636 closest distance to " O   HOH Z 421 " =    2.300
peak=    3.632 closest distance to " O  BHOH Z 338 " =    2.419
peak=    3.623 closest distance to " O   HOH Z 265 " =    2.001
peak=    3.616 closest distance to " O   HOH Z 344 " =    1.337
peak=    3.613 closest distance to " O   HOH Z   7 " =    1.115
peak=    3.609 closest distance to " O   HOH Z 398 " =    1.399
peak=    3.600 closest distance to " O   HOH Z 222 " =    2.374
peak=    3.592 closest distance to " O   HOH Z 156 " =    3.107
peak=    3.589 closest distance to " CB  ASN A  39 " =    0.849
peak=    3.587 closest distance to " O   HOH Z 405 " =    1.432
peak=    3.584 closest distance to " O   HOH Z  11 " =    1.536
peak=    3.564 closest distance to " O   HOH Z 298 " =    1.660
peak=    3.555 closest distance to " O   HOH Z 334 " =    1.423
peak=    3.555 closest distance to " O   HOH Z 365 " =    2.674
peak=    3.544 closest distance to " CA  GLY A 241 " =    4.071
peak=    3.544 closest distance to " CE3 TRP A 150 " =    1.035
peak=    3.540 closest distance to " CA  ASN A 217 " =    1.164
peak=    3.538 closest distance to " O   HOH Z  59 " =    1.797
peak=    3.538 closest distance to " O   HOH Z 153 " =    3.714
peak=    3.538 closest distance to " O   HOH Z 130 " =    2.053
peak=    3.535 closest distance to " CG2 ILE A  20 " =    1.665
peak=    3.527 closest distance to " O   HOH Z 415 " =    3.418
peak=    3.525 closest distance to " O   HOH Z 154 " =    2.221
peak=    3.524 closest distance to " O   HOH Z  44 " =    1.892
peak=    3.519 closest distance to " CB  SER A   3 " =    1.209
peak=    3.519 closest distance to " N   ARG A 156 " =    1.302
peak=    3.516 closest distance to " O   THR A 182 " =    1.434
peak=    3.516 closest distance to " CB  ASN A 110 " =    1.099
peak=    3.515 closest distance to " CA  TYR A  30 " =    1.085
peak=    3.511 closest distance to " CB  ARG A 156 " =    1.185
peak=    3.503 closest distance to " CG2 ILE A 120 " =    1.209
peak=    3.496 closest distance to " CA  ASP A 162 " =    0.919
peak=    3.496 closest distance to " CG  PRO A 213 " =    1.239
peak=    3.494 closest distance to " O   HOH Z 158 " =    3.136
peak=    3.482 closest distance to " CB  ALA A 248 " =    1.364
peak=    3.476 closest distance to " O   HOH Z  59 " =    1.934
peak=    3.474 closest distance to " O   HOH Z 141 " =    1.616
peak=    3.473 closest distance to " CA  ASN A 215 " =    0.951
peak=    3.471 closest distance to " O   HOH Z  76 " =    1.133
peak=    3.466 closest distance to " CB  PHE A 204 " =    0.773
peak=    3.462 closest distance to " CA  TRP A 150 " =    0.829
peak=    3.462 closest distance to " O   HOH Z 214 " =    2.728
peak=    3.460 closest distance to " CB  LEU A 300 " =    0.991
peak=    3.451 closest distance to " O   HOH Z 249 " =    1.052
peak=    3.446 closest distance to " O   HOH Z 385 " =    3.885
peak=    3.443 closest distance to " O   HOH Z 128 " =    2.018
peak=    3.442 closest distance to " CA  GLY A 267 " =    0.977
peak=    3.432 closest distance to " O   HOH Z 272 " =    2.095
peak=    3.430 closest distance to " O   HOH Z 299 " =    4.152
peak=    3.425 closest distance to " CB  ASP A 124 " =    0.856
peak=    3.424 closest distance to " O   HOH Z  88 " =    2.989
peak=    3.421 closest distance to " CE  LYS A 119 " =    1.185
peak=    3.421 closest distance to " CG  GLN A  88 " =    1.141
peak=    3.417 closest distance to " CB  ALA A 114 " =    1.216
peak=    3.410 closest distance to " CG  LYS A 119 " =    0.992
peak=    3.410 closest distance to " O   HOH Z   9 " =    1.825
peak=    3.402 closest distance to " CA  ARG A 195 " =    1.232
peak=    3.399 closest distance to " O   HOH Z 254 " =    1.439
peak=    3.393 closest distance to " O   HOH Z 273 " =    3.150
peak=    3.391 closest distance to " CA  ILE A 234 " =    1.069
peak=    3.388 closest distance to " O   HOH Z  97 " =    1.914
peak=    3.388 closest distance to " O   HOH Z 222 " =    2.131
peak=    3.388 closest distance to " CB  TRP A 266 " =    1.175
peak=    3.385 closest distance to " CB  SER A 216 " =    0.793
peak=    3.384 closest distance to " CB  ASN A 215 " =    1.102
peak=    3.383 closest distance to " O   HOH Z 423 " =    1.431
peak=    3.381 closest distance to " CB  TYR A 169 " =    0.727
peak=    3.379 closest distance to " O   HOH Z 425 " =    1.863
peak=    3.378 closest distance to " O   HOH Z 284 " =    2.882
peak=    3.372 closest distance to " O   HOH Z 298 " =    4.204
peak=    3.368 closest distance to " CD  LYS A 166 " =    1.277
peak=    3.365 closest distance to " O   HOH Z 193 " =    1.534
peak=    3.363 closest distance to " O   HOH Z  68 " =    2.065
peak=    3.352 closest distance to " O   HOH Z 132 " =    2.130
peak=    3.352 closest distance to " O   HOH Z 162 " =    2.367
peak=    3.351 closest distance to " CG  LYS A 289 " =    1.417
peak=    3.351 closest distance to " O   HOH Z 337 " =    2.063
peak=    3.350 closest distance to " NE2 GLN A  73 " =    1.403
peak=    3.349 closest distance to " NE  ARG A  56 " =    3.438
peak=    3.348 closest distance to " CA  LYS A 117 " =    1.095
peak=    3.344 closest distance to " O   HOH Z 128 " =    1.899
peak=    3.343 closest distance to " CA  ASP A 149 " =    1.126
peak=    3.330 closest distance to " OG  SER A  62 " =    2.778
peak=    3.328 closest distance to " CA  ASN A 127 " =    0.962
peak=    3.327 closest distance to " CB  ASP A 191 " =    1.149
peak=    3.326 closest distance to " O   HOH Z 355 " =    1.643
peak=    3.323 closest distance to " CG  GLU A 277 " =    1.785
peak=    3.315 closest distance to " O   HOH Z 371 " =    1.534
peak=    3.315 closest distance to " CD1 ILE A  33 " =    1.701
peak=    3.314 closest distance to " CG  GLN A  77 " =    1.092
peak=    3.312 closest distance to " OG1 THR A 221 " =    1.375
peak=    3.308 closest distance to " CE1 TYR A 186 " =    1.214
peak=    3.308 closest distance to " O   HOH Z 146 " =    1.413
peak=    3.307 closest distance to " CB  ARG A 190 " =    1.622
peak=    3.304 closest distance to " N   SER A 135 " =    1.381
peak=    3.303 closest distance to " O   HOH Z 323 " =    1.463
peak=    3.301 closest distance to " CB  ASN A 187 " =    1.073
peak=    3.301 closest distance to " O   HOH Z  55 " =    2.114
peak=    3.299 closest distance to " CG2 VAL A 197 " =    1.135
peak=    3.297 closest distance to " CE  LYS A  76 " =    0.922
peak=    3.294 closest distance to " O   HOH Z 250 " =    1.525
peak=    3.292 closest distance to " O   HOH Z  92 " =    2.126
peak=    3.289 closest distance to " O   HOH Z 158 " =    3.151
peak=    3.287 closest distance to " O   HOH Z 196 " =    1.169
peak=    3.280 closest distance to " O   HOH Z 305 " =    3.445
peak=    3.280 closest distance to " O   HOH Z 368 " =    2.251
peak=    3.271 closest distance to " O   HOH Z  26 " =    1.103
peak=    3.265 closest distance to " O   HOH Z   6 " =    1.997
peak=    3.262 closest distance to " O   HOH Z 132 " =    2.615
peak=    3.255 closest distance to " O   HOH Z  50 " =    1.749
peak=    3.255 closest distance to " CG  MET A 113 " =    0.840
peak=    3.252 closest distance to " O   PRO A 198 " =    1.578
peak=    3.249 closest distance to " O   HOH Z 137 " =    1.557
peak=    3.246 closest distance to " CB  ALA A 114 " =    1.106
peak=    3.244 closest distance to " O   HOH Z   5 " =    2.216
peak=    3.242 closest distance to " CG  ARG A 138 " =    1.077
peak=    3.239 closest distance to " CA  ARG A 159 " =    1.097
peak=    3.237 closest distance to " CD  ARG A 195 " =    3.592
peak=    3.235 closest distance to " CB  SER A 212 " =    1.530
peak=    3.234 closest distance to " O   HOH Z 368 " =    3.544
peak=    3.232 closest distance to " O   HOH Z 148 " =    2.292
peak=    3.229 closest distance to " CG  GLU A  37 " =    0.902
peak=    3.229 closest distance to " CG  PHE A 204 " =    0.914
peak=    3.228 closest distance to " O   HOH Z 325 " =    2.042
peak=    3.226 closest distance to " O   THR A 220 " =    1.280
peak=    3.226 closest distance to " O   HOH Z 180 " =    2.163
peak=    3.225 closest distance to " O   HOH Z  78 " =    2.035
peak=    3.225 closest distance to " O   HOH Z 283 " =    2.097
peak=    3.224 closest distance to " O   HOH Z   1 " =    1.625
peak=    3.223 closest distance to " CB  PRO A  90 " =    1.186
peak=    3.222 closest distance to " N   GLN A 278 " =    1.463
peak=    3.220 closest distance to " O   HOH Z 394 " =    1.714
peak=    3.218 closest distance to " N   CYS A 260 " =    0.884
peak=    3.216 closest distance to " NE AARG A 145 " =    0.870
peak=    3.214 closest distance to " O   HOH Z 191 " =    3.159
peak=    3.210 closest distance to " CB  ARG A 102 " =    0.895
peak=    3.210 closest distance to " OE1 GLN A 223 " =    2.467
peak=    3.206 closest distance to " O   HOH Z 223 " =    1.405
peak=    3.205 closest distance to " CG1 ILE A 120 " =    1.380
peak=    3.200 closest distance to " OG BSER A 210 " =    1.526
peak=    3.199 closest distance to " O   HOH Z 329 " =    4.047
peak=    3.198 closest distance to " ND1 HIS A  81 " =    1.634
peak=    3.197 closest distance to " CG1 ILE A  49 " =    1.544
peak=    3.196 closest distance to " O   HOH Z 129 " =    1.088
peak=    3.195 closest distance to " CD  ARG A 195 " =    0.878
peak=    3.195 closest distance to " O   HOH Z 281 " =    1.614
peak=    3.191 closest distance to " CA  GLY A 118 " =    0.705
peak=    3.190 closest distance to " O   HOH Z  41 " =    2.057
peak=    3.190 closest distance to " CG1 ILE A 120 " =    1.087
peak=    3.186 closest distance to " O   HOH Z 106 " =    3.089
peak=    3.186 closest distance to " N   ASN A 148 " =    1.106
peak=    3.180 closest distance to " O   HOH Z 213 " =    1.666
peak=    3.178 closest distance to " CA  LEU A 282 " =    1.194
peak=    3.177 closest distance to " NZ  LYS A 117 " =    1.222
peak=    3.177 closest distance to " O   HOH Z 344 " =    2.709
peak=    3.174 closest distance to " O   HOH Z 392 " =    2.770
peak=    3.172 closest distance to " CA  VAL A 125 " =    1.030
peak=    3.171 closest distance to " O   GLN A 194 " =    1.607
peak=    3.168 closest distance to " CA  ARG A  36 " =    0.996
peak=    3.168 closest distance to " O   HOH Z 421 " =    3.430
peak=    3.167 closest distance to " CB  ALA A  10 " =    0.718
peak=    3.153 closest distance to " CB  ARG A 219 " =    1.086
peak=    3.152 closest distance to " O   HOH Z 371 " =    2.435
peak=    3.148 closest distance to " O   ASP A 124 " =    1.182
peak=    3.145 closest distance to " O   GLY A  23 " =    2.406
peak=    3.144 closest distance to " OG BSER A 164 " =    2.145
peak=    3.142 closest distance to " O   HOH Z  39 " =    1.222
peak=    3.135 closest distance to " O   ASN A  74 " =    1.499
peak=    3.134 closest distance to " CG2 THR A 221 " =    1.170
peak=    3.131 closest distance to " CB  ALA A 160 " =    1.384
peak=    3.130 closest distance to " CG BARG A 102 " =    1.847
peak=    3.129 closest distance to " O   HOH Z 291 " =    1.409
peak=    3.123 closest distance to " O   HOH Z 172 " =    3.124
peak=    3.121 closest distance to " O   HOH Z  94 " =    2.091
peak=    3.119 closest distance to " O   HOH Z 194 " =    2.200
peak=    3.116 closest distance to " CA  LYS A 290 " =    1.191
peak=    3.113 closest distance to " O   HOH Z 365 " =    1.539
peak=    3.111 closest distance to " O   HOH Z  59 " =    2.237
peak=    3.111 closest distance to " NE2 GLN A 223 " =    1.869
peak=    3.104 closest distance to " CB  GLU A 128 " =    0.985
peak=    3.104 closest distance to " O   ASN A 284 " =    1.665
peak=    3.098 closest distance to " O   HOH Z 359 " =    4.052
peak=    3.096 closest distance to " CD  LYS A 119 " =    1.828
peak=    3.091 closest distance to " O   HOH Z 322 " =    1.916
peak=    3.091 closest distance to " O   HOH Z 200 " =    1.698
peak=    3.086 closest distance to " N   ARG A 190 " =    1.033
peak=    3.080 closest distance to " O   LEU A 228 " =    1.777
peak=    3.078 closest distance to " NH2BARG A 190 " =    1.391
peak=    3.067 closest distance to " CZ  PHE A  38 " =    1.036
peak=    3.065 closest distance to " CA  SER A  87 " =    0.976
peak=    3.048 closest distance to " O   GLY A 302 " =    1.869
peak=    3.034 closest distance to " CB  ALA A 295 " =    1.386
peak=    3.033 closest distance to " O   HOH Z 303 " =    2.380
peak=    3.010 closest distance to " O   HOH Z 293 " =    1.570

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.427 - 5.761
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 197
   mapped sites are within: 0.728 - 5.761

peak=   -4.740 closest distance to " O   HOH Z 193 " =    0.734
peak=   -4.712 closest distance to " O   HOH Z 211 " =    1.041
peak=   -4.643 closest distance to " O   HOH Z  69 " =    1.549
peak=   -4.582 closest distance to " C   HIS A 108 " =    1.203
peak=   -4.581 closest distance to " CG  GLN A  58 " =    0.899
peak=   -4.275 closest distance to " CD1 LEU A 255 " =    2.741
peak=   -4.163 closest distance to " CB  ALA A  43 " =    2.422
peak=   -4.139 closest distance to " O   PRO A 198 " =    1.234
peak=   -4.077 closest distance to " O   HOH Z 290 " =    1.046
peak=   -4.048 closest distance to " CD  ARG A  14 " =    3.009
peak=   -4.041 closest distance to " OG BSER A 134 " =    1.325
peak=   -4.036 closest distance to " CD  ARG A 156 " =    1.954
peak=   -4.015 closest distance to " O   PRO A 163 " =    1.953
peak=   -4.009 closest distance to " O   HOH Z 394 " =    1.451
peak=   -3.998 closest distance to " O   HOH Z 100 " =    0.828
peak=   -3.957 closest distance to " O   HOH Z 131 " =    4.140
peak=   -3.883 closest distance to " O   HOH Z 429 " =    1.632
peak=   -3.860 closest distance to " NE2 GLN A  88 " =    1.166
peak=   -3.857 closest distance to " CD  PRO A 213 " =    2.014
peak=   -3.796 closest distance to " O   HOH Z 134 " =    4.167
peak=   -3.783 closest distance to " O   HOH Z  26 " =    1.024
peak=   -3.759 closest distance to " CE2 TYR A  30 " =    2.748
peak=   -3.734 closest distance to " CD1 ILE A 263 " =    2.673
peak=   -3.718 closest distance to " O   HOH Z 267 " =    5.437
peak=   -3.715 closest distance to " CB  ASP A 132 " =    2.429
peak=   -3.714 closest distance to " CB  SER A 210 " =    1.175
peak=   -3.706 closest distance to " O   HOH Z 203 " =    1.742
peak=   -3.704 closest distance to " CD2 TYR A 293 " =    1.950
peak=   -3.697 closest distance to " CG  GLN A 223 " =    2.107
peak=   -3.690 closest distance to " CE  MET A 105 " =    2.447
peak=   -3.688 closest distance to " O   HOH Z 191 " =    5.587
peak=   -3.682 closest distance to " O   HOH Z 166 " =    2.060
peak=   -3.681 closest distance to " CG2 ILE A  20 " =    2.915
peak=   -3.668 closest distance to " O   VAL A 189 " =    2.540
peak=   -3.664 closest distance to " O   VAL A  67 " =    2.357
peak=   -3.662 closest distance to " OH  TYR A 172 " =    1.802
peak=   -3.649 closest distance to " C   ASN A 285 " =    2.101
peak=   -3.646 closest distance to " OD1 ASN A 301 " =    1.909
peak=   -3.640 closest distance to " CB  GLN A  55 " =    1.416
peak=   -3.628 closest distance to " O   ALA A 227 " =    1.346
peak=   -3.617 closest distance to " CD1 LEU A 101 " =    2.269
peak=   -3.616 closest distance to " NE2 GLN A  55 " =    1.402
peak=   -3.615 closest distance to " N   PHE A  59 " =    2.087
peak=   -3.604 closest distance to " O   HOH Z 185 " =    1.500
peak=   -3.602 closest distance to " OE1 GLN A 183 " =    1.607
peak=   -3.592 closest distance to " CG1 VAL A 112 " =    2.789
peak=   -3.591 closest distance to " CG  LEU A   5 " =    0.845
peak=   -3.590 closest distance to " CG2 ILE A  49 " =    2.847
peak=   -3.590 closest distance to " O   HOH Z 351 " =    1.686
peak=   -3.575 closest distance to " O   HOH Z 281 " =    3.043
peak=   -3.570 closest distance to " O   HOH Z 221 " =    0.950
peak=   -3.568 closest distance to " CG2 VAL A 202 " =    2.704
peak=   -3.555 closest distance to " CB  TRP A 266 " =    1.867
peak=   -3.549 closest distance to " NH2 ARG A  79 " =    2.084
peak=   -3.547 closest distance to " OG  SER A  87 " =    1.371
peak=   -3.546 closest distance to " CE1 TYR A 247 " =    2.560
peak=   -3.542 closest distance to " OG  SER A  97 " =    2.306
peak=   -3.533 closest distance to " O   HOH Z  11 " =    1.768
peak=   -3.528 closest distance to " CB  PRO A 163 " =    2.487
peak=   -3.528 closest distance to " ND2 ASN A 249 " =    2.156
peak=   -3.522 closest distance to " O   SER A 276 " =    1.588
peak=   -3.515 closest distance to " ND2 ASN A 173 " =    1.365
peak=   -3.507 closest distance to " CD2 PHE A 225 " =    1.046
peak=   -3.501 closest distance to " CG  PHE A 283 " =    2.611
peak=   -3.499 closest distance to " CB  ALA A 114 " =    2.431
peak=   -3.494 closest distance to " O   HOH Z 423 " =    2.433
peak=   -3.486 closest distance to " O   HOH Z 198 " =    0.772
peak=   -3.484 closest distance to " O   HOH Z 116 " =    1.611
peak=   -3.484 closest distance to " O   HOH Z  28 " =    2.409
peak=   -3.478 closest distance to " N   ALA A 248 " =    1.635
peak=   -3.475 closest distance to " CD  PRO A 243 " =    1.965
peak=   -3.474 closest distance to " O   ILE A  49 " =    1.689
peak=   -3.472 closest distance to " O   HOH Z 295 " =    1.705
peak=   -3.467 closest distance to " N   ALA A 244 " =    1.442
peak=   -3.467 closest distance to " CE  MET A 113 " =    2.822
peak=   -3.458 closest distance to " O   HOH Z 421 " =    3.064
peak=   -3.457 closest distance to " O   HOH Z 437 " =    1.451
peak=   -3.455 closest distance to " CD1 ILE A 199 " =    2.325
peak=   -3.454 closest distance to " SG BCYS A 201 " =    2.201
peak=   -3.451 closest distance to " O   HOH Z  64 " =    2.736
peak=   -3.446 closest distance to " O   HOH Z 375 " =    1.689
peak=   -3.443 closest distance to " OXT GLY A 302 " =    2.992
peak=   -3.443 closest distance to " O   HOH Z 130 " =    1.840
peak=   -3.443 closest distance to " O   HOH Z 185 " =    2.007
peak=   -3.434 closest distance to " CB  PHE A 192 " =    2.016
peak=   -3.430 closest distance to " O   VAL A 174 " =    2.216
peak=   -3.430 closest distance to " OD2 ASP A 191 " =    1.375
peak=   -3.420 closest distance to " CB  ALA A 248 " =    2.392
peak=   -3.415 closest distance to " CG  LEU A 228 " =    0.844
peak=   -3.410 closest distance to " CB  ALA A  51 " =    1.869
peak=   -3.410 closest distance to " CG2 ILE A 151 " =    2.482
peak=   -3.405 closest distance to " O   HOH Z 398 " =    1.325
peak=   -3.401 closest distance to " CD  LYS A 289 " =    2.260
peak=   -3.393 closest distance to " CG  ASP A 231 " =    0.755
peak=   -3.386 closest distance to " CG2 THR A  18 " =    2.807
peak=   -3.384 closest distance to " CD2 TYR A 247 " =    2.489
peak=   -3.377 closest distance to " NE2 GLN A  11 " =    1.816
peak=   -3.370 closest distance to " O   HOH Z 313 " =    1.274
peak=   -3.368 closest distance to " CG2 VAL A 296 " =    2.211
peak=   -3.357 closest distance to " OG ASER A 134 " =    1.464
peak=   -3.354 closest distance to " O   HOH Z 372 " =    2.316
peak=   -3.352 closest distance to " O   HOH Z 236 " =    1.609
peak=   -3.344 closest distance to " C   LEU A 222 " =    1.353
peak=   -3.339 closest distance to " CA  GLY A 241 " =    2.404
peak=   -3.338 closest distance to " O   HOH Z 252 " =    3.812
peak=   -3.336 closest distance to " OG  SER A 271 " =    1.141
peak=   -3.333 closest distance to " O   HOH Z 404 " =    1.410
peak=   -3.332 closest distance to " CG1BVAL A  72 " =    2.324
peak=   -3.328 closest distance to " O   SER A 135 " =    1.570
peak=   -3.324 closest distance to " O   HOH Z 107 " =    0.926
peak=   -3.324 closest distance to " O   HOH Z 183 " =    1.690
peak=   -3.315 closest distance to " CA  GLY A 133 " =    1.888
peak=   -3.304 closest distance to " O   HOH Z 142 " =    1.106
peak=   -3.302 closest distance to " O   HOH Z 372 " =    0.948
peak=   -3.301 closest distance to " O   HOH Z 340 " =    2.328
peak=   -3.299 closest distance to " C   MET A 188 " =    1.440
peak=   -3.295 closest distance to " O   HOH Z 187 " =    1.862
peak=   -3.294 closest distance to " ND2 ASN A 209 " =    1.925
peak=   -3.293 closest distance to " N   ASN A 127 " =    1.356
peak=   -3.293 closest distance to " CZ2 TRP A 274 " =    1.002
peak=   -3.291 closest distance to " O   HOH Z 377 " =    0.728
peak=   -3.288 closest distance to " CZ  ARG A 259 " =    0.993
peak=   -3.287 closest distance to " O   SER A 146 " =    1.378
peak=   -3.285 closest distance to " O   HOH Z 313 " =    1.533
peak=   -3.276 closest distance to " O   HOH Z 384 " =    1.828
peak=   -3.274 closest distance to " O   HOH Z 216 " =    1.101
peak=   -3.268 closest distance to " CG2 VAL A 189 " =    1.966
peak=   -3.267 closest distance to " O   HOH Z 352 " =    1.455
peak=   -3.264 closest distance to " O   HOH Z 140 " =    1.484
peak=   -3.263 closest distance to " C   LYS A  76 " =    1.707
peak=   -3.261 closest distance to " O   HOH Z 117 " =    1.770
peak=   -3.261 closest distance to " O   HOH Z 111 " =    1.600
peak=   -3.259 closest distance to " CG  GLN A 103 " =    2.281
peak=   -3.258 closest distance to " O   HOH Z 387 " =    2.170
peak=   -3.258 closest distance to " O   HOH Z 359 " =    3.093
peak=   -3.242 closest distance to " NZ  LYS A 119 " =    0.783
peak=   -3.241 closest distance to " O   HOH Z 164 " =    5.761
peak=   -3.237 closest distance to " OE2 GLU A 152 " =    1.389
peak=   -3.234 closest distance to " CG  GLU A 152 " =    0.977
peak=   -3.234 closest distance to " O   LYS A  76 " =    1.880
peak=   -3.229 closest distance to " ND2 ASN A 187 " =    1.525
peak=   -3.227 closest distance to " CA  GLY A  98 " =    1.809
peak=   -3.226 closest distance to " O   HOH Z 232 " =    2.009
peak=   -3.225 closest distance to " N   HIS A 115 " =    2.238
peak=   -3.224 closest distance to " NE2 GLN A 240 " =    1.734
peak=   -3.222 closest distance to " O   TRP A  70 " =    1.536
peak=   -3.219 closest distance to " CB  ALA A 131 " =    1.996
peak=   -3.214 closest distance to " O   HOH Z  73 " =    2.527
peak=   -3.213 closest distance to " C   ARG A 269 " =    1.219
peak=   -3.211 closest distance to " NE2 GLN A  88 " =    1.955
peak=   -3.206 closest distance to " CZ  PHE A  38 " =    2.361
peak=   -3.205 closest distance to " CE3 TRP A 179 " =    1.322
peak=   -3.203 closest distance to " O   HOH Z 407 " =    2.640
peak=   -3.203 closest distance to " CA  GLY A 302 " =    3.033
peak=   -3.201 closest distance to " CD  GLN A 223 " =    0.779
peak=   -3.199 closest distance to " O   HOH Z 286 " =    1.521
peak=   -3.197 closest distance to " CB  ALA A 161 " =    2.382
peak=   -3.193 closest distance to " CE BMET A  47 " =    1.395
peak=   -3.191 closest distance to " CB  ALA A  64 " =    2.630
peak=   -3.191 closest distance to " O   HOH Z 244 " =    1.809
peak=   -3.189 closest distance to " O   HOH Z 140 " =    0.906
peak=   -3.187 closest distance to " CD  GLU A 277 " =    1.060
peak=   -3.185 closest distance to " OE2 GLU A   2 " =    1.105
peak=   -3.184 closest distance to " O   HOH Z   9 " =    1.234
peak=   -3.180 closest distance to " CA  GLY A  57 " =    2.193
peak=   -3.176 closest distance to " CA  GLY A  23 " =    1.759
peak=   -3.175 closest distance to " CG  LEU A  83 " =    2.127
peak=   -3.171 closest distance to " O   HOH Z 427 " =    1.535
peak=   -3.160 closest distance to " O   HOH Z 111 " =    4.490
peak=   -3.159 closest distance to " CD2 LEU A   5 " =    1.146
peak=   -3.156 closest distance to " O   ALA A  10 " =    1.672
peak=   -3.154 closest distance to " OG  SER A  87 " =    1.343
peak=   -3.147 closest distance to " O   HOH Z   9 " =    2.776
peak=   -3.142 closest distance to " O   HOH Z 174 " =    3.962
peak=   -3.137 closest distance to " N   ALA A 226 " =    1.878
peak=   -3.137 closest distance to " CA  TRP A 274 " =    1.132
peak=   -3.133 closest distance to " CG  MET A 105 " =    0.940
peak=   -3.121 closest distance to " CA  ASP A  27 " =    2.354
peak=   -3.120 closest distance to " O   SER A  87 " =    2.126
peak=   -3.119 closest distance to " CG  ARG A 219 " =    2.622
peak=   -3.116 closest distance to " CD2 LEU A 237 " =    2.615
peak=   -3.108 closest distance to " O   LYS A 117 " =    1.621
peak=   -3.102 closest distance to " O   HOH Z 119 " =    2.394
peak=   -3.091 closest distance to " C   ASP A 124 " =    1.903
peak=   -3.090 closest distance to " O   HOH Z 147 " =    1.269
peak=   -3.079 closest distance to " OE1 GLN A  88 " =    1.034
peak=   -3.079 closest distance to " O   HOH Z  88 " =    2.607
peak=   -3.077 closest distance to " O   ASN A 187 " =    1.571
peak=   -3.063 closest distance to " CG AMET A  47 " =    2.963
peak=   -3.057 closest distance to " O   HOH Z 368 " =    1.521
peak=   -3.055 closest distance to " O   HOH Z 179 " =    1.881
peak=   -3.050 closest distance to " O   PRO A 198 " =    1.194
peak=   -3.048 closest distance to " CB  TRP A  85 " =    2.562
peak=   -3.008 closest distance to " O   HOH Z 231 " =    1.931

================= 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    :  0.5027 0.4962   6.299172e+00   6.295816e+00
   1_bss:  0.4941 0.4865   6.292548e+00   6.289143e+00
   1_xyz:  0.4283 0.4481   6.216851e+00   6.249993e+00
   1_adp:  0.3840 0.4445   6.159559e+00   6.240254e+00
   1_occ:  0.3842 0.4451   6.158975e+00   6.241153e+00
   2_bss:  0.3821 0.4437   6.161153e+00   6.242501e+00
   2_xyz:  0.3096 0.3715   5.995143e+00   6.138977e+00
   2_adp:  0.2850 0.3527   5.934057e+00   6.086918e+00
   2_occ:  0.2848 0.3522   5.934085e+00   6.086298e+00
   3_bss:  0.2833 0.3499   5.932850e+00   6.085135e+00
   3_xyz:  0.2086 0.2659   5.675299e+00   5.867939e+00
   3_adp:  0.1844 0.2478   5.583011e+00   5.798952e+00
   3_occ:  0.1841 0.2473   5.582059e+00   5.798593e+00
   4_bss:  0.1828 0.2479   5.580562e+00   5.798175e+00
   4_xyz:  0.1468 0.2026   5.385358e+00   5.618000e+00
   4_adp:  0.1387 0.1889   5.326043e+00   5.552064e+00
   4_occ:  0.1385 0.1887   5.324981e+00   5.550984e+00
   5_bss:  0.1386 0.1890   5.324830e+00   5.550546e+00
   5_xyz:  0.1222 0.1718   5.228023e+00   5.469602e+00
   5_adp:  0.1206 0.1665   5.209631e+00   5.442730e+00
   5_occ:  0.1204 0.1664   5.208575e+00   5.441913e+00
   5_bss:  0.1204 0.1664   5.208575e+00   5.441913e+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:  0.359  20.000   6.978   7.351   9.743   0.000   0.000   0.000
   1_xyz:  0.359  20.000   6.978   7.351   9.743   0.000   0.000   0.000
   1_adp:  0.359  20.000   6.978   7.351   9.743   0.000   0.000   0.000
   1_occ:  0.359  20.000   6.978   7.351   9.743   0.000   0.000   0.000
   2_bss:  0.341  39.011   3.641   3.709   6.385   0.000   0.000   0.000
   2_xyz:  0.341  39.011   3.641   3.709   6.385   0.000   0.000   0.000
   2_adp:  0.341  39.011   3.641   3.709   6.385   0.000   0.000   0.000
   2_occ:  0.341  39.011   3.641   3.709   6.385   0.000   0.000   0.000
   3_bss:  0.348  51.879   1.567   2.039   4.153   0.000   0.000   0.000
   3_xyz:  0.348  51.879   1.567   2.039   4.153   0.000   0.000   0.000
   3_adp:  0.348  51.879   1.567   2.039   4.153   0.000   0.000   0.000
   3_occ:  0.348  51.879   1.567   2.039   4.153   0.000   0.000   0.000
   4_bss:  0.322  46.364   0.148   0.892   2.840   0.000   0.000   0.000
   4_xyz:  0.322  46.364   0.148   0.892   2.840   0.000   0.000   0.000
   4_adp:  0.322  46.364   0.148   0.892   2.840   0.000   0.000   0.000
   4_occ:  0.322  46.364   0.148   0.892   2.840   0.000   0.000   0.000
   5_bss:  0.318  46.364  -0.364   0.476   2.327   0.000   0.000   0.000
   5_xyz:  0.318  46.364  -0.364   0.476   2.327   0.000   0.000   0.000
   5_adp:  0.318  46.364  -0.364   0.476   2.327   0.000   0.000   0.000
   5_occ:  0.318  46.364  -0.364   0.476   2.327   0.000   0.000   0.000
   5_bss:  0.318  47.177  -1.177  -0.337   1.514   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  63.214 0.3519  0.4244    81029.317
   1_bss:  63.720 0.3438  0.5225    79370.366
   1_xyz:  53.007 0.4817  0.7164    61415.197
   1_adp:  50.941 0.5078  0.8277    58666.348
   1_occ:  51.001 0.5070  0.8244    58767.468
   2_bss:  50.939 0.5079  0.7340    58941.561
   2_xyz:  40.713 0.6329  0.8976    38944.306
   2_adp:  37.105 0.6765  0.9472    33678.571
   2_occ:  37.131 0.6762  0.9467    33680.909
   3_bss:  36.916 0.6785  0.8840    33359.649
   3_xyz:  26.802 0.7920  0.9941    18592.964
   3_adp:  24.233 0.8197  1.0104    15994.936
   3_occ:  24.228 0.8197  1.0102    15954.394
   4_bss:  24.155 0.8204  0.9639    15885.289
   4_xyz:  19.278 0.8685  0.9899    10509.192
   4_adp:  17.684 0.8836  0.9906     9238.280
   4_occ:  17.670 0.8837  0.9904     9207.836
   5_bss:  17.632 0.8840  0.9735     9194.945
   5_xyz:  15.811 0.8998  0.9822     7644.757
   5_adp:  15.202 0.9052  0.9824     7284.036
   5_occ:  15.178 0.9054  0.9824     7262.191
   5_bss:  15.178 0.9054  0.9824     7262.191
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.086   5.3222e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.086   5.3222e+01
   1_xyz:   1.743  0.014  0.106 18.380  0.007  4.104   1.4976e-01
   1_adp:   1.743  0.014  0.106 18.380  0.007  4.104   1.4976e-01
   1_occ:   1.743  0.014  0.106 18.380  0.007  4.104   1.4976e-01
   2_bss:   1.743  0.014  0.106 18.380  0.007  4.104   1.4976e-01
   2_xyz:   1.277  0.009  0.083 16.400  0.005  4.105   9.5802e-02
   2_adp:   1.277  0.009  0.083 16.400  0.005  4.105   9.5802e-02
   2_occ:   1.277  0.009  0.083 16.400  0.005  4.105   9.5802e-02
   3_bss:   1.277  0.009  0.083 16.400  0.005  4.105   9.5802e-02
   3_xyz:   1.135  0.008  0.082 15.654  0.004  4.124   7.5057e-02
   3_adp:   1.135  0.008  0.082 15.654  0.004  4.124   7.5057e-02
   3_occ:   1.135  0.008  0.082 15.654  0.004  4.124   7.5057e-02
   4_bss:   1.135  0.008  0.082 15.654  0.004  4.124   7.5057e-02
   4_xyz:   1.043  0.007  0.074 15.333  0.005  4.121   6.5357e-02
   4_adp:   1.043  0.007  0.074 15.333  0.005  4.121   6.5357e-02
   4_occ:   1.043  0.007  0.074 15.333  0.005  4.121   6.5357e-02
   5_bss:   1.043  0.007  0.074 15.333  0.005  4.121   6.5357e-02
   5_xyz:   1.108  0.008  0.080 15.522  0.005  4.110   7.1645e-02
   5_adp:   1.108  0.008  0.080 15.522  0.005  4.110   7.1645e-02
   5_occ:   1.108  0.008  0.080 15.522  0.005  4.110   7.1645e-02
   5_bss:   1.108  0.008  0.080 15.522  0.005  4.110   7.1645e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.113   6.8890e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.113   6.8890e+00
   1_xyz:  14.710  0.167  0.434 86.212  0.053  2.094   9.9923e-02
   1_adp:  14.710  0.167  0.434 86.212  0.053  2.094   9.9923e-02
   1_occ:  14.710  0.167  0.434 86.212  0.053  2.094   9.9923e-02
   2_bss:  14.710  0.167  0.434 86.212  0.053  2.094   9.9923e-02
   2_xyz:   6.827  0.121  0.318 88.000  0.046  2.061   8.4944e-02
   2_adp:   6.827  0.121  0.318 88.000  0.046  2.061   8.4944e-02
   2_occ:   6.827  0.121  0.318 88.000  0.046  2.061   8.4944e-02
   3_bss:   6.827  0.121  0.318 88.000  0.046  2.061   8.4944e-02
   3_xyz:   7.346  0.088  0.292 86.243  0.041  2.234   5.0010e-02
   3_adp:   7.346  0.088  0.292 86.243  0.041  2.234   5.0010e-02
   3_occ:   7.346  0.088  0.292 86.243  0.041  2.234   5.0010e-02
   4_bss:   7.346  0.088  0.292 86.243  0.041  2.234   5.0010e-02
   4_xyz:   7.015  0.050  0.233 83.923  0.046  2.275   5.1196e-02
   4_adp:   7.015  0.050  0.233 83.923  0.046  2.275   5.1196e-02
   4_occ:   7.015  0.050  0.233 83.923  0.046  2.275   5.1196e-02
   5_bss:   7.015  0.050  0.233 83.923  0.046  2.275   5.1196e-02
   5_xyz:   7.052  0.054  0.259 83.178  0.046  2.335   6.0066e-02
   5_adp:   7.052  0.054  0.259 83.178  0.046  2.335   6.0066e-02
   5_occ:   7.052  0.054  0.259 83.178  0.046  2.335   6.0066e-02
   5_bss:   7.052  0.054  0.259 83.178  0.046  2.335   6.0066e-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:  66.01   0.00  15.28  60.04   0.00  13.55  66.01   0.00  24.68
   1_occ:  66.01   0.00  15.28  60.04   0.00  13.55  66.01   0.00  24.68
   2_bss:  66.01   0.00  15.28  60.04   0.00  13.55  66.01   0.00  24.68
   2_xyz:  66.01   0.00  15.28  60.04   0.00  13.55  66.01   0.00  24.68
   2_adp:  69.91   0.00  15.00  65.72   0.00  11.96  69.91   0.00  31.57
   2_occ:  69.91   0.00  15.00  65.72   0.00  11.96  69.91   0.00  31.57
   3_bss:  69.91   0.00  15.00  65.72   0.00  11.96  69.91   0.00  31.57
   3_xyz:  69.91   0.00  15.00  65.72   0.00  11.96  69.91   0.00  31.57
   3_adp:  87.68   0.00  15.58  80.17   0.00  11.01  87.68   0.00  40.45
   3_occ:  87.68   0.00  15.58  80.17   0.00  11.01  87.68   0.00  40.45
   4_bss:  87.68   0.00  15.58  80.17   0.00  11.01  87.68   0.00  40.45
   4_xyz:  87.68   0.00  15.58  80.17   0.00  11.01  87.68   0.00  40.45
   4_adp:  91.22   0.00  15.02  91.22   0.00  10.42  89.67   2.33  40.12
   4_occ:  91.22   0.00  15.02  91.22   0.00  10.42  89.67   2.33  40.12
   5_bss:  91.22   0.00  15.02  91.22   0.00  10.42  89.67   2.33  40.12
   5_xyz:  91.22   0.00  15.02  91.22   0.00  10.42  89.67   2.33  40.12
   5_adp:  91.29   0.61  14.51  91.29   0.61  10.17  85.67   3.13  38.13
   5_occ:  91.29   0.61  14.51  91.29   0.61  10.17  85.67   3.13  38.13
   5_bss:  92.10   1.42  15.32  92.10   1.42  10.99  86.48   3.94  38.94
------------------------------------------------------------------------
 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:    1.293    0.020    0.413
   1_adp:    1.293    0.020    0.413
   1_occ:    1.293    0.020    0.413
   2_bss:    1.293    0.020    0.413
   2_xyz:    1.853    0.043    0.583
   2_adp:    1.853    0.043    0.583
   2_occ:    1.853    0.043    0.583
   3_bss:    1.853    0.043    0.583
   3_xyz:    1.591    0.023    0.705
   3_adp:    1.591    0.023    0.705
   3_occ:    1.591    0.023    0.705
   4_bss:    1.591    0.023    0.705
   4_xyz:    1.778    0.068    0.770
   4_adp:    1.778    0.068    0.770
   4_occ:    1.778    0.068    0.770
   5_bss:    1.778    0.068    0.770
   5_xyz:    2.021    0.064    0.799
   5_adp:    2.021    0.064    0.799
   5_occ:    2.021    0.064    0.799
   5_bss:    2.021    0.064    0.799
------------------------------------------------------------------------

CPU time actual refinement: 286.46


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_42/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_42/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_42/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_42/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_42/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 286.33 
  Macro-tasks:
    bulk solvent and scale       = 36.08  
    individual site refinement   = 115.96 
    weights calculation          = 27.48  
    collect and process          = 5.44   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 185.08 
  Micro-tasks:
    mask                            = 2.05   
    f_calc                          = 88.32  
    alpha_beta                      = 7.03   
    target                          = 0.96   
    gradients_wrt_atomic_parameters = 96.48  
    fmodel                         = 6.05   
    r_factors                      = 0.22   
    phase_errors                   = 8.44   
    foms                           = 0.23   
    TOTAL for micro-tasks          = 209.78 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.068 micro seconds
Total CPU time: 4.97 minutes
from_scatterers_fft:    648 calls, 88.04 s
gradients_fft:          593 calls, 85.24 s

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

# Date 2008-01-16 Time 00:37:08 PST -0800 (1200472628.59 s)
Start R-work = 0.5027, R-free = 0.4962 (no bulk solvent and anisotropic scale)
Final R-work = 0.1389, R-free = 0.1823 (no bulk solvent and anisotropic scale)

Start R-work = 0.4941, R-free = 0.4865
Final R-work = 0.1204, R-free = 0.1664