# Date 2008-01-16 Time 02:19:43 PST -0800 (1200478783.23 s)
#phil __OFF__

Command line arguments: "../780.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27732
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 780

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 46.6953, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.6953, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1485 1.99255
Completeness in resolution range: 0.950922
Completeness with d_max=infinity: 0.948023

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1485
                             d_min =   1.9926

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.6953, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1485 1.99255
Completeness in resolution range: 0.950922
Completeness with d_max=infinity: 0.948023

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1489 -  4.2639 [2164/2188]  1944   220  10.2%
  bin  2:  4.2639 -  3.3969 [2067/2087]  1863   204   9.9%
  bin  3:  3.3969 -  2.9712 [2068/2087]  1863   205   9.9%
  bin  4:  2.9712 -  2.7012 [2022/2052]  1819   203  10.0%
  bin  5:  2.7012 -  2.5086 [2019/2038]  1817   202  10.0%
  bin  6:  2.5086 -  2.3612 [2008/2033]  1805   203  10.1%
  bin  7:  2.3612 -  2.2434 [2007/2035]  1805   202  10.1%
  bin  8:  2.2434 -  2.1460 [1986/2022]  1790   196   9.9%
  bin  9:  2.1460 -  2.0636 [1988/2030]  1791   197   9.9%
  bin 10:  2.0636 -  1.9925 [1260/2028]  1133   127  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_780/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: 0.15 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:
        1.57 -     2.24: 10
        2.24 -     2.90: 1386
        2.90 -     3.57: 4406
        3.57 -     4.23: 9059
        4.23 -     4.90: 13102
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.575 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.736 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.736 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.739 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 27958 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_780/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_780/model_refine_001.geo

CPU time processing inputs: 9.07


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.69535 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4710   r_free= 0.4592   ksol= 0.00   Bsol= 0.00   scale= 0.790    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.273720                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7559 0.99   1405  154 0.3963 0.3589      6.6166      6.5094|
|  2:  4.7559 -  3.7944 0.99   1356  153 0.3747 0.4038      6.7493      6.8347|
|  3:  3.7944 -  3.3205 0.99   1320  144 0.4289 0.4045      6.6626      6.6327|
|  4:  3.3205 -  3.0196 0.99   1318  152 0.4698 0.4155      6.5264      6.4352|
|  5:  3.0196 -  2.8046 0.99   1306  144 0.5002 0.4490      6.3557      6.3658|
|  6:  2.8046 -  2.6402 0.99   1308  142 0.4907 0.5730      6.2662      6.2149|
|  7:  2.6402 -  2.5086 0.99   1293  145 0.5115 0.5013      6.2247       6.203|
|  8:  2.5086 -  2.3998 0.98   1293  146 0.5254 0.4749      6.1927      6.1541|
|  9:  2.3998 -  2.3077 0.98   1275  140 0.5012 0.5574      6.0958      6.1736|
| 10:  2.3077 -  2.2284 1.00   1285  143 0.5244 0.4823       6.113      6.0749|
| 11:  2.2284 -  2.1589 0.98   1294  144 0.5121 0.4977      6.0289      6.0484|
| 12:  2.1589 -  2.0973 0.98   1268  142 0.5299 0.4827      5.9746      5.9722|
| 13:  2.0973 -  2.0423 0.99   1278  137 0.5135 0.5188      5.8672      5.8104|
| 14:  2.0423 -  1.9925 0.48    631   73 0.5189 0.5037      5.8729      5.7897|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1489 -  4.7559  1405   154  0.73  32.00   0.79     0.76      63106.08|
|  2:  4.7559 -  3.7944  1356   153  0.74  32.08   0.87     0.80      94620.47|
|  3:  3.7944 -  3.3205  1320   144  0.64  40.23   0.83     0.75      99380.40|
|  4:  3.3205 -  3.0196  1318   152  0.56  47.20   0.78     0.64      89268.61|
|  5:  3.0196 -  2.8046  1306   144  0.46  54.94   0.75     0.53      74563.14|
|  6:  2.8046 -  2.6402  1308   142  0.40  59.68   0.72     0.45      70625.93|
|  7:  2.6402 -  2.5086  1293   145  0.37  62.01   0.73     0.43      65479.30|
|  8:  2.5086 -  2.3998  1293   146  0.38  61.39   0.72     0.43      57610.74|
|  9:  2.3998 -  2.3077  1275   140  0.40  60.14   0.73     0.46      51860.88|
| 10:  2.3077 -  2.2284  1285   143  0.40  60.38   0.74     0.46      46220.30|
| 11:  2.2284 -  2.1589  1294   144  0.38  61.78   0.76     0.47      44578.91|
| 12:  2.1589 -  2.0973  1268   142  0.38  61.87   0.73     0.46      39971.84|
| 13:  2.0973 -  2.0423  1278   137  0.36  63.45   0.72     0.44      35392.23|
| 14:  2.0423 -  1.9925   631    73  0.36  62.96   0.75     0.40      30291.42|
|alpha:            min =        0.40 max =            0.80 mean =         0.54|
|beta:             min =    30291.42 max =        99380.40 mean =     63128.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           90.00 mean =        53.69|
|phase err.(test): min =        0.00 max =           89.97 mean =        54.01|
|-----------------------------------------------------------------------------|

============================== 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 = 12.063896             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.059   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.053935              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.702   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      164 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      678 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1488 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2586 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3868 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5042 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6483 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7627 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.268 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.774 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.138)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 12.138)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4776   r_free= 0.4637   ksol= 0.00   Bsol= 0.00   scale= 0.760    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.276826                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4621   r_free= 0.4482   ksol= 0.33   Bsol= 20.61   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.75,7.19,12.33,0.00,0.00,0.00); trace/3= 8.76                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.267598                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.643395             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.070   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.943349              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.038   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4621      final r-factor (work) = 0.3746          |
| start r-factor (free) = 0.4482      final r-factor (free) = 0.3964          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 87.6413 = 10.64 * 0.50 * 6.2712 + 1.00 * 54.2678                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.9663 = 10.64 * 0.50 * 6.1689 + 1.00 * 0.1375                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3746      final r-factor (work) = 0.3242          |
| start r-factor (free) = 0.3964      final r-factor (free) = 0.3737          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8338 = 0.94 * 1.00 * 6.1689 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7378 = 0.94 * 1.00 * 6.0661 + 1.00 * 0.0153                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.138)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.96   12.94    None  None   None       |
|    all(noH): 2823   0      0.00    69.96   12.94    None  None   None       |
|    Sol.    : 438    0      0.00    69.96   27.19    None  None   None       |
|    Mac.    : 2385   0      0.00    59.53   10.33    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 -   6.997: 1112   |   5:    34.982 -  41.979:   90        |
|      1:     6.997 -  13.993:  729   |   6:    41.979 -  48.975:   44        |
|      2:    13.993 -  20.989:  418   |   7:    48.975 -  55.972:   36        |
|      3:    20.989 -  27.986:  250   |   8:    55.972 -  62.968:   18        |
|      4:    27.986 -  34.982:  124   |   9:    62.968 -  69.965:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3242 r_free = 0.3737             target_work(ml) = 6.042         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3238 r_free = 0.3750             target_work(ml) = 6.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3238   r_free= 0.3750   ksol= 0.33   Bsol= 20.61   scale= 1.095   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.75,7.19,12.33,0.00,0.00,0.00); trace/3= 8.76                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.041094                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3213   r_free= 0.3718   ksol= 0.34   Bsol= 50.00   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.75,3.94,8.90,0.00,0.00,0.00); trace/3= 5.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.042112                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.397473              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.280   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.482821              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.166  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3213      final r-factor (work) = 0.2440          |
| start r-factor (free) = 0.3718      final r-factor (free) = 0.2996          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.4984 = 5.40 * 0.50 * 6.0625 + 1.00 * 0.1375                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.0499 = 5.40 * 0.50 * 5.9176 + 1.00 * 0.0798                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2440      final r-factor (work) = 0.2233          |
| start r-factor (free) = 0.2996      final r-factor (free) = 0.2770          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8728 = 0.48 * 1.00 * 5.9176 + 1.00 * 0.0156                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7971 = 0.48 * 1.00 * 5.7680 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.138)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.48   12.70    None  None   None       |
|    all(noH): 2823   0      0.00    70.48   12.70    None  None   None       |
|    Sol.    : 438    0      0.00    70.48   32.75    None  None   None       |
|    Mac.    : 2385   0      0.00    64.57   9.02     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 -   7.048: 1258   |   5:    35.242 -  42.290:  110        |
|      1:     7.048 -  14.097:  736   |   6:    42.290 -  49.339:   71        |
|      2:    14.097 -  21.145:  326   |   7:    49.339 -  56.387:   48        |
|      3:    21.145 -  28.194:  150   |   8:    56.387 -  63.435:   15        |
|      4:    28.194 -  35.242:  103   |   9:    63.435 -  70.484:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2233 r_free = 0.2770             target_work(ml) = 5.738         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2230 r_free = 0.2766             target_work(ml) = 5.738         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2230   r_free= 0.2766   ksol= 0.34   Bsol= 50.00   scale= 1.048   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.75,3.94,8.90,0.00,0.00,0.00); trace/3= 5.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.737753                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2216   r_free= 0.2770   ksol= 0.34   Bsol= 67.49   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.39,2.64,5.79,0.00,0.00,0.00); trace/3= 3.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.739030                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.570645              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.207  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.167396              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.019  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2216      final r-factor (work) = 0.1584          |
| start r-factor (free) = 0.2770      final r-factor (free) = 0.2116          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.1622 = 5.57 * 0.50 * 5.7740 + 1.00 * 0.0798                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.6939 = 5.57 * 0.50 * 5.6043 + 1.00 * 0.0841                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1584      final r-factor (work) = 0.1407          |
| start r-factor (free) = 0.2116      final r-factor (free) = 0.1945          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5546 = 1.17 * 1.00 * 5.6043 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3081 = 1.17 * 1.00 * 5.3908 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.138)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.40   13.40    None  None   None       |
|    all(noH): 2823   0      0.00    89.40   13.40    None  None   None       |
|    Sol.    : 438    0      1.34    89.40   38.97    None  None   None       |
|    Mac.    : 2385   0      0.00    75.51   8.70     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.941: 1626   |   5:    44.702 -  53.643:   90        |
|      1:     8.941 -  17.881:  610   |   6:    53.643 -  62.583:   62        |
|      2:    17.881 -  26.821:  169   |   7:    62.583 -  71.524:   42        |
|      3:    26.821 -  35.762:  109   |   8:    71.524 -  80.464:    9        |
|      4:    35.762 -  44.702:  103   |   9:    80.464 -  89.405:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1407 r_free = 0.1945             target_work(ml) = 5.346         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1405 r_free = 0.1945             target_work(ml) = 5.346         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1405   r_free= 0.1945   ksol= 0.34   Bsol= 67.49   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.39,2.64,5.79,0.00,0.00,0.00); trace/3= 3.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.346242                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1403   r_free= 0.1940   ksol= 0.33   Bsol= 67.49   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.01,2.20,4.53,0.00,0.00,0.00); trace/3= 2.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.345003                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.724301              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.937  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.208633              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.457  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1403      final r-factor (work) = 0.1316          |
| start r-factor (free) = 0.1940      final r-factor (free) = 0.1807          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7337 = 1.72 * 0.50 * 5.3930 + 1.00 * 0.0841                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6455 = 1.72 * 0.50 * 5.3220 + 1.00 * 0.0571                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1316      final r-factor (work) = 0.1316          |
| start r-factor (free) = 0.1807      final r-factor (free) = 0.1770          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1251 = 0.21 * 1.00 * 5.3220 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1165 = 0.21 * 1.00 * 5.2917 + 1.00 * 0.0125                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.138)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.56   12.71    None  None   None       |
|    all(noH): 2823   0      0.00    85.56   12.71    None  None   None       |
|    Sol.    : 438    0      1.46    85.56   36.18    None  None   None       |
|    Mac.    : 2385   0      0.00    75.51   8.40     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 -   8.556: 1625   |   5:    42.781 -  51.338:   86        |
|      1:     8.556 -  17.113:  632   |   6:    51.338 -  59.894:   56        |
|      2:    17.113 -  25.669:  164   |   7:    59.894 -  68.450:   31        |
|      3:    25.669 -  34.225:  113   |   8:    68.450 -  77.007:   10        |
|      4:    34.225 -  42.781:  102   |   9:    77.007 -  85.563:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1316 r_free = 0.1770             target_work(ml) = 5.280         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1315 r_free = 0.1767             target_work(ml) = 5.279         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1315   r_free= 0.1767   ksol= 0.33   Bsol= 67.49   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.01,2.20,4.53,0.00,0.00,0.00); trace/3= 2.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.278816                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1314   r_free= 0.1767   ksol= 0.33   Bsol= 61.58   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.87,2.03,4.13,0.00,0.00,0.00); trace/3= 2.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.278614                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.464183              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 131.216  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.112373              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.570   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1314      final r-factor (work) = 0.1207          |
| start r-factor (free) = 0.1767      final r-factor (free) = 0.1667          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5760 = 2.46 * 0.50 * 5.2909 + 1.00 * 0.0571                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5305 = 2.46 * 0.50 * 5.2412 + 1.00 * 0.0728                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1207      final r-factor (work) = 0.1185          |
| start r-factor (free) = 0.1667      final r-factor (free) = 0.1672          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8419 = 1.11 * 1.00 * 5.2412 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8216 = 1.11 * 1.00 * 5.2010 + 1.00 * 0.0362                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.138)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.63   13.00    None  None   None       |
|    all(noH): 2823   0      0.00    93.63   13.00    None  None   None       |
|    Sol.    : 438    0      1.12    93.63   37.52    None  None   None       |
|    Mac.    : 2385   0      0.00    80.64   8.50     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 -   9.363: 1739   |   5:    46.814 -  56.176:   88        |
|      1:     9.363 -  18.725:  539   |   6:    56.176 -  65.539:   47        |
|      2:    18.725 -  28.088:  157   |   7:    65.539 -  74.902:   24        |
|      3:    28.088 -  37.451:  128   |   8:    74.902 -  84.264:   10        |
|      4:    37.451 -  46.814:   89   |   9:    84.264 -  93.627:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1185 r_free = 0.1672             target_work(ml) = 5.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1182 r_free = 0.1672             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1182   r_free= 0.1672   ksol= 0.33   Bsol= 61.58   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.87,2.03,4.13,0.00,0.00,0.00); trace/3= 2.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.202045                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7559 0.99   1405  154 0.1004 0.1347      5.4096      5.5717|
|  2:  4.7559 -  3.7944 0.99   1356  153 0.0875 0.1203      5.4691      5.7073|
|  3:  3.7944 -  3.3205 0.99   1320  144 0.1131 0.1542      5.5385      5.8481|
|  4:  3.3205 -  3.0196 0.99   1318  152 0.1275 0.1834      5.4917      5.6982|
|  5:  3.0196 -  2.8046 0.99   1306  144 0.1419 0.1685      5.3878      5.5865|
|  6:  2.8046 -  2.6402 0.99   1308  142 0.1296 0.2211      5.2559      5.5539|
|  7:  2.6402 -  2.5086 0.99   1293  145 0.1369 0.1671       5.242      5.3848|
|  8:  2.5086 -  2.3998 0.98   1293  146 0.1245 0.1753      5.1404      5.4074|
|  9:  2.3998 -  2.3077 0.98   1275  140 0.1286 0.2002      5.1074      5.4045|
| 10:  2.3077 -  2.2284 1.00   1285  143 0.1219 0.1641      5.0145      5.1978|
| 11:  2.2284 -  2.1589 0.98   1294  144 0.1238 0.1953      5.0086      5.3345|
| 12:  2.1589 -  2.0973 0.98   1268  142 0.1224 0.1808      4.9375      5.2463|
| 13:  2.0973 -  2.0423 0.99   1278  137 0.1161 0.1773      4.8211      5.0363|
| 14:  2.0423 -  1.9925 0.48    631   73 0.0976 0.1688      4.6786      4.9605|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1489 -  4.7559  1405   154  0.94   9.41   0.97     0.94       7658.68|
|  2:  4.7559 -  3.7944  1356   153  0.95   8.59   1.01     0.99       9952.65|
|  3:  3.7944 -  3.3205  1320   144  0.93  12.41   1.02     1.02      11847.87|
|  4:  3.3205 -  3.0196  1318   152  0.91  14.61   1.00     0.98      11185.11|
|  5:  3.0196 -  2.8046  1306   144  0.90  16.71   1.00     0.98       9308.87|
|  6:  2.8046 -  2.6402  1308   142  0.89  17.14   0.97     0.94       7768.64|
|  7:  2.6402 -  2.5086  1293   145  0.89  17.06   0.98     0.94       7223.32|
|  8:  2.5086 -  2.3998  1293   146  0.90  16.72   0.99     0.96       6207.67|
|  9:  2.3998 -  2.3077  1275   140  0.90  16.79   0.99     0.95       5809.15|
| 10:  2.3077 -  2.2284  1285   143  0.89  16.72   0.99     0.95       4898.94|
| 11:  2.2284 -  2.1589  1294   144  0.89  17.72   0.98     0.94       5025.46|
| 12:  2.1589 -  2.0973  1268   142  0.89  17.14   0.99     0.98       4483.51|
| 13:  2.0973 -  2.0423  1278   137  0.89  17.31   0.98     0.96       3713.14|
| 14:  2.0423 -  1.9925   631    73  0.92  14.22   0.97     0.93       2684.09|
|alpha:            min =        0.93 max =            1.02 mean =         0.96|
|beta:             min =     2684.09 max =        11847.87 mean =      7183.85|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.15|
|phase err.(test): min =        0.00 max =           89.20 mean =        14.54|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1182   r_free= 0.1672   ksol= 0.33   Bsol= 64.41   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.73,-0.65,1.37,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.202112                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1182   r_free= 0.1672   ksol= 0.33   Bsol= 64.41   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.73,-0.65,1.37,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.202112                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7559 0.99   1405  154 0.1004 0.1348      5.4101      5.5728|
|  2:  4.7559 -  3.7944 0.99   1356  153 0.0876 0.1203      5.4696      5.7076|
|  3:  3.7944 -  3.3205 0.99   1320  144 0.1131 0.1544      5.5389      5.8491|
|  4:  3.3205 -  3.0196 0.99   1318  152 0.1275 0.1835      5.4919      5.6984|
|  5:  3.0196 -  2.8046 0.99   1306  144 0.1418 0.1683      5.3875      5.5859|
|  6:  2.8046 -  2.6402 0.99   1308  142 0.1296 0.2212      5.2559      5.5543|
|  7:  2.6402 -  2.5086 0.99   1293  145 0.1369 0.1675      5.2421      5.3859|
|  8:  2.5086 -  2.3998 0.98   1293  146 0.1245 0.1754      5.1409      5.4069|
|  9:  2.3998 -  2.3077 0.98   1275  140 0.1285 0.2003      5.1074      5.4048|
| 10:  2.3077 -  2.2284 1.00   1285  143 0.1219 0.1642      5.0145      5.1978|
| 11:  2.2284 -  2.1589 0.98   1294  144 0.1238 0.1949      5.0081      5.3334|
| 12:  2.1589 -  2.0973 0.98   1268  142 0.1224 0.1805      4.9371      5.2453|
| 13:  2.0973 -  2.0423 0.99   1278  137 0.1160 0.1774      4.8208      5.0363|
| 14:  2.0423 -  1.9925 0.48    631   73 0.0977 0.1688       4.679      4.9604|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1489 -  4.7559  1405   154  0.94   9.42   0.97     0.94       7669.58|
|  2:  4.7559 -  3.7944  1356   153  0.95   8.60   1.01     0.99       9967.06|
|  3:  3.7944 -  3.3205  1320   144  0.93  12.41   1.02     1.02      11863.50|
|  4:  3.3205 -  3.0196  1318   152  0.91  14.61   1.01     0.98      11189.37|
|  5:  3.0196 -  2.8046  1306   144  0.90  16.70   1.00     0.98       9309.41|
|  6:  2.8046 -  2.6402  1308   142  0.89  17.14   0.97     0.95       7767.83|
|  7:  2.6402 -  2.5086  1293   145  0.89  17.06   0.98     0.95       7226.89|
|  8:  2.5086 -  2.3998  1293   146  0.90  16.73   0.99     0.96       6215.13|
|  9:  2.3998 -  2.3077  1275   140  0.90  16.80   1.00     0.95       5816.46|
| 10:  2.3077 -  2.2284  1285   143  0.89  16.72   1.00     0.96       4895.18|
| 11:  2.2284 -  2.1589  1294   144  0.89  17.70   0.99     0.95       5017.76|
| 12:  2.1589 -  2.0973  1268   142  0.89  17.12   1.00     0.99       4477.24|
| 13:  2.0973 -  2.0423  1278   137  0.89  17.30   0.99     0.97       3709.44|
| 14:  2.0423 -  1.9925   631    73  0.92  14.22   0.98     0.94       2682.22|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2682.22 max =        11863.50 mean =      7187.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.15|
|phase err.(test): min =        0.00 max =           89.20 mean =        14.54|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.138)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.83    96.46   15.83    None  None   None       |
|    all(noH): 2823   0      2.83    96.46   15.83    None  None   None       |
|    Sol.    : 438    0      3.95    96.46   40.35    None  None   None       |
|    Mac.    : 2385   0      2.83    83.47   11.33    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:     2.830 -  12.193: 1739   |   5:    49.644 -  59.006:   88        |
|      1:    12.193 -  21.556:  539   |   6:    59.006 -  68.369:   47        |
|      2:    21.556 -  30.918:  157   |   7:    68.369 -  77.732:   24        |
|      3:    30.918 -  40.281:  128   |   8:    77.732 -  87.094:   10        |
|      4:    40.281 -  49.644:   89   |   9:    87.094 -  96.457:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 310         
Filter by distance & map next to the model:
   mapped sites are within: 0.261 - 4.986
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 308 from: 310
   mapped sites are within: 0.700 - 4.986

peak=   10.589 closest distance to " CB  VAL A 230 " =    1.450
peak=    7.880 closest distance to " CG2 VAL A 296 " =    1.258
peak=    6.287 closest distance to " CD2 LEU A   5 " =    1.231
peak=    5.723 closest distance to " NE2 GLN A  11 " =    1.172
peak=    5.544 closest distance to " NH2 ARG A  56 " =    2.099
peak=    5.504 closest distance to " O   HOH Z 142 " =    2.145
peak=    5.280 closest distance to " CG  LEU A   5 " =    1.245
peak=    5.234 closest distance to " O   HOH Z 232 " =    2.299
peak=    5.158 closest distance to " CB  GLN A 223 " =    1.505
peak=    5.148 closest distance to " CG  LEU A 228 " =    1.148
peak=    4.942 closest distance to " CB  GLN A 183 " =    1.275
peak=    4.840 closest distance to " O   HOH Z 248 " =    1.390
peak=    4.742 closest distance to " O   HOH Z   9 " =    1.794
peak=    4.600 closest distance to " CZ  PHE A 218 " =    1.125
peak=    4.535 closest distance to " O   HOH Z 265 " =    2.066
peak=    4.532 closest distance to " CB  ASN A 148 " =    1.422
peak=    4.502 closest distance to " O   HOH Z 427 " =    2.913
peak=    4.461 closest distance to " O   HOH Z 369 " =    2.188
peak=    4.375 closest distance to " CB  ASN A 142 " =    1.081
peak=    4.370 closest distance to " O   HOH Z 313 " =    1.971
peak=    4.365 closest distance to " CG  PRO A 243 " =    1.123
peak=    4.357 closest distance to " O   HOH Z 425 " =    1.461
peak=    4.347 closest distance to " O   HOH Z 303 " =    2.065
peak=    4.319 closest distance to " CZ3 TRP A 266 " =    1.149
peak=    4.312 closest distance to " CB  ASP A 124 " =    0.824
peak=    4.279 closest distance to " CB  ARG A 190 " =    1.510
peak=    4.239 closest distance to " O   SER A  87 " =    2.378
peak=    4.202 closest distance to " CG  PRO A 213 " =    1.207
peak=    4.187 closest distance to " CE  LYS A  76 " =    0.895
peak=    4.167 closest distance to " O   PRO A 198 " =    1.572
peak=    4.162 closest distance to " CA  ALA A  51 " =    1.003
peak=    4.158 closest distance to " O   HOH Z  92 " =    2.375
peak=    4.125 closest distance to " CB  VAL A 265 " =    1.307
peak=    4.122 closest distance to " CB  SER A  63 " =    1.233
peak=    4.113 closest distance to " CG  PRO A 198 " =    1.278
peak=    4.100 closest distance to " ND2 ASN A 187 " =    1.584
peak=    4.067 closest distance to " O   HOH Z  61 " =    1.787
peak=    4.060 closest distance to " CD2 LEU A 228 " =    1.152
peak=    4.051 closest distance to " CB  GLU A 277 " =    3.710
peak=    4.043 closest distance to " N   PHE A 130 " =    1.300
peak=    4.023 closest distance to " NH2AARG A 145 " =    1.177
peak=    4.022 closest distance to " CG  LEU A 167 " =    1.198
peak=    4.017 closest distance to " CG2 VAL A 257 " =    0.893
peak=    4.015 closest distance to " O   HOH Z 422 " =    2.605
peak=    4.011 closest distance to " O   HOH Z 359 " =    1.603
peak=    4.010 closest distance to " O   HOH Z 126 " =    2.027
peak=    4.009 closest distance to " CD  ARG A 159 " =    0.734
peak=    4.008 closest distance to " CB  TYR A 169 " =    0.700
peak=    3.992 closest distance to " CB  TRP A 266 " =    1.091
peak=    3.988 closest distance to " O   HOH Z 287 " =    2.158
peak=    3.978 closest distance to " O  BHOH Z 338 " =    2.355
peak=    3.965 closest distance to " NH1AARG A 145 " =    1.150
peak=    3.961 closest distance to " O   HOH Z 406 " =    1.607
peak=    3.957 closest distance to " O   HOH Z 353 " =    2.570
peak=    3.951 closest distance to " O   HOH Z 188 " =    2.919
peak=    3.937 closest distance to " O   HOH Z 222 " =    2.362
peak=    3.934 closest distance to " CA  ARG A 195 " =    1.188
peak=    3.932 closest distance to " O   HOH Z 346 " =    1.629
peak=    3.931 closest distance to " CD2 TRP A 179 " =    1.214
peak=    3.911 closest distance to " O   HOH Z 298 " =    1.782
peak=    3.898 closest distance to " CB  ASN A  39 " =    0.921
peak=    3.888 closest distance to " CB  ARG A  79 " =    1.496
peak=    3.885 closest distance to " O   HOH Z 290 " =    1.136
peak=    3.865 closest distance to " CA  TYR A  30 " =    1.019
peak=    3.856 closest distance to " O   HOH Z 251 " =    1.572
peak=    3.853 closest distance to " CA  SER A  87 " =    0.985
peak=    3.850 closest distance to " O   HOH Z 411 " =    3.692
peak=    3.850 closest distance to " CB  ARG A 275 " =    0.963
peak=    3.839 closest distance to " O   HOH Z 207 " =    1.201
peak=    3.837 closest distance to " CB  SER A 216 " =    0.886
peak=    3.832 closest distance to " O   HOH Z  90 " =    2.257
peak=    3.813 closest distance to " O   HOH Z   3 " =    2.047
peak=    3.809 closest distance to " O   HOH Z 126 " =    1.599
peak=    3.798 closest distance to " CG2 ILE A  20 " =    1.554
peak=    3.791 closest distance to " CG2 ILE A 234 " =    0.973
peak=    3.784 closest distance to " CB AVAL A  41 " =    1.249
peak=    3.782 closest distance to " CB  VAL A 296 " =    1.029
peak=    3.774 closest distance to " CB  SER A 212 " =    1.318
peak=    3.768 closest distance to " CG  GLN A  58 " =    0.961
peak=    3.765 closest distance to " CA  LYS A 117 " =    1.273
peak=    3.764 closest distance to " CG  MET A 185 " =    1.192
peak=    3.760 closest distance to " O   PHE A 192 " =    1.367
peak=    3.751 closest distance to " O   HOH Z 158 " =    3.149
peak=    3.746 closest distance to " CB  VAL A 230 " =    1.155
peak=    3.738 closest distance to " CB  PRO A  54 " =    0.832
peak=    3.737 closest distance to " O   HOH Z   7 " =    1.224
peak=    3.735 closest distance to " CB  PRO A  90 " =    1.180
peak=    3.727 closest distance to " O   HOH Z 368 " =    2.218
peak=    3.724 closest distance to " O   HOH Z 273 " =    2.936
peak=    3.717 closest distance to " CB  ASP A 140 " =    0.941
peak=    3.702 closest distance to " CA  VAL A 125 " =    1.203
peak=    3.700 closest distance to " CB  VAL A 202 " =    1.605
peak=    3.686 closest distance to " CB  GLU A  46 " =    0.916
peak=    3.684 closest distance to " CA  MET A 105 " =    0.958
peak=    3.681 closest distance to " CD  LYS A 166 " =    1.336
peak=    3.680 closest distance to " OG1 THR A 279 " =    1.408
peak=    3.679 closest distance to " O   HOH Z 214 " =    2.560
peak=    3.679 closest distance to " ND2 ASN A 249 " =    0.876
peak=    3.675 closest distance to " CG  GLU A  37 " =    0.917
peak=    3.669 closest distance to " CB  GLU A 152 " =    1.191
peak=    3.666 closest distance to " O   HOH Z 261 " =    1.784
peak=    3.661 closest distance to " CB  THR A  52 " =    0.860
peak=    3.656 closest distance to " O   HOH Z 258 " =    1.939
peak=    3.655 closest distance to " O   HOH Z  78 " =    1.645
peak=    3.648 closest distance to " O   HOH Z 127 " =    1.166
peak=    3.646 closest distance to " CE3 TRP A 150 " =    1.073
peak=    3.644 closest distance to " CZ  PHE A  38 " =    1.145
peak=    3.622 closest distance to " N   ASN A  39 " =    1.259
peak=    3.620 closest distance to " O   HOH Z 365 " =    3.011
peak=    3.618 closest distance to " CB  ALA A   9 " =    1.618
peak=    3.610 closest distance to " CB  GLN A  89 " =    1.257
peak=    3.603 closest distance to " O   HOH Z  43 " =    2.006
peak=    3.602 closest distance to " O   HOH Z  10 " =    1.761
peak=    3.600 closest distance to " CD  ARG A 269 " =    0.977
peak=    3.600 closest distance to " CG AARG A 275 " =    1.317
peak=    3.589 closest distance to " CA  LEU A 282 " =    1.140
peak=    3.587 closest distance to " O   HOH Z 280 " =    2.994
peak=    3.586 closest distance to " O   HOH Z  21 " =    1.725
peak=    3.572 closest distance to " O   ASP A 124 " =    1.154
peak=    3.562 closest distance to " NE2 HIS A 207 " =    1.199
peak=    3.556 closest distance to " CB  SER A   3 " =    1.412
peak=    3.552 closest distance to " O   HOH Z 234 " =    3.624
peak=    3.552 closest distance to " CD1 ILE A  33 " =    1.886
peak=    3.548 closest distance to " CA  ARG A  36 " =    1.133
peak=    3.544 closest distance to " O   HOH Z  59 " =    1.972
peak=    3.543 closest distance to " CA  TYR A 116 " =    1.430
peak=    3.536 closest distance to " N   ALA A 256 " =    1.126
peak=    3.517 closest distance to " O   HOH Z 371 " =    2.738
peak=    3.499 closest distance to " OG1 THR A 264 " =    0.704
peak=    3.495 closest distance to " O   HOH Z 211 " =    1.188
peak=    3.493 closest distance to " CA  ASN A  74 " =    1.246
peak=    3.485 closest distance to " CG1 ILE A  49 " =    1.567
peak=    3.479 closest distance to " O   HOH Z 261 " =    1.777
peak=    3.479 closest distance to " O   PHE A  61 " =    1.393
peak=    3.476 closest distance to " OD1 ASN A  69 " =    2.549
peak=    3.471 closest distance to " O   HOH Z 193 " =    1.827
peak=    3.469 closest distance to " O   HOH Z  69 " =    0.737
peak=    3.465 closest distance to " CB  ASN A 215 " =    1.257
peak=    3.459 closest distance to " OG ASER A 258 " =    3.133
peak=    3.449 closest distance to " CD  ARG A  66 " =    2.693
peak=    3.445 closest distance to " CA  ARG A 159 " =    1.238
peak=    3.434 closest distance to " O   HOH Z 368 " =    3.450
peak=    3.429 closest distance to " CG  LYS A 119 " =    1.055
peak=    3.427 closest distance to " O   ASN A  74 " =    1.418
peak=    3.427 closest distance to " CD1 LEU A  96 " =    0.785
peak=    3.426 closest distance to " CB  THR A  31 " =    1.627
peak=    3.425 closest distance to " CA  ALA A 129 " =    1.479
peak=    3.419 closest distance to " O   HOH Z 180 " =    2.185
peak=    3.418 closest distance to " O   HOH Z 417 " =    3.428
peak=    3.414 closest distance to " CB  SER A  62 " =    0.878
peak=    3.408 closest distance to " O   HOH Z  88 " =    3.102
peak=    3.406 closest distance to " O   HOH Z 403 " =    1.526
peak=    3.404 closest distance to " CA  ASN A 217 " =    1.213
peak=    3.401 closest distance to " CG2 ILE A 120 " =    1.289
peak=    3.401 closest distance to " CB  MET A  40 " =    0.823
peak=    3.399 closest distance to " CD BLYS A 290 " =    1.064
peak=    3.398 closest distance to " CB  ARG A 102 " =    1.002
peak=    3.398 closest distance to " CB  THR A  82 " =    1.312
peak=    3.396 closest distance to " CG  LYS A  76 " =    1.922
peak=    3.393 closest distance to " OE2 GLU A  53 " =    1.982
peak=    3.392 closest distance to " O   HOH Z  68 " =    2.263
peak=    3.391 closest distance to " OG  SER A  62 " =    2.937
peak=    3.387 closest distance to " CA  THR A 264 " =    0.851
peak=    3.381 closest distance to " CB  ASP A 298 " =    1.162
peak=    3.381 closest distance to " CB  LYS A 117 " =    1.231
peak=    3.380 closest distance to " CE1 TYR A 186 " =    1.250
peak=    3.379 closest distance to " CA  ASP A 162 " =    1.017
peak=    3.377 closest distance to " O   HOH Z  30 " =    1.481
peak=    3.372 closest distance to " CA  ALA A 291 " =    0.867
peak=    3.370 closest distance to " O   HOH Z  40 " =    1.718
peak=    3.370 closest distance to " O   ALA A 165 " =    1.490
peak=    3.369 closest distance to " O   HOH Z 329 " =    4.254
peak=    3.366 closest distance to " CB  ARG A 138 " =    0.964
peak=    3.364 closest distance to " CA  ASN A 215 " =    1.087
peak=    3.359 closest distance to " CA  ASN A 127 " =    1.088
peak=    3.359 closest distance to " O   HOH Z  80 " =    1.672
peak=    3.359 closest distance to " OE2 GLU A   2 " =    2.067
peak=    3.358 closest distance to " CG2 THR A 221 " =    1.106
peak=    3.358 closest distance to " CB  ALA A  43 " =    0.808
peak=    3.357 closest distance to " CB  ASN A 110 " =    1.219
peak=    3.357 closest distance to " O   HOH Z 403 " =    1.572
peak=    3.355 closest distance to " O   HOH Z 272 " =    1.751
peak=    3.353 closest distance to " CB  SER A  97 " =    0.991
peak=    3.350 closest distance to " CB  LEU A 143 " =    1.219
peak=    3.336 closest distance to " CB  ALA A 104 " =    0.736
peak=    3.336 closest distance to " CA  ALA A 160 " =    1.017
peak=    3.328 closest distance to " O   HOH Z 299 " =    4.313
peak=    3.328 closest distance to " CD1 ILE A 199 " =    1.151
peak=    3.327 closest distance to " CB  ASP A 171 " =    1.161
peak=    3.326 closest distance to " N   ASN A 127 " =    1.327
peak=    3.320 closest distance to " CG2AVAL A  72 " =    1.667
peak=    3.319 closest distance to " CA  ILE A 234 " =    1.027
peak=    3.318 closest distance to " O   HOH Z 285 " =    2.143
peak=    3.312 closest distance to " NZ  LYS A  48 " =    1.166
peak=    3.310 closest distance to " CG1 ILE A 151 " =    1.152
peak=    3.309 closest distance to " O   HOH Z 258 " =    1.118
peak=    3.309 closest distance to " O   HOH Z 166 " =    3.979
peak=    3.308 closest distance to " CG1 VAL A 153 " =    0.908
peak=    3.305 closest distance to " CB  LEU A  83 " =    0.742
peak=    3.300 closest distance to " O   HOH Z   1 " =    1.896
peak=    3.299 closest distance to " CG  ARG A 159 " =    0.954
peak=    3.299 closest distance to " CA  ALA A 158 " =    1.297
peak=    3.296 closest distance to " O   HOH Z 216 " =    3.685
peak=    3.288 closest distance to " CB  PRO A 243 " =    1.638
peak=    3.286 closest distance to " N   ASP A 162 " =    1.165
peak=    3.286 closest distance to " CB  TRP A 150 " =    1.257
peak=    3.285 closest distance to " CB  HIS A 108 " =    0.794
peak=    3.284 closest distance to " O   HOH Z 392 " =    3.094
peak=    3.284 closest distance to " O   HOH Z  88 " =    3.510
peak=    3.283 closest distance to " O   HOH Z 145 " =    1.343
peak=    3.283 closest distance to " CB  ASN A 173 " =    1.033
peak=    3.275 closest distance to " CB  TRP A 179 " =    1.478
peak=    3.268 closest distance to " OG BSER A 134 " =    2.857
peak=    3.266 closest distance to " O   HOH Z 193 " =    1.656
peak=    3.262 closest distance to " NH1 ARG A 138 " =    1.144
peak=    3.261 closest distance to " CD  ARG A 195 " =    3.544
peak=    3.260 closest distance to " O   ASN A 284 " =    1.672
peak=    3.259 closest distance to " CB  SER A 210 " =    0.750
peak=    3.259 closest distance to " O   HOH Z 112 " =    0.926
peak=    3.258 closest distance to " CA  HIS A  86 " =    0.711
peak=    3.257 closest distance to " O   HOH Z 171 " =    4.121
peak=    3.254 closest distance to " O   HOH Z 148 " =    3.556
peak=    3.254 closest distance to " O   HOH Z   4 " =    1.558
peak=    3.251 closest distance to " CG  GLN A  88 " =    1.093
peak=    3.251 closest distance to " O   HOH Z  76 " =    1.196
peak=    3.249 closest distance to " CB  ALA A 227 " =    1.043
peak=    3.248 closest distance to " CA  ARG A 102 " =    1.160
peak=    3.247 closest distance to " CB  VAL A 268 " =    0.866
peak=    3.246 closest distance to " CE  LYS A  48 " =    1.196
peak=    3.245 closest distance to " O   THR A 182 " =    1.456
peak=    3.243 closest distance to " CG2 VAL A 197 " =    1.094
peak=    3.242 closest distance to " O   HOH Z 350 " =    1.627
peak=    3.242 closest distance to " CB  GLN A  88 " =    1.258
peak=    3.240 closest distance to " O   MET A 105 " =    1.801
peak=    3.238 closest distance to " CD  ARG A  66 " =    2.357
peak=    3.237 closest distance to " O   HOH Z 337 " =    1.685
peak=    3.226 closest distance to " CA  GLN A  94 " =    0.753
peak=    3.224 closest distance to " CB  ALA A   1 " =    4.986
peak=    3.220 closest distance to " CA  ALA A 295 " =    1.173
peak=    3.219 closest distance to " C   ALA A 299 " =    0.905
peak=    3.218 closest distance to " O   HOH Z 281 " =    2.528
peak=    3.217 closest distance to " O   HOH Z 305 " =    3.414
peak=    3.215 closest distance to " CB  GLU A 128 " =    0.999
peak=    3.211 closest distance to " O   HOH Z   1 " =    1.647
peak=    3.209 closest distance to " OG BSER A 164 " =    2.261
peak=    3.207 closest distance to " O   HOH Z 133 " =    2.929
peak=    3.207 closest distance to " CA  ALA A 154 " =    1.099
peak=    3.206 closest distance to " CB  GLN A 205 " =    1.036
peak=    3.204 closest distance to " CB  LEU A 228 " =    1.299
peak=    3.202 closest distance to " CA  ALA A 100 " =    0.869
peak=    3.200 closest distance to " O   GLN A  88 " =    1.635
peak=    3.195 closest distance to " O   HOH Z 380 " =    1.693
peak=    3.194 closest distance to " CD  LYS A 119 " =    2.136
peak=    3.192 closest distance to " O   HOH Z 409 " =    3.005
peak=    3.190 closest distance to " O   HOH Z 419 " =    1.937
peak=    3.187 closest distance to " O   HOH Z 187 " =    2.318
peak=    3.186 closest distance to " CA  GLY A 267 " =    0.964
peak=    3.186 closest distance to " CG2BVAL A 121 " =    0.804
peak=    3.184 closest distance to " O   HOH Z 213 " =    1.952
peak=    3.182 closest distance to " CB  LEU A 300 " =    0.873
peak=    3.177 closest distance to " CA  ALA A  21 " =    1.188
peak=    3.177 closest distance to " CA  ALA A 233 " =    1.225
peak=    3.170 closest distance to " O   ASP A 200 " =    1.528
peak=    3.168 closest distance to " O   HOH Z 222 " =    2.245
peak=    3.168 closest distance to " CB  TYR A 116 " =    0.853
peak=    3.168 closest distance to " O   HOH Z 203 " =    1.711
peak=    3.167 closest distance to " CA  GLY A 118 " =    0.751
peak=    3.164 closest distance to " CG2 ILE A 151 " =    0.926
peak=    3.161 closest distance to " O   HOH Z 423 " =    1.778
peak=    3.161 closest distance to " CZ3 TRP A  92 " =    1.286
peak=    3.161 closest distance to " CA  ILE A 106 " =    0.785
peak=    3.159 closest distance to " O   THR A 220 " =    1.301
peak=    3.159 closest distance to " CD1 LEU A 300 " =    1.063
peak=    3.157 closest distance to " CB  PHE A 204 " =    0.913
peak=    3.156 closest distance to " O   HOH Z 126 " =    1.740
peak=    3.154 closest distance to " N   ARG A 156 " =    1.358
peak=    3.153 closest distance to " CB  ALA A 291 " =    1.252
peak=    3.153 closest distance to " CG  GLN A 278 " =    1.315
peak=    3.152 closest distance to " N   SER A 135 " =    1.322
peak=    3.147 closest distance to " N   GLN A 278 " =    1.436
peak=    3.140 closest distance to " ND1 HIS A  86 " =    1.649
peak=    3.139 closest distance to " CG  LEU A 281 " =    1.013
peak=    3.137 closest distance to " CB  ALA A  34 " =    1.189
peak=    3.135 closest distance to " CA  LEU A 101 " =    1.294
peak=    3.128 closest distance to " CB  LEU A  96 " =    1.373
peak=    3.125 closest distance to " CA  LYS A 290 " =    1.258
peak=    3.125 closest distance to " O   HOH Z 213 " =    2.857
peak=    3.124 closest distance to " O   HOH Z 263 " =    1.715
peak=    3.122 closest distance to " O   HOH Z 162 " =    3.849
peak=    3.118 closest distance to " CG  MET A 185 " =    1.009
peak=    3.117 closest distance to " O   HOH Z 389 " =    1.813
peak=    3.115 closest distance to " OH  TYR A 214 " =    1.295
peak=    3.114 closest distance to " CD  ARG A 195 " =    0.988
peak=    3.104 closest distance to " OG BSER A  99 " =    2.228
peak=    3.100 closest distance to " CA  ARG A 139 " =    1.040
peak=    3.086 closest distance to " O   HOH Z 148 " =    2.231
peak=    3.084 closest distance to " CA  LEU A  83 " =    1.128
peak=    3.082 closest distance to " O   HOH Z 394 " =    3.603
peak=    3.077 closest distance to " O   HOH Z 172 " =    3.458
peak=    3.067 closest distance to " O   HOH Z 128 " =    2.147
peak=    3.062 closest distance to " O   HOH Z 258 " =    1.401
peak=    3.054 closest distance to " CB  ALA A 180 " =    1.303
peak=    3.047 closest distance to " O   HOH Z 425 " =    2.119
peak=    3.041 closest distance to " N   ALA A   7 " =    1.206
peak=    3.034 closest distance to " CG  GLN A  55 " =    2.484
peak=    3.020 closest distance to " O   HOH Z 412 " =    3.991
peak=    3.019 closest distance to " O   HOH Z 116 " =    1.793
peak=    3.019 closest distance to " O   HOH Z 393 " =    3.150

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 213         
Filter by distance & map next to the model:
   mapped sites are within: 0.629 - 5.633
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 212 from: 213
   mapped sites are within: 0.722 - 5.633

peak=   -4.604 closest distance to " CG2 VAL A 230 " =    0.768
peak=   -4.511 closest distance to " CD  ARG A  14 " =    3.315
peak=   -4.461 closest distance to " CG1 VAL A 250 " =    2.762
peak=   -4.381 closest distance to " O   HOH Z 162 " =    2.678
peak=   -4.343 closest distance to " CG1 VAL A 112 " =    2.677
peak=   -4.294 closest distance to " O   HOH Z 193 " =    1.064
peak=   -4.218 closest distance to " CD  ARG A 156 " =    2.041
peak=   -4.140 closest distance to " CD  GLN A  58 " =    0.969
peak=   -4.132 closest distance to " CZ2 TRP A  92 " =    2.814
peak=   -4.082 closest distance to " O   HOH Z 231 " =    2.052
peak=   -4.039 closest distance to " CB  VAL A 230 " =    1.134
peak=   -4.012 closest distance to " O   HOH Z 411 " =    5.479
peak=   -3.951 closest distance to " CG2 VAL A 296 " =    1.400
peak=   -3.941 closest distance to " CB  PHE A 192 " =    1.951
peak=   -3.935 closest distance to " O   HOH Z  73 " =    2.469
peak=   -3.912 closest distance to " OG  SER A  97 " =    2.326
peak=   -3.909 closest distance to " CB  ALA A  43 " =    2.684
peak=   -3.897 closest distance to " OG BSER A 134 " =    1.409
peak=   -3.870 closest distance to " O   PRO A 198 " =    1.249
peak=   -3.857 closest distance to " O   HOH Z 149 " =    2.182
peak=   -3.840 closest distance to " O   HOH Z 394 " =    1.568
peak=   -3.826 closest distance to " CE2 TYR A  30 " =    2.622
peak=   -3.822 closest distance to " CG1 VAL A 112 " =    2.873
peak=   -3.821 closest distance to " C   HIS A 108 " =    1.282
peak=   -3.821 closest distance to " O   HOH Z  52 " =    1.546
peak=   -3.819 closest distance to " CD1 LEU A 101 " =    2.384
peak=   -3.796 closest distance to " O   HOH Z 166 " =    2.003
peak=   -3.796 closest distance to " O   HOH Z 295 " =    1.627
peak=   -3.777 closest distance to " CG2 VAL A 202 " =    2.751
peak=   -3.777 closest distance to " CG  GLN A 223 " =    2.238
peak=   -3.773 closest distance to " O   HOH Z 115 " =    1.786
peak=   -3.759 closest distance to " CE3 TRP A 150 " =    2.288
peak=   -3.756 closest distance to " O   HOH Z 359 " =    2.886
peak=   -3.753 closest distance to " CB  ALA A 161 " =    2.561
peak=   -3.744 closest distance to " CD  PRO A 213 " =    2.114
peak=   -3.738 closest distance to " O   VAL A  67 " =    2.608
peak=   -3.727 closest distance to " CG2 THR A  18 " =    2.854
peak=   -3.714 closest distance to " O   HOH Z 131 " =    4.025
peak=   -3.697 closest distance to " CA  GLY A 241 " =    2.370
peak=   -3.693 closest distance to " CE BMET A  47 " =    1.355
peak=   -3.689 closest distance to " OG  SER A  87 " =    1.522
peak=   -3.679 closest distance to " O   HOH Z 127 " =    1.047
peak=   -3.674 closest distance to " O   HOH Z  69 " =    1.907
peak=   -3.670 closest distance to " O   HOH Z 106 " =    1.738
peak=   -3.665 closest distance to " CG2 THR A 178 " =    2.463
peak=   -3.660 closest distance to " CD2 LEU A 237 " =    2.823
peak=   -3.659 closest distance to " O   HOH Z 166 " =    2.290
peak=   -3.648 closest distance to " CA  GLY A  98 " =    1.972
peak=   -3.645 closest distance to " CA  VAL A  67 " =    2.829
peak=   -3.636 closest distance to " CD2 TYR A 293 " =    2.017
peak=   -3.629 closest distance to " O   HOH Z 100 " =    0.997
peak=   -3.623 closest distance to " OG  SER A  62 " =    4.279
peak=   -3.620 closest distance to " CB  PRO A 280 " =    2.142
peak=   -3.595 closest distance to " O   GLY A  17 " =    1.144
peak=   -3.590 closest distance to " O   HOH Z 147 " =    2.036
peak=   -3.576 closest distance to " CB  HIS A  86 " =    1.100
peak=   -3.572 closest distance to " O   HOH Z 429 " =    1.920
peak=   -3.564 closest distance to " CG  GLU A 277 " =    1.262
peak=   -3.562 closest distance to " O   HOH Z 216 " =    1.020
peak=   -3.561 closest distance to " N   ALA A 226 " =    2.068
peak=   -3.559 closest distance to " O   VAL A 189 " =    2.669
peak=   -3.559 closest distance to " O   HOH Z 357 " =    2.103
peak=   -3.557 closest distance to " O   PRO A 163 " =    1.998
peak=   -3.550 closest distance to " O   HOH Z 252 " =    3.788
peak=   -3.548 closest distance to " CG  TRP A 266 " =    1.857
peak=   -3.546 closest distance to " CA  ASP A 298 " =    1.098
peak=   -3.545 closest distance to " NH2AARG A 275 " =    5.277
peak=   -3.523 closest distance to " O   HOH Z 351 " =    1.585
peak=   -3.521 closest distance to " O   HOH Z 185 " =    2.351
peak=   -3.521 closest distance to " O   HOH Z 290 " =    1.295
peak=   -3.511 closest distance to " CE2 TRP A  70 " =    2.289
peak=   -3.507 closest distance to " ND2 ASN A  45 " =    2.035
peak=   -3.506 closest distance to " CD2 PHE A 225 " =    1.140
peak=   -3.505 closest distance to " CA  ASP A  27 " =    2.503
peak=   -3.502 closest distance to " N   THR A  52 " =    1.670
peak=   -3.488 closest distance to " CD1 LEU A 255 " =    2.907
peak=   -3.485 closest distance to " O   HOH Z 238 " =    0.902
peak=   -3.483 closest distance to " CB  PRO A 163 " =    2.458
peak=   -3.476 closest distance to " OH  TYR A 172 " =    1.780
peak=   -3.468 closest distance to " OD1 ASN A 148 " =    1.345
peak=   -3.455 closest distance to " O   HOH Z 198 " =    1.911
peak=   -3.452 closest distance to " O   HOH Z 103 " =    1.731
peak=   -3.451 closest distance to " CB  ALA A 248 " =    2.324
peak=   -3.444 closest distance to " O   HOH Z 191 " =    5.633
peak=   -3.441 closest distance to " CG1 VAL A 112 " =    2.818
peak=   -3.439 closest distance to " OD1 ASP A 171 " =    1.614
peak=   -3.435 closest distance to " O   HOH Z 189 " =    2.404
peak=   -3.435 closest distance to " CA  GLY A 241 " =    3.227
peak=   -3.433 closest distance to " CG1BVAL A  72 " =    2.577
peak=   -3.432 closest distance to " O   HOH Z  44 " =    0.973
peak=   -3.428 closest distance to " N   ALA A  43 " =    2.676
peak=   -3.422 closest distance to " CG1 VAL A 257 " =    2.324
peak=   -3.418 closest distance to " O   HOH Z 407 " =    2.918
peak=   -3.418 closest distance to " O   HOH Z 138 " =    1.319
peak=   -3.412 closest distance to " O   HOH Z 426 " =    1.649
peak=   -3.408 closest distance to " O   HOH Z  11 " =    1.862
peak=   -3.403 closest distance to " CH2 TRP A 179 " =    1.225
peak=   -3.399 closest distance to " O   ALA A 227 " =    1.502
peak=   -3.398 closest distance to " CD2 PHE A  61 " =    2.071
peak=   -3.398 closest distance to " O   TYR A 186 " =    1.742
peak=   -3.395 closest distance to " CD2 LEU A   5 " =    1.052
peak=   -3.393 closest distance to " O   HOH Z 431 " =    1.891
peak=   -3.390 closest distance to " O   HOH Z  68 " =    1.369
peak=   -3.390 closest distance to " O   SER A 271 " =    2.228
peak=   -3.388 closest distance to " CA  ASN A 127 " =    1.190
peak=   -3.387 closest distance to " NE2 GLN A  11 " =    1.777
peak=   -3.387 closest distance to " C   ALA A 158 " =    1.328
peak=   -3.381 closest distance to " O   HOH Z   9 " =    1.664
peak=   -3.379 closest distance to " CG2 ILE A 263 " =    2.446
peak=   -3.377 closest distance to " CD1 ILE A 151 " =    2.517
peak=   -3.368 closest distance to " O   HOH Z 389 " =    1.527
peak=   -3.368 closest distance to " CE  MET A 105 " =    2.320
peak=   -3.367 closest distance to " O   HOH Z 102 " =    1.592
peak=   -3.348 closest distance to " CG  PHE A 283 " =    2.630
peak=   -3.341 closest distance to " O   HOH Z 292 " =    1.651
peak=   -3.338 closest distance to " CD1 LEU A 228 " =    2.314
peak=   -3.337 closest distance to " O   PHE A 218 " =    1.602
peak=   -3.335 closest distance to " NE2 GLN A 194 " =    1.901
peak=   -3.323 closest distance to " OE1 GLN A  88 " =    1.043
peak=   -3.322 closest distance to " O   HOH Z   9 " =    3.122
peak=   -3.321 closest distance to " CB  ALA A  10 " =    2.301
peak=   -3.318 closest distance to " CG  ASP A 231 " =    0.779
peak=   -3.316 closest distance to " SG BCYS A 201 " =    2.393
peak=   -3.314 closest distance to " CG  ARG A 269 " =    2.371
peak=   -3.312 closest distance to " O   SER A 276 " =    1.699
peak=   -3.305 closest distance to " O   HOH Z 123 " =    2.489
peak=   -3.300 closest distance to " O   HOH Z 100 " =    1.159
peak=   -3.295 closest distance to " C   LEU A 143 " =    1.101
peak=   -3.292 closest distance to " O   HOH Z 371 " =    2.302
peak=   -3.292 closest distance to " CA  GLY A 133 " =    2.302
peak=   -3.290 closest distance to " CA  SER A 135 " =    1.289
peak=   -3.285 closest distance to " ND2 ASN A 249 " =    2.199
peak=   -3.281 closest distance to " OG  SER A 141 " =    1.703
peak=   -3.279 closest distance to " O   HOH Z 412 " =    4.308
peak=   -3.279 closest distance to " CG2 THR A  29 " =    2.590
peak=   -3.272 closest distance to " O   HOH Z 111 " =    1.541
peak=   -3.268 closest distance to " CD  PRO A 243 " =    1.998
peak=   -3.265 closest distance to " O   HOH Z 232 " =    1.859
peak=   -3.260 closest distance to " CG2 VAL A 189 " =    1.862
peak=   -3.258 closest distance to " ND2 ASN A  60 " =    1.373
peak=   -3.258 closest distance to " O   HOH Z 275 " =    1.844
peak=   -3.258 closest distance to " O   HOH Z 285 " =    2.129
peak=   -3.253 closest distance to " O   HOH Z 275 " =    1.498
peak=   -3.249 closest distance to " OD1 ASP A 200 " =    1.615
peak=   -3.245 closest distance to " CD2 HIS A 207 " =    2.185
peak=   -3.240 closest distance to " O   ASP A  27 " =    1.845
peak=   -3.239 closest distance to " C   MET A 188 " =    1.466
peak=   -3.238 closest distance to " CD1 LEU A   5 " =    2.509
peak=   -3.234 closest distance to " O   HOH Z  63 " =    1.838
peak=   -3.229 closest distance to " O   HOH Z  64 " =    1.589
peak=   -3.227 closest distance to " O   GLY A  80 " =    2.568
peak=   -3.226 closest distance to " O   HOH Z 140 " =    1.665
peak=   -3.226 closest distance to " O   LYS A 117 " =    1.787
peak=   -3.215 closest distance to " O   HOH Z 253 " =    4.097
peak=   -3.214 closest distance to " O   HOH Z 176 " =    0.722
peak=   -3.207 closest distance to " O   HOH Z 136 " =    2.571
peak=   -3.206 closest distance to " CE2 PHE A  61 " =    2.702
peak=   -3.206 closest distance to " CZ2 TRP A 274 " =    1.000
peak=   -3.202 closest distance to " N   THR A 157 " =    1.544
peak=   -3.202 closest distance to " O   HOH Z 350 " =    1.570
peak=   -3.200 closest distance to " CE1 PHE A 218 " =    2.664
peak=   -3.191 closest distance to " O   ALA A  51 " =    1.308
peak=   -3.191 closest distance to " O   HOH Z 134 " =    4.100
peak=   -3.185 closest distance to " CA  GLY A 203 " =    2.574
peak=   -3.185 closest distance to " O   HOH Z 410 " =    2.078
peak=   -3.183 closest distance to " N   SER A 276 " =    1.431
peak=   -3.180 closest distance to " O   HOH Z 174 " =    2.457
peak=   -3.180 closest distance to " CD  GLN A 223 " =    1.335
peak=   -3.174 closest distance to " O   HOH Z  65 " =    1.521
peak=   -3.168 closest distance to " O   SER A 210 " =    1.832
peak=   -3.167 closest distance to " O   HOH Z  43 " =    1.679
peak=   -3.167 closest distance to " CG2 VAL A 296 " =    1.891
peak=   -3.165 closest distance to " O   HOH Z 200 " =    3.059
peak=   -3.163 closest distance to " O   HOH Z 251 " =    5.047
peak=   -3.161 closest distance to " O   HOH Z 364 " =    2.767
peak=   -3.155 closest distance to " CG  GLN A 103 " =    2.420
peak=   -3.154 closest distance to " O   HOH Z 256 " =    1.434
peak=   -3.152 closest distance to " CB  ASN A 148 " =    1.878
peak=   -3.151 closest distance to " CA  ASN A 110 " =    1.034
peak=   -3.148 closest distance to " CE3 TRP A  70 " =    1.634
peak=   -3.148 closest distance to " CG  PRO A 163 " =    2.149
peak=   -3.142 closest distance to " CA  GLY A 302 " =    2.866
peak=   -3.140 closest distance to " C   ASP A 270 " =    1.354
peak=   -3.136 closest distance to " CG1 VAL A 125 " =    1.832
peak=   -3.135 closest distance to " CD1 TRP A  70 " =    1.113
peak=   -3.127 closest distance to " O   HOH Z 389 " =    2.219
peak=   -3.126 closest distance to " ND2 ASN A 173 " =    1.798
peak=   -3.125 closest distance to " OG BSER A 134 " =    1.847
peak=   -3.123 closest distance to " O   HOH Z 110 " =    1.333
peak=   -3.120 closest distance to " O   HOH Z 326 " =    5.109
peak=   -3.118 closest distance to " CE1 TYR A 247 " =    2.648
peak=   -3.113 closest distance to " CG  PRO A 163 " =    2.674
peak=   -3.110 closest distance to " OH  TYR A 247 " =    1.841
peak=   -3.109 closest distance to " CA  GLY A 241 " =    2.910
peak=   -3.108 closest distance to " O   HOH Z 278 " =    1.197
peak=   -3.107 closest distance to " O   SER A  22 " =    2.517
peak=   -3.105 closest distance to " O   HOH Z 411 " =    1.095
peak=   -3.102 closest distance to " O   HOH Z 128 " =    2.589
peak=   -3.101 closest distance to " CD1 ILE A 199 " =    2.512
peak=   -3.098 closest distance to " CG  ARG A 259 " =    2.329
peak=   -3.096 closest distance to " O   HOH Z 145 " =    1.082
peak=   -3.092 closest distance to " O   HOH Z  10 " =    1.513
peak=   -3.087 closest distance to " OG  SER A 245 " =    1.328
peak=   -3.085 closest distance to " O   HOH Z 390 " =    2.292
peak=   -3.081 closest distance to " CB  TYR A  15 " =    2.250
peak=   -3.070 closest distance to " CG1 VAL A 197 " =    2.377
peak=   -3.069 closest distance to " O   HOH Z 318 " =    2.020
peak=   -3.068 closest distance to " O   GLN A 240 " =    2.540
peak=   -3.065 closest distance to " NH2 ARG A 219 " =    1.641
peak=   -3.062 closest distance to " O   HOH Z 340 " =    1.956
peak=   -3.036 closest distance to " O   HOH Z 166 " =    1.680
peak=   -3.019 closest distance to " CD  GLU A 236 " =    1.144

================= 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    :  0.4710 0.4592   6.273720e+00   6.252815e+00
   1_bss:  0.4621 0.4482   6.267598e+00   6.241488e+00
   1_xyz:  0.3746 0.3964   6.141290e+00   6.169717e+00
   1_adp:  0.3242 0.3737   6.041638e+00   6.128882e+00
   1_occ:  0.3238 0.3750   6.041094e+00   6.131187e+00
   2_bss:  0.3213 0.3718   6.042112e+00   6.130489e+00
   2_xyz:  0.2440 0.2996   5.809441e+00   5.962401e+00
   2_adp:  0.2233 0.2770   5.738354e+00   5.906033e+00
   2_occ:  0.2230 0.2766   5.737753e+00   5.905445e+00
   3_bss:  0.2216 0.2770   5.739030e+00   5.906319e+00
   3_xyz:  0.1584 0.2116   5.443818e+00   5.660632e+00
   3_adp:  0.1407 0.1945   5.346299e+00   5.580645e+00
   3_occ:  0.1405 0.1945   5.346242e+00   5.581218e+00
   4_bss:  0.1403 0.1940   5.345003e+00   5.579498e+00
   4_xyz:  0.1316 0.1807   5.289205e+00   5.518783e+00
   4_adp:  0.1316 0.1770   5.279733e+00   5.496114e+00
   4_occ:  0.1315 0.1767   5.278816e+00   5.495014e+00
   5_bss:  0.1314 0.1767   5.278614e+00   5.495013e+00
   5_xyz:  0.1207 0.1667   5.210753e+00   5.444414e+00
   5_adp:  0.1185 0.1672   5.202842e+00   5.446079e+00
   5_occ:  0.1182 0.1672   5.202045e+00   5.445648e+00
   5_bss:  0.1182 0.1672   5.202112e+00   5.445744e+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:  0.327  20.606   6.753   7.189  12.327   0.000   0.000   0.000
   1_xyz:  0.327  20.606   6.753   7.189  12.327   0.000   0.000   0.000
   1_adp:  0.327  20.606   6.753   7.189  12.327   0.000   0.000   0.000
   1_occ:  0.327  20.606   6.753   7.189  12.327   0.000   0.000   0.000
   2_bss:  0.336  50.000   3.750   3.936   8.903   0.000   0.000   0.000
   2_xyz:  0.336  50.000   3.750   3.936   8.903   0.000   0.000   0.000
   2_adp:  0.336  50.000   3.750   3.936   8.903   0.000   0.000   0.000
   2_occ:  0.336  50.000   3.750   3.936   8.903   0.000   0.000   0.000
   3_bss:  0.339  67.493   2.388   2.642   5.786   0.000   0.000   0.000
   3_xyz:  0.339  67.493   2.388   2.642   5.786   0.000   0.000   0.000
   3_adp:  0.339  67.493   2.388   2.642   5.786   0.000   0.000   0.000
   3_occ:  0.339  67.493   2.388   2.642   5.786   0.000   0.000   0.000
   4_bss:  0.333  67.493   2.006   2.198   4.530   0.000   0.000   0.000
   4_xyz:  0.333  67.493   2.006   2.198   4.530   0.000   0.000   0.000
   4_adp:  0.333  67.493   2.006   2.198   4.530   0.000   0.000   0.000
   4_occ:  0.333  67.493   2.006   2.198   4.530   0.000   0.000   0.000
   5_bss:  0.329  61.584   1.869   2.035   4.125   0.000   0.000   0.000
   5_xyz:  0.329  61.584   1.869   2.035   4.125   0.000   0.000   0.000
   5_adp:  0.329  61.584   1.869   2.035   4.125   0.000   0.000   0.000
   5_occ:  0.329  61.584   1.869   2.035   4.125   0.000   0.000   0.000
   5_bss:  0.329  64.414  -0.726  -0.646   1.372  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.726 0.4742  0.5419    63133.562
   1_bss:  53.093 0.4813  0.7119    60942.125
   1_xyz:  44.417 0.5890  0.8447    44809.204
   1_adp:  40.288 0.6393  0.9451    39080.826
   1_occ:  40.438 0.6375  0.9415    39321.813
   2_bss:  40.259 0.6397  0.8441    39121.548
   2_xyz:  30.838 0.7482  0.9628    23789.044
   2_adp:  28.058 0.7794  0.9855    20448.136
   2_occ:  28.062 0.7793  0.9850    20413.691
   3_bss:  27.956 0.7806  0.9223    20452.997
   3_xyz:  20.398 0.8573  0.9836    11356.175
   3_adp:  18.333 0.8771  0.9904     9620.033
   3_occ:  18.346 0.8770  0.9904     9622.419
   4_bss:  18.298 0.8774  0.9666     9595.697
   4_xyz:  16.828 0.8911  0.9694     8386.804
   4_adp:  16.254 0.8965  0.9685     8069.903
   4_occ:  16.233 0.8967  0.9687     8049.661
   5_bss:  16.228 0.8967  0.9608     8046.714
   5_xyz:  15.083 0.9064  0.9678     7206.133
   5_adp:  15.087 0.9065  0.9630     7189.631
   5_occ:  15.087 0.9065  0.9629     7184.434
   5_bss:  15.088 0.9065  0.9682     7187.592
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4268e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4268e+01
   1_xyz:   1.664  0.013  0.106 18.355  0.006  4.111   1.3746e-01
   1_adp:   1.664  0.013  0.106 18.355  0.006  4.111   1.3746e-01
   1_occ:   1.664  0.013  0.106 18.355  0.006  4.111   1.3746e-01
   2_bss:   1.664  0.013  0.106 18.355  0.006  4.111   1.3746e-01
   2_xyz:   1.158  0.008  0.081 16.598  0.005  4.129   7.9755e-02
   2_adp:   1.158  0.008  0.081 16.598  0.005  4.129   7.9755e-02
   2_occ:   1.158  0.008  0.081 16.598  0.005  4.129   7.9755e-02
   3_bss:   1.158  0.008  0.081 16.598  0.005  4.129   7.9755e-02
   3_xyz:   1.175  0.010  0.089 16.608  0.004  4.121   8.4147e-02
   3_adp:   1.175  0.010  0.089 16.608  0.004  4.121   8.4147e-02
   3_occ:   1.175  0.010  0.089 16.608  0.004  4.121   8.4147e-02
   4_bss:   1.175  0.010  0.089 16.608  0.004  4.121   8.4147e-02
   4_xyz:   0.927  0.007  0.072 15.864  0.003  4.126   5.7120e-02
   4_adp:   0.927  0.007  0.072 15.864  0.003  4.126   5.7120e-02
   4_occ:   0.927  0.007  0.072 15.864  0.003  4.126   5.7120e-02
   5_bss:   0.927  0.007  0.072 15.864  0.003  4.126   5.7120e-02
   5_xyz:   1.091  0.009  0.085 15.864  0.004  4.134   7.2814e-02
   5_adp:   1.091  0.009  0.085 15.864  0.004  4.134   7.2814e-02
   5_occ:   1.091  0.009  0.085 15.864  0.004  4.134   7.2814e-02
   5_bss:   1.091  0.009  0.085 15.864  0.004  4.134   7.2814e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0355e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0355e+00
   1_xyz:  13.783  0.167  0.408 86.485  0.033  2.128   1.0095e-01
   1_adp:  13.783  0.167  0.408 86.485  0.033  2.128   1.0095e-01
   1_occ:  13.783  0.167  0.408 86.485  0.033  2.128   1.0095e-01
   2_bss:  13.783  0.167  0.408 86.485  0.033  2.128   1.0095e-01
   2_xyz:   6.513  0.069  0.272 87.441  0.060  2.291   5.2198e-02
   2_adp:   6.513  0.069  0.272 87.441  0.060  2.291   5.2198e-02
   2_occ:   6.513  0.069  0.272 87.441  0.060  2.291   5.2198e-02
   3_bss:   6.513  0.069  0.272 87.441  0.060  2.291   5.2198e-02
   3_xyz:  10.103  0.062  0.413 87.172  0.037  2.240   6.7682e-02
   3_adp:  10.103  0.062  0.413 87.172  0.037  2.240   6.7682e-02
   3_occ:  10.103  0.062  0.413 87.172  0.037  2.240   6.7682e-02
   4_bss:  10.103  0.062  0.413 87.172  0.037  2.240   6.7682e-02
   4_xyz:   7.279  0.050  0.344 83.057  0.038  2.426   3.5163e-02
   4_adp:   7.279  0.050  0.344 83.057  0.038  2.426   3.5163e-02
   4_occ:   7.279  0.050  0.344 83.057  0.038  2.426   3.5163e-02
   5_bss:   7.279  0.050  0.344 83.057  0.038  2.426   3.5163e-02
   5_xyz:   7.043  0.053  0.472 87.852  0.038  2.321   4.4672e-02
   5_adp:   7.043  0.053  0.472 87.852  0.038  2.321   4.4672e-02
   5_occ:   7.043  0.053  0.472 87.852  0.038  2.321   4.4672e-02
   5_bss:   7.043  0.053  0.472 87.852  0.038  2.321   4.4672e-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:  69.96   0.00  12.94  59.53   0.00  10.33  69.96   0.00  27.19
   1_occ:  69.96   0.00  12.94  59.53   0.00  10.33  69.96   0.00  27.19
   2_bss:  69.96   0.00  12.94  59.53   0.00  10.33  69.96   0.00  27.19
   2_xyz:  69.96   0.00  12.94  59.53   0.00  10.33  69.96   0.00  27.19
   2_adp:  70.48   0.00  12.70  64.57   0.00   9.02  70.48   0.00  32.75
   2_occ:  70.48   0.00  12.70  64.57   0.00   9.02  70.48   0.00  32.75
   3_bss:  70.48   0.00  12.70  64.57   0.00   9.02  70.48   0.00  32.75
   3_xyz:  70.48   0.00  12.70  64.57   0.00   9.02  70.48   0.00  32.75
   3_adp:  89.40   0.00  13.40  75.51   0.00   8.70  89.40   1.34  38.97
   3_occ:  89.40   0.00  13.40  75.51   0.00   8.70  89.40   1.34  38.97
   4_bss:  89.40   0.00  13.40  75.51   0.00   8.70  89.40   1.34  38.97
   4_xyz:  89.40   0.00  13.40  75.51   0.00   8.70  89.40   1.34  38.97
   4_adp:  85.56   0.00  12.71  75.51   0.00   8.40  85.56   1.46  36.18
   4_occ:  85.56   0.00  12.71  75.51   0.00   8.40  85.56   1.46  36.18
   5_bss:  85.56   0.00  12.71  75.51   0.00   8.40  85.56   1.46  36.18
   5_xyz:  85.56   0.00  12.71  75.51   0.00   8.40  85.56   1.46  36.18
   5_adp:  93.63   0.00  13.00  80.64   0.00   8.50  93.63   1.12  37.52
   5_occ:  93.63   0.00  13.00  80.64   0.00   8.50  93.63   1.12  37.52
   5_bss:  96.46   2.83  15.83  83.47   2.83  11.33  96.46   3.95  40.35
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.255    0.015    0.410
   1_adp:    1.255    0.015    0.410
   1_occ:    1.255    0.015    0.410
   2_bss:    1.255    0.015    0.410
   2_xyz:    1.799    0.028    0.559
   2_adp:    1.799    0.028    0.559
   2_occ:    1.799    0.028    0.559
   3_bss:    1.799    0.028    0.559
   3_xyz:    1.683    0.028    0.660
   3_adp:    1.683    0.028    0.660
   3_occ:    1.683    0.028    0.660
   4_bss:    1.683    0.028    0.660
   4_xyz:    1.868    0.050    0.670
   4_adp:    1.868    0.050    0.670
   4_occ:    1.868    0.050    0.670
   5_bss:    1.868    0.050    0.670
   5_xyz:    1.869    0.022    0.690
   5_adp:    1.869    0.022    0.690
   5_occ:    1.869    0.022    0.690
   5_bss:    1.869    0.022    0.690
------------------------------------------------------------------------

CPU time actual refinement: 346.41


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_780/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_780/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_780/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_780/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_780/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 346.25 
  Macro-tasks:
    bulk solvent and scale       = 40.52  
    individual site refinement   = 152.67 
    weights calculation          = 31.60  
    collect and process          = 6.63   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 231.56 
  Micro-tasks:
    mask                            = 1.73   
    f_calc                          = 106.48 
    alpha_beta                      = 8.59   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 120.76 
    fmodel                         = 7.74   
    r_factors                      = 0.17   
    phase_errors                   = 10.72  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 257.64 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.714 micro seconds
Total CPU time: 6.00 minutes
from_scatterers_fft:    685 calls, 106.19 s
gradients_fft:          630 calls, 105.91 s

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

# Date 2008-01-16 Time 02:25:42 PST -0800 (1200479142.34 s)
Start R-work = 0.4710, R-free = 0.4592 (no bulk solvent and anisotropic scale)
Final R-work = 0.1357, R-free = 0.1835 (no bulk solvent and anisotropic scale)

Start R-work = 0.4621, R-free = 0.4482
Final R-work = 0.1182, R-free = 0.1672