# Date 2008-01-16 Time 01:37:03 PST -0800 (1200476223.83 s)
#phil __OFF__

Command line arguments: "../489.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 9222
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 489

-------------------------------------------------------------------------------
  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: (69.8988, 45.7567, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.80, per 1000 atoms: 0.99


================================== 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: (69.8988, 45.7567, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9392 1.953
Completeness in resolution range: 0.9461
Completeness with d_max=infinity: 0.943275

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9392
                             d_min =   1.9530

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: (69.8988, 45.7567, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9392 1.953
Completeness in resolution range: 0.9461
Completeness with d_max=infinity: 0.943275

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9396 -  4.1798 [2176/2201]  1956   220  10.1%
  bin  2:  4.1798 -  3.3297 [2090/2110]  1885   205   9.8%
  bin  3:  3.3297 -  2.9123 [2070/2089]  1862   208  10.0%
  bin  4:  2.9123 -  2.6477 [2031/2061]  1825   206  10.1%
  bin  5:  2.6477 -  2.4588 [2024/2043]  1828   196   9.7%
  bin  6:  2.4588 -  2.3144 [2021/2046]  1814   207  10.2%
  bin  7:  2.3144 -  2.1989 [2014/2042]  1809   205  10.2%
  bin  8:  2.1989 -  2.1034 [1997/2033]  1798   199  10.0%
  bin  9:  2.1034 -  2.0226 [1992/2034]  1797   195   9.8%
  bin 10:  2.0226 -  1.9530 [1174/2046]  1056   118  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_489/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.55 -     2.22: 25
        2.22 -     2.89: 1389
        2.89 -     3.56: 4564
        3.56 -     4.23: 9371
        4.23 -     4.90: 13369
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.554 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28713 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_489/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_489/model_refine_001.geo

CPU time processing inputs: 8.15


============================ 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 = 69.89875 45.75675 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4868   r_free= 0.4845   ksol= 0.00   Bsol= 0.00   scale= 0.793    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.294598                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.6623 0.99   1410  156 0.4238 0.4244       6.636       6.699|
|  2:  4.6623 -  3.7194 0.99   1361  153 0.4218 0.3847       6.833      6.7556|
|  3:  3.7194 -  3.2548 0.99   1329  142 0.4458 0.4151       6.697      6.6928|
|  4:  3.2548 -  2.9597 0.99   1329  152 0.4795 0.4544      6.5504      6.5054|
|  5:  2.9597 -  2.7490 0.99   1317  149 0.5143 0.5170       6.372      6.4014|
|  6:  2.7490 -  2.5878 0.99   1312  143 0.5201 0.5552      6.2894      6.2306|
|  7:  2.5878 -  2.4588 0.99   1298  140 0.5099 0.5097      6.2505      6.1942|
|  8:  2.4588 -  2.3522 0.98   1289  147 0.5306 0.5186      6.1815      6.1889|
|  9:  2.3522 -  2.2620 0.98   1289  148 0.5252 0.5472      6.1208      6.1745|
| 10:  2.2620 -  2.1841 1.00   1291  143 0.5298 0.5481      6.1071      6.0857|
| 11:  2.1841 -  2.1160 0.98   1309  138 0.5009 0.4877      6.0383      6.0423|
| 12:  2.1160 -  2.0557 0.98   1261  143 0.5151 0.5560      5.9548      6.0262|
| 13:  2.0557 -  2.0017 0.99   1286  141 0.5382 0.5186      5.8841      5.8028|
| 14:  2.0017 -  1.9530 0.41    549   64 0.5495 0.5226      5.8884      5.8262|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9396 -  4.6623  1410   156  0.62  41.36   0.78     0.68      98923.82|
|  2:  4.6623 -  3.7194  1361   153  0.67  37.57   0.86     0.76     120373.79|
|  3:  3.7194 -  3.2548  1329   142  0.58  45.50   0.85     0.72     121902.93|
|  4:  3.2548 -  2.9597  1329   152  0.48  53.28   0.80     0.58     107578.92|
|  5:  2.9597 -  2.7490  1317   149  0.36  62.76   0.74     0.45      90604.57|
|  6:  2.7490 -  2.5878  1312   143  0.32  66.10   0.72     0.37      79594.41|
|  7:  2.5878 -  2.4588  1298   140  0.28  69.27   0.76     0.33      73680.11|
|  8:  2.4588 -  2.3522  1289   147  0.26  70.22   0.73     0.32      65982.66|
|  9:  2.3522 -  2.2620  1289   148  0.29  68.57   0.73     0.35      58881.16|
| 10:  2.2620 -  2.1841  1291   143  0.31  66.74   0.76     0.37      50289.01|
| 11:  2.1841 -  2.1160  1309   138  0.30  67.84   0.80     0.37      50097.42|
| 12:  2.1160 -  2.0557  1261   143  0.24  71.95   0.78     0.32      47428.28|
| 13:  2.0557 -  2.0017  1286   141  0.23  73.09   0.72     0.31      41961.71|
| 14:  2.0017 -  1.9530   549    64  0.33  65.81   0.73     0.37      30883.65|
|alpha:            min =        0.31 max =            0.76 mean =         0.46|
|beta:             min =    30883.65 max =       121902.93 mean =     76566.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.38|
|phase err.(work): min =        0.00 max =           89.99 mean =        60.96|
|phase err.(test): min =        0.00 max =           90.00 mean =        61.10|
|-----------------------------------------------------------------------------|

============================== 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 = 19.607094             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.018   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.622529              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.265   (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:        7 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       34 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      175 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      720 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1529 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2692 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3991 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5148 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6628 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7862 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.080 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.196 |       2.447 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.511)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.511)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4911   r_free= 0.4854   ksol= 0.00   Bsol= 0.00   scale= 0.763    |
|                                                                             |
| 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:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.295861                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4778   r_free= 0.4716   ksol= 0.37   Bsol= 9.22   scale= 0.977    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.25,9.90,7.22,0.00,0.00,0.00); trace/3= 7.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.289126                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.773668             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.111   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.557778              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.679   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4778      final r-factor (work) = 0.4127          |
| start r-factor (free) = 0.4716      final r-factor (free) = 0.4411          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 102.6923 = 15.77 * 0.50 * 6.2905 + 1.00 * 53.0801                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 49.3009 = 15.77 * 0.50 * 6.2330 + 1.00 * 0.1425                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4127      final r-factor (work) = 0.3722          |
| start r-factor (free) = 0.4411      final r-factor (free) = 0.4356          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.7240 = 1.56 * 1.00 * 6.2330 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6423 = 1.56 * 1.00 * 6.1772 + 1.00 * 0.0197                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.511)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.80   14.24    None  None   None       |
|    all(noH): 2823   0      0.00    78.80   14.24    None  None   None       |
|    Sol.    : 438    0      0.00    71.32   22.44    None  None   None       |
|    Mac.    : 2385   0      0.00    78.80   12.74    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 -   7.880:  984   |   5:    39.401 -  47.282:   64        |
|      1:     7.880 -  15.761:  844   |   6:    47.282 -  55.162:   23        |
|      2:    15.761 -  23.641:  472   |   7:    55.162 -  63.042:   11        |
|      3:    23.641 -  31.521:  293   |   8:    63.042 -  70.923:    9        |
|      4:    31.521 -  39.401:  120   |   9:    70.923 -  78.803:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3722 r_free = 0.4356             target_work(ml) = 6.170         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3717 r_free = 0.4358             target_work(ml) = 6.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3717   r_free= 0.4358   ksol= 0.37   Bsol= 9.22   scale= 1.092    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.25,9.90,7.22,0.00,0.00,0.00); trace/3= 7.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.169677                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3703   r_free= 0.4325   ksol= 0.36   Bsol= 34.13   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.44,6.11,4.38,0.00,0.00,0.00); trace/3= 4.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.170191                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.748640              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.027  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.774998              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.823  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3703      final r-factor (work) = 0.3294          |
| start r-factor (free) = 0.4325      final r-factor (free) = 0.4060          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.1448 = 8.75 * 0.50 * 6.1729 + 1.00 * 0.1425                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.8545 = 8.75 * 0.50 * 6.1197 + 1.00 * 0.0848                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3294      final r-factor (work) = 0.3170          |
| start r-factor (free) = 0.4060      final r-factor (free) = 0.3929          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7658 = 0.77 * 1.00 * 6.1197 + 1.00 * 0.0230                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7266 = 0.77 * 1.00 * 6.0687 + 1.00 * 0.0234                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.511)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.91   13.75    None  None   None       |
|    all(noH): 2823   0      0.00    80.91   13.75    None  None   None       |
|    Sol.    : 438    0      0.00    72.21   24.82    None  None   None       |
|    Mac.    : 2385   0      0.00    80.91   11.72    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 -   8.091: 1086   |   5:    40.456 -  48.547:   48        |
|      1:     8.091 -  16.183:  846   |   6:    48.547 -  56.639:   19        |
|      2:    16.183 -  24.274:  432   |   7:    56.639 -  64.730:   11        |
|      3:    24.274 -  32.365:  256   |   8:    64.730 -  72.821:    7        |
|      4:    32.365 -  40.456:  117   |   9:    72.821 -  80.912:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3170 r_free = 0.3929             target_work(ml) = 6.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3169 r_free = 0.3935             target_work(ml) = 6.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3169   r_free= 0.3935   ksol= 0.36   Bsol= 34.13   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.44,6.11,4.38,0.00,0.00,0.00); trace/3= 4.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.056252                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3173   r_free= 0.3911   ksol= 0.36   Bsol= 52.36   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.62,4.16,3.61,0.00,0.00,0.00); trace/3= 3.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.056506                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.612994              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.460  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.027228              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.519   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3173      final r-factor (work) = 0.2614          |
| start r-factor (free) = 0.3911      final r-factor (free) = 0.3345          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.1850 = 7.61 * 0.50 * 6.0687 + 1.00 * 0.0846                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.8646 = 7.61 * 0.50 * 5.9812 + 1.00 * 0.0973                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2614      final r-factor (work) = 0.2388          |
| start r-factor (free) = 0.3345      final r-factor (free) = 0.3212          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1592 = 1.03 * 1.00 * 5.9812 + 1.00 * 0.0152                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0311 = 1.03 * 1.00 * 5.8555 + 1.00 * 0.0161                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.511)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.00   14.80    None  None   None       |
|    all(noH): 2823   0      0.00    87.00   14.80    None  None   None       |
|    Sol.    : 438    0      0.00    82.28   34.17    None  None   None       |
|    Mac.    : 2385   0      0.00    87.00   11.25    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 -   8.700: 1255   |   5:    43.501 -  52.201:   80        |
|      1:     8.700 -  17.400:  733   |   6:    52.201 -  60.901:   45        |
|      2:    17.400 -  26.101:  357   |   7:    60.901 -  69.601:   19        |
|      3:    26.101 -  34.801:  188   |   8:    69.601 -  78.302:    9        |
|      4:    34.801 -  43.501:  133   |   9:    78.302 -  87.002:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2388 r_free = 0.3212             target_work(ml) = 5.833         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2384 r_free = 0.3211             target_work(ml) = 5.833         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2384   r_free= 0.3211   ksol= 0.36   Bsol= 52.36   scale= 1.048   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.62,4.16,3.61,0.00,0.00,0.00); trace/3= 3.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.833342                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2378   r_free= 0.3198   ksol= 0.34   Bsol= 50.02   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.70,2.37,2.84,0.00,0.00,0.00); trace/3= 2.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.831231                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.578331              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.753  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.261986              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.818  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2378      final r-factor (work) = 0.2028          |
| start r-factor (free) = 0.3198      final r-factor (free) = 0.2694          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5726 = 3.58 * 0.50 * 5.8549 + 1.00 * 0.0973                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3714 = 3.58 * 0.50 * 5.7638 + 1.00 * 0.0590                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2028      final r-factor (work) = 0.1921          |
| start r-factor (free) = 0.2694      final r-factor (free) = 0.2477          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5260 = 0.26 * 1.00 * 5.7638 + 1.00 * 0.0159                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4917 = 0.26 * 1.00 * 5.6507 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.511)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.11   13.89    None  None   None       |
|    all(noH): 2823   0      0.00    86.11   13.89    None  None   None       |
|    Sol.    : 438    0      2.57    81.01   34.99    None  None   None       |
|    Mac.    : 2385   0      0.00    86.11   10.01    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.611: 1382   |   5:    43.054 -  51.664:   90        |
|      1:     8.611 -  17.221:  730   |   6:    51.664 -  60.275:   39        |
|      2:    17.221 -  25.832:  264   |   7:    60.275 -  68.886:   13        |
|      3:    25.832 -  34.443:  168   |   8:    68.886 -  77.496:    5        |
|      4:    34.443 -  43.054:  129   |   9:    77.496 -  86.107:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1921 r_free = 0.2477             target_work(ml) = 5.614         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1917 r_free = 0.2466             target_work(ml) = 5.612         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1917   r_free= 0.2466   ksol= 0.34   Bsol= 50.02   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.70,2.37,2.84,0.00,0.00,0.00); trace/3= 2.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.611838                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1914   r_free= 0.2465   ksol= 0.33   Bsol= 42.59   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.14,1.34,2.57,0.00,0.00,0.00); trace/3= 1.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.611943                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.500311              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.190  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.317885              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.221   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1914      final r-factor (work) = 0.1531          |
| start r-factor (free) = 0.2465      final r-factor (free) = 0.2042          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1219 = 2.50 * 0.50 * 5.6496 + 1.00 * 0.0590                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9505 = 2.50 * 0.50 * 5.5117 + 1.00 * 0.0601                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1531      final r-factor (work) = 0.1459          |
| start r-factor (free) = 0.2042      final r-factor (free) = 0.1989          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7621 = 0.32 * 1.00 * 5.5117 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7343 = 0.32 * 1.00 * 5.3892 + 1.00 * 0.0211                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.511)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.88  13.75    None  None   None       |
|    all(noH): 2823   0      0.00    113.88  13.75    None  None   None       |
|    Sol.    : 438    0      2.53    81.52   35.93    None  None   None       |
|    Mac.    : 2385   0      0.00    113.88  9.68     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.388: 1807   |   5:    56.940 -  68.328:   24        |
|      1:    11.388 -  22.776:  507   |   6:    68.328 -  79.717:    5        |
|      2:    22.776 -  34.164:  209   |   7:    79.717 -  91.105:    3        |
|      3:    34.164 -  45.552:  164   |   8:    91.105 - 102.493:    0        |
|      4:    45.552 -  56.940:  103   |   9:   102.493 - 113.881:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1459 r_free = 0.1989             target_work(ml) = 5.375         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1457 r_free = 0.1987             target_work(ml) = 5.375         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1457   r_free= 0.1987   ksol= 0.33   Bsol= 42.59   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.14,1.34,2.57,0.00,0.00,0.00); trace/3= 1.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.374708                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.6623 0.99   1410  156 0.1101 0.1489      5.4811      5.6903|
|  2:  4.6623 -  3.7194 0.99   1361  153 0.1062 0.1491      5.6284      5.9008|
|  3:  3.7194 -  3.2548 0.99   1329  142 0.1405 0.1769       5.718      5.9965|
|  4:  3.2548 -  2.9597 0.99   1329  152 0.1647 0.2117      5.7049        5.84|
|  5:  2.9597 -  2.7490 0.99   1317  149 0.1730 0.2263      5.5759      5.8063|
|  6:  2.7490 -  2.5878 0.99   1312  143 0.1613 0.2476      5.4307      5.6811|
|  7:  2.5878 -  2.4588 0.99   1298  140 0.1659 0.1951      5.4008      5.5129|
|  8:  2.4588 -  2.3522 0.98   1289  147 0.1596 0.2252      5.3349      5.6033|
|  9:  2.3522 -  2.2620 0.98   1289  148 0.1585 0.2287      5.2766      5.5306|
| 10:  2.2620 -  2.1841 1.00   1291  143 0.1473 0.2169      5.1739      5.4032|
| 11:  2.1841 -  2.1160 0.98   1309  138 0.1482 0.2243      5.1712      5.4466|
| 12:  2.1160 -  2.0557 0.98   1261  143 0.1580 0.2336       5.129       5.455|
| 13:  2.0557 -  2.0017 0.99   1286  141 0.1531 0.1972      5.0092       5.175|
| 14:  2.0017 -  1.9530 0.41    549   64 0.1312 0.1768      4.8657      5.0595|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9396 -  4.6623  1410   156  0.93  10.93   0.98     0.96       9192.90|
|  2:  4.6623 -  3.7194  1361   153  0.93  10.69   1.03     1.02      13199.11|
|  3:  3.7194 -  3.2548  1329   142  0.90  15.75   1.05     1.03      17061.48|
|  4:  3.2548 -  2.9597  1329   152  0.87  19.19   1.02     0.98      17246.94|
|  5:  2.9597 -  2.7490  1317   149  0.86  20.75   1.01     0.97      13803.57|
|  6:  2.7490 -  2.5878  1312   143  0.85  21.58   0.99     0.94      11070.37|
|  7:  2.5878 -  2.4588  1298   140  0.85  21.16   1.01     0.96      10188.86|
|  8:  2.4588 -  2.3522  1289   147  0.85  21.25   1.01     0.98       9425.61|
|  9:  2.3522 -  2.2620  1289   148  0.86  20.77   1.01     0.94       8274.02|
| 10:  2.2620 -  2.1841  1291   143  0.85  21.46   1.02     0.97       7184.23|
| 11:  2.1841 -  2.1160  1309   138  0.86  21.00   1.02     0.96       7044.98|
| 12:  2.1160 -  2.0557  1261   143  0.85  21.63   1.03     1.01       6700.47|
| 13:  2.0557 -  2.0017  1286   141  0.85  21.42   1.02     0.98       5119.99|
| 14:  2.0017 -  1.9530   549    64  0.90  17.01   1.01     0.97       3553.57|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     3553.57 max =        17246.94 mean =     10252.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.97 mean =        18.89|
|phase err.(test): min =        0.00 max =           89.12 mean =        18.04|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1460   r_free= 0.1983   ksol= 0.33   Bsol= 44.07   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,-0.53,1.01,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.373103                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1460   r_free= 0.1983   ksol= 0.33   Bsol= 44.07   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,-0.53,1.01,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.373103                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.6623 0.99   1410  156 0.1096 0.1447      5.4663      5.6745|
|  2:  4.6623 -  3.7194 0.99   1361  153 0.1072 0.1488      5.6283      5.9014|
|  3:  3.7194 -  3.2548 0.99   1329  142 0.1410 0.1769      5.7194      5.9931|
|  4:  3.2548 -  2.9597 0.99   1329  152 0.1646 0.2127      5.7052      5.8419|
|  5:  2.9597 -  2.7490 0.99   1317  149 0.1735 0.2256      5.5761      5.8027|
|  6:  2.7490 -  2.5878 0.99   1312  143 0.1617 0.2473      5.4299      5.6793|
|  7:  2.5878 -  2.4588 0.99   1298  140 0.1662 0.1942      5.4003      5.5103|
|  8:  2.4588 -  2.3522 0.98   1289  147 0.1592 0.2243      5.3327       5.601|
|  9:  2.3522 -  2.2620 0.98   1289  148 0.1586 0.2276      5.2753      5.5268|
| 10:  2.2620 -  2.1841 1.00   1291  143 0.1470 0.2169      5.1733      5.4049|
| 11:  2.1841 -  2.1160 0.98   1309  138 0.1478 0.2252      5.1715      5.4501|
| 12:  2.1160 -  2.0557 0.98   1261  143 0.1578 0.2337      5.1288       5.455|
| 13:  2.0557 -  2.0017 0.99   1286  141 0.1532 0.1953      5.0082      5.1712|
| 14:  2.0017 -  1.9530 0.41    549   64 0.1310 0.1767      4.8628      5.0588|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9396 -  4.6623  1410   156  0.93  10.64   0.98     0.95       8687.98|
|  2:  4.6623 -  3.7194  1361   153  0.94  10.47   1.03     1.02      12875.86|
|  3:  3.7194 -  3.2548  1329   142  0.90  15.73   1.04     1.03      17010.71|
|  4:  3.2548 -  2.9597  1329   152  0.87  19.17   1.02     0.98      17237.85|
|  5:  2.9597 -  2.7490  1317   149  0.86  20.71   1.00     0.97      13741.52|
|  6:  2.7490 -  2.5878  1312   143  0.85  21.52   0.98     0.93      11017.85|
|  7:  2.5878 -  2.4588  1298   140  0.85  21.11   1.00     0.96      10143.37|
|  8:  2.4588 -  2.3522  1289   147  0.85  21.20   1.00     0.98       9382.33|
|  9:  2.3522 -  2.2620  1289   148  0.86  20.74   1.00     0.94       8248.61|
| 10:  2.2620 -  2.1841  1291   143  0.85  21.46   1.01     0.96       7189.60|
| 11:  2.1841 -  2.1160  1309   138  0.86  21.04   1.01     0.95       7070.22|
| 12:  2.1160 -  2.0557  1261   143  0.85  21.66   1.02     1.00       6710.58|
| 13:  2.0557 -  2.0017  1286   141  0.85  21.39   1.00     0.97       5104.39|
| 14:  2.0017 -  1.9530   549    64  0.90  16.91   0.99     0.95       3521.17|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     3521.17 max =        17237.85 mean =     10166.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.97 mean =        18.83|
|phase err.(test): min =        0.00 max =           89.85 mean =        17.99|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.511)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.48    115.36  15.23    None  None   None       |
|    all(noH): 2823   0      1.48    115.36  15.23    None  None   None       |
|    Sol.    : 438    0      4.02    83.00   37.41    None  None   None       |
|    Mac.    : 2385   0      1.48    115.36  11.16    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.482 -  12.870: 1807   |   5:    58.422 -  69.810:   24        |
|      1:    12.870 -  24.258:  507   |   6:    69.810 -  81.199:    5        |
|      2:    24.258 -  35.646:  209   |   7:    81.199 -  92.587:    3        |
|      3:    35.646 -  47.034:  164   |   8:    92.587 - 103.975:    0        |
|      4:    47.034 -  58.422:  103   |   9:   103.975 - 115.363:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 346         
Filter by distance & map next to the model:
   mapped sites are within: 0.325 - 5.729
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 341 from: 346
   mapped sites are within: 0.753 - 5.729

peak=    7.711 closest distance to " O   HOH Z 390 " =    1.253
peak=    7.630 closest distance to " CB  VAL A 230 " =    1.511
peak=    7.187 closest distance to " O   HOH Z 268 " =    1.317
peak=    6.517 closest distance to " CG  LEU A   5 " =    1.593
peak=    6.438 closest distance to " CG1 VAL A 296 " =    1.245
peak=    6.262 closest distance to " OD1 ASP A  27 " =    1.012
peak=    6.240 closest distance to " O   HOH Z 387 " =    1.861
peak=    6.171 closest distance to " O   HOH Z 130 " =    2.001
peak=    5.979 closest distance to " NH1 ARG A 138 " =    1.001
peak=    5.950 closest distance to " CG  ARG A 138 " =    1.223
peak=    5.617 closest distance to " O   HOH Z 415 " =    1.519
peak=    5.572 closest distance to " NH2 ARG A  56 " =    2.104
peak=    5.495 closest distance to " O   HOH Z 350 " =    1.446
peak=    5.420 closest distance to " CD  ARG A 138 " =    0.896
peak=    5.347 closest distance to " O   HOH Z  65 " =    1.943
peak=    5.323 closest distance to " NZ BLYS A 290 " =    1.059
peak=    5.198 closest distance to " O   PRO A 198 " =    1.463
peak=    5.166 closest distance to " CD1AILE A 234 " =    1.073
peak=    5.074 closest distance to " NE2 GLN A  11 " =    1.300
peak=    5.047 closest distance to " O   HOH Z 403 " =    1.733
peak=    5.014 closest distance to " O   HOH Z  46 " =    1.342
peak=    4.998 closest distance to " O   HOH Z  24 " =    2.011
peak=    4.977 closest distance to " O   HOH Z   9 " =    1.740
peak=    4.969 closest distance to " O   HOH Z 139 " =    1.863
peak=    4.943 closest distance to " O   HOH Z 375 " =    1.402
peak=    4.941 closest distance to " O   HOH Z 124 " =    1.870
peak=    4.932 closest distance to " O   HOH Z 142 " =    1.949
peak=    4.924 closest distance to " CB  SER A   3 " =    1.458
peak=    4.890 closest distance to " CB  ARG A 275 " =    1.203
peak=    4.885 closest distance to " O   HOH Z  15 " =    1.001
peak=    4.860 closest distance to " O   HOH Z   7 " =    1.870
peak=    4.814 closest distance to " O   HOH Z 105 " =    1.209
peak=    4.795 closest distance to " O   HOH Z 225 " =    1.897
peak=    4.790 closest distance to " O   HOH Z 358 " =    1.465
peak=    4.790 closest distance to " O   HOH Z  69 " =    2.372
peak=    4.761 closest distance to " O   HOH Z 422 " =    1.296
peak=    4.687 closest distance to " O   HOH Z 428 " =    1.725
peak=    4.683 closest distance to " CB  PRO A  54 " =    1.111
peak=    4.682 closest distance to " O   HOH Z 417 " =    1.845
peak=    4.663 closest distance to " O   HOH Z 222 " =    1.588
peak=    4.662 closest distance to " O   HOH Z 381 " =    0.977
peak=    4.620 closest distance to " O   VAL A  72 " =    0.936
peak=    4.589 closest distance to " O   HOH Z  63 " =    1.717
peak=    4.554 closest distance to " O   HOH Z  27 " =    1.144
peak=    4.545 closest distance to " CB  VAL A 296 " =    1.257
peak=    4.537 closest distance to " O   HOH Z 400 " =    0.866
peak=    4.536 closest distance to " O   HOH Z  59 " =    1.567
peak=    4.500 closest distance to " O   HOH Z 418 " =    1.505
peak=    4.453 closest distance to " O   HOH Z  78 " =    1.920
peak=    4.433 closest distance to " CB  VAL A 230 " =    1.268
peak=    4.417 closest distance to " NH2 ARG A 269 " =    0.983
peak=    4.409 closest distance to " O   HOH Z 127 " =    1.209
peak=    4.407 closest distance to " O   HOH Z 215 " =    1.553
peak=    4.403 closest distance to " O   HOH Z 410 " =    1.534
peak=    4.397 closest distance to " O   HOH Z 427 " =    2.088
peak=    4.395 closest distance to " OG  SER A 276 " =    0.902
peak=    4.381 closest distance to " O   HOH Z 416 " =    1.391
peak=    4.363 closest distance to " CB  LYS A 290 " =    0.867
peak=    4.330 closest distance to " CG  PRO A 280 " =    0.988
peak=    4.327 closest distance to " O   HOH Z 112 " =    1.574
peak=    4.321 closest distance to " O   HOH Z 425 " =    1.703
peak=    4.293 closest distance to " OE1 GLU A   2 " =    1.998
peak=    4.260 closest distance to " O   HOH Z 133 " =    1.579
peak=    4.258 closest distance to " O   HOH Z 250 " =    2.220
peak=    4.179 closest distance to " O   HOH Z 214 " =    1.342
peak=    4.175 closest distance to " O   HOH Z 126 " =    1.777
peak=    4.165 closest distance to " O   HOH Z  77 " =    1.192
peak=    4.153 closest distance to " CG  LEU A   5 " =    1.188
peak=    4.153 closest distance to " NH2BARG A 145 " =    1.590
peak=    4.143 closest distance to " O   HOH Z 423 " =    1.956
peak=    4.135 closest distance to " N   GLN A 278 " =    0.938
peak=    4.126 closest distance to " CA  ILE A 234 " =    1.147
peak=    4.102 closest distance to " CD1 LEU A   5 " =    1.338
peak=    4.092 closest distance to " O   HOH Z 158 " =    2.716
peak=    4.086 closest distance to " O   HOH Z  66 " =    1.248
peak=    4.070 closest distance to " O   HOH Z 361 " =    1.760
peak=    4.061 closest distance to " O   HOH Z 356 " =    2.006
peak=    4.038 closest distance to " CB  ALA A 114 " =    1.261
peak=    4.031 closest distance to " O   HOH Z 293 " =    1.549
peak=    4.028 closest distance to " O   ASP A 286 " =    2.368
peak=    4.022 closest distance to " O   HOH Z 123 " =    1.362
peak=    4.022 closest distance to " O   HOH Z 360 " =    1.195
peak=    4.008 closest distance to " O   HOH Z  47 " =    1.619
peak=    4.008 closest distance to " O   HOH Z 371 " =    2.946
peak=    4.007 closest distance to " CB  GLN A 223 " =    1.538
peak=    4.006 closest distance to " O   HOH Z   1 " =    1.910
peak=    3.992 closest distance to " O   HOH Z 359 " =    1.343
peak=    3.987 closest distance to " O   HOH Z 119 " =    1.495
peak=    3.962 closest distance to " O   HOH Z  15 " =    1.320
peak=    3.961 closest distance to " O   HOH Z 428 " =    1.227
peak=    3.959 closest distance to " CG2 ILE A 234 " =    0.960
peak=    3.957 closest distance to " O  BHOH Z  74 " =    1.178
peak=    3.948 closest distance to " CE  MET A  93 " =    1.518
peak=    3.946 closest distance to " NE2 GLN A  58 " =    5.611
peak=    3.944 closest distance to " CB  SER A 216 " =    0.983
peak=    3.936 closest distance to " O   HOH Z 130 " =    2.346
peak=    3.930 closest distance to " C   GLN A  73 " =    1.038
peak=    3.927 closest distance to " O   HOH Z  28 " =    1.582
peak=    3.927 closest distance to " OD1 ASP A 286 " =    1.083
peak=    3.926 closest distance to " CG  PRO A  54 " =    1.382
peak=    3.922 closest distance to " CG1BVAL A 121 " =    2.223
peak=    3.917 closest distance to " O   HOH Z 236 " =    1.916
peak=    3.916 closest distance to " O   HOH Z 426 " =    1.201
peak=    3.899 closest distance to " O   HOH Z   2 " =    1.799
peak=    3.892 closest distance to " NE1 TRP A 274 " =    1.079
peak=    3.886 closest distance to " O   HOH Z 263 " =    1.541
peak=    3.881 closest distance to " O   HOH Z 257 " =    2.249
peak=    3.869 closest distance to " O   HOH Z 287 " =    1.715
peak=    3.868 closest distance to " O   HOH Z  65 " =    1.684
peak=    3.858 closest distance to " O   HOH Z 244 " =    1.381
peak=    3.852 closest distance to " O   HOH Z  54 " =    1.216
peak=    3.846 closest distance to " CZ3 TRP A 274 " =    1.504
peak=    3.843 closest distance to " N   CYS A 260 " =    1.208
peak=    3.839 closest distance to " CD2 LEU A 228 " =    1.411
peak=    3.836 closest distance to " CB  ASN A 148 " =    1.317
peak=    3.835 closest distance to " N   GLU A   2 " =    1.323
peak=    3.829 closest distance to " O   HOH Z 380 " =    2.310
peak=    3.827 closest distance to " N   ARG A 275 " =    0.762
peak=    3.817 closest distance to " CB  ASN A 187 " =    1.004
peak=    3.810 closest distance to " O   HOH Z 137 " =    1.580
peak=    3.806 closest distance to " OG ASER A 258 " =    2.998
peak=    3.784 closest distance to " O   ARG A 275 " =    1.019
peak=    3.777 closest distance to " O   HOH Z 389 " =    1.656
peak=    3.771 closest distance to " O   HOH Z 272 " =    1.866
peak=    3.766 closest distance to " O   HOH Z 366 " =    2.772
peak=    3.764 closest distance to " OG BSER A 258 " =    1.033
peak=    3.757 closest distance to " O   HOH Z 132 " =    1.124
peak=    3.756 closest distance to " N   TYR A  15 " =    0.949
peak=    3.746 closest distance to " CA  GLY A 136 " =    1.090
peak=    3.737 closest distance to " O   HOH Z 422 " =    2.383
peak=    3.736 closest distance to " CG2 ILE A 120 " =    0.983
peak=    3.735 closest distance to " O   HOH Z 240 " =    2.105
peak=    3.730 closest distance to " O   HOH Z 153 " =    3.536
peak=    3.724 closest distance to " O   HOH Z 369 " =    2.187
peak=    3.722 closest distance to " CB  GLU A 277 " =    1.022
peak=    3.721 closest distance to " O   HOH Z 414 " =    1.848
peak=    3.718 closest distance to " O   HOH Z 193 " =    1.575
peak=    3.715 closest distance to " CB  SER A  62 " =    1.173
peak=    3.709 closest distance to " O   HOH Z 353 " =    1.946
peak=    3.692 closest distance to " CG  PRO A 243 " =    1.123
peak=    3.692 closest distance to " O   HOH Z  51 " =    1.618
peak=    3.688 closest distance to " O   HOH Z 233 " =    1.474
peak=    3.686 closest distance to " N   ARG A 156 " =    1.303
peak=    3.685 closest distance to " O   HOH Z 205 " =    1.311
peak=    3.683 closest distance to " CA  ASN A 284 " =    0.962
peak=    3.679 closest distance to " ND2BASN A 224 " =    0.921
peak=    3.678 closest distance to " O   HOH Z 178 " =    1.281
peak=    3.664 closest distance to " CB  SER A  63 " =    1.260
peak=    3.661 closest distance to " CG2 THR A 221 " =    1.331
peak=    3.651 closest distance to " CG2 THR A 279 " =    1.035
peak=    3.613 closest distance to " C   GLN A  11 " =    1.318
peak=    3.604 closest distance to " NE2 GLN A  73 " =    1.612
peak=    3.603 closest distance to " C   ASN A 285 " =    0.961
peak=    3.600 closest distance to " O   HOH Z 172 " =    1.723
peak=    3.591 closest distance to " O   HOH Z 368 " =    1.758
peak=    3.589 closest distance to " O   HOH Z 425 " =    2.052
peak=    3.585 closest distance to " O   HOH Z  95 " =    1.391
peak=    3.582 closest distance to " CG2 ILE A  49 " =    1.257
peak=    3.581 closest distance to " O   HOH Z 429 " =    0.897
peak=    3.580 closest distance to " CB  TRP A 266 " =    0.833
peak=    3.574 closest distance to " CA  ARG A 159 " =    1.169
peak=    3.573 closest distance to " CA  ARG A 195 " =    1.278
peak=    3.571 closest distance to " O   HOH Z 114 " =    2.089
peak=    3.568 closest distance to " CG2 THR A 178 " =    1.202
peak=    3.561 closest distance to " O   HOH Z 128 " =    2.027
peak=    3.559 closest distance to " NH2 ARG A 138 " =    1.320
peak=    3.553 closest distance to " O   HOH Z 128 " =    1.995
peak=    3.552 closest distance to " CA  ALA A 295 " =    0.904
peak=    3.552 closest distance to " CA  ASN A 127 " =    1.082
peak=    3.551 closest distance to " CB  GLU A 128 " =    0.889
peak=    3.547 closest distance to " CB  SER A 210 " =    1.098
peak=    3.545 closest distance to " CG  LEU A 228 " =    0.995
peak=    3.545 closest distance to " O   HOH Z 248 " =    2.097
peak=    3.543 closest distance to " CD2 LEU A 297 " =    0.867
peak=    3.538 closest distance to " CD1 LEU A   5 " =    0.846
peak=    3.536 closest distance to " CA  PHE A 283 " =    1.309
peak=    3.534 closest distance to " NH2AARG A 145 " =    2.194
peak=    3.533 closest distance to " CA  ARG A  36 " =    1.015
peak=    3.528 closest distance to " O   HOH Z  58 " =    1.906
peak=    3.524 closest distance to " O   HOH Z 125 " =    1.860
peak=    3.519 closest distance to " CG2AVAL A  72 " =    0.873
peak=    3.515 closest distance to " O   HOH Z  68 " =    2.054
peak=    3.512 closest distance to " O   HOH Z 406 " =    1.884
peak=    3.511 closest distance to " O   HOH Z 363 " =    1.206
peak=    3.509 closest distance to " OG  SER A  62 " =    3.053
peak=    3.508 closest distance to " CB  ASP A 124 " =    1.045
peak=    3.503 closest distance to " CG2 ILE A  20 " =    1.268
peak=    3.500 closest distance to " OD1 ASN A  45 " =    1.224
peak=    3.499 closest distance to " CB  ASN A  39 " =    0.763
peak=    3.496 closest distance to " CZ3 TRP A 266 " =    1.247
peak=    3.495 closest distance to " CD1 ILE A  49 " =    2.602
peak=    3.494 closest distance to " O   HOH Z 371 " =    2.278
peak=    3.488 closest distance to " CB  ALA A   1 " =    1.128
peak=    3.487 closest distance to " N   GLY A 302 " =    0.989
peak=    3.483 closest distance to " O   HOH Z 245 " =    1.339
peak=    3.481 closest distance to " CG2 THR A 251 " =    1.703
peak=    3.478 closest distance to " CA  ALA A  21 " =    1.055
peak=    3.471 closest distance to " CB  LEU A 300 " =    0.846
peak=    3.470 closest distance to " N   PHE A 130 " =    1.285
peak=    3.467 closest distance to " O   HOH Z 303 " =    2.195
peak=    3.467 closest distance to " OG BSER A 212 " =    2.592
peak=    3.462 closest distance to " CG  GLN A 278 " =    3.926
peak=    3.460 closest distance to " NE AARG A 275 " =    1.801
peak=    3.459 closest distance to " O   HOH Z   6 " =    1.997
peak=    3.459 closest distance to " O   HOH Z 197 " =    2.140
peak=    3.451 closest distance to " CA  THR A 235 " =    0.841
peak=    3.450 closest distance to " CG1 ILE A  33 " =    1.405
peak=    3.445 closest distance to " CG2 THR A 294 " =    1.132
peak=    3.441 closest distance to " O   HOH Z  22 " =    2.002
peak=    3.440 closest distance to " O   HOH Z 427 " =    1.268
peak=    3.437 closest distance to " ND2 ASN A 249 " =    0.788
peak=    3.437 closest distance to " CB  ALA A  10 " =    1.068
peak=    3.436 closest distance to " N   VAL A 296 " =    1.724
peak=    3.430 closest distance to " O   HOH Z 214 " =    1.966
peak=    3.426 closest distance to " CA  GLN A  55 " =    0.938
peak=    3.422 closest distance to " N   SER A  97 " =    0.879
peak=    3.419 closest distance to " CB  ASP A 132 " =    3.775
peak=    3.418 closest distance to " CB  GLN A 183 " =    1.105
peak=    3.418 closest distance to " O   HOH Z  61 " =    1.450
peak=    3.417 closest distance to " O   HOH Z  30 " =    1.305
peak=    3.417 closest distance to " O   HOH Z   1 " =    1.626
peak=    3.408 closest distance to " O   HOH Z  52 " =    1.191
peak=    3.405 closest distance to " CB  ASN A 110 " =    0.971
peak=    3.404 closest distance to " O   HOH Z  39 " =    1.558
peak=    3.402 closest distance to " O   ILE A  20 " =    1.805
peak=    3.401 closest distance to " CE2 PHE A  16 " =    0.831
peak=    3.399 closest distance to " CG1AVAL A 121 " =    0.765
peak=    3.398 closest distance to " O   HOH Z  11 " =    1.701
peak=    3.396 closest distance to " CG BARG A 102 " =    1.968
peak=    3.394 closest distance to " O   HOH Z 145 " =    2.368
peak=    3.386 closest distance to " CG  ARG A 156 " =    1.237
peak=    3.385 closest distance to " CB  ASP A 140 " =    0.944
peak=    3.383 closest distance to " O   HOH Z 342 " =    1.089
peak=    3.381 closest distance to " O   HOH Z  21 " =    1.484
peak=    3.366 closest distance to " O   HOH Z  61 " =    2.006
peak=    3.365 closest distance to " O   HOH Z 305 " =    3.371
peak=    3.354 closest distance to " NH1 ARG A  14 " =    0.925
peak=    3.354 closest distance to " N   GLN A  73 " =    1.083
peak=    3.350 closest distance to " C   VAL A 153 " =    1.082
peak=    3.347 closest distance to " O   HOH Z 405 " =    1.926
peak=    3.347 closest distance to " CG  GLN A  88 " =    0.994
peak=    3.346 closest distance to " O   HOH Z 344 " =    2.922
peak=    3.332 closest distance to " O   HOH Z 434 " =    5.729
peak=    3.331 closest distance to " O   ASN A 301 " =    2.071
peak=    3.329 closest distance to " NH1AARG A 275 " =    1.272
peak=    3.327 closest distance to " O   HOH Z 193 " =    2.027
peak=    3.323 closest distance to " OG BSER A 164 " =    1.302
peak=    3.318 closest distance to " O   HOH Z 213 " =    1.719
peak=    3.311 closest distance to " O   HOH Z 111 " =    1.817
peak=    3.310 closest distance to " NZ  LYS A 117 " =    1.333
peak=    3.307 closest distance to " ND2 ASN A 110 " =    1.592
peak=    3.305 closest distance to " O   HOH Z 362 " =    1.826
peak=    3.303 closest distance to " O   HOH Z 151 " =    1.661
peak=    3.299 closest distance to " CB  GLU A 277 " =    3.686
peak=    3.295 closest distance to " CB  VAL A 202 " =    1.678
peak=    3.293 closest distance to " CA  ALA A 299 " =    0.940
peak=    3.290 closest distance to " O   HOH Z  91 " =    1.209
peak=    3.283 closest distance to " OG  SER A  26 " =    1.488
peak=    3.282 closest distance to " O   HOH Z 204 " =    1.242
peak=    3.274 closest distance to " CG  LEU A 167 " =    1.261
peak=    3.267 closest distance to " CB  GLN A  73 " =    0.950
peak=    3.267 closest distance to " N   TYR A 116 " =    1.538
peak=    3.264 closest distance to " O   HOH Z 289 " =    1.167
peak=    3.259 closest distance to " CA  ALA A 158 " =    1.069
peak=    3.257 closest distance to " CD1 LEU A 281 " =    1.135
peak=    3.249 closest distance to " O   HOH Z 352 " =    1.796
peak=    3.247 closest distance to " CA  ALA A  51 " =    1.086
peak=    3.247 closest distance to " O   ASN A 142 " =    1.010
peak=    3.245 closest distance to " O   HOH Z 185 " =    1.500
peak=    3.243 closest distance to " O   HOH Z 402 " =    1.523
peak=    3.240 closest distance to " CG  LYS A 119 " =    0.999
peak=    3.236 closest distance to " O   HOH Z 331 " =    1.280
peak=    3.235 closest distance to " O   HOH Z 143 " =    1.601
peak=    3.228 closest distance to " CB  TRP A 179 " =    1.403
peak=    3.225 closest distance to " CE1 TYR A  15 " =    1.229
peak=    3.225 closest distance to " OE1 GLN A  77 " =    1.216
peak=    3.223 closest distance to " O   HOH Z 167 " =    1.624
peak=    3.220 closest distance to " NE BARG A 275 " =    1.167
peak=    3.216 closest distance to " O   HOH Z  44 " =    2.529
peak=    3.215 closest distance to " CA  LEU A 282 " =    1.083
peak=    3.214 closest distance to " CB  ARG A  79 " =    0.768
peak=    3.214 closest distance to " CD2 LEU A 167 " =    1.193
peak=    3.205 closest distance to " O   HOH Z 294 " =    1.494
peak=    3.204 closest distance to " O   HOH Z  88 " =    3.598
peak=    3.203 closest distance to " CG  LYS A  76 " =    1.626
peak=    3.202 closest distance to " O   HOH Z 184 " =    1.560
peak=    3.199 closest distance to " CB  ALA A 248 " =    1.439
peak=    3.197 closest distance to " O   HOH Z 282 " =    2.337
peak=    3.193 closest distance to " O   HOH Z  26 " =    1.719
peak=    3.192 closest distance to " N   SER A 210 " =    0.940
peak=    3.191 closest distance to " O   HOH Z 158 " =    2.786
peak=    3.190 closest distance to " O   HOH Z 220 " =    1.578
peak=    3.189 closest distance to " O   ALA A 291 " =    1.663
peak=    3.189 closest distance to " CG2 VAL A 232 " =    1.473
peak=    3.180 closest distance to " CE  LYS A  48 " =    1.083
peak=    3.176 closest distance to " O   GLY A 302 " =    1.573
peak=    3.174 closest distance to " O   HOH Z 145 " =    2.794
peak=    3.171 closest distance to " NE2 GLN A 194 " =    1.876
peak=    3.169 closest distance to " O   HOH Z 434 " =    1.531
peak=    3.168 closest distance to " CB  PHE A 204 " =    0.820
peak=    3.165 closest distance to " CG1 ILE A 120 " =    1.530
peak=    3.163 closest distance to " NH1BARG A 145 " =    1.507
peak=    3.162 closest distance to " O   SER A 164 " =    1.434
peak=    3.161 closest distance to " O   HOH Z 419 " =    1.828
peak=    3.159 closest distance to " NH2AARG A 190 " =    1.811
peak=    3.155 closest distance to " CG2 THR A 246 " =    1.306
peak=    3.152 closest distance to " NH2AARG A 145 " =    1.031
peak=    3.151 closest distance to " O   HOH Z 211 " =    1.389
peak=    3.146 closest distance to " O   HOH Z 388 " =    2.283
peak=    3.145 closest distance to " O   HOH Z 215 " =    2.125
peak=    3.144 closest distance to " N   VAL A 125 " =    1.253
peak=    3.142 closest distance to " O   HOH Z 384 " =    1.658
peak=    3.141 closest distance to " CZ3 TRP A 123 " =    1.631
peak=    3.138 closest distance to " O   HOH Z 329 " =    3.873
peak=    3.137 closest distance to " OD2 ASP A 286 " =    2.329
peak=    3.137 closest distance to " NH2BARG A 145 " =    1.428
peak=    3.133 closest distance to " CB  GLN A 278 " =    0.756
peak=    3.127 closest distance to " O   HOH Z  41 " =    2.355
peak=    3.120 closest distance to " OD1 ASN A 170 " =    1.428
peak=    3.120 closest distance to " O   THR A 251 " =    0.984
peak=    3.118 closest distance to " O   HOH Z  59 " =    1.865
peak=    3.117 closest distance to " O   HOH Z 185 " =    1.839
peak=    3.110 closest distance to " CD1 LEU A 228 " =    1.681
peak=    3.109 closest distance to " CD1 ILE A  33 " =    1.831
peak=    3.104 closest distance to " CZ3 TRP A  70 " =    0.955
peak=    3.095 closest distance to " CG  LYS A 193 " =    1.531
peak=    3.093 closest distance to " CA  SER A  87 " =    1.104
peak=    3.092 closest distance to " O   HOH Z 291 " =    1.430
peak=    3.083 closest distance to " CB  PRO A  90 " =    1.277
peak=    3.079 closest distance to " O   HOH Z 196 " =    1.353
peak=    3.074 closest distance to " N   ALA A 256 " =    0.753
peak=    3.074 closest distance to " O   HOH Z 357 " =    2.027
peak=    3.071 closest distance to " OE1 GLN A 240 " =    1.646
peak=    3.070 closest distance to " CB  ASN A 215 " =    1.556
peak=    3.067 closest distance to " CD2 PHE A 204 " =    0.976
peak=    3.063 closest distance to " CB  ARG A 138 " =    0.756
peak=    3.056 closest distance to " CB  VAL A 265 " =    1.356
peak=    3.047 closest distance to " CE3 TRP A 274 " =    1.610
peak=    3.047 closest distance to " O   HOH Z  15 " =    2.288
peak=    3.035 closest distance to " CB  ALA A 131 " =    1.540
peak=    3.034 closest distance to " O   HOH Z  97 " =    1.956

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 215         
Filter by distance & map next to the model:
   mapped sites are within: 0.410 - 5.218
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 210 from: 215
   mapped sites are within: 0.723 - 5.218

peak=   -6.074 closest distance to " CD  ARG A 138 " =    1.064
peak=   -4.854 closest distance to " CG2 VAL A 230 " =    0.723
peak=   -4.785 closest distance to " CD  ARG A  14 " =    2.989
peak=   -4.540 closest distance to " O   PRO A 198 " =    1.058
peak=   -4.438 closest distance to " O   HOH Z 231 " =    0.776
peak=   -4.327 closest distance to " O   HOH Z 385 " =    0.843
peak=   -4.296 closest distance to " OG  SER A  97 " =    2.173
peak=   -4.189 closest distance to " OE1 GLU A 277 " =    2.419
peak=   -4.160 closest distance to " O   HOH Z 242 " =    1.588
peak=   -4.145 closest distance to " O   GLN A  11 " =    1.529
peak=   -4.131 closest distance to " O   HOH Z 300 " =    0.852
peak=   -4.091 closest distance to " O   HOH Z  52 " =    0.767
peak=   -4.083 closest distance to " CG1 VAL A 296 " =    0.865
peak=   -4.026 closest distance to " OD1 ASP A  27 " =    0.742
peak=   -3.998 closest distance to " O   ALA A  51 " =    1.408
peak=   -3.968 closest distance to " O   HOH Z 313 " =    0.793
peak=   -3.967 closest distance to " N   VAL A  72 " =    2.152
peak=   -3.962 closest distance to " O   HOH Z  24 " =    1.071
peak=   -3.951 closest distance to " CD2 LEU A   5 " =    0.901
peak=   -3.909 closest distance to " O   VAL A  72 " =    0.862
peak=   -3.890 closest distance to " O   HOH Z 163 " =    1.737
peak=   -3.851 closest distance to " O   HOH Z 377 " =    1.102
peak=   -3.832 closest distance to " O   HOH Z  39 " =    0.846
peak=   -3.824 closest distance to " CA  GLY A 133 " =    2.129
peak=   -3.819 closest distance to " O   HOH Z 205 " =    1.394
peak=   -3.765 closest distance to " O   HOH Z 268 " =    0.876
peak=   -3.762 closest distance to " CD  GLN A  77 " =    1.031
peak=   -3.760 closest distance to " O   HOH Z 131 " =    3.640
peak=   -3.758 closest distance to " OG ASER A 134 " =    0.959
peak=   -3.753 closest distance to " CG  TRP A 266 " =    1.767
peak=   -3.736 closest distance to " O   HOH Z  76 " =    1.061
peak=   -3.733 closest distance to " CA  GLY A  98 " =    1.714
peak=   -3.713 closest distance to " O   SER A 245 " =    1.203
peak=   -3.710 closest distance to " O   HOH Z  60 " =    1.630
peak=   -3.709 closest distance to " O   ASP A 191 " =    1.896
peak=   -3.705 closest distance to " CA  GLY A  35 " =    1.832
peak=   -3.695 closest distance to " O   HOH Z 389 " =    2.423
peak=   -3.690 closest distance to " O   HOH Z 359 " =    1.659
peak=   -3.687 closest distance to " CG BLYS A 290 " =    0.903
peak=   -3.685 closest distance to " CG  ASN A 284 " =    1.317
peak=   -3.676 closest distance to " OG BSER A 134 " =    1.627
peak=   -3.667 closest distance to " O   TRP A 179 " =    1.739
peak=   -3.653 closest distance to " O   HOH Z 413 " =    4.196
peak=   -3.649 closest distance to " O   HOH Z 286 " =    1.515
peak=   -3.642 closest distance to " O   HOH Z 186 " =    1.391
peak=   -3.638 closest distance to " CG  PRO A 163 " =    2.462
peak=   -3.624 closest distance to " OG  SER A 276 " =    0.983
peak=   -3.614 closest distance to " O   HOH Z  95 " =    1.112
peak=   -3.607 closest distance to " O   TRP A  92 " =    1.525
peak=   -3.605 closest distance to " O   HOH Z 331 " =    0.950
peak=   -3.593 closest distance to " C   PHE A 155 " =    0.798
peak=   -3.591 closest distance to " O   HIS A 108 " =    1.231
peak=   -3.589 closest distance to " CD  GLN A  11 " =    0.821
peak=   -3.587 closest distance to " CE2 TYR A  30 " =    2.601
peak=   -3.587 closest distance to " CD1 TRP A 179 " =    1.076
peak=   -3.583 closest distance to " CZ  ARG A  56 " =    0.753
peak=   -3.577 closest distance to " O   HOH Z 415 " =    0.781
peak=   -3.574 closest distance to " CA  TYR A  68 " =    1.281
peak=   -3.568 closest distance to " O   HOH Z 431 " =    1.114
peak=   -3.556 closest distance to " O   HOH Z 298 " =    0.730
peak=   -3.550 closest distance to " O   HOH Z 197 " =    2.081
peak=   -3.539 closest distance to " CG2AVAL A  41 " =    2.733
peak=   -3.528 closest distance to " CG  PRO A 213 " =    2.267
peak=   -3.524 closest distance to " CA  GLY A 203 " =    2.338
peak=   -3.523 closest distance to " CZ2 TRP A 274 " =    0.914
peak=   -3.514 closest distance to " CB  PHE A 130 " =    1.145
peak=   -3.512 closest distance to " CG  GLU A 277 " =    1.152
peak=   -3.506 closest distance to " N   ARG A 275 " =    0.776
peak=   -3.503 closest distance to " O   HOH Z  16 " =    1.126
peak=   -3.495 closest distance to " CB  ASP A  27 " =    2.369
peak=   -3.492 closest distance to " CB  PRO A 243 " =    2.511
peak=   -3.478 closest distance to " O   HOH Z 298 " =    2.826
peak=   -3.472 closest distance to " CD2 LEU A 297 " =    1.156
peak=   -3.466 closest distance to " CG2 ILE A 120 " =    1.339
peak=   -3.448 closest distance to " O   ARG A 275 " =    0.759
peak=   -3.442 closest distance to " CD1 TRP A 274 " =    0.956
peak=   -3.440 closest distance to " O   HOH Z 428 " =    1.506
peak=   -3.439 closest distance to " O   HOH Z 235 " =    0.940
peak=   -3.437 closest distance to " O   HOH Z  28 " =    1.275
peak=   -3.435 closest distance to " N   ALA A   1 " =    1.035
peak=   -3.429 closest distance to " O   HOH Z 207 " =    2.136
peak=   -3.427 closest distance to " CA  GLY A  57 " =    2.142
peak=   -3.421 closest distance to " C   ARG A  79 " =    2.600
peak=   -3.420 closest distance to " O   HOH Z 222 " =    4.633
peak=   -3.417 closest distance to " OG  SER A  63 " =    1.545
peak=   -3.410 closest distance to " O   HOH Z  30 " =    0.847
peak=   -3.410 closest distance to " O   HOH Z 185 " =    2.199
peak=   -3.410 closest distance to " O   THR A 178 " =    0.896
peak=   -3.408 closest distance to " O   HOH Z 102 " =    1.701
peak=   -3.406 closest distance to " CG2 VAL A  78 " =    2.646
peak=   -3.400 closest distance to " C   ASN A 285 " =    1.965
peak=   -3.396 closest distance to " CD1 ILE A 239 " =    2.337
peak=   -3.395 closest distance to " CE2 PHE A 218 " =    2.492
peak=   -3.395 closest distance to " CG1 ILE A 234 " =    1.734
peak=   -3.394 closest distance to " O   HOH Z 389 " =    0.956
peak=   -3.392 closest distance to " O   HOH Z  60 " =    1.446
peak=   -3.392 closest distance to " O   HOH Z 244 " =    1.376
peak=   -3.381 closest distance to " N   GLN A  11 " =    1.000
peak=   -3.376 closest distance to " CA  GLN A  55 " =    1.205
peak=   -3.366 closest distance to " CG  MET A 105 " =    0.849
peak=   -3.365 closest distance to " CD  GLN A  58 " =    0.819
peak=   -3.361 closest distance to " O   HOH Z 364 " =    0.835
peak=   -3.358 closest distance to " O   HOH Z 271 " =    0.778
peak=   -3.350 closest distance to " O   ALA A  10 " =    1.626
peak=   -3.349 closest distance to " O   SER A  22 " =    2.563
peak=   -3.349 closest distance to " O   HOH Z  34 " =    2.126
peak=   -3.343 closest distance to " O   GLN A  77 " =    1.620
peak=   -3.342 closest distance to " CB  SER A 276 " =    1.485
peak=   -3.339 closest distance to " CD  GLU A 277 " =    0.806
peak=   -3.338 closest distance to " O   HOH Z 429 " =    1.733
peak=   -3.336 closest distance to " ND2 ASN A 252 " =    2.136
peak=   -3.335 closest distance to " O   LYS A  76 " =    1.120
peak=   -3.330 closest distance to " N   THR A 157 " =    1.577
peak=   -3.329 closest distance to " OE1 GLU A  44 " =    1.172
peak=   -3.329 closest distance to " C   GLU A   2 " =    1.828
peak=   -3.323 closest distance to " O   HOH Z 347 " =    0.856
peak=   -3.322 closest distance to " O   HOH Z  75 " =    1.769
peak=   -3.319 closest distance to " O   HOH Z 308 " =    1.597
peak=   -3.313 closest distance to " O   HOH Z 390 " =    2.484
peak=   -3.312 closest distance to " O   HOH Z 151 " =    0.791
peak=   -3.308 closest distance to " OD2 ASP A 272 " =    1.355
peak=   -3.307 closest distance to " O   HOH Z 174 " =    2.877
peak=   -3.301 closest distance to " NE1 TRP A 177 " =    1.647
peak=   -3.301 closest distance to " OE2 GLU A 152 " =    1.044
peak=   -3.297 closest distance to " N   HIS A 115 " =    2.136
peak=   -3.293 closest distance to " O   ILE A  49 " =    1.614
peak=   -3.289 closest distance to " O   SER A 271 " =    1.636
peak=   -3.287 closest distance to " NE2 GLN A  11 " =    1.205
peak=   -3.286 closest distance to " O   HOH Z 290 " =    0.939
peak=   -3.283 closest distance to " OD1 ASP A  27 " =    1.038
peak=   -3.278 closest distance to " O   HOH Z 136 " =    2.688
peak=   -3.275 closest distance to " ND2BASN A 224 " =    1.402
peak=   -3.274 closest distance to " CB  TRP A 274 " =    2.749
peak=   -3.271 closest distance to " CB  ASN A  45 " =    1.938
peak=   -3.269 closest distance to " CB  ALA A  43 " =    2.199
peak=   -3.268 closest distance to " CG  ASP A 140 " =    0.988
peak=   -3.254 closest distance to " CG  PRO A 243 " =    1.584
peak=   -3.250 closest distance to " O   HOH Z 387 " =    1.138
peak=   -3.249 closest distance to " O   HOH Z  69 " =    2.075
peak=   -3.247 closest distance to " O   HOH Z 189 " =    3.044
peak=   -3.246 closest distance to " OG  SER A  87 " =    1.437
peak=   -3.245 closest distance to " O   HOH Z 404 " =    1.254
peak=   -3.245 closest distance to " CB  ASN A 301 " =    1.633
peak=   -3.243 closest distance to " O   HOH Z 353 " =    1.154
peak=   -3.242 closest distance to " O   HOH Z 351 " =    1.509
peak=   -3.232 closest distance to " O   HOH Z 376 " =    2.231
peak=   -3.230 closest distance to " ND2 ASN A 285 " =    2.197
peak=   -3.228 closest distance to " NH2 ARG A  79 " =    2.075
peak=   -3.226 closest distance to " CA  ASN A 142 " =    2.017
peak=   -3.225 closest distance to " ND2 ASN A 173 " =    1.511
peak=   -3.221 closest distance to " O   HOH Z 422 " =    3.346
peak=   -3.220 closest distance to " O   HOH Z  47 " =    1.613
peak=   -3.216 closest distance to " O   HOH Z 134 " =    2.944
peak=   -3.207 closest distance to " O   HOH Z  77 " =    1.950
peak=   -3.206 closest distance to " C   ILE A 239 " =    1.644
peak=   -3.203 closest distance to " O   HOH Z 111 " =    2.354
peak=   -3.202 closest distance to " CG  LEU A   5 " =    0.945
peak=   -3.201 closest distance to " CZ  TYR A 169 " =    1.703
peak=   -3.197 closest distance to " C   ASP A 124 " =    1.143
peak=   -3.192 closest distance to " O   HOH Z 214 " =    1.172
peak=   -3.191 closest distance to " O   HOH Z 266 " =    4.677
peak=   -3.190 closest distance to " CD2 TYR A 293 " =    1.789
peak=   -3.183 closest distance to " N   PRO A 163 " =    1.458
peak=   -3.181 closest distance to " O   ILE A 106 " =    2.153
peak=   -3.180 closest distance to " CB  ALA A   9 " =    2.508
peak=   -3.180 closest distance to " OE1 GLN A 183 " =    1.635
peak=   -3.177 closest distance to " ND2 ASN A 249 " =    1.295
peak=   -3.174 closest distance to " O   HOH Z 140 " =    1.702
peak=   -3.172 closest distance to " N   GLN A 122 " =    1.414
peak=   -3.170 closest distance to " O   GLY A 136 " =    1.522
peak=   -3.168 closest distance to " OG  SER A 245 " =    1.505
peak=   -3.167 closest distance to " N   GLU A 277 " =    1.357
peak=   -3.163 closest distance to " CB  TYR A 172 " =    2.134
peak=   -3.161 closest distance to " O   GLY A 211 " =    1.091
peak=   -3.159 closest distance to " O   HOH Z 132 " =    0.926
peak=   -3.156 closest distance to " O   HOH Z 256 " =    1.187
peak=   -3.156 closest distance to " O   HOH Z 401 " =    1.161
peak=   -3.155 closest distance to " CG  PHE A 283 " =    2.419
peak=   -3.154 closest distance to " CG2 ILE A 120 " =    0.926
peak=   -3.154 closest distance to " O   TYR A  30 " =    1.899
peak=   -3.150 closest distance to " N   GLN A  58 " =    1.085
peak=   -3.149 closest distance to " O   HOH Z 409 " =    1.749
peak=   -3.147 closest distance to " O   HOH Z 350 " =    1.945
peak=   -3.146 closest distance to " C   GLN A  89 " =    1.761
peak=   -3.145 closest distance to " N   MET A  40 " =    2.040
peak=   -3.141 closest distance to " CG2 ILE A  20 " =    2.819
peak=   -3.139 closest distance to " CZ  PHE A  38 " =    2.640
peak=   -3.135 closest distance to " OG  SER A   3 " =    1.133
peak=   -3.132 closest distance to " C   TRP A 179 " =    1.043
peak=   -3.126 closest distance to " CB  ALA A 114 " =    2.341
peak=   -3.123 closest distance to " O   LEU A 300 " =    2.450
peak=   -3.123 closest distance to " ND2 ASN A  60 " =    1.124
peak=   -3.121 closest distance to " CZ3 TRP A 123 " =    1.604
peak=   -3.119 closest distance to " CG1 ILE A 263 " =    1.917
peak=   -3.115 closest distance to " O   HOH Z 126 " =    1.659
peak=   -3.115 closest distance to " CG  ASP A 231 " =    0.782
peak=   -3.112 closest distance to " N   THR A 235 " =    1.135
peak=   -3.108 closest distance to " O   HOH Z  56 " =    2.419
peak=   -3.101 closest distance to " CG2 THR A   4 " =    2.077
peak=   -3.100 closest distance to " O   HOH Z 201 " =    1.307
peak=   -3.100 closest distance to " O   HOH Z 414 " =    1.863
peak=   -3.096 closest distance to " OD1 ASN A 249 " =    1.407
peak=   -3.093 closest distance to " OD2 ASP A 253 " =    0.990
peak=   -3.090 closest distance to " O   HOH Z  95 " =    2.448
peak=   -3.088 closest distance to " CD  ARG A 139 " =    1.665
peak=   -3.083 closest distance to " CD  LYS A 166 " =    2.622
peak=   -3.081 closest distance to " NH2AARG A 275 " =    5.218
peak=   -3.050 closest distance to " N   VAL A 189 " =    1.738
peak=   -3.039 closest distance to " O   HOH Z 335 " =    1.244
peak=   -3.030 closest distance to " CA  HIS A  86 " =    2.139

================= 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    :  0.4868 0.4845   6.294598e+00   6.283986e+00
   1_bss:  0.4778 0.4716   6.289126e+00   6.275452e+00
   1_xyz:  0.4127 0.4411   6.216510e+00   6.246544e+00
   1_adp:  0.3722 0.4356   6.170177e+00   6.243618e+00
   1_occ:  0.3717 0.4358   6.169677e+00   6.244162e+00
   2_bss:  0.3703 0.4325   6.170191e+00   6.242645e+00
   2_xyz:  0.3294 0.4060   6.077210e+00   6.194263e+00
   2_adp:  0.3170 0.3929   6.055959e+00   6.176763e+00
   2_occ:  0.3169 0.3935   6.056252e+00   6.177344e+00
   3_bss:  0.3173 0.3911   6.056506e+00   6.176560e+00
   3_xyz:  0.2614 0.3345   5.892718e+00   6.051526e+00
   3_adp:  0.2388 0.3212   5.833494e+00   6.019382e+00
   3_occ:  0.2384 0.3211   5.833342e+00   6.019712e+00
   4_bss:  0.2378 0.3198   5.831231e+00   6.017284e+00
   4_xyz:  0.2028 0.2694   5.671858e+00   5.875959e+00
   4_adp:  0.1921 0.2477   5.613623e+00   5.810164e+00
   4_occ:  0.1917 0.2466   5.611838e+00   5.807610e+00
   5_bss:  0.1914 0.2465   5.611943e+00   5.807610e+00
   5_xyz:  0.1531 0.2042   5.411932e+00   5.632525e+00
   5_adp:  0.1459 0.1989   5.375485e+00   5.605122e+00
   5_occ:  0.1457 0.1987   5.374708e+00   5.604436e+00
   5_bss:  0.1460 0.1983   5.373103e+00   5.602144e+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:  0.374   9.225   6.247   9.898   7.221   0.000   0.000   0.000
   1_xyz:  0.374   9.225   6.247   9.898   7.221   0.000   0.000   0.000
   1_adp:  0.374   9.225   6.247   9.898   7.221   0.000   0.000   0.000
   1_occ:  0.374   9.225   6.247   9.898   7.221   0.000   0.000   0.000
   2_bss:  0.364  34.126   3.439   6.106   4.379   0.000   0.000   0.000
   2_xyz:  0.364  34.126   3.439   6.106   4.379   0.000   0.000   0.000
   2_adp:  0.364  34.126   3.439   6.106   4.379   0.000   0.000   0.000
   2_occ:  0.364  34.126   3.439   6.106   4.379   0.000   0.000   0.000
   3_bss:  0.361  52.362   2.617   4.160   3.608   0.000   0.000   0.000
   3_xyz:  0.361  52.362   2.617   4.160   3.608   0.000   0.000   0.000
   3_adp:  0.361  52.362   2.617   4.160   3.608   0.000   0.000   0.000
   3_occ:  0.361  52.362   2.617   4.160   3.608   0.000   0.000   0.000
   4_bss:  0.338  50.023   1.698   2.373   2.837   0.000   0.000   0.000
   4_xyz:  0.338  50.023   1.698   2.373   2.837   0.000   0.000   0.000
   4_adp:  0.338  50.023   1.698   2.373   2.837   0.000   0.000   0.000
   4_occ:  0.338  50.023   1.698   2.373   2.837   0.000   0.000   0.000
   5_bss:  0.327  42.588   1.136   1.335   2.569   0.000   0.000   0.000
   5_xyz:  0.327  42.588   1.136   1.335   2.569   0.000   0.000   0.000
   5_adp:  0.327  42.588   1.136   1.335   2.569   0.000   0.000   0.000
   5_occ:  0.327  42.588   1.136   1.335   2.569   0.000   0.000   0.000
   5_bss:  0.327  44.070  -0.477  -0.529   1.006  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  60.975 0.3814  0.4564    76561.409
   1_bss:  59.911 0.3942  0.5881    73529.408
   1_xyz:  53.649 0.4738  0.6966    62572.223
   1_adp:  52.852 0.4838  0.7605    61679.658
   1_occ:  52.930 0.4828  0.7576    61866.157
   2_bss:  52.482 0.4885  0.6911    61132.761
   2_xyz:  46.326 0.5650  0.7972    49805.873
   2_adp:  44.137 0.5925  0.8369    46626.483
   2_occ:  44.224 0.5914  0.8352    46767.627
   3_bss:  43.964 0.5944  0.8051    46275.792
   3_xyz:  35.138 0.6996  0.9291    30901.680
   3_adp:  32.990 0.7246  0.9493    28133.098
   3_occ:  33.002 0.7245  0.9492    28168.745
   4_bss:  32.864 0.7259  0.9116    27897.959
   4_xyz:  26.955 0.7902  0.9608    18837.665
   4_adp:  24.117 0.8209  0.9741    15843.370
   4_occ:  24.032 0.8218  0.9742    15727.837
   5_bss:  24.048 0.8216  0.9517    15723.303
   5_xyz:  19.523 0.8663  0.9816    10810.071
   5_adp:  18.815 0.8732  0.9785    10286.019
   5_occ:  18.804 0.8733  0.9781    10252.076
   5_bss:  18.744 0.8737  0.9710    10166.139
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3080e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3080e+01
   1_xyz:   1.677  0.013  0.105 18.274  0.006  4.105   1.4249e-01
   1_adp:   1.677  0.013  0.105 18.274  0.006  4.105   1.4249e-01
   1_occ:   1.677  0.013  0.105 18.274  0.006  4.105   1.4249e-01
   2_bss:   1.677  0.013  0.105 18.274  0.006  4.105   1.4249e-01
   2_xyz:   1.136  0.008  0.075 16.116  0.005  4.119   8.4815e-02
   2_adp:   1.136  0.008  0.075 16.116  0.005  4.119   8.4815e-02
   2_occ:   1.136  0.008  0.075 16.116  0.005  4.119   8.4815e-02
   3_bss:   1.136  0.008  0.075 16.116  0.005  4.119   8.4815e-02
   3_xyz:   1.271  0.010  0.089 16.399  0.005  4.119   9.7304e-02
   3_adp:   1.271  0.010  0.089 16.399  0.005  4.119   9.7304e-02
   3_occ:   1.271  0.010  0.089 16.399  0.005  4.119   9.7304e-02
   4_bss:   1.271  0.010  0.089 16.399  0.005  4.119   9.7304e-02
   4_xyz:   0.937  0.006  0.067 15.580  0.003  4.106   5.9000e-02
   4_adp:   0.937  0.006  0.067 15.580  0.003  4.106   5.9000e-02
   4_occ:   0.937  0.006  0.067 15.580  0.003  4.106   5.9000e-02
   5_bss:   0.937  0.006  0.067 15.580  0.003  4.106   5.9000e-02
   5_xyz:   0.976  0.006  0.069 15.284  0.004  4.107   6.0118e-02
   5_adp:   0.976  0.006  0.069 15.284  0.004  4.107   6.0118e-02
   5_occ:   0.976  0.006  0.069 15.284  0.004  4.107   6.0118e-02
   5_bss:   0.976  0.006  0.069 15.284  0.004  4.107   6.0118e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8766e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8766e+00
   1_xyz:  13.037  0.190  0.407 85.234  0.038  2.137   9.6729e-02
   1_adp:  13.037  0.190  0.407 85.234  0.038  2.137   9.6729e-02
   1_occ:  13.037  0.190  0.407 85.234  0.038  2.137   9.6729e-02
   2_bss:  13.037  0.190  0.407 85.234  0.038  2.137   9.6729e-02
   2_xyz:   7.341  0.099  0.303 76.562  0.044  2.025   5.9528e-02
   2_adp:   7.341  0.099  0.303 76.562  0.044  2.025   5.9528e-02
   2_occ:   7.341  0.099  0.303 76.562  0.044  2.025   5.9528e-02
   3_bss:   7.341  0.099  0.303 76.562  0.044  2.025   5.9528e-02
   3_xyz:   8.988  0.108  0.319 76.198  0.029  2.136   1.1110e-01
   3_adp:   8.988  0.108  0.319 76.198  0.029  2.136   1.1110e-01
   3_occ:   8.988  0.108  0.319 76.198  0.029  2.136   1.1110e-01
   4_bss:   8.988  0.108  0.319 76.198  0.029  2.136   1.1110e-01
   4_xyz:   7.459  0.094  0.244 73.714  0.022  2.310   5.1834e-02
   4_adp:   7.459  0.094  0.244 73.714  0.022  2.310   5.1834e-02
   4_occ:   7.459  0.094  0.244 73.714  0.022  2.310   5.1834e-02
   5_bss:   7.459  0.094  0.244 73.714  0.022  2.310   5.1834e-02
   5_xyz:   6.948  0.058  0.206 81.490  0.038  2.352   8.0294e-02
   5_adp:   6.948  0.058  0.206 81.490  0.038  2.352   8.0294e-02
   5_occ:   6.948  0.058  0.206 81.490  0.038  2.352   8.0294e-02
   5_bss:   6.948  0.058  0.206 81.490  0.038  2.352   8.0294e-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:  78.80   0.00  14.24  78.80   0.00  12.74  71.32   0.00  22.44
   1_occ:  78.80   0.00  14.24  78.80   0.00  12.74  71.32   0.00  22.44
   2_bss:  78.80   0.00  14.24  78.80   0.00  12.74  71.32   0.00  22.44
   2_xyz:  78.80   0.00  14.24  78.80   0.00  12.74  71.32   0.00  22.44
   2_adp:  80.91   0.00  13.75  80.91   0.00  11.72  72.21   0.00  24.82
   2_occ:  80.91   0.00  13.75  80.91   0.00  11.72  72.21   0.00  24.82
   3_bss:  80.91   0.00  13.75  80.91   0.00  11.72  72.21   0.00  24.82
   3_xyz:  80.91   0.00  13.75  80.91   0.00  11.72  72.21   0.00  24.82
   3_adp:  87.00   0.00  14.80  87.00   0.00  11.25  82.28   0.00  34.17
   3_occ:  87.00   0.00  14.80  87.00   0.00  11.25  82.28   0.00  34.17
   4_bss:  87.00   0.00  14.80  87.00   0.00  11.25  82.28   0.00  34.17
   4_xyz:  87.00   0.00  14.80  87.00   0.00  11.25  82.28   0.00  34.17
   4_adp:  86.11   0.00  13.89  86.11   0.00  10.01  81.01   2.57  34.99
   4_occ:  86.11   0.00  13.89  86.11   0.00  10.01  81.01   2.57  34.99
   5_bss:  86.11   0.00  13.89  86.11   0.00  10.01  81.01   2.57  34.99
   5_xyz:  86.11   0.00  13.89  86.11   0.00  10.01  81.01   2.57  34.99
   5_adp: 113.88   0.00  13.75 113.88   0.00   9.68  81.52   2.53  35.93
   5_occ: 113.88   0.00  13.75 113.88   0.00   9.68  81.52   2.53  35.93
   5_bss: 115.36   1.48  15.23 115.36   1.48  11.16  83.00   4.02  37.41
------------------------------------------------------------------------
 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:    1.256    0.005    0.410
   1_adp:    1.256    0.005    0.410
   1_occ:    1.256    0.005    0.410
   2_bss:    1.256    0.005    0.410
   2_xyz:    1.576    0.034    0.539
   2_adp:    1.576    0.034    0.539
   2_occ:    1.576    0.034    0.539
   3_bss:    1.576    0.034    0.539
   3_xyz:    1.592    0.034    0.677
   3_adp:    1.592    0.034    0.677
   3_occ:    1.592    0.034    0.677
   4_bss:    1.592    0.034    0.677
   4_xyz:    1.876    0.095    0.762
   4_adp:    1.876    0.095    0.762
   4_occ:    1.876    0.095    0.762
   5_bss:    1.876    0.095    0.762
   5_xyz:    1.942    0.084    0.831
   5_adp:    1.942    0.084    0.831
   5_occ:    1.942    0.084    0.831
   5_bss:    1.942    0.084    0.831
------------------------------------------------------------------------

CPU time actual refinement: 296.67


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_489/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_489/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_489/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_489/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_489/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 296.55 
  Macro-tasks:
    bulk solvent and scale       = 36.86  
    individual site refinement   = 123.63 
    weights calculation          = 27.21  
    collect and process          = 5.35   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 193.15 
  Micro-tasks:
    mask                            = 2.50   
    f_calc                          = 92.02  
    alpha_beta                      = 7.05   
    target                          = 0.97   
    gradients_wrt_atomic_parameters = 101.70 
    fmodel                         = 6.17   
    r_factors                      = 0.22   
    phase_errors                   = 8.28   
    foms                           = 0.20   
    TOTAL for micro-tasks          = 219.11 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.113 micro seconds
Total CPU time: 5.14 minutes
from_scatterers_fft:    676 calls, 91.72 s
gradients_fft:          620 calls, 89.81 s

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

# Date 2008-01-16 Time 01:42:12 PST -0800 (1200476532.05 s)
Start R-work = 0.4868, R-free = 0.4845 (no bulk solvent and anisotropic scale)
Final R-work = 0.1612, R-free = 0.2122 (no bulk solvent and anisotropic scale)

Start R-work = 0.4778, R-free = 0.4716
Final R-work = 0.1460, R-free = 0.1983