# Date 2008-01-16 Time 01:27:50 PST -0800 (1200475670.17 s)
#phil __OFF__

Command line arguments: "../432.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8879
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 432

-------------------------------------------------------------------------------
  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: (69.5475, 47.1647, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.1647, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.844 1.98047
Completeness in resolution range: 0.971725
Completeness with d_max=infinity: 0.96865

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8440
                             d_min =   1.9805

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: (69.5475, 47.1647, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.844 1.98047
Completeness in resolution range: 0.971725
Completeness with d_max=infinity: 0.96865

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8444 -  4.2368 [2114/2141]  1903   211  10.0%
  bin  2:  4.2368 -  3.3759 [2031/2047]  1827   204  10.0%
  bin  3:  3.3759 -  2.9530 [2013/2032]  1810   203  10.1%
  bin  4:  2.9530 -  2.6847 [1984/2014]  1792   192   9.7%
  bin  5:  2.6847 -  2.4933 [1968/1987]  1767   201  10.2%
  bin  6:  2.4933 -  2.3469 [1963/1999]  1768   195   9.9%
  bin  7:  2.3469 -  2.2297 [1959/1992]  1765   194   9.9%
  bin  8:  2.2297 -  2.1330 [1942/1977]  1744   198  10.2%
  bin  9:  2.1330 -  2.0511 [1940/1967]  1746   194  10.0%
  bin 10:  2.0511 -  1.9805 [1675/2003]  1508   167  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_432/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: 0.13 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:
        1.81 -     2.42: 25
        2.42 -     3.04: 2220
        3.04 -     3.66: 4724
        3.66 -     4.28: 9093
        4.28 -     4.90: 12413
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.856 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.965 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  2.008 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  2.106 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28470 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_432/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_432/model_refine_001.geo

CPU time processing inputs: 9.13


============================ 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 = 69.5475 47.16465 85.5261 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: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4350   r_free= 0.4263   ksol= 0.00   Bsol= 0.00   scale= 0.827    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.227100                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.7251 0.99   1374  153 0.3622 0.3477      6.5122      6.5018|
|  2:  4.7251 -  3.7707 0.99   1322  146 0.3371 0.3335      6.6506      6.6633|
|  3:  3.7707 -  3.3000 0.99   1298  146 0.3716 0.3545      6.5642      6.5939|
|  4:  3.3000 -  3.0010 0.99   1285  138 0.4068 0.3868      6.4448      6.3719|
|  5:  3.0010 -  2.7874 0.99   1275  143 0.4449 0.4833      6.3181      6.3626|
|  6:  2.7874 -  2.6240 0.99   1279  146 0.4560 0.5052      6.2399      6.2269|
|  7:  2.6240 -  2.4933 0.99   1266  139 0.4784 0.4532      6.2168      6.1145|
|  8:  2.4933 -  2.3852 0.98   1269  142 0.4827 0.4560      6.1606      6.1428|
|  9:  2.3852 -  2.2937 0.98   1259  139 0.4961 0.5036      6.0909      6.1052|
| 10:  2.2937 -  2.2148 0.98   1249  136 0.4881 0.4804      6.1044      6.0624|
| 11:  2.2148 -  2.1458 1.00   1266  147 0.4912 0.4387      6.0268      6.0257|
| 12:  2.1458 -  2.0846 0.97   1253  128 0.5016 0.4747      5.9678      6.0078|
| 13:  2.0846 -  2.0299 0.98   1239  138 0.5092 0.5479      5.8952      5.8939|
| 14:  2.0299 -  1.9805 0.79    996  118 0.5064 0.4441      5.8361      5.7169|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8444 -  4.7251  1374   153  0.72  32.83   0.82     0.73      63384.43|
|  2:  4.7251 -  3.7707  1322   146  0.76  29.66   0.92     0.81      78272.36|
|  3:  3.7707 -  3.3000  1298   146  0.70  35.63   0.88     0.79      80702.72|
|  4:  3.3000 -  3.0010  1285   138  0.64  40.57   0.84     0.71      70538.78|
|  5:  3.0010 -  2.7874  1275   143  0.54  48.50   0.78     0.62      64043.69|
|  6:  2.7874 -  2.6240  1279   146  0.52  50.27   0.77     0.58      56379.96|
|  7:  2.6240 -  2.4933  1266   139  0.50  51.84   0.76     0.57      52998.51|
|  8:  2.4933 -  2.3852  1269   142  0.51  51.36   0.77     0.57      46307.36|
|  9:  2.3852 -  2.2937  1259   139  0.49  52.61   0.75     0.58      42501.43|
| 10:  2.2937 -  2.2148  1249   136  0.51  51.32   0.78     0.58      38034.06|
| 11:  2.2148 -  2.1458  1266   147  0.48  53.40   0.78     0.57      36971.04|
| 12:  2.1458 -  2.0846  1253   128  0.45  56.24   0.77     0.54      36371.28|
| 13:  2.0846 -  2.0299  1239   138  0.42  58.79   0.77     0.50      32603.33|
| 14:  2.0299 -  1.9805   996   118  0.44  56.97   0.75     0.48      25550.51|
|alpha:            min =        0.48 max =            0.81 mean =         0.62|
|beta:             min =    25550.51 max =        80702.72 mean =     52457.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.55|
|phase err.(work): min =        0.00 max =           89.99 mean =        47.51|
|phase err.(test): min =        0.00 max =           89.71 mean =        47.47|
|-----------------------------------------------------------------------------|

============================== 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 = 7.833063              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.659   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.655168              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.655   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      161 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      705 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1535 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2645 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3949 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5116 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6622 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7743 |
|-----------------------------------------------------------------------------|
|-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 |       53.458 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.865 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.718)------------------------------------------|
|    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 = 11.718)------------------------------------------|
|    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: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4432   r_free= 0.4341   ksol= 0.00   Bsol= 0.00   scale= 0.795    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.232448                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4260   r_free= 0.4177   ksol= 0.36   Bsol= 20.00   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.45,8.50,8.34,0.00,0.00,0.00); trace/3= 8.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.219856                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.357795              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.355   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.680988              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.268   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4260      final r-factor (work) = 0.3196          |
| start r-factor (free) = 0.4177      final r-factor (free) = 0.3429          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 76.4173 = 7.36 * 0.50 * 6.2409 + 1.00 * 53.4576                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.4655 = 7.36 * 0.50 * 6.0739 + 1.00 * 0.1204                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3196      final r-factor (work) = 0.2563          |
| start r-factor (free) = 0.3429      final r-factor (free) = 0.2924          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1509 = 0.68 * 1.00 * 6.0739 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0264 = 0.68 * 1.00 * 5.8947 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.718)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    63.93   10.78    None  None   None       |
|    all(noH): 2823   0      0.00    63.93   10.78    None  None   None       |
|    Sol.    : 438    0      0.00    62.45   27.80    None  None   None       |
|    Mac.    : 2385   0      0.00    63.93   7.65     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.393: 1375   |   5:    31.964 -  38.356:  108        |
|      1:     6.393 -  12.786:  707   |   6:    38.356 -  44.749:   54        |
|      2:    12.786 -  19.178:  255   |   7:    44.749 -  51.142:   36        |
|      3:    19.178 -  25.571:  148   |   8:    51.142 -  57.535:   20        |
|      4:    25.571 -  31.964:  112   |   9:    57.535 -  63.927:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2563 r_free = 0.2924             target_work(ml) = 5.827         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2558 r_free = 0.2925             target_work(ml) = 5.825         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2558   r_free= 0.2925   ksol= 0.36   Bsol= 20.00   scale= 1.091   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.45,8.50,8.34,0.00,0.00,0.00); trace/3= 8.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.825343                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2513   r_free= 0.2870   ksol= 0.33   Bsol= 35.43   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.07,4.84,5.41,0.00,0.00,0.00); trace/3= 4.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.824568                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.641138              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.838   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.338478              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.262  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2513      final r-factor (work) = 0.1715          |
| start r-factor (free) = 0.2870      final r-factor (free) = 0.2058          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9136 = 2.64 * 0.50 * 5.9019 + 1.00 * 0.1197                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5147 = 2.64 * 0.50 * 5.6471 + 1.00 * 0.0573                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1715      final r-factor (work) = 0.1560          |
| start r-factor (free) = 0.2058      final r-factor (free) = 0.1938          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9256 = 0.34 * 1.00 * 5.6471 + 1.00 * 0.0142                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8566 = 0.34 * 1.00 * 5.4310 + 1.00 * 0.0183                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.718)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.52   11.50    None  None   None       |
|    all(noH): 2823   0      0.00    77.52   11.50    None  None   None       |
|    Sol.    : 438    0      0.00    63.49   32.50    None  None   None       |
|    Mac.    : 2385   0      0.00    77.52   7.64     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 -   7.753: 1633   |   5:    38.763 -  46.515:  103        |
|      1:     7.753 -  15.505:  593   |   6:    46.515 -  54.267:   59        |
|      2:    15.505 -  23.258:  171   |   7:    54.267 -  62.020:   25        |
|      3:    23.258 -  31.010:  105   |   8:    62.020 -  69.772:    6        |
|      4:    31.010 -  38.763:  126   |   9:    69.772 -  77.525:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1560 r_free = 0.1938             target_work(ml) = 5.403         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1558 r_free = 0.1936             target_work(ml) = 5.402         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1558   r_free= 0.1936   ksol= 0.33   Bsol= 35.43   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.07,4.84,5.41,0.00,0.00,0.00); trace/3= 4.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.402034                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1549   r_free= 0.1936   ksol= 0.32   Bsol= 35.43   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.75,3.63,4.18,0.00,0.00,0.00); trace/3= 3.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.401519                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.814226              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.348  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.244921              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.463   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1549      final r-factor (work) = 0.1226          |
| start r-factor (free) = 0.1936      final r-factor (free) = 0.1630          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7122 = 2.81 * 0.50 * 5.4402 + 1.00 * 0.0573                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5157 = 2.81 * 0.50 * 5.2967 + 1.00 * 0.0626                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1226      final r-factor (work) = 0.1188          |
| start r-factor (free) = 0.1630      final r-factor (free) = 0.1578          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3154 = 0.24 * 1.00 * 5.2967 + 1.00 * 0.0181                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2809 = 0.24 * 1.00 * 5.1889 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.718)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.11   11.42    None  None   None       |
|    all(noH): 2823   0      0.00    77.11   11.42    None  None   None       |
|    Sol.    : 438    0      1.10    64.43   32.86    None  None   None       |
|    Mac.    : 2385   0      0.00    77.11   7.49     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 -   7.711: 1663   |   5:    38.556 -  46.267:  105        |
|      1:     7.711 -  15.422:  582   |   6:    46.267 -  53.978:   64        |
|      2:    15.422 -  23.133:  148   |   7:    53.978 -  61.689:   26        |
|      3:    23.133 -  30.844:  114   |   8:    61.689 -  69.400:    4        |
|      4:    30.844 -  38.556:  113   |   9:    69.400 -  77.111:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1188 r_free = 0.1578             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1187 r_free = 0.1577             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1577   ksol= 0.32   Bsol= 35.43   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.75,3.63,4.18,0.00,0.00,0.00); trace/3= 3.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.173843                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1193   r_free= 0.1576   ksol= 0.32   Bsol= 37.42   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.54,3.36,3.93,0.00,0.00,0.00); trace/3= 3.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.176167                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.888930              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.458  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.169032              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.140  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1193      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1576      final r-factor (free) = 0.1557          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9645 = 1.89 * 0.50 * 5.1902 + 1.00 * 0.0625                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9288 = 1.89 * 0.50 * 5.1567 + 1.00 * 0.0584                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1139          |
| start r-factor (free) = 0.1557      final r-factor (free) = 0.1558          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8816 = 0.17 * 1.00 * 5.1567 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8793 = 0.17 * 1.00 * 5.1488 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.718)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.15   11.17    None  None   None       |
|    all(noH): 2823   0      0.00    76.15   11.17    None  None   None       |
|    Sol.    : 438    0      1.01    63.58   31.77    None  None   None       |
|    Mac.    : 2385   0      0.00    76.15   7.39     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 -   7.615: 1671   |   5:    38.075 -  45.690:   95        |
|      1:     7.615 -  15.230:  585   |   6:    45.690 -  53.305:   61        |
|      2:    15.230 -  22.845:  145   |   7:    53.305 -  60.920:   17        |
|      3:    22.845 -  30.460:  123   |   8:    60.920 -  68.536:    7        |
|      4:    30.460 -  38.075:  115   |   9:    68.536 -  76.151:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1139 r_free = 0.1558             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1139 r_free = 0.1559             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1559   ksol= 0.32   Bsol= 37.42   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.54,3.36,3.93,0.00,0.00,0.00); trace/3= 3.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.147842                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1559   ksol= 0.32   Bsol= 37.42   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.46,3.25,3.84,0.00,0.00,0.00); trace/3= 3.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.147833                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.517032              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.168  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.596514              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 162.573  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1139      final r-factor (work) = 0.1101          |
| start r-factor (free) = 0.1559      final r-factor (free) = 0.1533          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5376 = 2.52 * 0.50 * 5.1483 + 1.00 * 0.0584                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5264 = 2.52 * 0.50 * 5.1324 + 1.00 * 0.0672                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1101      final r-factor (work) = 0.1085          |
| start r-factor (free) = 0.1533      final r-factor (free) = 0.1542          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0706 = 0.60 * 1.00 * 5.1324 + 1.00 * 0.0091                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0629 = 0.60 * 1.00 * 5.1159 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.718)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.60   11.36    None  None   None       |
|    all(noH): 2823   0      0.00    77.60   11.36    None  None   None       |
|    Sol.    : 438    0      1.04    64.55   32.86    None  None   None       |
|    Mac.    : 2385   0      0.00    77.60   7.42     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.760: 1681   |   5:    38.798 -  46.558:  102        |
|      1:     7.760 -  15.519:  561   |   6:    46.558 -  54.318:   65        |
|      2:    15.519 -  23.279:  151   |   7:    54.318 -  62.077:   22        |
|      3:    23.279 -  31.039:  116   |   8:    62.077 -  69.837:    5        |
|      4:    31.039 -  38.798:  114   |   9:    69.837 -  77.597:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1085 r_free = 0.1542             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1085 r_free = 0.1542             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1085   r_free= 0.1542   ksol= 0.32   Bsol= 37.42   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.46,3.25,3.84,0.00,0.00,0.00); trace/3= 3.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.120495                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.7251 0.99   1374  153 0.1010 0.1271       5.385      5.5059|
|  2:  4.7251 -  3.7707 0.99   1322  146 0.0852 0.1125       5.432      5.6368|
|  3:  3.7707 -  3.3000 0.99   1298  146 0.1032 0.1486       5.456      5.8444|
|  4:  3.3000 -  3.0010 0.99   1285  138 0.1165 0.1476      5.4246       5.574|
|  5:  3.0010 -  2.7874 0.99   1275  143 0.1244 0.1662      5.2944      5.5061|
|  6:  2.7874 -  2.6240 0.99   1279  146 0.1180 0.1780      5.1912       5.443|
|  7:  2.6240 -  2.4933 0.99   1266  139 0.1186 0.1565      5.1363      5.3263|
|  8:  2.4933 -  2.3852 0.98   1269  142 0.1138 0.1786      5.0646      5.3746|
|  9:  2.3852 -  2.2937 0.98   1259  139 0.1142 0.1754      5.0071      5.2466|
| 10:  2.2937 -  2.2148 0.98   1249  136 0.1069 0.1678        4.95      5.2048|
| 11:  2.2148 -  2.1458 1.00   1266  147 0.1085 0.1669      4.8982      5.2688|
| 12:  2.1458 -  2.0846 0.97   1253  128 0.1056 0.1616      4.8394      5.1223|
| 13:  2.0846 -  2.0299 0.98   1239  138 0.1091 0.1649      4.7715      5.0275|
| 14:  2.0299 -  1.9805 0.79    996  118 0.1047 0.1788      4.6778        4.96|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8444 -  4.7251  1374   153  0.94   8.96   0.98     0.96       7011.05|
|  2:  4.7251 -  3.7707  1322   146  0.95   7.75   1.02     1.01       8839.47|
|  3:  3.7707 -  3.3000  1298   146  0.94  10.90   1.03     1.02      10083.66|
|  4:  3.3000 -  3.0010  1285   138  0.93  12.80   1.00     0.99       9699.19|
|  5:  3.0010 -  2.7874  1275   143  0.91  15.23   0.99     0.96       7882.91|
|  6:  2.7874 -  2.6240  1279   146  0.91  15.40   0.98     0.95       6698.21|
|  7:  2.6240 -  2.4933  1266   139  0.91  15.18   0.98     0.95       5961.14|
|  8:  2.4933 -  2.3852  1269   142  0.91  14.84   0.99     0.97       5286.34|
|  9:  2.3852 -  2.2937  1259   139  0.91  15.45   1.00     0.97       4840.65|
| 10:  2.2937 -  2.2148  1249   136  0.90  15.29   1.00     0.97       4387.54|
| 11:  2.2148 -  2.1458  1266   147  0.91  15.28   1.00     0.97       4048.50|
| 12:  2.1458 -  2.0846  1253   128  0.92  14.39   1.01     0.99       3670.06|
| 13:  2.0846 -  2.0299  1239   138  0.91  15.18   1.00     0.99       3227.27|
| 14:  2.0299 -  1.9805   996   118  0.91  15.11   0.98     0.95       2657.41|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2657.41 max =        10083.66 mean =      6108.21|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.62|
|phase err.(test): min =        0.00 max =           88.60 mean =        13.17|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1085   r_free= 0.1542   ksol= 0.32   Bsol= 41.94   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.71,0.05,0.66,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.120410                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1085   r_free= 0.1542   ksol= 0.32   Bsol= 41.94   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.71,0.05,0.66,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.120410                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.7251 0.99   1374  153 0.1010 0.1273      5.3855      5.5068|
|  2:  4.7251 -  3.7707 0.99   1322  146 0.0853 0.1126      5.4335      5.6381|
|  3:  3.7707 -  3.3000 0.99   1298  146 0.1032 0.1486      5.4567      5.8446|
|  4:  3.3000 -  3.0010 0.99   1285  138 0.1165 0.1475      5.4243      5.5737|
|  5:  3.0010 -  2.7874 0.99   1275  143 0.1243 0.1662      5.2937      5.5054|
|  6:  2.7874 -  2.6240 0.99   1279  146 0.1179 0.1779      5.1906      5.4424|
|  7:  2.6240 -  2.4933 0.99   1266  139 0.1186 0.1565      5.1358      5.3259|
|  8:  2.4933 -  2.3852 0.98   1269  142 0.1137 0.1785      5.0643       5.374|
|  9:  2.3852 -  2.2937 0.98   1259  139 0.1142 0.1755      5.0069      5.2469|
| 10:  2.2937 -  2.2148 0.98   1249  136 0.1068 0.1679      4.9499      5.2046|
| 11:  2.2148 -  2.1458 1.00   1266  147 0.1084 0.1669       4.898      5.2686|
| 12:  2.1458 -  2.0846 0.97   1253  128 0.1056 0.1616      4.8391       5.122|
| 13:  2.0846 -  2.0299 0.98   1239  138 0.1091 0.1649      4.7712      5.0273|
| 14:  2.0299 -  1.9805 0.79    996  118 0.1047 0.1787      4.6773      4.9592|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8444 -  4.7251  1374   153  0.94   8.97   0.98     0.96       7023.21|
|  2:  4.7251 -  3.7707  1322   146  0.95   7.76   1.02     1.01       8857.95|
|  3:  3.7707 -  3.3000  1298   146  0.94  10.92   1.03     1.02      10100.47|
|  4:  3.3000 -  3.0010  1285   138  0.93  12.79   1.01     1.00       9694.03|
|  5:  3.0010 -  2.7874  1275   143  0.91  15.22   1.00     0.96       7873.54|
|  6:  2.7874 -  2.6240  1279   146  0.91  15.39   0.98     0.95       6689.32|
|  7:  2.6240 -  2.4933  1266   139  0.91  15.17   0.99     0.96       5954.00|
|  8:  2.4933 -  2.3852  1269   142  0.91  14.83   1.00     0.97       5282.45|
|  9:  2.3852 -  2.2937  1259   139  0.91  15.45   1.01     0.98       4838.73|
| 10:  2.2937 -  2.2148  1249   136  0.90  15.29   1.01     0.98       4386.39|
| 11:  2.2148 -  2.1458  1266   147  0.91  15.28   1.00     0.97       4046.61|
| 12:  2.1458 -  2.0846  1253   128  0.92  14.39   1.01     1.00       3667.62|
| 13:  2.0846 -  2.0299  1239   138  0.91  15.17   1.01     1.00       3223.67|
| 14:  2.0299 -  1.9805   996   118  0.91  15.10   0.99     0.96       2652.89|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2652.89 max =        10100.47 mean =      6108.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.62|
|phase err.(test): min =        0.00 max =           88.56 mean =        13.17|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.718)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.32    80.91   14.68    None  None   None       |
|    all(noH): 2823   0      3.32    80.91   14.68    None  None   None       |
|    Sol.    : 438    0      4.36    67.86   36.18    None  None   None       |
|    Mac.    : 2385   0      3.32    80.91   10.73    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:     3.316 -  11.076: 1681   |   5:    42.115 -  49.874:  102        |
|      1:    11.076 -  18.836:  561   |   6:    49.874 -  57.634:   65        |
|      2:    18.836 -  26.595:  151   |   7:    57.634 -  65.394:   22        |
|      3:    26.595 -  34.355:  116   |   8:    65.394 -  73.153:    5        |
|      4:    34.355 -  42.115:  114   |   9:    73.153 -  80.913:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 305         
Filter by distance & map next to the model:
   mapped sites are within: 0.354 - 4.746
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 301 from: 305
   mapped sites are within: 0.721 - 4.746

peak=   10.955 closest distance to " CB  VAL A 230 " =    1.458
peak=    6.398 closest distance to " CG  LEU A   5 " =    1.169
peak=    6.328 closest distance to " CG2 VAL A 296 " =    1.087
peak=    5.871 closest distance to " CB  VAL A 296 " =    1.054
peak=    5.676 closest distance to " CG  LEU A 228 " =    1.180
peak=    5.201 closest distance to " NH2 ARG A  56 " =    2.178
peak=    5.129 closest distance to " CG  PRO A  54 " =    1.199
peak=    5.102 closest distance to " CB  ARG A 275 " =    0.920
peak=    5.074 closest distance to " NE2 GLN A  11 " =    1.100
peak=    4.999 closest distance to " CD2 LEU A   5 " =    1.118
peak=    4.980 closest distance to " O   HOH Z 126 " =    1.918
peak=    4.975 closest distance to " O   HOH Z 142 " =    1.716
peak=    4.968 closest distance to " CB  GLN A 183 " =    1.302
peak=    4.947 closest distance to " CB  GLN A 223 " =    1.431
peak=    4.913 closest distance to " O   HOH Z 193 " =    1.764
peak=    4.857 closest distance to " O   HOH Z 232 " =    2.356
peak=    4.850 closest distance to " CB  SER A  63 " =    1.216
peak=    4.772 closest distance to " CB  VAL A 230 " =    1.179
peak=    4.680 closest distance to " CB  GLU A 152 " =    1.188
peak=    4.573 closest distance to " C   PRO A 198 " =    1.468
peak=    4.519 closest distance to " O   HOH Z 402 " =    1.454
peak=    4.496 closest distance to " O   HOH Z 272 " =    1.892
peak=    4.461 closest distance to " O   HOH Z 236 " =    1.887
peak=    4.440 closest distance to " O   SER A  87 " =    2.198
peak=    4.411 closest distance to " CB  TYR A 169 " =    0.722
peak=    4.392 closest distance to " O   HOH Z 124 " =    1.353
peak=    4.377 closest distance to " O   HOH Z 298 " =    1.801
peak=    4.359 closest distance to " O   HOH Z 209 " =    2.343
peak=    4.355 closest distance to " CG  PRO A 213 " =    1.237
peak=    4.329 closest distance to " O   HOH Z 234 " =    3.517
peak=    4.328 closest distance to " CB  ARG A  79 " =    1.425
peak=    4.319 closest distance to " CB  SER A   3 " =    1.269
peak=    4.318 closest distance to " CB  PRO A  54 " =    0.879
peak=    4.267 closest distance to " O   HOH Z 303 " =    2.089
peak=    4.262 closest distance to " O   HOH Z 403 " =    1.730
peak=    4.258 closest distance to " O   HOH Z  59 " =    2.186
peak=    4.256 closest distance to " O   HOH Z 346 " =    1.557
peak=    4.248 closest distance to " O   HOH Z 316 " =    2.943
peak=    4.213 closest distance to " O   HOH Z  85 " =    1.428
peak=    4.197 closest distance to " CB  ASN A 148 " =    1.396
peak=    4.196 closest distance to " O   HOH Z  97 " =    2.497
peak=    4.193 closest distance to " O   HOH Z 369 " =    2.205
peak=    4.186 closest distance to " OD1 ASN A  69 " =    2.581
peak=    4.169 closest distance to " O   HOH Z 368 " =    2.190
peak=    4.146 closest distance to " O   HOH Z  97 " =    1.901
peak=    4.135 closest distance to " O   HOH Z 423 " =    1.829
peak=    4.131 closest distance to " O   HOH Z  61 " =    1.617
peak=    4.130 closest distance to " O   HOH Z 427 " =    2.836
peak=    4.123 closest distance to " ND2 ASN A 187 " =    1.492
peak=    4.098 closest distance to " O   HOH Z 203 " =    1.634
peak=    4.092 closest distance to " CB  GLU A 277 " =    3.519
peak=    4.089 closest distance to " O   HOH Z  54 " =    1.583
peak=    4.069 closest distance to " O   HOH Z  78 " =    1.645
peak=    4.054 closest distance to " CA  TYR A  30 " =    0.942
peak=    4.037 closest distance to " CB  ARG A 139 " =    0.972
peak=    4.020 closest distance to " O   HOH Z  43 " =    2.140
peak=    4.011 closest distance to " O   HOH Z 158 " =    3.024
peak=    4.010 closest distance to " CB  TRP A 179 " =    1.298
peak=    3.993 closest distance to " CG  PRO A 243 " =    1.149
peak=    3.983 closest distance to " CG1BVAL A  72 " =    1.607
peak=    3.946 closest distance to " CD2 LEU A 228 " =    1.144
peak=    3.943 closest distance to " O   HOH Z 371 " =    3.220
peak=    3.933 closest distance to " O   HOH Z 280 " =    2.907
peak=    3.927 closest distance to " CB  ASN A  39 " =    0.844
peak=    3.924 closest distance to " O   HOH Z 197 " =    3.005
peak=    3.906 closest distance to " CB  VAL A 265 " =    1.259
peak=    3.899 closest distance to " CA  ALA A  21 " =    1.160
peak=    3.888 closest distance to " O   HOH Z 411 " =    3.802
peak=    3.878 closest distance to " O   HOH Z 128 " =    2.003
peak=    3.870 closest distance to " O   HOH Z 128 " =    2.078
peak=    3.864 closest distance to " O   HOH Z 250 " =    1.360
peak=    3.851 closest distance to " CG  GLN A  77 " =    2.160
peak=    3.850 closest distance to " N   ASN A  39 " =    1.233
peak=    3.847 closest distance to " CG2 ILE A  20 " =    1.456
peak=    3.842 closest distance to " O   TRP A 274 " =    1.904
peak=    3.834 closest distance to " O   HOH Z 248 " =    1.624
peak=    3.830 closest distance to " O   HOH Z 389 " =    1.875
peak=    3.829 closest distance to " O   HOH Z 345 " =    3.050
peak=    3.816 closest distance to " OD2 ASP A 286 " =    2.726
peak=    3.808 closest distance to " CZ  PHE A 218 " =    1.119
peak=    3.808 closest distance to " O   HOH Z 407 " =    2.630
peak=    3.799 closest distance to " CA  ASN A 215 " =    1.190
peak=    3.782 closest distance to " O   HOH Z 126 " =    2.248
peak=    3.780 closest distance to " O   HOH Z  48 " =    1.569
peak=    3.780 closest distance to " O   HOH Z  66 " =    2.177
peak=    3.777 closest distance to " O   HOH Z  15 " =    2.112
peak=    3.773 closest distance to " O   HOH Z 189 " =    2.590
peak=    3.769 closest distance to " O   HOH Z 344 " =    2.873
peak=    3.762 closest distance to " O   HOH Z 245 " =    1.402
peak=    3.755 closest distance to " CG  ARG A  66 " =    2.840
peak=    3.749 closest distance to " CB  GLU A 128 " =    1.014
peak=    3.749 closest distance to " CD2 TRP A 179 " =    1.407
peak=    3.746 closest distance to " O   HOH Z 417 " =    3.199
peak=    3.743 closest distance to " O   HOH Z 261 " =    2.155
peak=    3.743 closest distance to " NZ  LYS A 117 " =    3.091
peak=    3.738 closest distance to " CB  TRP A 266 " =    0.980
peak=    3.731 closest distance to " CB  SER A  26 " =    1.664
peak=    3.730 closest distance to " CA  LYS A 117 " =    1.257
peak=    3.711 closest distance to " CG  PRO A 198 " =    1.161
peak=    3.707 closest distance to " O   HOH Z 130 " =    2.344
peak=    3.689 closest distance to " CB  VAL A 202 " =    1.514
peak=    3.683 closest distance to " O   HOH Z 193 " =    1.939
peak=    3.679 closest distance to " O   HOH Z 263 " =    1.643
peak=    3.674 closest distance to " CA  VAL A  41 " =    0.839
peak=    3.672 closest distance to " CB  ASP A 140 " =    0.937
peak=    3.669 closest distance to " O   HOH Z  80 " =    1.646
peak=    3.665 closest distance to " O   HOH Z  54 " =    2.411
peak=    3.658 closest distance to " O   HOH Z 227 " =    1.574
peak=    3.652 closest distance to " O   HOH Z 251 " =    1.623
peak=    3.646 closest distance to " O   HOH Z  40 " =    1.597
peak=    3.642 closest distance to " O   HOH Z 322 " =    2.065
peak=    3.639 closest distance to " CB  ASN A 148 " =    1.905
peak=    3.636 closest distance to " O   HOH Z 273 " =    2.699
peak=    3.624 closest distance to " O   HOH Z 366 " =    2.968
peak=    3.618 closest distance to " CB  ARG A 190 " =    1.676
peak=    3.618 closest distance to " OD2 ASP A 298 " =    3.892
peak=    3.613 closest distance to " CB  ALA A   9 " =    1.597
peak=    3.608 closest distance to " O   ASP A 124 " =    1.197
peak=    3.603 closest distance to " CG1 ILE A  33 " =    1.292
peak=    3.581 closest distance to " O   HOH Z 209 " =    2.377
peak=    3.578 closest distance to " CB  ALA A 248 " =    1.388
peak=    3.574 closest distance to " O   HOH Z  44 " =    1.803
peak=    3.572 closest distance to " CA  ASP A 140 " =    1.204
peak=    3.566 closest distance to " OG BSER A 164 " =    2.182
peak=    3.566 closest distance to " CB  ALA A 295 " =    1.254
peak=    3.556 closest distance to " O   HOH Z 214 " =    2.346
peak=    3.552 closest distance to " OE1 GLU A   2 " =    2.151
peak=    3.543 closest distance to " O   HOH Z 421 " =    1.676
peak=    3.543 closest distance to " CE1 TYR A 186 " =    1.299
peak=    3.542 closest distance to " O   HOH Z 134 " =    1.360
peak=    3.533 closest distance to " CG1 ILE A  49 " =    1.400
peak=    3.532 closest distance to " O   HOH Z 145 " =    2.189
peak=    3.528 closest distance to " CB  THR A  31 " =    1.634
peak=    3.528 closest distance to " CG2 ILE A 120 " =    1.258
peak=    3.514 closest distance to " O   HOH Z 147 " =    1.683
peak=    3.510 closest distance to " O   HOH Z 422 " =    2.663
peak=    3.501 closest distance to " O   HOH Z 227 " =    2.132
peak=    3.499 closest distance to " CD  ARG A 269 " =    1.003
peak=    3.495 closest distance to " O   MET A 105 " =    1.835
peak=    3.488 closest distance to " O   HOH Z 426 " =    1.483
peak=    3.485 closest distance to " CB  ALA A 291 " =    1.389
peak=    3.484 closest distance to " O   HOH Z 250 " =    1.444
peak=    3.483 closest distance to " NH2 ARG A 156 " =    1.068
peak=    3.477 closest distance to " O   HOH Z 187 " =    2.287
peak=    3.474 closest distance to " O   HOH Z 291 " =    1.513
peak=    3.472 closest distance to " O   HOH Z 425 " =    2.067
peak=    3.472 closest distance to " O   HOH Z 286 " =    2.261
peak=    3.465 closest distance to " CB  ALA A   1 " =    1.181
peak=    3.461 closest distance to " CB  GLN A 205 " =    1.232
peak=    3.461 closest distance to " CA  ALA A 158 " =    1.280
peak=    3.459 closest distance to " CA  ALA A  51 " =    0.955
peak=    3.458 closest distance to " ND2 ASN A 110 " =    1.647
peak=    3.455 closest distance to " CA  ASP A 162 " =    1.091
peak=    3.453 closest distance to " O   HOH Z 383 " =    1.948
peak=    3.448 closest distance to " O   HOH Z 327 " =    1.540
peak=    3.447 closest distance to " O   HOH Z  88 " =    2.878
peak=    3.441 closest distance to " O   HOH Z 132 " =    2.602
peak=    3.435 closest distance to " CD BLYS A 290 " =    1.124
peak=    3.434 closest distance to " O   HOH Z 180 " =    2.134
peak=    3.430 closest distance to " CA  PHE A 283 " =    1.220
peak=    3.429 closest distance to " CG2 THR A 221 " =    1.252
peak=    3.428 closest distance to " CB  HIS A 108 " =    0.817
peak=    3.426 closest distance to " O   HOH Z 423 " =    3.157
peak=    3.414 closest distance to " O   HOH Z 166 " =    3.698
peak=    3.411 closest distance to " CD  LYS A 166 " =    1.320
peak=    3.397 closest distance to " O   HOH Z 329 " =    3.857
peak=    3.394 closest distance to " N   SER A 288 " =    1.789
peak=    3.392 closest distance to " CD1 ILE A 106 " =    1.106
peak=    3.391 closest distance to " CA  ARG A 195 " =    1.190
peak=    3.390 closest distance to " CG  MET A 185 " =    1.143
peak=    3.389 closest distance to " O   HOH Z 261 " =    1.705
peak=    3.385 closest distance to " CA  ASN A 176 " =    1.087
peak=    3.384 closest distance to " O   HOH Z 148 " =    3.220
peak=    3.384 closest distance to " CD2 TYR A  30 " =    0.921
peak=    3.381 closest distance to " O   HOH Z 419 " =    1.606
peak=    3.380 closest distance to " O   HOH Z 357 " =    1.840
peak=    3.378 closest distance to " O   HOH Z 123 " =    2.074
peak=    3.371 closest distance to " CB  GLN A 278 " =    0.920
peak=    3.369 closest distance to " O   HOH Z  35 " =    2.373
peak=    3.367 closest distance to " O   HOH Z 406 " =    1.583
peak=    3.361 closest distance to " O   HOH Z  10 " =    1.729
peak=    3.359 closest distance to " CB BVAL A  41 " =    1.084
peak=    3.359 closest distance to " CA  ARG A  36 " =    1.000
peak=    3.356 closest distance to " CG1 VAL A 296 " =    1.216
peak=    3.354 closest distance to " O   HOH Z 299 " =    4.274
peak=    3.353 closest distance to " O   HOH Z 435 " =    1.924
peak=    3.347 closest distance to " CB  GLU A  46 " =    1.082
peak=    3.347 closest distance to " CA  ALA A 291 " =    0.948
peak=    3.344 closest distance to " O   HOH Z  49 " =    2.311
peak=    3.334 closest distance to " CG  ARG A  66 " =    0.959
peak=    3.332 closest distance to " O   HOH Z  21 " =    1.732
peak=    3.323 closest distance to " O   HOH Z 374 " =    2.541
peak=    3.323 closest distance to " OE2 GLU A  53 " =    2.007
peak=    3.321 closest distance to " O   HOH Z 222 " =    2.483
peak=    3.319 closest distance to " O   HOH Z  48 " =    1.614
peak=    3.315 closest distance to " CA  THR A 221 " =    0.907
peak=    3.314 closest distance to " CD2 HIS A  81 " =    1.062
peak=    3.314 closest distance to " CD  ARG A 159 " =    0.721
peak=    3.313 closest distance to " O   HOH Z 313 " =    1.790
peak=    3.310 closest distance to " OG1 THR A 294 " =    2.316
peak=    3.309 closest distance to " NH2 ARG A  79 " =    1.290
peak=    3.305 closest distance to " CB  ILE A 120 " =    1.358
peak=    3.304 closest distance to " O   HOH Z  61 " =    1.545
peak=    3.304 closest distance to " O   HOH Z 367 " =    3.427
peak=    3.299 closest distance to " O   HOH Z 411 " =    1.774
peak=    3.299 closest distance to " CG AARG A 275 " =    1.134
peak=    3.292 closest distance to " CA  ALA A 233 " =    1.149
peak=    3.291 closest distance to " O   HOH Z 298 " =    4.746
peak=    3.289 closest distance to " O   ALA A 165 " =    1.475
peak=    3.283 closest distance to " O   HOH Z 175 " =    2.122
peak=    3.281 closest distance to " CB  LEU A 143 " =    1.144
peak=    3.277 closest distance to " N   SER A 135 " =    1.395
peak=    3.274 closest distance to " CB  THR A 157 " =    1.125
peak=    3.265 closest distance to " O   HOH Z 388 " =    2.026
peak=    3.263 closest distance to " O   HOH Z   9 " =    2.117
peak=    3.261 closest distance to " CD  LYS A 119 " =    1.783
peak=    3.258 closest distance to " OD1 ASN A 217 " =    1.772
peak=    3.257 closest distance to " CG BARG A 102 " =    1.780
peak=    3.256 closest distance to " O   GLN A 278 " =    1.146
peak=    3.256 closest distance to " CG  GLN A  58 " =    2.728
peak=    3.253 closest distance to " CG2 THR A 294 " =    1.662
peak=    3.252 closest distance to " CD  GLN A 194 " =    1.428
peak=    3.251 closest distance to " CA  ASP A 191 " =    1.065
peak=    3.249 closest distance to " O   HOH Z  88 " =    2.543
peak=    3.246 closest distance to " O   HOH Z 189 " =    2.626
peak=    3.240 closest distance to " O   HOH Z 392 " =    1.574
peak=    3.237 closest distance to " CB  ASN A 110 " =    1.123
peak=    3.229 closest distance to " CA  VAL A 126 " =    0.928
peak=    3.225 closest distance to " NZ  LYS A  76 " =    1.375
peak=    3.224 closest distance to " N   PHE A 130 " =    1.338
peak=    3.223 closest distance to " O   HOH Z 337 " =    3.606
peak=    3.218 closest distance to " NE2 GLN A  77 " =    3.246
peak=    3.215 closest distance to " CG  MET A 185 " =    1.100
peak=    3.209 closest distance to " O   HOH Z 279 " =    2.121
peak=    3.209 closest distance to " CE1 HIS A 108 " =    1.128
peak=    3.208 closest distance to " N   ASP A 162 " =    1.278
peak=    3.208 closest distance to " O   HOH Z 420 " =    1.972
peak=    3.205 closest distance to " O   HOH Z 109 " =    2.512
peak=    3.204 closest distance to " CB  ASN A 142 " =    1.112
peak=    3.200 closest distance to " O   HOH Z 185 " =    1.697
peak=    3.199 closest distance to " CD1 LEU A 228 " =    1.877
peak=    3.197 closest distance to " CG2 ILE A 234 " =    2.044
peak=    3.194 closest distance to " CB  LYS A 290 " =    1.033
peak=    3.193 closest distance to " CZ2 TRP A 179 " =    1.767
peak=    3.193 closest distance to " CZ3 TRP A  85 " =    0.946
peak=    3.190 closest distance to " N   VAL A 126 " =    1.325
peak=    3.189 closest distance to " CG2 VAL A 257 " =    0.828
peak=    3.187 closest distance to " O   HOH Z 302 " =    1.871
peak=    3.186 closest distance to " O   HOH Z 234 " =    1.833
peak=    3.185 closest distance to " O   HOH Z 112 " =    1.602
peak=    3.183 closest distance to " CD1 PHE A 204 " =    1.287
peak=    3.182 closest distance to " O   HOH Z 132 " =    2.724
peak=    3.182 closest distance to " O   HOH Z 108 " =    2.516
peak=    3.181 closest distance to " CB  SER A 212 " =    1.168
peak=    3.180 closest distance to " CA  THR A  52 " =    1.026
peak=    3.179 closest distance to " NH2BARG A 145 " =    2.013
peak=    3.178 closest distance to " CB  ASN A 215 " =    1.161
peak=    3.176 closest distance to " CD1 ILE A  33 " =    1.595
peak=    3.173 closest distance to " CB  ARG A 259 " =    1.917
peak=    3.172 closest distance to " CB  TYR A 169 " =    1.179
peak=    3.171 closest distance to " CZ2 TRP A 274 " =    1.546
peak=    3.168 closest distance to " CA  ALA A  84 " =    1.408
peak=    3.166 closest distance to " CA  THR A 264 " =    0.786
peak=    3.164 closest distance to " O   HOH Z 437 " =    1.973
peak=    3.163 closest distance to " O   HOH Z 303 " =    1.617
peak=    3.161 closest distance to " O   HOH Z 368 " =    3.615
peak=    3.157 closest distance to " OG  SER A  22 " =    2.690
peak=    3.152 closest distance to " O   HOH Z 271 " =    1.516
peak=    3.151 closest distance to " O   ALA A   1 " =    1.746
peak=    3.148 closest distance to " O   HOH Z 257 " =    2.275
peak=    3.147 closest distance to " O   HOH Z  85 " =    2.006
peak=    3.146 closest distance to " CA  LYS A 290 " =    1.233
peak=    3.143 closest distance to " O   GLY A  91 " =    1.489
peak=    3.140 closest distance to " NH1BARG A 190 " =    2.083
peak=    3.139 closest distance to " CA  GLY A  80 " =    0.793
peak=    3.137 closest distance to " O   HOH Z  19 " =    1.899
peak=    3.125 closest distance to " O   HOH Z  83 " =    1.574
peak=    3.122 closest distance to " OG  SER A  62 " =    2.876
peak=    3.120 closest distance to " CG  LYS A  76 " =    1.050
peak=    3.120 closest distance to " O   SER A 164 " =    1.101
peak=    3.117 closest distance to " CB  LEU A 255 " =    0.767
peak=    3.116 closest distance to " O   HOH Z 365 " =    3.407
peak=    3.114 closest distance to " O   HOH Z 305 " =    3.559
peak=    3.112 closest distance to " O   HOH Z 392 " =    2.131
peak=    3.108 closest distance to " NZ  LYS A 166 " =    3.008
peak=    3.107 closest distance to " O   HOH Z 116 " =    1.685
peak=    3.106 closest distance to " O   HOH Z 409 " =    3.630
peak=    3.105 closest distance to " O   HOH Z 433 " =    1.803
peak=    3.102 closest distance to " O   ALA A 158 " =    1.341
peak=    3.099 closest distance to " O   HOH Z 438 " =    1.842
peak=    3.092 closest distance to " NH1AARG A 145 " =    0.896
peak=    3.077 closest distance to " O   HOH Z 256 " =    2.400
peak=    3.065 closest distance to " CB  ALA A 100 " =    1.139
peak=    3.063 closest distance to " CG  LEU A 281 " =    1.036
peak=    3.047 closest distance to " O   HOH Z  48 " =    1.264
peak=    3.046 closest distance to " ND1 HIS A  81 " =    1.592
peak=    3.032 closest distance to " O   ASP A 124 " =    1.751
peak=    3.029 closest distance to " CA  ILE A 106 " =    0.758
peak=    3.020 closest distance to " O   HOH Z 258 " =    1.798
peak=    3.019 closest distance to " O   HOH Z 389 " =    1.769
peak=    3.005 closest distance to " O   HOH Z  28 " =    2.167

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.600 - 5.423
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 204
   mapped sites are within: 0.771 - 5.423

peak=   -5.339 closest distance to " CG2 VAL A 230 " =    0.771
peak=   -4.733 closest distance to " SG  CYS A 254 " =    3.251
peak=   -4.659 closest distance to " CD  ARG A 156 " =    2.038
peak=   -4.442 closest distance to " CA  SER A 164 " =    2.156
peak=   -4.347 closest distance to " O   HOH Z 266 " =    4.781
peak=   -4.248 closest distance to " C   HIS A 108 " =    1.227
peak=   -4.247 closest distance to " O   HOH Z 290 " =    1.097
peak=   -4.217 closest distance to " CG  GLN A 223 " =    2.035
peak=   -4.161 closest distance to " CG2BVAL A  41 " =    2.632
peak=   -4.128 closest distance to " O   ILE A 109 " =    2.590
peak=   -4.086 closest distance to " OXT GLY A 302 " =    2.733
peak=   -4.061 closest distance to " CD  GLN A  58 " =    1.195
peak=   -4.048 closest distance to " OG BSER A 134 " =    1.206
peak=   -3.969 closest distance to " CG  ASP A 231 " =    0.835
peak=   -3.942 closest distance to " CE2 TYR A  30 " =    2.775
peak=   -3.925 closest distance to " CG2 VAL A 296 " =    1.160
peak=   -3.919 closest distance to " N   GLN A  58 " =    1.680
peak=   -3.899 closest distance to " O   HOH Z 114 " =    3.142
peak=   -3.896 closest distance to " O   HOH Z 351 " =    1.515
peak=   -3.893 closest distance to " CB  PHE A 192 " =    1.946
peak=   -3.880 closest distance to " O   VAL A  67 " =    2.763
peak=   -3.870 closest distance to " CB  PRO A 243 " =    2.620
peak=   -3.860 closest distance to " CD1 LEU A 101 " =    2.416
peak=   -3.856 closest distance to " CB  ALA A 291 " =    2.292
peak=   -3.839 closest distance to " O   HOH Z  11 " =    1.876
peak=   -3.823 closest distance to " ND2 ASN A  45 " =    1.044
peak=   -3.805 closest distance to " CB  ALA A 248 " =    2.027
peak=   -3.804 closest distance to " CG1 VAL A 112 " =    2.701
peak=   -3.802 closest distance to " O   HOH Z 231 " =    2.065
peak=   -3.795 closest distance to " O   HOH Z 196 " =    2.093
peak=   -3.791 closest distance to " CZ3 TRP A 179 " =    1.277
peak=   -3.789 closest distance to " ND2 ASN A 187 " =    1.594
peak=   -3.771 closest distance to " OG  SER A  97 " =    2.220
peak=   -3.763 closest distance to " O   HOH Z 389 " =    1.806
peak=   -3.760 closest distance to " ND2 ASN A  45 " =    1.356
peak=   -3.759 closest distance to " CD2 LEU A 300 " =    2.830
peak=   -3.729 closest distance to " OG  SER A   3 " =    1.676
peak=   -3.728 closest distance to " CB  PRO A 163 " =    2.553
peak=   -3.716 closest distance to " OD1 ASN A  39 " =    2.196
peak=   -3.714 closest distance to " O   HOH Z 166 " =    1.820
peak=   -3.699 closest distance to " N   ALA A 226 " =    1.969
peak=   -3.699 closest distance to " O   HOH Z 407 " =    2.921
peak=   -3.691 closest distance to " C   ASP A 231 " =    2.566
peak=   -3.670 closest distance to " CD  ARG A 139 " =    1.585
peak=   -3.661 closest distance to " C   ILE A 239 " =    2.159
peak=   -3.661 closest distance to " CB  ALA A 248 " =    2.311
peak=   -3.656 closest distance to " CD  LYS A 289 " =    2.475
peak=   -3.637 closest distance to " O   HOH Z  13 " =    1.523
peak=   -3.633 closest distance to " CD1 LEU A 255 " =    2.798
peak=   -3.629 closest distance to " NE2 GLN A  88 " =    1.972
peak=   -3.623 closest distance to " CG2 THR A 178 " =    2.171
peak=   -3.618 closest distance to " N   THR A 235 " =    1.393
peak=   -3.613 closest distance to " O   HOH Z 353 " =    2.067
peak=   -3.605 closest distance to " CZ  TYR A 169 " =    1.709
peak=   -3.587 closest distance to " O   HOH Z 166 " =    1.457
peak=   -3.579 closest distance to " OG ASER A 134 " =    1.198
peak=   -3.574 closest distance to " NH2AARG A 275 " =    4.992
peak=   -3.569 closest distance to " CD1 PHE A  59 " =    1.819
peak=   -3.565 closest distance to " CD1 ILE A 263 " =    2.723
peak=   -3.554 closest distance to " CE2 PHE A 218 " =    2.595
peak=   -3.551 closest distance to " O   SER A 210 " =    1.936
peak=   -3.547 closest distance to " CE  MET A 105 " =    2.040
peak=   -3.540 closest distance to " O   GLY A  75 " =    1.789
peak=   -3.537 closest distance to " CA  ASP A 298 " =    1.063
peak=   -3.537 closest distance to " CB  ASP A 132 " =    2.351
peak=   -3.535 closest distance to " N   THR A 157 " =    1.467
peak=   -3.530 closest distance to " O   HOH Z 165 " =    1.925
peak=   -3.499 closest distance to " O   HOH Z 394 " =    1.576
peak=   -3.494 closest distance to " O   HOH Z 185 " =    2.395
peak=   -3.494 closest distance to " O   ALA A 161 " =    1.659
peak=   -3.472 closest distance to " O   GLY A  80 " =    2.397
peak=   -3.470 closest distance to " O   HOH Z  52 " =    1.567
peak=   -3.464 closest distance to " N   PHE A  59 " =    2.269
peak=   -3.462 closest distance to " NH2 ARG A  66 " =    1.697
peak=   -3.461 closest distance to " O   HOH Z 193 " =    1.691
peak=   -3.460 closest distance to " C   ALA A 158 " =    1.259
peak=   -3.451 closest distance to " O   MET A  40 " =    2.686
peak=   -3.450 closest distance to " O   HOH Z 102 " =    1.659
peak=   -3.450 closest distance to " N   ALA A 248 " =    1.719
peak=   -3.447 closest distance to " O   ALA A  51 " =    1.369
peak=   -3.444 closest distance to " O   HOH Z 103 " =    1.801
peak=   -3.442 closest distance to " CB  GLN A  11 " =    1.888
peak=   -3.427 closest distance to " CG  ASP A  50 " =    2.344
peak=   -3.422 closest distance to " CZ  PHE A  59 " =    1.545
peak=   -3.419 closest distance to " O   PHE A 218 " =    1.694
peak=   -3.414 closest distance to " N   SER A 276 " =    1.332
peak=   -3.413 closest distance to " O   VAL A 125 " =    2.280
peak=   -3.406 closest distance to " C   MET A 188 " =    1.448
peak=   -3.403 closest distance to " O   PRO A 198 " =    1.225
peak=   -3.398 closest distance to " CG1 VAL A 230 " =    1.802
peak=   -3.396 closest distance to " CG  PHE A 283 " =    2.717
peak=   -3.395 closest distance to " CB  ASP A 132 " =    2.258
peak=   -3.394 closest distance to " CA  GLY A 133 " =    1.964
peak=   -3.392 closest distance to " CB  ASN A  39 " =    2.206
peak=   -3.388 closest distance to " O   GLY A 196 " =    1.090
peak=   -3.386 closest distance to " CG  LEU A 228 " =    1.041
peak=   -3.386 closest distance to " NH2 ARG A  79 " =    1.970
peak=   -3.385 closest distance to " OG  SER A  62 " =    1.528
peak=   -3.378 closest distance to " OG  SER A  26 " =    1.227
peak=   -3.376 closest distance to " O   HOH Z 211 " =    1.697
peak=   -3.376 closest distance to " CB  ASN A  69 " =    1.122
peak=   -3.370 closest distance to " OD1 ASN A 148 " =    1.490
peak=   -3.369 closest distance to " O   HOH Z 234 " =    3.972
peak=   -3.365 closest distance to " NZ  LYS A 119 " =    3.473
peak=   -3.365 closest distance to " O   LYS A 117 " =    1.571
peak=   -3.365 closest distance to " O   HOH Z  17 " =    1.476
peak=   -3.364 closest distance to " CG1 VAL A 112 " =    2.825
peak=   -3.357 closest distance to " CB  ALA A 291 " =    2.135
peak=   -3.357 closest distance to " OG BSER A 134 " =    1.664
peak=   -3.355 closest distance to " CD1 LEU A  25 " =    2.487
peak=   -3.352 closest distance to " CG  GLU A 277 " =    1.103
peak=   -3.351 closest distance to " NE2 GLN A  88 " =    1.096
peak=   -3.343 closest distance to " O   HOH Z 426 " =    1.669
peak=   -3.340 closest distance to " CD1 LEU A 101 " =    2.625
peak=   -3.335 closest distance to " O   LEU A 167 " =    1.545
peak=   -3.327 closest distance to " CG2 ILE A 263 " =    2.288
peak=   -3.316 closest distance to " CD1 LEU A 228 " =    2.097
peak=   -3.315 closest distance to " O   HOH Z 283 " =    1.873
peak=   -3.311 closest distance to " CG1 VAL A  78 " =    2.607
peak=   -3.311 closest distance to " O   HOH Z 423 " =    2.143
peak=   -3.299 closest distance to " O   HOH Z  88 " =    4.333
peak=   -3.298 closest distance to " CA  GLY A 203 " =    2.342
peak=   -3.292 closest distance to " O   HOH Z  47 " =    1.542
peak=   -3.291 closest distance to " N   HIS A 115 " =    2.005
peak=   -3.286 closest distance to " O   HOH Z 174 " =    4.344
peak=   -3.286 closest distance to " CG1 VAL A 197 " =    2.208
peak=   -3.283 closest distance to " O   HOH Z 198 " =    2.164
peak=   -3.283 closest distance to " CD1 TYR A 247 " =    2.396
peak=   -3.282 closest distance to " C   THR A 279 " =    1.161
peak=   -3.279 closest distance to " O   HOH Z 191 " =    5.423
peak=   -3.277 closest distance to " O   HOH Z  43 " =    1.792
peak=   -3.276 closest distance to " O   HOH Z 123 " =    2.321
peak=   -3.272 closest distance to " CG1 VAL A 296 " =    1.218
peak=   -3.269 closest distance to " OD2 ASP A 171 " =    2.292
peak=   -3.269 closest distance to " C   GLN A 205 " =    1.908
peak=   -3.269 closest distance to " NH1 ARG A 195 " =    2.553
peak=   -3.264 closest distance to " CG  GLU A   2 " =    1.798
peak=   -3.261 closest distance to " OXT GLY A 302 " =    3.361
peak=   -3.257 closest distance to " O   HOH Z 339 " =    1.800
peak=   -3.253 closest distance to " O   HOH Z 431 " =    1.776
peak=   -3.253 closest distance to " OG  SER A 206 " =    1.579
peak=   -3.251 closest distance to " CG  TRP A 266 " =    1.993
peak=   -3.248 closest distance to " O   HOH Z 372 " =    2.239
peak=   -3.248 closest distance to " O   VAL A 189 " =    2.600
peak=   -3.242 closest distance to " CD  ARG A 195 " =    5.150
peak=   -3.241 closest distance to " O   HOH Z 313 " =    1.804
peak=   -3.239 closest distance to " N   GLY A  23 " =    2.185
peak=   -3.239 closest distance to " C   SER A 206 " =    1.594
peak=   -3.238 closest distance to " O   HOH Z 126 " =    1.907
peak=   -3.237 closest distance to " C   LEU A 143 " =    1.029
peak=   -3.232 closest distance to " O   HOH Z  19 " =    2.130
peak=   -3.230 closest distance to " O   SER A  95 " =    1.596
peak=   -3.230 closest distance to " O   HOH Z 139 " =    3.160
peak=   -3.222 closest distance to " O   HOH Z 311 " =    3.601
peak=   -3.222 closest distance to " N   ALA A  43 " =    2.550
peak=   -3.217 closest distance to " O   HOH Z 369 " =    2.220
peak=   -3.197 closest distance to " O   HOH Z 131 " =    4.035
peak=   -3.196 closest distance to " O   SER A  22 " =    2.193
peak=   -3.194 closest distance to " O   SER A 258 " =    1.904
peak=   -3.194 closest distance to " OG1 THR A  82 " =    1.452
peak=   -3.190 closest distance to " N   VAL A 230 " =    1.163
peak=   -3.186 closest distance to " O   HOH Z  38 " =    1.769
peak=   -3.186 closest distance to " CG  ARG A 269 " =    2.206
peak=   -3.185 closest distance to " O   HOH Z 385 " =    2.142
peak=   -3.183 closest distance to " OH  TYR A 214 " =    1.265
peak=   -3.180 closest distance to " CE3 TRP A 150 " =    2.029
peak=   -3.178 closest distance to " O   HOH Z   6 " =    1.762
peak=   -3.177 closest distance to " O   HOH Z 422 " =    1.589
peak=   -3.174 closest distance to " O   HOH Z  11 " =    2.025
peak=   -3.173 closest distance to " O   HOH Z 389 " =    4.771
peak=   -3.172 closest distance to " O   HOH Z 313 " =    1.112
peak=   -3.168 closest distance to " CB  ALA A  43 " =    2.343
peak=   -3.165 closest distance to " O   ASN A  45 " =    1.899
peak=   -3.163 closest distance to " SG ACYS A 201 " =    2.085
peak=   -3.161 closest distance to " NE2 GLN A 194 " =    1.710
peak=   -3.161 closest distance to " CB  ALA A 256 " =    2.602
peak=   -3.160 closest distance to " CE  LYS A 166 " =    3.053
peak=   -3.160 closest distance to " CG  PRO A 163 " =    2.674
peak=   -3.157 closest distance to " N   GLN A  77 " =    1.451
peak=   -3.155 closest distance to " CG  MET A 105 " =    0.898
peak=   -3.154 closest distance to " O   VAL A 197 " =    1.330
peak=   -3.152 closest distance to " O   VAL A 174 " =    2.022
peak=   -3.150 closest distance to " NE2 GLN A 103 " =    1.706
peak=   -3.135 closest distance to " CD2 LEU A 237 " =    2.627
peak=   -3.133 closest distance to " CB  VAL A 296 " =    1.087
peak=   -3.127 closest distance to " O   HOH Z 295 " =    1.489
peak=   -3.124 closest distance to " O   HOH Z  97 " =    1.206
peak=   -3.121 closest distance to " OD1 ASN A 301 " =    2.020
peak=   -3.116 closest distance to " CG  GLU A  53 " =    1.574
peak=   -3.114 closest distance to " ND2 ASN A  39 " =    1.219
peak=   -3.110 closest distance to " CD2 TYR A 293 " =    2.085
peak=   -3.107 closest distance to " CA  GLY A 133 " =    2.251
peak=   -3.105 closest distance to " CE BMET A  47 " =    1.717
peak=   -3.101 closest distance to " O   PRO A 198 " =    1.312
peak=   -3.095 closest distance to " OD1 ASN A 176 " =    1.252
peak=   -3.090 closest distance to " O   HOH Z 407 " =    3.038
peak=   -3.071 closest distance to " CG  GLU A 152 " =    1.309
peak=   -3.060 closest distance to " O   HOH Z 111 " =    2.539
peak=   -3.060 closest distance to " C   LEU A 222 " =    0.833
peak=   -3.054 closest distance to " N   MET A 105 " =    2.626
peak=   -3.019 closest distance to " C   ASP A 270 " =    1.234

================= 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    :  0.4350 0.4263   6.227100e+00   6.210657e+00
   1_bss:  0.4260 0.4177   6.219856e+00   6.195597e+00
   1_xyz:  0.3196 0.3429   6.015232e+00   6.061542e+00
   1_adp:  0.2563 0.2924   5.826528e+00   5.932940e+00
   1_occ:  0.2558 0.2925   5.825343e+00   5.932618e+00
   2_bss:  0.2513 0.2870   5.824568e+00   5.927650e+00
   2_xyz:  0.1715 0.2058   5.482706e+00   5.649368e+00
   2_adp:  0.1560 0.1938   5.402579e+00   5.584329e+00
   2_occ:  0.1558 0.1936   5.402034e+00   5.584064e+00
   3_bss:  0.1549 0.1936   5.401519e+00   5.581071e+00
   3_xyz:  0.1226 0.1630   5.203837e+00   5.420137e+00
   3_adp:  0.1188 0.1578   5.174357e+00   5.391143e+00
   3_occ:  0.1187 0.1577   5.173843e+00   5.390942e+00
   4_bss:  0.1193 0.1576   5.176167e+00   5.391611e+00
   4_xyz:  0.1138 0.1557   5.148230e+00   5.379940e+00
   4_adp:  0.1139 0.1558   5.147552e+00   5.378342e+00
   4_occ:  0.1139 0.1559   5.147842e+00   5.379152e+00
   5_bss:  0.1139 0.1559   5.147833e+00   5.379157e+00
   5_xyz:  0.1101 0.1533   5.123911e+00   5.364534e+00
   5_adp:  0.1085 0.1542   5.120488e+00   5.369905e+00
   5_occ:  0.1085 0.1542   5.120495e+00   5.369990e+00
   5_bss:  0.1085 0.1542   5.120410e+00   5.369914e+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:  0.355  20.001   7.449   8.497   8.336   0.000   0.000   0.000
   1_xyz:  0.355  20.001   7.449   8.497   8.336   0.000   0.000   0.000
   1_adp:  0.355  20.001   7.449   8.497   8.336   0.000   0.000   0.000
   1_occ:  0.355  20.001   7.449   8.497   8.336   0.000   0.000   0.000
   2_bss:  0.332  35.435   4.069   4.841   5.414   0.000   0.000   0.000
   2_xyz:  0.332  35.435   4.069   4.841   5.414   0.000   0.000   0.000
   2_adp:  0.332  35.435   4.069   4.841   5.414   0.000   0.000   0.000
   2_occ:  0.332  35.435   4.069   4.841   5.414   0.000   0.000   0.000
   3_bss:  0.323  35.435   2.745   3.632   4.185   0.000   0.000   0.000
   3_xyz:  0.323  35.435   2.745   3.632   4.185   0.000   0.000   0.000
   3_adp:  0.323  35.435   2.745   3.632   4.185   0.000   0.000   0.000
   3_occ:  0.323  35.435   2.745   3.632   4.185   0.000   0.000   0.000
   4_bss:  0.320  37.416   2.545   3.358   3.930   0.000   0.000   0.000
   4_xyz:  0.320  37.416   2.545   3.358   3.930   0.000   0.000   0.000
   4_adp:  0.320  37.416   2.545   3.358   3.930   0.000   0.000   0.000
   4_occ:  0.320  37.416   2.545   3.358   3.930   0.000   0.000   0.000
   5_bss:  0.322  37.416   2.456   3.246   3.838   0.000   0.000   0.000
   5_xyz:  0.322  37.416   2.456   3.246   3.838   0.000   0.000   0.000
   5_adp:  0.322  37.416   2.456   3.246   3.838   0.000   0.000   0.000
   5_occ:  0.322  37.416   2.456   3.246   3.838   0.000   0.000   0.000
   5_bss:  0.321  41.939  -0.709   0.053   0.656   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.507 0.5534  0.6214    52452.003
   1_bss:  47.749 0.5478  0.7832    50112.544
   1_xyz:  37.120 0.6754  0.9446    31940.697
   1_adp:  29.199 0.7673  1.0481    21748.708
   1_occ:  29.168 0.7676  1.0479    21700.272
   2_bss:  28.965 0.7697  0.9310    21403.474
   2_xyz:  19.969 0.8616  1.0065    10851.276
   2_adp:  18.275 0.8782  1.0213     9563.998
   2_occ:  18.268 0.8783  1.0210     9555.058
   3_bss:  18.234 0.8785  0.9743     9501.042
   3_xyz:  14.772 0.9084  0.9888     6752.494
   3_adp:  14.126 0.9140  0.9915     6422.070
   3_occ:  14.118 0.9141  0.9913     6417.834
   4_bss:  14.139 0.9139  0.9821     6443.405
   4_xyz:  13.762 0.9172  0.9822     6235.842
   4_adp:  13.683 0.9180  0.9814     6218.283
   4_occ:  13.696 0.9179  0.9811     6227.816
   5_bss:  13.696 0.9179  0.9776     6228.147
   5_xyz:  13.438 0.9197  0.9786     6051.185
   5_adp:  13.572 0.9187  0.9752     6105.327
   5_occ:  13.573 0.9186  0.9751     6107.484
   5_bss:  13.571 0.9187  0.9801     6107.525
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3458e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3458e+01
   1_xyz:   1.546  0.012  0.103 17.826  0.006  4.119   1.2038e-01
   1_adp:   1.546  0.012  0.103 17.826  0.006  4.119   1.2038e-01
   1_occ:   1.546  0.012  0.103 17.826  0.006  4.119   1.2038e-01
   2_bss:   1.546  0.012  0.103 17.826  0.006  4.119   1.2038e-01
   2_xyz:   0.944  0.006  0.070 15.868  0.003  4.118   5.7319e-02
   2_adp:   0.944  0.006  0.070 15.868  0.003  4.118   5.7319e-02
   2_occ:   0.944  0.006  0.070 15.868  0.003  4.118   5.7319e-02
   3_bss:   0.944  0.006  0.070 15.868  0.003  4.118   5.7319e-02
   3_xyz:   1.018  0.007  0.081 15.683  0.004  4.124   6.2570e-02
   3_adp:   1.018  0.007  0.081 15.683  0.004  4.124   6.2570e-02
   3_occ:   1.018  0.007  0.081 15.683  0.004  4.124   6.2570e-02
   4_bss:   1.018  0.007  0.081 15.683  0.004  4.124   6.2570e-02
   4_xyz:   0.976  0.006  0.079 15.504  0.004  4.113   5.8419e-02
   4_adp:   0.976  0.006  0.079 15.504  0.004  4.113   5.8419e-02
   4_occ:   0.976  0.006  0.079 15.504  0.004  4.113   5.8419e-02
   5_bss:   0.976  0.006  0.079 15.504  0.004  4.113   5.8419e-02
   5_xyz:   1.065  0.008  0.087 15.538  0.004  4.118   6.7209e-02
   5_adp:   1.065  0.008  0.087 15.538  0.004  4.118   6.7209e-02
   5_occ:   1.065  0.008  0.087 15.538  0.004  4.118   6.7209e-02
   5_bss:   1.065  0.008  0.087 15.538  0.004  4.118   6.7209e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9299e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9299e+00
   1_xyz:  13.594  0.144  0.467 86.860  0.045  2.262   8.9761e-02
   1_adp:  13.594  0.144  0.467 86.860  0.045  2.262   8.9761e-02
   1_occ:  13.594  0.144  0.467 86.860  0.045  2.262   8.9761e-02
   2_bss:  13.594  0.144  0.467 86.860  0.045  2.262   8.9761e-02
   2_xyz:   6.599  0.071  0.285 82.088  0.029  2.382   4.9657e-02
   2_adp:   6.599  0.071  0.285 82.088  0.029  2.382   4.9657e-02
   2_occ:   6.599  0.071  0.285 82.088  0.029  2.382   4.9657e-02
   3_bss:   6.599  0.071  0.285 82.088  0.029  2.382   4.9657e-02
   3_xyz:   6.506  0.044  0.587 82.606  0.037  2.340   5.8783e-02
   3_adp:   6.506  0.044  0.587 82.606  0.037  2.340   5.8783e-02
   3_occ:   6.506  0.044  0.587 82.606  0.037  2.340   5.8783e-02
   4_bss:   6.506  0.044  0.587 82.606  0.037  2.340   5.8783e-02
   4_xyz:   6.764  0.041  0.548 82.243  0.035  2.361   3.7197e-02
   4_adp:   6.764  0.041  0.548 82.243  0.035  2.361   3.7197e-02
   4_occ:   6.764  0.041  0.548 82.243  0.035  2.361   3.7197e-02
   5_bss:   6.764  0.041  0.548 82.243  0.035  2.361   3.7197e-02
   5_xyz:   7.190  0.047  0.666 82.565  0.037  2.286   4.8306e-02
   5_adp:   7.190  0.047  0.666 82.565  0.037  2.286   4.8306e-02
   5_occ:   7.190  0.047  0.666 82.565  0.037  2.286   4.8306e-02
   5_bss:   7.190  0.047  0.666 82.565  0.037  2.286   4.8306e-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:  63.93   0.00  10.78  63.93   0.00   7.65  62.45   0.00  27.80
   1_occ:  63.93   0.00  10.78  63.93   0.00   7.65  62.45   0.00  27.80
   2_bss:  63.93   0.00  10.78  63.93   0.00   7.65  62.45   0.00  27.80
   2_xyz:  63.93   0.00  10.78  63.93   0.00   7.65  62.45   0.00  27.80
   2_adp:  77.52   0.00  11.50  77.52   0.00   7.64  63.49   0.00  32.50
   2_occ:  77.52   0.00  11.50  77.52   0.00   7.64  63.49   0.00  32.50
   3_bss:  77.52   0.00  11.50  77.52   0.00   7.64  63.49   0.00  32.50
   3_xyz:  77.52   0.00  11.50  77.52   0.00   7.64  63.49   0.00  32.50
   3_adp:  77.11   0.00  11.42  77.11   0.00   7.49  64.43   1.10  32.86
   3_occ:  77.11   0.00  11.42  77.11   0.00   7.49  64.43   1.10  32.86
   4_bss:  77.11   0.00  11.42  77.11   0.00   7.49  64.43   1.10  32.86
   4_xyz:  77.11   0.00  11.42  77.11   0.00   7.49  64.43   1.10  32.86
   4_adp:  76.15   0.00  11.17  76.15   0.00   7.39  63.58   1.01  31.77
   4_occ:  76.15   0.00  11.17  76.15   0.00   7.39  63.58   1.01  31.77
   5_bss:  76.15   0.00  11.17  76.15   0.00   7.39  63.58   1.01  31.77
   5_xyz:  76.15   0.00  11.17  76.15   0.00   7.39  63.58   1.01  31.77
   5_adp:  77.60   0.00  11.36  77.60   0.00   7.42  64.55   1.04  32.86
   5_occ:  77.60   0.00  11.36  77.60   0.00   7.42  64.55   1.04  32.86
   5_bss:  80.91   3.32  14.68  80.91   3.32  10.73  67.86   4.36  36.18
------------------------------------------------------------------------
 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:    1.183    0.018    0.404
   1_adp:    1.183    0.018    0.404
   1_occ:    1.183    0.018    0.404
   2_bss:    1.183    0.018    0.404
   2_xyz:    1.541    0.017    0.500
   2_adp:    1.541    0.017    0.500
   2_occ:    1.541    0.017    0.500
   3_bss:    1.541    0.017    0.500
   3_xyz:    1.513    0.040    0.542
   3_adp:    1.513    0.040    0.542
   3_occ:    1.513    0.040    0.542
   4_bss:    1.513    0.040    0.542
   4_xyz:    1.599    0.037    0.559
   4_adp:    1.599    0.037    0.559
   4_occ:    1.599    0.037    0.559
   5_bss:    1.599    0.037    0.559
   5_xyz:    1.576    0.045    0.568
   5_adp:    1.576    0.045    0.568
   5_occ:    1.576    0.045    0.568
   5_bss:    1.576    0.045    0.568
------------------------------------------------------------------------

CPU time actual refinement: 332.91


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_432/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_432/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_432/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_432/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_432/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 332.76 
  Macro-tasks:
    bulk solvent and scale       = 41.46  
    individual site refinement   = 134.75 
    weights calculation          = 32.86  
    collect and process          = 6.57   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 215.73 
  Micro-tasks:
    mask                            = 1.73   
    f_calc                          = 102.11 
    alpha_beta                      = 8.15   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 112.82 
    fmodel                         = 7.34   
    r_factors                      = 0.17   
    phase_errors                   = 10.97  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 244.67 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.654 micro seconds
Total CPU time: 5.77 minutes
from_scatterers_fft:    663 calls, 101.79 s
gradients_fft:          607 calls,  99.26 s

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

# Date 2008-01-16 Time 01:33:35 PST -0800 (1200476015.23 s)
Start R-work = 0.4350, R-free = 0.4263 (no bulk solvent and anisotropic scale)
Final R-work = 0.1264, R-free = 0.1701 (no bulk solvent and anisotropic scale)

Start R-work = 0.4260, R-free = 0.4177
Final R-work = 0.1085, R-free = 0.1542