# Date 2008-01-16 Time 01:10:15 PST -0800 (1200474615.62 s)
#phil __OFF__

Command line arguments: "../318.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18145
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 318

-------------------------------------------------------------------------------
  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: (69.1963, 47.1647, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.36, per 1000 atoms: 1.19


================================== 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: (69.1963, 47.1647, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9516 1.97089
Completeness in resolution range: 0.931169
Completeness with d_max=infinity: 0.928345

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9516
                             d_min =   1.9709

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: (69.1963, 47.1647, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9516 1.97089
Completeness in resolution range: 0.931169
Completeness with d_max=infinity: 0.928345

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9520 -  4.2174 [2207/2235]  1985   222  10.1%
  bin  2:  4.2174 -  3.3599 [2127/2146]  1911   216  10.2%
  bin  3:  3.3599 -  2.9389 [2095/2115]  1893   202   9.6%
  bin  4:  2.9389 -  2.6719 [2078/2103]  1866   212  10.2%
  bin  5:  2.6719 -  2.4813 [2053/2073]  1843   210  10.2%
  bin  6:  2.4813 -  2.3356 [2039/2086]  1837   202   9.9%
  bin  7:  2.3356 -  2.2190 [2048/2081]  1852   196   9.6%
  bin  8:  2.2190 -  2.1227 [2050/2084]  1835   215  10.5%
  bin  9:  2.1227 -  2.0412 [2010/2051]  1816   194   9.7%
  bin 10:  2.0412 -  1.9709 [ 882/2063]   792    90  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_318/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:
        1.33 -     2.04: 14
        2.04 -     2.76: 387
        2.76 -     3.47: 4552
        3.47 -     4.19: 9301
        4.19 -     4.90: 13893
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.330 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.440 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.537 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.603 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.698 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28142 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_318/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_318/model_refine_001.geo

CPU time processing inputs: 9.12


============================ 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 = 69.19625 47.16465 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4853   r_free= 0.4708   ksol= 0.00   Bsol= 0.00   scale= 0.786    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.286350                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9520 -  4.7039 0.99   1437  158 0.3888 0.3766      6.6026      6.5749|
|  2:  4.7039 -  3.7531 0.99   1389  155 0.3979 0.4504      6.7706      6.9144|
|  3:  3.7531 -  3.2844 0.99   1341  153 0.4580 0.4149      6.6822      6.6557|
|  4:  3.2844 -  2.9867 0.99   1358  140 0.4746 0.4581      6.5157      6.4781|
|  5:  2.9867 -  2.7741 0.99   1325  154 0.5129 0.4894      6.3629      6.4059|
|  6:  2.7741 -  2.6114 0.98   1322  147 0.5141 0.5485      6.2815      6.2092|
|  7:  2.6114 -  2.4813 0.99   1326  155 0.5202 0.4815      6.2338      6.1299|
|  8:  2.4813 -  2.3737 0.98   1334  143 0.5350 0.4489        6.18      6.1527|
|  9:  2.3737 -  2.2827 0.98   1308  142 0.5378 0.5074      6.1347      6.1691|
| 10:  2.2827 -  2.2041 0.98   1320  142 0.5442 0.5291      6.0982      6.0989|
| 11:  2.2041 -  2.1354 0.99   1301  156 0.5206 0.5318      6.0064      6.0333|
| 12:  2.1354 -  2.0745 0.98   1322  143 0.5326 0.5023      5.9588       5.943|
| 13:  2.0745 -  2.0201 0.89   1182  121 0.5377 0.5159      5.8841      5.8474|
| 14:  2.0201 -  1.9709 0.28    365   50 0.5156 0.3966      5.9207       5.687|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9520 -  4.7039  1437   158  0.70  33.98   0.80     0.71      69373.23|
|  2:  4.7039 -  3.7531  1389   155  0.69  36.17   0.88     0.75     109991.55|
|  3:  3.7531 -  3.2844  1341   153  0.59  44.62   0.81     0.70     116493.97|
|  4:  3.2844 -  2.9867  1358   140  0.48  53.43   0.79     0.58     105256.10|
|  5:  2.9867 -  2.7741  1325   154  0.38  61.52   0.73     0.45      86432.57|
|  6:  2.7741 -  2.6114  1322   147  0.32  66.18   0.72     0.38      79399.30|
|  7:  2.6114 -  2.4813  1326   155  0.35  63.76   0.73     0.40      66624.37|
|  8:  2.4813 -  2.3737  1334   143  0.40  59.97   0.71     0.47      55605.25|
|  9:  2.3737 -  2.2827  1308   142  0.42  58.25   0.71     0.51      49502.86|
| 10:  2.2827 -  2.2041  1320   142  0.38  61.61   0.73     0.45      45909.18|
| 11:  2.2041 -  2.1354  1301   156  0.30  67.38   0.73     0.38      49056.27|
| 12:  2.1354 -  2.0745  1322   143  0.29  68.34   0.74     0.38      44743.10|
| 13:  2.0745 -  2.0201  1182   121  0.32  66.26   0.72     0.42      37941.03|
| 14:  2.0201 -  1.9709   365    50  0.46  55.38   0.78     0.46      25060.84|
|alpha:            min =        0.38 max =            0.75 mean =         0.51|
|beta:             min =    25060.84 max =       116493.97 mean =     70104.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.95 mean =        56.67|
|phase err.(test): min =        0.00 max =           89.93 mean =        57.01|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.173793             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.855   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.218924              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.594   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        7 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       26 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      171 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      700 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1506 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2608 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3891 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5043 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6569 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7669 |
|-----------------------------------------------------------------------------|
|-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 |       53.948 |
| 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 |       2.134 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.945)------------------------------------------|
|    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 = 11.945)------------------------------------------|
|    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: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4903   r_free= 0.4730   ksol= 0.00   Bsol= 0.00   scale= 0.757    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.288645                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4747   r_free= 0.4621   ksol= 0.33   Bsol= 10.03   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.26,7.78,12.23,0.00,0.00,0.00); trace/3= 9.09                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.279586                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.562914             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.920   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.179529              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.335   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4747      final r-factor (work) = 0.3956          |
| start r-factor (free) = 0.4621      final r-factor (free) = 0.4181          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 93.4259 = 12.56 * 0.50 * 6.2849 + 1.00 * 53.9477                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.0888 = 12.56 * 0.50 * 6.2002 + 1.00 * 0.1426                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3956      final r-factor (work) = 0.3528          |
| start r-factor (free) = 0.4181      final r-factor (free) = 0.4018          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3277 = 1.18 * 1.00 * 6.2002 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2286 = 1.18 * 1.00 * 6.1145 + 1.00 * 0.0163                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.945)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.69   13.71    None  None   None       |
|    all(noH): 2823   0      0.00    74.69   13.71    None  None   None       |
|    Sol.    : 438    0      0.00    74.69   26.26    None  None   None       |
|    Mac.    : 2385   0      0.00    62.60   11.40    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.469: 1048   |   5:    37.345 -  44.814:   79        |
|      1:     7.469 -  14.938:  755   |   6:    44.814 -  52.283:   46        |
|      2:    14.938 -  22.407:  470   |   7:    52.283 -  59.752:   20        |
|      3:    22.407 -  29.876:  252   |   8:    59.752 -  67.221:    7        |
|      4:    29.876 -  37.345:  143   |   9:    67.221 -  74.690:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3528 r_free = 0.4018             target_work(ml) = 6.094         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3525 r_free = 0.4029             target_work(ml) = 6.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3525   r_free= 0.4029   ksol= 0.33   Bsol= 10.03   scale= 1.112   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.26,7.78,12.23,0.00,0.00,0.00); trace/3= 9.09                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.093874                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3489   r_free= 0.3988   ksol= 0.32   Bsol= 43.06   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.08,3.80,7.98,0.00,0.00,0.00); trace/3= 4.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.094183                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.622993              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.703   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.518495              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.609  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3489      final r-factor (work) = 0.2739          |
| start r-factor (free) = 0.3988      final r-factor (free) = 0.3278          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.3240 = 5.62 * 0.50 * 6.1111 + 1.00 * 0.1426                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.9262 = 5.62 * 0.50 * 5.9917 + 1.00 * 0.0804                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2739      final r-factor (work) = 0.2552          |
| start r-factor (free) = 0.3278      final r-factor (free) = 0.3109          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1232 = 0.52 * 1.00 * 5.9917 + 1.00 * 0.0165                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0558 = 0.52 * 1.00 * 5.8682 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.945)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.00   13.92    None  None   None       |
|    all(noH): 2823   0      0.00    74.00   13.92    None  None   None       |
|    Sol.    : 438    0      0.00    74.00   32.04    None  None   None       |
|    Mac.    : 2385   0      0.00    67.74   10.59    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 -   7.400: 1077   |   5:    36.999 -  44.399:  111        |
|      1:     7.400 -  14.800:  812   |   6:    44.399 -  51.799:   63        |
|      2:    14.800 -  22.199:  383   |   7:    51.799 -  59.198:   27        |
|      3:    22.199 -  29.599:  217   |   8:    59.198 -  66.598:   15        |
|      4:    29.599 -  36.999:  114   |   9:    66.598 -  73.998:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2552 r_free = 0.3109             target_work(ml) = 5.848         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2549 r_free = 0.3108             target_work(ml) = 5.848         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2549   r_free= 0.3108   ksol= 0.32   Bsol= 43.06   scale= 1.054   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.08,3.80,7.98,0.00,0.00,0.00); trace/3= 4.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.847990                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2532   r_free= 0.3103   ksol= 0.33   Bsol= 59.04   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.29,2.37,5.20,0.00,0.00,0.00); trace/3= 2.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.849504                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.908341              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.998  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.293449              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 107.420  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2532      final r-factor (work) = 0.1789          |
| start r-factor (free) = 0.3103      final r-factor (free) = 0.2347          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.3621 = 6.91 * 0.50 * 5.8717 + 1.00 * 0.0803                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.8096 = 6.91 * 0.50 * 5.7103 + 1.00 * 0.0851                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1789      final r-factor (work) = 0.1603          |
| start r-factor (free) = 0.2347      final r-factor (free) = 0.2122          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6883 = 0.29 * 1.00 * 5.7103 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8050 = 0.29 * 1.00 * 5.4976 + 1.00 * 0.1917                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.945)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.12   13.57    None  None   None       |
|    all(noH): 2823   0      0.00    76.12   13.57    None  None   None       |
|    Sol.    : 438    0      2.62    76.12   35.38    None  None   None       |
|    Mac.    : 2385   0      0.00    72.14   9.57     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 -   7.612: 1232   |   5:    38.058 -  45.670:  116        |
|      1:     7.612 -  15.223:  868   |   6:    45.670 -  53.282:   76        |
|      2:    15.223 -  22.835:  245   |   7:    53.282 -  60.893:   28        |
|      3:    22.835 -  30.447:  123   |   8:    60.893 -  68.505:   14        |
|      4:    30.447 -  38.058:  115   |   9:    68.505 -  76.116:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1603 r_free = 0.2122             target_work(ml) = 5.445         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1601 r_free = 0.2121             target_work(ml) = 5.445         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1601   r_free= 0.2121   ksol= 0.33   Bsol= 59.04   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.29,2.37,5.20,0.00,0.00,0.00); trace/3= 2.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.444984                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1593   r_free= 0.2112   ksol= 0.33   Bsol= 58.56   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.48,1.45,3.51,0.00,0.00,0.00); trace/3= 1.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.444611                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.748009              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.351  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 12.196583             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.394   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1593      final r-factor (work) = 0.1357          |
| start r-factor (free) = 0.2112      final r-factor (free) = 0.1798          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6491 = 2.75 * 0.50 * 5.5051 + 1.00 * 0.0851                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4601 = 2.75 * 0.50 * 5.3813 + 1.00 * 0.0662                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1357      final r-factor (work) = 0.1279          |
| start r-factor (free) = 0.1798      final r-factor (free) = 0.1766          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 65.6465 = 12.20 * 1.00 * 5.3813 + 1.00 * 0.0133                             |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 64.3789 = 12.20 * 1.00 * 5.2759 + 1.00 * 0.0312                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.945)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.58  14.57    None  None   None       |
|    all(noH): 2823   0      0.00    101.58  14.57    None  None   None       |
|    Sol.    : 438    0      1.46    101.58  41.40    None  None   None       |
|    Mac.    : 2385   0      0.00    86.62   9.64     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 -  10.158: 1669   |   5:    50.788 -  60.945:   92        |
|      1:    10.158 -  20.315:  602   |   6:    60.945 -  71.103:   49        |
|      2:    20.315 -  30.473:  164   |   7:    71.103 -  81.260:   28        |
|      3:    30.473 -  40.630:  107   |   8:    81.260 -  91.418:   11        |
|      4:    40.630 -  50.788:   99   |   9:    91.418 - 101.575:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1279 r_free = 0.1766             target_work(ml) = 5.269         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1278 r_free = 0.1766             target_work(ml) = 5.269         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1278   r_free= 0.1766   ksol= 0.33   Bsol= 58.56   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.48,1.45,3.51,0.00,0.00,0.00); trace/3= 1.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.268984                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1277   r_free= 0.1772   ksol= 0.32   Bsol= 58.56   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.57,1.53,3.32,0.00,0.00,0.00); trace/3= 1.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.268687                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.952478              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.320  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.110222              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.002   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1277      final r-factor (work) = 0.1228          |
| start r-factor (free) = 0.1772      final r-factor (free) = 0.1719          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2160 = 1.95 * 0.50 * 5.2751 + 1.00 * 0.0662                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1876 = 1.95 * 0.50 * 5.2518 + 1.00 * 0.0606                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1228      final r-factor (work) = 0.1217          |
| start r-factor (free) = 0.1719      final r-factor (free) = 0.1715          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.6034 = 4.11 * 1.00 * 5.2518 + 1.00 * 0.0174                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.5322 = 4.11 * 1.00 * 5.2348 + 1.00 * 0.0158                              |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.945)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.02  14.35    None  None   None       |
|    all(noH): 2823   0      0.00    104.02  14.35    None  None   None       |
|    Sol.    : 438    0      1.61    104.02  40.88    None  None   None       |
|    Mac.    : 2385   0      0.00    91.27   9.48     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.402: 1751   |   5:    52.008 -  62.410:   86        |
|      1:    10.402 -  20.803:  535   |   6:    62.410 -  72.812:   39        |
|      2:    20.803 -  31.205:  172   |   7:    72.812 -  83.213:   25        |
|      3:    31.205 -  41.607:  105   |   8:    83.213 -  93.615:   11        |
|      4:    41.607 -  52.008:   97   |   9:    93.615 - 104.017:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1217 r_free = 0.1715             target_work(ml) = 5.235         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1217 r_free = 0.1715             target_work(ml) = 5.235         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1217   r_free= 0.1715   ksol= 0.32   Bsol= 58.56   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.57,1.53,3.32,0.00,0.00,0.00); trace/3= 1.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.234597                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9520 -  4.7039 0.99   1437  158 0.0986 0.1352      5.4191      5.5882|
|  2:  4.7039 -  3.7531 0.99   1389  155 0.0872 0.1153      5.4727      5.6951|
|  3:  3.7531 -  3.2844 0.99   1341  153 0.1149 0.1611      5.5432      5.8719|
|  4:  3.2844 -  2.9867 0.99   1358  140 0.1333 0.1764       5.509      5.6963|
|  5:  2.9867 -  2.7741 0.99   1325  154 0.1449 0.1713      5.4131      5.5797|
|  6:  2.7741 -  2.6114 0.98   1322  147 0.1370 0.2284      5.3026       5.625|
|  7:  2.6114 -  2.4813 0.99   1326  155 0.1394 0.1763      5.2654      5.3847|
|  8:  2.4813 -  2.3737 0.98   1334  143 0.1293 0.1832      5.1747      5.3996|
|  9:  2.3737 -  2.2827 0.98   1308  142 0.1294 0.2052      5.1153      5.4591|
| 10:  2.2827 -  2.2041 0.98   1320  142 0.1255 0.1909      5.0443      5.2679|
| 11:  2.2041 -  2.1354 0.99   1301  156 0.1284 0.2024      5.0194      5.3677|
| 12:  2.1354 -  2.0745 0.98   1322  143 0.1275 0.1770       4.979      5.1895|
| 13:  2.0745 -  2.0201 0.89   1182  121 0.1195 0.1842        4.85      5.0699|
| 14:  2.0201 -  1.9709 0.28    365   50 0.0991 0.1795      4.7142      4.9775|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9520 -  4.7039  1437   158  0.93   9.99   0.97     0.94       8296.14|
|  2:  4.7039 -  3.7531  1389   155  0.95   8.75   1.01     0.99      10079.60|
|  3:  3.7531 -  3.2844  1341   153  0.93  12.48   1.03     1.02      11919.51|
|  4:  3.2844 -  2.9867  1358   140  0.91  14.82   1.01     1.00      11331.47|
|  5:  2.9867 -  2.7741  1325   154  0.88  17.87   1.00     0.97      10223.38|
|  6:  2.7741 -  2.6114  1322   147  0.88  18.57   0.97     0.93       8637.71|
|  7:  2.6114 -  2.4813  1326   155  0.88  17.94   0.98     0.93       7670.79|
|  8:  2.4813 -  2.3737  1334   143  0.89  17.77   0.99     0.96       6862.68|
|  9:  2.3737 -  2.2827  1308   142  0.89  17.94   0.99     0.95       6063.17|
| 10:  2.2827 -  2.2041  1320   142  0.89  17.74   0.98     0.94       5397.99|
| 11:  2.2041 -  2.1354  1301   156  0.88  18.71   0.98     0.93       5338.15|
| 12:  2.1354 -  2.0745  1322   143  0.88  18.51   0.99     0.98       4996.62|
| 13:  2.0745 -  2.0201  1182   121  0.89  18.02   0.97     0.94       3933.49|
| 14:  2.0201 -  1.9709   365    50  0.91  14.43   0.96     0.92       2833.18|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2833.18 max =        11919.51 mean =      7707.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.96|
|phase err.(test): min =        0.00 max =           89.92 mean =        15.46|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1215   r_free= 0.1713   ksol= 0.33   Bsol= 62.23   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.18,-0.27,1.44,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.234924                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1215   r_free= 0.1713   ksol= 0.33   Bsol= 62.23   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.18,-0.27,1.44,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.234924                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9520 -  4.7039 0.99   1437  158 0.0988 0.1354      5.4208      5.5909|
|  2:  4.7039 -  3.7531 0.99   1389  155 0.0873 0.1155      5.4742      5.6959|
|  3:  3.7531 -  3.2844 0.99   1341  153 0.1149 0.1613      5.5436      5.8725|
|  4:  3.2844 -  2.9867 0.99   1358  140 0.1332 0.1764      5.5087      5.6964|
|  5:  2.9867 -  2.7741 0.99   1325  154 0.1449 0.1711      5.4127      5.5786|
|  6:  2.7741 -  2.6114 0.98   1322  147 0.1369 0.2283      5.3024      5.6252|
|  7:  2.6114 -  2.4813 0.99   1326  155 0.1394 0.1762      5.2654      5.3847|
|  8:  2.4813 -  2.3737 0.98   1334  143 0.1292 0.1834      5.1753      5.4002|
|  9:  2.3737 -  2.2827 0.98   1308  142 0.1294 0.2053      5.1156      5.4595|
| 10:  2.2827 -  2.2041 0.98   1320  142 0.1255 0.1908      5.0446      5.2675|
| 11:  2.2041 -  2.1354 0.99   1301  156 0.1285 0.2022      5.0193      5.3672|
| 12:  2.1354 -  2.0745 0.98   1322  143 0.1275 0.1770      4.9791      5.1896|
| 13:  2.0745 -  2.0201 0.89   1182  121 0.1195 0.1843        4.85      5.0699|
| 14:  2.0201 -  1.9709 0.28    365   50 0.0990 0.1793      4.7148      4.9773|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9520 -  4.7039  1437   158  0.93  10.03   0.97     0.94       8327.19|
|  2:  4.7039 -  3.7531  1389   155  0.95   8.77   1.02     1.00      10109.07|
|  3:  3.7531 -  3.2844  1341   153  0.93  12.50   1.03     1.03      11944.83|
|  4:  3.2844 -  2.9867  1358   140  0.91  14.83   1.02     1.00      11331.72|
|  5:  2.9867 -  2.7741  1325   154  0.88  17.87   1.01     0.98      10220.41|
|  6:  2.7741 -  2.6114  1322   147  0.88  18.57   0.98     0.94       8632.33|
|  7:  2.6114 -  2.4813  1326   155  0.88  17.95   0.99     0.94       7672.68|
|  8:  2.4813 -  2.3737  1334   143  0.89  17.79   1.00     0.97       6871.80|
|  9:  2.3737 -  2.2827  1308   142  0.89  17.95   1.00     0.96       6067.36|
| 10:  2.2827 -  2.2041  1320   142  0.89  17.75   0.99     0.95       5397.73|
| 11:  2.2041 -  2.1354  1301   156  0.88  18.70   0.99     0.94       5330.84|
| 12:  2.1354 -  2.0745  1322   143  0.88  18.52   1.01     0.99       4998.05|
| 13:  2.0745 -  2.0201  1182   121  0.89  18.02   0.98     0.95       3931.90|
| 14:  2.0201 -  1.9709   365    50  0.91  14.43   0.98     0.94       2830.74|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     2830.74 max =        11944.83 mean =      7713.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.97|
|phase err.(test): min =        0.00 max =           89.86 mean =        15.47|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.945)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.07    106.08  16.42    None  None   None       |
|    all(noH): 2823   0      2.07    106.08  16.42    None  None   None       |
|    Sol.    : 438    0      3.67    106.08  42.95    None  None   None       |
|    Mac.    : 2385   0      2.07    93.34   11.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.068 -  12.469: 1751   |   5:    54.076 -  64.478:   86        |
|      1:    12.469 -  22.871:  535   |   6:    64.478 -  74.879:   39        |
|      2:    22.871 -  33.273:  172   |   7:    74.879 -  85.281:   25        |
|      3:    33.273 -  43.674:  105   |   8:    85.281 -  95.683:   11        |
|      4:    43.674 -  54.076:   97   |   9:    95.683 - 106.084:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 313         
Filter by distance & map next to the model:
   mapped sites are within: 0.322 - 5.574
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 304 from: 313
   mapped sites are within: 0.716 - 5.574

peak=   10.421 closest distance to " CB  VAL A 230 " =    1.441
peak=    6.840 closest distance to " CD1AILE A 234 " =    1.342
peak=    6.069 closest distance to " CD2 LEU A   5 " =    1.162
peak=    5.324 closest distance to " CG  PRO A  54 " =    1.436
peak=    5.212 closest distance to " NE2 GLN A  11 " =    1.060
peak=    5.205 closest distance to " CB  VAL A 296 " =    1.049
peak=    5.142 closest distance to " CG  LEU A   5 " =    1.245
peak=    5.140 closest distance to " CB  GLN A 223 " =    1.513
peak=    5.075 closest distance to " O   HOH Z 248 " =    1.279
peak=    5.039 closest distance to " CG  LEU A 228 " =    1.261
peak=    5.016 closest distance to " O   HOH Z  76 " =    1.342
peak=    5.014 closest distance to " NH2 ARG A  56 " =    2.091
peak=    5.007 closest distance to " CG1 VAL A 296 " =    1.181
peak=    4.926 closest distance to " CG  PRO A 280 " =    0.959
peak=    4.882 closest distance to " CG2 VAL A 296 " =    1.053
peak=    4.742 closest distance to " O   HOH Z 232 " =    2.337
peak=    4.732 closest distance to " O   HOH Z 142 " =    1.728
peak=    4.720 closest distance to " CZ  PHE A 218 " =    1.128
peak=    4.685 closest distance to " CB  ARG A 275 " =    1.013
peak=    4.535 closest distance to " O   HOH Z 128 " =    1.254
peak=    4.492 closest distance to " O   HOH Z 188 " =    1.389
peak=    4.491 closest distance to " CB  ASN A 148 " =    1.414
peak=    4.465 closest distance to " CD2 LEU A 228 " =    1.251
peak=    4.423 closest distance to " NH2AARG A 145 " =    1.152
peak=    4.398 closest distance to " O   HOH Z 403 " =    1.572
peak=    4.384 closest distance to " O   HOH Z 126 " =    1.614
peak=    4.376 closest distance to " CB  ASN A 142 " =    1.218
peak=    4.363 closest distance to " O   HOH Z 251 " =    1.734
peak=    4.357 closest distance to " O   HOH Z 425 " =    1.543
peak=    4.345 closest distance to " CG  PRO A 243 " =    1.148
peak=    4.304 closest distance to " O   HOH Z 402 " =    1.404
peak=    4.290 closest distance to " CD2 TRP A 179 " =    1.357
peak=    4.286 closest distance to " CE  LYS A  76 " =    0.943
peak=    4.280 closest distance to " O   HOH Z 193 " =    1.728
peak=    4.272 closest distance to " O   HOH Z 313 " =    2.080
peak=    4.239 closest distance to " CB  ARG A  79 " =    1.442
peak=    4.231 closest distance to " CG  GLN A  58 " =    0.982
peak=    4.212 closest distance to " CA  TYR A  30 " =    0.956
peak=    4.209 closest distance to " CB  PRO A  54 " =    0.944
peak=    4.201 closest distance to " O   PRO A 198 " =    1.570
peak=    4.170 closest distance to " CZ3 TRP A 266 " =    1.102
peak=    4.167 closest distance to " CB  VAL A 230 " =    1.215
peak=    4.155 closest distance to " CB  ARG A 190 " =    1.730
peak=    4.145 closest distance to " O   HOH Z 427 " =    2.911
peak=    4.141 closest distance to " O   HOH Z 214 " =    1.241
peak=    4.140 closest distance to " CB  GLU A 277 " =    3.750
peak=    4.136 closest distance to " O   HOH Z 246 " =    1.219
peak=    4.113 closest distance to " O   HOH Z 238 " =    1.302
peak=    4.107 closest distance to " CG2 ILE A 234 " =    1.107
peak=    4.085 closest distance to " CA  ALA A  51 " =    1.025
peak=    4.048 closest distance to " O   HOH Z 411 " =    3.964
peak=    4.007 closest distance to " O   HOH Z 265 " =    2.058
peak=    4.006 closest distance to " O   HOH Z 142 " =    2.376
peak=    4.003 closest distance to " O   HOH Z 346 " =    1.532
peak=    4.003 closest distance to " O   HOH Z  85 " =    1.263
peak=    4.002 closest distance to " CB  ASP A 124 " =    0.943
peak=    3.999 closest distance to " ND2 ASN A 249 " =    0.946
peak=    3.996 closest distance to " O   HOH Z 369 " =    2.266
peak=    3.989 closest distance to " O   HOH Z 365 " =    2.442
peak=    3.988 closest distance to " O   HOH Z 207 " =    1.157
peak=    3.987 closest distance to " O   HOH Z  91 " =    2.441
peak=    3.978 closest distance to " CB  GLN A 183 " =    1.250
peak=    3.975 closest distance to " CG  ARG A  66 " =    2.451
peak=    3.970 closest distance to " CB  SER A  63 " =    1.187
peak=    3.961 closest distance to " OG ASER A 258 " =    3.096
peak=    3.960 closest distance to " CB  TRP A 266 " =    1.092
peak=    3.942 closest distance to " CG AARG A 275 " =    1.276
peak=    3.939 closest distance to " O   HOH Z 126 " =    1.900
peak=    3.937 closest distance to " CA  ARG A  36 " =    1.007
peak=    3.932 closest distance to " O   HOH Z 280 " =    2.937
peak=    3.930 closest distance to " O   HOH Z 107 " =    0.971
peak=    3.930 closest distance to " O   HOH Z  78 " =    1.705
peak=    3.928 closest distance to " CA  ALA A 160 " =    0.952
peak=    3.923 closest distance to " CG  PRO A 213 " =    1.174
peak=    3.908 closest distance to " CZ  PHE A  38 " =    1.167
peak=    3.898 closest distance to " CG  PRO A 198 " =    1.191
peak=    3.887 closest distance to " CB  ASN A  39 " =    0.904
peak=    3.881 closest distance to " O   HOH Z 303 " =    2.190
peak=    3.880 closest distance to " CB  VAL A 265 " =    1.230
peak=    3.874 closest distance to " CB  THR A  52 " =    0.818
peak=    3.872 closest distance to " CB  PRO A  90 " =    1.115
peak=    3.871 closest distance to " CD  ARG A 159 " =    0.748
peak=    3.869 closest distance to " O   HOH Z 365 " =    2.637
peak=    3.867 closest distance to " O   HOH Z 188 " =    2.559
peak=    3.862 closest distance to " CB  SER A  26 " =    1.829
peak=    3.854 closest distance to " CD  ARG A 269 " =    1.020
peak=    3.853 closest distance to " O   HOH Z 422 " =    2.661
peak=    3.842 closest distance to " O   HOH Z 258 " =    1.241
peak=    3.832 closest distance to " CD  LYS A 166 " =    1.393
peak=    3.817 closest distance to " CG2AVAL A 121 " =    2.235
peak=    3.817 closest distance to " O  BHOH Z 338 " =    2.199
peak=    3.815 closest distance to " O   ASP A 124 " =    1.194
peak=    3.803 closest distance to " O   HOH Z 359 " =    1.875
peak=    3.799 closest distance to " O   HOH Z 287 " =    1.696
peak=    3.796 closest distance to " CG  PHE A 204 " =    0.899
peak=    3.782 closest distance to " CB  TRP A 179 " =    1.482
peak=    3.780 closest distance to " O   HOH Z 406 " =    1.564
peak=    3.768 closest distance to " CD1 ILE A 199 " =    1.174
peak=    3.763 closest distance to " O   HOH Z  63 " =    1.854
peak=    3.759 closest distance to " O   HOH Z 329 " =    4.133
peak=    3.753 closest distance to " CB  SER A 273 " =    0.935
peak=    3.741 closest distance to " O   HOH Z 162 " =    1.611
peak=    3.740 closest distance to " O   HOH Z 290 " =    1.052
peak=    3.737 closest distance to " CA  ILE A 234 " =    1.024
peak=    3.726 closest distance to " CB  TYR A 169 " =    0.762
peak=    3.726 closest distance to " O   HOH Z 368 " =    3.442
peak=    3.725 closest distance to " O   HOH Z 258 " =    1.951
peak=    3.707 closest distance to " CA  ARG A 195 " =    1.208
peak=    3.698 closest distance to " O   HOH Z 353 " =    2.672
peak=    3.696 closest distance to " CA  ASN A 217 " =    1.070
peak=    3.695 closest distance to " CG2 VAL A 257 " =    0.716
peak=    3.691 closest distance to " NH1AARG A 145 " =    1.295
peak=    3.677 closest distance to " O   HOH Z 236 " =    1.583
peak=    3.675 closest distance to " NZ  LYS A 117 " =    2.852
peak=    3.670 closest distance to " O   HOH Z  59 " =    2.165
peak=    3.670 closest distance to " O   HOH Z 117 " =    1.017
peak=    3.667 closest distance to " CB BVAL A  41 " =    1.295
peak=    3.665 closest distance to " O   HOH Z 272 " =    1.833
peak=    3.662 closest distance to " O   HOH Z 214 " =    3.154
peak=    3.655 closest distance to " CD  LYS A  76 " =    1.920
peak=    3.640 closest distance to " O   HOH Z 371 " =    2.748
peak=    3.639 closest distance to " CB  GLU A 152 " =    1.109
peak=    3.637 closest distance to " O   HOH Z 337 " =    1.865
peak=    3.630 closest distance to " CB  ASN A 110 " =    1.158
peak=    3.627 closest distance to " CB  LYS A 117 " =    1.200
peak=    3.626 closest distance to " CA  ALA A 295 " =    1.022
peak=    3.621 closest distance to " OG BSER A 164 " =    2.265
peak=    3.616 closest distance to " CD2 LEU A 297 " =    0.856
peak=    3.613 closest distance to " O   HOH Z 234 " =    3.555
peak=    3.609 closest distance to " CB  ASP A 298 " =    1.200
peak=    3.607 closest distance to " O   HOH Z 227 " =    1.439
peak=    3.607 closest distance to " O   HOH Z 130 " =    2.814
peak=    3.591 closest distance to " O   HOH Z   4 " =    1.519
peak=    3.586 closest distance to " O   HOH Z   3 " =    1.901
peak=    3.585 closest distance to " CA  TYR A 116 " =    1.473
peak=    3.577 closest distance to " CA  VAL A 125 " =    1.142
peak=    3.571 closest distance to " O   HOH Z 124 " =    1.211
peak=    3.570 closest distance to " CB  ALA A 248 " =    1.349
peak=    3.568 closest distance to " O   HOH Z 200 " =    2.227
peak=    3.555 closest distance to " O   HOH Z 298 " =    1.789
peak=    3.554 closest distance to " CB  VAL A 202 " =    1.567
peak=    3.552 closest distance to " CB  THR A 235 " =    1.435
peak=    3.543 closest distance to " O   HOH Z 154 " =    1.586
peak=    3.540 closest distance to " O   HOH Z  80 " =    1.989
peak=    3.539 closest distance to " OG  SER A 276 " =    1.389
peak=    3.528 closest distance to " CB  THR A  31 " =    1.443
peak=    3.527 closest distance to " CE1 TYR A 186 " =    1.307
peak=    3.522 closest distance to " CB  ALA A 114 " =    0.770
peak=    3.520 closest distance to " O   HOH Z  92 " =    1.868
peak=    3.520 closest distance to " CB  ASP A 191 " =    1.296
peak=    3.519 closest distance to " N   ASN A  39 " =    1.281
peak=    3.518 closest distance to " CD1 LEU A  96 " =    0.752
peak=    3.506 closest distance to " O   HOH Z   9 " =    1.094
peak=    3.501 closest distance to " CG AARG A 102 " =    1.183
peak=    3.497 closest distance to " O   ASN A  74 " =    1.311
peak=    3.495 closest distance to " CG2 ILE A  20 " =    1.488
peak=    3.493 closest distance to " O   HOH Z 193 " =    1.657
peak=    3.492 closest distance to " CB  GLN A  89 " =    1.221
peak=    3.487 closest distance to " O   THR A 182 " =    1.413
peak=    3.470 closest distance to " O   HOH Z 203 " =    1.356
peak=    3.461 closest distance to " CG  MET A 185 " =    1.275
peak=    3.459 closest distance to " CB  PRO A 198 " =    1.165
peak=    3.457 closest distance to " CB  SER A   3 " =    1.345
peak=    3.457 closest distance to " O   HOH Z 193 " =    1.570
peak=    3.456 closest distance to " O   HOH Z 209 " =    2.261
peak=    3.455 closest distance to " O   HOH Z 423 " =    1.837
peak=    3.455 closest distance to " OE2 GLU A  53 " =    1.931
peak=    3.447 closest distance to " O   HOH Z  43 " =    2.166
peak=    3.442 closest distance to " CG  GLU A  37 " =    0.932
peak=    3.442 closest distance to " CG2 ILE A 120 " =    1.434
peak=    3.440 closest distance to " O   HOH Z 394 " =    1.454
peak=    3.438 closest distance to " CE  LYS A  48 " =    1.153
peak=    3.436 closest distance to " O   HOH Z  40 " =    1.742
peak=    3.433 closest distance to " O   HOH Z 383 " =    1.850
peak=    3.431 closest distance to " CA  ALA A 158 " =    1.382
peak=    3.428 closest distance to " O   HOH Z 438 " =    2.700
peak=    3.426 closest distance to " N   ASP A 162 " =    1.259
peak=    3.426 closest distance to " NZ  LYS A  48 " =    1.087
peak=    3.425 closest distance to " O   ALA A 165 " =    1.491
peak=    3.423 closest distance to " CA  MET A 105 " =    1.094
peak=    3.421 closest distance to " CG1 ILE A  20 " =    1.227
peak=    3.413 closest distance to " N   PHE A 130 " =    1.294
peak=    3.411 closest distance to " O   HOH Z 133 " =    2.748
peak=    3.410 closest distance to " CG  LEU A 167 " =    1.207
peak=    3.409 closest distance to " CA  ASP A 162 " =    0.991
peak=    3.409 closest distance to " O   HOH Z 112 " =    0.881
peak=    3.406 closest distance to " CG1 VAL A 153 " =    0.973
peak=    3.403 closest distance to " O   HOH Z  83 " =    1.475
peak=    3.399 closest distance to " CD1 ILE A  33 " =    1.682
peak=    3.398 closest distance to " CG  ARG A 138 " =    1.326
peak=    3.397 closest distance to " O   HOH Z 180 " =    2.090
peak=    3.397 closest distance to " CB  PHE A 204 " =    1.051
peak=    3.397 closest distance to " NE2 HIS A 207 " =    1.062
peak=    3.392 closest distance to " O   THR A 220 " =    1.268
peak=    3.392 closest distance to " O   HOH Z 410 " =    3.015
peak=    3.390 closest distance to " CB  ARG A 138 " =    0.795
peak=    3.385 closest distance to " CB  ASN A 173 " =    1.021
peak=    3.378 closest distance to " CA  ARG A 102 " =    1.144
peak=    3.377 closest distance to " CG2 VAL A 197 " =    1.027
peak=    3.377 closest distance to " O   HOH Z 357 " =    2.150
peak=    3.374 closest distance to " CA  ALA A 291 " =    0.870
peak=    3.366 closest distance to " CB  ASP A 140 " =    1.266
peak=    3.366 closest distance to " O   HOH Z  92 " =    0.949
peak=    3.364 closest distance to " O   HOH Z 263 " =    1.721
peak=    3.362 closest distance to " CE3 TRP A 150 " =    1.186
peak=    3.359 closest distance to " O   HOH Z  35 " =    2.380
peak=    3.356 closest distance to " O   HOH Z 299 " =    4.333
peak=    3.353 closest distance to " ND2 ASN A 187 " =    1.713
peak=    3.352 closest distance to " NE2 GLN A  77 " =    3.203
peak=    3.337 closest distance to " O   HOH Z  49 " =    1.012
peak=    3.330 closest distance to " O   HOH Z 361 " =    2.623
peak=    3.326 closest distance to " CD  LYS A 119 " =    1.886
peak=    3.325 closest distance to " O   HOH Z 361 " =    3.716
peak=    3.324 closest distance to " CG  GLN A  11 " =    1.809
peak=    3.322 closest distance to " O   HOH Z 325 " =    2.076
peak=    3.321 closest distance to " CB  ARG A 156 " =    1.269
peak=    3.321 closest distance to " O   HOH Z  78 " =    1.992
peak=    3.317 closest distance to " CG1 VAL A 257 " =    1.323
peak=    3.317 closest distance to " CA  ILE A 106 " =    0.783
peak=    3.315 closest distance to " CA  LEU A 282 " =    1.230
peak=    3.312 closest distance to " NH2 ARG A  56 " =    1.116
peak=    3.310 closest distance to " CE  LYS A 119 " =    1.088
peak=    3.309 closest distance to " CB  ASN A 215 " =    1.199
peak=    3.294 closest distance to " O   HOH Z 293 " =    1.972
peak=    3.293 closest distance to " CB  ALA A   9 " =    1.625
peak=    3.284 closest distance to " O   HOH Z 172 " =    3.801
peak=    3.282 closest distance to " CA  ALA A 154 " =    1.076
peak=    3.281 closest distance to " CA  ALA A 129 " =    1.460
peak=    3.280 closest distance to " CA  THR A 221 " =    1.030
peak=    3.280 closest distance to " O   HOH Z 417 " =    3.303
peak=    3.278 closest distance to " CA  SER A  87 " =    0.980
peak=    3.277 closest distance to " O   HOH Z 199 " =    1.603
peak=    3.275 closest distance to " OD1 ASP A 231 " =    1.922
peak=    3.274 closest distance to " CB  GLU A 128 " =    1.064
peak=    3.264 closest distance to " CB  SER A  62 " =    0.961
peak=    3.263 closest distance to " ND2BASN A 224 " =    0.735
peak=    3.254 closest distance to " N   ASP A 231 " =    1.603
peak=    3.253 closest distance to " O   HOH Z 132 " =    2.628
peak=    3.250 closest distance to " CA  ASN A  74 " =    1.076
peak=    3.246 closest distance to " N   ALA A 256 " =    1.177
peak=    3.245 closest distance to " O   HOH Z 407 " =    2.364
peak=    3.245 closest distance to " CA  VAL A  41 " =    0.750
peak=    3.236 closest distance to " CB  ALA A 291 " =    0.802
peak=    3.235 closest distance to " O   HOH Z 305 " =    3.426
peak=    3.231 closest distance to " O   HOH Z  88 " =    3.456
peak=    3.229 closest distance to " O   HOH Z 368 " =    4.110
peak=    3.226 closest distance to " O   GLN A  88 " =    1.631
peak=    3.225 closest distance to " O   HOH Z 421 " =    2.969
peak=    3.225 closest distance to " CB  SER A 216 " =    0.998
peak=    3.222 closest distance to " O   HOH Z 372 " =    0.877
peak=    3.216 closest distance to " O   HOH Z 371 " =    1.254
peak=    3.215 closest distance to " O   HOH Z 162 " =    2.949
peak=    3.214 closest distance to " N   TYR A 247 " =    1.350
peak=    3.213 closest distance to " CD1 LEU A 101 " =    1.129
peak=    3.205 closest distance to " O   HOH Z 272 " =    2.375
peak=    3.205 closest distance to " CB  GLU A  46 " =    0.930
peak=    3.202 closest distance to " OD2 ASP A  50 " =    2.810
peak=    3.202 closest distance to " OG  SER A  62 " =    2.786
peak=    3.201 closest distance to " O   ALA A 158 " =    1.110
peak=    3.197 closest distance to " NH2AARG A 275 " =    3.437
peak=    3.197 closest distance to " CD2 LEU A  83 " =    1.399
peak=    3.190 closest distance to " C   VAL A 153 " =    1.133
peak=    3.184 closest distance to " OG BSER A 134 " =    2.913
peak=    3.183 closest distance to " O   HOH Z 189 " =    2.847
peak=    3.183 closest distance to " CA  LYS A 290 " =    1.234
peak=    3.176 closest distance to " N   HIS A 108 " =    1.855
peak=    3.176 closest distance to " O   HOH Z 394 " =    3.598
peak=    3.175 closest distance to " O   HOH Z 344 " =    2.977
peak=    3.169 closest distance to " O   HOH Z 158 " =    3.109
peak=    3.169 closest distance to " O   HOH Z   9 " =    1.896
peak=    3.164 closest distance to " O   HOH Z 163 " =    2.021
peak=    3.160 closest distance to " O   HOH Z 156 " =    3.097
peak=    3.156 closest distance to " O   HOH Z 430 " =    5.574
peak=    3.155 closest distance to " O   HOH Z 392 " =    2.741
peak=    3.144 closest distance to " O   HOH Z  80 " =    1.924
peak=    3.142 closest distance to " CA  ASP A 253 " =    1.540
peak=    3.138 closest distance to " CB  SER A 288 " =    1.557
peak=    3.136 closest distance to " CA  LYS A 117 " =    1.287
peak=    3.134 closest distance to " O   HOH Z  88 " =    2.990
peak=    3.128 closest distance to " CB  PRO A 243 " =    1.067
peak=    3.127 closest distance to " NH2BARG A 190 " =    1.729
peak=    3.125 closest distance to " O   HOH Z 420 " =    2.080
peak=    3.125 closest distance to " CA  ARG A 139 " =    1.145
peak=    3.119 closest distance to " O   HOH Z 345 " =    3.395
peak=    3.117 closest distance to " CG  LEU A 281 " =    1.020
peak=    3.111 closest distance to " CD  ARG A  66 " =    2.485
peak=    3.109 closest distance to " CB  ARG A 219 " =    1.103
peak=    3.108 closest distance to " O   LEU A 228 " =    1.796
peak=    3.106 closest distance to " CD2 TYR A 186 " =    1.082
peak=    3.105 closest distance to " O   HOH Z 151 " =    1.570
peak=    3.104 closest distance to " O   HOH Z 421 " =    2.327
peak=    3.103 closest distance to " O   HOH Z 285 " =    2.213
peak=    3.101 closest distance to " OG  SER A 245 " =    1.599
peak=    3.092 closest distance to " N   TYR A  15 " =    1.060
peak=    3.088 closest distance to " CB  SER A 212 " =    1.345
peak=    3.087 closest distance to " O   HOH Z 173 " =    2.212
peak=    3.082 closest distance to " O   HOH Z 213 " =    1.804
peak=    3.072 closest distance to " CA  GLU A 152 " =    0.790
peak=    3.071 closest distance to " CE1 HIS A 108 " =    1.173
peak=    3.064 closest distance to " CB  ASP A 132 " =    0.946
peak=    3.058 closest distance to " CG2 THR A 221 " =    1.352
peak=    3.053 closest distance to " O   HOH Z 371 " =    2.478
peak=    3.039 closest distance to " CB  HIS A 108 " =    0.836
peak=    3.026 closest distance to " OG BSER A 164 " =    2.527

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.658 - 5.703
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 206
   mapped sites are within: 0.705 - 5.703

peak=   -4.648 closest distance to " SG  CYS A 254 " =    3.305
peak=   -4.488 closest distance to " O   PRO A 198 " =    1.289
peak=   -4.487 closest distance to " CG  GLN A  58 " =    1.009
peak=   -4.416 closest distance to " C   HIS A 108 " =    1.162
peak=   -4.305 closest distance to " O   HOH Z 193 " =    0.705
peak=   -4.273 closest distance to " CG2BVAL A  41 " =    2.629
peak=   -4.185 closest distance to " CD2 TYR A 293 " =    1.922
peak=   -4.150 closest distance to " OG BSER A 134 " =    1.463
peak=   -4.106 closest distance to " OE1 GLN A 223 " =    2.460
peak=   -4.106 closest distance to " CB  PRO A 243 " =    2.816
peak=   -4.082 closest distance to " CG2 VAL A 230 " =    0.743
peak=   -4.025 closest distance to " O   HOH Z 211 " =    1.077
peak=   -3.990 closest distance to " CZ2 TRP A  92 " =    2.885
peak=   -3.990 closest distance to " OXT GLY A 302 " =    3.021
peak=   -3.988 closest distance to " O   PRO A 163 " =    2.188
peak=   -3.979 closest distance to " O   HOH Z  69 " =    1.841
peak=   -3.979 closest distance to " O   HOH Z 267 " =    5.703
peak=   -3.976 closest distance to " O   HOH Z 166 " =    1.884
peak=   -3.944 closest distance to " CD  ARG A 156 " =    2.083
peak=   -3.943 closest distance to " CD1 LEU A 101 " =    2.351
peak=   -3.939 closest distance to " O   HOH Z 214 " =    2.476
peak=   -3.922 closest distance to " O   HOH Z 131 " =    4.141
peak=   -3.904 closest distance to " CG1 VAL A 250 " =    2.715
peak=   -3.874 closest distance to " NE2 GLN A  88 " =    1.108
peak=   -3.837 closest distance to " O   HOH Z 394 " =    1.756
peak=   -3.836 closest distance to " N   THR A  52 " =    1.644
peak=   -3.825 closest distance to " O   HOH Z 216 " =    1.187
peak=   -3.823 closest distance to " CG2 VAL A 189 " =    2.069
peak=   -3.818 closest distance to " O   SER A 271 " =    2.029
peak=   -3.814 closest distance to " O   HOH Z 191 " =    5.696
peak=   -3.813 closest distance to " O   HOH Z 231 " =    2.225
peak=   -3.799 closest distance to " NE2 GLN A  11 " =    1.680
peak=   -3.790 closest distance to " CE3 TRP A 150 " =    2.238
peak=   -3.785 closest distance to " CB  HIS A  86 " =    1.179
peak=   -3.760 closest distance to " OG  SER A  97 " =    2.319
peak=   -3.755 closest distance to " CG  PRO A 243 " =    1.593
peak=   -3.750 closest distance to " CE2 TRP A  70 " =    2.194
peak=   -3.739 closest distance to " O   HOH Z 285 " =    2.050
peak=   -3.732 closest distance to " O   HOH Z 283 " =    2.551
peak=   -3.714 closest distance to " CE1 PHE A 192 " =    1.954
peak=   -3.713 closest distance to " O   ASN A 252 " =    1.399
peak=   -3.693 closest distance to " CD1 ILE A 199 " =    2.425
peak=   -3.693 closest distance to " CG2 ILE A  20 " =    2.756
peak=   -3.692 closest distance to " O   HOH Z 119 " =    2.114
peak=   -3.686 closest distance to " CG1 VAL A 112 " =    2.694
peak=   -3.684 closest distance to " CB  ALA A  43 " =    2.612
peak=   -3.653 closest distance to " CA  ASP A 298 " =    1.070
peak=   -3.649 closest distance to " O   HOH Z 133 " =    1.106
peak=   -3.643 closest distance to " ND2 ASN A  45 " =    1.223
peak=   -3.633 closest distance to " O   HOH Z 203 " =    1.239
peak=   -3.622 closest distance to " O   HOH Z 359 " =    2.785
peak=   -3.619 closest distance to " O   HOH Z 295 " =    1.545
peak=   -3.615 closest distance to " CG1 VAL A 296 " =    1.060
peak=   -3.613 closest distance to " CE BMET A  47 " =    1.266
peak=   -3.606 closest distance to " CE  MET A 105 " =    2.540
peak=   -3.606 closest distance to " O   HOH Z 196 " =    2.233
peak=   -3.587 closest distance to " CG2 VAL A 296 " =    1.265
peak=   -3.580 closest distance to " O   HOH Z 275 " =    1.775
peak=   -3.578 closest distance to " O   HOH Z 106 " =    1.732
peak=   -3.571 closest distance to " O   HOH Z 128 " =    2.394
peak=   -3.571 closest distance to " CE2 TYR A  30 " =    2.739
peak=   -3.569 closest distance to " O   HOH Z 107 " =    1.046
peak=   -3.565 closest distance to " CA  GLY A 241 " =    2.367
peak=   -3.557 closest distance to " CG  GLN A 103 " =    2.446
peak=   -3.541 closest distance to " O   HOH Z 348 " =    2.288
peak=   -3.538 closest distance to " O   HOH Z 351 " =    1.740
peak=   -3.533 closest distance to " CG2 THR A 178 " =    2.397
peak=   -3.532 closest distance to " O   HOH Z 431 " =    1.984
peak=   -3.531 closest distance to " O   ILE A 106 " =    1.828
peak=   -3.526 closest distance to " O   HOH Z 110 " =    1.409
peak=   -3.516 closest distance to " O   ALA A 227 " =    1.308
peak=   -3.497 closest distance to " CB  PHE A 192 " =    2.100
peak=   -3.484 closest distance to " O   HOH Z 128 " =    1.054
peak=   -3.477 closest distance to " O   HOH Z 102 " =    1.492
peak=   -3.473 closest distance to " O   SER A 210 " =    1.711
peak=   -3.468 closest distance to " O   HOH Z  64 " =    1.635
peak=   -3.466 closest distance to " NE  ARG A  66 " =    4.304
peak=   -3.460 closest distance to " O   HOH Z 100 " =    0.994
peak=   -3.459 closest distance to " ND2 ASN A  69 " =    1.957
peak=   -3.440 closest distance to " O   HOH Z 149 " =    1.830
peak=   -3.437 closest distance to " O   HOH Z 165 " =    1.965
peak=   -3.425 closest distance to " O   TYR A 186 " =    1.755
peak=   -3.424 closest distance to " CD  PRO A 243 " =    1.820
peak=   -3.424 closest distance to " CG  ARG A 269 " =    2.277
peak=   -3.422 closest distance to " O   HOH Z 236 " =    1.591
peak=   -3.422 closest distance to " CG  TRP A 266 " =    1.883
peak=   -3.417 closest distance to " O   HOH Z 265 " =    2.386
peak=   -3.415 closest distance to " CB  ALA A 248 " =    2.218
peak=   -3.413 closest distance to " O   HOH Z  91 " =    1.312
peak=   -3.412 closest distance to " CG1 VAL A 112 " =    2.713
peak=   -3.404 closest distance to " O   MET A  40 " =    2.916
peak=   -3.401 closest distance to " OH  TYR A 172 " =    1.885
peak=   -3.400 closest distance to " O   HOH Z 116 " =    1.563
peak=   -3.397 closest distance to " O   HOH Z 252 " =    3.662
peak=   -3.397 closest distance to " CZ3 TRP A 274 " =    2.252
peak=   -3.395 closest distance to " CZ  PHE A  38 " =    2.378
peak=   -3.393 closest distance to " O   HOH Z   6 " =    2.135
peak=   -3.390 closest distance to " O   HOH Z 429 " =    1.465
peak=   -3.387 closest distance to " O   HOH Z 423 " =    2.411
peak=   -3.381 closest distance to " O   HOH Z 210 " =    1.068
peak=   -3.376 closest distance to " O   HOH Z   6 " =    1.530
peak=   -3.372 closest distance to " ND2 ASN A 187 " =    1.591
peak=   -3.370 closest distance to " ND2 ASN A 249 " =    2.285
peak=   -3.368 closest distance to " O   HOH Z 198 " =    1.823
peak=   -3.367 closest distance to " CB  TRP A  85 " =    2.586
peak=   -3.367 closest distance to " O   HOH Z 154 " =    1.548
peak=   -3.366 closest distance to " CD  GLN A 223 " =    1.792
peak=   -3.364 closest distance to " N   SER A 276 " =    1.373
peak=   -3.363 closest distance to " O   HOH Z 109 " =    1.129
peak=   -3.357 closest distance to " O   HOH Z  68 " =    1.218
peak=   -3.356 closest distance to " O   HOH Z 185 " =    2.428
peak=   -3.352 closest distance to " O   HOH Z 377 " =    2.078
peak=   -3.352 closest distance to " CG1 VAL A 125 " =    1.877
peak=   -3.349 closest distance to " NE  ARG A  79 " =    1.202
peak=   -3.349 closest distance to " CB  ASN A  39 " =    2.374
peak=   -3.348 closest distance to " O   HOH Z 260 " =    1.812
peak=   -3.346 closest distance to " CA  GLY A 203 " =    2.475
peak=   -3.344 closest distance to " OD1 ASN A  39 " =    2.135
peak=   -3.339 closest distance to " O   TRP A  70 " =    1.637
peak=   -3.336 closest distance to " CG  GLU A 277 " =    1.268
peak=   -3.332 closest distance to " O   HOH Z 275 " =    1.595
peak=   -3.326 closest distance to " O   GLU A 152 " =    1.478
peak=   -3.321 closest distance to " CD  LYS A 289 " =    2.417
peak=   -3.318 closest distance to " O   HOH Z 351 " =    1.519
peak=   -3.316 closest distance to " CB  ALA A  10 " =    2.289
peak=   -3.309 closest distance to " CG  LEU A   5 " =    1.020
peak=   -3.306 closest distance to " CB  ALA A  51 " =    1.914
peak=   -3.303 closest distance to " O   GLY A  80 " =    2.704
peak=   -3.297 closest distance to " CG2AVAL A  72 " =    2.628
peak=   -3.295 closest distance to " CA  VAL A 296 " =    0.973
peak=   -3.290 closest distance to " O   PHE A 218 " =    1.360
peak=   -3.288 closest distance to " CD2 HIS A 207 " =    2.221
peak=   -3.284 closest distance to " C   ASN A 285 " =    2.218
peak=   -3.279 closest distance to " O   HOH Z  38 " =    1.804
peak=   -3.273 closest distance to " N   ALA A 226 " =    1.965
peak=   -3.270 closest distance to " CZ2 TRP A 274 " =    1.062
peak=   -3.269 closest distance to " O   HOH Z   9 " =    1.683
peak=   -3.260 closest distance to " O   GLY A 196 " =    1.150
peak=   -3.257 closest distance to " OG  SER A  63 " =    1.120
peak=   -3.257 closest distance to " O   HOH Z 357 " =    1.922
peak=   -3.255 closest distance to " OE1 GLN A  88 " =    1.063
peak=   -3.254 closest distance to " O   HOH Z  52 " =    1.735
peak=   -3.254 closest distance to " CE  LYS A  76 " =    0.854
peak=   -3.252 closest distance to " CA  ASN A 127 " =    1.134
peak=   -3.251 closest distance to " O   HOH Z 215 " =    1.814
peak=   -3.247 closest distance to " O   HOH Z 201 " =    2.170
peak=   -3.242 closest distance to " O   HOH Z 278 " =    1.202
peak=   -3.239 closest distance to " O   HOH Z 103 " =    1.856
peak=   -3.238 closest distance to " O   HOH Z 301 " =    2.498
peak=   -3.234 closest distance to " CB  ASN A  45 " =    2.119
peak=   -3.233 closest distance to " CD2 PHE A 225 " =    1.018
peak=   -3.229 closest distance to " O   HOH Z 111 " =    1.605
peak=   -3.228 closest distance to " O   ALA A  34 " =    2.613
peak=   -3.226 closest distance to " O   HOH Z 244 " =    2.039
peak=   -3.225 closest distance to " ND2 ASN A  39 " =    1.295
peak=   -3.225 closest distance to " O   HOH Z 139 " =    5.225
peak=   -3.221 closest distance to " O   HOH Z 105 " =    1.958
peak=   -3.221 closest distance to " O   HOH Z 136 " =    1.488
peak=   -3.214 closest distance to " CG2 VAL A 202 " =    2.722
peak=   -3.212 closest distance to " CB  ALA A 161 " =    2.446
peak=   -3.211 closest distance to " CB  GLN A  55 " =    1.239
peak=   -3.209 closest distance to " O   HOH Z 137 " =    1.781
peak=   -3.208 closest distance to " O   SER A 146 " =    1.351
peak=   -3.205 closest distance to " OXT GLY A 302 " =    3.414
peak=   -3.200 closest distance to " O   HOH Z  60 " =    1.676
peak=   -3.198 closest distance to " ND2BASN A 224 " =    1.876
peak=   -3.189 closest distance to " O   HOH Z  35 " =    2.459
peak=   -3.185 closest distance to " NH2 ARG A  66 " =    1.346
peak=   -3.176 closest distance to " O   HOH Z 429 " =    2.195
peak=   -3.174 closest distance to " CZ3 TRP A 179 " =    1.331
peak=   -3.173 closest distance to " O   HOH Z 162 " =    3.043
peak=   -3.169 closest distance to " O   ALA A 161 " =    1.827
peak=   -3.167 closest distance to " CA  HIS A 207 " =    1.278
peak=   -3.165 closest distance to " O   HOH Z 256 " =    2.333
peak=   -3.164 closest distance to " C   ALA A 158 " =    1.115
peak=   -3.164 closest distance to " CG1BVAL A  72 " =    2.397
peak=   -3.155 closest distance to " O   HOH Z  88 " =    1.822
peak=   -3.155 closest distance to " CA  GLY A 133 " =    2.304
peak=   -3.152 closest distance to " CG  LYS A 193 " =    2.707
peak=   -3.150 closest distance to " OD1 ASP A 200 " =    1.584
peak=   -3.149 closest distance to " CE3 TRP A  70 " =    1.747
peak=   -3.148 closest distance to " ND2 ASN A  45 " =    2.091
peak=   -3.144 closest distance to " NH2 ARG A 156 " =    2.977
peak=   -3.143 closest distance to " O   HOH Z 251 " =    4.969
peak=   -3.140 closest distance to " O   HOH Z 371 " =    2.487
peak=   -3.134 closest distance to " O   HOH Z 290 " =    1.124
peak=   -3.134 closest distance to " OG BSER A  99 " =    1.220
peak=   -3.120 closest distance to " CB  SER A 210 " =    1.052
peak=   -3.119 closest distance to " O   HOH Z  78 " =    1.891
peak=   -3.103 closest distance to " CD  GLU A 236 " =    1.174
peak=   -3.091 closest distance to " O   HOH Z 231 " =    2.074
peak=   -3.082 closest distance to " O   HOH Z 221 " =    1.507
peak=   -3.078 closest distance to " NH2AARG A 275 " =    4.900
peak=   -3.076 closest distance to " O   HOH Z 357 " =    2.167
peak=   -3.074 closest distance to " CZ  TYR A 169 " =    1.851
peak=   -3.073 closest distance to " O   HOH Z 426 " =    1.670
peak=   -3.070 closest distance to " CE1 TYR A 247 " =    2.627
peak=   -3.062 closest distance to " O   SER A 276 " =    1.756
peak=   -3.053 closest distance to " OD1 ASN A 173 " =    1.488
peak=   -3.047 closest distance to " O   HOH Z 407 " =    2.753
peak=   -3.039 closest distance to " OD2 ASP A  50 " =    2.264
peak=   -3.035 closest distance to " O   HOH Z 265 " =    1.907
peak=   -3.013 closest distance to " ND2 ASN A  45 " =    1.579
peak=   -3.011 closest distance to " CH2 TRP A 150 " =    1.176

================= 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    :  0.4853 0.4708   6.286350e+00   6.273636e+00
   1_bss:  0.4747 0.4621   6.279586e+00   6.266028e+00
   1_xyz:  0.3956 0.4181   6.172967e+00   6.207371e+00
   1_adp:  0.3528 0.4018   6.094457e+00   6.173615e+00
   1_occ:  0.3525 0.4029   6.093874e+00   6.175175e+00
   2_bss:  0.3489 0.3988   6.094183e+00   6.174525e+00
   2_xyz:  0.2739 0.3278   5.900366e+00   6.038050e+00
   2_adp:  0.2552 0.3109   5.848394e+00   6.004173e+00
   2_occ:  0.2549 0.3108   5.847990e+00   6.003860e+00
   3_bss:  0.2532 0.3103   5.849504e+00   6.005182e+00
   3_xyz:  0.1789 0.2347   5.546413e+00   5.753439e+00
   3_adp:  0.1603 0.2122   5.445433e+00   5.656521e+00
   3_occ:  0.1601 0.2121   5.444984e+00   5.656337e+00
   4_bss:  0.1593 0.2112   5.444611e+00   5.653395e+00
   4_xyz:  0.1357 0.1798   5.303491e+00   5.514589e+00
   4_adp:  0.1279 0.1766   5.269297e+00   5.496402e+00
   4_occ:  0.1278 0.1766   5.268984e+00   5.496247e+00
   5_bss:  0.1277 0.1772   5.268687e+00   5.497055e+00
   5_xyz:  0.1228 0.1719   5.239633e+00   5.475169e+00
   5_adp:  0.1217 0.1715   5.234819e+00   5.472061e+00
   5_occ:  0.1217 0.1715   5.234597e+00   5.471931e+00
   5_bss:  0.1215 0.1713   5.234924e+00   5.472205e+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:  0.330  10.033   7.261   7.781  12.228   0.000   0.000   0.000
   1_xyz:  0.330  10.033   7.261   7.781  12.228   0.000   0.000   0.000
   1_adp:  0.330  10.033   7.261   7.781  12.228   0.000   0.000   0.000
   1_occ:  0.330  10.033   7.261   7.781  12.228   0.000   0.000   0.000
   2_bss:  0.320  43.056   3.084   3.800   7.978   0.000   0.000   0.000
   2_xyz:  0.320  43.056   3.084   3.800   7.978   0.000   0.000   0.000
   2_adp:  0.320  43.056   3.084   3.800   7.978   0.000   0.000   0.000
   2_occ:  0.320  43.056   3.084   3.800   7.978   0.000   0.000   0.000
   3_bss:  0.334  59.036   1.291   2.368   5.202   0.000   0.000   0.000
   3_xyz:  0.334  59.036   1.291   2.368   5.202   0.000   0.000   0.000
   3_adp:  0.334  59.036   1.291   2.368   5.202   0.000   0.000   0.000
   3_occ:  0.334  59.036   1.291   2.368   5.202   0.000   0.000   0.000
   4_bss:  0.327  58.563   0.478   1.449   3.514   0.000   0.000   0.000
   4_xyz:  0.327  58.563   0.478   1.449   3.514   0.000   0.000   0.000
   4_adp:  0.327  58.563   0.478   1.449   3.514   0.000   0.000   0.000
   4_occ:  0.327  58.563   0.478   1.449   3.514   0.000   0.000   0.000
   5_bss:  0.324  58.563   0.573   1.526   3.317   0.000   0.000   0.000
   5_xyz:  0.324  58.563   0.573   1.526   3.317   0.000   0.000   0.000
   5_adp:  0.324  58.563   0.573   1.526   3.317   0.000   0.000   0.000
   5_occ:  0.324  58.563   0.573   1.526   3.317   0.000   0.000   0.000
   5_bss:  0.325  62.230  -1.177  -0.268   1.445   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.702 0.4365  0.5080    70101.754
   1_bss:  56.536 0.4374  0.6692    68833.312
   1_xyz:  47.955 0.5451  0.8098    51621.897
   1_adp:  44.254 0.5914  0.9277    46449.290
   1_occ:  44.358 0.5901  0.9239    46604.957
   2_bss:  43.939 0.5953  0.8090    46238.557
   2_xyz:  34.325 0.7090  0.9410    29410.642
   2_adp:  31.981 0.7362  0.9757    26534.596
   2_occ:  31.974 0.7362  0.9755    26513.745
   3_bss:  31.880 0.7374  0.9103    26542.256
   3_xyz:  23.143 0.8302  0.9865    14130.302
   3_adp:  20.373 0.8582  1.0004    11620.452
   3_occ:  20.373 0.8582  1.0005    11604.844
   4_bss:  20.257 0.8592  0.9616    11504.904
   4_xyz:  16.893 0.8905  0.9727     8456.030
   4_adp:  16.474 0.8944  0.9632     8154.734
   4_occ:  16.471 0.8944  0.9632     8156.016
   5_bss:  16.486 0.8943  0.9629     8173.893
   5_xyz:  15.973 0.8988  0.9671     7754.104
   5_adp:  15.915 0.8994  0.9592     7710.256
   5_occ:  15.909 0.8994  0.9592     7706.654
   5_bss:  15.918 0.8994  0.9681     7713.354
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3948e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3948e+01
   1_xyz:   1.702  0.013  0.106 18.237  0.007  4.110   1.4258e-01
   1_adp:   1.702  0.013  0.106 18.237  0.007  4.110   1.4258e-01
   1_occ:   1.702  0.013  0.106 18.237  0.007  4.110   1.4258e-01
   2_bss:   1.702  0.013  0.106 18.237  0.007  4.110   1.4258e-01
   2_xyz:   1.201  0.008  0.079 16.087  0.004  4.126   8.0438e-02
   2_adp:   1.201  0.008  0.079 16.087  0.004  4.126   8.0438e-02
   2_occ:   1.201  0.008  0.079 16.087  0.004  4.126   8.0438e-02
   3_bss:   1.201  0.008  0.079 16.087  0.004  4.126   8.0438e-02
   3_xyz:   1.218  0.010  0.087 16.046  0.004  4.133   8.5072e-02
   3_adp:   1.218  0.010  0.087 16.046  0.004  4.133   8.5072e-02
   3_occ:   1.218  0.010  0.087 16.046  0.004  4.133   8.5072e-02
   4_bss:   1.218  0.010  0.087 16.046  0.004  4.133   8.5072e-02
   4_xyz:   1.043  0.008  0.080 15.543  0.004  4.115   6.6204e-02
   4_adp:   1.043  0.008  0.080 15.543  0.004  4.115   6.6204e-02
   4_occ:   1.043  0.008  0.080 15.543  0.004  4.115   6.6204e-02
   5_bss:   1.043  0.008  0.080 15.543  0.004  4.115   6.6204e-02
   5_xyz:   1.006  0.007  0.078 15.239  0.003  4.119   6.0567e-02
   5_adp:   1.006  0.007  0.078 15.239  0.003  4.119   6.0567e-02
   5_occ:   1.006  0.007  0.078 15.239  0.003  4.119   6.0567e-02
   5_bss:   1.006  0.007  0.078 15.239  0.003  4.119   6.0567e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9910e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9910e+00
   1_xyz:  14.095  0.166  0.440 86.118  0.066  2.150   1.0341e-01
   1_adp:  14.095  0.166  0.440 86.118  0.066  2.150   1.0341e-01
   1_occ:  14.095  0.166  0.440 86.118  0.066  2.150   1.0341e-01
   2_bss:  14.095  0.166  0.440 86.118  0.066  2.150   1.0341e-01
   2_xyz:   7.638  0.081  0.253 84.211  0.032  2.237   5.7329e-02
   2_adp:   7.638  0.081  0.253 84.211  0.032  2.237   5.7329e-02
   2_occ:   7.638  0.081  0.253 84.211  0.032  2.237   5.7329e-02
   3_bss:   7.638  0.081  0.253 84.211  0.032  2.237   5.7329e-02
   3_xyz:   9.248  0.060  0.366 85.523  0.032  2.127   6.9937e-02
   3_adp:   9.248  0.060  0.366 85.523  0.032  2.127   6.9937e-02
   3_occ:   9.248  0.060  0.366 85.523  0.032  2.127   6.9937e-02
   4_bss:   9.248  0.060  0.366 85.523  0.032  2.127   6.9937e-02
   4_xyz:   6.495  0.044  0.351 83.547  0.037  2.271   6.3944e-02
   4_adp:   6.495  0.044  0.351 83.547  0.037  2.271   6.3944e-02
   4_occ:   6.495  0.044  0.351 83.547  0.037  2.271   6.3944e-02
   5_bss:   6.495  0.044  0.351 83.547  0.037  2.271   6.3944e-02
   5_xyz:   6.801  0.040  0.380 81.763  0.030  2.354   3.5889e-02
   5_adp:   6.801  0.040  0.380 81.763  0.030  2.354   3.5889e-02
   5_occ:   6.801  0.040  0.380 81.763  0.030  2.354   3.5889e-02
   5_bss:   6.801  0.040  0.380 81.763  0.030  2.354   3.5889e-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:  74.69   0.00  13.71  62.60   0.00  11.40  74.69   0.00  26.26
   1_occ:  74.69   0.00  13.71  62.60   0.00  11.40  74.69   0.00  26.26
   2_bss:  74.69   0.00  13.71  62.60   0.00  11.40  74.69   0.00  26.26
   2_xyz:  74.69   0.00  13.71  62.60   0.00  11.40  74.69   0.00  26.26
   2_adp:  74.00   0.00  13.92  67.74   0.00  10.59  74.00   0.00  32.04
   2_occ:  74.00   0.00  13.92  67.74   0.00  10.59  74.00   0.00  32.04
   3_bss:  74.00   0.00  13.92  67.74   0.00  10.59  74.00   0.00  32.04
   3_xyz:  74.00   0.00  13.92  67.74   0.00  10.59  74.00   0.00  32.04
   3_adp:  76.12   0.00  13.57  72.14   0.00   9.57  76.12   2.62  35.38
   3_occ:  76.12   0.00  13.57  72.14   0.00   9.57  76.12   2.62  35.38
   4_bss:  76.12   0.00  13.57  72.14   0.00   9.57  76.12   2.62  35.38
   4_xyz:  76.12   0.00  13.57  72.14   0.00   9.57  76.12   2.62  35.38
   4_adp: 101.58   0.00  14.57  86.62   0.00   9.64 101.58   1.46  41.40
   4_occ: 101.58   0.00  14.57  86.62   0.00   9.64 101.58   1.46  41.40
   5_bss: 101.58   0.00  14.57  86.62   0.00   9.64 101.58   1.46  41.40
   5_xyz: 101.58   0.00  14.57  86.62   0.00   9.64 101.58   1.46  41.40
   5_adp: 104.02   0.00  14.35  91.27   0.00   9.48 104.02   1.61  40.88
   5_occ: 104.02   0.00  14.35  91.27   0.00   9.48 104.02   1.61  40.88
   5_bss: 106.08   2.07  16.42  93.34   2.07  11.55 106.08   3.67  42.95
------------------------------------------------------------------------
 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:    1.286    0.025    0.411
   1_adp:    1.286    0.025    0.411
   1_occ:    1.286    0.025    0.411
   2_bss:    1.286    0.025    0.411
   2_xyz:    1.965    0.037    0.549
   2_adp:    1.965    0.037    0.549
   2_occ:    1.965    0.037    0.549
   3_bss:    1.965    0.037    0.549
   3_xyz:    1.782    0.037    0.677
   3_adp:    1.782    0.037    0.677
   3_occ:    1.782    0.037    0.677
   4_bss:    1.782    0.037    0.677
   4_xyz:    1.904    0.067    0.719
   4_adp:    1.904    0.067    0.719
   4_occ:    1.904    0.067    0.719
   5_bss:    1.904    0.067    0.719
   5_xyz:    2.030    0.027    0.733
   5_adp:    2.030    0.027    0.733
   5_occ:    2.030    0.027    0.733
   5_bss:    2.030    0.027    0.733
------------------------------------------------------------------------

CPU time actual refinement: 335.17


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_318/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_318/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_318/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_318/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_318/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 335.03 
  Macro-tasks:
    bulk solvent and scale       = 43.56  
    individual site refinement   = 133.29 
    weights calculation          = 32.29  
    collect and process          = 6.52   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 215.75 
  Micro-tasks:
    mask                            = 2.20   
    f_calc                          = 104.11 
    alpha_beta                      = 8.20   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 109.10 
    fmodel                         = 7.75   
    r_factors                      = 0.21   
    phase_errors                   = 11.24  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 244.19 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.733 micro seconds
Total CPU time: 5.81 minutes
from_scatterers_fft:    651 calls, 103.68 s
gradients_fft:          596 calls,  97.97 s

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

# Date 2008-01-16 Time 01:16:05 PST -0800 (1200474965.59 s)
Start R-work = 0.4853, R-free = 0.4708 (no bulk solvent and anisotropic scale)
Final R-work = 0.1392, R-free = 0.1866 (no bulk solvent and anisotropic scale)

Start R-work = 0.4747, R-free = 0.4621
Final R-work = 0.1215, R-free = 0.1713