# Date 2008-01-16 Time 01:52:46 PST -0800 (1200477166.36 s)
#phil __OFF__

Command line arguments: "../611.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 = 30585
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 611

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 45.7567, 86.822, 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: 3.38, per 1000 atoms: 1.20


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 45.7567, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0142 1.95335
Completeness in resolution range: 0.938081
Completeness with d_max=infinity: 0.935304

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0142
                             d_min =   1.9534

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 45.7567, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0142 1.95335
Completeness in resolution range: 0.938081
Completeness with d_max=infinity: 0.935304

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0146 -  4.1809 [2193/2218]  1972   221  10.1%
  bin  2:  4.1809 -  3.3304 [2110/2130]  1902   208   9.9%
  bin  3:  3.3304 -  2.9129 [2081/2100]  1873   208  10.0%
  bin  4:  2.9129 -  2.6482 [2059/2089]  1849   210  10.2%
  bin  5:  2.6482 -  2.4593 [2049/2068]  1852   197   9.6%
  bin  6:  2.4593 -  2.3148 [2044/2069]  1833   211  10.3%
  bin  7:  2.3148 -  2.1993 [2024/2052]  1820   204  10.1%
  bin  8:  2.1993 -  2.1038 [2029/2065]  1823   206  10.2%
  bin  9:  2.1038 -  2.0230 [2012/2054]  1817   195   9.7%
  bin 10:  2.0230 -  1.9534 [ 988/2037]   889    99  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_611/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:
        1.63 -     2.29: 28
        2.29 -     2.94: 1637
        2.94 -     3.59: 4562
        3.59 -     4.25: 9308
        4.25 -     4.90: 13044
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.631 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28574 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_611/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_611/model_refine_001.geo

CPU time processing inputs: 9.08


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 45.75675 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4886   r_free= 0.4838   ksol= 0.00   Bsol= 0.00   scale= 0.789    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.295772                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.6638 0.99   1420  157 0.4243 0.4186      6.6367      6.6858|
|  2:  4.6638 -  3.7203 0.99   1373  156 0.4223 0.3789      6.8419      6.7685|
|  3:  3.7203 -  3.2555 0.99   1345  144 0.4471 0.4243      6.6914      6.6566|
|  4:  3.2555 -  2.9603 0.99   1344  152 0.4789 0.4619      6.5502      6.5104|
|  5:  2.9603 -  2.7495 0.99   1328  150 0.5220 0.5254        6.37      6.3982|
|  6:  2.7495 -  2.5883 0.99   1312  145 0.5177 0.5511      6.2801       6.214|
|  7:  2.5883 -  2.4593 0.99   1326  140 0.5117 0.5280      6.2506      6.1932|
|  8:  2.4593 -  2.3526 0.98   1297  151 0.5311 0.4945      6.1709      6.1921|
|  9:  2.3526 -  2.2624 0.98   1308  143 0.5336 0.5573      6.1301      6.2036|
| 10:  2.2624 -  2.1846 1.00   1308  152 0.5299 0.5086      6.0942      6.0488|
| 11:  2.1846 -  2.1164 0.98   1303  140 0.4990 0.5067      6.0376      6.0397|
| 12:  2.1164 -  2.0561 0.98   1289  142 0.5152 0.5731      5.9454      5.9995|
| 13:  2.0561 -  2.0021 0.98   1268  141 0.5539 0.5497      5.8854      5.8013|
| 14:  2.0021 -  1.9534 0.31    409   46 0.5533 0.4455      5.8669       5.833|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0146 -  4.6638  1420   157  0.63  40.59   0.78     0.68      94501.84|
|  2:  4.6638 -  3.7203  1373   156  0.68  36.71   0.85     0.77     116897.95|
|  3:  3.7203 -  3.2555  1345   144  0.58  45.34   0.85     0.72     119541.59|
|  4:  3.2555 -  2.9603  1344   152  0.49  53.05   0.78     0.58     107014.79|
|  5:  2.9603 -  2.7495  1328   150  0.36  63.05   0.73     0.45      90615.34|
|  6:  2.7495 -  2.5883  1312   145  0.32  65.82   0.71     0.38      79102.82|
|  7:  2.5883 -  2.4593  1326   140  0.28  68.99   0.76     0.33      73384.70|
|  8:  2.4593 -  2.3526  1297   151  0.27  69.79   0.71     0.32      65398.45|
|  9:  2.3526 -  2.2624  1308   143  0.28  68.88   0.73     0.35      59919.44|
| 10:  2.2624 -  2.1846  1308   152  0.31  66.54   0.76     0.38      50531.87|
| 11:  2.1846 -  2.1164  1303   140  0.31  66.94   0.79     0.38      49351.57|
| 12:  2.1164 -  2.0561  1289   142  0.26  70.64   0.77     0.34      46020.70|
| 13:  2.0561 -  2.0021  1268   141  0.24  72.36   0.71     0.32      41086.59|
| 14:  2.0021 -  1.9534   409    46  0.31  67.24   0.71     0.35      31401.83|
|alpha:            min =        0.32 max =            0.77 mean =         0.46|
|beta:             min =    31401.83 max =       119541.59 mean =     75926.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.39|
|phase err.(work): min =        0.00 max =           89.99 mean =        60.53|
|phase err.(test): min =        0.00 max =           89.89 mean =        60.79|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.319766             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.790   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.600659              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.634   (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:        6 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       34 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      174 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      715 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1513 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2668 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3971 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5151 |
| 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:     7819 |
|-----------------------------------------------------------------------------|
|-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 |       53.319 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.196 |       2.355 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.621)------------------------------------------|
|    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 = 11.621)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4933   r_free= 0.4850   ksol= 0.00   Bsol= 0.00   scale= 0.759    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.297161                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4799   r_free= 0.4709   ksol= 0.36   Bsol= 3.77   scale= 0.981    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.55,9.99,7.98,0.00,0.00,0.00); trace/3= 8.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.291581                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.752574             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.014   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.536811              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.974   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4799      final r-factor (work) = 0.4126          |
| start r-factor (free) = 0.4709      final r-factor (free) = 0.4377          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 102.8703 = 15.75 * 0.50 * 6.2913 + 1.00 * 53.3186                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 49.2410 = 15.75 * 0.50 * 6.2334 + 1.00 * 0.1449                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4126      final r-factor (work) = 0.3734          |
| start r-factor (free) = 0.4377      final r-factor (free) = 0.4365          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.5940 = 1.54 * 1.00 * 6.2334 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.5138 = 1.54 * 1.00 * 6.1783 + 1.00 * 0.0189                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.621)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.54   14.33    None  None   None       |
|    all(noH): 2823   0      0.00    78.54   14.33    None  None   None       |
|    Sol.    : 438    0      0.00    74.18   22.34    None  None   None       |
|    Mac.    : 2385   0      0.00    78.54   12.85    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 -   7.855:  969   |   5:    39.272 -  47.127:   59        |
|      1:     7.855 -  15.709:  844   |   6:    47.127 -  54.981:   34        |
|      2:    15.709 -  23.564:  513   |   7:    54.981 -  62.836:   18        |
|      3:    23.564 -  31.418:  231   |   8:    62.836 -  70.690:    4        |
|      4:    31.418 -  39.272:  148   |   9:    70.690 -  78.545:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3734 r_free = 0.4365             target_work(ml) = 6.172         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3732 r_free = 0.4365             target_work(ml) = 6.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3732   r_free= 0.4365   ksol= 0.36   Bsol= 3.77   scale= 1.101    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.55,9.99,7.98,0.00,0.00,0.00); trace/3= 8.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.171931                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3708   r_free= 0.4323   ksol= 0.38   Bsol= 50.00   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.49,6.02,4.53,0.00,0.00,0.00); trace/3= 4.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.173071                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.575443              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.147  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.782864              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.089  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3708      final r-factor (work) = 0.3285          |
| start r-factor (free) = 0.4323      final r-factor (free) = 0.4064          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.7091 = 9.58 * 0.50 * 6.1750 + 1.00 * 0.1449                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.3899 = 9.58 * 0.50 * 6.1201 + 1.00 * 0.0888                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3285      final r-factor (work) = 0.3163          |
| start r-factor (free) = 0.4064      final r-factor (free) = 0.3957          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8100 = 0.78 * 1.00 * 6.1201 + 1.00 * 0.0188                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7636 = 0.78 * 1.00 * 6.0684 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.621)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.82   14.20    None  None   None       |
|    all(noH): 2823   0      0.00    74.82   14.20    None  None   None       |
|    Sol.    : 438    0      0.00    69.68   24.75    None  None   None       |
|    Mac.    : 2385   0      0.00    74.82   12.26    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 -   7.482:  927   |   5:    37.409 -  44.891:   63        |
|      1:     7.482 -  14.964:  869   |   6:    44.891 -  52.373:   30        |
|      2:    14.964 -  22.446:  476   |   7:    52.373 -  59.855:   14        |
|      3:    22.446 -  29.927:  268   |   8:    59.855 -  67.337:    7        |
|      4:    29.927 -  37.409:  165   |   9:    67.337 -  74.819:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3163 r_free = 0.3957             target_work(ml) = 6.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3162 r_free = 0.3960             target_work(ml) = 6.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3162   r_free= 0.3960   ksol= 0.38   Bsol= 50.00   scale= 1.050   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.49,6.02,4.53,0.00,0.00,0.00); trace/3= 4.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.056482                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3164   r_free= 0.3935   ksol= 0.35   Bsol= 50.00   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.52,3.73,3.47,0.00,0.00,0.00); trace/3= 3.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.056397                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.436426              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.031  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.018611              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.866  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3164      final r-factor (work) = 0.2588          |
| start r-factor (free) = 0.3935      final r-factor (free) = 0.3330          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.7179 = 9.44 * 0.50 * 6.0678 + 1.00 * 0.0888                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.3197 = 9.44 * 0.50 * 5.9814 + 1.00 * 0.0981                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2588      final r-factor (work) = 0.2332          |
| start r-factor (free) = 0.3330      final r-factor (free) = 0.3221          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 30.0313 = 5.02 * 1.00 * 5.9814 + 1.00 * 0.0128                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 29.3225 = 5.02 * 1.00 * 5.8377 + 1.00 * 0.0252                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.621)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.59  16.55    None  None   None       |
|    all(noH): 2823   0      0.00    102.59  16.55    None  None   None       |
|    Sol.    : 438    0      0.00    102.59  38.60    None  None   None       |
|    Mac.    : 2385   0      0.00    95.29   12.50    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.260: 1364   |   5:    51.297 -  61.557:   86        |
|      1:    10.260 -  20.519:  661   |   6:    61.557 -  71.816:   48        |
|      2:    20.519 -  30.778:  321   |   7:    71.816 -  82.076:   22        |
|      3:    30.778 -  41.038:  201   |   8:    82.076 -  92.335:    4        |
|      4:    41.038 -  51.297:  111   |   9:    92.335 - 102.595:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2332 r_free = 0.3221             target_work(ml) = 5.819         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2330 r_free = 0.3224             target_work(ml) = 5.819         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2330   r_free= 0.3224   ksol= 0.35   Bsol= 50.00   scale= 1.050   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.52,3.73,3.47,0.00,0.00,0.00); trace/3= 3.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.819159                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2326   r_free= 0.3219   ksol= 0.33   Bsol= 50.00   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.95,2.32,3.07,0.00,0.00,0.00); trace/3= 2.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.817783                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.499588              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.878  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.441987              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.886  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2326      final r-factor (work) = 0.2026          |
| start r-factor (free) = 0.3219      final r-factor (free) = 0.2793          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3113 = 3.50 * 0.50 * 5.8368 + 1.00 * 0.0981                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1416 = 3.50 * 0.50 * 5.7643 + 1.00 * 0.0554                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2026      final r-factor (work) = 0.1919          |
| start r-factor (free) = 0.2793      final r-factor (free) = 0.2511          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5732 = 0.44 * 1.00 * 5.7643 + 1.00 * 0.0254                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5347 = 0.44 * 1.00 * 5.6667 + 1.00 * 0.0301                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.621)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.64  15.40    None  None   None       |
|    all(noH): 2823   0      0.00    101.64  15.40    None  None   None       |
|    Sol.    : 438    0      1.60    101.64  39.18    None  None   None       |
|    Mac.    : 2385   0      0.00    93.89   11.03    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 -  10.164: 1529   |   5:    50.821 -  60.985:   70        |
|      1:    10.164 -  20.328:  616   |   6:    60.985 -  71.149:   40        |
|      2:    20.328 -  30.493:  241   |   7:    71.149 -  81.313:   16        |
|      3:    30.493 -  40.657:  170   |   8:    81.313 -  91.477:    4        |
|      4:    40.657 -  50.821:  133   |   9:    91.477 - 101.642:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1919 r_free = 0.2511             target_work(ml) = 5.618         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1916 r_free = 0.2506             target_work(ml) = 5.616         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1916   r_free= 0.2506   ksol= 0.33   Bsol= 50.00   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.95,2.32,3.07,0.00,0.00,0.00); trace/3= 2.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.616084                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1916   r_free= 0.2503   ksol= 0.33   Bsol= 50.00   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.33,1.31,2.76,0.00,0.00,0.00); trace/3= 1.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.616324                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.423777              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.359  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.625945              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.111   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1916      final r-factor (work) = 0.1594          |
| start r-factor (free) = 0.2503      final r-factor (free) = 0.2176          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9221 = 2.42 * 0.50 * 5.6662 + 1.00 * 0.0554                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7636 = 2.42 * 0.50 * 5.5351 + 1.00 * 0.0557                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1594      final r-factor (work) = 0.1492          |
| start r-factor (free) = 0.2176      final r-factor (free) = 0.2064          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4871 = 0.63 * 1.00 * 5.5351 + 1.00 * 0.0224                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4220 = 0.63 * 1.00 * 5.4335 + 1.00 * 0.0209                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.621)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.10  14.97    None  None   None       |
|    all(noH): 2823   0      0.00    102.10  14.97    None  None   None       |
|    Sol.    : 438    0      2.99    102.10  41.56    None  None   None       |
|    Mac.    : 2385   0      0.00    98.24   10.08    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 -  10.210: 1634   |   5:    51.050 -  61.260:   91        |
|      1:    10.210 -  20.420:  603   |   6:    61.260 -  71.470:   49        |
|      2:    20.420 -  30.630:  178   |   7:    71.470 -  81.680:   19        |
|      3:    30.630 -  40.840:  125   |   8:    81.680 -  91.890:    4        |
|      4:    40.840 -  51.050:  117   |   9:    91.890 - 102.100:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1492 r_free = 0.2064             target_work(ml) = 5.407         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1491 r_free = 0.2065             target_work(ml) = 5.406         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1491   r_free= 0.2065   ksol= 0.33   Bsol= 50.00   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.33,1.31,2.76,0.00,0.00,0.00); trace/3= 1.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.406326                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.6638 0.99   1420  157 0.1086 0.1440      5.4714      5.6829|
|  2:  4.6638 -  3.7203 0.99   1373  156 0.1033 0.1450      5.6232      5.9133|
|  3:  3.7203 -  3.2555 0.99   1345  144 0.1405 0.1949      5.7232      6.0107|
|  4:  3.2555 -  2.9603 0.99   1344  152 0.1664 0.2184      5.7182      5.8685|
|  5:  2.9603 -  2.7495 0.99   1328  150 0.1773 0.2341      5.5964      5.8397|
|  6:  2.7495 -  2.5883 0.99   1312  145 0.1638 0.2561      5.4544      5.6936|
|  7:  2.5883 -  2.4593 0.99   1326  140 0.1709 0.2117      5.4245      5.5709|
|  8:  2.4593 -  2.3526 0.98   1297  151 0.1694 0.2258        5.38       5.611|
|  9:  2.3526 -  2.2624 0.98   1308  143 0.1676 0.2478      5.3182      5.5896|
| 10:  2.2624 -  2.1846 1.00   1308  152 0.1493 0.2329      5.2131      5.4423|
| 11:  2.1846 -  2.1164 0.98   1303  140 0.1530 0.2430      5.2115      5.5602|
| 12:  2.1164 -  2.0561 0.98   1289  142 0.1664 0.2360      5.1687       5.434|
| 13:  2.0561 -  2.0021 0.98   1268  141 0.1621 0.2130      5.0701      5.2235|
| 14:  2.0021 -  1.9534 0.31    409   46 0.1489 0.2112      4.9505       5.154|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0146 -  4.6638  1420   157  0.93  10.73   0.97     0.96       9126.44|
|  2:  4.6638 -  3.7203  1373   156  0.93  10.76   1.04     1.02      13276.43|
|  3:  3.7203 -  3.2555  1345   144  0.89  16.34   1.06     1.05      17795.86|
|  4:  3.2555 -  2.9603  1344   152  0.87  19.84   1.03     0.99      18152.04|
|  5:  2.9603 -  2.7495  1328   150  0.85  21.47   1.02     0.99      14659.92|
|  6:  2.7495 -  2.5883  1312   145  0.84  22.12   1.00     0.94      11890.66|
|  7:  2.5883 -  2.4593  1326   140  0.85  21.94   1.01     0.97      10889.21|
|  8:  2.4593 -  2.3526  1297   151  0.84  23.10   1.01     0.97      10498.22|
|  9:  2.3526 -  2.2624  1308   143  0.84  22.52   1.00     0.93       9078.01|
| 10:  2.2624 -  2.1846  1308   152  0.84  22.23   1.02     0.96       7912.70|
| 11:  2.1846 -  2.1164  1303   140  0.84  22.47   1.03     0.95       7770.94|
| 12:  2.1164 -  2.0561  1289   142  0.84  23.31   1.03     0.99       7485.87|
| 13:  2.0561 -  2.0021  1268   141  0.83  23.57   1.02     0.97       6066.31|
| 14:  2.0021 -  1.9534   409    46  0.88  19.24   1.01     0.96       4251.92|
|alpha:            min =        0.93 max =            1.05 mean =         0.98|
|beta:             min =     4251.92 max =        18152.04 mean =     11008.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.86|
|phase err.(work): min =        0.00 max =           89.92 mean =        19.90|
|phase err.(test): min =        0.00 max =           89.13 mean =        19.00|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1494   r_free= 0.2067   ksol= 0.32   Bsol= 47.06   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.39,-0.64,1.04,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.405778                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1494   r_free= 0.2067   ksol= 0.32   Bsol= 47.06   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.39,-0.64,1.04,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.405778                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.6638 0.99   1420  157 0.1084 0.1439      5.4648      5.6805|
|  2:  4.6638 -  3.7203 0.99   1373  156 0.1039 0.1460      5.6249      5.9175|
|  3:  3.7203 -  3.2555 0.99   1345  144 0.1409 0.1944       5.724      6.0035|
|  4:  3.2555 -  2.9603 0.99   1344  152 0.1667 0.2194      5.7177      5.8701|
|  5:  2.9603 -  2.7495 0.99   1328  150 0.1773 0.2333       5.596      5.8391|
|  6:  2.7495 -  2.5883 0.99   1312  145 0.1639 0.2564      5.4538      5.6937|
|  7:  2.5883 -  2.4593 0.99   1326  140 0.1710 0.2113       5.424      5.5699|
|  8:  2.4593 -  2.3526 0.98   1297  151 0.1691 0.2259      5.3794      5.6112|
|  9:  2.3526 -  2.2624 0.98   1308  143 0.1676 0.2471      5.3179       5.587|
| 10:  2.2624 -  2.1846 1.00   1308  152 0.1491 0.2335      5.2133      5.4451|
| 11:  2.1846 -  2.1164 0.98   1303  140 0.1527 0.2435      5.2118      5.5633|
| 12:  2.1164 -  2.0561 0.98   1289  142 0.1664 0.2360      5.1692      5.4341|
| 13:  2.0561 -  2.0021 0.98   1268  141 0.1623 0.2121      5.0698      5.2219|
| 14:  2.0021 -  1.9534 0.31    409   46 0.1491 0.2111      4.9487      5.1513|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0146 -  4.6638  1420   157  0.93  10.62   0.97     0.95       8878.24|
|  2:  4.6638 -  3.7203  1373   156  0.93  10.64   1.03     1.02      13143.49|
|  3:  3.7203 -  3.2555  1345   144  0.89  16.32   1.05     1.04      17784.71|
|  4:  3.2555 -  2.9603  1344   152  0.87  19.80   1.02     0.98      18082.88|
|  5:  2.9603 -  2.7495  1328   150  0.85  21.44   1.01     0.98      14621.81|
|  6:  2.7495 -  2.5883  1312   145  0.84  22.10   0.99     0.93      11865.83|
|  7:  2.5883 -  2.4593  1326   140  0.85  21.90   1.00     0.96      10868.11|
|  8:  2.4593 -  2.3526  1297   151  0.84  23.09   1.00     0.96      10497.31|
|  9:  2.3526 -  2.2624  1308   143  0.84  22.51   0.99     0.92       9072.86|
| 10:  2.2624 -  2.1846  1308   152  0.84  22.24   1.00     0.95       7928.30|
| 11:  2.1846 -  2.1164  1303   140  0.84  22.50   1.01     0.93       7800.32|
| 12:  2.1164 -  2.0561  1289   142  0.83  23.34   1.01     0.98       7502.84|
| 13:  2.0561 -  2.0021  1268   141  0.83  23.56   1.00     0.96       6060.03|
| 14:  2.0021 -  1.9534   409    46  0.88  19.16   0.98     0.94       4231.23|
|alpha:            min =        0.92 max =            1.04 mean =         0.97|
|beta:             min =     4231.23 max =        18082.88 mean =     10968.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.86|
|phase err.(work): min =        0.00 max =           89.99 mean =        19.87|
|phase err.(test): min =        0.00 max =           89.85 mean =        18.98|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.621)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.54    103.64  16.51    None  None   None       |
|    all(noH): 2823   0      1.54    103.64  16.51    None  None   None       |
|    Sol.    : 438    0      4.53    103.64  43.10    None  None   None       |
|    Mac.    : 2385   0      1.54    99.79   11.63    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.543 -  11.753: 1634   |   5:    52.593 -  62.803:   91        |
|      1:    11.753 -  21.963:  603   |   6:    62.803 -  73.013:   49        |
|      2:    21.963 -  32.173:  178   |   7:    73.013 -  83.223:   19        |
|      3:    32.173 -  42.383:  125   |   8:    83.223 -  93.433:    4        |
|      4:    42.383 -  52.593:  117   |   9:    93.433 - 103.643:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 355         
Filter by distance & map next to the model:
   mapped sites are within: 0.319 - 5.636
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 350 from: 355
   mapped sites are within: 0.706 - 5.636

peak=    7.246 closest distance to " CB  VAL A 230 " =    1.510
peak=    7.229 closest distance to " O   HOH Z 268 " =    1.335
peak=    6.875 closest distance to " O   HOH Z 390 " =    1.204
peak=    6.320 closest distance to " O   HOH Z 130 " =    2.157
peak=    6.278 closest distance to " CG  LEU A   5 " =    1.532
peak=    6.028 closest distance to " NH1 ARG A 138 " =    1.024
peak=    5.970 closest distance to " CG  ARG A 138 " =    1.188
peak=    5.939 closest distance to " O   HOH Z 385 " =    1.733
peak=    5.697 closest distance to " O   HOH Z 381 " =    1.122
peak=    5.611 closest distance to " NZ BLYS A 290 " =    1.108
peak=    5.584 closest distance to " O   HOH Z 350 " =    1.536
peak=    5.419 closest distance to " CG1 VAL A 296 " =    1.249
peak=    5.377 closest distance to " NH2 ARG A  56 " =    2.182
peak=    5.321 closest distance to " O   HOH Z  46 " =    1.313
peak=    5.310 closest distance to " O   HOH Z 415 " =    1.357
peak=    5.273 closest distance to " O   HOH Z 105 " =    1.358
peak=    5.269 closest distance to " CD  ARG A 138 " =    0.885
peak=    5.269 closest distance to " O   HOH Z  65 " =    1.938
peak=    5.246 closest distance to " O   HOH Z 375 " =    1.273
peak=    5.164 closest distance to " O   PRO A 198 " =    1.383
peak=    5.156 closest distance to " CD1AILE A 234 " =    1.082
peak=    5.111 closest distance to " NE2 GLN A  11 " =    1.321
peak=    5.087 closest distance to " O   HOH Z 124 " =    1.756
peak=    5.047 closest distance to " OD1 ASP A  27 " =    1.032
peak=    5.037 closest distance to " O   HOH Z  69 " =    2.416
peak=    5.025 closest distance to " O   HOH Z  24 " =    1.999
peak=    4.943 closest distance to " NH2 ARG A 269 " =    0.956
peak=    4.916 closest distance to " O   HOH Z  59 " =    1.647
peak=    4.885 closest distance to " O   HOH Z   7 " =    1.917
peak=    4.870 closest distance to " O   HOH Z 139 " =    1.824
peak=    4.821 closest distance to " O   HOH Z 127 " =    1.252
peak=    4.808 closest distance to " O   VAL A  72 " =    0.981
peak=    4.790 closest distance to " CB  LYS A 290 " =    0.915
peak=    4.786 closest distance to " O   HOH Z 403 " =    1.639
peak=    4.745 closest distance to " O   HOH Z 103 " =    1.112
peak=    4.721 closest distance to " CB  PRO A  54 " =    1.183
peak=    4.718 closest distance to " OG  SER A 276 " =    0.952
peak=    4.707 closest distance to " O   HOH Z 360 " =    1.210
peak=    4.687 closest distance to " O   ASN A 285 " =    0.921
peak=    4.684 closest distance to " O   HOH Z 417 " =    1.850
peak=    4.673 closest distance to " O   HOH Z   9 " =    1.897
peak=    4.652 closest distance to " O   HOH Z 142 " =    2.069
peak=    4.617 closest distance to " O   HOH Z 358 " =    1.503
peak=    4.614 closest distance to " CB  VAL A 296 " =    1.278
peak=    4.607 closest distance to " O   HOH Z 418 " =    1.468
peak=    4.605 closest distance to " O   HOH Z 427 " =    1.308
peak=    4.589 closest distance to " N   GLN A 278 " =    0.937
peak=    4.585 closest distance to " O   HOH Z 225 " =    1.971
peak=    4.584 closest distance to " O   HOH Z  27 " =    1.138
peak=    4.569 closest distance to " O   HOH Z  63 " =    1.702
peak=    4.555 closest distance to " O   HOH Z 214 " =    1.414
peak=    4.547 closest distance to " CB  SER A   3 " =    1.483
peak=    4.544 closest distance to " O   HOH Z 410 " =    1.557
peak=    4.536 closest distance to " O   HOH Z 232 " =    2.100
peak=    4.486 closest distance to " O   HOH Z 400 " =    0.883
peak=    4.476 closest distance to " CG2 ILE A 120 " =    1.117
peak=    4.465 closest distance to " CB  ARG A 275 " =    1.197
peak=    4.446 closest distance to " O   HOH Z  77 " =    1.225
peak=    4.436 closest distance to " N   TYR A  15 " =    1.013
peak=    4.351 closest distance to " O   HOH Z 361 " =    1.847
peak=    4.330 closest distance to " O   HOH Z 126 " =    1.965
peak=    4.322 closest distance to " O   HOH Z 425 " =    1.554
peak=    4.302 closest distance to " CE3 TRP A 274 " =    1.410
peak=    4.294 closest distance to " O   HOH Z 427 " =    1.948
peak=    4.275 closest distance to " O   HOH Z 342 " =    1.162
peak=    4.257 closest distance to " C   GLN A  73 " =    1.059
peak=    4.239 closest distance to " O   HOH Z 293 " =    1.524
peak=    4.233 closest distance to " CB  VAL A 230 " =    1.242
peak=    4.219 closest distance to " CA  ASN A 284 " =    0.965
peak=    4.214 closest distance to " O   HOH Z 424 " =    1.767
peak=    4.209 closest distance to " O   HOH Z 359 " =    1.330
peak=    4.202 closest distance to " O   HOH Z 133 " =    1.754
peak=    4.197 closest distance to " O   HOH Z 422 " =    1.080
peak=    4.197 closest distance to " N   ARG A 156 " =    1.328
peak=    4.192 closest distance to " CD1 LEU A   5 " =    1.020
peak=    4.182 closest distance to " O   HOH Z 245 " =    1.164
peak=    4.152 closest distance to " O   HOH Z 222 " =    1.523
peak=    4.151 closest distance to " CZ  PHE A  16 " =    0.919
peak=    4.138 closest distance to " O   HOH Z  78 " =    1.956
peak=    4.127 closest distance to " CB  SER A 216 " =    1.059
peak=    4.122 closest distance to " O  BHOH Z  74 " =    1.169
peak=    4.112 closest distance to " CE  MET A  93 " =    1.505
peak=    4.092 closest distance to " O   HOH Z  66 " =    1.279
peak=    4.064 closest distance to " CG  PRO A 280 " =    0.997
peak=    4.064 closest distance to " O   HOH Z  21 " =    1.325
peak=    4.063 closest distance to " O   HOH Z 158 " =    2.613
peak=    4.063 closest distance to " O   HOH Z 215 " =    1.608
peak=    4.062 closest distance to " NH2AARG A 145 " =    2.231
peak=    4.040 closest distance to " CG  PRO A 243 " =    1.195
peak=    4.016 closest distance to " OG ASER A 258 " =    2.969
peak=    4.006 closest distance to " CB  ASN A  39 " =    0.813
peak=    3.995 closest distance to " CZ  PHE A  16 " =    1.029
peak=    3.994 closest distance to " CG2AVAL A  72 " =    0.857
peak=    3.974 closest distance to " N   GLN A  73 " =    1.200
peak=    3.961 closest distance to " OE1 GLU A   2 " =    1.804
peak=    3.955 closest distance to " CG  PRO A  54 " =    1.412
peak=    3.943 closest distance to " O   HOH Z  43 " =    1.406
peak=    3.937 closest distance to " CG2 THR A 279 " =    1.082
peak=    3.936 closest distance to " O   ASN A 142 " =    1.107
peak=    3.932 closest distance to " O   ASP A 286 " =    2.290
peak=    3.918 closest distance to " O   HOH Z  15 " =    0.950
peak=    3.911 closest distance to " CG1BVAL A 121 " =    2.231
peak=    3.885 closest distance to " CB  ALA A 114 " =    1.226
peak=    3.872 closest distance to " O   HOH Z 287 " =    1.706
peak=    3.869 closest distance to " CG  LEU A 167 " =    1.356
peak=    3.865 closest distance to " O   HOH Z 257 " =    2.327
peak=    3.860 closest distance to " O   HOH Z 416 " =    1.463
peak=    3.857 closest distance to " CB  ASP A 124 " =    1.054
peak=    3.856 closest distance to " O   HOH Z 205 " =    1.361
peak=    3.855 closest distance to " CB  ASN A 148 " =    1.368
peak=    3.829 closest distance to " CA  ILE A 234 " =    1.201
peak=    3.827 closest distance to " CB  GLU A 277 " =    0.964
peak=    3.820 closest distance to " CB  GLU A 128 " =    0.991
peak=    3.813 closest distance to " O   HOH Z 233 " =    1.577
peak=    3.810 closest distance to " OD1 ASN A  69 " =    1.113
peak=    3.803 closest distance to " O   HOH Z 321 " =    1.144
peak=    3.792 closest distance to " CB  SER A  62 " =    1.293
peak=    3.782 closest distance to " NE2 GLN A  58 " =    5.636
peak=    3.780 closest distance to " O   HOH Z  52 " =    1.171
peak=    3.771 closest distance to " CD2 LEU A 297 " =    0.944
peak=    3.764 closest distance to " O   HOH Z 232 " =    2.061
peak=    3.762 closest distance to " OD2 ASP A 253 " =    0.985
peak=    3.759 closest distance to " O   HOH Z  11 " =    2.400
peak=    3.751 closest distance to " O   HOH Z 366 " =    2.978
peak=    3.743 closest distance to " CA  LEU A 222 " =    1.112
peak=    3.738 closest distance to " CG BASN A 224 " =    0.920
peak=    3.732 closest distance to " NH2 ARG A 138 " =    1.331
peak=    3.718 closest distance to " O   HOH Z 112 " =    1.313
peak=    3.716 closest distance to " CG  LEU A 228 " =    1.056
peak=    3.712 closest distance to " O   HOH Z 353 " =    1.963
peak=    3.711 closest distance to " O   HOH Z 371 " =    2.973
peak=    3.708 closest distance to " CD  ARG A  66 " =    2.279
peak=    3.704 closest distance to " CG  LEU A   5 " =    1.144
peak=    3.696 closest distance to " CZ3 TRP A 266 " =    1.236
peak=    3.690 closest distance to " CB  GLN A 223 " =    1.612
peak=    3.685 closest distance to " O   HOH Z 303 " =    2.041
peak=    3.679 closest distance to " O   HOH Z 371 " =    2.411
peak=    3.676 closest distance to " O   HOH Z  91 " =    1.185
peak=    3.672 closest distance to " OG BSER A 258 " =    1.044
peak=    3.670 closest distance to " CA  ALA A 295 " =    0.908
peak=    3.670 closest distance to " CG1 VAL A 265 " =    0.974
peak=    3.666 closest distance to " N   CYS A 260 " =    1.202
peak=    3.666 closest distance to " O   HOH Z 153 " =    3.483
peak=    3.662 closest distance to " O   HOH Z  53 " =    2.198
peak=    3.659 closest distance to " CB  ASN A 187 " =    1.065
peak=    3.657 closest distance to " CB  SER A 210 " =    1.094
peak=    3.652 closest distance to " O   HOH Z 422 " =    2.421
peak=    3.646 closest distance to " CB  SER A  63 " =    1.283
peak=    3.629 closest distance to " O   HOH Z  97 " =    1.455
peak=    3.626 closest distance to " CA  GLY A 136 " =    1.061
peak=    3.625 closest distance to " O   HOH Z 380 " =    2.381
peak=    3.619 closest distance to " CD2 LEU A 228 " =    1.308
peak=    3.619 closest distance to " NE AARG A 275 " =    1.695
peak=    3.616 closest distance to " N   GLU A   2 " =    1.300
peak=    3.607 closest distance to " N   GLY A 302 " =    1.025
peak=    3.606 closest distance to " CG1 ILE A  33 " =    1.410
peak=    3.602 closest distance to " CD1 LEU A 228 " =    1.680
peak=    3.595 closest distance to " OD1 ASP A  50 " =    1.036
peak=    3.594 closest distance to " C   VAL A 153 " =    1.052
peak=    3.589 closest distance to " O   HOH Z 245 " =    0.765
peak=    3.588 closest distance to " O   HOH Z 272 " =    1.889
peak=    3.588 closest distance to " O   HOH Z 167 " =    1.408
peak=    3.586 closest distance to " OD1 ASN A  45 " =    1.290
peak=    3.585 closest distance to " CB  TRP A 179 " =    1.426
peak=    3.581 closest distance to " OE1 GLN A  73 " =    2.347
peak=    3.580 closest distance to " OD2 ASP A  50 " =    1.016
peak=    3.575 closest distance to " CG2 THR A 294 " =    1.165
peak=    3.570 closest distance to " O   HOH Z 172 " =    1.841
peak=    3.564 closest distance to " O   HOH Z  61 " =    2.155
peak=    3.561 closest distance to " O   HOH Z   6 " =    1.834
peak=    3.556 closest distance to " O   HOH Z 146 " =    1.728
peak=    3.554 closest distance to " O   HOH Z 279 " =    2.602
peak=    3.552 closest distance to " N   VAL A 296 " =    1.790
peak=    3.547 closest distance to " CG2 ILE A 234 " =    0.823
peak=    3.544 closest distance to " O   HOH Z 423 " =    2.204
peak=    3.542 closest distance to " O   HOH Z  66 " =    2.216
peak=    3.539 closest distance to " O   HOH Z 368 " =    1.661
peak=    3.539 closest distance to " O   HOH Z 120 " =    1.050
peak=    3.536 closest distance to " CG2 VAL A 296 " =    0.999
peak=    3.534 closest distance to " O   HOH Z 414 " =    1.820
peak=    3.532 closest distance to " CA  ALA A  51 " =    1.129
peak=    3.529 closest distance to " O   HOH Z 132 " =    1.169
peak=    3.526 closest distance to " O   HOH Z  88 " =    3.757
peak=    3.525 closest distance to " CD1 ILE A  33 " =    1.952
peak=    3.512 closest distance to " O   ARG A 275 " =    1.122
peak=    3.510 closest distance to " O   HOH Z 428 " =    1.150
peak=    3.509 closest distance to " N   ARG A 275 " =    0.832
peak=    3.492 closest distance to " CE1 TYR A  68 " =    1.213
peak=    3.490 closest distance to " O   HOH Z 368 " =    3.055
peak=    3.487 closest distance to " O   HOH Z   1 " =    1.870
peak=    3.485 closest distance to " O   HOH Z   7 " =    3.224
peak=    3.483 closest distance to " CA  LEU A 282 " =    1.040
peak=    3.476 closest distance to " NH2 ARG A 269 " =    1.096
peak=    3.476 closest distance to " O   HOH Z 159 " =    0.982
peak=    3.476 closest distance to " O   HOH Z 369 " =    2.265
peak=    3.475 closest distance to " CE  LYS A  48 " =    1.087
peak=    3.475 closest distance to " CB  ALA A  10 " =    1.054
peak=    3.475 closest distance to " CG2 THR A 178 " =    1.296
peak=    3.474 closest distance to " CG  LYS A 119 " =    1.081
peak=    3.474 closest distance to " O   HOH Z 244 " =    1.437
peak=    3.470 closest distance to " O   HOH Z  57 " =    1.208
peak=    3.464 closest distance to " O   HOH Z  11 " =    1.107
peak=    3.452 closest distance to " NH2BARG A 145 " =    1.685
peak=    3.452 closest distance to " O   HOH Z 119 " =    1.474
peak=    3.452 closest distance to " C   GLY A 111 " =    1.727
peak=    3.450 closest distance to " CB  ALA A 244 " =    1.072
peak=    3.449 closest distance to " CG2 THR A 221 " =    1.310
peak=    3.448 closest distance to " O   HOH Z 125 " =    1.884
peak=    3.445 closest distance to " O   HOH Z  61 " =    1.463
peak=    3.444 closest distance to " O   SER A 273 " =    0.842
peak=    3.443 closest distance to " NH1AARG A 145 " =    1.016
peak=    3.441 closest distance to " O   GLY A 302 " =    1.618
peak=    3.439 closest distance to " O   HOH Z 298 " =    1.960
peak=    3.437 closest distance to " O   HOH Z 426 " =    1.155
peak=    3.430 closest distance to " O   HOH Z  39 " =    1.554
peak=    3.423 closest distance to " CA  ALA A 299 " =    0.885
peak=    3.420 closest distance to " N   ASN A 285 " =    0.806
peak=    3.418 closest distance to " O   HOH Z 389 " =    1.379
peak=    3.417 closest distance to " CA  MET A  47 " =    1.238
peak=    3.415 closest distance to " CG1AVAL A 121 " =    0.870
peak=    3.415 closest distance to " OD1 ASP A 286 " =    1.064
peak=    3.411 closest distance to " CB  VAL A 202 " =    1.672
peak=    3.407 closest distance to " CD2 LEU A 101 " =    1.245
peak=    3.407 closest distance to " CB  ALA A 248 " =    1.471
peak=    3.406 closest distance to " O   HOH Z  47 " =    1.723
peak=    3.406 closest distance to " O   HOH Z 211 " =    1.479
peak=    3.406 closest distance to " CA  GLN A  55 " =    1.002
peak=    3.405 closest distance to " O   HOH Z  30 " =    1.322
peak=    3.402 closest distance to " O   HOH Z   1 " =    1.542
peak=    3.402 closest distance to " CD2 LEU A 300 " =    1.256
peak=    3.399 closest distance to " CB  TRP A 266 " =    0.873
peak=    3.395 closest distance to " NZ  LYS A 117 " =    1.137
peak=    3.391 closest distance to " N   VAL A  72 " =    0.912
peak=    3.390 closest distance to " CG2 ILE A  20 " =    1.423
peak=    3.388 closest distance to " O   HOH Z 363 " =    1.171
peak=    3.378 closest distance to " C   GLN A  11 " =    1.188
peak=    3.377 closest distance to " CZ AARG A 102 " =    1.992
peak=    3.374 closest distance to " O   HOH Z 197 " =    2.081
peak=    3.374 closest distance to " OE1 GLN A  77 " =    1.266
peak=    3.368 closest distance to " O   HOH Z 219 " =    2.067
peak=    3.360 closest distance to " CA  ARG A 195 " =    1.287
peak=    3.357 closest distance to " CB  LYS A 289 " =    1.034
peak=    3.357 closest distance to " N   PHE A 130 " =    1.256
peak=    3.356 closest distance to " O   ALA A  10 " =    1.088
peak=    3.355 closest distance to " O   HOH Z 313 " =    1.758
peak=    3.354 closest distance to " OG  SER A  32 " =    1.090
peak=    3.353 closest distance to " NH2AARG A 145 " =    1.087
peak=    3.353 closest distance to " NE2 GLN A  73 " =    1.439
peak=    3.352 closest distance to " CG  ARG A 156 " =    1.206
peak=    3.347 closest distance to " O   HOH Z 110 " =    1.809
peak=    3.346 closest distance to " NE1 TRP A 274 " =    1.106
peak=    3.345 closest distance to " O   HOH Z 389 " =    1.531
peak=    3.341 closest distance to " CB  ASN A 215 " =    1.519
peak=    3.340 closest distance to " CZ  PHE A 218 " =    1.189
peak=    3.334 closest distance to " O   HOH Z  26 " =    1.805
peak=    3.334 closest distance to " CA  ARG A 159 " =    1.285
peak=    3.331 closest distance to " O   HOH Z 143 " =    1.557
peak=    3.326 closest distance to " O   HOH Z 368 " =    0.908
peak=    3.324 closest distance to " O   HOH Z  49 " =    2.820
peak=    3.323 closest distance to " CB  LEU A 300 " =    0.892
peak=    3.323 closest distance to " O   HOH Z 217 " =    3.347
peak=    3.322 closest distance to " CB  ASN A 110 " =    1.001
peak=    3.321 closest distance to " CB  ARG A 138 " =    0.832
peak=    3.320 closest distance to " ND2 ASN A  60 " =    3.117
peak=    3.319 closest distance to " O   HOH Z 412 " =    2.959
peak=    3.318 closest distance to " CG  GLN A 278 " =    4.026
peak=    3.313 closest distance to " CA  ASN A 127 " =    1.180
peak=    3.309 closest distance to " O   HOH Z 248 " =    2.047
peak=    3.309 closest distance to " O   HOH Z 128 " =    2.147
peak=    3.307 closest distance to " O   HOH Z  51 " =    1.604
peak=    3.301 closest distance to " CG2 THR A 251 " =    1.698
peak=    3.298 closest distance to " CD2 LEU A 167 " =    1.307
peak=    3.291 closest distance to " O   HOH Z  48 " =    1.615
peak=    3.289 closest distance to " NH1 ARG A  79 " =    0.962
peak=    3.288 closest distance to " N   SER A  26 " =    1.064
peak=    3.285 closest distance to " OD1 ASP A 200 " =    1.553
peak=    3.274 closest distance to " O   HOH Z 423 " =    1.876
peak=    3.272 closest distance to " O   HOH Z 123 " =    1.207
peak=    3.270 closest distance to " O   HOH Z 238 " =    1.290
peak=    3.270 closest distance to " O   HOH Z 369 " =    1.506
peak=    3.270 closest distance to " CB  LEU A  83 " =    0.734
peak=    3.268 closest distance to " O   HOH Z 303 " =    1.215
peak=    3.264 closest distance to " OD2 ASP A  65 " =    2.022
peak=    3.263 closest distance to " O   SER A 288 " =    1.040
peak=    3.262 closest distance to " CG2 THR A 246 " =    1.483
peak=    3.262 closest distance to " O   HOH Z 404 " =    1.336
peak=    3.258 closest distance to " CA  ALA A 158 " =    1.135
peak=    3.252 closest distance to " OG  SER A  26 " =    1.352
peak=    3.252 closest distance to " O   ASN A 301 " =    2.094
peak=    3.251 closest distance to " O   HOH Z 384 " =    1.648
peak=    3.251 closest distance to " CA  SER A  87 " =    0.882
peak=    3.246 closest distance to " O   HOH Z 193 " =    1.833
peak=    3.246 closest distance to " CG1 VAL A 153 " =    1.029
peak=    3.244 closest distance to " O   HOH Z  58 " =    2.012
peak=    3.243 closest distance to " CG2 VAL A 232 " =    1.278
peak=    3.237 closest distance to " CE AMET A  47 " =    1.404
peak=    3.235 closest distance to " OD1 ASN A 170 " =    1.279
peak=    3.233 closest distance to " CG  PRO A 198 " =    1.368
peak=    3.230 closest distance to " O   HOH Z 204 " =    1.232
peak=    3.228 closest distance to " O   HOH Z 240 " =    1.969
peak=    3.226 closest distance to " CB  ALA A 104 " =    0.905
peak=    3.224 closest distance to " O   GLY A 211 " =    1.205
peak=    3.220 closest distance to " O   HOH Z 392 " =    1.590
peak=    3.216 closest distance to " CG  LYS A 193 " =    1.510
peak=    3.215 closest distance to " CD1 PHE A 283 " =    1.028
peak=    3.214 closest distance to " CA  ALA A 160 " =    1.129
peak=    3.209 closest distance to " ND2 ASN A 249 " =    0.706
peak=    3.202 closest distance to " CB  ALA A 233 " =    1.177
peak=    3.200 closest distance to " O   HOH Z 178 " =    1.286
peak=    3.200 closest distance to " N   SER A  97 " =    0.813
peak=    3.197 closest distance to " CB  ARG A  79 " =    0.887
peak=    3.192 closest distance to " O   HOH Z 158 " =    2.843
peak=    3.186 closest distance to " O   PRO A 213 " =    1.286
peak=    3.186 closest distance to " CA  ASP A 162 " =    0.989
peak=    3.178 closest distance to " O   HOH Z 115 " =    1.641
peak=    3.171 closest distance to " O   HOH Z 364 " =    1.273
peak=    3.167 closest distance to " CB  LEU A 228 " =    1.438
peak=    3.161 closest distance to " O   THR A 220 " =    1.810
peak=    3.161 closest distance to " OE1 GLN A 240 " =    1.679
peak=    3.159 closest distance to " N   LYS A  76 " =    1.310
peak=    3.158 closest distance to " O   HOH Z 362 " =    1.648
peak=    3.156 closest distance to " O   HOH Z 341 " =    2.785
peak=    3.152 closest distance to " CB  ASP A 140 " =    1.135
peak=    3.152 closest distance to " O   HOH Z 332 " =    1.395
peak=    3.151 closest distance to " N   TYR A 116 " =    1.645
peak=    3.150 closest distance to " O   HOH Z 116 " =    2.028
peak=    3.149 closest distance to " O   SER A  87 " =    2.540
peak=    3.147 closest distance to " O   THR A 251 " =    1.008
peak=    3.143 closest distance to " CB  GLN A  73 " =    0.994
peak=    3.143 closest distance to " O   HOH Z 331 " =    1.113
peak=    3.139 closest distance to " NZ  LYS A 289 " =    1.201
peak=    3.139 closest distance to " CA  TRP A  92 " =    1.264
peak=    3.138 closest distance to " ND1 HIS A  81 " =    1.515
peak=    3.137 closest distance to " CB  ALA A 131 " =    1.510
peak=    3.134 closest distance to " O   HOH Z 384 " =    1.572
peak=    3.129 closest distance to " N   ALA A 295 " =    1.651
peak=    3.126 closest distance to " CG2 VAL A 202 " =    1.272
peak=    3.125 closest distance to " O   HOH Z 294 " =    1.390
peak=    3.119 closest distance to " O   HOH Z 258 " =    2.736
peak=    3.112 closest distance to " CE1 PHE A  38 " =    0.935
peak=    3.104 closest distance to " N   THR A 294 " =    1.068
peak=    3.100 closest distance to " CZ3 TRP A  70 " =    0.939
peak=    3.099 closest distance to " O   HOH Z 196 " =    1.316
peak=    3.091 closest distance to " CB  GLU A 277 " =    3.727
peak=    3.065 closest distance to " CG  GLN A  88 " =    0.981
peak=    3.064 closest distance to " CZ3 TRP A 123 " =    1.558
peak=    3.055 closest distance to " CB  ALA A 292 " =    0.999
peak=    3.034 closest distance to " CG2 VAL A 202 " =    1.430
peak=    3.022 closest distance to " CB  GLU A 152 " =    1.382
peak=    3.010 closest distance to " O   HOH Z 363 " =    1.548

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.500 - 5.312
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 211
   mapped sites are within: 0.704 - 5.312

peak=   -6.294 closest distance to " CD  ARG A 138 " =    1.142
peak=   -4.616 closest distance to " O   HOH Z 163 " =    1.676
peak=   -4.446 closest distance to " OD1 ASP A  27 " =    0.704
peak=   -4.445 closest distance to " O   PRO A 198 " =    1.142
peak=   -4.331 closest distance to " O   HOH Z 242 " =    1.549
peak=   -4.309 closest distance to " O   ASP A 191 " =    1.755
peak=   -4.298 closest distance to " CD  ARG A  14 " =    2.986
peak=   -4.245 closest distance to " OG  SER A  97 " =    2.278
peak=   -4.183 closest distance to " O   ALA A  51 " =    1.339
peak=   -4.151 closest distance to " O   VAL A  72 " =    0.934
peak=   -4.052 closest distance to " CG2 VAL A 230 " =    0.847
peak=   -4.046 closest distance to " O   HOH Z 186 " =    1.402
peak=   -4.038 closest distance to " O   GLN A  11 " =    1.520
peak=   -4.015 closest distance to " O   HOH Z 381 " =    1.010
peak=   -4.011 closest distance to " OD2 ASP A 253 " =    0.889
peak=   -3.985 closest distance to " CG BLYS A 290 " =    0.817
peak=   -3.979 closest distance to " OG BSER A 134 " =    1.779
peak=   -3.977 closest distance to " CG  MET A 105 " =    0.868
peak=   -3.973 closest distance to " CG1 VAL A 296 " =    0.940
peak=   -3.949 closest distance to " N   ARG A 275 " =    0.824
peak=   -3.949 closest distance to " CG  ASN A 284 " =    1.222
peak=   -3.935 closest distance to " O   HOH Z 300 " =    0.929
peak=   -3.929 closest distance to " CG1AVAL A  72 " =    2.163
peak=   -3.902 closest distance to " O   LYS A  76 " =    1.102
peak=   -3.893 closest distance to " OE1 GLU A 277 " =    2.439
peak=   -3.873 closest distance to " CE2 TYR A  30 " =    2.558
peak=   -3.870 closest distance to " CA  LYS A 290 " =    1.043
peak=   -3.860 closest distance to " OD2 ASP A 272 " =    1.233
peak=   -3.844 closest distance to " O   HOH Z 385 " =    0.918
peak=   -3.837 closest distance to " CG  ASP A  50 " =    0.938
peak=   -3.834 closest distance to " CB  PHE A 130 " =    1.091
peak=   -3.821 closest distance to " CG2 ILE A 120 " =    1.203
peak=   -3.813 closest distance to " CG  PRO A 163 " =    2.431
peak=   -3.806 closest distance to " CD2 LEU A   5 " =    0.901
peak=   -3.804 closest distance to " CA  HIS A  86 " =    2.129
peak=   -3.802 closest distance to " N   THR A 157 " =    1.663
peak=   -3.802 closest distance to " CA  GLY A 203 " =    2.501
peak=   -3.798 closest distance to " CG  PRO A 213 " =    2.088
peak=   -3.785 closest distance to " ND2 ASN A 252 " =    2.264
peak=   -3.765 closest distance to " CB  ASP A  27 " =    2.449
peak=   -3.747 closest distance to " NE1 TRP A 179 " =    1.048
peak=   -3.741 closest distance to " O   HOH Z 205 " =    1.405
peak=   -3.739 closest distance to " O   HOH Z  39 " =    0.942
peak=   -3.737 closest distance to " OG  SER A 276 " =    0.884
peak=   -3.730 closest distance to " C   SER A 276 " =    1.305
peak=   -3.697 closest distance to " CD2 LEU A 297 " =    1.097
peak=   -3.694 closest distance to " O   HOH Z  24 " =    1.199
peak=   -3.692 closest distance to " O   THR A 178 " =    0.840
peak=   -3.688 closest distance to " O   HOH Z 222 " =    4.643
peak=   -3.686 closest distance to " CG  TRP A 266 " =    1.748
peak=   -3.682 closest distance to " O   HOH Z  28 " =    1.032
peak=   -3.679 closest distance to " CG2 ILE A 120 " =    0.846
peak=   -3.666 closest distance to " O   HOH Z 313 " =    0.911
peak=   -3.660 closest distance to " O   HOH Z  77 " =    2.045
peak=   -3.657 closest distance to " O   HOH Z 389 " =    2.529
peak=   -3.649 closest distance to " OG  SER A   3 " =    1.006
peak=   -3.638 closest distance to " CA  GLY A 133 " =    2.111
peak=   -3.632 closest distance to " CA  GLY A  57 " =    2.173
peak=   -3.632 closest distance to " O   ALA A  84 " =    1.663
peak=   -3.626 closest distance to " CG2AVAL A  41 " =    2.763
peak=   -3.625 closest distance to " O   SER A 245 " =    1.255
peak=   -3.608 closest distance to " O   HOH Z 151 " =    2.236
peak=   -3.607 closest distance to " CD2 TYR A 116 " =    2.248
peak=   -3.606 closest distance to " OD2 ASP A 140 " =    0.853
peak=   -3.595 closest distance to " O   HOH Z 413 " =    4.182
peak=   -3.580 closest distance to " O   HOH Z 231 " =    0.793
peak=   -3.546 closest distance to " OG1 THR A 178 " =    1.115
peak=   -3.544 closest distance to " O   HOH Z 131 " =    3.670
peak=   -3.542 closest distance to " C   GLU A   2 " =    1.802
peak=   -3.540 closest distance to " O   HOH Z 435 " =    2.394
peak=   -3.539 closest distance to " OG  SER A  63 " =    1.387
peak=   -3.538 closest distance to " O   HOH Z 216 " =    1.656
peak=   -3.534 closest distance to " CD  GLN A  77 " =    1.127
peak=   -3.532 closest distance to " O   HOH Z 377 " =    1.357
peak=   -3.525 closest distance to " O   HOH Z 286 " =    1.487
peak=   -3.522 closest distance to " NE2 GLN A  11 " =    1.316
peak=   -3.511 closest distance to " CB  ALA A 248 " =    2.065
peak=   -3.492 closest distance to " CG  ASP A 140 " =    1.035
peak=   -3.473 closest distance to " CD1 LEU A 297 " =    2.191
peak=   -3.465 closest distance to " N   THR A 235 " =    1.040
peak=   -3.464 closest distance to " N   GLN A  11 " =    0.968
peak=   -3.461 closest distance to " NH2AARG A 275 " =    5.312
peak=   -3.458 closest distance to " O   HOH Z  60 " =    1.733
peak=   -3.453 closest distance to " O   HOH Z 390 " =    2.472
peak=   -3.451 closest distance to " O   HOH Z 409 " =    1.904
peak=   -3.449 closest distance to " N   VAL A 189 " =    1.760
peak=   -3.447 closest distance to " O   HOH Z 241 " =    1.114
peak=   -3.447 closest distance to " O   HOH Z 415 " =    0.968
peak=   -3.441 closest distance to " O   HOH Z 266 " =    4.831
peak=   -3.433 closest distance to " O   ARG A 275 " =    0.795
peak=   -3.428 closest distance to " OG  SER A   3 " =    0.986
peak=   -3.426 closest distance to " OG ASER A 134 " =    0.985
peak=   -3.420 closest distance to " O   HOH Z 353 " =    1.230
peak=   -3.418 closest distance to " O   CYS A 260 " =    1.242
peak=   -3.418 closest distance to " O   ALA A  10 " =    1.560
peak=   -3.416 closest distance to " CD2 TYR A 293 " =    1.772
peak=   -3.411 closest distance to " CA  GLY A  35 " =    1.829
peak=   -3.406 closest distance to " O   SER A 273 " =    0.916
peak=   -3.399 closest distance to " C   ASP A 124 " =    1.187
peak=   -3.397 closest distance to " O   GLY A  80 " =    2.588
peak=   -3.394 closest distance to " O   HOH Z  54 " =    1.384
peak=   -3.387 closest distance to " O   GLY A  98 " =    2.065
peak=   -3.379 closest distance to " O   HIS A 108 " =    1.202
peak=   -3.377 closest distance to " OE2 GLU A 152 " =    0.999
peak=   -3.376 closest distance to " O   ALA A 226 " =    1.259
peak=   -3.373 closest distance to " NE1 TRP A 177 " =    1.755
peak=   -3.367 closest distance to " O   HOH Z 331 " =    0.969
peak=   -3.361 closest distance to " O   HOH Z 428 " =    1.376
peak=   -3.356 closest distance to " O   TYR A  30 " =    1.772
peak=   -3.351 closest distance to " O   HOH Z 185 " =    2.011
peak=   -3.351 closest distance to " O   ASP A 286 " =    0.911
peak=   -3.346 closest distance to " CD1 ILE A  33 " =    2.192
peak=   -3.344 closest distance to " N   LYS A 289 " =    1.181
peak=   -3.341 closest distance to " O   HOH Z 268 " =    0.938
peak=   -3.339 closest distance to " OE1 GLU A  44 " =    1.123
peak=   -3.335 closest distance to " O   HOH Z 422 " =    3.765
peak=   -3.335 closest distance to " O   HOH Z 404 " =    1.013
peak=   -3.328 closest distance to " O   HOH Z 102 " =    1.791
peak=   -3.327 closest distance to " CA  GLY A 133 " =    2.043
peak=   -3.326 closest distance to " O   HOH Z 275 " =    1.837
peak=   -3.322 closest distance to " OG  SER A 245 " =    1.728
peak=   -3.322 closest distance to " O   HOH Z  60 " =    1.612
peak=   -3.320 closest distance to " O   HOH Z 235 " =    0.934
peak=   -3.315 closest distance to " O   VAL A 125 " =    2.429
peak=   -3.313 closest distance to " O   HOH Z 255 " =    2.638
peak=   -3.305 closest distance to " O   HOH Z 111 " =    1.953
peak=   -3.303 closest distance to " O   HOH Z 201 " =    1.532
peak=   -3.300 closest distance to " O   HOH Z 352 " =    1.726
peak=   -3.291 closest distance to " CB  PRO A 243 " =    2.593
peak=   -3.291 closest distance to " O   TRP A  70 " =    1.408
peak=   -3.288 closest distance to " CA  GLN A  55 " =    1.241
peak=   -3.284 closest distance to " O   HOH Z 207 " =    2.100
peak=   -3.283 closest distance to " O   HOH Z 412 " =    2.196
peak=   -3.281 closest distance to " O   HOH Z 256 " =    0.963
peak=   -3.275 closest distance to " O   HOH Z 431 " =    1.043
peak=   -3.274 closest distance to " OD1 ASN A 249 " =    1.485
peak=   -3.272 closest distance to " O   PHE A 218 " =    1.554
peak=   -3.267 closest distance to " CE2 PHE A 218 " =    2.432
peak=   -3.263 closest distance to " O   HOH Z 159 " =    1.333
peak=   -3.263 closest distance to " CB  ASN A 285 " =    2.084
peak=   -3.262 closest distance to " O   HOH Z 416 " =    0.812
peak=   -3.260 closest distance to " O   SER A  22 " =    2.707
peak=   -3.259 closest distance to " O   HOH Z  54 " =    0.980
peak=   -3.258 closest distance to " CD  ARG A 139 " =    1.726
peak=   -3.258 closest distance to " CG  PRO A 243 " =    1.642
peak=   -3.252 closest distance to " NE2 GLN A 223 " =    1.568
peak=   -3.250 closest distance to " O   ILE A  49 " =    1.632
peak=   -3.247 closest distance to " CA  ASN A 127 " =    1.266
peak=   -3.244 closest distance to " CB  PHE A 283 " =    2.434
peak=   -3.237 closest distance to " CZ  ARG A  24 " =    1.931
peak=   -3.232 closest distance to " OG  SER A  87 " =    1.310
peak=   -3.232 closest distance to " O   TRP A  92 " =    1.563
peak=   -3.231 closest distance to " O   GLY A 136 " =    1.589
peak=   -3.231 closest distance to " CD1 TRP A 274 " =    1.006
peak=   -3.225 closest distance to " O   HOH Z  76 " =    1.261
peak=   -3.224 closest distance to " O   SER A  22 " =    1.082
peak=   -3.223 closest distance to " O   HOH Z 105 " =    2.135
peak=   -3.219 closest distance to " O   HOH Z 174 " =    2.810
peak=   -3.217 closest distance to " C   PHE A 155 " =    0.848
peak=   -3.216 closest distance to " CA  TYR A  68 " =    1.214
peak=   -3.205 closest distance to " C   GLN A 205 " =    2.086
peak=   -3.203 closest distance to " CG1 VAL A 112 " =    2.839
peak=   -3.199 closest distance to " CA  LEU A 143 " =    1.055
peak=   -3.197 closest distance to " O   HOH Z  34 " =    2.202
peak=   -3.196 closest distance to " CA  MET A 113 " =    1.031
peak=   -3.192 closest distance to " O   HOH Z 368 " =    1.662
peak=   -3.189 closest distance to " O   HOH Z 376 " =    2.249
peak=   -3.189 closest distance to " O   HOH Z  16 " =    1.358
peak=   -3.188 closest distance to " CG2 VAL A  78 " =    2.711
peak=   -3.182 closest distance to " CD  LYS A 166 " =    2.593
peak=   -3.179 closest distance to " C   PHE A  61 " =    1.004
peak=   -3.177 closest distance to " CA  GLY A  57 " =    2.198
peak=   -3.175 closest distance to " CG  GLU A 277 " =    1.232
peak=   -3.173 closest distance to " O   HOH Z  53 " =    1.764
peak=   -3.171 closest distance to " O   HOH Z 350 " =    1.946
peak=   -3.169 closest distance to " O   ASN A 301 " =    1.320
peak=   -3.164 closest distance to " O   LEU A 222 " =    1.469
peak=   -3.162 closest distance to " O   HOH Z 414 " =    1.970
peak=   -3.161 closest distance to " O   HOH Z 231 " =    1.803
peak=   -3.157 closest distance to " O   HOH Z   1 " =    3.588
peak=   -3.155 closest distance to " O   GLU A 277 " =    2.058
peak=   -3.155 closest distance to " O   HOH Z 140 " =    1.919
peak=   -3.149 closest distance to " O   HOH Z  52 " =    0.803
peak=   -3.137 closest distance to " CG  TYR A 172 " =    2.101
peak=   -3.136 closest distance to " CG2 ILE A  20 " =    2.743
peak=   -3.136 closest distance to " O   GLN A  88 " =    1.615
peak=   -3.134 closest distance to " O   HOH Z 135 " =    1.389
peak=   -3.130 closest distance to " O   HOH Z 132 " =    4.620
peak=   -3.130 closest distance to " O   VAL A  72 " =    1.088
peak=   -3.130 closest distance to " O   HOH Z 298 " =    2.753
peak=   -3.129 closest distance to " CZ  ARG A  66 " =    2.051
peak=   -3.127 closest distance to " O   HOH Z  64 " =    2.626
peak=   -3.112 closest distance to " OG  SER A 206 " =    1.791
peak=   -3.110 closest distance to " N   ALA A  43 " =    2.717
peak=   -3.107 closest distance to " OE2 GLU A 277 " =    3.502
peak=   -3.104 closest distance to " N   PRO A 163 " =    1.434
peak=   -3.102 closest distance to " OE2 GLU A 152 " =    2.189
peak=   -3.102 closest distance to " ND2 ASN A 249 " =    1.325
peak=   -3.097 closest distance to " O   HOH Z 100 " =    0.840
peak=   -3.096 closest distance to " O   ILE A 106 " =    2.158
peak=   -3.093 closest distance to " NE  ARG A  79 " =    0.888
peak=   -3.089 closest distance to " CG  HIS A 108 " =    0.941
peak=   -3.081 closest distance to " N   ALA A   1 " =    1.126
peak=   -3.074 closest distance to " O   HOH Z 189 " =    3.378
peak=   -3.056 closest distance to " N   LEU A 282 " =    2.399
peak=   -3.054 closest distance to " O   HOH Z  11 " =    2.076
peak=   -3.048 closest distance to " SG BCYS A 201 " =    2.232
peak=   -3.024 closest distance to " O   HOH Z 268 " =    1.248

================= 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    :  0.4886 0.4838   6.295772e+00   6.282214e+00
   1_bss:  0.4799 0.4709   6.291581e+00   6.275155e+00
   1_xyz:  0.4126 0.4377   6.217414e+00   6.247332e+00
   1_adp:  0.3734 0.4365   6.172183e+00   6.244641e+00
   1_occ:  0.3732 0.4365   6.171931e+00   6.245227e+00
   2_bss:  0.3708 0.4323   6.173071e+00   6.244102e+00
   2_xyz:  0.3285 0.4064   6.077320e+00   6.196595e+00
   2_adp:  0.3163 0.3957   6.056403e+00   6.182334e+00
   2_occ:  0.3162 0.3960   6.056482e+00   6.182767e+00
   3_bss:  0.3164 0.3935   6.056397e+00   6.181319e+00
   3_xyz:  0.2588 0.3330   5.881491e+00   6.045176e+00
   3_adp:  0.2332 0.3221   5.819012e+00   6.019386e+00
   3_occ:  0.2330 0.3224   5.819159e+00   6.020056e+00
   4_bss:  0.2326 0.3219   5.817783e+00   6.018706e+00
   4_xyz:  0.2026 0.2793   5.685653e+00   5.905427e+00
   4_adp:  0.1919 0.2511   5.617703e+00   5.826462e+00
   4_occ:  0.1916 0.2506   5.616084e+00   5.824506e+00
   5_bss:  0.1916 0.2503   5.616324e+00   5.823717e+00
   5_xyz:  0.1594 0.2176   5.460846e+00   5.691937e+00
   5_adp:  0.1492 0.2064   5.406709e+00   5.641402e+00
   5_occ:  0.1491 0.2065   5.406326e+00   5.641210e+00
   5_bss:  0.1494 0.2067   5.405778e+00   5.640943e+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:  0.363   3.771   6.548   9.989   7.981   0.000   0.000   0.000
   1_xyz:  0.363   3.771   6.548   9.989   7.981   0.000   0.000   0.000
   1_adp:  0.363   3.771   6.548   9.989   7.981   0.000   0.000   0.000
   1_occ:  0.363   3.771   6.548   9.989   7.981   0.000   0.000   0.000
   2_bss:  0.376  50.000   3.491   6.018   4.528   0.000   0.000   0.000
   2_xyz:  0.376  50.000   3.491   6.018   4.528   0.000   0.000   0.000
   2_adp:  0.376  50.000   3.491   6.018   4.528   0.000   0.000   0.000
   2_occ:  0.376  50.000   3.491   6.018   4.528   0.000   0.000   0.000
   3_bss:  0.347  50.000   2.518   3.729   3.474   0.000   0.000   0.000
   3_xyz:  0.347  50.000   2.518   3.729   3.474   0.000   0.000   0.000
   3_adp:  0.347  50.000   2.518   3.729   3.474   0.000   0.000   0.000
   3_occ:  0.347  50.000   2.518   3.729   3.474   0.000   0.000   0.000
   4_bss:  0.330  50.000   1.953   2.322   3.074   0.000   0.000   0.000
   4_xyz:  0.330  50.000   1.953   2.322   3.074   0.000   0.000   0.000
   4_adp:  0.330  50.000   1.953   2.322   3.074   0.000   0.000   0.000
   4_occ:  0.330  50.000   1.953   2.322   3.074   0.000   0.000   0.000
   5_bss:  0.328  50.000   1.326   1.308   2.762   0.000   0.000   0.000
   5_xyz:  0.328  50.000   1.326   1.308   2.762   0.000   0.000   0.000
   5_adp:  0.328  50.000   1.326   1.308   2.762   0.000   0.000   0.000
   5_occ:  0.328  50.000   1.326   1.308   2.762   0.000   0.000   0.000
   5_bss:  0.317  47.056  -0.393  -0.643   1.036   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  60.552 0.3867  0.4635    75924.629
   1_bss:  59.643 0.3976  0.6016    73443.462
   1_xyz:  53.624 0.4741  0.7042    62551.681
   1_adp:  53.061 0.4809  0.7684    61858.830
   1_occ:  53.160 0.4797  0.7657    62112.012
   2_bss:  52.710 0.4855  0.6926    61633.008
   2_xyz:  46.792 0.5589  0.7938    50222.579
   2_adp:  44.845 0.5834  0.8357    47446.231
   2_occ:  44.890 0.5829  0.8348    47494.593
   3_bss:  44.643 0.5857  0.7968    46957.386
   3_xyz:  35.124 0.6991  0.9299    30481.319
   3_adp:  33.353 0.7196  0.9395    28156.295
   3_occ:  33.385 0.7193  0.9390    28208.148
   4_bss:  33.298 0.7202  0.9140    28052.532
   4_xyz:  28.331 0.7747  0.9580    20258.163
   4_adp:  24.828 0.8130  0.9810    16500.194
   4_occ:  24.755 0.8138  0.9808    16384.972
   5_bss:  24.734 0.8140  0.9581    16367.319
   5_xyz:  21.179 0.8497  0.9806    12221.636
   5_adp:  19.813 0.8634  0.9776    11023.206
   5_occ:  19.811 0.8634  0.9772    11007.971
   5_bss:  19.784 0.8636  0.9678    10968.368
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3319e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3319e+01
   1_xyz:   1.689  0.013  0.105 18.391  0.006  4.104   1.4492e-01
   1_adp:   1.689  0.013  0.105 18.391  0.006  4.104   1.4492e-01
   1_occ:   1.689  0.013  0.105 18.391  0.006  4.104   1.4492e-01
   2_bss:   1.689  0.013  0.105 18.391  0.006  4.104   1.4492e-01
   2_xyz:   1.158  0.008  0.077 16.299  0.005  4.104   8.8801e-02
   2_adp:   1.158  0.008  0.077 16.299  0.005  4.104   8.8801e-02
   2_occ:   1.158  0.008  0.077 16.299  0.005  4.104   8.8801e-02
   3_bss:   1.158  0.008  0.077 16.299  0.005  4.104   8.8801e-02
   3_xyz:   1.290  0.010  0.090 16.356  0.005  4.104   9.8058e-02
   3_adp:   1.290  0.010  0.090 16.356  0.005  4.104   9.8058e-02
   3_occ:   1.290  0.010  0.090 16.356  0.005  4.104   9.8058e-02
   4_bss:   1.290  0.010  0.090 16.356  0.005  4.104   9.8058e-02
   4_xyz:   0.897  0.006  0.065 15.487  0.003  4.110   5.5357e-02
   4_adp:   0.897  0.006  0.065 15.487  0.003  4.110   5.5357e-02
   4_occ:   0.897  0.006  0.065 15.487  0.003  4.110   5.5357e-02
   5_bss:   0.897  0.006  0.065 15.487  0.003  4.110   5.5357e-02
   5_xyz:   0.939  0.006  0.069 15.208  0.004  4.115   5.5726e-02
   5_adp:   0.939  0.006  0.069 15.208  0.004  4.115   5.5726e-02
   5_occ:   0.939  0.006  0.069 15.208  0.004  4.115   5.5726e-02
   5_bss:   0.939  0.006  0.069 15.208  0.004  4.115   5.5726e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9082e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9082e+00
   1_xyz:  13.012  0.189  0.403 85.623  0.034  2.112   9.8191e-02
   1_adp:  13.012  0.189  0.403 85.623  0.034  2.112   9.8191e-02
   1_occ:  13.012  0.189  0.403 85.623  0.034  2.112   9.8191e-02
   2_bss:  13.012  0.189  0.403 85.623  0.034  2.112   9.8191e-02
   2_xyz:   7.749  0.095  0.330 77.040  0.048  1.948   5.7869e-02
   2_adp:   7.749  0.095  0.330 77.040  0.048  1.948   5.7869e-02
   2_occ:   7.749  0.095  0.330 77.040  0.048  1.948   5.7869e-02
   3_bss:   7.749  0.095  0.330 77.040  0.048  1.948   5.7869e-02
   3_xyz:   6.888  0.092  0.315 83.575  0.033  2.081   9.4884e-02
   3_adp:   6.888  0.092  0.315 83.575  0.033  2.081   9.4884e-02
   3_occ:   6.888  0.092  0.315 83.575  0.033  2.081   9.4884e-02
   4_bss:   6.888  0.092  0.315 83.575  0.033  2.081   9.4884e-02
   4_xyz:   6.890  0.072  0.223 80.253  0.022  2.311   4.0053e-02
   4_adp:   6.890  0.072  0.223 80.253  0.022  2.311   4.0053e-02
   4_occ:   6.890  0.072  0.223 80.253  0.022  2.311   4.0053e-02
   5_bss:   6.890  0.072  0.223 80.253  0.022  2.311   4.0053e-02
   5_xyz:   7.119  0.050  0.204 79.930  0.050  2.375   3.8584e-02
   5_adp:   7.119  0.050  0.204 79.930  0.050  2.375   3.8584e-02
   5_occ:   7.119  0.050  0.204 79.930  0.050  2.375   3.8584e-02
   5_bss:   7.119  0.050  0.204 79.930  0.050  2.375   3.8584e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  78.54   0.00  14.33  78.54   0.00  12.85  74.18   0.00  22.34
   1_occ:  78.54   0.00  14.33  78.54   0.00  12.85  74.18   0.00  22.34
   2_bss:  78.54   0.00  14.33  78.54   0.00  12.85  74.18   0.00  22.34
   2_xyz:  78.54   0.00  14.33  78.54   0.00  12.85  74.18   0.00  22.34
   2_adp:  74.82   0.00  14.20  74.82   0.00  12.26  69.68   0.00  24.75
   2_occ:  74.82   0.00  14.20  74.82   0.00  12.26  69.68   0.00  24.75
   3_bss:  74.82   0.00  14.20  74.82   0.00  12.26  69.68   0.00  24.75
   3_xyz:  74.82   0.00  14.20  74.82   0.00  12.26  69.68   0.00  24.75
   3_adp: 102.59   0.00  16.55  95.29   0.00  12.50 102.59   0.00  38.60
   3_occ: 102.59   0.00  16.55  95.29   0.00  12.50 102.59   0.00  38.60
   4_bss: 102.59   0.00  16.55  95.29   0.00  12.50 102.59   0.00  38.60
   4_xyz: 102.59   0.00  16.55  95.29   0.00  12.50 102.59   0.00  38.60
   4_adp: 101.64   0.00  15.40  93.89   0.00  11.03 101.64   1.60  39.18
   4_occ: 101.64   0.00  15.40  93.89   0.00  11.03 101.64   1.60  39.18
   5_bss: 101.64   0.00  15.40  93.89   0.00  11.03 101.64   1.60  39.18
   5_xyz: 101.64   0.00  15.40  93.89   0.00  11.03 101.64   1.60  39.18
   5_adp: 102.10   0.00  14.97  98.24   0.00  10.08 102.10   2.99  41.56
   5_occ: 102.10   0.00  14.97  98.24   0.00  10.08 102.10   2.99  41.56
   5_bss: 103.64   1.54  16.51  99.79   1.54  11.63 103.64   4.53  43.10
------------------------------------------------------------------------
 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:    1.273    0.018    0.410
   1_adp:    1.273    0.018    0.410
   1_occ:    1.273    0.018    0.410
   2_bss:    1.273    0.018    0.410
   2_xyz:    1.594    0.041    0.549
   2_adp:    1.594    0.041    0.549
   2_occ:    1.594    0.041    0.549
   3_bss:    1.594    0.041    0.549
   3_xyz:    1.582    0.031    0.689
   3_adp:    1.582    0.031    0.689
   3_occ:    1.582    0.031    0.689
   4_bss:    1.582    0.031    0.689
   4_xyz:    1.895    0.047    0.764
   4_adp:    1.895    0.047    0.764
   4_occ:    1.895    0.047    0.764
   5_bss:    1.895    0.047    0.764
   5_xyz:    1.958    0.078    0.824
   5_adp:    1.958    0.078    0.824
   5_occ:    1.958    0.078    0.824
   5_bss:    1.958    0.078    0.824
------------------------------------------------------------------------

CPU time actual refinement: 339.20


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_611/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_611/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_611/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_611/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_611/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 339.06 
  Macro-tasks:
    bulk solvent and scale       = 45.96  
    individual site refinement   = 137.63 
    weights calculation          = 32.18  
    collect and process          = 6.42   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 222.29 
  Micro-tasks:
    mask                            = 2.77   
    f_calc                          = 105.45 
    alpha_beta                      = 8.38   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 110.16 
    fmodel                         = 7.29   
    r_factors                      = 0.22   
    phase_errors                   = 10.69  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 246.34 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.815 micro seconds
Total CPU time: 5.88 minutes
from_scatterers_fft:    629 calls, 105.05 s
gradients_fft:          574 calls,  99.17 s

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

# Date 2008-01-16 Time 01:58:39 PST -0800 (1200477519.47 s)
Start R-work = 0.4886, R-free = 0.4838 (no bulk solvent and anisotropic scale)
Final R-work = 0.1637, R-free = 0.2198 (no bulk solvent and anisotropic scale)

Start R-work = 0.4799, R-free = 0.4709
Final R-work = 0.1494, R-free = 0.2067