# Date 2008-01-16 Time 01:56:08 PST -0800 (1200477368.29 s)
#phil __OFF__

Command line arguments: "../617.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 12624
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 617

-------------------------------------------------------------------------------
  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, 45.9914, 84.6622, 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: 3.29, per 1000 atoms: 1.17


================================== 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, 45.9914, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9109 1.96037
Completeness in resolution range: 0.967167
Completeness with d_max=infinity: 0.964215

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9109
                             d_min =   1.9604

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, 45.9914, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9109 1.96037
Completeness in resolution range: 0.967167
Completeness with d_max=infinity: 0.964215

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9113 -  4.1951 [2122/2147]  1912   210   9.9%
  bin  2:  4.1951 -  3.3421 [2047/2067]  1842   205  10.0%
  bin  3:  3.3421 -  2.9232 [2020/2039]  1815   205  10.1%
  bin  4:  2.9232 -  2.6576 [1993/2023]  1797   196   9.8%
  bin  5:  2.6576 -  2.4680 [1988/2007]  1794   194   9.8%
  bin  6:  2.4680 -  2.3231 [1992/2017]  1788   204  10.2%
  bin  7:  2.3231 -  2.2071 [1937/1965]  1741   196  10.1%
  bin  8:  2.2071 -  2.1113 [1976/2012]  1777   199  10.1%
  bin  9:  2.1113 -  2.0303 [1952/1994]  1756   196  10.0%
  bin 10:  2.0303 -  1.9604 [1562/1983]  1408   154   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_617/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: 0.14 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:
        1.67 -     2.32: 35
        2.32 -     2.96: 1783
        2.96 -     3.61: 4678
        3.61 -     4.25: 9351
        4.25 -     4.90: 13040
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.674 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.714 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.760 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  ... (remaining 28882 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_617/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_617/model_refine_001.geo

CPU time processing inputs: 9.18


============================ 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 45.9914 84.6622 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: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5000   r_free= 0.4999   ksol= 0.00   Bsol= 0.00   scale= 0.788    |
|                                                                             |
| 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:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.297956                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9113 -  4.6791 0.99   1386  155 0.4259 0.4394      6.6295      6.6798|
|  2:  4.6791 -  3.7332 0.99   1331  146 0.4423 0.4109      6.8494      6.8038|
|  3:  3.7332 -  3.2669 0.99   1299  142 0.4659 0.4488      6.7164      6.7827|
|  4:  3.2669 -  2.9708 0.99   1294  153 0.4878 0.4525      6.5707      6.5035|
|  5:  2.9708 -  2.7593 0.99   1289  138 0.5269 0.5519      6.3942      6.3853|
|  6:  2.7593 -  2.5975 0.99   1283  141 0.5220 0.5731      6.2999      6.2723|
|  7:  2.5975 -  2.4680 0.99   1278  135 0.5259 0.4844      6.2563      6.2299|
|  8:  2.4680 -  2.3610 0.98   1268  151 0.5475 0.4906      6.1941      6.1727|
|  9:  2.3610 -  2.2705 0.98   1242  138 0.5319 0.5560       6.136      6.1579|
| 10:  2.2705 -  2.1924 1.00   1294  140 0.5358 0.5754      6.1231      6.1508|
| 11:  2.1924 -  2.1240 0.97   1254  140 0.5231 0.5266      6.0536       6.068|
| 12:  2.1240 -  2.0635 0.98   1253  140 0.5176 0.5603      5.9862      6.0338|
| 13:  2.0635 -  2.0093 1.00   1261  137 0.5479 0.5275      5.8954      5.8418|
| 14:  2.0093 -  1.9604 0.70    898  103 0.5687 0.5349      5.8529      5.7771|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9113 -  4.6791  1386   155  0.60  42.74   0.78     0.67     101409.75|
|  2:  4.6791 -  3.7332  1331   146  0.64  40.32   0.85     0.74     135013.42|
|  3:  3.7332 -  3.2669  1299   142  0.54  48.99   0.84     0.69     138946.41|
|  4:  3.2669 -  2.9708  1294   153  0.45  55.59   0.80     0.57     119670.66|
|  5:  2.9708 -  2.7593  1289   138  0.35  63.67   0.73     0.44      94229.37|
|  6:  2.7593 -  2.5975  1283   141  0.33  65.17   0.72     0.39      80324.51|
|  7:  2.5975 -  2.4680  1278   135  0.28  68.87   0.74     0.33      72441.32|
|  8:  2.4680 -  2.3610  1268   151  0.24  71.76   0.72     0.30      67761.30|
|  9:  2.3610 -  2.2705  1242   138  0.23  73.01   0.72     0.27      61986.22|
| 10:  2.2705 -  2.1924  1294   140  0.24  72.27   0.76     0.29      55882.51|
| 11:  2.1924 -  2.1240  1254   140  0.24  72.44   0.78     0.29      52450.62|
| 12:  2.1240 -  2.0635  1253   140  0.24  72.51   0.79     0.30      48302.79|
| 13:  2.0635 -  2.0093  1261   137  0.22  73.81   0.73     0.29      41790.23|
| 14:  2.0093 -  1.9604   898   103  0.24  72.32   0.71     0.27      32198.39|
|alpha:            min =        0.27 max =            0.74 mean =         0.42|
|beta:             min =    32198.39 max =       138946.41 mean =     80307.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.35|
|phase err.(work): min =        0.00 max =           89.98 mean =        63.36|
|phase err.(test): min =        0.00 max =           89.95 mean =        63.62|
|-----------------------------------------------------------------------------|

============================== 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 = 21.136740             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.074   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.293279              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.526   (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:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       37 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      177 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      729 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1545 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2694 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     4006 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5175 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6654 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7872 |
|-----------------------------------------------------------------------------|
|-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 |       52.911 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.087    4.900  1.196 |       2.242 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.438)------------------------------------------|
|    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 = 11.438)------------------------------------------|
|    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: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5049   r_free= 0.5012   ksol= 0.00   Bsol= 0.00   scale= 0.758    |
|                                                                             |
| 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:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.298883                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4915   r_free= 0.4863   ksol= 0.41   Bsol= 20.00   scale= 0.968   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.79,9.00,8.03,0.00,0.00,0.00); trace/3= 7.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.292406                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.416988             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.891   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.890181              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.038   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4915      final r-factor (work) = 0.4329          |
| start r-factor (free) = 0.4863      final r-factor (free) = 0.4532          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 104.5778 = 16.42 * 0.50 * 6.2943 + 1.00 * 52.9113                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 51.3874 = 16.42 * 0.50 * 6.2429 + 1.00 * 0.1428                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4329      final r-factor (work) = 0.3921          |
| start r-factor (free) = 0.4532      final r-factor (free) = 0.4472          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.8145 = 1.89 * 1.00 * 6.2429 + 1.00 * 0.0143                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.7190 = 1.89 * 1.00 * 6.1880 + 1.00 * 0.0225                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.438)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.27  15.84    None  None   None       |
|    all(noH): 2823   0      0.00    114.27  15.84    None  None   None       |
|    Sol.    : 438    0      0.00    114.27  25.15    None  None   None       |
|    Mac.    : 2385   0      0.00    100.88  14.13    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.427: 1297   |   5:    57.135 -  68.562:   20        |
|      1:    11.427 -  22.854:  837   |   6:    68.562 -  79.989:    5        |
|      2:    22.854 -  34.281:  416   |   7:    79.989 -  91.416:    3        |
|      3:    34.281 -  45.708:  160   |   8:    91.416 - 102.843:    2        |
|      4:    45.708 -  57.135:   82   |   9:   102.843 - 114.270:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3921 r_free = 0.4472             target_work(ml) = 6.180         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3918 r_free = 0.4478             target_work(ml) = 6.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3918   r_free= 0.4478   ksol= 0.41   Bsol= 20.00   scale= 1.106   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.79,9.00,8.03,0.00,0.00,0.00); trace/3= 7.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.179821                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3896   r_free= 0.4442   ksol= 0.37   Bsol= 37.79   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.86,4.89,4.98,0.00,0.00,0.00); trace/3= 4.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.180094                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.983144             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.185  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.725803              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.005  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3896      final r-factor (work) = 0.3233          |
| start r-factor (free) = 0.4442      final r-factor (free) = 0.3822          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.1877 = 11.98 * 0.50 * 6.1828 + 1.00 * 0.1428                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.6839 = 11.98 * 0.50 * 6.1057 + 1.00 * 0.1011                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3233      final r-factor (work) = 0.2990          |
| start r-factor (free) = 0.3822      final r-factor (free) = 0.3643          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4540 = 0.73 * 1.00 * 6.1057 + 1.00 * 0.0224                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3694 = 0.73 * 1.00 * 6.0012 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.438)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.50  15.39    None  None   None       |
|    all(noH): 2823   0      0.00    114.50  15.39    None  None   None       |
|    Sol.    : 438    0      0.00    114.50  29.96    None  None   None       |
|    Mac.    : 2385   0      0.00    101.58  12.72    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.450: 1363   |   5:    57.252 -  68.702:   16        |
|      1:    11.450 -  22.901:  862   |   6:    68.702 -  80.152:    2        |
|      2:    22.901 -  34.351:  354   |   7:    80.152 -  91.603:    3        |
|      3:    34.351 -  45.801:  150   |   8:    91.603 - 103.053:    3        |
|      4:    45.801 -  57.252:   69   |   9:   103.053 - 114.503:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2990 r_free = 0.3643             target_work(ml) = 5.980         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2987 r_free = 0.3643             target_work(ml) = 5.979         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2987   r_free= 0.3643   ksol= 0.37   Bsol= 37.79   scale= 1.076   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.86,4.89,4.98,0.00,0.00,0.00); trace/3= 4.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.979370                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2971   r_free= 0.3637   ksol= 0.35   Bsol= 45.09   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.71,2.39,2.80,0.00,0.00,0.00); trace/3= 2.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.979294                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.520657              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.355  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.745987              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.626  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2971      final r-factor (work) = 0.2377          |
| start r-factor (free) = 0.3637      final r-factor (free) = 0.3026          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.6621 = 4.52 * 0.50 * 5.9996 + 1.00 * 0.1011                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.3865 = 4.52 * 0.50 * 5.8912 + 1.00 * 0.0704                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2377      final r-factor (work) = 0.2157          |
| start r-factor (free) = 0.3026      final r-factor (free) = 0.2861          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4084 = 0.75 * 1.00 * 5.8912 + 1.00 * 0.0137                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3043 = 0.75 * 1.00 * 5.7516 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.438)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.30  15.49    None  None   None       |
|    all(noH): 2823   0      0.00    115.30  15.49    None  None   None       |
|    Sol.    : 438    0      2.46    115.30  37.41    None  None   None       |
|    Mac.    : 2385   0      0.00    107.12  11.47    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.530: 1558   |   5:    57.649 -  69.179:   46        |
|      1:    11.530 -  23.060:  683   |   6:    69.179 -  80.709:    6        |
|      2:    23.060 -  34.589:  247   |   7:    80.709 -  92.238:    1        |
|      3:    34.589 -  46.119:  179   |   8:    92.238 - 103.768:    3        |
|      4:    46.119 -  57.649:   97   |   9:   103.768 - 115.298:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2157 r_free = 0.2861             target_work(ml) = 5.724         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2153 r_free = 0.2858             target_work(ml) = 5.723         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2153   r_free= 0.2858   ksol= 0.35   Bsol= 45.09   scale= 1.049   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.71,2.39,2.80,0.00,0.00,0.00); trace/3= 2.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.722982                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2148   r_free= 0.2838   ksol= 0.33   Bsol= 40.97   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.86,1.09,1.82,0.00,0.00,0.00); trace/3= 1.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.721141                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.287599              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.965  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.281826              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.186  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2148      final r-factor (work) = 0.1659          |
| start r-factor (free) = 0.2838      final r-factor (free) = 0.2252          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.4035 = 4.29 * 0.50 * 5.7529 + 1.00 * 0.0704                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1022 = 4.29 * 0.50 * 5.6145 + 1.00 * 0.0657                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1659      final r-factor (work) = 0.1528          |
| start r-factor (free) = 0.2252      final r-factor (free) = 0.2061          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5961 = 0.28 * 1.00 * 5.6145 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5470 = 0.28 * 1.00 * 5.4554 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.438)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.66  14.80    None  None   None       |
|    all(noH): 2823   0      0.00    112.66  14.80    None  None   None       |
|    Sol.    : 438    0      3.69    112.66  38.42    None  None   None       |
|    Mac.    : 2385   0      0.00    104.71  10.46    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.266: 1717   |   5:    56.328 -  67.594:   45        |
|      1:    11.266 -  22.531:  583   |   6:    67.594 -  78.859:   14        |
|      2:    22.531 -  33.797:  186   |   7:    78.859 -  90.125:    1        |
|      3:    33.797 -  45.062:  157   |   8:    90.125 - 101.391:    2        |
|      4:    45.062 -  56.328:  115   |   9:   101.391 - 112.656:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1528 r_free = 0.2061             target_work(ml) = 5.409         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1524 r_free = 0.2054             target_work(ml) = 5.407         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1524   r_free= 0.2054   ksol= 0.33   Bsol= 40.97   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.86,1.09,1.82,0.00,0.00,0.00); trace/3= 1.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.406747                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1526   r_free= 0.2055   ksol= 0.32   Bsol= 36.52   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.44,0.22,1.29,0.00,0.00,0.00); trace/3= 0.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.405647                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.628390              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.740  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.344428              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.709  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1526      final r-factor (work) = 0.1286          |
| start r-factor (free) = 0.2055      final r-factor (free) = 0.1774          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9650 = 3.63 * 0.50 * 5.4566 + 1.00 * 0.0657                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7492 = 3.63 * 0.50 * 5.3366 + 1.00 * 0.0675                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1286      final r-factor (work) = 0.1225          |
| start r-factor (free) = 0.1774      final r-factor (free) = 0.1727          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1842 = 1.34 * 1.00 * 5.3366 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0543 = 1.34 * 1.00 * 5.2383 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.438)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.16  15.16    None  None   None       |
|    all(noH): 2823   0      0.00    112.16  15.16    None  None   None       |
|    Sol.    : 438    0      4.10    112.16  41.36    None  None   None       |
|    Mac.    : 2385   0      0.00    105.17  10.35    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.216: 1746   |   5:    56.081 -  67.297:   77        |
|      1:    11.216 -  22.432:  574   |   6:    67.297 -  78.513:   34        |
|      2:    22.432 -  33.648:  153   |   7:    78.513 -  89.729:    7        |
|      3:    33.648 -  44.865:  119   |   8:    89.729 - 100.945:    3        |
|      4:    44.865 -  56.081:  107   |   9:   100.945 - 112.161:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1225 r_free = 0.1727             target_work(ml) = 5.223         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1224 r_free = 0.1726             target_work(ml) = 5.223         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1224   r_free= 0.1726   ksol= 0.32   Bsol= 36.52   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.44,0.22,1.29,0.00,0.00,0.00); trace/3= 0.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.222783                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9113 -  4.6791 0.99   1386  155 0.1037 0.1377      5.4404      5.5951|
|  2:  4.6791 -  3.7332 0.99   1331  146 0.0917 0.1276      5.5055      5.7443|
|  3:  3.7332 -  3.2669 0.99   1299  142 0.1175 0.1554      5.5774      5.8825|
|  4:  3.2669 -  2.9708 0.99   1294  153 0.1370 0.1875      5.5684      5.7286|
|  5:  2.9708 -  2.7593 0.99   1289  138 0.1442 0.2021      5.4176      5.6645|
|  6:  2.7593 -  2.5975 0.99   1283  141 0.1325 0.1789       5.303      5.4903|
|  7:  2.5975 -  2.4680 0.99   1278  135 0.1389 0.1910      5.2684      5.5269|
|  8:  2.4680 -  2.3610 0.98   1268  151 0.1346 0.1844      5.1675      5.4323|
|  9:  2.3610 -  2.2705 0.98   1242  138 0.1290 0.1843      5.1116      5.3199|
| 10:  2.2705 -  2.1924 1.00   1294  140 0.1205 0.1907      5.0275      5.3302|
| 11:  2.1924 -  2.1240 0.97   1254  140 0.1226 0.1997      5.0183      5.3751|
| 12:  2.1240 -  2.0635 0.98   1253  140 0.1194 0.1715      4.9596      5.2093|
| 13:  2.0635 -  2.0093 1.00   1261  137 0.1193 0.1986      4.8404      5.1624|
| 14:  2.0093 -  1.9604 0.70    898  103 0.1131 0.1648      4.7008      4.9352|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9113 -  4.6791  1386   155  0.93  10.18   0.98     0.96       8526.94|
|  2:  4.6791 -  3.7332  1331   146  0.94   9.15   1.04     1.02      10649.45|
|  3:  3.7332 -  3.2669  1299   142  0.92  12.96   1.05     1.04      12614.00|
|  4:  3.2669 -  2.9708  1294   153  0.90  15.86   1.03     1.01      13054.19|
|  5:  2.9708 -  2.7593  1289   138  0.88  17.72   1.00     0.96      10014.79|
|  6:  2.7593 -  2.5975  1283   141  0.88  17.93   0.99     0.95       8680.62|
|  7:  2.5975 -  2.4680  1278   135  0.88  18.32   1.01     0.97       7946.34|
|  8:  2.4680 -  2.3610  1268   151  0.89  17.50   1.00     0.97       6391.74|
|  9:  2.3610 -  2.2705  1242   138  0.90  16.74   1.02     1.00       5857.95|
| 10:  2.2705 -  2.1924  1294   140  0.89  16.82   1.01     0.98       5113.40|
| 11:  2.1924 -  2.1240  1254   140  0.88  18.06   1.02     0.97       5185.52|
| 12:  2.1240 -  2.0635  1253   140  0.90  17.12   1.03     1.00       4844.30|
| 13:  2.0635 -  2.0093  1261   137  0.89  17.70   1.02     1.01       3811.74|
| 14:  2.0093 -  1.9604   898   103  0.91  14.93   1.00     0.98       2684.38|
|alpha:            min =        0.95 max =            1.04 mean =         0.99|
|beta:             min =     2684.38 max =        13054.19 mean =      7672.09|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.74|
|phase err.(test): min =        0.00 max =           90.00 mean =        15.11|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1227   r_free= 0.1725   ksol= 0.32   Bsol= 39.42   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.20,-0.38,0.58,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.222854                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1227   r_free= 0.1725   ksol= 0.32   Bsol= 39.42   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.20,-0.38,0.58,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.222854                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9113 -  4.6791 0.99   1386  155 0.1038 0.1371      5.4384      5.5874|
|  2:  4.6791 -  3.7332 0.99   1331  146 0.0929 0.1297      5.5148      5.7594|
|  3:  3.7332 -  3.2669 0.99   1299  142 0.1182 0.1555      5.5833      5.8879|
|  4:  3.2669 -  2.9708 0.99   1294  153 0.1375 0.1861      5.5699      5.7247|
|  5:  2.9708 -  2.7593 0.99   1289  138 0.1442 0.2014      5.4169        5.66|
|  6:  2.7593 -  2.5975 0.99   1283  141 0.1328 0.1783      5.3019      5.4887|
|  7:  2.5975 -  2.4680 0.99   1278  135 0.1391 0.1908      5.2674      5.5263|
|  8:  2.4680 -  2.3610 0.98   1268  151 0.1344 0.1831      5.1644      5.4277|
|  9:  2.3610 -  2.2705 0.98   1242  138 0.1288 0.1840      5.1098      5.3198|
| 10:  2.2705 -  2.1924 1.00   1294  140 0.1204 0.1907      5.0261      5.3302|
| 11:  2.1924 -  2.1240 0.97   1254  140 0.1220 0.1996      5.0171      5.3726|
| 12:  2.1240 -  2.0635 0.98   1253  140 0.1192 0.1717      4.9586      5.2099|
| 13:  2.0635 -  2.0093 1.00   1261  137 0.1192 0.1984      4.8387       5.161|
| 14:  2.0093 -  1.9604 0.70    898  103 0.1130 0.1645      4.6992      4.9331|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9113 -  4.6791  1386   155  0.93  10.05   0.98     0.96       8472.97|
|  2:  4.6791 -  3.7332  1331   146  0.94   9.25   1.04     1.02      10801.75|
|  3:  3.7332 -  3.2669  1299   142  0.92  13.09   1.05     1.04      12845.73|
|  4:  3.2669 -  2.9708  1294   153  0.90  15.81   1.03     1.00      12994.02|
|  5:  2.9708 -  2.7593  1289   138  0.89  17.69   1.00     0.96       9991.74|
|  6:  2.7593 -  2.5975  1283   141  0.89  17.89   0.99     0.95       8633.47|
|  7:  2.5975 -  2.4680  1278   135  0.88  18.26   1.00     0.97       7909.74|
|  8:  2.4680 -  2.3610  1268   151  0.89  17.44   1.00     0.97       6340.02|
|  9:  2.3610 -  2.2705  1242   138  0.90  16.72   1.01     1.00       5836.43|
| 10:  2.2705 -  2.1924  1294   140  0.89  16.78   1.01     0.98       5094.04|
| 11:  2.1924 -  2.1240  1254   140  0.88  18.05   1.01     0.96       5178.97|
| 12:  2.1240 -  2.0635  1253   140  0.90  17.10   1.02     1.00       4834.79|
| 13:  2.0635 -  2.0093  1261   137  0.89  17.68   1.02     1.00       3799.23|
| 14:  2.0093 -  1.9604   898   103  0.91  14.89   1.00     0.98       2672.72|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     2672.72 max =        12994.02 mean =      7674.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        15.72|
|phase err.(test): min =        0.00 max =           89.98 mean =        15.08|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.438)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.56    112.72  15.72    None  None   None       |
|    all(noH): 2823   0      0.56    112.72  15.72    None  None   None       |
|    Sol.    : 438    0      4.66    112.72  41.91    None  None   None       |
|    Mac.    : 2385   0      0.56    105.73  10.91    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:     0.560 -  11.776: 1746   |   5:    56.640 -  67.856:   77        |
|      1:    11.776 -  22.992:  574   |   6:    67.856 -  79.072:   34        |
|      2:    22.992 -  34.208:  153   |   7:    79.072 -  90.289:    7        |
|      3:    34.208 -  45.424:  119   |   8:    90.289 - 101.505:    3        |
|      4:    45.424 -  56.640:  107   |   9:   101.505 - 112.721:    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)= 324         
Filter by distance & map next to the model:
   mapped sites are within: 0.699 - 5.303
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 323 from: 324
   mapped sites are within: 0.729 - 5.303

peak=    9.458 closest distance to " CB  VAL A 230 " =    1.415
peak=    9.113 closest distance to " CG2 VAL A 296 " =    1.354
peak=    8.279 closest distance to " O   HOH Z 390 " =    1.278
peak=    7.803 closest distance to " O   HOH Z 130 " =    1.560
peak=    7.406 closest distance to " O   HOH Z 385 " =    1.378
peak=    7.303 closest distance to " CG  ARG A 138 " =    1.119
peak=    6.381 closest distance to " O   HOH Z  65 " =    1.428
peak=    5.933 closest distance to " CD2 LEU A   5 " =    1.303
peak=    5.891 closest distance to " O   HOH Z 278 " =    1.627
peak=    5.818 closest distance to " O   HOH Z 124 " =    1.747
peak=    5.806 closest distance to " O   HOH Z   7 " =    1.886
peak=    5.630 closest distance to " O   HOH Z 289 " =    1.311
peak=    5.604 closest distance to " NE2 GLN A  11 " =    1.237
peak=    5.573 closest distance to " O   HOH Z 142 " =    2.021
peak=    5.560 closest distance to " NH2 ARG A  56 " =    2.069
peak=    5.516 closest distance to " CB  VAL A 230 " =    1.183
peak=    5.454 closest distance to " O   HOH Z  28 " =    1.591
peak=    5.380 closest distance to " O   HOH Z 132 " =    1.380
peak=    5.275 closest distance to " O   HOH Z 403 " =    1.412
peak=    5.203 closest distance to " O   HOH Z 193 " =    1.860
peak=    5.098 closest distance to " O   PRO A 198 " =    1.298
peak=    5.061 closest distance to " O   HOH Z 424 " =    1.412
peak=    4.947 closest distance to " O   HOH Z 414 " =    1.350
peak=    4.945 closest distance to " O   HOH Z 427 " =    2.433
peak=    4.929 closest distance to " CD1AILE A 234 " =    1.000
peak=    4.917 closest distance to " O   HOH Z 375 " =    1.062
peak=    4.903 closest distance to " CG  PRO A 213 " =    1.233
peak=    4.877 closest distance to " CG  LEU A   5 " =    1.204
peak=    4.876 closest distance to " O   HOH Z 143 " =    1.543
peak=    4.872 closest distance to " CB  PRO A  54 " =    1.098
peak=    4.819 closest distance to " O   HOH Z  63 " =    1.661
peak=    4.711 closest distance to " O   HOH Z 344 " =    1.307
peak=    4.700 closest distance to " O   HOH Z 214 " =    1.513
peak=    4.677 closest distance to " O   HOH Z 374 " =    1.194
peak=    4.667 closest distance to " O   HOH Z 126 " =    1.830
peak=    4.598 closest distance to " O   HOH Z 427 " =    1.267
peak=    4.556 closest distance to " O   HOH Z 123 " =    1.259
peak=    4.540 closest distance to " O   HOH Z 222 " =    1.233
peak=    4.467 closest distance to " O   HOH Z 133 " =    1.540
peak=    4.456 closest distance to " O   HOH Z 316 " =    2.870
peak=    4.455 closest distance to " O   HOH Z 357 " =    1.391
peak=    4.447 closest distance to " O   HOH Z 202 " =    1.343
peak=    4.433 closest distance to " CD2 LEU A 228 " =    1.224
peak=    4.421 closest distance to " O   HOH Z 369 " =    2.262
peak=    4.411 closest distance to " CB  ARG A 275 " =    0.945
peak=    4.351 closest distance to " O   HOH Z  78 " =    1.669
peak=    4.334 closest distance to " O   HOH Z 425 " =    1.478
peak=    4.299 closest distance to " O   HOH Z 423 " =    1.651
peak=    4.290 closest distance to " O   HOH Z 232 " =    2.150
peak=    4.275 closest distance to " O   HOH Z 117 " =    1.888
peak=    4.259 closest distance to " CG  PRO A  54 " =    1.167
peak=    4.230 closest distance to " CB  GLN A 183 " =    1.216
peak=    4.221 closest distance to " O   HOH Z 112 " =    1.141
peak=    4.200 closest distance to " O   HOH Z 193 " =    1.585
peak=    4.194 closest distance to " CG  GLN A  11 " =    2.193
peak=    4.132 closest distance to " O   HOH Z   2 " =    1.983
peak=    4.121 closest distance to " CB  SER A   3 " =    1.297
peak=    4.119 closest distance to " CG  PRO A 198 " =    1.339
peak=    4.117 closest distance to " CB  VAL A 121 " =    1.043
peak=    4.111 closest distance to " O   HOH Z 260 " =    1.261
peak=    4.110 closest distance to " O   HOH Z   1 " =    1.824
peak=    4.105 closest distance to " OG  SER A  62 " =    3.194
peak=    4.082 closest distance to " O   HOH Z 236 " =    1.698
peak=    4.069 closest distance to " O   HOH Z  91 " =    2.510
peak=    4.064 closest distance to " CB  ASN A 148 " =    1.197
peak=    4.062 closest distance to " O   HOH Z 411 " =    3.570
peak=    4.062 closest distance to " CA  LEU A 282 " =    1.021
peak=    4.047 closest distance to " O   HOH Z 207 " =    2.240
peak=    4.042 closest distance to " OD2 ASP A 286 " =    2.537
peak=    4.021 closest distance to " CB  SER A 216 " =    0.991
peak=    4.019 closest distance to " O   HOH Z 227 " =    1.871
peak=    4.014 closest distance to " O   HOH Z 347 " =    0.964
peak=    4.012 closest distance to " O   HOH Z 158 " =    1.343
peak=    4.009 closest distance to " O   HOH Z  50 " =    1.356
peak=    4.006 closest distance to " O   HOH Z 298 " =    1.833
peak=    4.005 closest distance to " O   HOH Z 272 " =    1.809
peak=    4.001 closest distance to " O   HOH Z 426 " =    1.163
peak=    3.994 closest distance to " O   HOH Z 334 " =    2.857
peak=    3.983 closest distance to " O   HOH Z  97 " =    1.270
peak=    3.979 closest distance to " O   HOH Z 108 " =    1.561
peak=    3.975 closest distance to " CB  GLU A 277 " =    3.510
peak=    3.970 closest distance to " O   HOH Z  59 " =    1.508
peak=    3.961 closest distance to " CB  TYR A 169 " =    0.934
peak=    3.960 closest distance to " O   HOH Z  22 " =    2.034
peak=    3.940 closest distance to " CG  LEU A 228 " =    1.081
peak=    3.933 closest distance to " CB  VAL A 296 " =    1.033
peak=    3.922 closest distance to " O   HOH Z 259 " =    2.115
peak=    3.916 closest distance to " O   HOH Z 145 " =    2.199
peak=    3.910 closest distance to " CB  TRP A 179 " =    1.352
peak=    3.910 closest distance to " NE1 TRP A 274 " =    1.020
peak=    3.903 closest distance to " O   HOH Z  61 " =    1.519
peak=    3.889 closest distance to " O   HOH Z 263 " =    1.493
peak=    3.875 closest distance to " CG  TRP A 179 " =    2.254
peak=    3.871 closest distance to " O   HOH Z 422 " =    2.464
peak=    3.869 closest distance to " CE AMET A  47 " =    1.296
peak=    3.868 closest distance to " O   HOH Z 130 " =    2.455
peak=    3.853 closest distance to " O   HOH Z  37 " =    1.274
peak=    3.852 closest distance to " O   HOH Z 371 " =    2.905
peak=    3.849 closest distance to " CB  VAL A 265 " =    1.259
peak=    3.843 closest distance to " CB  SER A  63 " =    1.288
peak=    3.839 closest distance to " O   HOH Z 371 " =    1.804
peak=    3.825 closest distance to " O   HOH Z 147 " =    1.444
peak=    3.819 closest distance to " O   HOH Z 378 " =    1.098
peak=    3.812 closest distance to " O   HOH Z  88 " =    3.028
peak=    3.796 closest distance to " O   HOH Z   9 " =    1.045
peak=    3.792 closest distance to " O   HOH Z 128 " =    2.075
peak=    3.776 closest distance to " O   HOH Z 405 " =    1.545
peak=    3.775 closest distance to " O   HOH Z 220 " =    1.403
peak=    3.770 closest distance to " CG  GLN A  88 " =    1.131
peak=    3.769 closest distance to " O   HOH Z  51 " =    1.225
peak=    3.766 closest distance to " CB  GLN A 223 " =    1.454
peak=    3.766 closest distance to " CA  PHE A 283 " =    1.365
peak=    3.762 closest distance to " O   HOH Z 384 " =    1.700
peak=    3.745 closest distance to " O   HOH Z 251 " =    1.662
peak=    3.744 closest distance to " O   HOH Z 380 " =    1.830
peak=    3.743 closest distance to " O   HOH Z 406 " =    1.644
peak=    3.739 closest distance to " O   HOH Z 247 " =    1.258
peak=    3.734 closest distance to " O   HOH Z 217 " =    3.417
peak=    3.734 closest distance to " O   HOH Z 287 " =    1.922
peak=    3.733 closest distance to " O   HOH Z 390 " =    2.439
peak=    3.725 closest distance to " O   HOH Z 189 " =    2.372
peak=    3.722 closest distance to " O   HOH Z 359 " =    1.265
peak=    3.715 closest distance to " CG  GLN A  77 " =    2.179
peak=    3.715 closest distance to " CG2 THR A 221 " =    1.252
peak=    3.714 closest distance to " O   HOH Z 120 " =    1.057
peak=    3.706 closest distance to " O   HOH Z 225 " =    1.496
peak=    3.691 closest distance to " O   HOH Z 419 " =    2.057
peak=    3.685 closest distance to " CB  GLU A 128 " =    1.036
peak=    3.677 closest distance to " O   HOH Z 222 " =    1.968
peak=    3.675 closest distance to " CB  VAL A 202 " =    1.680
peak=    3.672 closest distance to " CB  MET A  40 " =    0.934
peak=    3.667 closest distance to " NH1 ARG A 138 " =    1.020
peak=    3.665 closest distance to " O   HOH Z 148 " =    1.764
peak=    3.660 closest distance to " O   HOH Z  97 " =    1.538
peak=    3.654 closest distance to " O   HOH Z 134 " =    1.476
peak=    3.653 closest distance to " O   HOH Z 245 " =    1.307
peak=    3.647 closest distance to " O   HOH Z 326 " =    1.389
peak=    3.635 closest distance to " O   HOH Z 368 " =    1.989
peak=    3.626 closest distance to " CB  ARG A  79 " =    1.410
peak=    3.621 closest distance to " O   HOH Z  64 " =    2.047
peak=    3.614 closest distance to " CG  LEU A 167 " =    1.154
peak=    3.607 closest distance to " CA  ASN A 127 " =    1.123
peak=    3.606 closest distance to " O   HOH Z 130 " =    1.749
peak=    3.604 closest distance to " NZ  LYS A 117 " =    1.040
peak=    3.600 closest distance to " O   HOH Z 108 " =    1.670
peak=    3.600 closest distance to " NH2 ARG A 219 " =    1.782
peak=    3.600 closest distance to " O   HOH Z 392 " =    1.346
peak=    3.599 closest distance to " O   HOH Z 250 " =    1.395
peak=    3.597 closest distance to " O   HOH Z 180 " =    2.172
peak=    3.595 closest distance to " CB  ALA A   1 " =    0.984
peak=    3.589 closest distance to " O   HOH Z 425 " =    2.060
peak=    3.588 closest distance to " CG2 VAL A 257 " =    0.873
peak=    3.583 closest distance to " CB  GLU A 152 " =    1.334
peak=    3.578 closest distance to " CG  LYS A 166 " =    1.296
peak=    3.577 closest distance to " O   HOH Z 184 " =    1.221
peak=    3.571 closest distance to " CG1 ILE A 120 " =    1.361
peak=    3.566 closest distance to " O   HOH Z 350 " =    1.390
peak=    3.565 closest distance to " O   HOH Z 358 " =    1.343
peak=    3.560 closest distance to " O   HOH Z 234 " =    3.500
peak=    3.559 closest distance to " O   HOH Z 410 " =    1.522
peak=    3.538 closest distance to " NH2BARG A 145 " =    1.416
peak=    3.533 closest distance to " O   HOH Z 302 " =    1.326
peak=    3.532 closest distance to " O   HOH Z 209 " =    2.280
peak=    3.527 closest distance to " CA  ILE A 234 " =    0.949
peak=    3.525 closest distance to " NH1AARG A 145 " =    0.915
peak=    3.523 closest distance to " OG BSER A 212 " =    2.749
peak=    3.515 closest distance to " CA  ALA A 158 " =    1.160
peak=    3.509 closest distance to " CB BVAL A  41 " =    1.140
peak=    3.508 closest distance to " CZ AARG A 102 " =    1.861
peak=    3.506 closest distance to " CA  ALA A 295 " =    1.031
peak=    3.498 closest distance to " O   ALA A 165 " =    1.260
peak=    3.494 closest distance to " CA  VAL A 126 " =    1.334
peak=    3.492 closest distance to " NH2BARG A 190 " =    1.578
peak=    3.485 closest distance to " O   HOH Z 130 " =    1.824
peak=    3.478 closest distance to " O   HOH Z 345 " =    3.165
peak=    3.464 closest distance to " O   HOH Z 428 " =    1.086
peak=    3.464 closest distance to " O   HOH Z 214 " =    1.791
peak=    3.463 closest distance to " O   HOH Z 290 " =    0.940
peak=    3.457 closest distance to " O   HOH Z 361 " =    1.623
peak=    3.455 closest distance to " O   HOH Z 365 " =    3.477
peak=    3.448 closest distance to " O   HOH Z  64 " =    2.097
peak=    3.434 closest distance to " O   HOH Z 303 " =    1.708
peak=    3.434 closest distance to " CG1 VAL A 153 " =    0.851
peak=    3.432 closest distance to " O   HOH Z  94 " =    2.512
peak=    3.426 closest distance to " O   HOH Z  39 " =    1.184
peak=    3.425 closest distance to " CG  LYS A  76 " =    1.456
peak=    3.419 closest distance to " OD1 ASN A 217 " =    1.692
peak=    3.412 closest distance to " CB  SER A 276 " =    1.139
peak=    3.407 closest distance to " CA  TYR A  30 " =    1.094
peak=    3.403 closest distance to " NE2 GLN A  73 " =    1.635
peak=    3.400 closest distance to " CA  LEU A 101 " =    1.640
peak=    3.396 closest distance to " O   HOH Z 293 " =    1.423
peak=    3.394 closest distance to " O   HOH Z  47 " =    1.750
peak=    3.389 closest distance to " O   HOH Z 402 " =    1.612
peak=    3.389 closest distance to " OD1 ASN A  69 " =    2.707
peak=    3.387 closest distance to " O   HOH Z 375 " =    2.100
peak=    3.374 closest distance to " O   HOH Z 155 " =    1.628
peak=    3.373 closest distance to " N   PHE A 130 " =    1.275
peak=    3.371 closest distance to " NE2 GLN A  58 " =    5.303
peak=    3.371 closest distance to " O   HOH Z 278 " =    1.196
peak=    3.368 closest distance to " O   HOH Z  55 " =    2.192
peak=    3.368 closest distance to " CB  PHE A 225 " =    1.249
peak=    3.366 closest distance to " O   HOH Z  49 " =    1.311
peak=    3.366 closest distance to " O   HOH Z 383 " =    2.322
peak=    3.362 closest distance to " O   HOH Z 393 " =    1.335
peak=    3.359 closest distance to " O   HOH Z  30 " =    1.760
peak=    3.354 closest distance to " NE2 GLN A  58 " =    2.987
peak=    3.352 closest distance to " O   ASN A 217 " =    1.140
peak=    3.348 closest distance to " O   HOH Z 152 " =    2.113
peak=    3.347 closest distance to " CG2 THR A 220 " =    1.028
peak=    3.342 closest distance to " O   GLY A 302 " =    1.913
peak=    3.335 closest distance to " OE2 GLU A  53 " =    2.049
peak=    3.331 closest distance to " O   HOH Z   9 " =    1.826
peak=    3.330 closest distance to " O   HOH Z 389 " =    1.226
peak=    3.326 closest distance to " N   TYR A  15 " =    1.021
peak=    3.325 closest distance to " NE AARG A 275 " =    1.453
peak=    3.324 closest distance to " O   HOH Z 276 " =    1.491
peak=    3.322 closest distance to " CB  ARG A 139 " =    1.055
peak=    3.321 closest distance to " CB  LEU A 255 " =    0.907
peak=    3.320 closest distance to " O   HOH Z 126 " =    1.462
peak=    3.320 closest distance to " O   HOH Z 281 " =    2.371
peak=    3.318 closest distance to " CG2 ILE A 234 " =    0.808
peak=    3.316 closest distance to " O   HOH Z 166 " =    1.252
peak=    3.316 closest distance to " O   HOH Z 258 " =    2.141
peak=    3.311 closest distance to " O   HOH Z 119 " =    1.491
peak=    3.307 closest distance to " O   HOH Z  94 " =    1.609
peak=    3.301 closest distance to " O   HOH Z 213 " =    2.032
peak=    3.298 closest distance to " CG  ARG A 159 " =    0.921
peak=    3.297 closest distance to " O   HOH Z 205 " =    0.934
peak=    3.294 closest distance to " O   GLY A 302 " =    1.621
peak=    3.290 closest distance to " O   HOH Z 305 " =    3.275
peak=    3.290 closest distance to " O   HOH Z 368 " =    3.652
peak=    3.290 closest distance to " O   HOH Z  29 " =    1.857
peak=    3.290 closest distance to " O   HOH Z 146 " =    1.609
peak=    3.289 closest distance to " CB  ARG A 138 " =    1.396
peak=    3.288 closest distance to " O   HOH Z 284 " =    1.498
peak=    3.285 closest distance to " CD  LYS A 119 " =    1.716
peak=    3.281 closest distance to " NH1 ARG A  14 " =    0.977
peak=    3.279 closest distance to " CB  PHE A  16 " =    0.932
peak=    3.277 closest distance to " O   HOH Z 176 " =    1.741
peak=    3.276 closest distance to " CA  ASN A  74 " =    1.230
peak=    3.276 closest distance to " O   HOH Z 279 " =    0.904
peak=    3.275 closest distance to " CG  MET A 185 " =    1.044
peak=    3.275 closest distance to " O   HOH Z 423 " =    1.256
peak=    3.272 closest distance to " OE2 GLU A   2 " =    1.946
peak=    3.272 closest distance to " CD2 LEU A 300 " =    0.931
peak=    3.266 closest distance to " CB  ASN A 142 " =    1.022
peak=    3.265 closest distance to " CA  ASN A 215 " =    1.123
peak=    3.260 closest distance to " CB  ASN A 148 " =    1.868
peak=    3.259 closest distance to " O   HOH Z 282 " =    1.478
peak=    3.258 closest distance to " O   HOH Z 248 " =    1.670
peak=    3.251 closest distance to " O   HOH Z 291 " =    1.456
peak=    3.249 closest distance to " OE1 GLU A   2 " =    2.130
peak=    3.248 closest distance to " CB  SER A 273 " =    0.822
peak=    3.243 closest distance to " CD1 LEU A 228 " =    1.549
peak=    3.243 closest distance to " O   HOH Z 327 " =    1.514
peak=    3.230 closest distance to " N   ALA A   1 " =    1.371
peak=    3.229 closest distance to " O   HOH Z  76 " =    0.976
peak=    3.229 closest distance to " CD  ARG A 269 " =    1.023
peak=    3.229 closest distance to " O   HOH Z  51 " =    1.720
peak=    3.223 closest distance to " CD BARG A 102 " =    1.159
peak=    3.221 closest distance to " CB  ASP A 124 " =    0.969
peak=    3.219 closest distance to " O   HOH Z 233 " =    1.636
peak=    3.219 closest distance to " OG BSER A  99 " =    2.184
peak=    3.217 closest distance to " O   HOH Z 433 " =    1.889
peak=    3.213 closest distance to " O   HOH Z 153 " =    3.625
peak=    3.213 closest distance to " CG1BVAL A 121 " =    2.274
peak=    3.208 closest distance to " CB  PHE A 204 " =    0.995
peak=    3.207 closest distance to " O   HOH Z 352 " =    1.572
peak=    3.202 closest distance to " CE  MET A  40 " =    1.088
peak=    3.200 closest distance to " O   HOH Z 417 " =    1.232
peak=    3.199 closest distance to " O   HOH Z 412 " =    1.644
peak=    3.198 closest distance to " OG  SER A  95 " =    1.455
peak=    3.197 closest distance to " O   HOH Z 389 " =    1.620
peak=    3.195 closest distance to " O   HOH Z  20 " =    1.338
peak=    3.195 closest distance to " O   HOH Z  61 " =    1.570
peak=    3.192 closest distance to " O   HOH Z 381 " =    1.056
peak=    3.190 closest distance to " CB  ASN A 187 " =    1.076
peak=    3.188 closest distance to " O   HOH Z  93 " =    2.035
peak=    3.187 closest distance to " O   HOH Z 353 " =    1.896
peak=    3.187 closest distance to " NE2 GLN A 223 " =    1.563
peak=    3.186 closest distance to " O   HOH Z 353 " =    2.235
peak=    3.181 closest distance to " CD  ARG A 159 " =    0.759
peak=    3.176 closest distance to " O   HOH Z 329 " =    3.388
peak=    3.174 closest distance to " OD1 ASP A 238 " =    0.885
peak=    3.174 closest distance to " CD1 ILE A  33 " =    1.686
peak=    3.173 closest distance to " CA  ALA A 114 " =    1.876
peak=    3.168 closest distance to " O   HOH Z  47 " =    1.829
peak=    3.161 closest distance to " O   HOH Z 143 " =    2.156
peak=    3.158 closest distance to " O   HOH Z 158 " =    3.327
peak=    3.157 closest distance to " O   HOH Z 110 " =    1.924
peak=    3.153 closest distance to " O   HOH Z 158 " =    2.352
peak=    3.151 closest distance to " O   HOH Z 385 " =    2.929
peak=    3.150 closest distance to " ND1 HIS A  86 " =    1.860
peak=    3.149 closest distance to " O   HOH Z 255 " =    1.793
peak=    3.142 closest distance to " O   GLY A 147 " =    1.499
peak=    3.138 closest distance to " O   HOH Z 128 " =    1.991
peak=    3.138 closest distance to " O   HOH Z 381 " =    0.951
peak=    3.135 closest distance to " CB  SER A  62 " =    1.202
peak=    3.131 closest distance to " O   HOH Z 344 " =    2.744
peak=    3.131 closest distance to " CB  LEU A 300 " =    0.914
peak=    3.130 closest distance to " ND1 HIS A  81 " =    1.577
peak=    3.129 closest distance to " C   ALA A 299 " =    0.919
peak=    3.126 closest distance to " CB  LYS A 290 " =    1.454
peak=    3.123 closest distance to " O   HOH Z 175 " =    2.165
peak=    3.123 closest distance to " O   HOH Z  89 " =    1.559
peak=    3.120 closest distance to " O   HOH Z 204 " =    1.668
peak=    3.111 closest distance to " O   MET A 105 " =    1.730
peak=    3.111 closest distance to " CB  ALA A 291 " =    1.515
peak=    3.110 closest distance to " OE1 GLN A 240 " =    1.528
peak=    3.110 closest distance to " CG  PRO A 280 " =    0.841
peak=    3.094 closest distance to " O   HOH Z 258 " =    1.374
peak=    3.085 closest distance to " NH1BARG A 145 " =    1.461
peak=    3.080 closest distance to " CA  ALA A  21 " =    1.013
peak=    3.078 closest distance to " CA  ARG A  56 " =    1.711
peak=    3.070 closest distance to " CB  TRP A 266 " =    1.051
peak=    3.070 closest distance to " O   HOH Z  48 " =    1.422
peak=    3.066 closest distance to " O   GLN A  58 " =    1.443
peak=    3.065 closest distance to " O   HOH Z 129 " =    0.729
peak=    3.064 closest distance to " O   HOH Z 102 " =    1.705
peak=    3.050 closest distance to " O   HOH Z   1 " =    1.463
peak=    3.049 closest distance to " O   HOH Z 392 " =    2.076
peak=    3.004 closest distance to " NH2BARG A 145 " =    0.818

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.447 - 5.662
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 198
   mapped sites are within: 0.738 - 5.662

peak=   -4.701 closest distance to " O   HOH Z  43 " =    1.853
peak=   -4.551 closest distance to " O   HOH Z 385 " =    0.873
peak=   -4.549 closest distance to " CD  ARG A 138 " =    1.283
peak=   -4.294 closest distance to " O   HOH Z 298 " =    1.032
peak=   -4.283 closest distance to " CG  ARG A 138 " =    0.936
peak=   -4.266 closest distance to " CG2 VAL A 230 " =    0.938
peak=   -4.205 closest distance to " CD  ARG A  14 " =    3.007
peak=   -4.183 closest distance to " NH2 ARG A  79 " =    1.921
peak=   -4.154 closest distance to " OG ASER A 134 " =    1.111
peak=   -4.109 closest distance to " OG BSER A 134 " =    1.195
peak=   -4.095 closest distance to " CA  TYR A  68 " =    2.743
peak=   -4.055 closest distance to " O   PRO A 198 " =    1.228
peak=   -4.040 closest distance to " NH1 ARG A  56 " =    2.427
peak=   -4.009 closest distance to " CA  GLY A 133 " =    1.923
peak=   -3.995 closest distance to " O   HOH Z 231 " =    1.656
peak=   -3.985 closest distance to " OD1 ASN A  39 " =    2.030
peak=   -3.980 closest distance to " O   HOH Z 111 " =    4.284
peak=   -3.960 closest distance to " CD  ARG A 156 " =    1.887
peak=   -3.941 closest distance to " O   GLY A  57 " =    1.306
peak=   -3.938 closest distance to " CD2 LEU A   5 " =    1.022
peak=   -3.913 closest distance to " O   HOH Z 162 " =    2.477
peak=   -3.902 closest distance to " O   PRO A 163 " =    2.049
peak=   -3.891 closest distance to " O   HOH Z 350 " =    1.808
peak=   -3.879 closest distance to " N   GLN A  58 " =    1.829
peak=   -3.847 closest distance to " O   HOH Z 407 " =    3.218
peak=   -3.842 closest distance to " O   HOH Z 266 " =    4.558
peak=   -3.838 closest distance to " O   GLY A  98 " =    2.061
peak=   -3.827 closest distance to " C   HIS A 108 " =    1.079
peak=   -3.824 closest distance to " O   VAL A  67 " =    2.828
peak=   -3.820 closest distance to " C   ILE A 239 " =    2.197
peak=   -3.796 closest distance to " N   HIS A 115 " =    1.992
peak=   -3.793 closest distance to " C   ASN A 285 " =    2.115
peak=   -3.790 closest distance to " CD1 LEU A 101 " =    2.277
peak=   -3.787 closest distance to " O   HOH Z 347 " =    0.967
peak=   -3.767 closest distance to " CG  PRO A 163 " =    2.578
peak=   -3.758 closest distance to " CD  LYS A 289 " =    2.526
peak=   -3.757 closest distance to " CD1 ILE A 239 " =    2.539
peak=   -3.742 closest distance to " OD2 ASP A  50 " =    1.539
peak=   -3.735 closest distance to " O   HOH Z 205 " =    0.843
peak=   -3.731 closest distance to " O   HOH Z 111 " =    1.021
peak=   -3.719 closest distance to " O   HOH Z  47 " =    1.501
peak=   -3.711 closest distance to " O   ILE A  49 " =    1.703
peak=   -3.696 closest distance to " O   SER A 146 " =    1.125
peak=   -3.680 closest distance to " CG2 THR A   4 " =    1.896
peak=   -3.679 closest distance to " O   SER A 135 " =    1.589
peak=   -3.673 closest distance to " O   HOH Z 385 " =    2.125
peak=   -3.670 closest distance to " O   HOH Z 388 " =    1.843
peak=   -3.655 closest distance to " OE1 GLU A 277 " =    2.228
peak=   -3.651 closest distance to " CG2 VAL A 257 " =    2.905
peak=   -3.648 closest distance to " O   HOH Z 359 " =    1.630
peak=   -3.634 closest distance to " CB  ALA A 248 " =    1.938
peak=   -3.626 closest distance to " C   ARG A 190 " =    1.141
peak=   -3.612 closest distance to " CG  PHE A 283 " =    2.539
peak=   -3.610 closest distance to " OG  SER A  87 " =    1.245
peak=   -3.608 closest distance to " O   HOH Z 126 " =    1.867
peak=   -3.596 closest distance to " OE2 GLU A 152 " =    0.909
peak=   -3.594 closest distance to " CA  GLY A  98 " =    1.861
peak=   -3.593 closest distance to " O   HOH Z 166 " =    1.917
peak=   -3.590 closest distance to " O   HOH Z 412 " =    5.662
peak=   -3.584 closest distance to " CE2 TYR A  30 " =    2.764
peak=   -3.583 closest distance to " O   HOH Z 140 " =    1.301
peak=   -3.567 closest distance to " O   SER A 216 " =    1.918
peak=   -3.567 closest distance to " O   HOH Z  13 " =    1.572
peak=   -3.566 closest distance to " CG2 THR A 178 " =    2.038
peak=   -3.563 closest distance to " O   ALA A  51 " =    1.335
peak=   -3.555 closest distance to " O   GLY A  80 " =    2.406
peak=   -3.552 closest distance to " CB  VAL A 230 " =    0.971
peak=   -3.547 closest distance to " N   ALA A   1 " =    1.147
peak=   -3.547 closest distance to " OG  SER A   3 " =    1.623
peak=   -3.545 closest distance to " ND2 ASN A  60 " =    1.257
peak=   -3.536 closest distance to " O   HOH Z  40 " =    4.245
peak=   -3.535 closest distance to " O   ALA A   1 " =    1.281
peak=   -3.532 closest distance to " O   HOH Z  88 " =    1.995
peak=   -3.530 closest distance to " CE3 TRP A 274 " =    2.483
peak=   -3.527 closest distance to " O   HOH Z 290 " =    1.166
peak=   -3.523 closest distance to " CB  ASP A  27 " =    2.481
peak=   -3.520 closest distance to " OH  TYR A 214 " =    1.233
peak=   -3.517 closest distance to " C   ALA A 158 " =    1.352
peak=   -3.515 closest distance to " CD1 LEU A 255 " =    2.814
peak=   -3.504 closest distance to " OG  SER A  26 " =    1.049
peak=   -3.503 closest distance to " O   HOH Z 414 " =    1.881
peak=   -3.497 closest distance to " O   HOH Z  75 " =    1.867
peak=   -3.489 closest distance to " CG  GLN A  88 " =    0.856
peak=   -3.481 closest distance to " O   HOH Z 131 " =    3.872
peak=   -3.475 closest distance to " O   HOH Z  51 " =    0.914
peak=   -3.472 closest distance to " CG  ARG A 219 " =    2.284
peak=   -3.462 closest distance to " N   ALA A 248 " =    1.673
peak=   -3.462 closest distance to " O   ASN A 301 " =    1.356
peak=   -3.459 closest distance to " O   HOH Z 339 " =    1.631
peak=   -3.450 closest distance to " CB  ASN A  39 " =    2.123
peak=   -3.448 closest distance to " N   GLN A  88 " =    1.686
peak=   -3.445 closest distance to " O   HOH Z 351 " =    1.458
peak=   -3.441 closest distance to " OG  SER A 245 " =    1.233
peak=   -3.423 closest distance to " C   TYR A  30 " =    1.040
peak=   -3.419 closest distance to " C   LEU A 143 " =    1.167
peak=   -3.417 closest distance to " O   HOH Z 365 " =    1.366
peak=   -3.417 closest distance to " CD  GLU A 152 " =    2.299
peak=   -3.414 closest distance to " O   HOH Z 189 " =    2.502
peak=   -3.412 closest distance to " CZ  PHE A  59 " =    1.476
peak=   -3.411 closest distance to " OG  SER A 206 " =    1.617
peak=   -3.410 closest distance to " O   HOH Z  76 " =    1.180
peak=   -3.408 closest distance to " CB  ALA A   7 " =    2.080
peak=   -3.403 closest distance to " CD1 ILE A 151 " =    2.341
peak=   -3.400 closest distance to " O   GLN A  11 " =    1.644
peak=   -3.398 closest distance to " O   PRO A 198 " =    1.217
peak=   -3.392 closest distance to " OG BSER A 134 " =    1.772
peak=   -3.387 closest distance to " CZ2 TRP A 179 " =    2.321
peak=   -3.385 closest distance to " O   HOH Z 137 " =    1.404
peak=   -3.383 closest distance to " O   HOH Z 198 " =    1.989
peak=   -3.382 closest distance to " N   LYS A 166 " =    1.888
peak=   -3.375 closest distance to " CE2 TYR A 116 " =    2.967
peak=   -3.372 closest distance to " O   HOH Z 103 " =    1.401
peak=   -3.370 closest distance to " O   SER A  22 " =    2.493
peak=   -3.365 closest distance to " OG1 THR A 178 " =    1.032
peak=   -3.361 closest distance to " CE2 PHE A 218 " =    2.577
peak=   -3.359 closest distance to " CG1 VAL A 268 " =    2.813
peak=   -3.354 closest distance to " O   ALA A 161 " =    1.850
peak=   -3.345 closest distance to " O   HOH Z  60 " =    1.758
peak=   -3.341 closest distance to " O   HOH Z 415 " =    1.288
peak=   -3.329 closest distance to " CG  ASN A 301 " =    1.951
peak=   -3.323 closest distance to " O   HOH Z 377 " =    1.069
peak=   -3.318 closest distance to " CG2AVAL A  41 " =    2.964
peak=   -3.317 closest distance to " N   GLN A  58 " =    1.376
peak=   -3.312 closest distance to " CG  MET A 105 " =    0.914
peak=   -3.308 closest distance to " O   HOH Z 222 " =    2.562
peak=   -3.304 closest distance to " NE2 GLN A 223 " =    1.419
peak=   -3.299 closest distance to " CG2 THR A  31 " =    2.231
peak=   -3.296 closest distance to " CG  ASP A 231 " =    0.738
peak=   -3.294 closest distance to " CA  GLY A  35 " =    1.982
peak=   -3.285 closest distance to " NH2 ARG A 159 " =    2.317
peak=   -3.284 closest distance to " O   VAL A 197 " =    1.483
peak=   -3.280 closest distance to " O   HOH Z 211 " =    1.607
peak=   -3.275 closest distance to " ND2BASN A 224 " =    1.627
peak=   -3.273 closest distance to " NH2AARG A 275 " =    5.329
peak=   -3.272 closest distance to " O   TRP A 179 " =    1.671
peak=   -3.269 closest distance to " N   PRO A 163 " =    1.587
peak=   -3.264 closest distance to " C   VAL A 265 " =    0.831
peak=   -3.264 closest distance to " N   SER A 276 " =    1.105
peak=   -3.263 closest distance to " O   HOH Z 389 " =    1.985
peak=   -3.262 closest distance to " O   GLN A  73 " =    1.526
peak=   -3.261 closest distance to " O   HOH Z  56 " =    1.831
peak=   -3.259 closest distance to " OD1 ASP A 200 " =    1.143
peak=   -3.259 closest distance to " CD2 LEU A 237 " =    2.563
peak=   -3.257 closest distance to " N   VAL A 125 " =    1.053
peak=   -3.255 closest distance to " O   HOH Z 125 " =    2.885
peak=   -3.254 closest distance to " CB  ALA A 227 " =    2.232
peak=   -3.253 closest distance to " O   HOH Z  54 " =    0.975
peak=   -3.249 closest distance to " C   GLY A 229 " =    1.222
peak=   -3.247 closest distance to " O   HOH Z 308 " =    1.663
peak=   -3.246 closest distance to " O   HOH Z 352 " =    1.822
peak=   -3.237 closest distance to " NE2 GLN A 194 " =    2.694
peak=   -3.235 closest distance to " CB  GLN A  55 " =    1.116
peak=   -3.235 closest distance to " CG  LEU A 228 " =    1.034
peak=   -3.234 closest distance to " CZ  PHE A  16 " =    1.485
peak=   -3.218 closest distance to " CD1 LEU A  96 " =    2.257
peak=   -3.217 closest distance to " O   HOH Z 185 " =    1.850
peak=   -3.215 closest distance to " CB  ALA A 244 " =    2.082
peak=   -3.214 closest distance to " O   HOH Z 424 " =    1.129
peak=   -3.207 closest distance to " O   HOH Z 158 " =    2.127
peak=   -3.206 closest distance to " OG ASER A 216 " =    1.109
peak=   -3.197 closest distance to " CG  ARG A  66 " =    2.127
peak=   -3.196 closest distance to " CG  LEU A 281 " =    1.705
peak=   -3.193 closest distance to " O   MET A  40 " =    2.738
peak=   -3.192 closest distance to " CB  PRO A  90 " =    1.404
peak=   -3.189 closest distance to " O   HOH Z 137 " =    1.581
peak=   -3.182 closest distance to " O   HOH Z 174 " =    4.864
peak=   -3.182 closest distance to " CG  GLU A 277 " =    1.172
peak=   -3.182 closest distance to " O   HOH Z 207 " =    1.973
peak=   -3.178 closest distance to " CA  SER A 245 " =    2.282
peak=   -3.176 closest distance to " C   ARG A 102 " =    1.482
peak=   -3.173 closest distance to " CD2 TRP A 150 " =    1.151
peak=   -3.169 closest distance to " O   HOH Z 235 " =    1.123
peak=   -3.163 closest distance to " CD1 TRP A 179 " =    1.217
peak=   -3.162 closest distance to " CB  PRO A 163 " =    2.555
peak=   -3.158 closest distance to " O   HOH Z 179 " =    1.969
peak=   -3.157 closest distance to " CG1 ILE A 263 " =    2.141
peak=   -3.156 closest distance to " CD2 LEU A 237 " =    2.296
peak=   -3.143 closest distance to " CG1 VAL A 296 " =    1.699
peak=   -3.143 closest distance to " O   HOH Z 317 " =    0.890
peak=   -3.135 closest distance to " O   HOH Z 210 " =    1.940
peak=   -3.132 closest distance to " O   HOH Z 364 " =    2.005
peak=   -3.130 closest distance to " O   HOH Z  61 " =    1.228
peak=   -3.124 closest distance to " O   HOH Z 396 " =    1.576
peak=   -3.119 closest distance to " O   HOH Z  60 " =    2.302
peak=   -3.119 closest distance to " O   HOH Z  97 " =    1.092
peak=   -3.116 closest distance to " CB  ALA A  51 " =    1.675
peak=   -3.116 closest distance to " C   PRO A  90 " =    1.564
peak=   -3.112 closest distance to " N   VAL A  72 " =    1.723
peak=   -3.108 closest distance to " ND2 ASN A 173 " =    1.655
peak=   -3.106 closest distance to " CE BMET A  47 " =    1.514
peak=   -3.105 closest distance to " O   HOH Z 404 " =    1.365
peak=   -3.095 closest distance to " OE1 GLN A  73 " =    2.462
peak=   -3.089 closest distance to " CD  GLN A  58 " =    1.051
peak=   -3.087 closest distance to " O   HOH Z 184 " =    0.872
peak=   -3.073 closest distance to " C   SER A 206 " =    1.364
peak=   -3.065 closest distance to " CB  CYS A 201 " =    2.520
peak=   -3.047 closest distance to " O   HOH Z 390 " =    2.347

================= 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    :  0.5000 0.4999   6.297956e+00   6.292037e+00
   1_bss:  0.4915 0.4863   6.292406e+00   6.282877e+00
   1_xyz:  0.4329 0.4532   6.226975e+00   6.249511e+00
   1_adp:  0.3921 0.4472   6.180046e+00   6.247004e+00
   1_occ:  0.3918 0.4478   6.179821e+00   6.247392e+00
   2_bss:  0.3896 0.4442   6.180094e+00   6.245465e+00
   2_xyz:  0.3233 0.3822   6.028236e+00   6.148244e+00
   2_adp:  0.2990 0.3643   5.979745e+00   6.115668e+00
   2_occ:  0.2987 0.3643   5.979370e+00   6.115468e+00
   3_bss:  0.2971 0.3637   5.979294e+00   6.115163e+00
   3_xyz:  0.2377 0.3026   5.796215e+00   5.962765e+00
   3_adp:  0.2157 0.2861   5.724079e+00   5.914545e+00
   3_occ:  0.2153 0.2858   5.722982e+00   5.914026e+00
   4_bss:  0.2148 0.2838   5.721141e+00   5.910812e+00
   4_xyz:  0.1659 0.2252   5.489762e+00   5.715077e+00
   4_adp:  0.1528 0.2061   5.408501e+00   5.631679e+00
   4_occ:  0.1524 0.2054   5.406747e+00   5.629495e+00
   5_bss:  0.1526 0.2055   5.405647e+00   5.627554e+00
   5_xyz:  0.1286 0.1774   5.259583e+00   5.498648e+00
   5_adp:  0.1225 0.1727   5.223426e+00   5.472124e+00
   5_occ:  0.1224 0.1726   5.222783e+00   5.471019e+00
   5_bss:  0.1227 0.1725   5.222854e+00   5.470434e+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:  0.411  19.999   5.786   9.002   8.027   0.000   0.000   0.000
   1_xyz:  0.411  19.999   5.786   9.002   8.027   0.000   0.000   0.000
   1_adp:  0.411  19.999   5.786   9.002   8.027   0.000   0.000   0.000
   1_occ:  0.411  19.999   5.786   9.002   8.027   0.000   0.000   0.000
   2_bss:  0.371  37.790   2.864   4.891   4.985   0.000   0.000   0.000
   2_xyz:  0.371  37.790   2.864   4.891   4.985   0.000   0.000   0.000
   2_adp:  0.371  37.790   2.864   4.891   4.985   0.000   0.000   0.000
   2_occ:  0.371  37.790   2.864   4.891   4.985   0.000   0.000   0.000
   3_bss:  0.351  45.090   1.710   2.389   2.800   0.000   0.000   0.000
   3_xyz:  0.351  45.090   1.710   2.389   2.800   0.000   0.000   0.000
   3_adp:  0.351  45.090   1.710   2.389   2.800   0.000   0.000   0.000
   3_occ:  0.351  45.090   1.710   2.389   2.800   0.000   0.000   0.000
   4_bss:  0.334  40.973   0.856   1.091   1.818   0.000   0.000   0.000
   4_xyz:  0.334  40.973   0.856   1.091   1.818   0.000   0.000   0.000
   4_adp:  0.334  40.973   0.856   1.091   1.818   0.000   0.000   0.000
   4_occ:  0.334  40.973   0.856   1.091   1.818   0.000   0.000   0.000
   5_bss:  0.319  36.521   0.437   0.222   1.294   0.000   0.000   0.000
   5_xyz:  0.319  36.521   0.437   0.222   1.294   0.000   0.000   0.000
   5_adp:  0.319  36.521   0.437   0.222   1.294   0.000   0.000   0.000
   5_occ:  0.319  36.521   0.437   0.222   1.294   0.000   0.000   0.000
   5_bss:  0.316  39.416  -0.196  -0.380   0.576   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  63.388 0.3501  0.4224    80308.568
   1_bss:  62.650 0.3585  0.5341    77064.811
   1_xyz:  54.702 0.4603  0.6766    63297.395
   1_adp:  53.287 0.4784  0.7696    62004.886
   1_occ:  53.402 0.4770  0.7669    62326.381
   2_bss:  53.170 0.4796  0.6877    61678.980
   2_xyz:  42.361 0.6132  0.8731    41614.216
   2_adp:  39.030 0.6540  0.9362    37223.471
   2_occ:  39.031 0.6539  0.9360    37201.109
   3_bss:  38.945 0.6548  0.8733    37094.655
   3_xyz:  30.628 0.7507  0.9681    23782.086
   3_adp:  28.129 0.7787  0.9821    21025.897
   3_occ:  28.103 0.7790  0.9816    20979.963
   4_bss:  28.015 0.7798  0.9448    20782.712
   4_xyz:  21.884 0.8429  0.9912    12892.099
   4_adp:  19.433 0.8675  0.9992    10869.639
   4_occ:  19.380 0.8680  0.9992    10791.913
   5_bss:  19.332 0.8683  0.9769    10705.383
   5_xyz:  16.332 0.8954  0.9918     8077.600
   5_adp:  15.694 0.9012  0.9874     7692.976
   5_occ:  15.676 0.9013  0.9874     7672.418
   5_bss:  15.654 0.9015  0.9842     7675.200
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.2911e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.2911e+01
   1_xyz:   1.694  0.013  0.106 18.384  0.007  4.106   1.4283e-01
   1_adp:   1.694  0.013  0.106 18.384  0.007  4.106   1.4283e-01
   1_occ:   1.694  0.013  0.106 18.384  0.007  4.106   1.4283e-01
   2_bss:   1.694  0.013  0.106 18.384  0.007  4.106   1.4283e-01
   2_xyz:   1.270  0.009  0.089 16.596  0.006  4.104   1.0105e-01
   2_adp:   1.270  0.009  0.089 16.596  0.006  4.104   1.0105e-01
   2_occ:   1.270  0.009  0.089 16.596  0.006  4.104   1.0105e-01
   3_bss:   1.270  0.009  0.089 16.596  0.006  4.104   1.0105e-01
   3_xyz:   1.100  0.007  0.077 15.745  0.004  4.106   7.0448e-02
   3_adp:   1.100  0.007  0.077 15.745  0.004  4.106   7.0448e-02
   3_occ:   1.100  0.007  0.077 15.745  0.004  4.106   7.0448e-02
   4_bss:   1.100  0.007  0.077 15.745  0.004  4.106   7.0448e-02
   4_xyz:   1.023  0.007  0.075 15.567  0.004  4.110   6.5741e-02
   4_adp:   1.023  0.007  0.075 15.567  0.004  4.110   6.5741e-02
   4_occ:   1.023  0.007  0.075 15.567  0.004  4.110   6.5741e-02
   5_bss:   1.023  0.007  0.075 15.567  0.004  4.110   6.5741e-02
   5_xyz:   1.072  0.007  0.077 15.786  0.004  4.115   6.7545e-02
   5_adp:   1.072  0.007  0.077 15.786  0.004  4.115   6.7545e-02
   5_occ:   1.072  0.007  0.077 15.786  0.004  4.115   6.7545e-02
   5_bss:   1.072  0.007  0.077 15.786  0.004  4.115   6.7545e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8562e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8562e+00
   1_xyz:  13.267  0.171  0.442 86.370  0.052  2.159   9.6497e-02
   1_adp:  13.267  0.171  0.442 86.370  0.052  2.159   9.6497e-02
   1_occ:  13.267  0.171  0.442 86.370  0.052  2.159   9.6497e-02
   2_bss:  13.267  0.171  0.442 86.370  0.052  2.159   9.6497e-02
   2_xyz:   7.674  0.068  0.401 82.341  0.054  2.223   6.9118e-02
   2_adp:   7.674  0.068  0.401 82.341  0.054  2.223   6.9118e-02
   2_occ:   7.674  0.068  0.401 82.341  0.054  2.223   6.9118e-02
   3_bss:   7.674  0.068  0.401 82.341  0.054  2.223   6.9118e-02
   3_xyz:   7.503  0.057  0.260 89.057  0.041  2.282   4.8044e-02
   3_adp:   7.503  0.057  0.260 89.057  0.041  2.282   4.8044e-02
   3_occ:   7.503  0.057  0.260 89.057  0.041  2.282   4.8044e-02
   4_bss:   7.503  0.057  0.260 89.057  0.041  2.282   4.8044e-02
   4_xyz:   7.191  0.044  0.316 79.362  0.033  2.323   5.7007e-02
   4_adp:   7.191  0.044  0.316 79.362  0.033  2.323   5.7007e-02
   4_occ:   7.191  0.044  0.316 79.362  0.033  2.323   5.7007e-02
   5_bss:   7.191  0.044  0.316 79.362  0.033  2.323   5.7007e-02
   5_xyz:   7.482  0.057  0.412 81.915  0.030  2.267   4.9189e-02
   5_adp:   7.482  0.057  0.412 81.915  0.030  2.267   4.9189e-02
   5_occ:   7.482  0.057  0.412 81.915  0.030  2.267   4.9189e-02
   5_bss:   7.482  0.057  0.412 81.915  0.030  2.267   4.9189e-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: 114.27   0.00  15.84 100.88   0.00  14.13 114.27   0.00  25.15
   1_occ: 114.27   0.00  15.84 100.88   0.00  14.13 114.27   0.00  25.15
   2_bss: 114.27   0.00  15.84 100.88   0.00  14.13 114.27   0.00  25.15
   2_xyz: 114.27   0.00  15.84 100.88   0.00  14.13 114.27   0.00  25.15
   2_adp: 114.50   0.00  15.39 101.58   0.00  12.72 114.50   0.00  29.96
   2_occ: 114.50   0.00  15.39 101.58   0.00  12.72 114.50   0.00  29.96
   3_bss: 114.50   0.00  15.39 101.58   0.00  12.72 114.50   0.00  29.96
   3_xyz: 114.50   0.00  15.39 101.58   0.00  12.72 114.50   0.00  29.96
   3_adp: 115.30   0.00  15.49 107.12   0.00  11.47 115.30   2.46  37.41
   3_occ: 115.30   0.00  15.49 107.12   0.00  11.47 115.30   2.46  37.41
   4_bss: 115.30   0.00  15.49 107.12   0.00  11.47 115.30   2.46  37.41
   4_xyz: 115.30   0.00  15.49 107.12   0.00  11.47 115.30   2.46  37.41
   4_adp: 112.66   0.00  14.80 104.71   0.00  10.46 112.66   3.69  38.42
   4_occ: 112.66   0.00  14.80 104.71   0.00  10.46 112.66   3.69  38.42
   5_bss: 112.66   0.00  14.80 104.71   0.00  10.46 112.66   3.69  38.42
   5_xyz: 112.66   0.00  14.80 104.71   0.00  10.46 112.66   3.69  38.42
   5_adp: 112.16   0.00  15.16 105.17   0.00  10.35 112.16   4.10  41.36
   5_occ: 112.16   0.00  15.16 105.17   0.00  10.35 112.16   4.10  41.36
   5_bss: 112.72   0.56  15.72 105.73   0.56  10.91 112.72   4.66  41.91
------------------------------------------------------------------------
 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:    1.248    0.023    0.409
   1_adp:    1.248    0.023    0.409
   1_occ:    1.248    0.023    0.409
   2_bss:    1.248    0.023    0.409
   2_xyz:    1.629    0.023    0.595
   2_adp:    1.629    0.023    0.595
   2_occ:    1.629    0.023    0.595
   3_bss:    1.629    0.023    0.595
   3_xyz:    1.644    0.046    0.701
   3_adp:    1.644    0.046    0.701
   3_occ:    1.644    0.046    0.701
   4_bss:    1.644    0.046    0.701
   4_xyz:    1.823    0.066    0.804
   4_adp:    1.823    0.066    0.804
   4_occ:    1.823    0.066    0.804
   5_bss:    1.823    0.066    0.804
   5_xyz:    2.020    0.063    0.846
   5_adp:    2.020    0.063    0.846
   5_occ:    2.020    0.063    0.846
   5_bss:    2.020    0.063    0.846
------------------------------------------------------------------------

CPU time actual refinement: 333.86


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_617/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_617/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_617/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_617/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_617/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 333.71 
  Macro-tasks:
    bulk solvent and scale       = 41.08  
    individual site refinement   = 132.56 
    weights calculation          = 31.93  
    collect and process          = 6.52   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 212.21 
  Micro-tasks:
    mask                            = 2.93   
    f_calc                          = 103.92 
    alpha_beta                      = 8.47   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 112.03 
    fmodel                         = 6.96   
    r_factors                      = 0.30   
    phase_errors                   = 10.11  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 246.18 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.775 micro seconds
Total CPU time: 5.79 minutes
from_scatterers_fft:    634 calls, 103.63 s
gradients_fft:          578 calls,  99.53 s

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

# Date 2008-01-16 Time 02:01:56 PST -0800 (1200477716.21 s)
Start R-work = 0.5000, R-free = 0.4999 (no bulk solvent and anisotropic scale)
Final R-work = 0.1382, R-free = 0.1877 (no bulk solvent and anisotropic scale)

Start R-work = 0.4915, R-free = 0.4863
Final R-work = 0.1227, R-free = 0.1725