# Date 2008-01-16 Time 05:22:21 PST -0800 (1200489741.23 s)
#phil __OFF__

Command line arguments: "../705.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 20133
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 705

-------------------------------------------------------------------------------
  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.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 47.8686, 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: 2.79, per 1000 atoms: 0.99


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.8686, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9307 1.9615
Completeness in resolution range: 0.93139
Completeness with d_max=infinity: 0.928609

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9307
                             d_min =   1.9615

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, 47.8686, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9307 1.9615
Completeness in resolution range: 0.93139
Completeness with d_max=infinity: 0.928609

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9311 -  4.1976 [2212/2241]  1990   222  10.0%
  bin  2:  4.1976 -  3.3440 [2110/2133]  1901   209   9.9%
  bin  3:  3.3440 -  2.9249 [2084/2109]  1873   211  10.1%
  bin  4:  2.9249 -  2.6591 [2074/2091]  1870   204   9.8%
  bin  5:  2.6591 -  2.4695 [2073/2116]  1864   209  10.1%
  bin  6:  2.4695 -  2.3244 [2050/2078]  1852   198   9.7%
  bin  7:  2.3244 -  2.2084 [2021/2057]  1816   205  10.1%
  bin  8:  2.2084 -  2.1126 [2030/2072]  1823   207  10.2%
  bin  9:  2.1126 -  2.0314 [2009/2066]  1804   205  10.2%
  bin 10:  2.0314 -  1.9615 [ 926/2069]   837    89   9.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_705/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.64 -     2.29: 25
        2.29 -     2.94: 1645
        2.94 -     3.60: 4473
        3.60 -     4.25: 9204
        4.25 -     4.90: 13029
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   TYR A 214 " - " O   HOH Z 204 "  1.638 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.641 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.654 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.706 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.716 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28371 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 =====================


==================== 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/noshake/run_705/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_705/model_refine_001.geo

CPU time processing inputs: 8.11


============================ 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 47.8686 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
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4413   r_free= 0.4326   ksol= 0.00   Bsol= 0.00   scale= 0.908    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.255014                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9311 -  4.6819 0.99   1434  163 0.3517 0.3632      6.5155      6.5298|
|  2:  4.6819 -  3.7353 0.99   1377  147 0.3730 0.3784      6.7717      6.7346|
|  3:  3.7353 -  3.2688 0.99   1349  153 0.4055 0.3821      6.6211      6.6558|
|  4:  3.2688 -  2.9725 0.99   1344  147 0.4189 0.3983      6.4635      6.4266|
|  5:  2.9725 -  2.7609 0.99   1339  149 0.4505 0.4259      6.3288       6.289|
|  6:  2.7609 -  2.5990 0.99   1325  150 0.4787 0.4373      6.2565      6.1448|
|  7:  2.5990 -  2.4695 0.98   1330  146 0.4713 0.4116      6.2203      6.1629|
|  8:  2.4695 -  2.3624 0.98   1311  144 0.4925 0.5309      6.1405      6.1869|
|  9:  2.3624 -  2.2718 0.99   1317  143 0.5208 0.4958      6.1287      6.1149|
| 10:  2.2718 -  2.1936 0.98   1311  148 0.4829 0.5138      6.0744      6.1255|
| 11:  2.1936 -  2.1252 0.97   1287  143 0.5099 0.5195      6.0264      6.0064|
| 12:  2.1252 -  2.0647 0.99   1301  150 0.4858 0.5243      5.9289      5.9867|
| 13:  2.0647 -  2.0104 0.91   1200  133 0.5012 0.4534       5.865      5.8255|
| 14:  2.0104 -  1.9615 0.30    405   43 0.5449 0.4573      5.8249       5.708|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9311 -  4.6819  1434   163  0.71  33.70   0.84     0.73      68871.24|
|  2:  4.6819 -  3.7353  1377   147  0.73  32.27   0.92     0.82      89015.86|
|  3:  3.7353 -  3.2688  1349   153  0.66  39.08   0.93     0.83      92362.06|
|  4:  3.2688 -  2.9725  1344   147  0.59  44.53   0.93     0.79      80560.21|
|  5:  2.9725 -  2.7609  1339   149  0.54  48.51   0.90     0.74      64811.94|
|  6:  2.7609 -  2.5990  1325   150  0.51  51.18   0.92     0.71      56036.35|
|  7:  2.5990 -  2.4695  1330   146  0.50  52.18   0.93     0.67      52230.57|
|  8:  2.4695 -  2.3624  1311   144  0.42  58.45   0.90     0.61      53495.76|
|  9:  2.3624 -  2.2718  1317   143  0.38  61.14   0.92     0.56      50559.00|
| 10:  2.2718 -  2.1936  1311   148  0.34  64.62   0.96     0.50      51244.71|
| 11:  2.1936 -  2.1252  1287   143  0.31  66.94   0.94     0.47      47900.54|
| 12:  2.1252 -  2.0647  1301   150  0.28  69.07   0.95     0.45      45681.73|
| 13:  2.0647 -  2.0104  1200   133  0.33  65.46   0.96     0.51      36009.41|
| 14:  2.0104 -  1.9615   405    43  0.41  58.98   0.91     0.63      27013.89|
|alpha:            min =        0.45 max =            0.83 mean =         0.65|
|beta:             min =    27013.89 max =        92362.06 mean =     60342.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           90.00 mean =        52.63|
|phase err.(test): min =        0.00 max =           89.98 mean =        52.79|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.013725             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.376   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.265852              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.004   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.638 -  1.964:       11 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.964 -  2.290:       14 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.290 -  2.616:       54 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.616 -  2.943:     1591 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.943 -  3.269:     1903 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.269 -  3.595:     2570 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.595 -  3.921:     4742 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.921 -  4.247:     4462 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.247 -  4.574:     5946 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.574 -  4.900:     7083 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.181 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.638 |       0.460 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.864)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    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:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4413   r_free= 0.4326   ksol= 0.00   Bsol= 0.00   scale= 0.908    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.255014                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4296   r_free= 0.4187   ksol= 0.29   Bsol= 24.13   scale= 0.946   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.40,4.15,1.33,0.00,0.00,0.00); trace/3= 0.69                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.243800                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.603245              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.133   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.037375              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.779   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4296      final r-factor (work) = 0.3173          |
| start r-factor (free) = 0.4187      final r-factor (free) = 0.3503          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.0388 = 8.60 * 0.50 * 6.2436 + 1.00 * 0.1813                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.3392 = 8.60 * 0.50 * 6.0894 + 1.00 * 0.1448                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3173      final r-factor (work) = 0.2894          |
| start r-factor (free) = 0.3503      final r-factor (free) = 0.3596          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3231 = 1.04 * 1.00 * 6.0894 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2003 = 1.04 * 1.00 * 5.9549 + 1.00 * 0.0228                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.864)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.35   18.24    None  None   None       |
|    all(noH): 2823   0      0.00    81.35   18.24    None  None   None       |
|    Sol.    : 438    0      0.43    81.35   37.94    None  None   None       |
|    Mac.    : 2385   0      0.00    75.69   14.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.135:  727   |   5:    40.673 -  48.808:  108        |
|      1:     8.135 -  16.269:  912   |   6:    48.808 -  56.942:   85        |
|      2:    16.269 -  24.404:  471   |   7:    56.942 -  65.077:   39        |
|      3:    24.404 -  32.539:  272   |   8:    65.077 -  73.212:   19        |
|      4:    32.539 -  40.673:  186   |   9:    73.212 -  81.346:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2894 r_free = 0.3596             target_work(ml) = 5.963         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2890 r_free = 0.3599             target_work(ml) = 5.962         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2890   r_free= 0.3599   ksol= 0.29   Bsol= 24.13   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.40,4.15,1.33,0.00,0.00,0.00); trace/3= 0.69                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.962478                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2865   r_free= 0.3556   ksol= 0.32   Bsol= 49.57   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,1.63,-0.36,0.00,-0.00,-0.00); trace/3= -0.31                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.959213                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.513280              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.968   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.476746              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 103.259  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2865      final r-factor (work) = 0.2221          |
| start r-factor (free) = 0.3556      final r-factor (free) = 0.2761          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.5569 = 5.51 * 0.50 * 5.9537 + 1.00 * 0.1448                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.2405 = 5.51 * 0.50 * 5.8634 + 1.00 * 0.0772                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2221      final r-factor (work) = 0.2056          |
| start r-factor (free) = 0.2761      final r-factor (free) = 0.2617          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8166 = 0.48 * 1.00 * 5.8634 + 1.00 * 0.0212                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7283 = 0.48 * 1.00 * 5.6995 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.864)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.20   17.68    None  None   None       |
|    all(noH): 2823   0      0.00    86.20   17.68    None  None   None       |
|    Sol.    : 438    0      5.17    86.20   39.51    None  None   None       |
|    Mac.    : 2385   0      0.00    78.79   13.67    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.620:  814   |   5:    43.101 -  51.721:  116        |
|      1:     8.620 -  17.241: 1062   |   6:    51.721 -  60.342:   63        |
|      2:    17.241 -  25.861:  397   |   7:    60.342 -  68.962:   42        |
|      3:    25.861 -  34.481:  161   |   8:    68.962 -  77.582:   18        |
|      4:    34.481 -  43.101:  147   |   9:    77.582 -  86.202:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2056 r_free = 0.2617             target_work(ml) = 5.677         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2055 r_free = 0.2618             target_work(ml) = 5.677         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2055   r_free= 0.2618   ksol= 0.32   Bsol= 49.57   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,1.63,-0.36,0.00,-0.00,-0.00); trace/3= -0.31                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.676813                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2051   r_free= 0.2611   ksol= 0.32   Bsol= 53.05   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,0.36,-0.95,0.00,-0.00,-0.00); trace/3= -0.87                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.675425                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.412703              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.622   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.304334              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.751  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2051      final r-factor (work) = 0.1491          |
| start r-factor (free) = 0.2611      final r-factor (free) = 0.1936          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.3526 = 6.41 * 0.50 * 5.6998 + 1.00 * 0.0772                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.8750 = 6.41 * 0.50 * 5.5507 + 1.00 * 0.0773                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1491      final r-factor (work) = 0.1328          |
| start r-factor (free) = 0.1936      final r-factor (free) = 0.1810          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.3526 = 3.30 * 1.00 * 5.5507 + 1.00 * 0.0111                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.6156 = 3.30 * 1.00 * 5.3272 + 1.00 * 0.0126                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.864)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.42   17.99    None  None   None       |
|    all(noH): 2823   0      0.00    99.42   17.99    None  None   None       |
|    Sol.    : 438    0      6.07    99.36   44.58    None  None   None       |
|    Mac.    : 2385   0      0.00    99.42   13.11    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 -   9.942: 1091   |   5:    49.711 -  59.654:  103        |
|      1:     9.942 -  19.885: 1049   |   6:    59.654 -  69.596:   69        |
|      2:    19.885 -  29.827:  233   |   7:    69.596 -  79.538:   32        |
|      3:    29.827 -  39.769:  120   |   8:    79.538 -  89.481:   20        |
|      4:    39.769 -  49.711:   99   |   9:    89.481 -  99.423:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1328 r_free = 0.1810             target_work(ml) = 5.290         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1328 r_free = 0.1809             target_work(ml) = 5.290         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1328   r_free= 0.1809   ksol= 0.32   Bsol= 53.05   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,0.36,-0.95,0.00,-0.00,-0.00); trace/3= -0.87                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.289985                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1329   r_free= 0.1809   ksol= 0.32   Bsol= 53.05   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,-0.73,-1.36,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.292683                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.501515              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.649  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.659218              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 111.005  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1329      final r-factor (work) = 0.1220          |
| start r-factor (free) = 0.1809      final r-factor (free) = 0.1711          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7465 = 2.50 * 0.50 * 5.3321 + 1.00 * 0.0773                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6396 = 2.50 * 0.50 * 5.2596 + 1.00 * 0.0611                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1220      final r-factor (work) = 0.1191          |
| start r-factor (free) = 0.1711      final r-factor (free) = 0.1671          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4798 = 0.66 * 1.00 * 5.2596 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4509 = 0.66 * 1.00 * 5.2178 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.864)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.97    104.78  17.48    None  None   None       |
|    all(noH): 2823   0      0.97    104.78  17.48    None  None   None       |
|    Sol.    : 438    0      5.24    99.54   43.22    None  None   None       |
|    Mac.    : 2385   0      0.97    104.78  12.75    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:     0.971 -  11.352: 1397   |   5:    52.876 -  63.257:   89        |
|      1:    11.352 -  21.733:  856   |   6:    63.257 -  73.638:   45        |
|      2:    21.733 -  32.114:  178   |   7:    73.638 -  84.019:   22        |
|      3:    32.114 -  42.495:  112   |   8:    84.019 -  94.400:   11        |
|      4:    42.495 -  52.876:  107   |   9:    94.400 - 104.781:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1191 r_free = 0.1671             target_work(ml) = 5.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1191 r_free = 0.1671             target_work(ml) = 5.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1191   r_free= 0.1671   ksol= 0.32   Bsol= 53.05   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,-0.73,-1.36,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.203965                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1671   ksol= 0.32   Bsol= 54.97   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-0.95,-1.33,-0.00,-0.00,-0.00); trace/3= -1.46                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.203876                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.649151              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.082  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.230422              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.200  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1190      final r-factor (work) = 0.1173          |
| start r-factor (free) = 0.1671      final r-factor (free) = 0.1640          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3633 = 1.65 * 0.50 * 5.2175 + 1.00 * 0.0611                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3400 = 1.65 * 0.50 * 5.1995 + 1.00 * 0.0526                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1173      final r-factor (work) = 0.1177          |
| start r-factor (free) = 0.1640      final r-factor (free) = 0.1623          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2092 = 0.23 * 1.00 * 5.1995 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2051 = 0.23 * 1.00 * 5.1920 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.864)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.38    100.91  16.71    None  None   None       |
|    all(noH): 2823   0      1.38    100.91  16.71    None  None   None       |
|    Sol.    : 438    0      4.82    90.12   39.99    None  None   None       |
|    Mac.    : 2385   0      1.38    100.91  12.44    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.381 -  11.335: 1437   |   5:    51.147 -  61.101:   71        |
|      1:    11.335 -  21.288:  823   |   6:    61.101 -  71.054:   31        |
|      2:    21.288 -  31.241:  187   |   7:    71.054 -  81.007:   19        |
|      3:    31.241 -  41.194:  124   |   8:    81.007 -  90.960:    8        |
|      4:    41.194 -  51.147:  119   |   9:    90.960 - 100.913:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1177 r_free = 0.1623             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1175 r_free = 0.1624             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1175   r_free= 0.1624   ksol= 0.32   Bsol= 54.97   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-0.95,-1.33,-0.00,-0.00,-0.00); trace/3= -1.46                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.185682                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9311 -  4.6819 0.99   1434  163 0.0998 0.1263      5.3737      5.5308|
|  2:  4.6819 -  3.7353 0.99   1377  147 0.0860 0.1080      5.4269      5.6204|
|  3:  3.7353 -  3.2688 0.99   1349  153 0.1076 0.1591      5.4795      5.8845|
|  4:  3.2688 -  2.9725 0.99   1344  147 0.1338 0.1591      5.5062       5.628|
|  5:  2.9725 -  2.7609 0.99   1339  149 0.1407 0.1878      5.3721      5.5372|
|  6:  2.7609 -  2.5990 0.99   1325  150 0.1340 0.1998       5.267      5.4905|
|  7:  2.5990 -  2.4695 0.98   1330  146 0.1305 0.1756      5.1972      5.4097|
|  8:  2.4695 -  2.3624 0.98   1311  144 0.1270 0.1763      5.1221      5.3228|
|  9:  2.3624 -  2.2718 0.99   1317  143 0.1260 0.1943      5.0775      5.3374|
| 10:  2.2718 -  2.1936 0.98   1311  148 0.1202 0.1750      5.0032      5.2557|
| 11:  2.1936 -  2.1252 0.97   1287  143 0.1172 0.1858       4.943      5.2414|
| 12:  2.1252 -  2.0647 0.99   1301  150 0.1197 0.1675      4.8785      5.0866|
| 13:  2.0647 -  2.0104 0.91   1200  133 0.1189 0.1884      4.8181       5.082|
| 14:  2.0104 -  1.9615 0.30    405   43 0.1245 0.1705      4.7334      4.9479|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9311 -  4.6819  1434   163  0.94   8.83   0.97     0.95       6767.17|
|  2:  4.6819 -  3.7353  1377   147  0.95   7.78   1.01     1.00       8594.44|
|  3:  3.7353 -  3.2688  1349   153  0.93  11.48   1.02     1.02      10364.32|
|  4:  3.2688 -  2.9725  1344   147  0.91  14.83   1.01     0.98      11132.06|
|  5:  2.9725 -  2.7609  1339   149  0.89  17.17   1.00     0.97       9055.51|
|  6:  2.7609 -  2.5990  1325   150  0.89  16.85   0.98     0.96       7649.85|
|  7:  2.5990 -  2.4695  1330   146  0.90  16.06   0.99     0.96       6557.98|
|  8:  2.4695 -  2.3624  1311   144  0.90  16.57   1.00     0.97       6028.41|
|  9:  2.3624 -  2.2718  1317   143  0.89  17.04   1.00     0.96       5404.22|
| 10:  2.2718 -  2.1936  1311   148  0.90  15.67   0.99     0.96       4717.93|
| 11:  2.1936 -  2.1252  1287   143  0.90  16.52   0.99     0.96       4358.75|
| 12:  2.1252 -  2.0647  1301   150  0.91  15.46   1.00     0.99       3834.50|
| 13:  2.0647 -  2.0104  1200   133  0.89  16.90   1.00     0.99       3516.28|
| 14:  2.0104 -  1.9615   405    43  0.88  17.50   0.97     0.94       2956.44|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2956.44 max =        11132.06 mean =      6732.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.89 mean =        14.69|
|phase err.(test): min =        0.00 max =           89.97 mean =        14.13|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1175   r_free= 0.1624   ksol= 0.32   Bsol= 52.57   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-0.99,-1.23,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.185765                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1175   r_free= 0.1624   ksol= 0.32   Bsol= 52.57   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-0.99,-1.23,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.185765                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9311 -  4.6819 0.99   1434  163 0.0997 0.1263      5.3738      5.5297|
|  2:  4.6819 -  3.7353 0.99   1377  147 0.0858 0.1080      5.4252      5.6183|
|  3:  3.7353 -  3.2688 0.99   1349  153 0.1075 0.1589      5.4784      5.8846|
|  4:  3.2688 -  2.9725 0.99   1344  147 0.1338 0.1590      5.5063      5.6278|
|  5:  2.9725 -  2.7609 0.99   1339  149 0.1408 0.1878      5.3725      5.5374|
|  6:  2.7609 -  2.5990 0.99   1325  150 0.1340 0.1997       5.267      5.4904|
|  7:  2.5990 -  2.4695 0.98   1330  146 0.1306 0.1756      5.1973      5.4094|
|  8:  2.4695 -  2.3624 0.98   1311  144 0.1270 0.1763      5.1226      5.3233|
|  9:  2.3624 -  2.2718 0.99   1317  143 0.1260 0.1942      5.0777      5.3382|
| 10:  2.2718 -  2.1936 0.98   1311  148 0.1203 0.1750      5.0039      5.2567|
| 11:  2.1936 -  2.1252 0.97   1287  143 0.1172 0.1858      4.9432      5.2414|
| 12:  2.1252 -  2.0647 0.99   1301  150 0.1197 0.1678      4.8793       5.088|
| 13:  2.0647 -  2.0104 0.91   1200  133 0.1189 0.1884      4.8187      5.0816|
| 14:  2.0104 -  1.9615 0.30    405   43 0.1246 0.1702      4.7338       4.947|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9311 -  4.6819  1434   163  0.94   8.82   0.97     0.95       6767.77|
|  2:  4.6819 -  3.7353  1377   147  0.95   7.76   1.01     1.00       8568.92|
|  3:  3.7353 -  3.2688  1349   153  0.93  11.44   1.02     1.02      10326.09|
|  4:  3.2688 -  2.9725  1344   147  0.91  14.82   1.01     0.98      11131.89|
|  5:  2.9725 -  2.7609  1339   149  0.89  17.15   1.00     0.97       9047.33|
|  6:  2.7609 -  2.5990  1325   150  0.89  16.85   0.98     0.96       7647.19|
|  7:  2.5990 -  2.4695  1330   146  0.90  16.05   0.99     0.96       6557.61|
|  8:  2.4695 -  2.3624  1311   144  0.90  16.59   1.00     0.97       6035.97|
|  9:  2.3624 -  2.2718  1317   143  0.89  17.05   1.00     0.96       5415.20|
| 10:  2.2718 -  2.1936  1311   148  0.90  15.68   0.99     0.96       4725.86|
| 11:  2.1936 -  2.1252  1287   143  0.90  16.53   0.99     0.96       4361.80|
| 12:  2.1252 -  2.0647  1301   150  0.91  15.48   1.00     0.99       3842.88|
| 13:  2.0647 -  2.0104  1200   133  0.89  16.92   1.00     0.99       3520.02|
| 14:  2.0104 -  1.9615   405    43  0.88  17.51   0.97     0.94       2954.70|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2954.70 max =        11131.89 mean =      6729.36|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.69|
|phase err.(test): min =        0.00 max =           89.97 mean =        14.13|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.864)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.33    100.86  16.66    None  None   None       |
|    all(noH): 2823   0      1.33    100.86  16.66    None  None   None       |
|    Sol.    : 438    0      4.77    90.07   39.94    None  None   None       |
|    Mac.    : 2385   0      1.33    100.86  12.39    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.333 -  11.286: 1437   |   5:    51.099 -  61.052:   71        |
|      1:    11.286 -  21.239:  823   |   6:    61.052 -  71.005:   31        |
|      2:    21.239 -  31.192:  187   |   7:    71.005 -  80.958:   19        |
|      3:    31.192 -  41.145:  124   |   8:    80.958 -  90.911:    8        |
|      4:    41.145 -  51.099:  119   |   9:    90.911 - 100.864:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 321         
Filter by distance & map next to the model:
   mapped sites are within: 0.647 - 4.214
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 317 from: 321
   mapped sites are within: 0.731 - 4.214

peak=    5.659 closest distance to " O   HOH Z 113 " =    2.337
peak=    5.535 closest distance to " CB  SER A  63 " =    1.200
peak=    5.490 closest distance to " CB  GLN A 223 " =    1.415
peak=    5.483 closest distance to " CG  PRO A  54 " =    1.290
peak=    5.131 closest distance to " CG  PRO A 198 " =    1.233
peak=    4.991 closest distance to " CG  PRO A  90 " =    1.210
peak=    4.971 closest distance to " O   PRO A 198 " =    1.558
peak=    4.965 closest distance to " O   HOH Z 124 " =    1.560
peak=    4.814 closest distance to " CA  TYR A  30 " =    0.993
peak=    4.755 closest distance to " CG  PRO A 213 " =    1.278
peak=    4.719 closest distance to " O   HOH Z  15 " =    2.091
peak=    4.697 closest distance to " CG  PRO A 280 " =    0.731
peak=    4.679 closest distance to " O   HOH Z  80 " =    1.751
peak=    4.657 closest distance to " O   HOH Z 134 " =    1.904
peak=    4.632 closest distance to " CB  ARG A 275 " =    0.863
peak=    4.585 closest distance to " O   HOH Z 210 " =    1.191
peak=    4.538 closest distance to " CB  GLU A 128 " =    1.157
peak=    4.527 closest distance to " O   HOH Z 209 " =    2.375
peak=    4.518 closest distance to " O   HOH Z 234 " =    3.840
peak=    4.451 closest distance to " CB  SER A   3 " =    1.322
peak=    4.429 closest distance to " O   HOH Z 232 " =    2.330
peak=    4.428 closest distance to " CB  PRO A  54 " =    0.841
peak=    4.421 closest distance to " O   HOH Z 402 " =    1.536
peak=    4.398 closest distance to " O   HOH Z 389 " =    1.960
peak=    4.344 closest distance to " O   HOH Z 298 " =    1.990
peak=    4.335 closest distance to " O   HOH Z 132 " =    1.140
peak=    4.330 closest distance to " O   HOH Z 279 " =    2.086
peak=    4.315 closest distance to " NH2 ARG A 156 " =    1.214
peak=    4.313 closest distance to " CB  GLN A 183 " =    1.294
peak=    4.278 closest distance to " O   HOH Z 433 " =    1.594
peak=    4.273 closest distance to " O   HOH Z 133 " =    1.642
peak=    4.270 closest distance to " CB  SER A 141 " =    1.056
peak=    4.265 closest distance to " O   HOH Z  20 " =    1.728
peak=    4.259 closest distance to " O   HOH Z 247 " =    1.447
peak=    4.248 closest distance to " O   HOH Z  97 " =    1.924
peak=    4.237 closest distance to " CG1 ILE A  33 " =    1.250
peak=    4.227 closest distance to " O   SER A  87 " =    2.178
peak=    4.226 closest distance to " O   HOH Z 426 " =    1.484
peak=    4.225 closest distance to " O   HOH Z 368 " =    2.050
peak=    4.213 closest distance to " O   HOH Z 126 " =    1.660
peak=    4.202 closest distance to " CB  GLU A 152 " =    1.155
peak=    4.201 closest distance to " CB  TYR A 169 " =    0.881
peak=    4.179 closest distance to " O   HOH Z 193 " =    1.867
peak=    4.169 closest distance to " NH2BARG A 145 " =    2.076
peak=    4.159 closest distance to " O   HOH Z 154 " =    1.407
peak=    4.159 closest distance to " CB  GLU A 277 " =    3.638
peak=    4.148 closest distance to " CA  ALA A  21 " =    1.334
peak=    4.133 closest distance to " O   HOH Z  40 " =    1.827
peak=    4.128 closest distance to " CG  PRO A 243 " =    1.142
peak=    4.123 closest distance to " O   HOH Z 142 " =    1.521
peak=    4.118 closest distance to " NZ  LYS A  76 " =    1.233
peak=    4.109 closest distance to " CB  ARG A 190 " =    1.731
peak=    4.100 closest distance to " O   HOH Z  39 " =    1.234
peak=    4.083 closest distance to " O   HOH Z 403 " =    1.829
peak=    4.081 closest distance to " O   HOH Z 316 " =    2.910
peak=    4.077 closest distance to " O   HOH Z 130 " =    2.808
peak=    4.073 closest distance to " N   ASN A  39 " =    1.304
peak=    4.050 closest distance to " OE1 GLN A  11 " =    1.921
peak=    4.039 closest distance to " CA  ASP A 191 " =    0.890
peak=    4.035 closest distance to " O   HOH Z 132 " =    2.577
peak=    4.025 closest distance to " O   HOH Z 108 " =    2.509
peak=    4.000 closest distance to " OD2 ASP A 286 " =    2.812
peak=    3.998 closest distance to " CA  ARG A  36 " =    1.127
peak=    3.986 closest distance to " NZ  LYS A 117 " =    3.145
peak=    3.973 closest distance to " O   HOH Z 145 " =    2.062
peak=    3.973 closest distance to " CB  LEU A 228 " =    1.196
peak=    3.973 closest distance to " CB  PRO A 198 " =    1.044
peak=    3.960 closest distance to " CD  ARG A 269 " =    1.003
peak=    3.959 closest distance to " O   HOH Z 374 " =    2.626
peak=    3.945 closest distance to " CB  ARG A  79 " =    1.353
peak=    3.941 closest distance to " O   HOH Z 189 " =    2.042
peak=    3.939 closest distance to " O   HOH Z 132 " =    2.043
peak=    3.937 closest distance to " O   HOH Z  11 " =    1.318
peak=    3.936 closest distance to " O   HOH Z  67 " =    1.871
peak=    3.929 closest distance to " CB  VAL A 202 " =    1.522
peak=    3.929 closest distance to " CB  PRO A  54 " =    1.314
peak=    3.927 closest distance to " O   HOH Z  63 " =    1.986
peak=    3.898 closest distance to " O   HOH Z 227 " =    1.783
peak=    3.896 closest distance to " O   HOH Z 411 " =    3.422
peak=    3.892 closest distance to " O   HOH Z 287 " =    1.970
peak=    3.890 closest distance to " O   HOH Z 272 " =    1.917
peak=    3.867 closest distance to " O   HOH Z 406 " =    1.613
peak=    3.865 closest distance to " O   HOH Z 163 " =    1.583
peak=    3.863 closest distance to " CB  TRP A 179 " =    1.258
peak=    3.859 closest distance to " O   HOH Z 326 " =    1.499
peak=    3.854 closest distance to " CG2 THR A 221 " =    1.109
peak=    3.853 closest distance to " O   HOH Z 371 " =    3.315
peak=    3.852 closest distance to " OD1 ASN A  69 " =    2.556
peak=    3.851 closest distance to " O   HOH Z  43 " =    1.508
peak=    3.843 closest distance to " O   HOH Z 214 " =    0.993
peak=    3.837 closest distance to " CG2BVAL A  41 " =    0.911
peak=    3.830 closest distance to " O   HOH Z 357 " =    2.007
peak=    3.823 closest distance to " CD  LYS A 166 " =    1.368
peak=    3.820 closest distance to " O   HOH Z 102 " =    1.233
peak=    3.820 closest distance to " O   HOH Z 203 " =    1.806
peak=    3.811 closest distance to " O   HOH Z 173 " =    2.134
peak=    3.799 closest distance to " O   HOH Z  48 " =    1.480
peak=    3.778 closest distance to " CB  SER A  62 " =    0.790
peak=    3.771 closest distance to " CB  ASN A 148 " =    1.219
peak=    3.763 closest distance to " O   HOH Z 196 " =    1.202
peak=    3.756 closest distance to " O   HOH Z 423 " =    1.861
peak=    3.756 closest distance to " O   HOH Z  61 " =    1.501
peak=    3.749 closest distance to " O   HOH Z 313 " =    1.898
peak=    3.746 closest distance to " O   HOH Z  44 " =    1.868
peak=    3.746 closest distance to " CD1 LEU A 300 " =    1.209
peak=    3.737 closest distance to " O   HOH Z   6 " =    2.113
peak=    3.736 closest distance to " O   HOH Z 128 " =    2.116
peak=    3.730 closest distance to " O   HOH Z 369 " =    2.295
peak=    3.727 closest distance to " O   HOH Z 345 " =    1.725
peak=    3.721 closest distance to " O   HOH Z 128 " =    2.113
peak=    3.716 closest distance to " O   HOH Z 291 " =    1.543
peak=    3.689 closest distance to " O   HOH Z  78 " =    1.907
peak=    3.681 closest distance to " O   HOH Z 383 " =    2.025
peak=    3.680 closest distance to " OD1 ASP A 238 " =    0.902
peak=    3.673 closest distance to " O   HOH Z  49 " =    1.837
peak=    3.652 closest distance to " NE2 GLN A  11 " =    1.074
peak=    3.649 closest distance to " O   TRP A 274 " =    1.772
peak=    3.641 closest distance to " ND2 ASN A 187 " =    1.622
peak=    3.639 closest distance to " CA  ARG A 195 " =    1.124
peak=    3.639 closest distance to " O   HOH Z 126 " =    1.900
peak=    3.635 closest distance to " O   HOH Z 394 " =    1.625
peak=    3.634 closest distance to " CD2 LEU A 297 " =    0.921
peak=    3.632 closest distance to " CG2 ILE A 120 " =    1.160
peak=    3.630 closest distance to " CA  ASP A 162 " =    1.190
peak=    3.626 closest distance to " CA  ASN A 176 " =    1.487
peak=    3.625 closest distance to " O   HOH Z 344 " =    3.027
peak=    3.623 closest distance to " O   HOH Z  30 " =    1.381
peak=    3.615 closest distance to " O   HOH Z 197 " =    1.937
peak=    3.614 closest distance to " O   HOH Z 123 " =    2.081
peak=    3.611 closest distance to " O   GLY A  23 " =    2.326
peak=    3.609 closest distance to " OG BSER A 164 " =    2.535
peak=    3.607 closest distance to " O   ALA A 165 " =    1.281
peak=    3.603 closest distance to " CG1BVAL A  72 " =    1.701
peak=    3.594 closest distance to " O   HOH Z 387 " =    2.409
peak=    3.591 closest distance to " O   HOH Z 346 " =    1.522
peak=    3.588 closest distance to " CB  ASN A 187 " =    1.166
peak=    3.588 closest distance to " CG AARG A 275 " =    0.973
peak=    3.583 closest distance to " O   HOH Z 336 " =    1.613
peak=    3.581 closest distance to " NE1 TRP A 274 " =    0.921
peak=    3.580 closest distance to " CG2 VAL A 197 " =    1.132
peak=    3.577 closest distance to " O   HOH Z 358 " =    1.986
peak=    3.575 closest distance to " O   HOH Z  88 " =    3.410
peak=    3.568 closest distance to " O   HOH Z 245 " =    1.409
peak=    3.567 closest distance to " O   HOH Z 362 " =    3.483
peak=    3.564 closest distance to " O   HOH Z 260 " =    1.331
peak=    3.560 closest distance to " O   HOH Z 427 " =    3.008
peak=    3.559 closest distance to " O   HOH Z  21 " =    1.827
peak=    3.545 closest distance to " O   HOH Z 408 " =    1.610
peak=    3.542 closest distance to " CB  ALA A 291 " =    1.258
peak=    3.541 closest distance to " CA  THR A 221 " =    0.942
peak=    3.539 closest distance to " O   HOH Z 284 " =    2.911
peak=    3.537 closest distance to " O   HOH Z 255 " =    1.759
peak=    3.533 closest distance to " O   HOH Z  54 " =    2.300
peak=    3.530 closest distance to " O   HOH Z 227 " =    1.651
peak=    3.530 closest distance to " O   HOH Z 147 " =    1.736
peak=    3.527 closest distance to " CG2 VAL A  78 " =    0.984
peak=    3.527 closest distance to " CA  ASP A 140 " =    1.169
peak=    3.524 closest distance to " O   HOH Z 154 " =    2.494
peak=    3.520 closest distance to " NH1 ARG A 269 " =    0.795
peak=    3.514 closest distance to " OG  SER A  62 " =    3.027
peak=    3.513 closest distance to " CB  GLN A  58 " =    0.823
peak=    3.510 closest distance to " O   HOH Z 261 " =    1.935
peak=    3.509 closest distance to " NH2AARG A 145 " =    2.200
peak=    3.503 closest distance to " CB  ALA A 256 " =    1.034
peak=    3.500 closest distance to " O   HOH Z 421 " =    1.598
peak=    3.492 closest distance to " CG  ARG A  66 " =    0.890
peak=    3.491 closest distance to " CB  ASN A 148 " =    1.620
peak=    3.488 closest distance to " O   HOH Z 427 " =    2.859
peak=    3.486 closest distance to " CG  GLN A  58 " =    2.378
peak=    3.483 closest distance to " O   HOH Z 214 " =    2.426
peak=    3.477 closest distance to " CD  PRO A  54 " =    1.157
peak=    3.476 closest distance to " O   HOH Z 345 " =    2.838
peak=    3.476 closest distance to " OG1 THR A 294 " =    2.470
peak=    3.468 closest distance to " CG1 VAL A 153 " =    1.057
peak=    3.465 closest distance to " O   HOH Z 250 " =    1.769
peak=    3.465 closest distance to " O   HOH Z  54 " =    1.660
peak=    3.463 closest distance to " O   HOH Z 386 " =    2.251
peak=    3.451 closest distance to " O   HOH Z 327 " =    2.341
peak=    3.449 closest distance to " O   HOH Z  35 " =    2.436
peak=    3.449 closest distance to " CB  ASN A 285 " =    0.910
peak=    3.438 closest distance to " O   HOH Z 425 " =    1.392
peak=    3.433 closest distance to " CD2 HIS A  81 " =    1.211
peak=    3.431 closest distance to " O   SER A  26 " =    1.691
peak=    3.430 closest distance to " O   HOH Z  97 " =    2.538
peak=    3.426 closest distance to " O   THR A 251 " =    1.184
peak=    3.422 closest distance to " CB  PHE A  16 " =    1.003
peak=    3.418 closest distance to " OH  TYR A  30 " =    1.265
peak=    3.414 closest distance to " CA  ALA A  51 " =    0.896
peak=    3.414 closest distance to " O   HOH Z 118 " =    1.370
peak=    3.412 closest distance to " CA  PRO A  90 " =    0.921
peak=    3.412 closest distance to " C   ILE A 106 " =    1.871
peak=    3.403 closest distance to " C   GLY A  80 " =    1.158
peak=    3.403 closest distance to " CB  MET A  47 " =    1.053
peak=    3.399 closest distance to " CA  ALA A 248 " =    1.223
peak=    3.395 closest distance to " NH2AARG A 190 " =    1.363
peak=    3.394 closest distance to " NZ  LYS A 117 " =    1.927
peak=    3.390 closest distance to " CA  GLU A 152 " =    0.861
peak=    3.389 closest distance to " O   HOH Z 108 " =    1.136
peak=    3.384 closest distance to " O   HOH Z 303 " =    2.143
peak=    3.383 closest distance to " O   HOH Z 334 " =    1.564
peak=    3.383 closest distance to " NZ  LYS A 119 " =    1.680
peak=    3.380 closest distance to " CB  ALA A 100 " =    1.293
peak=    3.379 closest distance to " C   SER A  32 " =    1.029
peak=    3.378 closest distance to " O   HOH Z 263 " =    2.164
peak=    3.377 closest distance to " CA  GLN A 223 " =    0.878
peak=    3.374 closest distance to " CB  ARG A 139 " =    0.886
peak=    3.372 closest distance to " O   HOH Z 404 " =    1.525
peak=    3.372 closest distance to " CG2 THR A 220 " =    0.763
peak=    3.368 closest distance to " CA  ARG A  66 " =    0.989
peak=    3.365 closest distance to " CB  ALA A  71 " =    1.203
peak=    3.364 closest distance to " CD  LYS A 119 " =    1.496
peak=    3.361 closest distance to " CZ  PHE A 218 " =    1.044
peak=    3.358 closest distance to " O   HOH Z 130 " =    2.301
peak=    3.357 closest distance to " O   HOH Z 419 " =    1.603
peak=    3.357 closest distance to " O   HOH Z 250 " =    1.417
peak=    3.353 closest distance to " O   HOH Z 438 " =    2.407
peak=    3.350 closest distance to " CD2 TRP A 179 " =    1.318
peak=    3.350 closest distance to " O   HOH Z 144 " =    1.828
peak=    3.347 closest distance to " CG2 ILE A 106 " =    1.037
peak=    3.342 closest distance to " O   HOH Z  66 " =    2.291
peak=    3.341 closest distance to " CD1 TRP A 266 " =    1.234
peak=    3.337 closest distance to " O   HOH Z 409 " =    3.145
peak=    3.334 closest distance to " O   HOH Z 295 " =    1.450
peak=    3.331 closest distance to " O   GLY A 211 " =    1.334
peak=    3.330 closest distance to " O   HOH Z 104 " =    3.134
peak=    3.329 closest distance to " CG2AVAL A 121 " =    2.148
peak=    3.329 closest distance to " O   HOH Z 365 " =    2.829
peak=    3.328 closest distance to " CD1 LEU A  96 " =    0.740
peak=    3.327 closest distance to " CA  ALA A 160 " =    0.854
peak=    3.325 closest distance to " CE  LYS A 119 " =    1.086
peak=    3.323 closest distance to " CA  ASP A 124 " =    0.761
peak=    3.320 closest distance to " O   HOH Z 418 " =    1.412
peak=    3.319 closest distance to " O   HOH Z 402 " =    2.861
peak=    3.314 closest distance to " O   HOH Z 261 " =    1.586
peak=    3.313 closest distance to " CD2 LEU A 255 " =    1.112
peak=    3.309 closest distance to " O   HOH Z 109 " =    2.319
peak=    3.304 closest distance to " O   HOH Z 211 " =    2.650
peak=    3.303 closest distance to " O   HOH Z 287 " =    1.760
peak=    3.303 closest distance to " N   ARG A 156 " =    1.424
peak=    3.301 closest distance to " CZ  PHE A  38 " =    1.435
peak=    3.298 closest distance to " CB  ASN A  39 " =    0.888
peak=    3.296 closest distance to " O   HOH Z 261 " =    2.042
peak=    3.294 closest distance to " CD BLYS A 290 " =    1.123
peak=    3.293 closest distance to " CA  LYS A 117 " =    1.217
peak=    3.293 closest distance to " CG  GLN A  58 " =    2.583
peak=    3.287 closest distance to " CA  VAL A  41 " =    0.843
peak=    3.287 closest distance to " CD  ARG A 159 " =    0.842
peak=    3.286 closest distance to " O   HOH Z 234 " =    1.887
peak=    3.285 closest distance to " O   HOH Z 280 " =    2.478
peak=    3.285 closest distance to " O   HOH Z  47 " =    1.304
peak=    3.278 closest distance to " O   GLY A  91 " =    1.225
peak=    3.275 closest distance to " CA  GLU A 152 " =    1.439
peak=    3.273 closest distance to " O   HOH Z 156 " =    2.561
peak=    3.271 closest distance to " O   ALA A 158 " =    1.184
peak=    3.268 closest distance to " CG  GLN A  11 " =    1.217
peak=    3.268 closest distance to " O   HOH Z 106 " =    2.329
peak=    3.262 closest distance to " OG BSER A 258 " =    3.451
peak=    3.256 closest distance to " CA  GLY A 211 " =    1.140
peak=    3.249 closest distance to " CA  THR A 221 " =    1.325
peak=    3.248 closest distance to " O   HOH Z 423 " =    3.314
peak=    3.246 closest distance to " CB  GLN A 194 " =    0.910
peak=    3.243 closest distance to " O   HOH Z 207 " =    2.383
peak=    3.240 closest distance to " CA  LEU A  83 " =    1.415
peak=    3.237 closest distance to " O   HOH Z 185 " =    1.646
peak=    3.234 closest distance to " CB  ILE A 199 " =    1.030
peak=    3.232 closest distance to " O   HOH Z 422 " =    0.924
peak=    3.232 closest distance to " ND2 ASN A 209 " =    3.757
peak=    3.232 closest distance to " O   HOH Z 437 " =    1.648
peak=    3.231 closest distance to " CB  VAL A 265 " =    1.186
peak=    3.227 closest distance to " CB  MET A  40 " =    0.849
peak=    3.219 closest distance to " O   HOH Z   1 " =    2.745
peak=    3.219 closest distance to " CD  ARG A 195 " =    1.034
peak=    3.218 closest distance to " O   HOH Z 434 " =    1.461
peak=    3.216 closest distance to " CZ  PHE A 192 " =    0.894
peak=    3.211 closest distance to " OG  SER A 245 " =    1.543
peak=    3.210 closest distance to " O   VAL A  72 " =    3.221
peak=    3.210 closest distance to " CA  GLU A  46 " =    0.757
peak=    3.205 closest distance to " O   HOH Z 150 " =    1.609
peak=    3.203 closest distance to " O   HOH Z 420 " =    1.990
peak=    3.200 closest distance to " CA  ALA A 295 " =    1.127
peak=    3.194 closest distance to " CA  GLY A 196 " =    1.058
peak=    3.193 closest distance to " CB  GLN A 103 " =    0.802
peak=    3.188 closest distance to " CB  ARG A 269 " =    1.002
peak=    3.186 closest distance to " O   HOH Z 281 " =    4.214
peak=    3.181 closest distance to " ND2 ASN A 110 " =    1.587
peak=    3.178 closest distance to " CD  ARG A 139 " =    1.314
peak=    3.178 closest distance to " NH1AARG A 145 " =    1.089
peak=    3.174 closest distance to " N   SER A 135 " =    1.408
peak=    3.172 closest distance to " NH1BARG A 145 " =    1.065
peak=    3.172 closest distance to " CB  TRP A 266 " =    0.921
peak=    3.170 closest distance to " O   HOH Z 352 " =    1.231
peak=    3.167 closest distance to " CB  PRO A  90 " =    1.138
peak=    3.165 closest distance to " CG2 ILE A  20 " =    1.372
peak=    3.162 closest distance to " CB  THR A  52 " =    1.125
peak=    3.159 closest distance to " O   HOH Z 162 " =    1.703
peak=    3.159 closest distance to " O   HOH Z 166 " =    3.439
peak=    3.156 closest distance to " CA  SER A  87 " =    0.913
peak=    3.153 closest distance to " OG  SER A  97 " =    3.614
peak=    3.149 closest distance to " OD1 ASP A 171 " =    1.352
peak=    3.143 closest distance to " CG  GLN A  77 " =    0.753
peak=    3.142 closest distance to " O   HOH Z 155 " =    2.964
peak=    3.137 closest distance to " CA  ILE A  33 " =    1.503
peak=    3.129 closest distance to " CG  MET A 185 " =    1.211
peak=    3.125 closest distance to " O   HOH Z  19 " =    1.559
peak=    3.123 closest distance to " CB  SER A 273 " =    0.819
peak=    3.121 closest distance to " CE1 TYR A 186 " =    1.301
peak=    3.111 closest distance to " O   HOH Z 273 " =    2.765
peak=    3.109 closest distance to " OG  SER A 206 " =    1.453
peak=    3.107 closest distance to " OD1 ASP A 231 " =    1.934
peak=    3.098 closest distance to " CG2 VAL A 257 " =    0.816
peak=    3.096 closest distance to " O   HOH Z  51 " =    1.503
peak=    3.095 closest distance to " OD2 ASP A 298 " =    4.012
peak=    3.085 closest distance to " CG1 VAL A 202 " =    2.067
peak=    3.080 closest distance to " O   HOH Z  22 " =    2.434
peak=    3.060 closest distance to " O   HOH Z 368 " =    2.520
peak=    3.048 closest distance to " O   HOH Z 377 " =    1.260
peak=    3.018 closest distance to " OD2 ASP A 286 " =    3.037

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.451 - 5.176
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 207
   mapped sites are within: 0.732 - 5.176

peak=   -4.543 closest distance to " O   HOH Z 266 " =    4.360
peak=   -4.357 closest distance to " O   HOH Z 377 " =    0.957
peak=   -4.336 closest distance to " OXT GLY A 302 " =    2.748
peak=   -4.311 closest distance to " CD  ARG A 156 " =    2.016
peak=   -4.271 closest distance to " O   HOH Z 290 " =    0.896
peak=   -4.216 closest distance to " O   HOH Z 210 " =    0.779
peak=   -4.196 closest distance to " N   ALA A  43 " =    2.619
peak=   -4.181 closest distance to " CA  SER A 164 " =    2.102
peak=   -4.153 closest distance to " NH2 ARG A  66 " =    1.532
peak=   -4.135 closest distance to " O   VAL A  67 " =    2.705
peak=   -4.102 closest distance to " O   PRO A 198 " =    1.280
peak=   -4.035 closest distance to " OG  SER A  97 " =    2.181
peak=   -4.025 closest distance to " O   HOH Z  13 " =    1.549
peak=   -4.013 closest distance to " O   HOH Z 221 " =    1.087
peak=   -3.975 closest distance to " CE2 TYR A  30 " =    2.708
peak=   -3.949 closest distance to " O   TRP A  92 " =    1.867
peak=   -3.942 closest distance to " CA  SER A 276 " =    1.471
peak=   -3.933 closest distance to " O   HOH Z 292 " =    4.483
peak=   -3.890 closest distance to " O   HOH Z 166 " =    1.896
peak=   -3.885 closest distance to " CD1 LEU A 101 " =    2.578
peak=   -3.884 closest distance to " O   HOH Z  10 " =    1.620
peak=   -3.881 closest distance to " C   HIS A 108 " =    1.074
peak=   -3.839 closest distance to " O   HOH Z 407 " =    3.547
peak=   -3.823 closest distance to " O   HOH Z 234 " =    4.281
peak=   -3.811 closest distance to " ND2 ASN A  45 " =    1.035
peak=   -3.796 closest distance to " C   THR A 279 " =    1.194
peak=   -3.785 closest distance to " C   SER A 206 " =    1.635
peak=   -3.769 closest distance to " O   HOH Z  93 " =    1.328
peak=   -3.763 closest distance to " CH2 TRP A 179 " =    1.196
peak=   -3.758 closest distance to " OG  SER A  62 " =    1.382
peak=   -3.757 closest distance to " O   HOH Z 185 " =    2.340
peak=   -3.749 closest distance to " O   HOH Z 423 " =    2.354
peak=   -3.745 closest distance to " CB  LEU A 167 " =    2.178
peak=   -3.723 closest distance to " O   HOH Z  71 " =    1.396
peak=   -3.719 closest distance to " O   ALA A 256 " =    1.486
peak=   -3.718 closest distance to " C   ASN A 285 " =    2.322
peak=   -3.710 closest distance to " CA  TYR A  68 " =    2.675
peak=   -3.710 closest distance to " O   HOH Z 165 " =    2.047
peak=   -3.705 closest distance to " O   HOH Z 353 " =    2.325
peak=   -3.700 closest distance to " O   HOH Z  52 " =    1.885
peak=   -3.699 closest distance to " CD2 LEU A 300 " =    2.854
peak=   -3.692 closest distance to " O   HOH Z 313 " =    1.086
peak=   -3.690 closest distance to " CD2 LEU A 237 " =    2.522
peak=   -3.676 closest distance to " C   ALA A 158 " =    1.237
peak=   -3.667 closest distance to " O   HOH Z 196 " =    2.200
peak=   -3.661 closest distance to " O   HOH Z 422 " =    1.274
peak=   -3.646 closest distance to " CD1 LEU A 228 " =    2.335
peak=   -3.627 closest distance to " CD1 LEU A  25 " =    2.460
peak=   -3.625 closest distance to " O   ALA A 160 " =    1.451
peak=   -3.623 closest distance to " ND2 ASN A 187 " =    1.643
peak=   -3.612 closest distance to " OE2 GLU A   2 " =    1.434
peak=   -3.612 closest distance to " ND2 ASN A  60 " =    1.421
peak=   -3.611 closest distance to " CA  VAL A 197 " =    0.971
peak=   -3.609 closest distance to " O   HOH Z 150 " =    1.484
peak=   -3.604 closest distance to " CG  GLU A  53 " =    1.374
peak=   -3.596 closest distance to " CG  GLN A  58 " =    1.291
peak=   -3.595 closest distance to " N   GLN A  58 " =    1.707
peak=   -3.591 closest distance to " SG  CYS A 254 " =    3.283
peak=   -3.584 closest distance to " CG  ASP A  50 " =    2.426
peak=   -3.579 closest distance to " CA  ASP A 298 " =    1.105
peak=   -3.578 closest distance to " CG2 ILE A  20 " =    2.950
peak=   -3.577 closest distance to " NH1 ARG A 195 " =    2.663
peak=   -3.576 closest distance to " CE  MET A 105 " =    1.880
peak=   -3.555 closest distance to " CG2 THR A   4 " =    1.911
peak=   -3.548 closest distance to " O   HOH Z 417 " =    2.755
peak=   -3.542 closest distance to " CG  ASP A 231 " =    0.842
peak=   -3.539 closest distance to " CB  PRO A 243 " =    2.591
peak=   -3.538 closest distance to " O   HOH Z  11 " =    1.524
peak=   -3.534 closest distance to " O   GLY A 196 " =    1.006
peak=   -3.533 closest distance to " OG ASER A 134 " =    1.349
peak=   -3.530 closest distance to " ND2 ASN A  45 " =    1.210
peak=   -3.530 closest distance to " OD1 ASN A 148 " =    1.660
peak=   -3.528 closest distance to " CE  MET A  93 " =    1.231
peak=   -3.523 closest distance to " CD1 PHE A  59 " =    1.845
peak=   -3.509 closest distance to " O   HOH Z 418 " =    1.264
peak=   -3.505 closest distance to " O   SER A 210 " =    1.835
peak=   -3.498 closest distance to " OD2 ASP A 171 " =    1.774
peak=   -3.493 closest distance to " O   HOH Z 118 " =    3.265
peak=   -3.492 closest distance to " CE3 TRP A 150 " =    2.185
peak=   -3.488 closest distance to " CD  GLN A  88 " =    0.732
peak=   -3.488 closest distance to " NE1 TRP A 266 " =    2.304
peak=   -3.482 closest distance to " CB  PHE A 208 " =    2.332
peak=   -3.477 closest distance to " CD2 LEU A 167 " =    1.681
peak=   -3.474 closest distance to " O   HOH Z 377 " =    2.098
peak=   -3.461 closest distance to " O  BHOH Z 338 " =    1.416
peak=   -3.460 closest distance to " O   HOH Z 145 " =    1.798
peak=   -3.449 closest distance to " OH  TYR A 169 " =    0.979
peak=   -3.448 closest distance to " O   HOH Z  17 " =    1.175
peak=   -3.448 closest distance to " N   MET A 188 " =    1.979
peak=   -3.444 closest distance to " CD1 LEU A 101 " =    2.818
peak=   -3.440 closest distance to " O   HOH Z  43 " =    1.733
peak=   -3.440 closest distance to " O   ALA A 161 " =    1.534
peak=   -3.439 closest distance to " NH2 ARG A  66 " =    5.176
peak=   -3.430 closest distance to " OD1 ASP A 191 " =    1.769
peak=   -3.422 closest distance to " O   HOH Z 396 " =    1.869
peak=   -3.413 closest distance to " CA  GLY A 203 " =    2.261
peak=   -3.407 closest distance to " CD  ARG A 139 " =    1.573
peak=   -3.400 closest distance to " O   ALA A 161 " =    2.781
peak=   -3.400 closest distance to " NE2 GLN A 103 " =    1.704
peak=   -3.400 closest distance to " O   HOH Z 392 " =    1.411
peak=   -3.397 closest distance to " CB  ASN A  39 " =    2.298
peak=   -3.389 closest distance to " CD  ARG A 195 " =    5.113
peak=   -3.388 closest distance to " CZ  TYR A 169 " =    1.845
peak=   -3.387 closest distance to " CB  ALA A 161 " =    2.592
peak=   -3.386 closest distance to " NH2 ARG A  79 " =    1.882
peak=   -3.382 closest distance to " O   HOH Z 151 " =    1.555
peak=   -3.379 closest distance to " CE  MET A 105 " =    1.995
peak=   -3.377 closest distance to " CB  TYR A  15 " =    2.299
peak=   -3.376 closest distance to " N   LEU A 281 " =    1.842
peak=   -3.370 closest distance to " O   HOH Z 360 " =    2.510
peak=   -3.368 closest distance to " O   ALA A   7 " =    1.586
peak=   -3.368 closest distance to " CB  ALA A 248 " =    1.979
peak=   -3.368 closest distance to " OE1 GLN A  58 " =    1.308
peak=   -3.363 closest distance to " OG BSER A 134 " =    1.815
peak=   -3.360 closest distance to " CG2 VAL A 189 " =    2.219
peak=   -3.359 closest distance to " O   HOH Z 380 " =    4.682
peak=   -3.355 closest distance to " CD2 PHE A  59 " =    2.497
peak=   -3.348 closest distance to " O   HOH Z 351 " =    1.439
peak=   -3.348 closest distance to " CD  GLN A  88 " =    0.881
peak=   -3.331 closest distance to " O   HOH Z 283 " =    1.723
peak=   -3.330 closest distance to " OG  SER A   3 " =    1.696
peak=   -3.325 closest distance to " O   HOH Z  97 " =    1.534
peak=   -3.323 closest distance to " O   ASN A 187 " =    1.526
peak=   -3.316 closest distance to " O   GLY A 118 " =    2.198
peak=   -3.313 closest distance to " CG2 ILE A 263 " =    2.293
peak=   -3.307 closest distance to " OD2 ASP A 171 " =    2.198
peak=   -3.305 closest distance to " OG  SER A  32 " =    1.181
peak=   -3.304 closest distance to " CD1 PHE A 130 " =    2.316
peak=   -3.302 closest distance to " NH2 ARG A  66 " =    1.338
peak=   -3.299 closest distance to " CA  GLY A  98 " =    2.201
peak=   -3.298 closest distance to " O   HOH Z 222 " =    1.214
peak=   -3.295 closest distance to " O   HOH Z 385 " =    3.757
peak=   -3.295 closest distance to " O   HOH Z 388 " =    2.138
peak=   -3.294 closest distance to " C   LEU A 143 " =    1.193
peak=   -3.291 closest distance to " O   HOH Z  19 " =    2.188
peak=   -3.291 closest distance to " ND2 ASN A  69 " =    1.493
peak=   -3.289 closest distance to " NH1 ARG A 195 " =    2.258
peak=   -3.288 closest distance to " CD2 LEU A 237 " =    2.829
peak=   -3.287 closest distance to " CB  ALA A 291 " =    2.472
peak=   -3.285 closest distance to " O   GLN A  11 " =    1.239
peak=   -3.284 closest distance to " CD  GLN A  58 " =    0.997
peak=   -3.284 closest distance to " O   HOH Z 166 " =    2.033
peak=   -3.282 closest distance to " O   ALA A   1 " =    2.045
peak=   -3.282 closest distance to " CB  ALA A 131 " =    2.330
peak=   -3.279 closest distance to " O   ALA A  10 " =    1.597
peak=   -3.278 closest distance to " N   ALA A 226 " =    2.097
peak=   -3.276 closest distance to " CB  ASP A 286 " =    2.287
peak=   -3.273 closest distance to " O   HOH Z  39 " =    1.618
peak=   -3.262 closest distance to " O   MET A  40 " =    2.697
peak=   -3.257 closest distance to " CG  ARG A 219 " =    2.343
peak=   -3.255 closest distance to " CD  PRO A 198 " =    1.235
peak=   -3.254 closest distance to " OG BSER A 210 " =    2.232
peak=   -3.252 closest distance to " O   LEU A 167 " =    1.575
peak=   -3.243 closest distance to " CB  PRO A 163 " =    2.812
peak=   -3.242 closest distance to " NH2AARG A 275 " =    5.065
peak=   -3.238 closest distance to " CB  LYS A 193 " =    2.498
peak=   -3.237 closest distance to " CD1 TYR A 247 " =    2.254
peak=   -3.235 closest distance to " CG1 VAL A 112 " =    2.595
peak=   -3.233 closest distance to " CB  SER A 210 " =    1.346
peak=   -3.231 closest distance to " O   PHE A 218 " =    1.474
peak=   -3.231 closest distance to " O   HOH Z 424 " =    2.966
peak=   -3.230 closest distance to " O   HOH Z 423 " =    1.147
peak=   -3.230 closest distance to " CB  CYS A 254 " =    2.513
peak=   -3.223 closest distance to " O   HOH Z  63 " =    1.111
peak=   -3.223 closest distance to " NE2 GLN A  88 " =    1.931
peak=   -3.220 closest distance to " CG  ASP A 132 " =    2.365
peak=   -3.215 closest distance to " CB  TRP A  85 " =    2.400
peak=   -3.210 closest distance to " CA  GLY A 133 " =    1.860
peak=   -3.209 closest distance to " O   SER A 135 " =    1.533
peak=   -3.209 closest distance to " N   VAL A 189 " =    1.858
peak=   -3.204 closest distance to " O   PRO A 198 " =    1.309
peak=   -3.202 closest distance to " O   HOH Z   6 " =    1.719
peak=   -3.194 closest distance to " O   HOH Z 298 " =    2.787
peak=   -3.193 closest distance to " O   SER A  26 " =    1.328
peak=   -3.192 closest distance to " CG  PRO A 243 " =    1.593
peak=   -3.190 closest distance to " O   HOH Z 412 " =    4.910
peak=   -3.184 closest distance to " O   HOH Z  37 " =    1.550
peak=   -3.182 closest distance to " O   VAL A 125 " =    2.135
peak=   -3.181 closest distance to " CD  GLN A 223 " =    0.925
peak=   -3.180 closest distance to " CD1 LEU A 167 " =    2.159
peak=   -3.174 closest distance to " O   HOH Z 414 " =    1.428
peak=   -3.172 closest distance to " N   ALA A 248 " =    1.830
peak=   -3.166 closest distance to " CG  LYS A 119 " =    2.980
peak=   -3.164 closest distance to " O   HOH Z 292 " =    2.919
peak=   -3.162 closest distance to " O   VAL A 174 " =    2.027
peak=   -3.161 closest distance to " O   ALA A  34 " =    2.489
peak=   -3.156 closest distance to " CA  GLY A 241 " =    2.256
peak=   -3.154 closest distance to " OG BSER A 210 " =    1.195
peak=   -3.148 closest distance to " O   HOH Z  78 " =    1.759
peak=   -3.132 closest distance to " CB  ALA A  43 " =    2.475
peak=   -3.131 closest distance to " O   GLY A  23 " =    1.740
peak=   -3.128 closest distance to " OG BSER A 134 " =    1.282
peak=   -3.126 closest distance to " OG  SER A 245 " =    1.004
peak=   -3.120 closest distance to " CE3 TRP A 274 " =    2.472
peak=   -3.111 closest distance to " O   HOH Z 140 " =    0.806
peak=   -3.099 closest distance to " O   HOH Z 198 " =    2.276
peak=   -3.099 closest distance to " O   HOH Z 427 " =    1.305
peak=   -3.090 closest distance to " OD2 ASP A  65 " =    1.756
peak=   -3.089 closest distance to " O   HOH Z 407 " =    1.207
peak=   -3.081 closest distance to " CH2 TRP A 177 " =    1.912
peak=   -3.076 closest distance to " O   ALA A  34 " =    2.024
peak=   -3.056 closest distance to " O   HOH Z 361 " =    3.409
peak=   -3.025 closest distance to " O   HOH Z 297 " =    2.893
peak=   -3.024 closest distance to " O   HOH Z 366 " =    1.709
peak=   -3.015 closest distance to " O   HOH Z 111 " =    3.517

================= 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    :  0.4413 0.4326   6.255014e+00   6.240437e+00
   1_bss:  0.4296 0.4187   6.243800e+00   6.223010e+00
   1_xyz:  0.3173 0.3503   6.012047e+00   6.079078e+00
   1_adp:  0.2894 0.3596   5.963293e+00   6.099006e+00
   1_occ:  0.2890 0.3599   5.962478e+00   6.098894e+00
   2_bss:  0.2865 0.3556   5.959213e+00   6.095971e+00
   2_xyz:  0.2221 0.2761   5.731909e+00   5.905252e+00
   2_adp:  0.2056 0.2617   5.677110e+00   5.860936e+00
   2_occ:  0.2055 0.2618   5.676813e+00   5.860710e+00
   3_bss:  0.2051 0.2611   5.675425e+00   5.859215e+00
   3_xyz:  0.1491 0.1936   5.379838e+00   5.591699e+00
   3_adp:  0.1328 0.1810   5.289984e+00   5.519938e+00
   3_occ:  0.1328 0.1809   5.289985e+00   5.520048e+00
   4_bss:  0.1329 0.1809   5.292683e+00   5.521222e+00
   4_xyz:  0.1220 0.1711   5.227128e+00   5.464896e+00
   4_adp:  0.1191 0.1671   5.204157e+00   5.439909e+00
   4_occ:  0.1191 0.1671   5.203965e+00   5.439982e+00
   5_bss:  0.1190 0.1671   5.203876e+00   5.440014e+00
   5_xyz:  0.1173 0.1640   5.189109e+00   5.422270e+00
   5_adp:  0.1177 0.1623   5.185926e+00   5.411994e+00
   5_occ:  0.1175 0.1624   5.185682e+00   5.412220e+00
   5_bss:  0.1175 0.1624   5.185765e+00   5.412188e+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:  0.295  24.129  -3.401   4.151   1.334   0.000   0.000   0.000
   1_xyz:  0.295  24.129  -3.401   4.151   1.334   0.000   0.000   0.000
   1_adp:  0.295  24.129  -3.401   4.151   1.334   0.000   0.000   0.000
   1_occ:  0.295  24.129  -3.401   4.151   1.334   0.000   0.000   0.000
   2_bss:  0.318  49.575  -2.185   1.628  -0.363   0.000  -0.000  -0.000
   2_xyz:  0.318  49.575  -2.185   1.628  -0.363   0.000  -0.000  -0.000
   2_adp:  0.318  49.575  -2.185   1.628  -0.363   0.000  -0.000  -0.000
   2_occ:  0.318  49.575  -2.185   1.628  -0.363   0.000  -0.000  -0.000
   3_bss:  0.321  53.049  -2.016   0.361  -0.945   0.000  -0.000  -0.000
   3_xyz:  0.321  53.049  -2.016   0.361  -0.945   0.000  -0.000  -0.000
   3_adp:  0.321  53.049  -2.016   0.361  -0.945   0.000  -0.000  -0.000
   3_occ:  0.321  53.049  -2.016   0.361  -0.945   0.000  -0.000  -0.000
   4_bss:  0.321  53.049  -2.202  -0.729  -1.359  -0.000  -0.000  -0.000
   4_xyz:  0.321  53.049  -2.202  -0.729  -1.359  -0.000  -0.000  -0.000
   4_adp:  0.321  53.049  -2.202  -0.729  -1.359  -0.000  -0.000  -0.000
   4_occ:  0.321  53.049  -2.202  -0.729  -1.359  -0.000  -0.000  -0.000
   5_bss:  0.323  54.972  -2.103  -0.945  -1.327  -0.000  -0.000  -0.000
   5_xyz:  0.323  54.972  -2.103  -0.945  -1.327  -0.000  -0.000  -0.000
   5_adp:  0.323  54.972  -2.103  -0.945  -1.327  -0.000  -0.000  -0.000
   5_occ:  0.323  54.972  -2.103  -0.945  -1.327  -0.000  -0.000  -0.000
   5_bss:  0.323  52.573  -2.031  -0.993  -1.231  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.644 0.4874  0.6492    60338.964
   1_bss:  50.855 0.5084  0.6912    55795.111
   1_xyz:  37.834 0.6682  0.8807    33871.118
   1_adp:  39.123 0.6521  0.8615    35735.721
   1_occ:  39.122 0.6521  0.8607    35707.785
   2_bss:  38.631 0.6579  0.8428    35132.587
   2_xyz:  28.631 0.7716  0.9525    20320.798
   2_adp:  26.566 0.7948  0.9598    18179.722
   2_occ:  26.568 0.7947  0.9595    18174.805
   3_bss:  26.436 0.7961  0.9427    18039.818
   3_xyz:  18.833 0.8717  0.9951     9631.468
   3_adp:  17.108 0.8879  0.9959     8381.150
   3_occ:  17.111 0.8879  0.9957     8383.999
   4_bss:  17.132 0.8878  0.9767     8433.376
   4_xyz:  15.833 0.8994  0.9803     7441.996
   4_adp:  15.263 0.9045  0.9762     7118.256
   4_occ:  15.263 0.9046  0.9761     7123.215
   5_bss:  15.259 0.9046  0.9755     7125.580
   5_xyz:  14.849 0.9080  0.9770     6812.829
   5_adp:  14.628 0.9099  0.9734     6725.144
   5_occ:  14.630 0.9099  0.9733     6731.402
   5_bss:  14.629 0.9099  0.9731     6728.699
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.8133e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.8133e-01
   1_xyz:   1.629  0.013  0.094 15.868  0.006  4.116   1.4484e-01
   1_adp:   1.629  0.013  0.094 15.868  0.006  4.116   1.4484e-01
   1_occ:   1.629  0.013  0.094 15.868  0.006  4.116   1.4484e-01
   2_bss:   1.629  0.013  0.094 15.868  0.006  4.116   1.4484e-01
   2_xyz:   1.237  0.008  0.078 14.367  0.005  4.110   7.7157e-02
   2_adp:   1.237  0.008  0.078 14.367  0.005  4.110   7.7157e-02
   2_occ:   1.237  0.008  0.078 14.367  0.005  4.110   7.7157e-02
   3_bss:   1.237  0.008  0.078 14.367  0.005  4.110   7.7157e-02
   3_xyz:   1.155  0.009  0.076 14.839  0.005  4.121   7.7338e-02
   3_adp:   1.155  0.009  0.076 14.839  0.005  4.121   7.7338e-02
   3_occ:   1.155  0.009  0.076 14.839  0.005  4.121   7.7338e-02
   4_bss:   1.155  0.009  0.076 14.839  0.005  4.121   7.7338e-02
   4_xyz:   1.029  0.007  0.073 14.611  0.004  4.113   6.1082e-02
   4_adp:   1.029  0.007  0.073 14.611  0.004  4.113   6.1082e-02
   4_occ:   1.029  0.007  0.073 14.611  0.004  4.113   6.1082e-02
   5_bss:   1.029  0.007  0.073 14.611  0.004  4.113   6.1082e-02
   5_xyz:   0.940  0.006  0.068 14.359  0.003  4.114   5.2625e-02
   5_adp:   0.940  0.006  0.068 14.359  0.003  4.114   5.2625e-02
   5_occ:   0.940  0.006  0.068 14.359  0.003  4.114   5.2625e-02
   5_bss:   0.940  0.006  0.068 14.359  0.003  4.114   5.2625e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.638   2.4143e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.638   2.4143e-01
   1_xyz:  10.128  0.080  0.490 88.893  0.024  1.996   2.2477e-01
   1_adp:  10.128  0.080  0.490 88.893  0.024  1.996   2.2477e-01
   1_occ:  10.128  0.080  0.490 88.893  0.024  1.996   2.2477e-01
   2_bss:  10.128  0.080  0.490 88.893  0.024  1.996   2.2477e-01
   2_xyz:   7.832  0.048  0.228 87.355  0.043  2.270   9.0983e-02
   2_adp:   7.832  0.048  0.228 87.355  0.043  2.270   9.0983e-02
   2_occ:   7.832  0.048  0.228 87.355  0.043  2.270   9.0983e-02
   3_bss:   7.832  0.048  0.228 87.355  0.043  2.270   9.0983e-02
   3_xyz:   7.607  0.075  0.258 83.274  0.032  2.246   7.3551e-02
   3_adp:   7.607  0.075  0.258 83.274  0.032  2.246   7.3551e-02
   3_occ:   7.607  0.075  0.258 83.274  0.032  2.246   7.3551e-02
   4_bss:   7.607  0.075  0.258 83.274  0.032  2.246   7.3551e-02
   4_xyz:   7.077  0.040  0.229 83.051  0.034  2.345   5.6053e-02
   4_adp:   7.077  0.040  0.229 83.051  0.034  2.345   5.6053e-02
   4_occ:   7.077  0.040  0.229 83.051  0.034  2.345   5.6053e-02
   5_bss:   7.077  0.040  0.229 83.051  0.034  2.345   5.6053e-02
   5_xyz:   6.953  0.043  0.230 81.030  0.028  2.365   3.3543e-02
   5_adp:   6.953  0.043  0.230 81.030  0.028  2.365   3.3543e-02
   5_occ:   6.953  0.043  0.230 81.030  0.028  2.365   3.3543e-02
   5_bss:   6.953  0.043  0.230 81.030  0.028  2.365   3.3543e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  81.35   0.00  18.24  75.69   0.00  14.62  81.35   0.43  37.94
   1_occ:  81.35   0.00  18.24  75.69   0.00  14.62  81.35   0.43  37.94
   2_bss:  81.35   0.00  18.24  75.69   0.00  14.62  81.35   0.43  37.94
   2_xyz:  81.35   0.00  18.24  75.69   0.00  14.62  81.35   0.43  37.94
   2_adp:  86.20   0.00  17.68  78.79   0.00  13.67  86.20   5.17  39.51
   2_occ:  86.20   0.00  17.68  78.79   0.00  13.67  86.20   5.17  39.51
   3_bss:  86.20   0.00  17.68  78.79   0.00  13.67  86.20   5.17  39.51
   3_xyz:  86.20   0.00  17.68  78.79   0.00  13.67  86.20   5.17  39.51
   3_adp:  99.42   0.00  17.99  99.42   0.00  13.11  99.36   6.07  44.58
   3_occ:  99.42   0.00  17.99  99.42   0.00  13.11  99.36   6.07  44.58
   4_bss:  99.42   0.00  17.99  99.42   0.00  13.11  99.36   6.07  44.58
   4_xyz:  99.42   0.00  17.99  99.42   0.00  13.11  99.36   6.07  44.58
   4_adp: 104.78   0.97  17.48 104.78   0.97  12.75  99.54   5.24  43.22
   4_occ: 104.78   0.97  17.48 104.78   0.97  12.75  99.54   5.24  43.22
   5_bss: 104.78   0.97  17.48 104.78   0.97  12.75  99.54   5.24  43.22
   5_xyz: 104.78   0.97  17.48 104.78   0.97  12.75  99.54   5.24  43.22
   5_adp: 100.91   1.38  16.71 100.91   1.38  12.44  90.12   4.82  39.99
   5_occ: 100.91   1.38  16.71 100.91   1.38  12.44  90.12   4.82  39.99
   5_bss: 100.86   1.33  16.66 100.86   1.33  12.39  90.07   4.77  39.94
------------------------------------------------------------------------
 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:    2.057    0.034    0.414
   1_adp:    2.057    0.034    0.414
   1_occ:    2.057    0.034    0.414
   2_bss:    2.057    0.034    0.414
   2_xyz:    1.541    0.050    0.538
   2_adp:    1.541    0.050    0.538
   2_occ:    1.541    0.050    0.538
   3_bss:    1.541    0.050    0.538
   3_xyz:    1.399    0.070    0.695
   3_adp:    1.399    0.070    0.695
   3_occ:    1.399    0.070    0.695
   4_bss:    1.399    0.070    0.695
   4_xyz:    1.417    0.058    0.723
   4_adp:    1.417    0.058    0.723
   4_occ:    1.417    0.058    0.723
   5_bss:    1.417    0.058    0.723
   5_xyz:    1.442    0.113    0.738
   5_adp:    1.442    0.113    0.738
   5_occ:    1.442    0.113    0.738
   5_bss:    1.442    0.113    0.738
------------------------------------------------------------------------

CPU time actual refinement: 279.86


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_705/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/noshake/run_705/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_705/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_705/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_705/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 279.73 
  Macro-tasks:
    bulk solvent and scale       = 36.97  
    individual site refinement   = 111.75 
    weights calculation          = 24.50  
    collect and process          = 5.45   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 178.76 
  Micro-tasks:
    mask                            = 1.50   
    f_calc                          = 88.34  
    alpha_beta                      = 6.95   
    target                          = 1.00   
    gradients_wrt_atomic_parameters = 95.11  
    fmodel                         = 5.94   
    r_factors                      = 0.12   
    phase_errors                   = 8.74   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 207.94 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.011 micro seconds
Total CPU time: 4.86 minutes
from_scatterers_fft:    632 calls, 88.04 s
gradients_fft:          577 calls, 84.00 s

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

# Date 2008-01-16 Time 05:27:12 PST -0800 (1200490032.46 s)
Start R-work = 0.4413, R-free = 0.4326 (no bulk solvent and anisotropic scale)
Final R-work = 0.1385, R-free = 0.1813 (no bulk solvent and anisotropic scale)

Start R-work = 0.4296, R-free = 0.4187
Final R-work = 0.1175, R-free = 0.1624