# Date 2008-01-16 Time 05:52:39 PST -0800 (1200491559.02 s)
#phil __OFF__

Command line arguments: "../914.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29996
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 914

-------------------------------------------------------------------------------
  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: (70.9525, 47.1647, 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: 2.76, per 1000 atoms: 0.98


================================== 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: (70.9525, 47.1647, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.96131
Completeness in resolution range: 0.935482
Completeness with d_max=infinity: 0.932676

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0179
                             d_min =   1.9613

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: (70.9525, 47.1647, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.96131
Completeness in resolution range: 0.935482
Completeness with d_max=infinity: 0.932676

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0183 -  4.1977 [2202/2231]  1984   218   9.9%
  bin  2:  4.1977 -  3.3439 [2097/2120]  1888   209  10.0%
  bin  3:  3.3439 -  2.9248 [2089/2111]  1873   216  10.3%
  bin  4:  2.9248 -  2.6590 [2068/2087]  1873   195   9.4%
  bin  5:  2.6590 -  2.4693 [2058/2087]  1842   216  10.5%
  bin  6:  2.4693 -  2.3242 [2029/2071]  1833   196   9.7%
  bin  7:  2.3242 -  2.2082 [2029/2065]  1826   203  10.0%
  bin  8:  2.2082 -  2.1124 [2017/2054]  1816   201  10.0%
  bin  9:  2.1124 -  2.0312 [2027/2059]  1821   206  10.2%
  bin 10:  2.0312 -  1.9613 [ 973/2055]   874    99  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_914/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:
        1.70 -     2.34: 26
        2.34 -     2.98: 1824
        2.98 -     3.62: 4594
        3.62 -     4.26: 9157
        4.26 -     4.90: 12785
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.704 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.727 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.992 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z  17 " - " O   HOH Z 333 "  2.059 3.040 -x,y+1/2,-z+1/2
  ... (remaining 28381 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_914/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_914/model_refine_001.geo

CPU time processing inputs: 7.87


============================ 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 = 70.9525 47.16465 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 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3636   r_free= 0.3676   ksol= 0.00   Bsol= 0.00   scale= 0.955    |
|                                                                             |
| 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:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.128927                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6823 0.99   1423  159 0.2957 0.2954      6.3887      6.3779|
|  2:  4.6823 -  3.7353 0.99   1375  146 0.2823 0.2707      6.5219      6.4804|
|  3:  3.7353 -  3.2687 0.99   1350  158 0.3175 0.3206      6.4258      6.5367|
|  4:  3.2687 -  2.9723 0.99   1344  148 0.3390 0.3434      6.3053      6.3057|
|  5:  2.9723 -  2.7607 0.99   1310  147 0.3672 0.3479      6.1785      6.1992|
|  6:  2.7607 -  2.5988 0.98   1332  146 0.4013 0.4040      6.1306      6.0691|
|  7:  2.5988 -  2.4693 0.99   1326  150 0.3812 0.3489      6.1005      6.0169|
|  8:  2.4693 -  2.3622 0.99   1290  143 0.4051 0.4264       6.036      6.1117|
|  9:  2.3622 -  2.2716 0.98   1326  148 0.4101 0.4182      6.0132      5.9654|
| 10:  2.2716 -  2.1934 0.98   1301  148 0.4253 0.4780      5.9895      6.0686|
| 11:  2.1934 -  2.1251 0.98   1303  137 0.4259 0.4905      5.9316      6.0263|
| 12:  2.1251 -  2.0645 0.99   1295  144 0.4281 0.4596      5.8729      5.9229|
| 13:  2.0645 -  2.0102 0.94   1253  146 0.4382 0.4163      5.8027      5.7558|
| 14:  2.0102 -  1.9613 0.30    402   39 0.5231 0.5342      5.8173      5.8085|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0183 -  4.6823  1423   159  0.78  26.66   0.86     0.79      44775.96|
|  2:  4.6823 -  3.7353  1375   146  0.81  25.41   0.97     0.89      56537.74|
|  3:  3.7353 -  3.2687  1350   158  0.76  30.45   0.97     0.92      59481.62|
|  4:  3.2687 -  2.9723  1344   148  0.70  35.39   0.99     0.89      54116.11|
|  5:  2.9723 -  2.7607  1310   147  0.64  40.31   0.95     0.84      45265.61|
|  6:  2.7607 -  2.5988  1332   146  0.63  41.44   0.97     0.83      38807.93|
|  7:  2.5988 -  2.4693  1326   150  0.65  39.57   0.99     0.84      34522.51|
|  8:  2.4693 -  2.3622  1290   143  0.62  42.19   0.96     0.85      33136.77|
|  9:  2.3622 -  2.2716  1326   148  0.60  43.94   1.00     0.82      32039.48|
| 10:  2.2716 -  2.1934  1301   148  0.55  48.23   1.02     0.77      34689.59|
| 11:  2.1934 -  2.1251  1303   137  0.51  51.20   1.01     0.74      33512.76|
| 12:  2.1251 -  2.0645  1295   144  0.49  52.72   1.01     0.75      32568.01|
| 13:  2.0645 -  2.0102  1253   146  0.50  52.37   0.99     0.74      26949.05|
| 14:  2.0102 -  1.9613   402    39  0.48  53.68   0.94     0.68      23131.87|
|alpha:            min =        0.68 max =            0.92 mean =         0.82|
|beta:             min =    23131.87 max =        59481.62 mean =     40302.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.63|
|phase err.(work): min =        0.00 max =           90.00 mean =        40.82|
|phase err.(test): min =        0.00 max =           89.78 mean =        40.79|
|-----------------------------------------------------------------------------|

============================== 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 = 3.954553              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.172   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.074514              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.067   (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 |  1.704 -  2.024:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.024 -  2.343:       22 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.343 -  2.663:       66 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.663 -  2.982:     1758 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.982 -  3.302:     1914 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.302 -  3.622:     2680 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.622 -  3.941:     4731 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.941 -  4.261:     4426 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.261 -  4.580:     5843 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.580 -  4.900:     6942 |
|-----------------------------------------------------------------------------|
|-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 |        0.169 |
| 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  1.704 |       0.284 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    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 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3636   r_free= 0.3676   ksol= 0.00   Bsol= 0.00   scale= 0.955    |
|                                                                             |
| 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:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.128927                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3515   r_free= 0.3558   ksol= 0.30   Bsol= 50.00   scale= 0.967   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.81,-2.06,2.16,-0.00,0.00,0.00); trace/3= -0.57                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.116128                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.244885              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.241   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.513107              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.963   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3515      final r-factor (work) = 0.2351          |
| start r-factor (free) = 0.3558      final r-factor (free) = 0.2639          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0901 = 3.24 * 0.50 * 6.1148 + 1.00 * 0.1693                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6520 = 3.24 * 0.50 * 5.9011 + 1.00 * 0.0777                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2351      final r-factor (work) = 0.2177          |
| start r-factor (free) = 0.2639      final r-factor (free) = 0.2707          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0344 = 0.51 * 1.00 * 5.9011 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9851 = 0.51 * 1.00 * 5.7156 + 1.00 * 0.0523                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.20   16.94    None  None   None       |
|    all(noH): 2823   0      0.00    98.20   16.94    None  None   None       |
|    Sol.    : 438    0      6.50    63.85   38.02    None  None   None       |
|    Mac.    : 2385   0      0.00    98.20   13.07    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 -   9.820:  904   |   5:    49.102 -  58.922:   95        |
|      1:     9.820 -  19.641: 1179   |   6:    58.922 -  68.743:   12        |
|      2:    19.641 -  29.461:  318   |   7:    68.743 -  78.563:    0        |
|      3:    29.461 -  39.282:  176   |   8:    78.563 -  88.383:    0        |
|      4:    39.282 -  49.102:  138   |   9:    88.383 -  98.204:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2177 r_free = 0.2707             target_work(ml) = 5.727         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2173 r_free = 0.2705             target_work(ml) = 5.726         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2173   r_free= 0.2705   ksol= 0.30   Bsol= 50.00   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.81,-2.06,2.16,-0.00,0.00,0.00); trace/3= -0.57                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.726003                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2156   r_free= 0.2678   ksol= 0.33   Bsol= 52.47   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.38,-0.55,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.721187                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.876682              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.804   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.507364              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.245   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2156      final r-factor (work) = 0.1550          |
| start r-factor (free) = 0.2678      final r-factor (free) = 0.2006          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3050 = 2.88 * 0.50 * 5.7200 + 1.00 * 0.0777                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0980 = 2.88 * 0.50 * 5.5916 + 1.00 * 0.0553                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1550      final r-factor (work) = 0.1417          |
| start r-factor (free) = 0.2006      final r-factor (free) = 0.1887          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8918 = 0.51 * 1.00 * 5.5916 + 1.00 * 0.0548                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7396 = 0.51 * 1.00 * 5.3808 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.73   17.55    None  None   None       |
|    all(noH): 2823   0      0.00    82.73   17.55    None  None   None       |
|    Sol.    : 438    0      6.05    77.91   41.25    None  None   None       |
|    Mac.    : 2385   0      0.00    82.73   13.20    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 -   8.273:  614   |   5:    41.365 -  49.638:  126        |
|      1:     8.273 -  16.546: 1336   |   6:    49.638 -  57.911:   94        |
|      2:    16.546 -  24.819:  351   |   7:    57.911 -  66.184:   44        |
|      3:    24.819 -  33.092:  127   |   8:    66.184 -  74.457:   23        |
|      4:    33.092 -  41.365:   99   |   9:    74.457 -  82.730:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1417 r_free = 0.1887             target_work(ml) = 5.348         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1415 r_free = 0.1887             target_work(ml) = 5.347         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1415   r_free= 0.1887   ksol= 0.33   Bsol= 52.47   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.38,-0.55,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.347313                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1415   r_free= 0.1880   ksol= 0.33   Bsol= 52.47   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-2.26,-1.42,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.344333                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.676983              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.633  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.312227              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.091  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1415      final r-factor (work) = 0.1242          |
| start r-factor (free) = 0.1880      final r-factor (free) = 0.1662          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5664 = 1.68 * 0.50 * 5.3800 + 1.00 * 0.0553                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4828 = 1.68 * 0.50 * 5.2891 + 1.00 * 0.0479                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1242      final r-factor (work) = 0.1208          |
| start r-factor (free) = 0.1662      final r-factor (free) = 0.1627          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6609 = 0.31 * 1.00 * 5.2891 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6373 = 0.31 * 1.00 * 5.2163 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.21    84.91   17.30    None  None   None       |
|    all(noH): 2823   0      1.21    84.91   17.30    None  None   None       |
|    Sol.    : 438    0      3.32    77.39   40.44    None  None   None       |
|    Mac.    : 2385   0      1.21    84.91   13.05    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:     1.210 -   9.580:  905   |   5:    43.060 -  51.430:  113        |
|      1:     9.580 -  17.950: 1179   |   6:    51.430 -  59.800:   74        |
|      2:    17.950 -  26.320:  256   |   7:    59.800 -  68.170:   38        |
|      3:    26.320 -  34.690:  119   |   8:    68.170 -  76.540:   18        |
|      4:    34.690 -  43.060:  115   |   9:    76.540 -  84.910:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1208 r_free = 0.1627             target_work(ml) = 5.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1207 r_free = 0.1625             target_work(ml) = 5.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1207   r_free= 0.1625   ksol= 0.33   Bsol= 52.47   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-2.26,-1.42,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.202522                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1623   ksol= 0.32   Bsol= 47.88   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.26,-1.78,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.201969                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.595322              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 120.083  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.894635              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.297  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1206      final r-factor (work) = 0.1091          |
| start r-factor (free) = 0.1623      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4242 = 3.60 * 0.50 * 5.2158 + 1.00 * 0.0480                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3455 = 3.60 * 0.50 * 5.1582 + 1.00 * 0.0729                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1091      final r-factor (work) = 0.1073          |
| start r-factor (free) = 0.1556      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6233 = 0.89 * 1.00 * 5.1582 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5927 = 0.89 * 1.00 * 5.1232 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.13    94.88   17.23    None  None   None       |
|    all(noH): 2823   0      1.13    94.88   17.23    None  None   None       |
|    Sol.    : 438    0      3.16    83.10   40.43    None  None   None       |
|    Mac.    : 2385   0      1.13    94.88   12.97    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:     1.125 -  10.501: 1156   |   5:    48.003 -  57.379:  112        |
|      1:    10.501 -  19.877: 1021   |   6:    57.379 -  66.755:   40        |
|      2:    19.877 -  29.252:  211   |   7:    66.755 -  76.130:   24        |
|      3:    29.252 -  38.628:  132   |   8:    76.130 -  85.506:    4        |
|      4:    38.628 -  48.003:  118   |   9:    85.506 -  94.882:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1073 r_free = 0.1561             target_work(ml) = 5.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1073 r_free = 0.1560             target_work(ml) = 5.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1073   r_free= 0.1560   ksol= 0.32   Bsol= 47.88   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.26,-1.78,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.125135                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1075   r_free= 0.1554   ksol= 0.32   Bsol= 47.88   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.12,-1.76,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.125889                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.511242              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 159.173  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.718396              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.824  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1075      final r-factor (work) = 0.1075          |
| start r-factor (free) = 0.1554      final r-factor (free) = 0.1565          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5062 = 2.51 * 0.50 * 5.1236 + 1.00 * 0.0729                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4994 = 2.51 * 0.50 * 5.1273 + 1.00 * 0.0614                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1075      final r-factor (work) = 0.1072          |
| start r-factor (free) = 0.1565      final r-factor (free) = 0.1570          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6926 = 0.72 * 1.00 * 5.1273 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6950 = 0.72 * 1.00 * 5.1306 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.09    100.89  17.00    None  None   None       |
|    all(noH): 2823   0      1.09    100.89  17.00    None  None   None       |
|    Sol.    : 438    0      4.85    84.60   39.82    None  None   None       |
|    Mac.    : 2385   0      1.09    100.89  12.81    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:     1.090 -  11.070: 1319   |   5:    50.989 -  60.969:   74        |
|      1:    11.070 -  21.050:  910   |   6:    60.969 -  70.949:   34        |
|      2:    21.050 -  31.030:  192   |   7:    70.949 -  80.929:   12        |
|      3:    31.030 -  41.010:  138   |   8:    80.929 -  90.909:    4        |
|      4:    41.010 -  50.989:  136   |   9:    90.909 - 100.889:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1072 r_free = 0.1570             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1072 r_free = 0.1570             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1570   ksol= 0.32   Bsol= 47.88   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.12,-1.76,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.133402                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6823 0.99   1423  159 0.0951 0.1276      5.3604      5.5386|
|  2:  4.6823 -  3.7353 0.99   1375  146 0.0821 0.1042      5.3997      5.6034|
|  3:  3.7353 -  3.2687 0.99   1350  158 0.1013 0.1563      5.4353      5.8549|
|  4:  3.2687 -  2.9723 0.99   1344  148 0.1177 0.1528      5.4329      5.5675|
|  5:  2.9723 -  2.7607 0.99   1310  147 0.1251 0.1739      5.2991      5.5059|
|  6:  2.7607 -  2.5988 0.98   1332  146 0.1201 0.1847       5.199      5.4379|
|  7:  2.5988 -  2.4693 0.99   1326  150 0.1164 0.1694      5.1317      5.3638|
|  8:  2.4693 -  2.3622 0.99   1290  143 0.1095 0.1664      5.0293      5.2672|
|  9:  2.3622 -  2.2716 0.98   1326  148 0.1124 0.1900      5.0068      5.3242|
| 10:  2.2716 -  2.1934 0.98   1301  148 0.1087 0.1675      4.9582      5.2139|
| 11:  2.1934 -  2.1251 0.98   1303  137 0.1113 0.1797      4.9275      5.3017|
| 12:  2.1251 -  2.0645 0.99   1295  144 0.1057 0.1718      4.8552      5.0903|
| 13:  2.0645 -  2.0102 0.94   1253  146 0.1118 0.1703      4.7752      5.0222|
| 14:  2.0102 -  1.9613 0.30    402   39 0.1036 0.1706      4.6508      4.8997|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0183 -  4.6823  1423   159  0.94   8.69   0.97     0.95       6838.93|
|  2:  4.6823 -  3.7353  1375   146  0.95   7.89   1.01     1.00       8563.02|
|  3:  3.7353 -  3.2687  1350   158  0.94  11.06   1.02     1.02       9900.66|
|  4:  3.2687 -  2.9723  1344   148  0.92  13.75   1.01     0.99      10269.55|
|  5:  2.9723 -  2.7607  1310   147  0.90  16.14   0.99     0.96       8264.76|
|  6:  2.7607 -  2.5988  1332   146  0.90  16.26   0.98     0.96       7097.94|
|  7:  2.5988 -  2.4693  1326   150  0.91  14.92   0.99     0.96       5969.11|
|  8:  2.4693 -  2.3622  1290   143  0.91  15.50   0.99     0.96       5213.29|
|  9:  2.3622 -  2.2716  1326   148  0.91  15.60   0.99     0.96       4860.45|
| 10:  2.2716 -  2.1934  1301   148  0.90  15.56   0.99     0.96       4560.78|
| 11:  2.1934 -  2.1251  1303   137  0.90  16.70   0.99     0.95       4434.49|
| 12:  2.1251 -  2.0645  1295   144  0.91  15.46   0.99     0.98       3961.93|
| 13:  2.0645 -  2.0102  1253   146  0.90  16.29   0.99     0.97       3346.15|
| 14:  2.0102 -  1.9613   402    39  0.90  16.12   0.98     0.95       2662.02|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2662.02 max =        10269.55 mean =      6361.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.11|
|phase err.(test): min =        0.00 max =           89.51 mean =        13.69|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1071   r_free= 0.1570   ksol= 0.32   Bsol= 47.84   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-1.89,-1.57,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.133524                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1071   r_free= 0.1570   ksol= 0.32   Bsol= 47.84   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-1.89,-1.57,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.133524                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6823 0.99   1423  159 0.0952 0.1278      5.3618      5.5401|
|  2:  4.6823 -  3.7353 0.99   1375  146 0.0821 0.1041      5.3999      5.6029|
|  3:  3.7353 -  3.2687 0.99   1350  158 0.1013 0.1563       5.435      5.8548|
|  4:  3.2687 -  2.9723 0.99   1344  148 0.1177 0.1528      5.4328      5.5675|
|  5:  2.9723 -  2.7607 0.99   1310  147 0.1251 0.1739      5.2991      5.5059|
|  6:  2.7607 -  2.5988 0.98   1332  146 0.1201 0.1848      5.1991      5.4382|
|  7:  2.5988 -  2.4693 0.99   1326  150 0.1165 0.1694       5.132       5.364|
|  8:  2.4693 -  2.3622 0.99   1290  143 0.1096 0.1664      5.0294      5.2673|
|  9:  2.3622 -  2.2716 0.98   1326  148 0.1124 0.1899      5.0069      5.3242|
| 10:  2.2716 -  2.1934 0.98   1301  148 0.1087 0.1675      4.9582      5.2135|
| 11:  2.1934 -  2.1251 0.98   1303  137 0.1113 0.1797      4.9276       5.302|
| 12:  2.1251 -  2.0645 0.99   1295  144 0.1057 0.1717      4.8549      5.0901|
| 13:  2.0645 -  2.0102 0.94   1253  146 0.1118 0.1702      4.7751      5.0218|
| 14:  2.0102 -  1.9613 0.30    402   39 0.1036 0.1707      4.6509      4.9003|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0183 -  4.6823  1423   159  0.94   8.71   0.98     0.95       6858.79|
|  2:  4.6823 -  3.7353  1375   146  0.95   7.90   1.02     1.00       8571.27|
|  3:  3.7353 -  3.2687  1350   158  0.94  11.06   1.03     1.03       9896.12|
|  4:  3.2687 -  2.9723  1344   148  0.92  13.75   1.01     0.99      10268.19|
|  5:  2.9723 -  2.7607  1310   147  0.90  16.14   0.99     0.97       8266.09|
|  6:  2.7607 -  2.5988  1332   146  0.90  16.27   0.99     0.96       7100.07|
|  7:  2.5988 -  2.4693  1326   150  0.91  14.92   0.99     0.96       5971.05|
|  8:  2.4693 -  2.3622  1290   143  0.91  15.50   1.00     0.97       5213.10|
|  9:  2.3622 -  2.2716  1326   148  0.91  15.61   1.00     0.96       4859.22|
| 10:  2.2716 -  2.1934  1301   148  0.90  15.56   1.00     0.96       4559.43|
| 11:  2.1934 -  2.1251  1303   137  0.90  16.70   1.00     0.96       4433.01|
| 12:  2.1251 -  2.0645  1295   144  0.91  15.46   1.00     0.99       3959.38|
| 13:  2.0645 -  2.0102  1253   146  0.90  16.29   1.00     0.98       3345.33|
| 14:  2.0102 -  1.9613   402    39  0.90  16.12   0.99     0.96       2662.91|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2662.91 max =        10268.19 mean =      6362.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.12|
|phase err.(test): min =        0.00 max =           89.51 mean =        13.69|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.05    100.85  16.96    None  None   None       |
|    all(noH): 2823   0      1.05    100.85  16.96    None  None   None       |
|    Sol.    : 438    0      4.81    84.57   39.78    None  None   None       |
|    Mac.    : 2385   0      1.05    100.85  12.77    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:     1.052 -  11.032: 1319   |   5:    50.952 -  60.931:   74        |
|      1:    11.032 -  21.012:  910   |   6:    60.931 -  70.911:   34        |
|      2:    21.012 -  30.992:  192   |   7:    70.911 -  80.891:   12        |
|      3:    30.992 -  40.972:  138   |   8:    80.891 -  90.871:    4        |
|      4:    40.972 -  50.952:  136   |   9:    90.871 - 100.851:    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)= 303         
Filter by distance & map next to the model:
   mapped sites are within: 0.530 - 4.429
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 297 from: 303
   mapped sites are within: 0.735 - 4.429

peak=    5.857 closest distance to " NH2 ARG A  56 " =    2.201
peak=    5.658 closest distance to " CB  GLN A 223 " =    1.432
peak=    5.441 closest distance to " CB  SER A  63 " =    1.219
peak=    5.379 closest distance to " CG  PRO A  54 " =    1.186
peak=    5.005 closest distance to " CG  PRO A 213 " =    1.201
peak=    4.866 closest distance to " O   HOH Z 126 " =    1.905
peak=    4.859 closest distance to " CB  PRO A  54 " =    0.932
peak=    4.824 closest distance to " CB  GLN A 183 " =    1.271
peak=    4.740 closest distance to " NE2 GLN A  11 " =    1.069
peak=    4.710 closest distance to " CB  ARG A 275 " =    0.895
peak=    4.634 closest distance to " CA  TYR A  30 " =    0.948
peak=    4.630 closest distance to " O   HOH Z 232 " =    2.278
peak=    4.625 closest distance to " CG  PRO A  90 " =    1.094
peak=    4.621 closest distance to " O   HOH Z 193 " =    1.932
peak=    4.599 closest distance to " O   HOH Z  15 " =    2.135
peak=    4.580 closest distance to " C   PRO A 198 " =    1.509
peak=    4.560 closest distance to " CB  GLU A 128 " =    1.117
peak=    4.517 closest distance to " O   HOH Z  78 " =    1.722
peak=    4.498 closest distance to " CB  GLU A 152 " =    1.180
peak=    4.487 closest distance to " OD1 ASN A  69 " =    2.571
peak=    4.463 closest distance to " O   HOH Z 298 " =    1.856
peak=    4.417 closest distance to " O   HOH Z 236 " =    1.968
peak=    4.357 closest distance to " CB  TYR A 169 " =    0.756
peak=    4.349 closest distance to " CB  ASN A 148 " =    1.483
peak=    4.337 closest distance to " O   HOH Z 142 " =    1.670
peak=    4.336 closest distance to " O   HOH Z 272 " =    1.861
peak=    4.332 closest distance to " O   HOH Z 427 " =    2.853
peak=    4.332 closest distance to " CB  LEU A 228 " =    1.110
peak=    4.315 closest distance to " CG  PRO A 198 " =    1.260
peak=    4.281 closest distance to " CB  SER A   3 " =    1.375
peak=    4.235 closest distance to " OD2 ASP A 286 " =    2.866
peak=    4.235 closest distance to " O   HOH Z 316 " =    3.023
peak=    4.210 closest distance to " O   HOH Z 368 " =    2.014
peak=    4.208 closest distance to " O   HOH Z 344 " =    3.063
peak=    4.202 closest distance to " CB  TRP A 179 " =    1.353
peak=    4.194 closest distance to " O   HOH Z 209 " =    2.278
peak=    4.163 closest distance to " O   HOH Z 352 " =    1.860
peak=    4.144 closest distance to " CG  PRO A 243 " =    1.149
peak=    4.131 closest distance to " O   HOH Z 369 " =    1.973
peak=    4.130 closest distance to " CB  ARG A  79 " =    1.463
peak=    4.122 closest distance to " O   HOH Z 234 " =    3.732
peak=    4.101 closest distance to " CA  ALA A  21 " =    1.206
peak=    4.093 closest distance to " O   HOH Z 389 " =    1.968
peak=    4.085 closest distance to " CA  THR A 221 " =    0.922
peak=    4.056 closest distance to " CB  VAL A 202 " =    1.654
peak=    4.045 closest distance to " O   HOH Z 426 " =    1.540
peak=    4.010 closest distance to " ND2 ASN A 187 " =    1.546
peak=    3.982 closest distance to " O   HOH Z 261 " =    2.151
peak=    3.981 closest distance to " O   MET A 105 " =    1.824
peak=    3.950 closest distance to " O   HOH Z 132 " =    2.599
peak=    3.936 closest distance to " O   HOH Z 207 " =    1.858
peak=    3.936 closest distance to " O   HOH Z 403 " =    1.722
peak=    3.924 closest distance to " CG1 ILE A  33 " =    1.284
peak=    3.921 closest distance to " NH2 ARG A 156 " =    1.182
peak=    3.917 closest distance to " CB  ARG A 190 " =    1.709
peak=    3.905 closest distance to " CD1 LEU A 300 " =    1.246
peak=    3.888 closest distance to " O   HOH Z 134 " =    1.375
peak=    3.887 closest distance to " O   HOH Z  21 " =    1.691
peak=    3.883 closest distance to " CB  GLU A 277 " =    3.582
peak=    3.879 closest distance to " CD BLYS A 290 " =    1.094
peak=    3.873 closest distance to " O   HOH Z 303 " =    1.988
peak=    3.864 closest distance to " O   HOH Z  54 " =    1.718
peak=    3.857 closest distance to " CA  MET A  40 " =    1.069
peak=    3.856 closest distance to " O   SER A  87 " =    2.232
peak=    3.850 closest distance to " O   HOH Z 371 " =    3.231
peak=    3.839 closest distance to " O   HOH Z  97 " =    1.890
peak=    3.827 closest distance to " CG2BVAL A  41 " =    0.745
peak=    3.826 closest distance to " O   HOH Z  93 " =    2.558
peak=    3.825 closest distance to " O   HOH Z 133 " =    2.340
peak=    3.824 closest distance to " NH2BARG A 145 " =    2.090
peak=    3.823 closest distance to " O   HOH Z  61 " =    1.607
peak=    3.819 closest distance to " O   HOH Z 346 " =    1.705
peak=    3.819 closest distance to " O   HOH Z  88 " =    3.467
peak=    3.811 closest distance to " O   HOH Z 193 " =    2.067
peak=    3.809 closest distance to " O   HOH Z  40 " =    1.640
peak=    3.801 closest distance to " O   HOH Z 180 " =    2.210
peak=    3.794 closest distance to " O   HOH Z  43 " =    1.924
peak=    3.791 closest distance to " NZ  LYS A 117 " =    3.351
peak=    3.779 closest distance to " O   HOH Z 135 " =    1.729
peak=    3.773 closest distance to " O   HOH Z 423 " =    1.916
peak=    3.768 closest distance to " O   HOH Z 214 " =    2.013
peak=    3.764 closest distance to " O   HOH Z 425 " =    1.309
peak=    3.758 closest distance to " O   HOH Z 133 " =    1.659
peak=    3.756 closest distance to " CB  VAL A 265 " =    1.218
peak=    3.751 closest distance to " NH1AARG A 145 " =    1.039
peak=    3.746 closest distance to " O   HOH Z 108 " =    2.073
peak=    3.743 closest distance to " CG2 THR A 221 " =    1.063
peak=    3.730 closest distance to " O   HOH Z 280 " =    3.060
peak=    3.728 closest distance to " CG  ARG A  66 " =    2.446
peak=    3.727 closest distance to " O   HOH Z 374 " =    2.631
peak=    3.727 closest distance to " O   HOH Z 247 " =    1.278
peak=    3.715 closest distance to " O   HOH Z 183 " =    1.448
peak=    3.711 closest distance to " CD  ARG A 159 " =    0.797
peak=    3.704 closest distance to " O   HOH Z 411 " =    3.809
peak=    3.694 closest distance to " O   HOH Z 197 " =    2.795
peak=    3.694 closest distance to " O   HOH Z 158 " =    3.077
peak=    3.690 closest distance to " O   HOH Z   6 " =    2.202
peak=    3.677 closest distance to " CD  LYS A 119 " =    1.247
peak=    3.666 closest distance to " CD  ARG A 269 " =    0.933
peak=    3.663 closest distance to " O   HOH Z  68 " =    1.656
peak=    3.663 closest distance to " O   HOH Z 108 " =    1.302
peak=    3.656 closest distance to " CA  ASN A 215 " =    1.233
peak=    3.654 closest distance to " O   HOH Z  59 " =    2.150
peak=    3.654 closest distance to " O   HOH Z 189 " =    2.097
peak=    3.645 closest distance to " O   HOH Z 250 " =    1.506
peak=    3.632 closest distance to " CB  ARG A 139 " =    0.866
peak=    3.629 closest distance to " CA  ALA A  51 " =    0.953
peak=    3.627 closest distance to " CB  TRP A 266 " =    0.928
peak=    3.620 closest distance to " O   HOH Z  44 " =    1.785
peak=    3.613 closest distance to " CG2 VAL A 257 " =    0.932
peak=    3.610 closest distance to " CB  ASP A 140 " =    0.946
peak=    3.608 closest distance to " O   HOH Z 128 " =    2.294
peak=    3.605 closest distance to " O   ALA A 165 " =    1.379
peak=    3.599 closest distance to " CB  MET A  47 " =    0.993
peak=    3.595 closest distance to " O   HOH Z  61 " =    1.561
peak=    3.592 closest distance to " O   HOH Z  20 " =    1.628
peak=    3.591 closest distance to " CD2 LEU A 297 " =    0.904
peak=    3.591 closest distance to " O   HOH Z 295 " =    1.471
peak=    3.589 closest distance to " O   HOH Z  10 " =    1.887
peak=    3.589 closest distance to " CA  ASP A 140 " =    1.137
peak=    3.586 closest distance to " CG  LEU A 167 " =    1.191
peak=    3.584 closest distance to " CD2 LEU A 255 " =    1.361
peak=    3.567 closest distance to " CZ  PHE A 218 " =    1.032
peak=    3.563 closest distance to " O   HOH Z 427 " =    3.090
peak=    3.563 closest distance to " CB  SER A 212 " =    1.069
peak=    3.558 closest distance to " N   ARG A 156 " =    1.341
peak=    3.551 closest distance to " N   ASN A 127 " =    1.266
peak=    3.549 closest distance to " O   HOH Z 147 " =    1.704
peak=    3.545 closest distance to " O   HOH Z 245 " =    1.320
peak=    3.543 closest distance to " OG BSER A 164 " =    2.444
peak=    3.543 closest distance to " O   HOH Z 172 " =    3.778
peak=    3.537 closest distance to " O   HOH Z 406 " =    1.689
peak=    3.535 closest distance to " O   TRP A 274 " =    1.868
peak=    3.534 closest distance to " CA  ASN A 176 " =    1.241
peak=    3.534 closest distance to " CB  SER A 141 " =    1.029
peak=    3.533 closest distance to " O   HOH Z 368 " =    3.749
peak=    3.518 closest distance to " CG1 VAL A 202 " =    2.032
peak=    3.517 closest distance to " O   HOH Z 345 " =    3.330
peak=    3.515 closest distance to " O   HOH Z 128 " =    2.150
peak=    3.504 closest distance to " O   HOH Z  54 " =    2.336
peak=    3.500 closest distance to " CD  LYS A 166 " =    1.309
peak=    3.499 closest distance to " CA  ARG A  36 " =    1.134
peak=    3.494 closest distance to " CA  THR A 264 " =    0.887
peak=    3.494 closest distance to " CG2 VAL A  78 " =    0.920
peak=    3.485 closest distance to " O   HOH Z  49 " =    2.261
peak=    3.482 closest distance to " O   HOH Z 411 " =    1.812
peak=    3.471 closest distance to " O   HOH Z 273 " =    2.762
peak=    3.466 closest distance to " ND1 HIS A  81 " =    1.604
peak=    3.463 closest distance to " CA  ALA A 291 " =    0.932
peak=    3.460 closest distance to " O   HOH Z 409 " =    3.104
peak=    3.458 closest distance to " CG2 ILE A 120 " =    1.166
peak=    3.453 closest distance to " O   HOH Z   1 " =    2.018
peak=    3.452 closest distance to " CA  LYS A 117 " =    1.222
peak=    3.449 closest distance to " N   ASN A  39 " =    1.305
peak=    3.448 closest distance to " CG1 ILE A 151 " =    0.911
peak=    3.444 closest distance to " O   HOH Z 403 " =    1.342
peak=    3.442 closest distance to " ND1 HIS A  86 " =    1.831
peak=    3.433 closest distance to " O   HOH Z 124 " =    1.374
peak=    3.430 closest distance to " CA  ARG A 195 " =    1.316
peak=    3.429 closest distance to " CG1BVAL A  72 " =    1.582
peak=    3.427 closest distance to " O   ALA A 158 " =    1.282
peak=    3.422 closest distance to " O   HOH Z 211 " =    2.549
peak=    3.421 closest distance to " CA  ALA A 160 " =    0.840
peak=    3.416 closest distance to " O   HOH Z 281 " =    4.429
peak=    3.415 closest distance to " O   HOH Z 437 " =    1.704
peak=    3.415 closest distance to " CD1 ILE A 106 " =    0.961
peak=    3.412 closest distance to " O   HOH Z 334 " =    1.501
peak=    3.410 closest distance to " CB  LEU A 255 " =    0.735
peak=    3.406 closest distance to " CE  LYS A  76 " =    0.853
peak=    3.403 closest distance to " O   HOH Z 227 " =    1.605
peak=    3.397 closest distance to " CB  GLN A  88 " =    1.306
peak=    3.391 closest distance to " O   HOH Z 425 " =    1.959
peak=    3.388 closest distance to " O   HOH Z  53 " =    2.467
peak=    3.382 closest distance to " O   HOH Z  66 " =    2.037
peak=    3.379 closest distance to " O   HOH Z  64 " =    2.250
peak=    3.378 closest distance to " CA  ALA A 248 " =    1.179
peak=    3.378 closest distance to " O   HOH Z 175 " =    2.150
peak=    3.375 closest distance to " CB  SER A 216 " =    0.796
peak=    3.374 closest distance to " OG  SER A  22 " =    2.768
peak=    3.371 closest distance to " CA  ASP A 191 " =    0.804
peak=    3.367 closest distance to " O   HOH Z 407 " =    2.689
peak=    3.366 closest distance to " CA  ALA A 154 " =    0.950
peak=    3.362 closest distance to " CA  VAL A 126 " =    1.192
peak=    3.361 closest distance to " NZ  LYS A 166 " =    3.026
peak=    3.360 closest distance to " CG  MET A 185 " =    1.095
peak=    3.360 closest distance to " O   HOH Z  63 " =    1.986
peak=    3.355 closest distance to " O   HOH Z 337 " =    3.671
peak=    3.351 closest distance to " CB  ALA A 248 " =    0.942
peak=    3.349 closest distance to " O   HOH Z 279 " =    2.218
peak=    3.347 closest distance to " O   ALA A   1 " =    1.472
peak=    3.345 closest distance to " O   HOH Z  78 " =    1.999
peak=    3.338 closest distance to " O   HOH Z 227 " =    2.149
peak=    3.337 closest distance to " CB  GLU A  46 " =    1.034
peak=    3.337 closest distance to " NH2 ARG A 219 " =    1.861
peak=    3.334 closest distance to " CB  LEU A 143 " =    1.104
peak=    3.329 closest distance to " CB  ALA A 291 " =    1.402
peak=    3.328 closest distance to " O   HOH Z 171 " =    2.329
peak=    3.327 closest distance to " O   HOH Z 286 " =    2.206
peak=    3.324 closest distance to " CB  PHE A  16 " =    0.966
peak=    3.323 closest distance to " O   HOH Z 327 " =    1.670
peak=    3.323 closest distance to " O   HOH Z 410 " =    1.897
peak=    3.313 closest distance to " CA  GLY A 267 " =    1.140
peak=    3.311 closest distance to " O   HOH Z 250 " =    1.621
peak=    3.309 closest distance to " NH2AARG A 190 " =    1.331
peak=    3.308 closest distance to " CG2 VAL A 197 " =    1.123
peak=    3.301 closest distance to " CD2 HIS A  81 " =    1.176
peak=    3.300 closest distance to " CB  SER A  62 " =    1.204
peak=    3.298 closest distance to " O   HOH Z 271 " =    2.330
peak=    3.297 closest distance to " O   HOH Z 173 " =    1.857
peak=    3.291 closest distance to " O   HOH Z 163 " =    1.655
peak=    3.287 closest distance to " O   HOH Z  48 " =    1.321
peak=    3.285 closest distance to " CB  GLU A 152 " =    1.536
peak=    3.277 closest distance to " CG  GLU A 277 " =    2.094
peak=    3.275 closest distance to " CA  SER A  87 " =    0.963
peak=    3.275 closest distance to " O   HOH Z 402 " =    1.462
peak=    3.272 closest distance to " OD1 ASP A 231 " =    1.825
peak=    3.272 closest distance to " O   THR A 220 " =    1.356
peak=    3.270 closest distance to " CB  ALA A  71 " =    1.321
peak=    3.269 closest distance to " CG  MET A 113 " =    1.341
peak=    3.268 closest distance to " O   HOH Z  20 " =    2.109
peak=    3.266 closest distance to " O   HOH Z 118 " =    1.443
peak=    3.263 closest distance to " O   HOH Z 329 " =    3.532
peak=    3.259 closest distance to " C   TYR A 214 " =    1.505
peak=    3.258 closest distance to " O   HOH Z 368 " =    2.576
peak=    3.249 closest distance to " CZ  PHE A 192 " =    0.968
peak=    3.247 closest distance to " O   HOH Z 267 " =    2.106
peak=    3.241 closest distance to " O   HOH Z 313 " =    1.656
peak=    3.236 closest distance to " NE2 GLN A  58 " =    4.331
peak=    3.233 closest distance to " CE1 TYR A 186 " =    1.221
peak=    3.231 closest distance to " CB  TYR A 116 " =    0.909
peak=    3.230 closest distance to " O   HOH Z 163 " =    1.441
peak=    3.229 closest distance to " CA  ALA A 158 " =    1.126
peak=    3.226 closest distance to " CA  ALA A 233 " =    1.457
peak=    3.225 closest distance to " O   HOH Z 234 " =    1.759
peak=    3.225 closest distance to " O   HOH Z 163 " =    1.844
peak=    3.217 closest distance to " CD2 TRP A 179 " =    1.357
peak=    3.215 closest distance to " CG2 VAL A 174 " =    1.347
peak=    3.215 closest distance to " O   HOH Z 171 " =    3.852
peak=    3.212 closest distance to " O   GLY A  57 " =    2.570
peak=    3.208 closest distance to " O   HOH Z  44 " =    3.451
peak=    3.207 closest distance to " O   HOH Z 366 " =    3.096
peak=    3.206 closest distance to " CG  LYS A  76 " =    1.026
peak=    3.205 closest distance to " CG BARG A 275 " =    1.408
peak=    3.198 closest distance to " O   HOH Z  66 " =    2.050
peak=    3.198 closest distance to " OG  SER A  62 " =    3.055
peak=    3.196 closest distance to " CZ2 TRP A 179 " =    1.682
peak=    3.194 closest distance to " O   HOH Z 263 " =    1.781
peak=    3.185 closest distance to " O   HOH Z 391 " =    2.966
peak=    3.184 closest distance to " O   HOH Z 116 " =    1.853
peak=    3.181 closest distance to " CD  ARG A  66 " =    2.919
peak=    3.179 closest distance to " OG1 THR A 294 " =    1.649
peak=    3.170 closest distance to " CG  MET A 185 " =    1.224
peak=    3.168 closest distance to " O   HOH Z 214 " =    2.452
peak=    3.168 closest distance to " O   HOH Z 388 " =    1.917
peak=    3.168 closest distance to " O   HOH Z 174 " =    2.619
peak=    3.166 closest distance to " O   HOH Z 112 " =    1.541
peak=    3.163 closest distance to " OG BSER A  99 " =    2.168
peak=    3.161 closest distance to " CB  ASN A  39 " =    0.868
peak=    3.160 closest distance to " O   HOH Z 305 " =    3.589
peak=    3.159 closest distance to " CG  GLN A  11 " =    1.757
peak=    3.158 closest distance to " CA  ILE A  33 " =    1.633
peak=    3.157 closest distance to " CA  TYR A 186 " =    1.390
peak=    3.154 closest distance to " O   HOH Z 125 " =    2.285
peak=    3.153 closest distance to " O   HOH Z  80 " =    1.600
peak=    3.147 closest distance to " CB  ALA A  34 " =    1.047
peak=    3.147 closest distance to " O   HOH Z   4 " =    1.850
peak=    3.145 closest distance to " CD  ARG A 219 " =    0.983
peak=    3.144 closest distance to " NH1BARG A 145 " =    1.057
peak=    3.141 closest distance to " O   HOH Z 166 " =    3.673
peak=    3.138 closest distance to " O   HOH Z 422 " =    2.690
peak=    3.132 closest distance to " CD1AILE A 234 " =    0.974
peak=    3.132 closest distance to " O   HOH Z 193 " =    1.616
peak=    3.132 closest distance to " O   THR A  31 " =    1.572
peak=    3.132 closest distance to " C   LYS A 290 " =    1.353
peak=    3.127 closest distance to " CA  LEU A  83 " =    1.484
peak=    3.127 closest distance to " O   HOH Z 368 " =    2.516
peak=    3.117 closest distance to " CD1 LEU A 228 " =    1.914
peak=    3.116 closest distance to " O   HOH Z 248 " =    1.550
peak=    3.110 closest distance to " CB  MET A  40 " =    0.875
peak=    3.109 closest distance to " O   HOH Z 345 " =    1.671
peak=    3.106 closest distance to " O   ALA A 233 " =    1.785
peak=    3.104 closest distance to " O   HOH Z 367 " =    3.537
peak=    3.101 closest distance to " CA  ASP A 162 " =    1.181
peak=    3.095 closest distance to " CA  ILE A 234 " =    0.924
peak=    3.094 closest distance to " O   HOH Z 261 " =    1.432
peak=    3.082 closest distance to " CB  ILE A 120 " =    1.296
peak=    3.076 closest distance to " O   THR A 251 " =    1.195
peak=    3.073 closest distance to " CG BARG A 102 " =    1.862
peak=    3.068 closest distance to " CA  MET A 105 " =    1.004
peak=    3.068 closest distance to " NZ  LYS A  76 " =    1.227
peak=    3.066 closest distance to " CD1 LEU A 222 " =    0.766
peak=    3.062 closest distance to " CA  LEU A 101 " =    1.531
peak=    3.059 closest distance to " O   HOH Z 301 " =    1.896
peak=    3.055 closest distance to " O   HOH Z 365 " =    2.848
peak=    3.048 closest distance to " CE  MET A 188 " =    2.175
peak=    3.039 closest distance to " OE2 GLU A  53 " =    2.199
peak=    3.019 closest distance to " O   HOH Z  88 " =    2.821

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 192         
Filter by distance & map next to the model:
   mapped sites are within: 0.832 - 5.849
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 191 from: 192
   mapped sites are within: 0.832 - 5.849

peak=   -4.775 closest distance to " O   HOH Z 266 " =    4.362
peak=   -4.458 closest distance to " CB  PRO A 243 " =    2.589
peak=   -4.445 closest distance to " O   HOH Z 377 " =    1.878
peak=   -4.438 closest distance to " O   HOH Z 372 " =    2.434
peak=   -4.407 closest distance to " O   ILE A 109 " =    2.637
peak=   -4.310 closest distance to " O   VAL A  67 " =    2.854
peak=   -4.309 closest distance to " CD  ARG A 156 " =    1.982
peak=   -4.166 closest distance to " N   ALA A  43 " =    2.527
peak=   -4.160 closest distance to " O   HOH Z 198 " =    2.205
peak=   -4.121 closest distance to " O   HOH Z 126 " =    1.900
peak=   -4.120 closest distance to " CD  ARG A  14 " =    3.448
peak=   -4.037 closest distance to " O   HOH Z 231 " =    2.150
peak=   -4.021 closest distance to " OE1 GLN A 223 " =    2.055
peak=   -3.995 closest distance to " O   HOH Z 118 " =    2.941
peak=   -3.979 closest distance to " C   HIS A 108 " =    1.072
peak=   -3.948 closest distance to " CE2 TYR A  30 " =    2.736
peak=   -3.932 closest distance to " ND2 ASN A  45 " =    0.958
peak=   -3.915 closest distance to " CD1 LEU A 228 " =    2.293
peak=   -3.905 closest distance to " O   HOH Z  19 " =    2.379
peak=   -3.899 closest distance to " O   HOH Z 290 " =    1.156
peak=   -3.889 closest distance to " O   PRO A 163 " =    2.088
peak=   -3.884 closest distance to " O   HOH Z  13 " =    1.491
peak=   -3.877 closest distance to " O   HOH Z 353 " =    2.242
peak=   -3.863 closest distance to " O   HOH Z  10 " =    1.518
peak=   -3.860 closest distance to " CD  ARG A 139 " =    1.612
peak=   -3.853 closest distance to " OG  SER A  97 " =    2.146
peak=   -3.836 closest distance to " CZ3 TRP A 179 " =    1.225
peak=   -3.828 closest distance to " C   ALA A 158 " =    1.241
peak=   -3.823 closest distance to " OXT GLY A 302 " =    2.833
peak=   -3.819 closest distance to " O   HOH Z  43 " =    1.622
peak=   -3.813 closest distance to " O   HOH Z  52 " =    1.408
peak=   -3.800 closest distance to " O   PRO A 198 " =    1.326
peak=   -3.796 closest distance to " CG1 VAL A 250 " =    2.680
peak=   -3.740 closest distance to " O   HOH Z 407 " =    3.247
peak=   -3.733 closest distance to " OG BSER A 134 " =    1.247
peak=   -3.730 closest distance to " CZ  PHE A  59 " =    1.640
peak=   -3.707 closest distance to " CD1 PHE A  59 " =    1.819
peak=   -3.699 closest distance to " SG ACYS A 201 " =    2.088
peak=   -3.695 closest distance to " CZ  TYR A 169 " =    1.734
peak=   -3.695 closest distance to " O   HOH Z 388 " =    1.908
peak=   -3.685 closest distance to " N   SER A 212 " =    2.012
peak=   -3.674 closest distance to " O   HOH Z 185 " =    2.232
peak=   -3.664 closest distance to " O   SER A 135 " =    1.557
peak=   -3.662 closest distance to " O   HOH Z  11 " =    2.018
peak=   -3.657 closest distance to " NE2 GLN A  88 " =    1.926
peak=   -3.638 closest distance to " O   HOH Z  11 " =    1.862
peak=   -3.635 closest distance to " CD1 LEU A 101 " =    2.496
peak=   -3.634 closest distance to " CG  PHE A 283 " =    2.590
peak=   -3.630 closest distance to " CG  ASP A 231 " =    0.832
peak=   -3.621 closest distance to " CA  VAL A  67 " =    2.740
peak=   -3.620 closest distance to " NH2AARG A 275 " =    5.365
peak=   -3.607 closest distance to " O   HOH Z  38 " =    1.481
peak=   -3.606 closest distance to " C   LEU A 143 " =    1.212
peak=   -3.596 closest distance to " O   HOH Z  93 " =    1.635
peak=   -3.595 closest distance to " N   GLN A  58 " =    1.734
peak=   -3.591 closest distance to " CB  ASN A  39 " =    2.220
peak=   -3.584 closest distance to " C   ASN A 285 " =    2.506
peak=   -3.576 closest distance to " NH1 ARG A 195 " =    2.622
peak=   -3.558 closest distance to " OG  SER A  62 " =    1.607
peak=   -3.551 closest distance to " CG  GLU A  53 " =    1.390
peak=   -3.548 closest distance to " O   HOH Z 351 " =    1.465
peak=   -3.539 closest distance to " OD1 ASP A 191 " =    1.678
peak=   -3.538 closest distance to " O   HOH Z 292 " =    4.520
peak=   -3.536 closest distance to " O   HOH Z 102 " =    1.684
peak=   -3.536 closest distance to " OG BSER A 134 " =    1.753
peak=   -3.532 closest distance to " CD2 LEU A 300 " =    2.871
peak=   -3.524 closest distance to " O   HOH Z 283 " =    1.920
peak=   -3.522 closest distance to " CB  ALA A 291 " =    2.394
peak=   -3.522 closest distance to " CD  LYS A 289 " =    2.525
peak=   -3.515 closest distance to " O   HOH Z 435 " =    2.711
peak=   -3.509 closest distance to " OE2 GLU A   2 " =    1.776
peak=   -3.506 closest distance to " O   HOH Z  98 " =    2.279
peak=   -3.500 closest distance to " OD1 ASN A 187 " =    1.685
peak=   -3.484 closest distance to " N   SER A 276 " =    1.310
peak=   -3.482 closest distance to " CD  ARG A 195 " =    5.201
peak=   -3.477 closest distance to " NH2 ARG A  66 " =    1.974
peak=   -3.473 closest distance to " NH2 ARG A  79 " =    1.859
peak=   -3.472 closest distance to " OD1 ASN A 148 " =    1.650
peak=   -3.468 closest distance to " CG1 VAL A 197 " =    2.268
peak=   -3.468 closest distance to " O   HOH Z 311 " =    3.578
peak=   -3.467 closest distance to " O   HOH Z 389 " =    1.765
peak=   -3.460 closest distance to " CG1 VAL A 112 " =    2.814
peak=   -3.459 closest distance to " CE  MET A 105 " =    2.116
peak=   -3.457 closest distance to " OE1 GLN A  88 " =    1.231
peak=   -3.456 closest distance to " O   HOH Z  76 " =    1.971
peak=   -3.451 closest distance to " O   HOH Z 166 " =    1.494
peak=   -3.450 closest distance to " O   HOH Z 385 " =    1.992
peak=   -3.450 closest distance to " O   GLY A 196 " =    1.093
peak=   -3.449 closest distance to " O   HOH Z 234 " =    4.126
peak=   -3.441 closest distance to " CG  PRO A 163 " =    2.477
peak=   -3.440 closest distance to " CB  TYR A  15 " =    2.175
peak=   -3.437 closest distance to " CB  CYS A 254 " =    2.412
peak=   -3.434 closest distance to " O   HOH Z 211 " =    1.612
peak=   -3.429 closest distance to " O   HOH Z 148 " =    3.380
peak=   -3.429 closest distance to " O   HOH Z 166 " =    1.815
peak=   -3.428 closest distance to " CG  ASP A  50 " =    2.553
peak=   -3.415 closest distance to " O   HOH Z 222 " =    1.178
peak=   -3.413 closest distance to " CE2 PHE A 218 " =    2.475
peak=   -3.411 closest distance to " CB  ASP A 132 " =    2.311
peak=   -3.411 closest distance to " OG  SER A  87 " =    1.322
peak=   -3.409 closest distance to " CG  LEU A  83 " =    1.930
peak=   -3.402 closest distance to " OG ASER A 134 " =    1.249
peak=   -3.396 closest distance to " CD2 TYR A 247 " =    2.460
peak=   -3.391 closest distance to " O   HOH Z 417 " =    2.529
peak=   -3.388 closest distance to " O   VAL A 153 " =    2.335
peak=   -3.387 closest distance to " NH2 ARG A  66 " =    5.155
peak=   -3.377 closest distance to " CA  GLY A 203 " =    2.140
peak=   -3.375 closest distance to " N   ALA A 226 " =    2.064
peak=   -3.364 closest distance to " CD1 ILE A 239 " =    2.060
peak=   -3.361 closest distance to " O   HOH Z 313 " =    2.081
peak=   -3.342 closest distance to " CG2 ILE A 263 " =    2.289
peak=   -3.339 closest distance to " O   HOH Z 436 " =    1.469
peak=   -3.336 closest distance to " CE  MET A  93 " =    1.213
peak=   -3.329 closest distance to " CB  ALA A 291 " =    2.180
peak=   -3.328 closest distance to " O   HOH Z 275 " =    1.507
peak=   -3.319 closest distance to " CE3 TRP A 150 " =    1.990
peak=   -3.317 closest distance to " O   HOH Z  97 " =    1.882
peak=   -3.313 closest distance to " CG  ARG A  66 " =    2.397
peak=   -3.309 closest distance to " CA  VAL A 232 " =    2.514
peak=   -3.307 closest distance to " CB  PHE A 192 " =    1.975
peak=   -3.305 closest distance to " O   HOH Z 266 " =    4.707
peak=   -3.296 closest distance to " OD1 ASP A 191 " =    1.514
peak=   -3.292 closest distance to " O   HOH Z 396 " =    1.622
peak=   -3.290 closest distance to " OD2 ASP A 171 " =    1.759
peak=   -3.289 closest distance to " O   HOH Z 207 " =    2.059
peak=   -3.288 closest distance to " O   PHE A 218 " =    1.545
peak=   -3.287 closest distance to " CB  ALA A 248 " =    1.950
peak=   -3.285 closest distance to " CE  MET A 105 " =    1.903
peak=   -3.284 closest distance to " CD2 TYR A 293 " =    2.076
peak=   -3.281 closest distance to " CA  GLY A  98 " =    2.069
peak=   -3.273 closest distance to " O   HOH Z 361 " =    3.405
peak=   -3.267 closest distance to " O   ASN A 249 " =    1.509
peak=   -3.266 closest distance to " O   GLY A 211 " =    1.534
peak=   -3.265 closest distance to " O   HOH Z 198 " =    1.481
peak=   -3.264 closest distance to " O   HOH Z 243 " =    2.048
peak=   -3.262 closest distance to " O   VAL A 174 " =    2.099
peak=   -3.258 closest distance to " CE3 TRP A 274 " =    2.493
peak=   -3.254 closest distance to " C   MET A 188 " =    1.605
peak=   -3.252 closest distance to " O   HOH Z 298 " =    1.224
peak=   -3.252 closest distance to " CG2 VAL A 189 " =    2.074
peak=   -3.251 closest distance to " N   ALA A 248 " =    1.586
peak=   -3.251 closest distance to " CG2AVAL A  41 " =    2.827
peak=   -3.241 closest distance to " CA  ASP A 298 " =    1.054
peak=   -3.229 closest distance to " OXT GLY A 302 " =    3.190
peak=   -3.225 closest distance to " ND2 ASN A 187 " =    1.529
peak=   -3.215 closest distance to " O   HOH Z 283 " =    5.849
peak=   -3.214 closest distance to " ND2 ASN A  60 " =    1.564
peak=   -3.213 closest distance to " O   GLY A  80 " =    2.452
peak=   -3.212 closest distance to " CA  GLY A 241 " =    3.091
peak=   -3.210 closest distance to " CA  GLY A 133 " =    2.002
peak=   -3.210 closest distance to " O   HOH Z  47 " =    1.459
peak=   -3.206 closest distance to " OG1 THR A 178 " =    1.270
peak=   -3.205 closest distance to " CG  GLU A 277 " =    1.150
peak=   -3.203 closest distance to " CB  SER A 245 " =    2.425
peak=   -3.201 closest distance to " NE2 GLN A  58 " =    1.148
peak=   -3.186 closest distance to " O   HOH Z 423 " =    2.239
peak=   -3.185 closest distance to " O   HOH Z 265 " =    1.996
peak=   -3.182 closest distance to " CZ  PHE A  38 " =    2.460
peak=   -3.181 closest distance to " ND2 ASN A 249 " =    2.126
peak=   -3.174 closest distance to " N   THR A 157 " =    1.580
peak=   -3.169 closest distance to " C   SER A 206 " =    1.512
peak=   -3.164 closest distance to " O   HOH Z 241 " =    1.423
peak=   -3.160 closest distance to " OE1 GLN A 223 " =    2.035
peak=   -3.158 closest distance to " OD2 ASP A 171 " =    2.293
peak=   -3.156 closest distance to " CG  TRP A 266 " =    1.672
peak=   -3.146 closest distance to " NH2 ARG A 159 " =    2.416
peak=   -3.134 closest distance to " O   HOH Z 210 " =    1.051
peak=   -3.134 closest distance to " O   HOH Z 111 " =    2.321
peak=   -3.131 closest distance to " CB  ASP A 132 " =    2.343
peak=   -3.130 closest distance to " CB  TRP A  85 " =    2.534
peak=   -3.129 closest distance to " O   HOH Z 295 " =    1.439
peak=   -3.129 closest distance to " CG  ASN A 301 " =    2.022
peak=   -3.125 closest distance to " O   HOH Z 252 " =    3.678
peak=   -3.118 closest distance to " O   HOH Z 252 " =    4.216
peak=   -3.114 closest distance to " CG  ARG A 259 " =    2.897
peak=   -3.114 closest distance to " O   HOH Z 165 " =    2.014
peak=   -3.113 closest distance to " OD1 ASP A 200 " =    1.396
peak=   -3.112 closest distance to " CB  CYS A 201 " =    2.551
peak=   -3.109 closest distance to " O   HOH Z 411 " =    3.577
peak=   -3.107 closest distance to " O   HOH Z 350 " =    1.731
peak=   -3.106 closest distance to " O   ASN A 301 " =    1.378
peak=   -3.100 closest distance to " CD2 LEU A 237 " =    2.438
peak=   -3.099 closest distance to " O   HOH Z 409 " =    4.636
peak=   -3.094 closest distance to " O   PRO A 198 " =    1.297
peak=   -3.089 closest distance to " CG  GLN A 278 " =    2.242
peak=   -3.062 closest distance to " O   HOH Z 298 " =    2.627
peak=   -3.059 closest distance to " CD  PRO A  90 " =    1.778
peak=   -3.054 closest distance to " O   HOH Z 139 " =    2.879
peak=   -3.051 closest distance to " CA  TRP A 274 " =    1.532
peak=   -3.047 closest distance to " CA  SER A 135 " =    1.286
peak=   -3.045 closest distance to " OH  TYR A 247 " =    2.061

================= 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    :  0.3636 0.3676   6.128927e+00   6.139128e+00
   1_bss:  0.3515 0.3558   6.116128e+00   6.114604e+00
   1_xyz:  0.2351 0.2639   5.767438e+00   5.864261e+00
   1_adp:  0.2177 0.2707   5.727388e+00   5.889348e+00
   1_occ:  0.2173 0.2705   5.726003e+00   5.888195e+00
   2_bss:  0.2156 0.2678   5.721187e+00   5.881343e+00
   2_xyz:  0.1550 0.2006   5.421204e+00   5.621990e+00
   2_adp:  0.1417 0.1887   5.348085e+00   5.559920e+00
   2_occ:  0.1415 0.1887   5.347313e+00   5.559329e+00
   3_bss:  0.1415 0.1880   5.344333e+00   5.555545e+00
   3_xyz:  0.1242 0.1662   5.227083e+00   5.445151e+00
   3_adp:  0.1208 0.1627   5.203220e+00   5.421031e+00
   3_occ:  0.1207 0.1625   5.202522e+00   5.420545e+00
   4_bss:  0.1206 0.1623   5.201969e+00   5.419998e+00
   4_xyz:  0.1091 0.1556   5.130270e+00   5.373200e+00
   4_adp:  0.1073 0.1561   5.125332e+00   5.374807e+00
   4_occ:  0.1073 0.1560   5.125135e+00   5.374790e+00
   5_bss:  0.1075 0.1554   5.125889e+00   5.374950e+00
   5_xyz:  0.1075 0.1565   5.132361e+00   5.382736e+00
   5_adp:  0.1072 0.1570   5.133482e+00   5.386424e+00
   5_occ:  0.1072 0.1570   5.133402e+00   5.386516e+00
   5_bss:  0.1071 0.1570   5.133524e+00   5.386602e+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:  0.300  50.000  -1.812  -2.063   2.160  -0.000   0.000   0.000
   1_xyz:  0.300  50.000  -1.812  -2.063   2.160  -0.000   0.000   0.000
   1_adp:  0.300  50.000  -1.812  -2.063   2.160  -0.000   0.000   0.000
   1_occ:  0.300  50.000  -1.812  -2.063   2.160  -0.000   0.000   0.000
   2_bss:  0.326  52.473  -2.398  -2.380  -0.549  -0.000  -0.000  -0.000
   2_xyz:  0.326  52.473  -2.398  -2.380  -0.549  -0.000  -0.000  -0.000
   2_adp:  0.326  52.473  -2.398  -2.380  -0.549  -0.000  -0.000  -0.000
   2_occ:  0.326  52.473  -2.398  -2.380  -0.549  -0.000  -0.000  -0.000
   3_bss:  0.326  52.473  -2.338  -2.255  -1.420  -0.000  -0.000  -0.000
   3_xyz:  0.326  52.473  -2.338  -2.255  -1.420  -0.000  -0.000  -0.000
   3_adp:  0.326  52.473  -2.338  -2.255  -1.420  -0.000  -0.000  -0.000
   3_occ:  0.326  52.473  -2.338  -2.255  -1.420  -0.000  -0.000  -0.000
   4_bss:  0.319  47.878  -2.399  -2.256  -1.779  -0.000  -0.000  -0.000
   4_xyz:  0.319  47.878  -2.399  -2.256  -1.779  -0.000  -0.000  -0.000
   4_adp:  0.319  47.878  -2.399  -2.256  -1.779  -0.000  -0.000  -0.000
   4_occ:  0.319  47.878  -2.399  -2.256  -1.779  -0.000  -0.000  -0.000
   5_bss:  0.318  47.878  -2.237  -2.115  -1.756  -0.000  -0.000  -0.000
   5_xyz:  0.318  47.878  -2.237  -2.115  -1.756  -0.000  -0.000  -0.000
   5_adp:  0.318  47.878  -2.237  -2.115  -1.756  -0.000  -0.000  -0.000
   5_occ:  0.318  47.878  -2.237  -2.115  -1.756  -0.000  -0.000  -0.000
   5_bss:  0.319  47.840  -2.031  -1.895  -1.574  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  40.816 0.6344  0.8196    40305.138
   1_bss:  39.324 0.6497  0.8255    36533.019
   1_xyz:  26.481 0.7971  0.9655    18554.683
   1_adp:  27.834 0.7815  0.9519    19811.149
   1_occ:  27.805 0.7818  0.9518    19751.446
   2_bss:  27.414 0.7859  0.9167    19333.456
   2_xyz:  19.557 0.8655  0.9753    10427.223
   2_adp:  17.851 0.8820  0.9808     9195.108
   2_occ:  17.834 0.8821  0.9807     9180.180
   3_bss:  17.733 0.8830  0.9728     9086.383
   3_xyz:  15.370 0.9034  0.9815     7155.488
   3_adp:  14.773 0.9089  0.9804     6862.549
   3_occ:  14.759 0.9090  0.9803     6854.070
   4_bss:  14.746 0.9091  0.9752     6843.482
   4_xyz:  13.889 0.9157  0.9789     6212.655
   4_adp:  13.890 0.9159  0.9744     6213.000
   4_occ:  13.886 0.9159  0.9743     6211.422
   5_bss:  13.896 0.9158  0.9776     6212.609
   5_xyz:  14.008 0.9151  0.9758     6314.806
   5_adp:  14.073 0.9146  0.9699     6361.919
   5_occ:  14.071 0.9146  0.9698     6361.960
   5_bss:  14.075 0.9146  0.9755     6363.616
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6926e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6926e-01
   1_xyz:   1.187  0.009  0.075 15.075  0.004  4.113   7.7723e-02
   1_adp:   1.187  0.009  0.075 15.075  0.004  4.113   7.7723e-02
   1_occ:   1.187  0.009  0.075 15.075  0.004  4.113   7.7723e-02
   2_bss:   1.187  0.009  0.075 15.075  0.004  4.113   7.7723e-02
   2_xyz:   1.006  0.006  0.068 13.973  0.004  4.122   5.5344e-02
   2_adp:   1.006  0.006  0.068 13.973  0.004  4.122   5.5344e-02
   2_occ:   1.006  0.006  0.068 13.973  0.004  4.122   5.5344e-02
   3_bss:   1.006  0.006  0.068 13.973  0.004  4.122   5.5344e-02
   3_xyz:   0.895  0.005  0.065 14.103  0.003  4.123   4.7899e-02
   3_adp:   0.895  0.005  0.065 14.103  0.003  4.123   4.7899e-02
   3_occ:   0.895  0.005  0.065 14.103  0.003  4.123   4.7899e-02
   4_bss:   0.895  0.005  0.065 14.103  0.003  4.123   4.7899e-02
   4_xyz:   1.134  0.009  0.082 14.821  0.005  4.115   7.2906e-02
   4_adp:   1.134  0.009  0.082 14.821  0.005  4.115   7.2906e-02
   4_occ:   1.134  0.009  0.082 14.821  0.005  4.115   7.2906e-02
   5_bss:   1.134  0.009  0.082 14.821  0.005  4.115   7.2906e-02
   5_xyz:   1.025  0.008  0.075 14.460  0.004  4.115   6.1438e-02
   5_adp:   1.025  0.008  0.075 14.460  0.004  4.115   6.1438e-02
   5_occ:   1.025  0.008  0.075 14.460  0.004  4.115   6.1438e-02
   5_bss:   1.025  0.008  0.075 14.460  0.004  4.115   6.1438e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.704   2.4065e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.704   2.4065e-01
   1_xyz:   7.940  0.052  0.270 87.213  0.021  2.220   6.8658e-02
   1_adp:   7.940  0.052  0.270 87.213  0.021  2.220   6.8658e-02
   1_occ:   7.940  0.052  0.270 87.213  0.021  2.220   6.8658e-02
   2_bss:   7.940  0.052  0.270 87.213  0.021  2.220   6.8658e-02
   2_xyz:   7.359  0.034  0.253 80.008  0.024  2.408   6.0970e-02
   2_adp:   7.359  0.034  0.253 80.008  0.024  2.408   6.0970e-02
   2_occ:   7.359  0.034  0.253 80.008  0.024  2.408   6.0970e-02
   3_bss:   7.359  0.034  0.253 80.008  0.024  2.408   6.0970e-02
   3_xyz:   7.113  0.038  0.227 83.248  0.034  2.332   4.2562e-02
   3_adp:   7.113  0.038  0.227 83.248  0.034  2.332   4.2562e-02
   3_occ:   7.113  0.038  0.227 83.248  0.034  2.332   4.2562e-02
   4_bss:   7.113  0.038  0.227 83.248  0.034  2.332   4.2562e-02
   4_xyz:   7.305  0.049  0.253 82.601  0.035  2.252   5.9613e-02
   4_adp:   7.305  0.049  0.253 82.601  0.035  2.252   5.9613e-02
   4_occ:   7.305  0.049  0.253 82.601  0.035  2.252   5.9613e-02
   5_bss:   7.305  0.049  0.253 82.601  0.035  2.252   5.9613e-02
   5_xyz:   6.903  0.040  0.235 82.619  0.034  2.354   5.0036e-02
   5_adp:   6.903  0.040  0.235 82.619  0.034  2.354   5.0036e-02
   5_occ:   6.903  0.040  0.235 82.619  0.034  2.354   5.0036e-02
   5_bss:   6.903  0.040  0.235 82.619  0.034  2.354   5.0036e-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:  98.20   0.00  16.94  98.20   0.00  13.07  63.85   6.50  38.02
   1_occ:  98.20   0.00  16.94  98.20   0.00  13.07  63.85   6.50  38.02
   2_bss:  98.20   0.00  16.94  98.20   0.00  13.07  63.85   6.50  38.02
   2_xyz:  98.20   0.00  16.94  98.20   0.00  13.07  63.85   6.50  38.02
   2_adp:  82.73   0.00  17.55  82.73   0.00  13.20  77.91   6.05  41.25
   2_occ:  82.73   0.00  17.55  82.73   0.00  13.20  77.91   6.05  41.25
   3_bss:  82.73   0.00  17.55  82.73   0.00  13.20  77.91   6.05  41.25
   3_xyz:  82.73   0.00  17.55  82.73   0.00  13.20  77.91   6.05  41.25
   3_adp:  84.91   1.21  17.30  84.91   1.21  13.05  77.39   3.32  40.44
   3_occ:  84.91   1.21  17.30  84.91   1.21  13.05  77.39   3.32  40.44
   4_bss:  84.91   1.21  17.30  84.91   1.21  13.05  77.39   3.32  40.44
   4_xyz:  84.91   1.21  17.30  84.91   1.21  13.05  77.39   3.32  40.44
   4_adp:  94.88   1.13  17.23  94.88   1.13  12.97  83.10   3.16  40.43
   4_occ:  94.88   1.13  17.23  94.88   1.13  12.97  83.10   3.16  40.43
   5_bss:  94.88   1.13  17.23  94.88   1.13  12.97  83.10   3.16  40.43
   5_xyz:  94.88   1.13  17.23  94.88   1.13  12.97  83.10   3.16  40.43
   5_adp: 100.89   1.09  17.00 100.89   1.09  12.81  84.60   4.85  39.82
   5_occ: 100.89   1.09  17.00 100.89   1.09  12.81  84.60   4.85  39.82
   5_bss: 100.85   1.05  16.96 100.85   1.05  12.77  84.57   4.81  39.78
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.826    0.008    0.284
   1_adp:    1.826    0.008    0.284
   1_occ:    1.826    0.008    0.284
   2_bss:    1.826    0.008    0.284
   2_xyz:    1.104    0.013    0.392
   2_adp:    1.104    0.013    0.392
   2_occ:    1.104    0.013    0.392
   3_bss:    1.104    0.013    0.392
   3_xyz:    1.114    0.028    0.442
   3_adp:    1.114    0.028    0.442
   3_occ:    1.114    0.028    0.442
   4_bss:    1.114    0.028    0.442
   4_xyz:    1.224    0.035    0.471
   4_adp:    1.224    0.035    0.471
   4_occ:    1.224    0.035    0.471
   5_bss:    1.224    0.035    0.471
   5_xyz:    1.299    0.072    0.480
   5_adp:    1.299    0.072    0.480
   5_occ:    1.299    0.072    0.480
   5_bss:    1.299    0.072    0.480
------------------------------------------------------------------------

CPU time actual refinement: 300.49


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_914/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_914/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_914/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_914/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_914/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 300.36 
  Macro-tasks:
    bulk solvent and scale       = 31.64  
    individual site refinement   = 129.41 
    weights calculation          = 25.40  
    collect and process          = 5.51   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 192.04 
  Micro-tasks:
    mask                            = 1.57   
    f_calc                          = 100.36 
    alpha_beta                      = 7.03   
    target                          = 1.01   
    gradients_wrt_atomic_parameters = 108.10 
    fmodel                         = 5.72   
    r_factors                      = 0.14   
    phase_errors                   = 9.03   
    foms                           = 0.22   
    TOTAL for micro-tasks          = 233.18 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.205 micro seconds
Total CPU time: 5.20 minutes
from_scatterers_fft:    660 calls, 100.09 s
gradients_fft:          605 calls,  96.07 s

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

# Date 2008-01-16 Time 05:57:50 PST -0800 (1200491870.20 s)
Start R-work = 0.3636, R-free = 0.3676 (no bulk solvent and anisotropic scale)
Final R-work = 0.1308, R-free = 0.1765 (no bulk solvent and anisotropic scale)

Start R-work = 0.3515, R-free = 0.3558
Final R-work = 0.1071, R-free = 0.1570