# Date 2008-01-16 Time 05:07:48 PST -0800 (1200488868.35 s)
#phil __OFF__

Command line arguments: "../608.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27716
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 608

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 45.7567, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 45.7567, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9529 1.95311
Completeness in resolution range: 0.951615
Completeness with d_max=infinity: 0.948804

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9529
                             d_min =   1.9531

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 45.7567, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9529 1.95311
Completeness in resolution range: 0.951615
Completeness with d_max=infinity: 0.948804

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9533 -  4.1801 [2163/2189]  1947   216  10.0%
  bin  2:  4.1801 -  3.3299 [2070/2090]  1864   206  10.0%
  bin  3:  3.3299 -  2.9125 [2062/2081]  1853   209  10.1%
  bin  4:  2.9125 -  2.6478 [2024/2054]  1821   203  10.0%
  bin  5:  2.6478 -  2.4589 [2021/2040]  1826   195   9.6%
  bin  6:  2.4589 -  2.3145 [2010/2035]  1798   212  10.5%
  bin  7:  2.3145 -  2.1990 [2003/2031]  1807   196   9.8%
  bin  8:  2.1990 -  2.1035 [1993/2029]  1796   197   9.9%
  bin  9:  2.1035 -  2.0228 [1968/2010]  1771   197  10.0%
  bin 10:  2.0228 -  1.9531 [1275/2026]  1147   128  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_608/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.68 -     2.32: 33
        2.32 -     2.97: 1818
        2.97 -     3.61: 4652
        3.61 -     4.26: 9321
        4.26 -     4.90: 12972
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.731 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.766 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 302 " - " O   HOH Z  70 "  1.766 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28791 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_608/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_608/model_refine_001.geo

CPU time processing inputs: 9.13


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 45.75675 85.5261 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: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4359   r_free= 0.4310   ksol= 0.00   Bsol= 0.00   scale= 0.919    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.255170                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.6627 0.99   1402  157 0.3689 0.3828      6.5558      6.5931|
|  2:  4.6627 -  3.7197 0.99   1348  150 0.3815 0.3506      6.7837       6.698|
|  3:  3.7197 -  3.2550 0.99   1330  143 0.4069 0.3931      6.6619      6.7156|
|  4:  3.2550 -  2.9599 0.99   1321  152 0.4221 0.4274        6.51      6.4739|
|  5:  2.9599 -  2.7492 0.99   1317  147 0.4602 0.4377      6.3382       6.359|
|  6:  2.7492 -  2.5880 0.99   1299  138 0.4565 0.4912      6.2517      6.2045|
|  7:  2.5880 -  2.4589 0.99   1294  142 0.4601 0.4641      6.2168      6.1754|
|  8:  2.4589 -  2.3523 0.98   1271  145 0.4774 0.4395      6.1443      6.1335|
|  9:  2.3523 -  2.2621 0.98   1282  151 0.4754 0.5007      6.1007      6.1885|
| 10:  2.2621 -  2.1843 1.00   1306  148 0.4668 0.4802      6.0649      6.0492|
| 11:  2.1843 -  2.1162 0.98   1284  132 0.4723 0.4653      6.0038      6.0063|
| 12:  2.1162 -  2.0558 0.98   1259  142 0.4589 0.4357      5.9322      5.9761|
| 13:  2.0558 -  2.0018 0.99   1284  138 0.4729 0.4424      5.8476      5.7593|
| 14:  2.0018 -  1.9531 0.48    633   74 0.5233 0.4425      5.8972       5.784|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9533 -  4.6627  1402   157  0.69  35.30   0.83     0.75      76769.55|
|  2:  4.6627 -  3.7197  1348   150  0.71  34.36   0.91     0.83     102146.39|
|  3:  3.7197 -  3.2550  1330   143  0.63  41.38   0.94     0.82     104984.49|
|  4:  3.2550 -  2.9599  1321   152  0.55  47.97   0.95     0.74      95074.74|
|  5:  2.9599 -  2.7492  1317   147  0.47  54.23   0.91     0.67      74890.43|
|  6:  2.7492 -  2.5880  1299   138  0.45  55.98   0.91     0.63      66737.15|
|  7:  2.5880 -  2.4589  1294   142  0.44  57.07   0.95     0.61      59092.92|
|  8:  2.4589 -  2.3523  1271   145  0.42  58.05   0.94     0.62      54323.13|
|  9:  2.3523 -  2.2621  1282   151  0.44  56.90   0.94     0.63      48004.34|
| 10:  2.2621 -  2.1843  1306   148  0.46  55.56   0.97     0.66      41953.00|
| 11:  2.1843 -  2.1162  1284   132  0.46  55.42   1.01     0.70      39161.87|
| 12:  2.1162 -  2.0558  1259   142  0.48  53.89   1.01     0.73      33844.18|
| 13:  2.0558 -  2.0018  1284   138  0.49  53.37   1.00     0.76      27850.87|
| 14:  2.0018 -  1.9531   633    74  0.57  46.97   0.99     0.81      19908.57|
|alpha:            min =        0.61 max =            0.83 mean =         0.71|
|beta:             min =    19908.57 max =       104984.49 mean =     62335.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           90.00 mean =        50.41|
|phase err.(test): min =        0.00 max =           89.99 mean =        50.49|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.075681             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.910   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.872917              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.806   (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 |  1.681 -  2.003:       14 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.003 -  2.325:       19 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.325 -  2.647:       89 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.647 -  2.969:     1729 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.969 -  3.290:     1954 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.290 -  3.612:     2698 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.612 -  3.934:     4813 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.934 -  4.256:     4508 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.256 -  4.578:     5927 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.578 -  4.900:     7045 |
|-----------------------------------------------------------------------------|
|-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 |        0.186 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.107    4.900  1.681 |       0.554 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.473)------------------------------------------|
|    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: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4359   r_free= 0.4310   ksol= 0.00   Bsol= 0.00   scale= 0.919    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.255170                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4234   r_free= 0.4198   ksol= 0.35   Bsol= 35.86   scale= 0.933   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.43,3.22,-1.07,0.00,-0.00,-0.00); trace/3= -0.43                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.244568                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.823238              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.737   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.035303              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.781   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4234      final r-factor (work) = 0.3502          |
| start r-factor (free) = 0.4198      final r-factor (free) = 0.3840          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.7363 = 8.82 * 0.50 * 6.2450 + 1.00 * 0.1856                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.2102 = 8.82 * 0.50 * 6.1409 + 1.00 * 0.1190                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3502      final r-factor (work) = 0.3217          |
| start r-factor (free) = 0.3840      final r-factor (free) = 0.3941          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3638 = 1.04 * 1.00 * 6.1409 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2963 = 1.04 * 1.00 * 6.0658 + 1.00 * 0.0164                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.473)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.16   17.95    None  None   None       |
|    all(noH): 2823   0      0.00    95.16   17.95    None  None   None       |
|    Sol.    : 438    0      0.00    95.16   34.00    None  None   None       |
|    Mac.    : 2385   0      0.00    82.94   15.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.516:  844   |   5:    47.582 -  57.098:   74        |
|      1:     9.516 -  19.033:  951   |   6:    57.098 -  66.614:   30        |
|      2:    19.033 -  28.549:  510   |   7:    66.614 -  76.130:    5        |
|      3:    28.549 -  38.065:  275   |   8:    76.130 -  85.647:    5        |
|      4:    38.065 -  47.582:  127   |   9:    85.647 -  95.163:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3217 r_free = 0.3941             target_work(ml) = 6.069         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3213 r_free = 0.3945             target_work(ml) = 6.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3213   r_free= 0.3945   ksol= 0.35   Bsol= 35.86   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.43,3.22,-1.07,0.00,-0.00,-0.00); trace/3= -0.43                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.068766                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3214   r_free= 0.3939   ksol= 0.36   Bsol= 57.40   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.59,1.17,-0.56,0.00,-0.00,-0.00); trace/3= -0.33                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.070599                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.016587             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.488  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.655938              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.346  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3214      final r-factor (work) = 0.2601          |
| start r-factor (free) = 0.3939      final r-factor (free) = 0.3274          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.5462 = 11.02 * 0.50 * 6.0685 + 1.00 * 0.1190                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.0909 = 11.02 * 0.50 * 5.9884 + 1.00 * 0.1049                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2601      final r-factor (work) = 0.2418          |
| start r-factor (free) = 0.3274      final r-factor (free) = 0.3195          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9443 = 0.66 * 1.00 * 5.9884 + 1.00 * 0.0163                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8583 = 0.66 * 1.00 * 5.8625 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.473)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.06   17.94    None  None   None       |
|    all(noH): 2823   0      0.00    90.06   17.94    None  None   None       |
|    Sol.    : 438    0      0.00    90.06   37.32    None  None   None       |
|    Mac.    : 2385   0      0.00    84.76   14.38    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 -   9.006:  835   |   5:    45.029 -  54.034:   94        |
|      1:     9.006 -  18.011:  957   |   6:    54.034 -  63.040:   56        |
|      2:    18.011 -  27.017:  459   |   7:    63.040 -  72.046:   10        |
|      3:    27.017 -  36.023:  234   |   8:    72.046 -  81.051:    9        |
|      4:    36.023 -  45.029:  164   |   9:    81.051 -  90.057:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2418 r_free = 0.3195             target_work(ml) = 5.848         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2416 r_free = 0.3191             target_work(ml) = 5.848         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2416   r_free= 0.3191   ksol= 0.36   Bsol= 57.40   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.59,1.17,-0.56,0.00,-0.00,-0.00); trace/3= -0.33                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.848284                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2413   r_free= 0.3169   ksol= 0.34   Bsol= 55.81   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.14,-0.42,-0.31,-0.00,-0.00,-0.00); trace/3= -0.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.843795                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.923869              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.836  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.472734              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.827  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2413      final r-factor (work) = 0.1939          |
| start r-factor (free) = 0.3169      final r-factor (free) = 0.2568          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.5368 = 4.92 * 0.50 * 5.8620 + 1.00 * 0.1049                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.2458 = 4.92 * 0.50 * 5.7569 + 1.00 * 0.0728                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1939      final r-factor (work) = 0.1756          |
| start r-factor (free) = 0.2568      final r-factor (free) = 0.2344          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7344 = 0.47 * 1.00 * 5.7569 + 1.00 * 0.0129                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6529 = 0.47 * 1.00 * 5.5891 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.473)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.53   17.63    None  None   None       |
|    all(noH): 2823   0      0.00    90.53   17.63    None  None   None       |
|    Sol.    : 438    0      3.16    87.79   41.76    None  None   None       |
|    Mac.    : 2385   0      0.00    90.53   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 -   9.053:  907   |   5:    45.266 -  54.319:  116        |
|      1:     9.053 -  18.106: 1091   |   6:    54.319 -  63.372:   72        |
|      2:    18.106 -  27.159:  303   |   7:    63.372 -  72.425:   35        |
|      3:    27.159 -  36.212:  162   |   8:    72.425 -  81.478:    6        |
|      4:    36.212 -  45.266:  126   |   9:    81.478 -  90.531:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1756 r_free = 0.2344             target_work(ml) = 5.547         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1753 r_free = 0.2338             target_work(ml) = 5.546         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1753   r_free= 0.2338   ksol= 0.34   Bsol= 55.81   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.14,-0.42,-0.31,-0.00,-0.00,-0.00); trace/3= -0.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.545680                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1750   r_free= 0.2324   ksol= 0.32   Bsol= 46.37   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-1.60,-0.75,-0.00,-0.00,-0.00); trace/3= -1.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.542043                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.898642              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.867   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.210249              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.873  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1750      final r-factor (work) = 0.1438          |
| start r-factor (free) = 0.2324      final r-factor (free) = 0.1964          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1751 = 2.90 * 0.50 * 5.5908 + 1.00 * 0.0723                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9693 = 2.90 * 0.50 * 5.4606 + 1.00 * 0.0551                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1438      final r-factor (work) = 0.1380          |
| start r-factor (free) = 0.1964      final r-factor (free) = 0.1869          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1588 = 0.21 * 1.00 * 5.4606 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5567 = 0.21 * 1.00 * 5.3491 + 1.00 * 0.4321                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.473)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.16   17.17    None  None   None       |
|    all(noH): 2823   0      0.00    90.16   17.17    None  None   None       |
|    Sol.    : 438    0      3.92    86.22   41.28    None  None   None       |
|    Mac.    : 2385   0      0.00    90.16   12.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.016:  882   |   5:    45.079 -  54.095:  111        |
|      1:     9.016 -  18.032: 1188   |   6:    54.095 -  63.110:   73        |
|      2:    18.032 -  27.047:  271   |   7:    63.110 -  72.126:   34        |
|      3:    27.047 -  36.063:  131   |   8:    72.126 -  81.142:    6        |
|      4:    36.063 -  45.079:  123   |   9:    81.142 -  90.157:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1380 r_free = 0.1869             target_work(ml) = 5.323         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1378 r_free = 0.1868             target_work(ml) = 5.322         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1378   r_free= 0.1868   ksol= 0.32   Bsol= 46.37   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-1.60,-0.75,-0.00,-0.00,-0.00); trace/3= -1.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.322172                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1381   r_free= 0.1869   ksol= 0.32   Bsol= 43.77   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-2.06,-0.88,-0.00,-0.00,-0.00); trace/3= -1.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.322628                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.561990              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.449  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 7.664440              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.310   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1381      final r-factor (work) = 0.1210          |
| start r-factor (free) = 0.1869      final r-factor (free) = 0.1690          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5828 = 3.56 * 0.50 * 5.3497 + 1.00 * 0.0551                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4489 = 3.56 * 0.50 * 5.2688 + 1.00 * 0.0651                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1210      final r-factor (work) = 0.1159          |
| start r-factor (free) = 0.1690      final r-factor (free) = 0.1677          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 40.3959 = 7.66 * 1.00 * 5.2688 + 1.00 * 0.0134                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 39.7941 = 7.66 * 1.00 * 5.1906 + 1.00 * 0.0110                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.473)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.72  17.45    None  None   None       |
|    all(noH): 2823   0      0.00    100.72  17.45    None  None   None       |
|    Sol.    : 438    0      4.01    91.17   44.09    None  None   None       |
|    Mac.    : 2385   0      0.00    100.72  12.56    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.072: 1180   |   5:    50.360 -  60.432:   88        |
|      1:    10.072 -  20.144: 1004   |   6:    60.432 -  70.504:   72        |
|      2:    20.144 -  30.216:  217   |   7:    70.504 -  80.576:   36        |
|      3:    30.216 -  40.288:  116   |   8:    80.576 -  90.648:    9        |
|      4:    40.288 -  50.360:   98   |   9:    90.648 - 100.720:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1159 r_free = 0.1677             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1159 r_free = 0.1677             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1159   r_free= 0.1677   ksol= 0.32   Bsol= 43.77   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-2.06,-0.88,-0.00,-0.00,-0.00); trace/3= -1.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.183299                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.6627 0.99   1402  157 0.0975 0.1343      5.3741       5.602|
|  2:  4.6627 -  3.7197 0.99   1348  150 0.0850 0.1175      5.4542      5.6723|
|  3:  3.7197 -  3.2550 0.99   1330  143 0.1115 0.1510      5.5241      5.8592|
|  4:  3.2550 -  2.9599 0.99   1321  152 0.1295 0.1830      5.5154      5.6928|
|  5:  2.9599 -  2.7492 0.99   1317  147 0.1405 0.1870      5.3758      5.6232|
|  6:  2.7492 -  2.5880 0.99   1299  138 0.1251 0.1787      5.2436      5.4313|
|  7:  2.5880 -  2.4589 0.99   1294  142 0.1313 0.1779      5.1908      5.4248|
|  8:  2.4589 -  2.3523 0.98   1271  145 0.1250 0.1877       5.106      5.3757|
|  9:  2.3523 -  2.2621 0.98   1282  151 0.1225 0.1742      5.0629       5.317|
| 10:  2.2621 -  2.1843 1.00   1306  148 0.1154 0.1893       4.987      5.2559|
| 11:  2.1843 -  2.1162 0.98   1284  132 0.1162 0.1924      4.9867      5.2862|
| 12:  2.1162 -  2.0558 0.98   1259  142 0.1158 0.1817      4.9197      5.2444|
| 13:  2.0558 -  2.0018 0.99   1284  138 0.1169 0.1938      4.8226      5.0931|
| 14:  2.0018 -  1.9531 0.48    633   74 0.1033 0.1612      4.6938      4.9285|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9533 -  4.6627  1402   157  0.94   9.43   0.98     0.96       7424.66|
|  2:  4.6627 -  3.7197  1348   150  0.95   8.47   1.03     1.02       9849.50|
|  3:  3.7197 -  3.2550  1330   143  0.93  12.48   1.05     1.04      11809.55|
|  4:  3.2550 -  2.9599  1321   152  0.91  15.25   1.03     1.01      12089.48|
|  5:  2.9599 -  2.7492  1317   147  0.89  16.92   1.01     0.98       9212.19|
|  6:  2.7492 -  2.5880  1299   138  0.89  16.97   1.00     0.97       7682.70|
|  7:  2.5880 -  2.4589  1294   142  0.89  16.66   1.01     0.98       6682.08|
|  8:  2.4589 -  2.3523  1271   145  0.90  16.36   1.00     0.98       5711.89|
|  9:  2.3523 -  2.2621  1282   151  0.90  16.07   1.01     0.97       5323.39|
| 10:  2.2621 -  2.1843  1306   148  0.89  16.84   1.00     0.97       4809.95|
| 11:  2.1843 -  2.1162  1284   132  0.89  17.25   1.00     0.96       4891.91|
| 12:  2.1162 -  2.0558  1259   142  0.90  16.87   1.02     1.01       4501.47|
| 13:  2.0558 -  2.0018  1284   138  0.89  17.41   1.01     0.99       3701.12|
| 14:  2.0018 -  1.9531   633    74  0.91  15.33   1.00     0.97       2870.74|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2870.74 max =        12089.48 mean =      7090.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        15.09|
|phase err.(test): min =        0.00 max =           89.53 mean =        14.65|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1676   ksol= 0.32   Bsol= 46.51   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-2.06,-0.83,-0.00,-0.00,-0.00); trace/3= -1.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.182807                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1676   ksol= 0.32   Bsol= 46.51   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-2.06,-0.83,-0.00,-0.00,-0.00); trace/3= -1.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.182807                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.6627 0.99   1402  157 0.0973 0.1343       5.371      5.6019|
|  2:  4.6627 -  3.7197 0.99   1348  150 0.0852 0.1177      5.4559      5.6751|
|  3:  3.7197 -  3.2550 0.99   1330  143 0.1116 0.1512      5.5259       5.862|
|  4:  3.2550 -  2.9599 0.99   1321  152 0.1295 0.1832      5.5158      5.6929|
|  5:  2.9599 -  2.7492 0.99   1317  147 0.1404 0.1867      5.3751      5.6213|
|  6:  2.7492 -  2.5880 0.99   1299  138 0.1250 0.1785      5.2425      5.4304|
|  7:  2.5880 -  2.4589 0.99   1294  142 0.1313 0.1779      5.1898       5.424|
|  8:  2.4589 -  2.3523 0.98   1271  145 0.1249 0.1873      5.1052      5.3736|
|  9:  2.3523 -  2.2621 0.98   1282  151 0.1224 0.1743      5.0622      5.3172|
| 10:  2.2621 -  2.1843 1.00   1306  148 0.1153 0.1893      4.9867      5.2558|
| 11:  2.1843 -  2.1162 0.98   1284  132 0.1162 0.1924      4.9863       5.286|
| 12:  2.1162 -  2.0558 0.98   1259  142 0.1158 0.1815       4.919      5.2438|
| 13:  2.0558 -  2.0018 0.99   1284  138 0.1169 0.1936      4.8218      5.0914|
| 14:  2.0018 -  1.9531 0.48    633   74 0.1032 0.1607       4.692      4.9262|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9533 -  4.6627  1402   157  0.94   9.39   0.98     0.96       7375.96|
|  2:  4.6627 -  3.7197  1348   150  0.95   8.46   1.03     1.02       9858.23|
|  3:  3.7197 -  3.2550  1330   143  0.92  12.53   1.05     1.04      11880.57|
|  4:  3.2550 -  2.9599  1321   152  0.91  15.27   1.03     1.01      12112.65|
|  5:  2.9599 -  2.7492  1317   147  0.89  16.90   1.01     0.98       9196.83|
|  6:  2.7492 -  2.5880  1299   138  0.89  16.95   1.00     0.97       7660.31|
|  7:  2.5880 -  2.4589  1294   142  0.89  16.62   1.01     0.98       6658.69|
|  8:  2.4589 -  2.3523  1271   145  0.90  16.35   1.00     0.98       5698.01|
|  9:  2.3523 -  2.2621  1282   151  0.90  16.06   1.01     0.98       5316.44|
| 10:  2.2621 -  2.1843  1306   148  0.89  16.83   1.01     0.97       4807.90|
| 11:  2.1843 -  2.1162  1284   132  0.89  17.25   1.01     0.97       4890.19|
| 12:  2.1162 -  2.0558  1259   142  0.90  16.85   1.02     1.01       4494.14|
| 13:  2.0558 -  2.0018  1284   138  0.89  17.39   1.02     1.00       3691.79|
| 14:  2.0018 -  1.9531   633    74  0.91  15.30   1.00     0.97       2858.92|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2858.92 max =        12112.65 mean =      7086.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        15.08|
|phase err.(test): min =        0.00 max =           89.61 mean =        14.64|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.473)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.72  17.45    None  None   None       |
|    all(noH): 2823   0      0.00    100.72  17.45    None  None   None       |
|    Sol.    : 438    0      4.01    91.17   44.09    None  None   None       |
|    Mac.    : 2385   0      0.00    100.72  12.56    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:     0.003 -  10.075: 1180   |   5:    50.363 -  60.435:   88        |
|      1:    10.075 -  20.147: 1004   |   6:    60.435 -  70.507:   72        |
|      2:    20.147 -  30.219:  217   |   7:    70.507 -  80.579:   36        |
|      3:    30.219 -  40.291:  116   |   8:    80.579 -  90.651:    9        |
|      4:    40.291 -  50.363:   98   |   9:    90.651 - 100.723:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 321         
Filter by distance & map next to the model:
   mapped sites are within: 0.586 - 4.180
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 316 from: 321
   mapped sites are within: 0.709 - 4.180

peak=    6.747 closest distance to " NE2 GLN A  11 " =    1.373
peak=    6.742 closest distance to " O   HOH Z 385 " =    1.471
peak=    6.580 closest distance to " O   HOH Z 431 " =    1.751
peak=    6.225 closest distance to " O   HOH Z  65 " =    1.603
peak=    6.076 closest distance to " O   HOH Z 390 " =    1.096
peak=    6.073 closest distance to " O   HOH Z 289 " =    1.309
peak=    5.914 closest distance to " O   HOH Z   7 " =    1.840
peak=    5.896 closest distance to " O   HOH Z 427 " =    1.367
peak=    5.672 closest distance to " O   HOH Z 214 " =    1.799
peak=    5.659 closest distance to " O   HOH Z 222 " =    1.239
peak=    5.455 closest distance to " O   HOH Z 417 " =    2.213
peak=    5.326 closest distance to " O   HOH Z 144 " =    1.767
peak=    5.268 closest distance to " O   HOH Z 287 " =    1.974
peak=    5.152 closest distance to " NH2 ARG A  56 " =    2.015
peak=    5.133 closest distance to " O   HOH Z 245 " =    1.177
peak=    5.110 closest distance to " O   HOH Z  78 " =    1.633
peak=    5.012 closest distance to " CG  PRO A  54 " =    1.238
peak=    4.998 closest distance to " O   HOH Z  63 " =    2.051
peak=    4.959 closest distance to " O   HOH Z 427 " =    1.825
peak=    4.871 closest distance to " O   HOH Z  29 " =    1.112
peak=    4.846 closest distance to " O   HOH Z 193 " =    1.791
peak=    4.835 closest distance to " CB  PRO A  54 " =    1.050
peak=    4.794 closest distance to " CA  TYR A  30 " =    1.029
peak=    4.789 closest distance to " O   HOH Z 236 " =    1.513
peak=    4.774 closest distance to " CB  ARG A 275 " =    1.006
peak=    4.758 closest distance to " O   HOH Z 403 " =    1.366
peak=    4.619 closest distance to " O   HOH Z  63 " =    1.933
peak=    4.599 closest distance to " O   HOH Z 298 " =    1.923
peak=    4.588 closest distance to " O   HOH Z 145 " =    1.617
peak=    4.550 closest distance to " O   HOH Z 232 " =    2.231
peak=    4.547 closest distance to " O   HOH Z 139 " =    1.420
peak=    4.545 closest distance to " O   HOH Z  28 " =    1.389
peak=    4.538 closest distance to " CB  GLN A 183 " =    1.149
peak=    4.526 closest distance to " O   HOH Z 424 " =    1.199
peak=    4.513 closest distance to " O   HOH Z 124 " =    1.454
peak=    4.504 closest distance to " O   PRO A 198 " =    1.246
peak=    4.498 closest distance to " O   HOH Z 272 " =    1.851
peak=    4.477 closest distance to " O   HOH Z 380 " =    1.959
peak=    4.472 closest distance to " CG  PRO A 213 " =    1.221
peak=    4.472 closest distance to " O   HOH Z  49 " =    1.350
peak=    4.440 closest distance to " O   ASP A 286 " =    2.602
peak=    4.420 closest distance to " O   HOH Z 316 " =    2.878
peak=    4.420 closest distance to " CB  GLN A 223 " =    1.470
peak=    4.419 closest distance to " O   HOH Z 158 " =    1.295
peak=    4.415 closest distance to " O   HOH Z 423 " =    1.733
peak=    4.389 closest distance to " O   HOH Z 392 " =    1.336
peak=    4.380 closest distance to " O   HOH Z 394 " =    1.807
peak=    4.328 closest distance to " O   HOH Z 371 " =    3.150
peak=    4.297 closest distance to " O   HOH Z  91 " =    2.374
peak=    4.267 closest distance to " O   HOH Z 425 " =    1.506
peak=    4.256 closest distance to " O   HOH Z 414 " =    1.268
peak=    4.252 closest distance to " O   HOH Z 369 " =    2.050
peak=    4.195 closest distance to " O   HOH Z 130 " =    0.936
peak=    4.193 closest distance to " O   HOH Z 217 " =    2.564
peak=    4.188 closest distance to " O   HOH Z  88 " =    2.909
peak=    4.159 closest distance to " O   HOH Z   2 " =    1.658
peak=    4.149 closest distance to " O   HOH Z 112 " =    1.232
peak=    4.148 closest distance to " CB  SER A   3 " =    1.286
peak=    4.132 closest distance to " CB  SER A  63 " =    1.295
peak=    4.120 closest distance to " O   HOH Z 261 " =    1.883
peak=    4.092 closest distance to " CB  GLU A 128 " =    1.083
peak=    4.083 closest distance to " O   HOH Z 166 " =    1.579
peak=    4.081 closest distance to " O   HOH Z 209 " =    2.289
peak=    4.070 closest distance to " O   HOH Z 327 " =    1.799
peak=    4.063 closest distance to " O   HOH Z 352 " =    1.562
peak=    4.039 closest distance to " CB  ASN A 148 " =    1.422
peak=    4.037 closest distance to " O   HOH Z 402 " =    1.458
peak=    3.987 closest distance to " CB  SER A 216 " =    1.002
peak=    3.970 closest distance to " OG BSER A  99 " =    2.277
peak=    3.966 closest distance to " O   HOH Z 368 " =    3.706
peak=    3.960 closest distance to " O   HOH Z 250 " =    1.424
peak=    3.960 closest distance to " O   HOH Z 359 " =    1.403
peak=    3.959 closest distance to " O   HOH Z 371 " =    1.917
peak=    3.951 closest distance to " CG  LEU A 167 " =    1.278
peak=    3.950 closest distance to " O   HOH Z 211 " =    1.124
peak=    3.947 closest distance to " O   HOH Z  44 " =    2.893
peak=    3.927 closest distance to " O   HOH Z 302 " =    1.343
peak=    3.916 closest distance to " CG  PRO A  90 " =    1.171
peak=    3.915 closest distance to " CD  ARG A  66 " =    2.369
peak=    3.911 closest distance to " O   HOH Z 405 " =    1.426
peak=    3.908 closest distance to " O   HOH Z  61 " =    1.523
peak=    3.896 closest distance to " O   HOH Z 171 " =    2.527
peak=    3.896 closest distance to " CG  TRP A 179 " =    2.104
peak=    3.895 closest distance to " NZ  LYS A 117 " =    1.304
peak=    3.883 closest distance to " N   ALA A   1 " =    2.624
peak=    3.876 closest distance to " CB  ASN A 148 " =    1.885
peak=    3.863 closest distance to " CB  TRP A 179 " =    1.421
peak=    3.840 closest distance to " CG  PRO A 198 " =    1.241
peak=    3.836 closest distance to " O   HOH Z 133 " =    2.551
peak=    3.833 closest distance to " O   HOH Z 431 " =    1.254
peak=    3.833 closest distance to " O   HOH Z 413 " =    1.479
peak=    3.824 closest distance to " N   GLU A   2 " =    1.303
peak=    3.823 closest distance to " CB  LYS A 117 " =    1.186
peak=    3.822 closest distance to " NE2 GLN A 278 " =    3.663
peak=    3.822 closest distance to " NE1 TRP A 274 " =    0.986
peak=    3.789 closest distance to " CB  GLU A 152 " =    1.247
peak=    3.783 closest distance to " NE2 GLN A  58 " =    3.692
peak=    3.778 closest distance to " O   HOH Z 207 " =    2.244
peak=    3.762 closest distance to " OD2 ASP A 286 " =    2.536
peak=    3.759 closest distance to " O   HOH Z  11 " =    1.926
peak=    3.759 closest distance to " CG2 VAL A 257 " =    0.864
peak=    3.744 closest distance to " CB  TRP A 266 " =    1.085
peak=    3.741 closest distance to " O   HOH Z 147 " =    1.318
peak=    3.734 closest distance to " O   HOH Z 151 " =    1.675
peak=    3.730 closest distance to " O   HOH Z   9 " =    2.100
peak=    3.728 closest distance to " O   HOH Z 115 " =    1.451
peak=    3.725 closest distance to " OG  SER A  62 " =    3.088
peak=    3.723 closest distance to " O   HOH Z 152 " =    2.063
peak=    3.723 closest distance to " O   HOH Z 363 " =    1.095
peak=    3.718 closest distance to " O   HOH Z 385 " =    3.307
peak=    3.712 closest distance to " O   HOH Z 425 " =    2.166
peak=    3.710 closest distance to " CB  GLU A 277 " =    3.510
peak=    3.707 closest distance to " O   HOH Z   9 " =    0.989
peak=    3.699 closest distance to " CB  ARG A 190 " =    1.694
peak=    3.694 closest distance to " CB  SER A 276 " =    1.113
peak=    3.693 closest distance to " O   HOH Z 119 " =    4.180
peak=    3.684 closest distance to " CA  ASN A 215 " =    1.227
peak=    3.681 closest distance to " N   GLN A 278 " =    1.113
peak=    3.673 closest distance to " O   HOH Z  44 " =    1.747
peak=    3.671 closest distance to " N   ALA A   1 " =    1.269
peak=    3.644 closest distance to " CG2 THR A 221 " =    1.244
peak=    3.641 closest distance to " O   HOH Z 258 " =    2.111
peak=    3.639 closest distance to " NH1AARG A 145 " =    1.077
peak=    3.634 closest distance to " CA  ILE A 234 " =    1.019
peak=    3.632 closest distance to " O   HOH Z 222 " =    2.174
peak=    3.627 closest distance to " O   HOH Z 155 " =    1.851
peak=    3.614 closest distance to " O   HOH Z 244 " =    1.544
peak=    3.612 closest distance to " O   HOH Z 422 " =    2.580
peak=    3.610 closest distance to " O   HOH Z 234 " =    3.743
peak=    3.608 closest distance to " O   ALA A 165 " =    1.322
peak=    3.608 closest distance to " CD  LYS A 166 " =    1.502
peak=    3.608 closest distance to " CB  MET A 105 " =    1.353
peak=    3.607 closest distance to " O   HOH Z  32 " =    2.139
peak=    3.603 closest distance to " CB  VAL A 202 " =    1.629
peak=    3.601 closest distance to " CG2AVAL A 121 " =    2.502
peak=    3.601 closest distance to " O   HOH Z 293 " =    1.351
peak=    3.595 closest distance to " CG1BVAL A 121 " =    2.108
peak=    3.593 closest distance to " O   HOH Z 415 " =    1.148
peak=    3.586 closest distance to " O   HOH Z  50 " =    1.959
peak=    3.583 closest distance to " O   HOH Z 365 " =    2.698
peak=    3.579 closest distance to " CA  ALA A 160 " =    0.775
peak=    3.578 closest distance to " O   HOH Z 412 " =    1.500
peak=    3.576 closest distance to " CB  VAL A 265 " =    1.302
peak=    3.575 closest distance to " O   HOH Z 358 " =    1.211
peak=    3.567 closest distance to " CA  PHE A 283 " =    1.453
peak=    3.561 closest distance to " OD1 ASN A  69 " =    2.592
peak=    3.553 closest distance to " CG  GLN A  11 " =    2.132
peak=    3.551 closest distance to " O   HOH Z 108 " =    1.803
peak=    3.551 closest distance to " O   HOH Z  30 " =    1.525
peak=    3.548 closest distance to " O   HOH Z 399 " =    0.796
peak=    3.546 closest distance to " O   HOH Z 193 " =    1.778
peak=    3.540 closest distance to " O  BHOH Z  74 " =    1.376
peak=    3.529 closest distance to " O   HOH Z 437 " =    2.042
peak=    3.518 closest distance to " O   HOH Z 345 " =    1.844
peak=    3.513 closest distance to " CD1 ILE A 263 " =    1.292
peak=    3.506 closest distance to " CA  GLY A 241 " =    3.694
peak=    3.504 closest distance to " O   HOH Z 290 " =    0.907
peak=    3.497 closest distance to " O   HOH Z 119 " =    1.493
peak=    3.494 closest distance to " O   HOH Z  97 " =    1.865
peak=    3.489 closest distance to " NZ BLYS A 290 " =    0.862
peak=    3.488 closest distance to " CD  ARG A 159 " =    0.847
peak=    3.481 closest distance to " NE AARG A 275 " =    1.493
peak=    3.481 closest distance to " O   HOH Z 156 " =    2.778
peak=    3.474 closest distance to " O   HOH Z  40 " =    1.980
peak=    3.473 closest distance to " CG1 ILE A 120 " =    1.422
peak=    3.468 closest distance to " CA  ARG A 195 " =    1.538
peak=    3.466 closest distance to " O   HOH Z 128 " =    2.162
peak=    3.459 closest distance to " CA  LEU A 282 " =    1.057
peak=    3.459 closest distance to " CE1 TYR A 186 " =    1.243
peak=    3.459 closest distance to " O   HOH Z   7 " =    3.337
peak=    3.447 closest distance to " O   HOH Z 175 " =    2.083
peak=    3.446 closest distance to " NH2 ARG A 219 " =    1.743
peak=    3.424 closest distance to " O   HOH Z  59 " =    1.410
peak=    3.423 closest distance to " CB  LYS A 290 " =    1.522
peak=    3.422 closest distance to " O   HOH Z 215 " =    1.384
peak=    3.414 closest distance to " CB  LEU A 228 " =    1.083
peak=    3.413 closest distance to " O   HOH Z   6 " =    1.986
peak=    3.405 closest distance to " ND1 HIS A  81 " =    1.508
peak=    3.403 closest distance to " O   HOH Z 389 " =    1.676
peak=    3.400 closest distance to " OG BSER A 212 " =    2.797
peak=    3.399 closest distance to " O   HOH Z 329 " =    3.469
peak=    3.395 closest distance to " O   HOH Z 368 " =    1.905
peak=    3.394 closest distance to " O   HOH Z 225 " =    1.336
peak=    3.388 closest distance to " O   HOH Z  73 " =    1.640
peak=    3.381 closest distance to " CB  GLU A 277 " =    1.089
peak=    3.373 closest distance to " O   ALA A   1 " =    1.692
peak=    3.373 closest distance to " CB  LEU A 300 " =    0.913
peak=    3.372 closest distance to " OG1 THR A 221 " =    1.380
peak=    3.372 closest distance to " CB  ASP A 124 " =    0.948
peak=    3.368 closest distance to " N   HIS A  86 " =    1.824
peak=    3.368 closest distance to " O   HOH Z 384 " =    1.257
peak=    3.367 closest distance to " O   HOH Z 158 " =    2.392
peak=    3.362 closest distance to " O   HOH Z 389 " =    1.130
peak=    3.362 closest distance to " O   HOH Z 434 " =    1.239
peak=    3.361 closest distance to " CD1 PHE A  16 " =    0.968
peak=    3.357 closest distance to " CA  ALA A 299 " =    0.920
peak=    3.350 closest distance to " CB  THR A  31 " =    1.614
peak=    3.346 closest distance to " O   HOH Z  64 " =    2.022
peak=    3.343 closest distance to " O   HOH Z 435 " =    1.869
peak=    3.343 closest distance to " O   HOH Z 135 " =    1.868
peak=    3.339 closest distance to " O   HOH Z  65 " =    1.478
peak=    3.338 closest distance to " O   HOH Z 130 " =    2.157
peak=    3.333 closest distance to " O   HOH Z 416 " =    1.173
peak=    3.333 closest distance to " CB  ASN A 187 " =    1.395
peak=    3.331 closest distance to " O   HOH Z  58 " =    1.544
peak=    3.327 closest distance to " CB  MET A 105 " =    1.122
peak=    3.320 closest distance to " CB  TYR A 169 " =    0.823
peak=    3.314 closest distance to " O   HOH Z 344 " =    3.092
peak=    3.313 closest distance to " O   HOH Z 282 " =    1.479
peak=    3.309 closest distance to " N   ASN A 127 " =    1.339
peak=    3.307 closest distance to " CD  ARG A 138 " =    0.733
peak=    3.306 closest distance to " CG  GLN A  89 " =    1.348
peak=    3.305 closest distance to " O   HOH Z 393 " =    1.334
peak=    3.304 closest distance to " OD1BASN A 224 " =    2.351
peak=    3.303 closest distance to " O   HOH Z 313 " =    1.892
peak=    3.302 closest distance to " OG BSER A 258 " =    0.928
peak=    3.301 closest distance to " O   HOH Z  17 " =    2.067
peak=    3.298 closest distance to " O   HOH Z  10 " =    1.627
peak=    3.298 closest distance to " O   HOH Z  61 " =    1.605
peak=    3.298 closest distance to " CG1 ILE A  33 " =    1.265
peak=    3.297 closest distance to " CG  LYS A 166 " =    1.363
peak=    3.295 closest distance to " O   HOH Z  80 " =    1.934
peak=    3.292 closest distance to " CB  TYR A 116 " =    1.002
peak=    3.291 closest distance to " CA  ALA A 291 " =    0.891
peak=    3.291 closest distance to " O   HOH Z 116 " =    2.671
peak=    3.287 closest distance to " O   HOH Z  93 " =    1.945
peak=    3.287 closest distance to " O   HOH Z 288 " =    2.049
peak=    3.281 closest distance to " CA  ALA A  21 " =    1.159
peak=    3.281 closest distance to " O   HOH Z  28 " =    2.086
peak=    3.278 closest distance to " O   HOH Z 213 " =    1.946
peak=    3.275 closest distance to " O   HOH Z 227 " =    1.797
peak=    3.274 closest distance to " O   HOH Z 193 " =    1.903
peak=    3.274 closest distance to " N   SER A 210 " =    1.162
peak=    3.274 closest distance to " CB  GLU A 236 " =    1.506
peak=    3.273 closest distance to " O   HOH Z 419 " =    1.898
peak=    3.273 closest distance to " O   HOH Z 357 " =    1.764
peak=    3.271 closest distance to " NZ  LYS A  76 " =    1.546
peak=    3.268 closest distance to " O   HOH Z 369 " =    1.630
peak=    3.267 closest distance to " O   HOH Z 361 " =    2.637
peak=    3.265 closest distance to " CZ3 TRP A 274 " =    2.170
peak=    3.264 closest distance to " O   HOH Z  55 " =    1.759
peak=    3.263 closest distance to " O   GLY A 147 " =    1.478
peak=    3.257 closest distance to " ND2 ASN A 187 " =    1.411
peak=    3.255 closest distance to " O   HOH Z 384 " =    1.615
peak=    3.252 closest distance to " OG  SER A  22 " =    2.853
peak=    3.251 closest distance to " O   HOH Z 158 " =    2.977
peak=    3.251 closest distance to " CG2 THR A 220 " =    0.961
peak=    3.249 closest distance to " O   THR A 220 " =    1.643
peak=    3.248 closest distance to " CA  MET A 105 " =    0.866
peak=    3.245 closest distance to " O   HOH Z 122 " =    1.710
peak=    3.241 closest distance to " O   GLY A 302 " =    2.320
peak=    3.239 closest distance to " OE1 GLU A  37 " =    1.214
peak=    3.238 closest distance to " O   HOH Z  57 " =    1.629
peak=    3.236 closest distance to " N   TYR A  15 " =    1.063
peak=    3.229 closest distance to " CE3 TRP A 274 " =    2.468
peak=    3.227 closest distance to " O   HOH Z 291 " =    1.433
peak=    3.225 closest distance to " CG2BVAL A  41 " =    1.003
peak=    3.225 closest distance to " O   HOH Z 299 " =    2.605
peak=    3.223 closest distance to " O   HOH Z 189 " =    2.803
peak=    3.222 closest distance to " O   HOH Z 430 " =    1.774
peak=    3.220 closest distance to " CA  GLY A 267 " =    1.275
peak=    3.220 closest distance to " CB  ALA A  34 " =    1.145
peak=    3.218 closest distance to " O   HOH Z 128 " =    2.128
peak=    3.217 closest distance to " CB  PHE A 225 " =    1.327
peak=    3.204 closest distance to " OG BSER A 164 " =    2.142
peak=    3.201 closest distance to " O   MET A 105 " =    1.825
peak=    3.200 closest distance to " O   HOH Z 311 " =    1.514
peak=    3.199 closest distance to " CE AMET A  47 " =    1.324
peak=    3.197 closest distance to " CB  ASP A 298 " =    1.178
peak=    3.197 closest distance to " CA  ASN A  74 " =    1.215
peak=    3.196 closest distance to " CG  GLN A  88 " =    1.093
peak=    3.192 closest distance to " CA  ASN A 127 " =    1.066
peak=    3.190 closest distance to " O   HOH Z 424 " =    2.903
peak=    3.187 closest distance to " CA  GLU A 152 " =    1.314
peak=    3.186 closest distance to " CB  PHE A 130 " =    1.075
peak=    3.185 closest distance to " O   HOH Z 248 " =    1.935
peak=    3.184 closest distance to " CB  ARG A 138 " =    0.867
peak=    3.181 closest distance to " O   HOH Z 380 " =    2.069
peak=    3.179 closest distance to " O   HOH Z 172 " =    2.262
peak=    3.177 closest distance to " CB  MET A  40 " =    0.930
peak=    3.172 closest distance to " O   HOH Z 189 " =    1.903
peak=    3.172 closest distance to " O   HOH Z 362 " =    1.650
peak=    3.163 closest distance to " OE2 GLU A  53 " =    2.068
peak=    3.163 closest distance to " O   HOH Z 258 " =    1.549
peak=    3.154 closest distance to " CZ  ARG A  14 " =    1.590
peak=    3.149 closest distance to " O   HOH Z 214 " =    3.083
peak=    3.142 closest distance to " OD1 ASN A  45 " =    1.284
peak=    3.135 closest distance to " O   HOH Z 426 " =    1.938
peak=    3.126 closest distance to " O   HOH Z 438 " =    2.497
peak=    3.126 closest distance to " O   HOH Z 213 " =    1.726
peak=    3.122 closest distance to " CB  ARG A  79 " =    1.269
peak=    3.122 closest distance to " CB  LEU A 237 " =    0.709
peak=    3.121 closest distance to " O   HOH Z 421 " =    2.716
peak=    3.119 closest distance to " O   HOH Z 326 " =    1.799
peak=    3.118 closest distance to " CE  MET A  93 " =    1.434
peak=    3.116 closest distance to " NH2AARG A 190 " =    1.322
peak=    3.114 closest distance to " CG  PRO A 243 " =    1.062
peak=    3.109 closest distance to " CG2 ILE A 234 " =    0.854
peak=    3.107 closest distance to " O   HOH Z 281 " =    1.904
peak=    3.103 closest distance to " O   HOH Z 104 " =    1.377
peak=    3.099 closest distance to " O   HOH Z 106 " =    2.515
peak=    3.095 closest distance to " CA  ALA A  51 " =    1.062
peak=    3.095 closest distance to " O   HOH Z 108 " =    1.538
peak=    3.094 closest distance to " CA  GLY A 136 " =    1.035
peak=    3.094 closest distance to " O   HOH Z 112 " =    2.441
peak=    3.079 closest distance to " O   HOH Z 325 " =    3.162
peak=    3.077 closest distance to " CE3 TRP A 274 " =    1.316
peak=    3.076 closest distance to " O   HOH Z 409 " =    2.073
peak=    3.074 closest distance to " CA  ALA A 158 " =    1.113
peak=    3.068 closest distance to " O   HOH Z 217 " =    1.661
peak=    3.066 closest distance to " N   ILE A  33 " =    1.041
peak=    3.062 closest distance to " CD  PRO A 243 " =    1.625
peak=    3.061 closest distance to " O   HOH Z 180 " =    2.107
peak=    3.042 closest distance to " O   HOH Z 227 " =    1.931
peak=    3.032 closest distance to " O   HOH Z 153 " =    3.788
peak=    3.028 closest distance to " O   HOH Z 216 " =    1.478

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.742 - 5.589
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 212 from: 212
   mapped sites are within: 0.742 - 5.589

peak=   -4.428 closest distance to " O   HOH Z 385 " =    1.281
peak=   -4.393 closest distance to " O   HOH Z 409 " =    3.296
peak=   -4.348 closest distance to " O   HOH Z  60 " =    2.010
peak=   -4.210 closest distance to " CB  PRO A 243 " =    2.522
peak=   -4.209 closest distance to " CA  GLY A  98 " =    1.753
peak=   -4.192 closest distance to " O   HOH Z 185 " =    1.852
peak=   -4.183 closest distance to " OG BSER A 134 " =    1.485
peak=   -4.109 closest distance to " O   SER A  22 " =    2.613
peak=   -4.078 closest distance to " CB  ALA A 248 " =    1.984
peak=   -4.030 closest distance to " N   THR A 157 " =    1.465
peak=   -4.020 closest distance to " CD  ARG A  14 " =    3.065
peak=   -3.962 closest distance to " CD  ARG A 156 " =    1.985
peak=   -3.952 closest distance to " NH2 ARG A 219 " =    1.837
peak=   -3.938 closest distance to " CZ  PHE A  59 " =    1.422
peak=   -3.937 closest distance to " O   PRO A 198 " =    1.256
peak=   -3.935 closest distance to " O   HOH Z 197 " =    3.270
peak=   -3.923 closest distance to " O   HOH Z 196 " =    1.851
peak=   -3.904 closest distance to " O   HOH Z  43 " =    1.807
peak=   -3.864 closest distance to " OE1 GLU A 277 " =    2.134
peak=   -3.861 closest distance to " O   HOH Z 166 " =    1.398
peak=   -3.845 closest distance to " OG  SER A  87 " =    1.238
peak=   -3.831 closest distance to " O   MET A  40 " =    2.791
peak=   -3.830 closest distance to " O   ARG A 145 " =    1.395
peak=   -3.818 closest distance to " CZ2 TRP A 274 " =    0.971
peak=   -3.805 closest distance to " CB  ALA A 291 " =    2.136
peak=   -3.802 closest distance to " O   HOH Z  88 " =    1.937
peak=   -3.788 closest distance to " CD2 TYR A 293 " =    1.742
peak=   -3.783 closest distance to " CD1 LEU A 255 " =    2.999
peak=   -3.753 closest distance to " O   HOH Z 415 " =    1.205
peak=   -3.746 closest distance to " CG  MET A 105 " =    0.917
peak=   -3.744 closest distance to " CA  GLY A 203 " =    2.231
peak=   -3.743 closest distance to " CG  GLN A  58 " =    1.340
peak=   -3.728 closest distance to " O   HOH Z 438 " =    0.890
peak=   -3.724 closest distance to " O   HOH Z 426 " =    1.574
peak=   -3.720 closest distance to " CA  ASP A  27 " =    2.362
peak=   -3.715 closest distance to " O   HOH Z  56 " =    2.008
peak=   -3.711 closest distance to " CE2 TYR A 116 " =    2.982
peak=   -3.680 closest distance to " O   HOH Z  65 " =    0.848
peak=   -3.674 closest distance to " OD2 ASP A 171 " =    1.887
peak=   -3.672 closest distance to " O   ALA A   1 " =    1.286
peak=   -3.661 closest distance to " O   SER A  95 " =    1.265
peak=   -3.648 closest distance to " O   HOH Z 377 " =    2.013
peak=   -3.640 closest distance to " OD2 ASP A 191 " =    1.571
peak=   -3.626 closest distance to " O   HOH Z 200 " =    3.827
peak=   -3.624 closest distance to " C   HIS A 108 " =    1.194
peak=   -3.624 closest distance to " O   HOH Z 435 " =    3.221
peak=   -3.606 closest distance to " O   HOH Z 211 " =    1.425
peak=   -3.597 closest distance to " O   PHE A 218 " =    1.382
peak=   -3.596 closest distance to " ND2 ASN A 209 " =    1.899
peak=   -3.573 closest distance to " CA  GLY A 133 " =    1.883
peak=   -3.569 closest distance to " O   HOH Z  90 " =    2.439
peak=   -3.568 closest distance to " O   HOH Z 372 " =    2.472
peak=   -3.566 closest distance to " O   HOH Z 416 " =    0.991
peak=   -3.565 closest distance to " CB  TYR A  15 " =    2.096
peak=   -3.564 closest distance to " O   SER A 135 " =    1.552
peak=   -3.563 closest distance to " O   HOH Z 111 " =    2.138
peak=   -3.560 closest distance to " OG  SER A  97 " =    2.110
peak=   -3.552 closest distance to " NE1 TRP A 179 " =    1.309
peak=   -3.544 closest distance to " CE3 TRP A 179 " =    1.279
peak=   -3.544 closest distance to " O   HOH Z  28 " =    1.978
peak=   -3.530 closest distance to " O   HOH Z 313 " =    1.497
peak=   -3.524 closest distance to " CB  ALA A 100 " =    1.887
peak=   -3.519 closest distance to " C   ALA A 114 " =    1.958
peak=   -3.517 closest distance to " CD2 LEU A 237 " =    2.567
peak=   -3.508 closest distance to " O   HOH Z 298 " =    1.093
peak=   -3.507 closest distance to " CD1 LEU A 101 " =    2.269
peak=   -3.499 closest distance to " C   ALA A 158 " =    1.518
peak=   -3.499 closest distance to " O   HOH Z  72 " =    1.636
peak=   -3.490 closest distance to " NH2 ARG A  79 " =    1.937
peak=   -3.484 closest distance to " CA  GLY A 241 " =    2.168
peak=   -3.483 closest distance to " O   SER A 216 " =    1.855
peak=   -3.482 closest distance to " O   HOH Z 266 " =    4.473
peak=   -3.481 closest distance to " O   HOH Z 236 " =    2.159
peak=   -3.479 closest distance to " O   HOH Z 418 " =    1.671
peak=   -3.479 closest distance to " N   GLN A  58 " =    1.261
peak=   -3.478 closest distance to " O   HOH Z 250 " =    1.324
peak=   -3.473 closest distance to " CG  ASP A 231 " =    0.822
peak=   -3.464 closest distance to " CG  ARG A 219 " =    2.385
peak=   -3.459 closest distance to " O   HOH Z 352 " =    1.700
peak=   -3.459 closest distance to " O   ALA A 180 " =    1.178
peak=   -3.459 closest distance to " O   TRP A  70 " =    1.428
peak=   -3.459 closest distance to " O   HOH Z 393 " =    2.920
peak=   -3.457 closest distance to " ND2 ASN A 285 " =    1.833
peak=   -3.457 closest distance to " N   GLN A  58 " =    1.788
peak=   -3.453 closest distance to " OE1 GLN A 223 " =    2.140
peak=   -3.450 closest distance to " O   ASN A 301 " =    1.409
peak=   -3.447 closest distance to " O   HOH Z 369 " =    2.238
peak=   -3.440 closest distance to " CZ3 TRP A 123 " =    1.817
peak=   -3.438 closest distance to " O   GLY A  80 " =    2.494
peak=   -3.436 closest distance to " CB  PRO A  90 " =    1.424
peak=   -3.432 closest distance to " CG  PHE A 283 " =    2.547
peak=   -3.429 closest distance to " CE3 TRP A 274 " =    2.398
peak=   -3.428 closest distance to " O   HOH Z 114 " =    0.827
peak=   -3.424 closest distance to " O   HOH Z 198 " =    1.978
peak=   -3.422 closest distance to " NE  ARG A  36 " =    1.820
peak=   -3.421 closest distance to " CD  GLN A 223 " =    1.543
peak=   -3.419 closest distance to " OG ASER A 134 " =    1.195
peak=   -3.418 closest distance to " O   HOH Z 351 " =    1.602
peak=   -3.417 closest distance to " O   HOH Z  24 " =    1.190
peak=   -3.411 closest distance to " CD  GLN A  88 " =    0.811
peak=   -3.404 closest distance to " CG  PRO A 163 " =    2.508
peak=   -3.402 closest distance to " O   PRO A 243 " =    2.411
peak=   -3.398 closest distance to " N   ARG A 159 " =    1.978
peak=   -3.398 closest distance to " O   HOH Z 359 " =    1.452
peak=   -3.398 closest distance to " O   ASP A 191 " =    1.874
peak=   -3.396 closest distance to " CB  PHE A 192 " =    1.693
peak=   -3.392 closest distance to " O   HOH Z 422 " =    0.844
peak=   -3.383 closest distance to " O   ILE A  49 " =    1.626
peak=   -3.378 closest distance to " O   ILE A 120 " =    1.892
peak=   -3.378 closest distance to " O   HOH Z   1 " =    1.267
peak=   -3.378 closest distance to " O   ALA A  10 " =    1.647
peak=   -3.370 closest distance to " O   PRO A 198 " =    1.286
peak=   -3.367 closest distance to " ND2 ASN A 249 " =    2.442
peak=   -3.359 closest distance to " C   ARG A 190 " =    1.035
peak=   -3.358 closest distance to " NE2 GLN A  58 " =    3.018
peak=   -3.356 closest distance to " OG  SER A 245 " =    1.258
peak=   -3.352 closest distance to " O   HOH Z  13 " =    1.764
peak=   -3.351 closest distance to " O   HOH Z  49 " =    1.660
peak=   -3.349 closest distance to " O   HOH Z 389 " =    1.976
peak=   -3.349 closest distance to " O   HOH Z 388 " =    2.110
peak=   -3.347 closest distance to " OG BSER A 134 " =    1.714
peak=   -3.346 closest distance to " ND2 ASN A 187 " =    1.375
peak=   -3.343 closest distance to " O   HOH Z 385 " =    2.299
peak=   -3.342 closest distance to " OE2 GLU A 152 " =    1.001
peak=   -3.339 closest distance to " OG  SER A   3 " =    1.637
peak=   -3.338 closest distance to " O   HOH Z 275 " =    1.850
peak=   -3.338 closest distance to " CG  GLU A 152 " =    1.589
peak=   -3.335 closest distance to " CB  ILE A  33 " =    2.818
peak=   -3.334 closest distance to " O   HOH Z  37 " =    1.645
peak=   -3.331 closest distance to " O   VAL A  67 " =    2.648
peak=   -3.331 closest distance to " CG2 ILE A  20 " =    2.911
peak=   -3.326 closest distance to " O   HOH Z   2 " =    1.058
peak=   -3.317 closest distance to " O   HOH Z 122 " =    2.358
peak=   -3.315 closest distance to " CB  MET A 185 " =    2.909
peak=   -3.314 closest distance to " O   HOH Z 427 " =    1.361
peak=   -3.312 closest distance to " CE  MET A 113 " =    2.256
peak=   -3.308 closest distance to " CD  LYS A 166 " =    2.337
peak=   -3.302 closest distance to " CD2 LEU A  25 " =    1.911
peak=   -3.301 closest distance to " O   HOH Z 364 " =    1.338
peak=   -3.300 closest distance to " OH  TYR A 214 " =    1.262
peak=   -3.298 closest distance to " CG  ARG A 259 " =    2.377
peak=   -3.286 closest distance to " CE3 TRP A  70 " =    2.058
peak=   -3.267 closest distance to " CD  GLN A  58 " =    0.978
peak=   -3.261 closest distance to " CE2 TYR A  30 " =    2.618
peak=   -3.255 closest distance to " CD2 LEU A 237 " =    2.656
peak=   -3.253 closest distance to " O   HOH Z 131 " =    4.078
peak=   -3.250 closest distance to " O   HOH Z 409 " =    5.589
peak=   -3.244 closest distance to " CB  ALA A 227 " =    2.367
peak=   -3.243 closest distance to " OG ASER A 216 " =    1.010
peak=   -3.242 closest distance to " CG2 VAL A 232 " =    1.953
peak=   -3.239 closest distance to " CB  SER A  62 " =    2.462
peak=   -3.234 closest distance to " OD1 ASN A 148 " =    1.756
peak=   -3.232 closest distance to " CB  ALA A   7 " =    1.865
peak=   -3.231 closest distance to " CB  ASP A 132 " =    2.363
peak=   -3.230 closest distance to " O   HOH Z 102 " =    1.598
peak=   -3.229 closest distance to " C   LEU A 143 " =    1.172
peak=   -3.229 closest distance to " OE2 GLU A 152 " =    2.197
peak=   -3.229 closest distance to " O   HOH Z  60 " =    2.158
peak=   -3.227 closest distance to " O   HOH Z  77 " =    1.762
peak=   -3.226 closest distance to " N   ALA A   1 " =    1.154
peak=   -3.223 closest distance to " N   GLN A  88 " =    1.749
peak=   -3.222 closest distance to " CB  ALA A  43 " =    2.185
peak=   -3.222 closest distance to " O   HOH Z 198 " =    1.802
peak=   -3.214 closest distance to " O   HOH Z 290 " =    1.253
peak=   -3.212 closest distance to " O   HOH Z 425 " =    1.013
peak=   -3.212 closest distance to " NH2AARG A 275 " =    5.367
peak=   -3.208 closest distance to " O   PRO A 163 " =    1.991
peak=   -3.205 closest distance to " O   HOH Z  93 " =    2.001
peak=   -3.204 closest distance to " O   HOH Z 231 " =    1.894
peak=   -3.204 closest distance to " CD  ARG A 139 " =    1.666
peak=   -3.202 closest distance to " O   HOH Z  71 " =    2.012
peak=   -3.201 closest distance to " OG  SER A 206 " =    1.907
peak=   -3.194 closest distance to " O   HOH Z 137 " =    1.493
peak=   -3.192 closest distance to " O   HOH Z 111 " =    1.154
peak=   -3.187 closest distance to " O   VAL A 125 " =    2.042
peak=   -3.185 closest distance to " CA  ALA A  34 " =    2.374
peak=   -3.182 closest distance to " O   HOH Z 298 " =    2.618
peak=   -3.181 closest distance to " O   HOH Z  52 " =    1.344
peak=   -3.177 closest distance to " CD2 TYR A 293 " =    2.139
peak=   -3.176 closest distance to " O   HOH Z 348 " =    1.746
peak=   -3.174 closest distance to " O   HOH Z 275 " =    1.523
peak=   -3.158 closest distance to " OG  SER A  26 " =    1.286
peak=   -3.156 closest distance to " CZ  TYR A 169 " =    1.811
peak=   -3.155 closest distance to " CB  PRO A 213 " =    2.088
peak=   -3.154 closest distance to " O   HOH Z 318 " =    1.842
peak=   -3.153 closest distance to " O   HOH Z 213 " =    1.223
peak=   -3.150 closest distance to " OE1 GLN A 183 " =    1.494
peak=   -3.149 closest distance to " O   HOH Z 414 " =    1.535
peak=   -3.144 closest distance to " O   HOH Z  51 " =    1.500
peak=   -3.144 closest distance to " CG1BVAL A  41 " =    2.976
peak=   -3.137 closest distance to " O   HOH Z 289 " =    1.802
peak=   -3.136 closest distance to " O   HOH Z 143 " =    2.195
peak=   -3.129 closest distance to " CB  ALA A 114 " =    2.381
peak=   -3.127 closest distance to " O   HOH Z 399 " =    2.109
peak=   -3.124 closest distance to " CB  CYS A 201 " =    2.110
peak=   -3.123 closest distance to " O   HOH Z  51 " =    1.174
peak=   -3.116 closest distance to " NE2 GLN A  55 " =    0.842
peak=   -3.101 closest distance to " NE2 GLN A 278 " =    1.864
peak=   -3.094 closest distance to " O   ALA A  34 " =    2.384
peak=   -3.092 closest distance to " O   HOH Z   4 " =    0.742
peak=   -3.091 closest distance to " CG  GLU A   2 " =    2.032
peak=   -3.089 closest distance to " O   HOH Z 426 " =    1.647
peak=   -3.084 closest distance to " OG  SER A  63 " =    1.279
peak=   -3.081 closest distance to " CG  ARG A  66 " =    1.960
peak=   -3.078 closest distance to " O   HOH Z 348 " =    2.126
peak=   -3.077 closest distance to " O   HOH Z 288 " =    1.363
peak=   -3.076 closest distance to " OD2 ASP A 171 " =    1.398
peak=   -3.065 closest distance to " CG2 THR A 178 " =    2.022
peak=   -3.050 closest distance to " CD1 ILE A 239 " =    2.262
peak=   -3.046 closest distance to " N   ALA A   1 " =    2.924
peak=   -3.039 closest distance to " O   SER A 146 " =    1.386
peak=   -3.030 closest distance to " CG  ARG A 259 " =    2.844

================= 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    :  0.4359 0.4310   6.255170e+00   6.245749e+00
   1_bss:  0.4234 0.4198   6.244568e+00   6.230242e+00
   1_xyz:  0.3502 0.3840   6.113094e+00   6.176027e+00
   1_adp:  0.3217 0.3941   6.069486e+00   6.183401e+00
   1_occ:  0.3213 0.3945   6.068766e+00   6.182988e+00
   2_bss:  0.3214 0.3939   6.070599e+00   6.183419e+00
   2_xyz:  0.2601 0.3274   5.894718e+00   6.045315e+00
   2_adp:  0.2418 0.3195   5.848475e+00   6.026108e+00
   2_occ:  0.2416 0.3191   5.848284e+00   6.026395e+00
   3_bss:  0.2413 0.3169   5.843795e+00   6.022305e+00
   3_xyz:  0.1939 0.2568   5.634256e+00   5.841185e+00
   3_adp:  0.1756 0.2344   5.547032e+00   5.765519e+00
   3_occ:  0.1753 0.2338   5.545680e+00   5.764085e+00
   4_bss:  0.1750 0.2324   5.542043e+00   5.758247e+00
   4_xyz:  0.1438 0.1964   5.364284e+00   5.602604e+00
   4_adp:  0.1380 0.1869   5.322850e+00   5.555066e+00
   4_occ:  0.1378 0.1868   5.322172e+00   5.554381e+00
   5_bss:  0.1381 0.1869   5.322628e+00   5.553573e+00
   5_xyz:  0.1210 0.1690   5.209296e+00   5.452367e+00
   5_adp:  0.1159 0.1677   5.183432e+00   5.436668e+00
   5_occ:  0.1159 0.1677   5.183299e+00   5.436561e+00
   5_bss:  0.1158 0.1676   5.182807e+00   5.436319e+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:  0.353  35.858  -3.429   3.216  -1.067   0.000  -0.000  -0.000
   1_xyz:  0.353  35.858  -3.429   3.216  -1.067   0.000  -0.000  -0.000
   1_adp:  0.353  35.858  -3.429   3.216  -1.067   0.000  -0.000  -0.000
   1_occ:  0.353  35.858  -3.429   3.216  -1.067   0.000  -0.000  -0.000
   2_bss:  0.356  57.397  -1.594   1.171  -0.556   0.000  -0.000  -0.000
   2_xyz:  0.356  57.397  -1.594   1.171  -0.556   0.000  -0.000  -0.000
   2_adp:  0.356  57.397  -1.594   1.171  -0.556   0.000  -0.000  -0.000
   2_occ:  0.356  57.397  -1.594   1.171  -0.556   0.000  -0.000  -0.000
   3_bss:  0.342  55.811  -1.145  -0.421  -0.310  -0.000  -0.000  -0.000
   3_xyz:  0.342  55.811  -1.145  -0.421  -0.310  -0.000  -0.000  -0.000
   3_adp:  0.342  55.811  -1.145  -0.421  -0.310  -0.000  -0.000  -0.000
   3_occ:  0.342  55.811  -1.145  -0.421  -0.310  -0.000  -0.000  -0.000
   4_bss:  0.322  46.375  -1.795  -1.596  -0.747  -0.000  -0.000  -0.000
   4_xyz:  0.322  46.375  -1.795  -1.596  -0.747  -0.000  -0.000  -0.000
   4_adp:  0.322  46.375  -1.795  -1.596  -0.747  -0.000  -0.000  -0.000
   4_occ:  0.322  46.375  -1.795  -1.596  -0.747  -0.000  -0.000  -0.000
   5_bss:  0.320  43.772  -1.901  -2.057  -0.883  -0.000  -0.000  -0.000
   5_xyz:  0.320  43.772  -1.901  -2.057  -0.883  -0.000  -0.000  -0.000
   5_adp:  0.320  43.772  -1.901  -2.057  -0.883  -0.000  -0.000  -0.000
   5_occ:  0.320  43.772  -1.901  -2.057  -0.883  -0.000  -0.000  -0.000
   5_bss:  0.318  46.507  -1.799  -2.060  -0.828  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.419 0.5175  0.7085    62333.157
   1_bss:  49.583 0.5267  0.7099    58850.061
   1_xyz:  44.285 0.5908  0.7786    46259.472
   1_adp:  44.712 0.5854  0.7717    47208.814
   1_occ:  44.724 0.5852  0.7714    47265.644
   2_bss:  44.436 0.5888  0.7820    46993.358
   2_xyz:  35.229 0.6984  0.9126    30675.335
   2_adp:  33.682 0.7165  0.9207    28878.266
   2_occ:  33.710 0.7161  0.9199    28877.926
   3_bss:  33.377 0.7197  0.9144    28276.176
   3_xyz:  25.730 0.8033  0.9859    17209.715
   3_adp:  23.178 0.8302  0.9925    14335.690
   3_occ:  23.129 0.8306  0.9922    14257.367
   4_bss:  22.983 0.8318  0.9661    14005.547
   4_xyz:  18.893 0.8715  0.9899     9934.377
   4_adp:  17.626 0.8839  0.9908     9077.943
   4_occ:  17.609 0.8840  0.9906     9056.712
   5_bss:  17.601 0.8841  0.9822     9047.009
   5_xyz:  15.440 0.9027  0.9912     7287.388
   5_adp:  15.053 0.9063  0.9859     7093.801
   5_occ:  15.050 0.9063  0.9859     7090.268
   5_bss:  15.039 0.9064  0.9881     7086.219
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.107   1.8555e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.107   1.8555e-01
   1_xyz:   1.538  0.011  0.101 15.425  0.006  4.104   1.1899e-01
   1_adp:   1.538  0.011  0.101 15.425  0.006  4.104   1.1899e-01
   1_occ:   1.538  0.011  0.101 15.425  0.006  4.104   1.1899e-01
   2_bss:   1.538  0.011  0.101 15.425  0.006  4.104   1.1899e-01
   2_xyz:   1.370  0.010  0.094 15.232  0.005  4.103   1.0491e-01
   2_adp:   1.370  0.010  0.094 15.232  0.005  4.103   1.0491e-01
   2_occ:   1.370  0.010  0.094 15.232  0.005  4.103   1.0491e-01
   3_bss:   1.370  0.010  0.094 15.232  0.005  4.103   1.0491e-01
   3_xyz:   1.093  0.008  0.077 14.423  0.004  4.108   7.2753e-02
   3_adp:   1.093  0.008  0.077 14.423  0.004  4.108   7.2753e-02
   3_occ:   1.093  0.008  0.077 14.423  0.004  4.108   7.2753e-02
   4_bss:   1.093  0.008  0.077 14.423  0.004  4.108   7.2753e-02
   4_xyz:   0.946  0.006  0.067 14.431  0.003  4.110   5.5085e-02
   4_adp:   0.946  0.006  0.067 14.431  0.003  4.110   5.5085e-02
   4_occ:   0.946  0.006  0.067 14.431  0.003  4.110   5.5085e-02
   5_bss:   0.946  0.006  0.067 14.431  0.003  4.110   5.5085e-02
   5_xyz:   1.056  0.007  0.075 14.641  0.004  4.107   6.5121e-02
   5_adp:   1.056  0.007  0.075 14.641  0.004  4.107   6.5121e-02
   5_occ:   1.056  0.007  0.075 14.641  0.004  4.107   6.5121e-02
   5_bss:   1.056  0.007  0.075 14.641  0.004  4.107   6.5121e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.681   2.3857e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.681   2.3857e-01
   1_xyz:   9.239  0.114  0.398 86.409  0.041  2.108   9.8324e-02
   1_adp:   9.239  0.114  0.398 86.409  0.041  2.108   9.8324e-02
   1_occ:   9.239  0.114  0.398 86.409  0.041  2.108   9.8324e-02
   2_bss:   9.239  0.114  0.398 86.409  0.041  2.108   9.8324e-02
   2_xyz:   9.652  0.050  0.334 80.962  0.049  2.015   1.0628e-01
   2_adp:   9.652  0.050  0.334 80.962  0.049  2.015   1.0628e-01
   2_occ:   9.652  0.050  0.334 80.962  0.049  2.015   1.0628e-01
   3_bss:   9.652  0.050  0.334 80.962  0.049  2.015   1.0628e-01
   3_xyz:   6.985  0.052  0.250 83.562  0.032  2.313   1.3977e-01
   3_adp:   6.985  0.052  0.250 83.562  0.032  2.313   1.3977e-01
   3_occ:   6.985  0.052  0.250 83.562  0.032  2.313   1.3977e-01
   4_bss:   6.985  0.052  0.250 83.562  0.032  2.313   1.3977e-01
   4_xyz:   7.064  0.043  0.212 79.220  0.030  2.307   4.3090e-02
   4_adp:   7.064  0.043  0.212 79.220  0.030  2.307   4.3090e-02
   4_occ:   7.064  0.043  0.212 79.220  0.030  2.307   4.3090e-02
   5_bss:   7.064  0.043  0.212 79.220  0.030  2.307   4.3090e-02
   5_xyz:   6.899  0.039  0.233 84.037  0.038  2.276   5.5264e-02
   5_adp:   6.899  0.039  0.233 84.037  0.038  2.276   5.5264e-02
   5_occ:   6.899  0.039  0.233 84.037  0.038  2.276   5.5264e-02
   5_bss:   6.899  0.039  0.233 84.037  0.038  2.276   5.5264e-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:  95.16   0.00  17.95  82.94   0.00  15.00  95.16   0.00  34.00
   1_occ:  95.16   0.00  17.95  82.94   0.00  15.00  95.16   0.00  34.00
   2_bss:  95.16   0.00  17.95  82.94   0.00  15.00  95.16   0.00  34.00
   2_xyz:  95.16   0.00  17.95  82.94   0.00  15.00  95.16   0.00  34.00
   2_adp:  90.06   0.00  17.94  84.76   0.00  14.38  90.06   0.00  37.32
   2_occ:  90.06   0.00  17.94  84.76   0.00  14.38  90.06   0.00  37.32
   3_bss:  90.06   0.00  17.94  84.76   0.00  14.38  90.06   0.00  37.32
   3_xyz:  90.06   0.00  17.94  84.76   0.00  14.38  90.06   0.00  37.32
   3_adp:  90.53   0.00  17.63  90.53   0.00  13.20  87.79   3.16  41.76
   3_occ:  90.53   0.00  17.63  90.53   0.00  13.20  87.79   3.16  41.76
   4_bss:  90.53   0.00  17.63  90.53   0.00  13.20  87.79   3.16  41.76
   4_xyz:  90.53   0.00  17.63  90.53   0.00  13.20  87.79   3.16  41.76
   4_adp:  90.16   0.00  17.17  90.16   0.00  12.75  86.22   3.92  41.28
   4_occ:  90.16   0.00  17.17  90.16   0.00  12.75  86.22   3.92  41.28
   5_bss:  90.16   0.00  17.17  90.16   0.00  12.75  86.22   3.92  41.28
   5_xyz:  90.16   0.00  17.17  90.16   0.00  12.75  86.22   3.92  41.28
   5_adp: 100.72   0.00  17.45 100.72   0.00  12.56  91.17   4.01  44.09
   5_occ: 100.72   0.00  17.45 100.72   0.00  12.56  91.17   4.01  44.09
   5_bss: 100.72   0.00  17.45 100.72   0.00  12.56  91.17   4.01  44.09
------------------------------------------------------------------------
 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:    1.601    0.021    0.312
   1_adp:    1.601    0.021    0.312
   1_occ:    1.601    0.021    0.312
   2_bss:    1.601    0.021    0.312
   2_xyz:    1.440    0.047    0.538
   2_adp:    1.440    0.047    0.538
   2_occ:    1.440    0.047    0.538
   3_bss:    1.440    0.047    0.538
   3_xyz:    1.646    0.050    0.665
   3_adp:    1.646    0.050    0.665
   3_occ:    1.646    0.050    0.665
   4_bss:    1.646    0.050    0.665
   4_xyz:    1.507    0.026    0.731
   4_adp:    1.507    0.026    0.731
   4_occ:    1.507    0.026    0.731
   5_bss:    1.507    0.026    0.731
   5_xyz:    1.585    0.050    0.775
   5_adp:    1.585    0.050    0.775
   5_occ:    1.585    0.050    0.775
   5_bss:    1.585    0.050    0.775
------------------------------------------------------------------------

CPU time actual refinement: 336.12


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_608/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_608/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_608/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_608/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_608/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 335.96 
  Macro-tasks:
    bulk solvent and scale       = 37.43  
    individual site refinement   = 146.39 
    weights calculation          = 29.20  
    collect and process          = 6.37   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 219.48 
  Micro-tasks:
    mask                            = 2.32   
    f_calc                          = 108.07 
    alpha_beta                      = 8.10   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 118.46 
    fmodel                         = 6.53   
    r_factors                      = 0.17   
    phase_errors                   = 10.63  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 255.66 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.678 micro seconds
Total CPU time: 5.82 minutes
from_scatterers_fft:    661 calls, 107.68 s
gradients_fft:          606 calls, 104.26 s

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

# Date 2008-01-16 Time 05:13:36 PST -0800 (1200489216.70 s)
Start R-work = 0.4359, R-free = 0.4310 (no bulk solvent and anisotropic scale)
Final R-work = 0.1370, R-free = 0.1838 (no bulk solvent and anisotropic scale)

Start R-work = 0.4234, R-free = 0.4198
Final R-work = 0.1158, R-free = 0.1676