# Date 2008-01-16 Time 03:52:55 PST -0800 (1200484375.41 s)
#phil __OFF__

Command line arguments: "../88.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29541
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 88

-------------------------------------------------------------------------------
  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: (68.4938, 47.6339, 84.2302, 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: 3.35, per 1000 atoms: 1.19


================================== 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: (68.4938, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8572 1.95055
Completeness in resolution range: 0.94839
Completeness with d_max=infinity: 0.945506

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8572
                             d_min =   1.9505

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: (68.4938, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8572 1.95055
Completeness in resolution range: 0.94839
Completeness with d_max=infinity: 0.945506

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8576 -  4.1742 [2169/2198]  1950   219  10.1%
  bin  2:  4.1742 -  3.3254 [2083/2106]  1875   208  10.0%
  bin  3:  3.3254 -  2.9086 [2052/2077]  1847   205  10.0%
  bin  4:  2.9086 -  2.6443 [2026/2045]  1828   198   9.8%
  bin  5:  2.6443 -  2.4557 [2016/2057]  1810   206  10.2%
  bin  6:  2.4557 -  2.3115 [2017/2045]  1823   194   9.6%
  bin  7:  2.3115 -  2.1961 [1987/2023]  1787   200  10.1%
  bin  8:  2.1961 -  2.1008 [2003/2045]  1804   199   9.9%
  bin  9:  2.1008 -  2.0201 [1963/2020]  1762   201  10.2%
  bin 10:  2.0201 -  1.9505 [1273/2039]  1144   129  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_88/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.18 -     1.92: 24
        1.92 -     2.67: 161
        2.67 -     3.41: 4501
        3.41 -     4.16: 9562
        4.16 -     4.90: 14689
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.175 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.247 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.352 3.040 -x+1,y-1/2,-z+1/2
  " CA  GLY A  91 " - " O   HOH Z 401 "  1.364 3.440 -x+1,y-1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.368 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28932 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_88/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_88/model_refine_001.geo

CPU time processing inputs: 9.05


============================ 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 = 68.49375 47.63395 84.23025 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 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4897   r_free= 0.4903   ksol= 0.00   Bsol= 0.00   scale= 0.891    |
|                                                                             |
| 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:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.290400                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8576 -  4.6559 0.99   1405  159 0.3932 0.4014      6.5926      6.6448|
|  2:  4.6559 -  3.7145 0.99   1354  148 0.4341 0.4158       6.827      6.8114|
|  3:  3.7145 -  3.2506 0.99   1331  149 0.4505 0.4527      6.6856      6.7811|
|  4:  3.2506 -  2.9559 0.99   1322  136 0.4732 0.4795      6.5267      6.5215|
|  5:  2.9559 -  2.7455 0.99   1308  151 0.5037 0.4738      6.3764        6.37|
|  6:  2.7455 -  2.5845 0.99   1304  147 0.5088 0.5180      6.2786      6.2061|
|  7:  2.5845 -  2.4557 0.98   1286  146 0.5313 0.4962      6.2668      6.1927|
|  8:  2.4557 -  2.3492 0.98   1314  138 0.5417 0.5538      6.1869       6.221|
|  9:  2.3492 -  2.2591 0.99   1276  145 0.5573 0.5606      6.1292      6.1594|
| 10:  2.2591 -  2.1814 0.98   1291  143 0.5384 0.5732      6.1234       6.139|
| 11:  2.1814 -  2.1134 0.97   1271  144 0.5522 0.5773      6.0404      6.0461|
| 12:  2.1134 -  2.0531 0.98   1287  143 0.5402 0.5464      5.9704      5.9985|
| 13:  2.0531 -  1.9992 0.93   1209  132 0.5373 0.5708      5.8913      5.8972|
| 14:  1.9992 -  1.9505 0.52    672   78 0.5523 0.5259      5.8636      5.7207|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8576 -  4.6559  1405   159  0.65  38.52   0.82     0.67      82959.04|
|  2:  4.6559 -  3.7145  1354   148  0.65  39.66   0.90     0.75     124370.30|
|  3:  3.7145 -  3.2506  1331   149  0.55  47.75   0.92     0.75     131186.59|
|  4:  3.2506 -  2.9559  1322   136  0.47  54.57   0.92     0.68     112937.19|
|  5:  2.9559 -  2.7455  1308   151  0.41  59.19   0.88     0.60      87559.79|
|  6:  2.7455 -  2.5845  1304   147  0.36  63.01   0.89     0.52      74583.10|
|  7:  2.5845 -  2.4557  1286   146  0.30  67.22   0.89     0.42      70530.97|
|  8:  2.4557 -  2.3492  1314   138  0.23  72.49   0.90     0.35      67808.57|
|  9:  2.3492 -  2.2591  1276   145  0.17  77.65   0.89     0.26      65783.29|
| 10:  2.2591 -  2.1814  1291   143  0.15  79.05   0.96     0.23      60394.01|
| 11:  2.1814 -  2.1134  1271   144  0.09  83.58   0.91     0.14      57462.11|
| 12:  2.1134 -  2.0531  1287   143  0.08  83.99   0.95     0.14      52722.48|
| 13:  2.0531 -  1.9992  1209   132  0.09  83.37   0.93     0.15      44677.10|
| 14:  1.9992 -  1.9505   672    78  0.17  77.61   0.93     0.24      34598.42|
|alpha:            min =        0.14 max =            0.75 mean =         0.43|
|beta:             min =    34598.42 max =       131186.59 mean =     78304.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.32|
|phase err.(work): min =        0.00 max =           90.00 mean =        65.41|
|phase err.(test): min =        0.00 max =           89.99 mean =        65.54|
|-----------------------------------------------------------------------------|

============================== 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 = 15.610559             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.056   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.211295              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.308   (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 |  1.175 -  1.548:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.548 -  1.920:       15 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.920 -  2.293:       48 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.293 -  2.665:      113 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.665 -  3.038:     2156 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.038 -  3.410:     2345 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.410 -  3.783:     4066 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.783 -  4.155:     5496 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.155 -  4.527:     6559 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.527 -  4.900:     8130 |
|-----------------------------------------------------------------------------|
|-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 |        0.266 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.106    4.900  1.175 |       1.764 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.370)------------------------------------------|
|    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 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4897   r_free= 0.4903   ksol= 0.00   Bsol= 0.00   scale= 0.891    |
|                                                                             |
| 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:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.290400                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4837   r_free= 0.4822   ksol= 0.33   Bsol= 20.00   scale= 0.925   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.79,0.82,1.25,0.00,0.00,0.00); trace/3= 0.43                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.286602                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.717847             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.813   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.802716              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.787   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4837      final r-factor (work) = 0.3831          |
| start r-factor (free) = 0.4822      final r-factor (free) = 0.4052          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.2402 = 12.72 * 0.50 * 6.2863 + 1.00 * 0.2661                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.5719 = 12.72 * 0.50 * 6.2009 + 1.00 * 0.1410                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3831      final r-factor (work) = 0.3434          |
| start r-factor (free) = 0.4052      final r-factor (free) = 0.4130          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.1845 = 1.80 * 1.00 * 6.2009 + 1.00 * 0.0061                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.9973 = 1.80 * 1.00 * 6.0858 + 1.00 * 0.0263                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.370)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.93   21.46    None  None   None       |
|    all(noH): 2823   0      0.00    93.93   21.46    None  None   None       |
|    Sol.    : 438    0      0.00    93.50   42.42    None  None   None       |
|    Mac.    : 2385   0      0.00    93.93   17.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.393:  793   |   5:    46.964 -  56.357:  156        |
|      1:     9.393 -  18.786:  799   |   6:    56.357 -  65.749:   75        |
|      2:    18.786 -  28.178:  454   |   7:    65.749 -  75.142:   44        |
|      3:    28.178 -  37.571:  291   |   8:    75.142 -  84.535:   28        |
|      4:    37.571 -  46.964:  172   |   9:    84.535 -  93.928:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3434 r_free = 0.4130             target_work(ml) = 6.093         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3429 r_free = 0.4128             target_work(ml) = 6.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3429   r_free= 0.4128   ksol= 0.33   Bsol= 20.00   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.79,0.82,1.25,0.00,0.00,0.00); trace/3= 0.43                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.092410                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3411   r_free= 0.4096   ksol= 0.33   Bsol= 46.79   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.77,0.80,0.88,0.00,0.00,0.00); trace/3= 0.30                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.088712                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.073892             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.704   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.797544              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.806  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3411      final r-factor (work) = 0.2696          |
| start r-factor (free) = 0.4096      final r-factor (free) = 0.3301          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.7895 = 10.07 * 0.50 * 6.0848 + 1.00 * 0.1408                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.3508 = 10.07 * 0.50 * 6.0076 + 1.00 * 0.0909                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2696      final r-factor (work) = 0.2437          |
| start r-factor (free) = 0.3301      final r-factor (free) = 0.3078          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8172 = 0.80 * 1.00 * 6.0076 + 1.00 * 0.0259                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6817 = 0.80 * 1.00 * 5.8510 + 1.00 * 0.0153                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.370)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.70   19.85    None  None   None       |
|    all(noH): 2823   0      0.00    98.70   19.85    None  None   None       |
|    Sol.    : 438    0      2.91    98.70   42.88    None  None   None       |
|    Mac.    : 2385   0      0.00    94.39   15.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.870:  938   |   5:    49.350 -  59.220:  112        |
|      1:     9.870 -  19.740:  896   |   6:    59.220 -  69.090:   70        |
|      2:    19.740 -  29.610:  384   |   7:    69.090 -  78.960:   29        |
|      3:    29.610 -  39.480:  226   |   8:    78.960 -  88.830:   17        |
|      4:    39.480 -  49.350:  146   |   9:    88.830 -  98.700:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2437 r_free = 0.3078             target_work(ml) = 5.819         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2434 r_free = 0.3075             target_work(ml) = 5.818         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2434   r_free= 0.3075   ksol= 0.33   Bsol= 46.79   scale= 1.064   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.77,0.80,0.88,0.00,0.00,0.00); trace/3= 0.30                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.817690                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2434   r_free= 0.3053   ksol= 0.32   Bsol= 45.69   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.59,-0.15,-0.11,-0.00,-0.00,-0.00); trace/3= -0.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.815190                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.460004              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.921   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 7.331712              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.965  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2434      final r-factor (work) = 0.1798          |
| start r-factor (free) = 0.3053      final r-factor (free) = 0.2380          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.9186 = 7.46 * 0.50 * 5.8519 + 1.00 * 0.0909                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.3636 = 7.46 * 0.50 * 5.7065 + 1.00 * 0.0784                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1798      final r-factor (work) = 0.1581          |
| start r-factor (free) = 0.2380      final r-factor (free) = 0.2159          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 41.8537 = 7.33 * 1.00 * 5.7065 + 1.00 * 0.0154                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 40.3781 = 7.33 * 1.00 * 5.5053 + 1.00 * 0.0149                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.370)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.10  19.40    None  None   None       |
|    all(noH): 2823   0      0.00    113.10  19.40    None  None   None       |
|    Sol.    : 438    0      3.91    113.10  47.58    None  None   None       |
|    Mac.    : 2385   0      0.00    104.36  14.23    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.310: 1267   |   5:    56.548 -  67.858:   91        |
|      1:    11.310 -  22.619:  892   |   6:    67.858 -  79.168:   67        |
|      2:    22.619 -  33.929:  214   |   7:    79.168 -  90.477:   26        |
|      3:    33.929 -  45.239:  125   |   8:    90.477 - 101.787:    9        |
|      4:    45.239 -  56.548:  126   |   9:   101.787 - 113.097:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1581 r_free = 0.2159             target_work(ml) = 5.446         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1580 r_free = 0.2159             target_work(ml) = 5.446         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1580   r_free= 0.2159   ksol= 0.32   Bsol= 45.69   scale= 1.053   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.59,-0.15,-0.11,-0.00,-0.00,-0.00); trace/3= -0.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.446410                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1580   r_free= 0.2141   ksol= 0.32   Bsol= 41.05   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-1.09,-1.37,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.444008                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.377481              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.056  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.387050              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.198   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1580      final r-factor (work) = 0.1379          |
| start r-factor (free) = 0.2141      final r-factor (free) = 0.1931          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6333 = 2.38 * 0.50 * 5.5144 + 1.00 * 0.0781                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4687 = 2.38 * 0.50 * 5.3943 + 1.00 * 0.0563                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1379      final r-factor (work) = 0.1314          |
| start r-factor (free) = 0.1931      final r-factor (free) = 0.1831          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1027 = 0.39 * 1.00 * 5.3943 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0706 = 0.39 * 1.00 * 5.3222 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.370)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.09    105.49  18.14    None  None   None       |
|    all(noH): 2823   0      1.09    105.49  18.14    None  None   None       |
|    Sol.    : 438    0      2.80    102.16  44.16    None  None   None       |
|    Mac.    : 2385   0      1.09    105.49  13.37    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.087 -  11.527: 1354   |   5:    53.286 -  63.726:   90        |
|      1:    11.527 -  21.967:  873   |   6:    63.726 -  74.166:   49        |
|      2:    21.967 -  32.406:  176   |   7:    74.166 -  84.606:   25        |
|      3:    32.406 -  42.846:  127   |   8:    84.606 -  95.046:   10        |
|      4:    42.846 -  53.286:  113   |   9:    95.046 - 105.485:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1314 r_free = 0.1831             target_work(ml) = 5.291         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1312 r_free = 0.1829             target_work(ml) = 5.290         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1312   r_free= 0.1829   ksol= 0.32   Bsol= 41.05   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-1.09,-1.37,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.289638                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1318   r_free= 0.1834   ksol= 0.32   Bsol= 41.94   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-1.37,-1.66,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.291575                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.964003              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 133.628  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.204370              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.508  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1318      final r-factor (work) = 0.1189          |
| start r-factor (free) = 0.1834      final r-factor (free) = 0.1721          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9455 = 2.96 * 0.50 * 5.3234 + 1.00 * 0.0563                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8494 = 2.96 * 0.50 * 5.2513 + 1.00 * 0.0670                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1189      final r-factor (work) = 0.1181          |
| start r-factor (free) = 0.1721      final r-factor (free) = 0.1689          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0838 = 0.20 * 1.00 * 5.2513 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0730 = 0.20 * 1.00 * 5.2096 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.370)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.39    102.56  17.17    None  None   None       |
|    all(noH): 2823   0      2.39    102.56  17.17    None  None   None       |
|    Sol.    : 438    0      4.31    93.66   40.69    None  None   None       |
|    Mac.    : 2385   0      2.39    102.56  12.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.394 -  12.411: 1564   |   5:    52.479 -  62.496:   76        |
|      1:    12.411 -  22.428:  713   |   6:    62.496 -  72.512:   31        |
|      2:    22.428 -  32.445:  164   |   7:    72.512 -  82.529:   12        |
|      3:    32.445 -  42.462:  135   |   8:    82.529 -  92.546:    7        |
|      4:    42.462 -  52.479:  116   |   9:    92.546 - 102.563:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1181 r_free = 0.1689             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1179 r_free = 0.1689             target_work(ml) = 5.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1689   ksol= 0.32   Bsol= 41.94   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-1.37,-1.66,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.199083                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8576 -  4.6559 0.99   1405  159 0.0984 0.1354      5.3914      5.5768|
|  2:  4.6559 -  3.7145 0.99   1354  148 0.0866 0.1095      5.4513      5.6489|
|  3:  3.7145 -  3.2506 0.99   1331  149 0.1075 0.1660       5.493       5.899|
|  4:  3.2506 -  2.9559 0.99   1322  136 0.1324 0.1646      5.5123        5.68|
|  5:  2.9559 -  2.7455 0.99   1308  151 0.1387 0.1732      5.3797      5.5441|
|  6:  2.7455 -  2.5845 0.99   1304  147 0.1383 0.2269      5.2966      5.5518|
|  7:  2.5845 -  2.4557 0.98   1286  146 0.1275 0.1735      5.2083      5.3993|
|  8:  2.4557 -  2.3492 0.98   1314  138 0.1261 0.1768      5.1432      5.3672|
|  9:  2.3492 -  2.2591 0.99   1276  145 0.1287 0.1971      5.0901      5.3481|
| 10:  2.2591 -  2.1814 0.98   1291  143 0.1192 0.1918      5.0409      5.2889|
| 11:  2.1814 -  2.1134 0.97   1271  144 0.1214 0.1877      4.9783      5.2638|
| 12:  2.1134 -  2.0531 0.98   1287  143 0.1205 0.1919      4.9163      5.1838|
| 13:  2.0531 -  1.9992 0.93   1209  132 0.1207 0.1848      4.8381      5.1099|
| 14:  1.9992 -  1.9505 0.52    672   78 0.1158 0.1819      4.7605      4.9714|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8576 -  4.6559  1405   159  0.94   9.54   0.98     0.96       7745.58|
|  2:  4.6559 -  3.7145  1354   148  0.95   8.36   1.03     1.01       9418.47|
|  3:  3.7145 -  3.2506  1331   149  0.93  11.60   1.04     1.03      10724.22|
|  4:  3.2506 -  2.9559  1322   136  0.91  14.92   1.02     1.01      11582.84|
|  5:  2.9559 -  2.7455  1308   151  0.89  17.40   1.01     0.98       9510.49|
|  6:  2.7455 -  2.5845  1304   147  0.89  17.72   0.99     0.95       8316.43|
|  7:  2.5845 -  2.4557  1286   146  0.90  16.68   0.99     0.95       6917.20|
|  8:  2.4557 -  2.3492  1314   138  0.90  16.77   1.01     0.99       6383.65|
|  9:  2.3492 -  2.2591  1276   145  0.89  17.29   1.01     0.97       5668.83|
| 10:  2.2591 -  2.1814  1291   143  0.89  16.74   1.00     0.97       5211.61|
| 11:  2.1814 -  2.1134  1271   144  0.89  17.30   1.01     0.97       4803.02|
| 12:  2.1134 -  2.0531  1287   143  0.90  16.43   1.01     1.00       4236.84|
| 13:  2.0531 -  1.9992  1209   132  0.89  17.13   1.00     1.00       3695.94|
| 14:  1.9992 -  1.9505   672    78  0.90  16.52   0.99     0.95       3099.09|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     3099.09 max =        11582.84 mean =      7138.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.19|
|phase err.(test): min =        0.00 max =           88.71 mean =        14.82|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1689   ksol= 0.32   Bsol= 41.85   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-1.28,-1.53,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.199373                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1689   ksol= 0.32   Bsol= 41.85   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-1.28,-1.53,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.199373                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8576 -  4.6559 0.99   1405  159 0.0987 0.1361      5.3955      5.5805|
|  2:  4.6559 -  3.7145 0.99   1354  148 0.0865 0.1093      5.4511      5.6471|
|  3:  3.7145 -  3.2506 0.99   1331  149 0.1074 0.1659      5.4921      5.8987|
|  4:  3.2506 -  2.9559 0.99   1322  136 0.1324 0.1646      5.5122        5.68|
|  5:  2.9559 -  2.7455 0.99   1308  151 0.1387 0.1732      5.3797      5.5438|
|  6:  2.7455 -  2.5845 0.99   1304  147 0.1383 0.2268      5.2966      5.5518|
|  7:  2.5845 -  2.4557 0.98   1286  146 0.1275 0.1735      5.2083      5.3994|
|  8:  2.4557 -  2.3492 0.98   1314  138 0.1260 0.1769      5.1433      5.3675|
|  9:  2.3492 -  2.2591 0.99   1276  145 0.1287 0.1971      5.0901      5.3483|
| 10:  2.2591 -  2.1814 0.98   1291  143 0.1192 0.1919      5.0411      5.2893|
| 11:  2.1814 -  2.1134 0.97   1271  144 0.1214 0.1877      4.9784      5.2639|
| 12:  2.1134 -  2.0531 0.98   1287  143 0.1206 0.1920      4.9165       5.184|
| 13:  2.0531 -  1.9992 0.93   1209  132 0.1208 0.1848      4.8383      5.1098|
| 14:  1.9992 -  1.9505 0.52    672   78 0.1158 0.1819      4.7605      4.9713|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8576 -  4.6559  1405   159  0.94   9.59   0.98     0.96       7844.74|
|  2:  4.6559 -  3.7145  1354   148  0.95   8.38   1.03     1.01       9439.05|
|  3:  3.7145 -  3.2506  1331   149  0.93  11.58   1.04     1.03      10692.89|
|  4:  3.2506 -  2.9559  1322   136  0.91  14.91   1.02     1.01      11577.56|
|  5:  2.9559 -  2.7455  1308   151  0.89  17.40   1.01     0.98       9506.46|
|  6:  2.7455 -  2.5845  1304   147  0.89  17.72   0.99     0.95       8315.07|
|  7:  2.5845 -  2.4557  1286   146  0.90  16.68   0.99     0.95       6918.15|
|  8:  2.4557 -  2.3492  1314   138  0.90  16.78   1.01     0.99       6386.56|
|  9:  2.3492 -  2.2591  1276   145  0.89  17.29   1.01     0.97       5672.23|
| 10:  2.2591 -  2.1814  1291   143  0.89  16.74   1.01     0.97       5212.59|
| 11:  2.1814 -  2.1134  1271   144  0.89  17.30   1.01     0.97       4804.14|
| 12:  2.1134 -  2.0531  1287   143  0.90  16.43   1.01     1.01       4238.55|
| 13:  2.0531 -  1.9992  1209   132  0.89  17.13   1.01     1.00       3696.47|
| 14:  1.9992 -  1.9505   672    78  0.90  16.52   1.00     0.96       3097.92|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     3097.92 max =        11577.56 mean =      7146.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.20|
|phase err.(test): min =        0.00 max =           88.81 mean =        14.83|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.370)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.31    102.48  17.08    None  None   None       |
|    all(noH): 2823   0      2.31    102.48  17.08    None  None   None       |
|    Sol.    : 438    0      4.22    93.58   40.60    None  None   None       |
|    Mac.    : 2385   0      2.31    102.48  12.76    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:     2.307 -  12.324: 1564   |   5:    52.392 -  62.409:   76        |
|      1:    12.324 -  22.341:  713   |   6:    62.409 -  72.426:   31        |
|      2:    22.341 -  32.358:  164   |   7:    72.426 -  82.442:   12        |
|      3:    32.358 -  42.375:  135   |   8:    82.442 -  92.459:    7        |
|      4:    42.375 -  52.392:  116   |   9:    92.459 - 102.476:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 326         
Filter by distance & map next to the model:
   mapped sites are within: 0.580 - 5.970
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 324 from: 326
   mapped sites are within: 0.723 - 5.970

peak=    9.333 closest distance to " CB  SER A 216 " =    1.131
peak=    9.325 closest distance to " O   HOH Z 138 " =    1.228
peak=    7.694 closest distance to " O   HOH Z  92 " =    2.015
peak=    7.579 closest distance to " O   HOH Z 178 " =    1.334
peak=    6.664 closest distance to " O   HOH Z 199 " =    1.501
peak=    5.627 closest distance to " CB  ARG A 275 " =    0.961
peak=    5.592 closest distance to " O   HOH Z  52 " =    1.533
peak=    5.570 closest distance to " O   HOH Z 124 " =    1.658
peak=    5.517 closest distance to " O   HOH Z 278 " =    1.460
peak=    5.293 closest distance to " O   HOH Z 404 " =    1.178
peak=    5.184 closest distance to " NH2 ARG A  56 " =    2.181
peak=    5.152 closest distance to " O   HOH Z 193 " =    1.931
peak=    5.130 closest distance to " O   HOH Z 402 " =    1.536
peak=    5.110 closest distance to " CG  PRO A  54 " =    1.209
peak=    5.091 closest distance to " O   HOH Z  65 " =    1.110
peak=    5.065 closest distance to " O   HOH Z  97 " =    1.636
peak=    5.061 closest distance to " O   HOH Z  80 " =    1.769
peak=    4.981 closest distance to " O   HOH Z 132 " =    1.845
peak=    4.954 closest distance to " O   HOH Z 406 " =    1.492
peak=    4.915 closest distance to " O   HOH Z 247 " =    1.410
peak=    4.882 closest distance to " O   HOH Z 389 " =    1.919
peak=    4.849 closest distance to " O   HOH Z 234 " =    3.620
peak=    4.840 closest distance to " C   PRO A 198 " =    1.602
peak=    4.818 closest distance to " CG  PRO A 213 " =    1.291
peak=    4.792 closest distance to " CB  SER A  63 " =    1.195
peak=    4.784 closest distance to " O   HOH Z 214 " =    1.273
peak=    4.774 closest distance to " CB  ASN A 187 " =    1.908
peak=    4.755 closest distance to " O   SER A  87 " =    2.170
peak=    4.740 closest distance to " O   HOH Z 272 " =    1.892
peak=    4.737 closest distance to " CG AARG A 275 " =    1.145
peak=    4.669 closest distance to " O   HOH Z 108 " =    1.512
peak=    4.659 closest distance to " O   HOH Z 117 " =    1.224
peak=    4.594 closest distance to " O   HOH Z 142 " =    1.671
peak=    4.509 closest distance to " CB  GLN A 223 " =    1.415
peak=    4.496 closest distance to " O   HOH Z  97 " =    2.044
peak=    4.445 closest distance to " CA  TYR A  30 " =    1.031
peak=    4.405 closest distance to " O   HOH Z 117 " =    2.082
peak=    4.369 closest distance to " CB  ARG A 275 " =    1.229
peak=    4.354 closest distance to " O   HOH Z  43 " =    1.435
peak=    4.352 closest distance to " O   HOH Z 411 " =    3.563
peak=    4.348 closest distance to " O   HOH Z 334 " =    1.509
peak=    4.329 closest distance to " O   HOH Z 154 " =    1.735
peak=    4.327 closest distance to " O   HOH Z 408 " =    1.830
peak=    4.324 closest distance to " O   HOH Z 128 " =    1.994
peak=    4.286 closest distance to " O   HOH Z 261 " =    1.765
peak=    4.284 closest distance to " O   HOH Z 155 " =    1.809
peak=    4.263 closest distance to " O   HOH Z 209 " =    2.390
peak=    4.249 closest distance to " O   HOH Z  85 " =    1.605
peak=    4.246 closest distance to " NE2 GLN A  11 " =    1.067
peak=    4.243 closest distance to " CB  SER A   3 " =    1.277
peak=    4.241 closest distance to " O   HOH Z 163 " =    1.463
peak=    4.237 closest distance to " O   HOH Z 316 " =    2.807
peak=    4.230 closest distance to " O   HOH Z 232 " =    2.228
peak=    4.225 closest distance to " CG  GLN A  77 " =    1.012
peak=    4.216 closest distance to " O   HOH Z 145 " =    2.090
peak=    4.197 closest distance to " O   HOH Z 394 " =    1.547
peak=    4.180 closest distance to " O   HOH Z  63 " =    1.905
peak=    4.174 closest distance to " CD  ARG A 269 " =    1.035
peak=    4.166 closest distance to " O   HOH Z 163 " =    2.097
peak=    4.150 closest distance to " CB  GLN A 183 " =    1.236
peak=    4.108 closest distance to " CB  GLU A 152 " =    1.136
peak=    4.108 closest distance to " CG1 ILE A  33 " =    1.198
peak=    4.101 closest distance to " O   HOH Z 368 " =    2.028
peak=    4.094 closest distance to " OE1 GLU A   2 " =    2.357
peak=    4.080 closest distance to " O   HOH Z 137 " =    1.419
peak=    4.069 closest distance to " O   HOH Z  47 " =    1.765
peak=    4.055 closest distance to " CG  ARG A  66 " =    1.182
peak=    4.053 closest distance to " NH2AARG A 145 " =    2.043
peak=    4.040 closest distance to " O   HOH Z  40 " =    1.718
peak=    4.032 closest distance to " O   HOH Z 403 " =    2.126
peak=    4.021 closest distance to " O   HOH Z 134 " =    1.932
peak=    4.020 closest distance to " O   HOH Z 279 " =    2.144
peak=    4.013 closest distance to " O   HOH Z 260 " =    1.482
peak=    4.004 closest distance to " O   HOH Z 416 " =    1.253
peak=    3.992 closest distance to " O   HOH Z  68 " =    1.803
peak=    3.991 closest distance to " O   HOH Z 128 " =    2.074
peak=    3.979 closest distance to " O   HOH Z  15 " =    2.179
peak=    3.964 closest distance to " O   HOH Z 130 " =    2.549
peak=    3.962 closest distance to " O   HOH Z 118 " =    1.424
peak=    3.949 closest distance to " O   HOH Z 114 " =    1.515
peak=    3.942 closest distance to " CB  ASN A 148 " =    1.375
peak=    3.936 closest distance to " O   HOH Z 156 " =    3.317
peak=    3.921 closest distance to " O   HOH Z  35 " =    2.243
peak=    3.918 closest distance to " O   HOH Z 227 " =    1.598
peak=    3.918 closest distance to " O   HOH Z  78 " =    1.979
peak=    3.911 closest distance to " N   ASN A  39 " =    1.327
peak=    3.906 closest distance to " O   HOH Z 315 " =    1.894
peak=    3.900 closest distance to " NZ  LYS A 117 " =    3.111
peak=    3.896 closest distance to " O   HOH Z 203 " =    1.845
peak=    3.891 closest distance to " O   HOH Z 127 " =    1.227
peak=    3.884 closest distance to " O   HOH Z 327 " =    1.930
peak=    3.878 closest distance to " O   HOH Z 192 " =    1.846
peak=    3.877 closest distance to " O   HOH Z 154 " =    2.138
peak=    3.874 closest distance to " O   HOH Z  59 " =    1.781
peak=    3.873 closest distance to " NH2BARG A 145 " =    2.137
peak=    3.869 closest distance to " O   HOH Z 326 " =    1.583
peak=    3.869 closest distance to " O   HOH Z 427 " =    2.644
peak=    3.851 closest distance to " CB  ARG A  79 " =    1.383
peak=    3.849 closest distance to " O   HOH Z 132 " =    1.962
peak=    3.845 closest distance to " O   HOH Z 298 " =    1.894
peak=    3.841 closest distance to " O   HOH Z 111 " =    3.449
peak=    3.832 closest distance to " CB  VAL A 265 " =    1.214
peak=    3.829 closest distance to " O   HOH Z 207 " =    1.645
peak=    3.818 closest distance to " NH1AARG A 275 " =    1.172
peak=    3.814 closest distance to " CG  PRO A  90 " =    1.222
peak=    3.795 closest distance to " O   HOH Z 345 " =    1.927
peak=    3.792 closest distance to " CG  PRO A 198 " =    1.364
peak=    3.790 closest distance to " CE  LYS A 119 " =    1.162
peak=    3.789 closest distance to " O   HOH Z 426 " =    1.409
peak=    3.780 closest distance to " CB  PRO A 163 " =    3.869
peak=    3.758 closest distance to " ND2 ASN A 187 " =    1.587
peak=    3.754 closest distance to " O   HOH Z 336 " =    1.651
peak=    3.746 closest distance to " O   HOH Z 427 " =    3.084
peak=    3.744 closest distance to " O   HOH Z 287 " =    1.913
peak=    3.740 closest distance to " O   HOH Z 369 " =    2.149
peak=    3.735 closest distance to " O   HOH Z  30 " =    2.014
peak=    3.734 closest distance to " CB  GLU A 128 " =    1.334
peak=    3.731 closest distance to " O   HOH Z 303 " =    2.094
peak=    3.729 closest distance to " O   HOH Z  78 " =    2.542
peak=    3.722 closest distance to " O   HOH Z 414 " =    1.638
peak=    3.715 closest distance to " CB  SER A 141 " =    1.000
peak=    3.713 closest distance to " CB  TYR A 169 " =    0.723
peak=    3.708 closest distance to " CE BMET A  47 " =    1.350
peak=    3.704 closest distance to " O   HOH Z 421 " =    1.887
peak=    3.703 closest distance to " CB  TRP A 179 " =    1.093
peak=    3.699 closest distance to " O   HOH Z 144 " =    2.000
peak=    3.679 closest distance to " CA  ALA A  21 " =    1.119
peak=    3.676 closest distance to " O   HOH Z 425 " =    1.460
peak=    3.674 closest distance to " OD1 ASP A 253 " =    1.904
peak=    3.667 closest distance to " CG1BVAL A  72 " =    1.560
peak=    3.659 closest distance to " NZ  LYS A 119 " =    1.452
peak=    3.652 closest distance to " O   HOH Z 287 " =    1.908
peak=    3.650 closest distance to " O   HOH Z 194 " =    1.814
peak=    3.650 closest distance to " CG2BVAL A  41 " =    0.892
peak=    3.648 closest distance to " O   HOH Z 313 " =    1.557
peak=    3.648 closest distance to " O   HOH Z 274 " =    2.281
peak=    3.642 closest distance to " O   HOH Z 108 " =    2.015
peak=    3.639 closest distance to " O   HOH Z 132 " =    2.400
peak=    3.628 closest distance to " O   HOH Z 274 " =    1.716
peak=    3.627 closest distance to " OE1 GLN A  11 " =    1.833
peak=    3.625 closest distance to " O   HOH Z 346 " =    1.444
peak=    3.622 closest distance to " CD  ARG A 139 " =    1.482
peak=    3.618 closest distance to " CD BLYS A 290 " =    1.118
peak=    3.608 closest distance to " CH2 TRP A 274 " =    2.141
peak=    3.606 closest distance to " CG  LYS A 166 " =    1.582
peak=    3.605 closest distance to " O   HOH Z  51 " =    2.027
peak=    3.601 closest distance to " O   HOH Z  66 " =    2.264
peak=    3.599 closest distance to " O   HOH Z 402 " =    2.625
peak=    3.582 closest distance to " O   HOH Z 337 " =    3.517
peak=    3.579 closest distance to " O   HOH Z 147 " =    1.708
peak=    3.577 closest distance to " CD  GLN A 194 " =    1.626
peak=    3.562 closest distance to " O   HOH Z  11 " =    1.331
peak=    3.559 closest distance to " CB  ASP A 191 " =    1.228
peak=    3.559 closest distance to " O   HOH Z  19 " =    1.475
peak=    3.557 closest distance to " CD  PRO A  54 " =    1.038
peak=    3.555 closest distance to " O   GLY A  23 " =    2.261
peak=    3.555 closest distance to " OD1 ASN A  60 " =    1.218
peak=    3.554 closest distance to " O   HOH Z  54 " =    1.560
peak=    3.552 closest distance to " NZ  LYS A 117 " =    1.099
peak=    3.539 closest distance to " O   HOH Z 245 " =    1.443
peak=    3.538 closest distance to " O   HOH Z 357 " =    1.657
peak=    3.536 closest distance to " O   HOH Z 425 " =    1.851
peak=    3.536 closest distance to " CA  LYS A 117 " =    1.280
peak=    3.534 closest distance to " CB  ALA A 100 " =    1.117
peak=    3.533 closest distance to " O   HOH Z  44 " =    1.967
peak=    3.527 closest distance to " O   HOH Z 343 " =    2.194
peak=    3.521 closest distance to " CD  LYS A  76 " =    1.639
peak=    3.518 closest distance to " O   HOH Z 428 " =    3.888
peak=    3.515 closest distance to " CD  ARG A 195 " =    0.939
peak=    3.515 closest distance to " O   HOH Z 365 " =    2.610
peak=    3.515 closest distance to " O   HOH Z 214 " =    2.873
peak=    3.512 closest distance to " OD2 ASP A 286 " =    2.622
peak=    3.511 closest distance to " CB  ARG A 139 " =    1.056
peak=    3.510 closest distance to " OH  TYR A  30 " =    1.143
peak=    3.503 closest distance to " CA  GLU A  37 " =    1.000
peak=    3.502 closest distance to " NH2AARG A 190 " =    1.460
peak=    3.501 closest distance to " CA  ASN A 176 " =    1.096
peak=    3.500 closest distance to " O   HOH Z 236 " =    1.547
peak=    3.496 closest distance to " O   GLY A 211 " =    1.449
peak=    3.492 closest distance to " O   HOH Z 155 " =    2.647
peak=    3.485 closest distance to " CB  LEU A 228 " =    1.244
peak=    3.480 closest distance to " O   HOH Z 345 " =    2.220
peak=    3.476 closest distance to " O   HOH Z 291 " =    1.666
peak=    3.463 closest distance to " O   HOH Z 215 " =    1.501
peak=    3.462 closest distance to " O   HOH Z 136 " =    1.057
peak=    3.462 closest distance to " O   MET A 105 " =    1.847
peak=    3.459 closest distance to " CG2 VAL A 197 " =    1.112
peak=    3.458 closest distance to " CD AARG A 102 " =    2.255
peak=    3.458 closest distance to " CB  PRO A  90 " =    2.055
peak=    3.453 closest distance to " O   GLY A  91 " =    1.466
peak=    3.452 closest distance to " O   HOH Z 284 " =    2.715
peak=    3.449 closest distance to " O   HOH Z 189 " =    1.677
peak=    3.447 closest distance to " CB  SER A  26 " =    1.688
peak=    3.447 closest distance to " O   HOH Z 173 " =    2.147
peak=    3.426 closest distance to " O   HOH Z 188 " =    1.089
peak=    3.424 closest distance to " CD2 TRP A 179 " =    1.462
peak=    3.423 closest distance to " O   HOH Z  10 " =    1.818
peak=    3.416 closest distance to " CD2 PHE A 225 " =    1.127
peak=    3.413 closest distance to " OD1 ASP A 238 " =    0.973
peak=    3.413 closest distance to " O   HOH Z 173 " =    1.790
peak=    3.411 closest distance to " O   HOH Z 249 " =    1.210
peak=    3.409 closest distance to " O   HOH Z 124 " =    2.739
peak=    3.401 closest distance to " CD  LYS A 166 " =    1.400
peak=    3.398 closest distance to " O   HOH Z  88 " =    3.428
peak=    3.383 closest distance to " OG BSER A 210 " =    1.333
peak=    3.383 closest distance to " O   ALA A 165 " =    1.240
peak=    3.382 closest distance to " O   HOH Z 189 " =    1.530
peak=    3.380 closest distance to " CA  THR A 221 " =    0.985
peak=    3.377 closest distance to " O   HOH Z 109 " =    1.422
peak=    3.374 closest distance to " CZ AARG A 102 " =    1.669
peak=    3.371 closest distance to " O   HOH Z  59 " =    1.795
peak=    3.366 closest distance to " CB  ARG A 190 " =    1.832
peak=    3.366 closest distance to " N   ASP A 162 " =    1.317
peak=    3.365 closest distance to " CA  ASP A 162 " =    1.055
peak=    3.364 closest distance to " OE1 GLN A  58 " =    5.970
peak=    3.364 closest distance to " O   ASN A 217 " =    1.168
peak=    3.359 closest distance to " O   HOH Z 261 " =    2.011
peak=    3.358 closest distance to " O   HOH Z 193 " =    2.374
peak=    3.358 closest distance to " CB  SER A  62 " =    0.865
peak=    3.357 closest distance to " CD2 HIS A  81 " =    1.178
peak=    3.352 closest distance to " O   HOH Z 144 " =    2.317
peak=    3.339 closest distance to " CG2 ILE A  33 " =    1.454
peak=    3.339 closest distance to " NH2 ARG A 156 " =    1.079
peak=    3.334 closest distance to " O   HOH Z 152 " =    1.893
peak=    3.332 closest distance to " O   HOH Z 365 " =    1.391
peak=    3.332 closest distance to " O   HOH Z 261 " =    1.980
peak=    3.332 closest distance to " O   HOH Z 344 " =    2.532
peak=    3.330 closest distance to " O   HOH Z 298 " =    2.361
peak=    3.325 closest distance to " O   HOH Z  89 " =    1.694
peak=    3.322 closest distance to " O   HOH Z 435 " =    1.816
peak=    3.312 closest distance to " O   HOH Z 217 " =    1.566
peak=    3.301 closest distance to " CA  ARG A  36 " =    1.104
peak=    3.301 closest distance to " CG2 ILE A 120 " =    1.222
peak=    3.299 closest distance to " O   HOH Z 423 " =    2.049
peak=    3.297 closest distance to " CZ2 TRP A 179 " =    1.786
peak=    3.295 closest distance to " CD  GLN A 240 " =    1.477
peak=    3.294 closest distance to " CB  SER A  62 " =    1.271
peak=    3.292 closest distance to " O   HOH Z  71 " =    1.447
peak=    3.284 closest distance to " O   HOH Z 280 " =    2.512
peak=    3.279 closest distance to " NH2 ARG A  56 " =    1.183
peak=    3.278 closest distance to " CB  PRO A 198 " =    1.117
peak=    3.277 closest distance to " O   HOH Z 282 " =    2.115
peak=    3.276 closest distance to " O   HOH Z 166 " =    1.148
peak=    3.275 closest distance to " O   HOH Z 367 " =    2.971
peak=    3.274 closest distance to " O   HOH Z 380 " =    1.699
peak=    3.274 closest distance to " CG  PRO A 243 " =    1.257
peak=    3.273 closest distance to " O   HOH Z 394 " =    2.376
peak=    3.265 closest distance to " O   HOH Z  64 " =    1.649
peak=    3.262 closest distance to " CB  VAL A 202 " =    1.649
peak=    3.261 closest distance to " CA  ARG A  66 " =    0.978
peak=    3.259 closest distance to " CA  ALA A 233 " =    1.280
peak=    3.245 closest distance to " O   HOH Z 305 " =    3.535
peak=    3.245 closest distance to " O   HOH Z  61 " =    1.498
peak=    3.244 closest distance to " CA  VAL A  41 " =    0.869
peak=    3.238 closest distance to " CB  ALA A  34 " =    0.965
peak=    3.237 closest distance to " OG  SER A 245 " =    1.387
peak=    3.235 closest distance to " O   HOH Z 233 " =    1.528
peak=    3.235 closest distance to " OG BSER A 164 " =    2.483
peak=    3.233 closest distance to " O   HOH Z  85 " =    1.843
peak=    3.231 closest distance to " O   HOH Z 433 " =    1.463
peak=    3.229 closest distance to " OG  SER A  62 " =    2.953
peak=    3.227 closest distance to " CA  ASN A 215 " =    1.115
peak=    3.227 closest distance to " CA  ALA A 299 " =    0.904
peak=    3.227 closest distance to " O   HOH Z 365 " =    4.865
peak=    3.227 closest distance to " CG1BVAL A  72 " =    3.345
peak=    3.217 closest distance to " O   PHE A 155 " =    1.827
peak=    3.212 closest distance to " NH1BARG A 145 " =    1.270
peak=    3.212 closest distance to " O   HOH Z 361 " =    2.922
peak=    3.212 closest distance to " O   HOH Z 417 " =    3.024
peak=    3.210 closest distance to " CD2 LEU A 297 " =    1.089
peak=    3.207 closest distance to " CB  ASP A 107 " =    1.053
peak=    3.207 closest distance to " O   HOH Z 197 " =    2.352
peak=    3.204 closest distance to " O   HOH Z 273 " =    2.482
peak=    3.204 closest distance to " O   HOH Z 128 " =    1.586
peak=    3.199 closest distance to " O   HOH Z 296 " =    1.446
peak=    3.198 closest distance to " CG2 THR A 294 " =    1.329
peak=    3.194 closest distance to " C   ALA A   1 " =    1.517
peak=    3.188 closest distance to " O   HOH Z 383 " =    1.969
peak=    3.186 closest distance to " O   HOH Z 325 " =    1.453
peak=    3.182 closest distance to " O   THR A 264 " =    1.517
peak=    3.180 closest distance to " CB  ARG A 102 " =    0.781
peak=    3.179 closest distance to " CG2 THR A 220 " =    0.868
peak=    3.173 closest distance to " CA  ILE A  20 " =    0.812
peak=    3.173 closest distance to " O   HOH Z 381 " =    1.591
peak=    3.172 closest distance to " CG  ARG A 269 " =    0.982
peak=    3.164 closest distance to " CD1 LEU A 228 " =    1.734
peak=    3.162 closest distance to " CB  SER A  26 " =    1.056
peak=    3.154 closest distance to " CZ  ARG A  14 " =    1.396
peak=    3.152 closest distance to " CB  GLN A 194 " =    0.851
peak=    3.152 closest distance to " CG  MET A  93 " =    1.035
peak=    3.151 closest distance to " O   HOH Z  61 " =    1.524
peak=    3.151 closest distance to " CB  ALA A   1 " =    1.222
peak=    3.149 closest distance to " N   PHE A 130 " =    1.384
peak=    3.148 closest distance to " CA  ASP A 140 " =    1.193
peak=    3.147 closest distance to " CG  MET A 185 " =    1.273
peak=    3.146 closest distance to " O   HOH Z 257 " =    2.029
peak=    3.145 closest distance to " CB  MET A  47 " =    1.207
peak=    3.142 closest distance to " CA  VAL A 126 " =    1.017
peak=    3.137 closest distance to " OG BSER A 216 " =    2.738
peak=    3.130 closest distance to " O   HOH Z  50 " =    1.511
peak=    3.127 closest distance to " CB  ALA A 248 " =    1.363
peak=    3.123 closest distance to " O   HOH Z   1 " =    2.459
peak=    3.111 closest distance to " O   HOH Z 434 " =    4.126
peak=    3.110 closest distance to " O   HOH Z 130 " =    2.345
peak=    3.109 closest distance to " O   SER A 164 " =    1.148
peak=    3.106 closest distance to " CE  MET A 188 " =    1.967
peak=    3.104 closest distance to " O   HOH Z 367 " =    3.483
peak=    3.094 closest distance to " O   HOH Z 434 " =    5.519
peak=    3.093 closest distance to " O   HOH Z 227 " =    1.945
peak=    3.092 closest distance to " NH2 ARG A 269 " =    1.143
peak=    3.076 closest distance to " O   HOH Z 357 " =    0.982
peak=    3.076 closest distance to " O   HOH Z 208 " =    1.465
peak=    3.075 closest distance to " OH  TYR A 116 " =    1.061
peak=    3.071 closest distance to " CA  ALA A  84 " =    1.202
peak=    3.064 closest distance to " O   HOH Z 259 " =    1.916
peak=    3.063 closest distance to " NH1 ARG A  14 " =    1.156
peak=    3.058 closest distance to " CB  ALA A   9 " =    1.514
peak=    3.044 closest distance to " O   HOH Z  63 " =    2.152
peak=    3.041 closest distance to " OG BSER A 258 " =    3.191
peak=    3.033 closest distance to " CE BLYS A 290 " =    0.947
peak=    3.029 closest distance to " O   HOH Z  71 " =    1.703
peak=    3.012 closest distance to " CA  ASP A 191 " =    0.812
peak=    3.009 closest distance to " O   HOH Z 130 " =    3.107
peak=    3.004 closest distance to " O   HOH Z 154 " =    2.810

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.565 - 5.380
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 199
   mapped sites are within: 0.721 - 5.380

peak=   -4.788 closest distance to " OG  SER A  63 " =    0.835
peak=   -4.759 closest distance to " O   HOH Z  13 " =    1.408
peak=   -4.746 closest distance to " C   HIS A 108 " =    1.126
peak=   -4.409 closest distance to " O   HOH Z  52 " =    1.325
peak=   -4.385 closest distance to " O   HOH Z 266 " =    4.144
peak=   -4.350 closest distance to " O   HOH Z 290 " =    0.753
peak=   -4.242 closest distance to " CA  VAL A  67 " =    2.836
peak=   -4.234 closest distance to " O   HOH Z 117 " =    0.721
peak=   -4.105 closest distance to " O   HOH Z 102 " =    0.966
peak=   -4.065 closest distance to " O   PRO A 163 " =    1.971
peak=   -4.013 closest distance to " O   HOH Z 377 " =    2.094
peak=   -4.004 closest distance to " O   HOH Z 198 " =    0.908
peak=   -3.997 closest distance to " O   HOH Z  71 " =    1.208
peak=   -3.989 closest distance to " CD2 LEU A 300 " =    2.827
peak=   -3.986 closest distance to " O   HOH Z 138 " =    0.881
peak=   -3.970 closest distance to " O   TRP A  92 " =    1.813
peak=   -3.916 closest distance to " N   ALA A 248 " =    1.833
peak=   -3.914 closest distance to " O   SER A 146 " =    0.846
peak=   -3.914 closest distance to " O   HOH Z 423 " =    2.421
peak=   -3.897 closest distance to " OG  SER A  97 " =    1.980
peak=   -3.877 closest distance to " O   VAL A  67 " =    2.661
peak=   -3.867 closest distance to " CG  MET A  93 " =    2.478
peak=   -3.852 closest distance to " CD  ARG A 156 " =    2.024
peak=   -3.845 closest distance to " CB  ALA A 291 " =    2.260
peak=   -3.844 closest distance to " NH2 ARG A  79 " =    1.931
peak=   -3.843 closest distance to " CD2 LEU A 237 " =    2.519
peak=   -3.834 closest distance to " OG BSER A 134 " =    1.579
peak=   -3.793 closest distance to " O   HOH Z 234 " =    4.046
peak=   -3.790 closest distance to " O   HOH Z 407 " =    3.034
peak=   -3.782 closest distance to " OXT GLY A 302 " =    2.995
peak=   -3.762 closest distance to " O   HOH Z 165 " =    1.929
peak=   -3.747 closest distance to " C   THR A 279 " =    1.299
peak=   -3.743 closest distance to " O   SER A 273 " =    1.134
peak=   -3.740 closest distance to " O   HOH Z 197 " =    1.959
peak=   -3.693 closest distance to " O   HOH Z 396 " =    1.691
peak=   -3.672 closest distance to " O   HOH Z  97 " =    1.218
peak=   -3.642 closest distance to " N   GLN A  58 " =    1.665
peak=   -3.631 closest distance to " O   ASN A 187 " =    1.441
peak=   -3.628 closest distance to " O   HOH Z 109 " =    5.380
peak=   -3.611 closest distance to " OG ASER A 216 " =    0.985
peak=   -3.602 closest distance to " CA  GLY A 133 " =    1.777
peak=   -3.595 closest distance to " CD  GLN A  88 " =    1.003
peak=   -3.590 closest distance to " ND2 ASN A  45 " =    0.962
peak=   -3.589 closest distance to " OG BSER A 134 " =    1.670
peak=   -3.584 closest distance to " O   ALA A 161 " =    1.511
peak=   -3.578 closest distance to " OE1 GLN A 103 " =    1.208
peak=   -3.574 closest distance to " CE1 HIS A  81 " =    1.200
peak=   -3.573 closest distance to " O   HOH Z 198 " =    1.317
peak=   -3.556 closest distance to " O   HOH Z  18 " =    2.791
peak=   -3.556 closest distance to " N   GLN A 122 " =    1.513
peak=   -3.552 closest distance to " O   ALA A  51 " =    1.506
peak=   -3.550 closest distance to " O   HOH Z 222 " =    1.216
peak=   -3.540 closest distance to " ND2 ASN A 209 " =    1.672
peak=   -3.535 closest distance to " O   PHE A 218 " =    1.498
peak=   -3.533 closest distance to " CD2 TYR A 293 " =    2.013
peak=   -3.530 closest distance to " O   VAL A 197 " =    1.118
peak=   -3.529 closest distance to " O   VAL A 174 " =    2.048
peak=   -3.529 closest distance to " CG  LYS A 193 " =    2.230
peak=   -3.526 closest distance to " CG2 THR A 182 " =    2.259
peak=   -3.519 closest distance to " ND2 ASN A  39 " =    1.171
peak=   -3.517 closest distance to " CA  GLY A 241 " =    2.339
peak=   -3.513 closest distance to " O   HOH Z 299 " =    1.885
peak=   -3.512 closest distance to " O   PRO A 198 " =    1.341
peak=   -3.511 closest distance to " CZ  TYR A 169 " =    2.013
peak=   -3.505 closest distance to " CD  GLN A  58 " =    0.976
peak=   -3.503 closest distance to " O   ARG A  56 " =    1.577
peak=   -3.502 closest distance to " CG  LEU A  83 " =    1.991
peak=   -3.496 closest distance to " O   HOH Z 412 " =    1.362
peak=   -3.490 closest distance to " CD  ARG A  14 " =    3.227
peak=   -3.485 closest distance to " O   HOH Z 137 " =    1.590
peak=   -3.485 closest distance to " ND2 ASN A 187 " =    1.275
peak=   -3.474 closest distance to " O   HOH Z  88 " =    4.396
peak=   -3.472 closest distance to " O   GLY A 196 " =    0.947
peak=   -3.466 closest distance to " O   HOH Z 251 " =    1.220
peak=   -3.464 closest distance to " O   PRO A 198 " =    1.250
peak=   -3.462 closest distance to " NE2 GLN A  55 " =    1.757
peak=   -3.448 closest distance to " O   HOH Z 395 " =    5.077
peak=   -3.447 closest distance to " O   HOH Z 265 " =    1.717
peak=   -3.446 closest distance to " CD1 TYR A 247 " =    2.388
peak=   -3.446 closest distance to " CD  GLN A  58 " =    1.394
peak=   -3.444 closest distance to " O   HOH Z 424 " =    3.145
peak=   -3.443 closest distance to " CE  MET A 105 " =    1.856
peak=   -3.435 closest distance to " O   LEU A 228 " =    2.303
peak=   -3.427 closest distance to " OE2 GLU A   2 " =    1.792
peak=   -3.426 closest distance to " O   HOH Z  24 " =    1.127
peak=   -3.424 closest distance to " CB  SER A  26 " =    1.358
peak=   -3.423 closest distance to " CB  PRO A 163 " =    2.835
peak=   -3.421 closest distance to " O   HOH Z  11 " =    1.667
peak=   -3.418 closest distance to " N   SER A 210 " =    1.342
peak=   -3.417 closest distance to " OD2 ASP A 171 " =    2.334
peak=   -3.416 closest distance to " CD2 LEU A 237 " =    2.084
peak=   -3.412 closest distance to " ND2 ASN A  69 " =    1.683
peak=   -3.407 closest distance to " NE2 GLN A  88 " =    2.134
peak=   -3.406 closest distance to " CD1 PHE A  59 " =    1.938
peak=   -3.391 closest distance to " C   ALA A 158 " =    1.102
peak=   -3.391 closest distance to " O   PRO A  54 " =    1.539
peak=   -3.390 closest distance to " N   ASP A 286 " =    2.092
peak=   -3.388 closest distance to " O   HOH Z 250 " =    1.345
peak=   -3.386 closest distance to " OD2 ASP A  50 " =    1.389
peak=   -3.379 closest distance to " CG1AVAL A  41 " =    2.555
peak=   -3.378 closest distance to " OD1 ASN A 176 " =    1.063
peak=   -3.378 closest distance to " CG  GLU A 152 " =    0.906
peak=   -3.378 closest distance to " O   LEU A 222 " =    1.336
peak=   -3.370 closest distance to " OD1 ASN A  39 " =    2.228
peak=   -3.365 closest distance to " O   GLN A  11 " =    1.322
peak=   -3.346 closest distance to " OD2 ASP A 191 " =    1.579
peak=   -3.341 closest distance to " CD  GLN A 223 " =    1.013
peak=   -3.340 closest distance to " CB  PHE A 208 " =    2.214
peak=   -3.335 closest distance to " CG  ASP A 132 " =    2.140
peak=   -3.324 closest distance to " O   ALA A 160 " =    1.449
peak=   -3.323 closest distance to " O   HOH Z 397 " =    1.253
peak=   -3.320 closest distance to " CE1 TYR A 169 " =    2.210
peak=   -3.317 closest distance to " CB  ALA A 161 " =    2.513
peak=   -3.313 closest distance to " O   SER A   3 " =    0.988
peak=   -3.309 closest distance to " CG2 VAL A 189 " =    2.148
peak=   -3.305 closest distance to " O   HOH Z  63 " =    1.141
peak=   -3.302 closest distance to " CD1 TRP A 179 " =    1.268
peak=   -3.302 closest distance to " O   ASN A  45 " =    1.778
peak=   -3.300 closest distance to " CH2 TRP A 274 " =    1.186
peak=   -3.295 closest distance to " CG1 VAL A 296 " =    2.234
peak=   -3.295 closest distance to " O   ALA A  34 " =    2.467
peak=   -3.288 closest distance to " O   HOH Z 364 " =    5.148
peak=   -3.287 closest distance to " O   HOH Z 384 " =    3.445
peak=   -3.284 closest distance to " OD1 ASP A 200 " =    1.196
peak=   -3.282 closest distance to " C   GLY A  91 " =    1.330
peak=   -3.281 closest distance to " O   HOH Z 367 " =    2.514
peak=   -3.280 closest distance to " O   HOH Z  51 " =    1.900
peak=   -3.279 closest distance to " O   HOH Z  20 " =    1.862
peak=   -3.276 closest distance to " O   HOH Z 221 " =    0.978
peak=   -3.275 closest distance to " CG  ASP A  50 " =    2.274
peak=   -3.275 closest distance to " CB  ASN A  39 " =    2.196
peak=   -3.275 closest distance to " N   ALA A 226 " =    1.920
peak=   -3.271 closest distance to " N   THR A  52 " =    1.682
peak=   -3.271 closest distance to " O   HOH Z 388 " =    1.960
peak=   -3.268 closest distance to " CD1 PHE A 130 " =    2.133
peak=   -3.268 closest distance to " CD2 TYR A  30 " =    2.870
peak=   -3.266 closest distance to " CD  LYS A 289 " =    2.445
peak=   -3.265 closest distance to " O   HOH Z 287 " =    2.030
peak=   -3.264 closest distance to " CG  GLU A  53 " =    1.478
peak=   -3.261 closest distance to " CB  PHE A 192 " =    1.987
peak=   -3.259 closest distance to " ND2 ASN A 142 " =    1.862
peak=   -3.256 closest distance to " O   HOH Z 166 " =    1.363
peak=   -3.251 closest distance to " N   GLN A 144 " =    1.949
peak=   -3.250 closest distance to " N   GLY A  17 " =    1.418
peak=   -3.250 closest distance to " N   SER A 276 " =    1.319
peak=   -3.249 closest distance to " O   HOH Z 202 " =    1.551
peak=   -3.247 closest distance to " O   HOH Z 427 " =    1.484
peak=   -3.244 closest distance to " O   HOH Z 418 " =    1.441
peak=   -3.239 closest distance to " O   HOH Z  47 " =    0.932
peak=   -3.238 closest distance to " O   HOH Z 126 " =    1.949
peak=   -3.228 closest distance to " O   LEU A 143 " =    1.636
peak=   -3.227 closest distance to " O   HOH Z 283 " =    1.740
peak=   -3.224 closest distance to " O   HOH Z 417 " =    2.696
peak=   -3.222 closest distance to " O   HOH Z  15 " =    1.614
peak=   -3.220 closest distance to " OG  SER A   3 " =    1.298
peak=   -3.219 closest distance to " C   GLY A  80 " =    2.367
peak=   -3.215 closest distance to " O   HOH Z  60 " =    0.857
peak=   -3.214 closest distance to " C   ALA A 242 " =    1.916
peak=   -3.213 closest distance to " OG  SER A  62 " =    1.267
peak=   -3.212 closest distance to " CG  PRO A 243 " =    1.658
peak=   -3.202 closest distance to " O   HOH Z 119 " =    1.968
peak=   -3.198 closest distance to " O   THR A 182 " =    1.096
peak=   -3.198 closest distance to " OD1 ASP A 171 " =    1.775
peak=   -3.195 closest distance to " N   ALA A  43 " =    2.436
peak=   -3.192 closest distance to " O   HOH Z  48 " =    1.061
peak=   -3.190 closest distance to " O   HOH Z  35 " =    1.731
peak=   -3.184 closest distance to " CA  ASP A 298 " =    1.126
peak=   -3.184 closest distance to " CB  ASP A 124 " =    2.146
peak=   -3.181 closest distance to " O   MET A  40 " =    2.819
peak=   -3.175 closest distance to " O   HOH Z 166 " =    2.121
peak=   -3.174 closest distance to " O   LEU A 167 " =    1.582
peak=   -3.166 closest distance to " O   HOH Z 313 " =    1.201
peak=   -3.165 closest distance to " CG  LYS A  76 " =    2.959
peak=   -3.162 closest distance to " CG1 VAL A 197 " =    1.809
peak=   -3.161 closest distance to " OE2 GLU A  44 " =    1.104
peak=   -3.155 closest distance to " CG  ASN A 110 " =    1.208
peak=   -3.145 closest distance to " CA  VAL A 232 " =    2.502
peak=   -3.143 closest distance to " O   HOH Z 219 " =    3.726
peak=   -3.125 closest distance to " CG  ARG A 269 " =    2.163
peak=   -3.120 closest distance to " NE2 GLN A 223 " =    1.282
peak=   -3.110 closest distance to " O   SER A 210 " =    1.899
peak=   -3.104 closest distance to " OG BSER A 212 " =    1.474
peak=   -3.093 closest distance to " O   HOH Z 216 " =    3.508
peak=   -3.091 closest distance to " CE2 TYR A 214 " =    1.404
peak=   -3.090 closest distance to " O   HOH Z 380 " =    4.620
peak=   -3.087 closest distance to " OG1 THR A 178 " =    1.174
peak=   -3.077 closest distance to " CG2 THR A 251 " =    1.993
peak=   -3.077 closest distance to " CD  ARG A 139 " =    1.529
peak=   -3.068 closest distance to " CD1 LEU A  96 " =    2.044
peak=   -3.057 closest distance to " O   HOH Z 109 " =    3.141
peak=   -3.053 closest distance to " CA  GLY A 211 " =    1.628
peak=   -3.047 closest distance to " CB  LEU A 167 " =    2.084
peak=   -3.046 closest distance to " N   ALA A 248 " =    2.252
peak=   -3.039 closest distance to " O   SER A 135 " =    1.611

================= 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    :  0.4897 0.4903   6.290400e+00   6.290335e+00
   1_bss:  0.4837 0.4822   6.286602e+00   6.278621e+00
   1_xyz:  0.3831 0.4052   6.144906e+00   6.183900e+00
   1_adp:  0.3434 0.4130   6.092963e+00   6.198980e+00
   1_occ:  0.3429 0.4128   6.092410e+00   6.198831e+00
   2_bss:  0.3411 0.4096   6.088712e+00   6.198629e+00
   2_xyz:  0.2696 0.3301   5.888009e+00   6.049377e+00
   2_adp:  0.2437 0.3078   5.818547e+00   5.994831e+00
   2_occ:  0.2434 0.3075   5.817690e+00   5.994338e+00
   3_bss:  0.2434 0.3053   5.815190e+00   5.989959e+00
   3_xyz:  0.1798 0.2380   5.559514e+00   5.774001e+00
   3_adp:  0.1581 0.2159   5.446382e+00   5.671891e+00
   3_occ:  0.1580 0.2159   5.446410e+00   5.672193e+00
   4_bss:  0.1580 0.2141   5.444008e+00   5.666530e+00
   4_xyz:  0.1379 0.1931   5.338542e+00   5.570535e+00
   4_adp:  0.1314 0.1831   5.290515e+00   5.515307e+00
   4_occ:  0.1312 0.1829   5.289638e+00   5.514988e+00
   5_bss:  0.1318 0.1834   5.291575e+00   5.516270e+00
   5_xyz:  0.1189 0.1721   5.211499e+00   5.452230e+00
   5_adp:  0.1181 0.1689   5.199719e+00   5.436232e+00
   5_occ:  0.1179 0.1689   5.199083e+00   5.436320e+00
   5_bss:  0.1179 0.1689   5.199373e+00   5.436518e+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:  0.332  20.001  -0.786   0.816   1.255   0.000   0.000   0.000
   1_xyz:  0.332  20.001  -0.786   0.816   1.255   0.000   0.000   0.000
   1_adp:  0.332  20.001  -0.786   0.816   1.255   0.000   0.000   0.000
   1_occ:  0.332  20.001  -0.786   0.816   1.255   0.000   0.000   0.000
   2_bss:  0.328  46.786  -0.769   0.796   0.880   0.000   0.000   0.000
   2_xyz:  0.328  46.786  -0.769   0.796   0.880   0.000   0.000   0.000
   2_adp:  0.328  46.786  -0.769   0.796   0.880   0.000   0.000   0.000
   2_occ:  0.328  46.786  -0.769   0.796   0.880   0.000   0.000   0.000
   3_bss:  0.325  45.692  -1.592  -0.153  -0.114  -0.000  -0.000  -0.000
   3_xyz:  0.325  45.692  -1.592  -0.153  -0.114  -0.000  -0.000  -0.000
   3_adp:  0.325  45.692  -1.592  -0.153  -0.114  -0.000  -0.000  -0.000
   3_occ:  0.325  45.692  -1.592  -0.153  -0.114  -0.000  -0.000  -0.000
   4_bss:  0.318  41.047  -2.590  -1.092  -1.367  -0.000  -0.000  -0.000
   4_xyz:  0.318  41.047  -2.590  -1.092  -1.367  -0.000  -0.000  -0.000
   4_adp:  0.318  41.047  -2.590  -1.092  -1.367  -0.000  -0.000  -0.000
   4_occ:  0.318  41.047  -2.590  -1.092  -1.367  -0.000  -0.000  -0.000
   5_bss:  0.318  41.936  -2.916  -1.366  -1.657  -0.000  -0.000  -0.000
   5_xyz:  0.318  41.936  -2.916  -1.366  -1.657  -0.000  -0.000  -0.000
   5_adp:  0.318  41.936  -2.916  -1.366  -1.657  -0.000  -0.000  -0.000
   5_occ:  0.318  41.936  -2.916  -1.366  -1.657  -0.000  -0.000  -0.000
   5_bss:  0.324  41.849  -2.794  -1.285  -1.528  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  65.426 0.3217  0.4337    78280.914
   1_bss:  64.345 0.3342  0.4607    74842.802
   1_xyz:  46.468 0.5634  0.7731    47784.909
   1_adp:  48.043 0.5431  0.7631    50228.545
   1_occ:  48.060 0.5429  0.7615    50212.781
   2_bss:  47.829 0.5455  0.7640    49565.487
   2_xyz:  36.425 0.6823  0.9372    30181.415
   2_adp:  32.719 0.7264  0.9619    25919.363
   2_occ:  32.681 0.7268  0.9620    25838.066
   3_bss:  32.482 0.7287  0.9315    25453.707
   3_xyz:  23.994 0.8203  1.0142    14714.903
   3_adp:  20.826 0.8532  1.0254    11921.726
   3_occ:  20.835 0.8531  1.0254    11934.953
   4_bss:  20.684 0.8544  0.9859    11726.040
   4_xyz:  18.296 0.8772  0.9937     9358.909
   4_adp:  16.943 0.8901  0.9910     8448.190
   4_occ:  16.939 0.8901  0.9910     8435.691
   5_bss:  16.964 0.8900  0.9804     8481.055
   5_xyz:  15.596 0.9016  0.9868     7346.054
   5_adp:  15.163 0.9056  0.9832     7142.435
   5_occ:  15.156 0.9056  0.9830     7136.765
   5_bss:  15.162 0.9056  0.9839     7143.899
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.106   2.6606e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.106   2.6606e-01
   1_xyz:   1.564  0.012  0.091 16.483  0.006  4.108   1.4096e-01
   1_adp:   1.564  0.012  0.091 16.483  0.006  4.108   1.4096e-01
   1_occ:   1.564  0.012  0.091 16.483  0.006  4.108   1.4096e-01
   2_bss:   1.564  0.012  0.091 16.483  0.006  4.108   1.4096e-01
   2_xyz:   1.302  0.009  0.085 15.135  0.006  4.105   9.0916e-02
   2_adp:   1.302  0.009  0.085 15.135  0.006  4.105   9.0916e-02
   2_occ:   1.302  0.009  0.085 15.135  0.006  4.105   9.0916e-02
   3_bss:   1.302  0.009  0.085 15.135  0.006  4.105   9.0916e-02
   3_xyz:   1.201  0.009  0.073 14.835  0.005  4.113   7.8370e-02
   3_adp:   1.201  0.009  0.073 14.835  0.005  4.113   7.8370e-02
   3_occ:   1.201  0.009  0.073 14.835  0.005  4.113   7.8370e-02
   4_bss:   1.201  0.009  0.073 14.835  0.005  4.113   7.8370e-02
   4_xyz:   0.988  0.006  0.067 14.509  0.004  4.112   5.6313e-02
   4_adp:   0.988  0.006  0.067 14.509  0.004  4.112   5.6313e-02
   4_occ:   0.988  0.006  0.067 14.509  0.004  4.112   5.6313e-02
   5_bss:   0.988  0.006  0.067 14.509  0.004  4.112   5.6313e-02
   5_xyz:   1.111  0.007  0.073 14.706  0.004  4.113   6.7045e-02
   5_adp:   1.111  0.007  0.073 14.706  0.004  4.113   6.7045e-02
   5_occ:   1.111  0.007  0.073 14.706  0.004  4.113   6.7045e-02
   5_bss:   1.111  0.007  0.073 14.706  0.004  4.113   6.7045e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.175   2.4561e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.175   2.4561e-01
   1_xyz:  10.535  0.092  0.280 87.376  0.056  1.785   9.2874e-02
   1_adp:  10.535  0.092  0.280 87.376  0.056  1.785   9.2874e-02
   1_occ:  10.535  0.092  0.280 87.376  0.056  1.785   9.2874e-02
   2_bss:  10.535  0.092  0.280 87.376  0.056  1.785   9.2874e-02
   2_xyz:   8.404  0.060  0.285 80.723  0.055  2.058   8.0437e-02
   2_adp:   8.404  0.060  0.285 80.723  0.055  2.058   8.0437e-02
   2_occ:   8.404  0.060  0.285 80.723  0.055  2.058   8.0437e-02
   3_bss:   8.404  0.060  0.285 80.723  0.055  2.058   8.0437e-02
   3_xyz:   8.128  0.059  0.232 80.439  0.038  2.164   6.8845e-02
   3_adp:   8.128  0.059  0.232 80.439  0.038  2.164   6.8845e-02
   3_occ:   8.128  0.059  0.232 80.439  0.038  2.164   6.8845e-02
   4_bss:   8.128  0.059  0.232 80.439  0.038  2.164   6.8845e-02
   4_xyz:   6.905  0.030  0.247 79.682  0.038  2.352   3.4812e-02
   4_adp:   6.905  0.030  0.247 79.682  0.038  2.352   3.4812e-02
   4_occ:   6.905  0.030  0.247 79.682  0.038  2.352   3.4812e-02
   5_bss:   6.905  0.030  0.247 79.682  0.038  2.352   3.4812e-02
   5_xyz:   7.587  0.039  0.236 83.141  0.034  2.165   4.8461e-02
   5_adp:   7.587  0.039  0.236 83.141  0.034  2.165   4.8461e-02
   5_occ:   7.587  0.039  0.236 83.141  0.034  2.165   4.8461e-02
   5_bss:   7.587  0.039  0.236 83.141  0.034  2.165   4.8461e-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:  93.93   0.00  21.46  93.93   0.00  17.62  93.50   0.00  42.42
   1_occ:  93.93   0.00  21.46  93.93   0.00  17.62  93.50   0.00  42.42
   2_bss:  93.93   0.00  21.46  93.93   0.00  17.62  93.50   0.00  42.42
   2_xyz:  93.93   0.00  21.46  93.93   0.00  17.62  93.50   0.00  42.42
   2_adp:  98.70   0.00  19.85  94.39   0.00  15.62  98.70   2.91  42.88
   2_occ:  98.70   0.00  19.85  94.39   0.00  15.62  98.70   2.91  42.88
   3_bss:  98.70   0.00  19.85  94.39   0.00  15.62  98.70   2.91  42.88
   3_xyz:  98.70   0.00  19.85  94.39   0.00  15.62  98.70   2.91  42.88
   3_adp: 113.10   0.00  19.40 104.36   0.00  14.23 113.10   3.91  47.58
   3_occ: 113.10   0.00  19.40 104.36   0.00  14.23 113.10   3.91  47.58
   4_bss: 113.10   0.00  19.40 104.36   0.00  14.23 113.10   3.91  47.58
   4_xyz: 113.10   0.00  19.40 104.36   0.00  14.23 113.10   3.91  47.58
   4_adp: 105.49   1.09  18.14 105.49   1.09  13.37 102.16   2.80  44.16
   4_occ: 105.49   1.09  18.14 105.49   1.09  13.37 102.16   2.80  44.16
   5_bss: 105.49   1.09  18.14 105.49   1.09  13.37 102.16   2.80  44.16
   5_xyz: 105.49   1.09  18.14 105.49   1.09  13.37 102.16   2.80  44.16
   5_adp: 102.56   2.39  17.17 102.56   2.39  12.85  93.66   4.31  40.69
   5_occ: 102.56   2.39  17.17 102.56   2.39  12.85  93.66   4.31  40.69
   5_bss: 102.48   2.31  17.08 102.48   2.31  12.76  93.58   4.22  40.60
------------------------------------------------------------------------
 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:    4.012    0.030    0.388
   1_adp:    4.012    0.030    0.388
   1_occ:    4.012    0.030    0.388
   2_bss:    4.012    0.030    0.388
   2_xyz:    1.824    0.045    0.601
   2_adp:    1.824    0.045    0.601
   2_occ:    1.824    0.045    0.601
   3_bss:    1.824    0.045    0.601
   3_xyz:    1.899    0.057    0.745
   3_adp:    1.899    0.057    0.745
   3_occ:    1.899    0.057    0.745
   4_bss:    1.899    0.057    0.745
   4_xyz:    1.953    0.080    0.795
   4_adp:    1.953    0.080    0.795
   4_occ:    1.953    0.080    0.795
   5_bss:    1.953    0.080    0.795
   5_xyz:    1.977    0.055    0.823
   5_adp:    1.977    0.055    0.823
   5_occ:    1.977    0.055    0.823
   5_bss:    1.977    0.055    0.823
------------------------------------------------------------------------

CPU time actual refinement: 351.01


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_88/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_88/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_88/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_88/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_88/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 350.86 
  Macro-tasks:
    bulk solvent and scale       = 47.00  
    individual site refinement   = 139.61 
    weights calculation          = 32.02  
    collect and process          = 6.63   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 225.34 
  Micro-tasks:
    mask                            = 2.28   
    f_calc                          = 112.78 
    alpha_beta                      = 8.83   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 114.21 
    fmodel                         = 7.68   
    r_factors                      = 0.21   
    phase_errors                   = 11.09  
    foms                           = 0.13   
    TOTAL for micro-tasks          = 258.41 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.033 micro seconds
Total CPU time: 6.07 minutes
from_scatterers_fft:    628 calls, 112.26 s
gradients_fft:          573 calls, 103.43 s

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

# Date 2008-01-16 Time 03:59:00 PST -0800 (1200484740.11 s)
Start R-work = 0.4897, R-free = 0.4903 (no bulk solvent and anisotropic scale)
Final R-work = 0.1427, R-free = 0.1896 (no bulk solvent and anisotropic scale)

Start R-work = 0.4837, R-free = 0.4822
Final R-work = 0.1179, R-free = 0.1689