# Date 2008-01-16 Time 06:31:38 PST -0800 (1200493898.68 s)
#phil __OFF__

Command line arguments: "../1184.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8504
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1184

-------------------------------------------------------------------------------
  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: (71.655, 47.6339, 87.2539, 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: 3.27, per 1000 atoms: 1.16


================================== 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: (71.655, 47.6339, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2528 2.02103
Completeness in resolution range: 0.972835
Completeness with d_max=infinity: 0.969752

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2528
                             d_min =   2.0210

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: (71.655, 47.6339, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2528 2.02103
Completeness in resolution range: 0.972835
Completeness with d_max=infinity: 0.969752

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2532 -  4.3242 [2104/2128]  1894   210  10.0%
  bin  2:  4.3242 -  3.4453 [2037/2056]  1833   204  10.0%
  bin  3:  3.4453 -  3.0136 [2006/2025]  1803   203  10.1%
  bin  4:  3.0136 -  2.7398 [1988/2018]  1793   195   9.8%
  bin  5:  2.7398 -  2.5444 [1980/1999]  1782   198  10.0%
  bin  6:  2.5444 -  2.3950 [1940/1965]  1746   194  10.0%
  bin  7:  2.3950 -  2.2754 [1971/1999]  1770   201  10.2%
  bin  8:  2.2754 -  2.1767 [1946/1982]  1755   191   9.8%
  bin  9:  2.1767 -  2.0931 [1935/1977]  1743   192   9.9%
  bin 10:  2.0931 -  2.0210 [1682/1987]  1511   171  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1184/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.41 -     2.11: 2
        2.11 -     2.81: 745
        2.81 -     3.51: 4371
        3.51 -     4.20: 9111
        4.20 -     4.90: 13489
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.413 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 343 " - " O   HOH Z 277 "  2.134 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  2.134 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 27713 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_1184/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1184/model_refine_001.geo

CPU time processing inputs: 9.20


============================ 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 = 71.655 47.63395 87.2539 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: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4235   r_free= 0.4114   ksol= 0.00   Bsol= 0.00   scale= 0.904    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.218945                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2532 -  4.8228 0.99   1376  153 0.3247 0.3237      6.4444      6.3714|
|  2:  4.8228 -  3.8483 0.99   1321  146 0.3485 0.3539      6.7079      6.7309|
|  3:  3.8483 -  3.3678 0.99   1298  144 0.3753 0.3545      6.5789      6.5342|
|  4:  3.3678 -  3.0626 0.99   1278  145 0.4141 0.3849      6.4709      6.3948|
|  5:  3.0626 -  2.8446 0.99   1283  141 0.4391 0.4309      6.3001      6.3335|
|  6:  2.8446 -  2.6778 0.99   1278  139 0.4600 0.4247       6.238      6.1684|
|  7:  2.6778 -  2.5444 0.99   1271  142 0.4576 0.4375      6.1773      6.1741|
|  8:  2.5444 -  2.4341 0.98   1261  145 0.4717 0.4275      6.1549      6.1127|
|  9:  2.4341 -  2.3407 0.98   1257  137 0.4712 0.4656      6.0823      6.1312|
| 10:  2.3407 -  2.2602 0.99   1240  141 0.4810 0.4697       6.082      6.0933|
| 11:  2.2602 -  2.1897 0.98   1266  134 0.4873 0.4798      6.0281       6.038|
| 12:  2.1897 -  2.1273 0.97   1235  140 0.4957 0.4802      5.9636      5.9914|
| 13:  2.1273 -  2.0715 1.00   1245  144 0.4883 0.4931      5.8746      5.8439|
| 14:  2.0715 -  2.0210 0.79   1021  108 0.4899 0.5090      5.8146      5.7654|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2532 -  4.8228  1376   153  0.76  28.99   0.84     0.78      52590.65|
|  2:  4.8228 -  3.8483  1321   146  0.78  28.33   0.93     0.84      71754.59|
|  3:  3.8483 -  3.3678  1298   144  0.71  34.68   0.92     0.83      77312.98|
|  4:  3.3678 -  3.0626  1278   145  0.64  40.25   0.91     0.78      70929.69|
|  5:  3.0626 -  2.8446  1283   141  0.55  47.72   0.91     0.72      60367.89|
|  6:  2.8446 -  2.6778  1278   139  0.54  49.14   0.90     0.69      53129.98|
|  7:  2.6778 -  2.5444  1271   142  0.51  51.30   0.92     0.67      49638.39|
|  8:  2.5444 -  2.4341  1261   145  0.49  52.56   0.92     0.67      47389.05|
|  9:  2.4341 -  2.3407  1257   137  0.47  54.07   0.92     0.64      44899.37|
| 10:  2.3407 -  2.2602  1240   141  0.46  55.44   0.94     0.63      42005.55|
| 11:  2.2602 -  2.1897  1266   134  0.44  56.67   0.93     0.63      39737.68|
| 12:  2.1897 -  2.1273  1235   140  0.43  57.42   0.92     0.63      37752.78|
| 13:  2.1273 -  2.0715  1245   144  0.40  59.63   0.91     0.59      33359.12|
| 14:  2.0715 -  2.0210  1021   108  0.40  59.99   0.91     0.52      27082.60|
|alpha:            min =        0.52 max =            0.84 mean =         0.69|
|beta:             min =    27082.60 max =        77312.98 mean =     51105.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.55|
|phase err.(work): min =        0.00 max =           90.00 mean =        47.88|
|phase err.(test): min =        0.00 max =           89.69 mean =        47.89|
|-----------------------------------------------------------------------------|

============================== 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 = 8.898076              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.308   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.633888              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.506   (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 |  1.413 -  1.761:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.761 -  2.110:        1 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.110 -  2.459:       12 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.459 -  2.808:      733 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.808 -  3.156:     2035 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.156 -  3.505:     2336 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.505 -  3.854:     4480 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.854 -  4.203:     4631 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.203 -  4.551:     6081 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.551 -  4.900:     7408 |
|-----------------------------------------------------------------------------|
|-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 |        0.165 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.115    4.900  1.413 |       0.180 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.432)------------------------------------------|
|    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: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4235   r_free= 0.4114   ksol= 0.00   Bsol= 0.00   scale= 0.904    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.218945                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4161   r_free= 0.4037   ksol= 0.30   Bsol= 67.98   scale= 0.947   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.52,2.14,-0.08,0.00,-0.00,-0.00); trace/3= 0.86                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.209687                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.949515              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.309   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.882867              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.202   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4161      final r-factor (work) = 0.2605          |
| start r-factor (free) = 0.4037      final r-factor (free) = 0.2840          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.8523 = 7.95 * 0.50 * 6.2109 + 1.00 * 0.1653                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.9975 = 7.95 * 0.50 * 6.0092 + 1.00 * 0.1125                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2605      final r-factor (work) = 0.2355          |
| start r-factor (free) = 0.2840      final r-factor (free) = 0.2884          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3117 = 0.88 * 1.00 * 6.0092 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1108 = 0.88 * 1.00 * 5.7713 + 1.00 * 0.0155                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.432)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.93   18.36    None  None   None       |
|    all(noH): 2823   0      0.00    98.93   18.36    None  None   None       |
|    Sol.    : 438    0      2.81    98.93   43.91    None  None   None       |
|    Mac.    : 2385   0      0.00    88.43   13.67    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.893: 1000   |   5:    49.467 -  59.360:   85        |
|      1:     9.893 -  19.787: 1020   |   6:    59.360 -  69.253:   60        |
|      2:    19.787 -  29.680:  328   |   7:    69.253 -  79.146:   36        |
|      3:    29.680 -  39.573:  161   |   8:    79.146 -  89.040:   16        |
|      4:    39.573 -  49.467:  111   |   9:    89.040 -  98.933:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2355 r_free = 0.2884             target_work(ml) = 5.775         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2351 r_free = 0.2884             target_work(ml) = 5.774         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2351   r_free= 0.2884   ksol= 0.30   Bsol= 67.98   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.52,2.14,-0.08,0.00,-0.00,-0.00); trace/3= 0.86                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.774240                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2334   r_free= 0.2862   ksol= 0.33   Bsol= 88.34   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.14,-0.17,-0.79,-0.00,-0.00,-0.00); trace/3= -0.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.772644                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.351851              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.134   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.389213              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.313  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2334      final r-factor (work) = 0.1644          |
| start r-factor (free) = 0.2862      final r-factor (free) = 0.2076          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.5742 = 5.35 * 0.50 * 5.7781 + 1.00 * 0.1125                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.1640 = 5.35 * 0.50 * 5.6370 + 1.00 * 0.0797                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1644      final r-factor (work) = 0.1480          |
| start r-factor (free) = 0.2076      final r-factor (free) = 0.1891          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2094 = 0.39 * 1.00 * 5.6370 + 1.00 * 0.0154                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1174 = 0.39 * 1.00 * 5.4113 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.432)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.31    97.74   17.81    None  None   None       |
|    all(noH): 2823   0      1.31    97.74   17.81    None  None   None       |
|    Sol.    : 438    0      4.64    97.74   43.79    None  None   None       |
|    Mac.    : 2385   0      1.31    91.39   13.04    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:     1.311 -  10.954: 1254   |   5:    49.525 -  59.168:   83        |
|      1:    10.954 -  20.596:  924   |   6:    59.168 -  68.810:   63        |
|      2:    20.596 -  30.239:  205   |   7:    68.810 -  78.453:   38        |
|      3:    30.239 -  39.882:  119   |   8:    78.453 -  88.096:    9        |
|      4:    39.882 -  49.525:  121   |   9:    88.096 -  97.739:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1480 r_free = 0.1891             target_work(ml) = 5.366         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1478 r_free = 0.1886             target_work(ml) = 5.365         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1478   r_free= 0.1886   ksol= 0.33   Bsol= 88.34   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.14,-0.17,-0.79,-0.00,-0.00,-0.00); trace/3= -0.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.365169                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1475   r_free= 0.1883   ksol= 0.33   Bsol= 80.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.60,-1.11,-0.68,-0.00,-0.00,-0.00); trace/3= -1.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.363214                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.832307              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.529  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.608756              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.522  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1475      final r-factor (work) = 0.1329          |
| start r-factor (free) = 0.1883      final r-factor (free) = 0.1762          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0385 = 1.83 * 0.50 * 5.4117 + 1.00 * 0.0806                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9325 = 1.83 * 0.50 * 5.3194 + 1.00 * 0.0591                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1329      final r-factor (work) = 0.1302          |
| start r-factor (free) = 0.1762      final r-factor (free) = 0.1752          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2497 = 0.61 * 1.00 * 5.3194 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4431 = 0.61 * 1.00 * 5.2722 + 1.00 * 0.2336                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.432)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.34   17.60    None  None   None       |
|    all(noH): 2823   0      0.00    97.34   17.60    None  None   None       |
|    Sol.    : 438    0      5.23    97.34   43.69    None  None   None       |
|    Mac.    : 2385   0      0.00    91.89   12.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.734: 1060   |   5:    48.672 -  58.406:   87        |
|      1:     9.734 -  19.469: 1081   |   6:    58.406 -  68.140:   70        |
|      2:    19.469 -  29.203:  227   |   7:    68.140 -  77.875:   37        |
|      3:    29.203 -  38.937:  130   |   8:    77.875 -  87.609:   11        |
|      4:    38.937 -  48.672:  113   |   9:    87.609 -  97.343:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1302 r_free = 0.1752             target_work(ml) = 5.267         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1301 r_free = 0.1751             target_work(ml) = 5.267         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1301   r_free= 0.1751   ksol= 0.33   Bsol= 80.00   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.60,-1.11,-0.68,-0.00,-0.00,-0.00); trace/3= -1.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.267132                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1301   r_free= 0.1752   ksol= 0.33   Bsol= 74.56   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.61,-1.27,-0.53,-0.00,-0.00,-0.00); trace/3= -1.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.266959                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.363850              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.271  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.727004              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.287   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1301      final r-factor (work) = 0.1211          |
| start r-factor (free) = 0.1752      final r-factor (free) = 0.1682          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2902 = 2.36 * 0.50 * 5.2720 + 1.00 * 0.0591                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2579 = 2.36 * 0.50 * 5.2339 + 1.00 * 0.0719                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1211      final r-factor (work) = 0.1190          |
| start r-factor (free) = 0.1682      final r-factor (free) = 0.1685          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.2891 = 2.73 * 1.00 * 5.2339 + 1.00 * 0.0162                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.1997 = 2.73 * 1.00 * 5.2023 + 1.00 * 0.0129                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.432)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.95  17.48    None  None   None       |
|    all(noH): 2823   0      0.00    100.95  17.48    None  None   None       |
|    Sol.    : 438    0      5.17    100.31  43.96    None  None   None       |
|    Mac.    : 2385   0      0.00    100.95  12.62    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 -  10.095: 1188   |   5:    50.475 -  60.570:   86        |
|      1:    10.095 -  20.190:  989   |   6:    60.570 -  70.665:   73        |
|      2:    20.190 -  30.285:  211   |   7:    70.665 -  80.760:   33        |
|      3:    30.285 -  40.380:  130   |   8:    80.760 -  90.855:    8        |
|      4:    40.380 -  50.475:   96   |   9:    90.855 - 100.950:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1190 r_free = 0.1685             target_work(ml) = 5.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1190 r_free = 0.1685             target_work(ml) = 5.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1685   ksol= 0.33   Bsol= 74.56   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.61,-1.27,-0.53,-0.00,-0.00,-0.00); trace/3= -1.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.202755                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1193   r_free= 0.1683   ksol= 0.33   Bsol= 74.56   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.49,-1.26,-0.43,-0.00,-0.00,-0.00); trace/3= -1.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.203127                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.547429              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 156.886  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.284371              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.299  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1193      final r-factor (work) = 0.1167          |
| start r-factor (free) = 0.1683      final r-factor (free) = 0.1689          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6985 = 2.55 * 0.50 * 5.2026 + 1.00 * 0.0719                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6872 = 2.55 * 0.50 * 5.1944 + 1.00 * 0.0710                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1167      final r-factor (work) = 0.1169          |
| start r-factor (free) = 0.1689      final r-factor (free) = 0.1658          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4900 = 0.28 * 1.00 * 5.1944 + 1.00 * 0.0128                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5495 = 0.28 * 1.00 * 5.1966 + 1.00 * 0.0717                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.432)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.94   17.01    None  None   None       |
|    all(noH): 2823   0      0.00    99.94   17.01    None  None   None       |
|    Sol.    : 438    0      5.30    98.53   42.69    None  None   None       |
|    Mac.    : 2385   0      0.00    99.94   12.29    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 -   9.994: 1238   |   5:    49.970 -  59.964:   85        |
|      1:     9.994 -  19.988:  964   |   6:    59.964 -  69.958:   64        |
|      2:    19.988 -  29.982:  202   |   7:    69.958 -  79.952:   31        |
|      3:    29.982 -  39.976:  127   |   8:    79.952 -  89.946:    8        |
|      4:    39.976 -  49.970:   95   |   9:    89.946 -  99.940:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1169 r_free = 0.1658             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1168 r_free = 0.1658             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1658   ksol= 0.33   Bsol= 74.56   scale= 0.982   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.49,-1.26,-0.43,-0.00,-0.00,-0.00); trace/3= -1.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.188139                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2532 -  4.8228 0.99   1376  153 0.1000 0.1343      5.4098      5.5596|
|  2:  4.8228 -  3.8483 0.99   1321  146 0.0850 0.1076      5.4347      5.6112|
|  3:  3.8483 -  3.3678 0.99   1298  144 0.1039 0.1531      5.4695      5.8739|
|  4:  3.3678 -  3.0626 0.99   1278  145 0.1265 0.1596      5.4985      5.6264|
|  5:  3.0626 -  2.8446 0.99   1283  141 0.1429 0.1906       5.399      5.6226|
|  6:  2.8446 -  2.6778 0.99   1278  139 0.1321 0.1950      5.2906      5.4929|
|  7:  2.6778 -  2.5444 0.99   1271  142 0.1348 0.1786      5.2246      5.4539|
|  8:  2.5444 -  2.4341 0.98   1261  145 0.1246 0.1755      5.1331      5.3922|
|  9:  2.4341 -  2.3407 0.98   1257  137 0.1223 0.1823      5.0862      5.3278|
| 10:  2.3407 -  2.2602 0.99   1240  141 0.1179 0.1918      5.0145      5.3015|
| 11:  2.2602 -  2.1897 0.98   1266  134 0.1229 0.1867      5.0045      5.2809|
| 12:  2.1897 -  2.1273 0.97   1235  140 0.1204 0.1847      4.9434      5.2847|
| 13:  2.1273 -  2.0715 1.00   1245  144 0.1223 0.1867      4.8594      5.1278|
| 14:  2.0715 -  2.0210 0.79   1021  108 0.1134 0.1861      4.7145      4.9771|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2532 -  4.8228  1376   153  0.93   9.86   0.96     0.93       8022.89|
|  2:  4.8228 -  3.8483  1321   146  0.95   8.11   0.99     0.97       9144.13|
|  3:  3.8483 -  3.3678  1298   144  0.93  11.14   1.01     1.00      10359.26|
|  4:  3.3678 -  3.0626  1278   145  0.92  14.16   1.00     0.97      11098.85|
|  5:  3.0626 -  2.8446  1283   141  0.89  16.98   0.99     0.96       9469.56|
|  6:  2.8446 -  2.6778  1278   139  0.89  17.03   0.98     0.96       8223.27|
|  7:  2.6778 -  2.5444  1271   142  0.89  17.15   0.98     0.95       7040.22|
|  8:  2.5444 -  2.4341  1261   145  0.90  16.16   0.98     0.95       6001.19|
|  9:  2.4341 -  2.3407  1257   137  0.90  16.26   0.98     0.94       5582.32|
| 10:  2.3407 -  2.2602  1240   141  0.90  16.05   0.98     0.93       4773.65|
| 11:  2.2602 -  2.1897  1266   134  0.89  17.44   0.97     0.93       4886.29|
| 12:  2.1897 -  2.1273  1235   140  0.91  15.91   0.98     0.96       4415.14|
| 13:  2.1273 -  2.0715  1245   144  0.90  16.91   0.97     0.96       3823.72|
| 14:  2.0715 -  2.0210  1021   108  0.91  15.23   0.94     0.90       2727.44|
|alpha:            min =        0.90 max =            1.00 mean =         0.95|
|beta:             min =     2727.44 max =        11098.85 mean =      6922.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.82|
|phase err.(test): min =        0.00 max =           89.83 mean =        14.25|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1658   ksol= 0.32   Bsol= 70.20   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.33,-1.15,-0.23,-0.00,-0.00,-0.00); trace/3= -0.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.188113                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1658   ksol= 0.32   Bsol= 70.20   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.33,-1.15,-0.23,-0.00,-0.00,-0.00); trace/3= -0.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.188113                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2532 -  4.8228 0.99   1376  153 0.0998 0.1343      5.4075      5.5588|
|  2:  4.8228 -  3.8483 0.99   1321  146 0.0848 0.1073      5.4335      5.6089|
|  3:  3.8483 -  3.3678 0.99   1298  144 0.1039 0.1531      5.4689      5.8743|
|  4:  3.3678 -  3.0626 0.99   1278  145 0.1267 0.1596      5.4993      5.6268|
|  5:  3.0626 -  2.8446 0.99   1283  141 0.1431 0.1909      5.3999      5.6233|
|  6:  2.8446 -  2.6778 0.99   1278  139 0.1322 0.1950      5.2911      5.4929|
|  7:  2.6778 -  2.5444 0.99   1271  142 0.1349 0.1787      5.2249      5.4545|
|  8:  2.5444 -  2.4341 0.98   1261  145 0.1247 0.1757      5.1333      5.3922|
|  9:  2.4341 -  2.3407 0.98   1257  137 0.1223 0.1821      5.0864      5.3278|
| 10:  2.3407 -  2.2602 0.99   1240  141 0.1179 0.1920       5.015      5.3026|
| 11:  2.2602 -  2.1897 0.98   1266  134 0.1229 0.1869       5.005      5.2815|
| 12:  2.1897 -  2.1273 0.97   1235  140 0.1204 0.1848      4.9435      5.2852|
| 13:  2.1273 -  2.0715 1.00   1245  144 0.1222 0.1865      4.8595      5.1279|
| 14:  2.0715 -  2.0210 0.79   1021  108 0.1135 0.1859      4.7144      4.9765|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2532 -  4.8228  1376   153  0.93   9.84   0.96     0.93       7998.63|
|  2:  4.8228 -  3.8483  1321   146  0.95   8.09   1.00     0.98       9118.46|
|  3:  3.8483 -  3.3678  1298   144  0.93  11.12   1.01     1.00      10340.52|
|  4:  3.3678 -  3.0626  1278   145  0.92  14.16   1.00     0.98      11107.53|
|  5:  3.0626 -  2.8446  1283   141  0.89  16.99   0.99     0.97       9477.84|
|  6:  2.8446 -  2.6778  1278   139  0.89  17.03   0.98     0.96       8231.23|
|  7:  2.6778 -  2.5444  1271   142  0.89  17.16   0.98     0.95       7043.31|
|  8:  2.5444 -  2.4341  1261   145  0.90  16.16   0.98     0.96       6001.64|
|  9:  2.4341 -  2.3407  1257   137  0.90  16.25   0.99     0.95       5585.23|
| 10:  2.3407 -  2.2602  1240   141  0.90  16.06   0.98     0.94       4776.45|
| 11:  2.2602 -  2.1897  1266   134  0.89  17.45   0.98     0.93       4893.87|
| 12:  2.1897 -  2.1273  1235   140  0.91  15.92   0.98     0.97       4418.21|
| 13:  2.1273 -  2.0715  1245   144  0.90  16.91   0.98     0.97       3824.21|
| 14:  2.0715 -  2.0210  1021   108  0.91  15.22   0.95     0.91       2725.31|
|alpha:            min =        0.91 max =            1.00 mean =         0.96|
|beta:             min =     2725.31 max =        11107.53 mean =      6920.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.82|
|phase err.(test): min =        0.00 max =           89.81 mean =        14.24|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.432)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.94   17.01    None  None   None       |
|    all(noH): 2823   0      0.00    99.94   17.01    None  None   None       |
|    Sol.    : 438    0      5.30    98.53   42.70    None  None   None       |
|    Mac.    : 2385   0      0.00    99.94   12.30    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.997: 1238   |   5:    49.973 -  59.967:   85        |
|      1:     9.997 -  19.991:  964   |   6:    59.967 -  69.961:   64        |
|      2:    19.991 -  29.985:  202   |   7:    69.961 -  79.955:   31        |
|      3:    29.985 -  39.979:  127   |   8:    79.955 -  89.949:    8        |
|      4:    39.979 -  49.973:   95   |   9:    89.949 -  99.943:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 309         
Filter by distance & map next to the model:
   mapped sites are within: 0.494 - 4.812
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 303 from: 309
   mapped sites are within: 0.704 - 4.812

peak=    5.596 closest distance to " O   HOH Z 111 " =    2.038
peak=    5.566 closest distance to " CB  GLN A 223 " =    1.441
peak=    5.087 closest distance to " CB  SER A  63 " =    1.253
peak=    4.904 closest distance to " CG  PRO A  54 " =    1.382
peak=    4.786 closest distance to " CB  ARG A 190 " =    1.700
peak=    4.695 closest distance to " CG  PRO A 213 " =    1.218
peak=    4.669 closest distance to " O   HOH Z 232 " =    2.298
peak=    4.664 closest distance to " CB  PRO A  54 " =    0.936
peak=    4.601 closest distance to " CG  PRO A 198 " =    1.282
peak=    4.588 closest distance to " CB  GLN A 183 " =    1.260
peak=    4.555 closest distance to " O   HOH Z 210 " =    0.841
peak=    4.541 closest distance to " CZ  PHE A 218 " =    1.083
peak=    4.501 closest distance to " O   HOH Z 369 " =    2.114
peak=    4.409 closest distance to " O   HOH Z 298 " =    2.035
peak=    4.390 closest distance to " NH2 ARG A 156 " =    1.201
peak=    4.364 closest distance to " C   PRO A 198 " =    1.525
peak=    4.344 closest distance to " CA  TYR A  30 " =    0.979
peak=    4.342 closest distance to " CD  ARG A 269 " =    0.901
peak=    4.315 closest distance to " CB  VAL A 202 " =    1.579
peak=    4.313 closest distance to " O   HOH Z 261 " =    1.908
peak=    4.303 closest distance to " CB  ARG A 275 " =    0.948
peak=    4.277 closest distance to " CB  LEU A 228 " =    1.063
peak=    4.238 closest distance to " CB  GLU A 128 " =    1.046
peak=    4.218 closest distance to " CB  TRP A 266 " =    0.993
peak=    4.177 closest distance to " O   HOH Z  15 " =    2.084
peak=    4.164 closest distance to " CB  ARG A  79 " =    1.373
peak=    4.155 closest distance to " O   HOH Z 234 " =    3.964
peak=    4.148 closest distance to " O   HOH Z 368 " =    2.147
peak=    4.146 closest distance to " CB  ASP A 124 " =    0.717
peak=    4.139 closest distance to " CD  LYS A 166 " =    1.312
peak=    4.136 closest distance to " CB  ASN A 148 " =    1.344
peak=    4.109 closest distance to " O   HOH Z 412 " =    3.781
peak=    4.108 closest distance to " CA  ALA A  51 " =    0.956
peak=    4.094 closest distance to " CG  PRO A 243 " =    1.131
peak=    4.085 closest distance to " CB  GLU A 277 " =    3.791
peak=    4.084 closest distance to " O   HOH Z 189 " =    2.849
peak=    4.078 closest distance to " CD ALYS A 290 " =    1.005
peak=    4.077 closest distance to " CG2 THR A 221 " =    1.031
peak=    4.073 closest distance to " O   HOH Z  40 " =    1.947
peak=    4.069 closest distance to " CB  GLU A 152 " =    1.155
peak=    4.050 closest distance to " O   HOH Z  19 " =    2.255
peak=    4.049 closest distance to " O   HOH Z 133 " =    2.502
peak=    4.039 closest distance to " CA  ASP A 191 " =    0.826
peak=    4.022 closest distance to " C   ILE A 106 " =    1.889
peak=    4.022 closest distance to " CD1 LEU A 300 " =    1.212
peak=    4.007 closest distance to " NE2 GLN A  11 " =    1.048
peak=    4.003 closest distance to " CB  TYR A 169 " =    0.823
peak=    3.998 closest distance to " CA  PRO A  54 " =    1.388
peak=    3.993 closest distance to " O   HOH Z 265 " =    2.172
peak=    3.971 closest distance to " O   HOH Z 271 " =    2.853
peak=    3.967 closest distance to " CD  ARG A 159 " =    0.809
peak=    3.966 closest distance to " O   HOH Z 134 " =    1.433
peak=    3.963 closest distance to " O   HOH Z 425 " =    1.372
peak=    3.951 closest distance to " NH1AARG A 145 " =    1.236
peak=    3.937 closest distance to " O   HOH Z  21 " =    1.832
peak=    3.936 closest distance to " O   HOH Z  49 " =    0.787
peak=    3.912 closest distance to " CZ  PHE A 192 " =    0.971
peak=    3.909 closest distance to " CA  ARG A  36 " =    1.185
peak=    3.887 closest distance to " O   THR A 251 " =    1.208
peak=    3.878 closest distance to " O   HOH Z  68 " =    1.952
peak=    3.876 closest distance to " O   HOH Z 287 " =    2.109
peak=    3.864 closest distance to " OD1 ASN A  69 " =    2.530
peak=    3.860 closest distance to " ND2 ASN A 187 " =    1.453
peak=    3.846 closest distance to " CA  ARG A 195 " =    1.172
peak=    3.845 closest distance to " N   ASN A 127 " =    1.299
peak=    3.841 closest distance to " O   HOH Z 126 " =    2.020
peak=    3.837 closest distance to " CB  ASP A 140 " =    0.874
peak=    3.817 closest distance to " CG1 ILE A  33 " =    1.246
peak=    3.816 closest distance to " O   HOH Z 285 " =    2.745
peak=    3.807 closest distance to " O   HOH Z 303 " =    2.204
peak=    3.806 closest distance to " O   HOH Z 126 " =    1.630
peak=    3.794 closest distance to " CA  ALA A 160 " =    0.950
peak=    3.790 closest distance to " O   HOH Z 214 " =    2.149
peak=    3.787 closest distance to " O   HOH Z  97 " =    2.101
peak=    3.784 closest distance to " CB  VAL A 265 " =    1.319
peak=    3.760 closest distance to " O   HOH Z 316 " =    3.205
peak=    3.753 closest distance to " CB  ASN A  39 " =    0.896
peak=    3.752 closest distance to " O   HOH Z 128 " =    2.213
peak=    3.749 closest distance to " O   HOH Z 383 " =    2.140
peak=    3.733 closest distance to " O   HOH Z  44 " =    2.070
peak=    3.730 closest distance to " CG2 VAL A 257 " =    0.917
peak=    3.725 closest distance to " CA  ALA A 295 " =    1.115
peak=    3.714 closest distance to " CB  SER A   3 " =    1.428
peak=    3.712 closest distance to " CG  GLU A  37 " =    0.905
peak=    3.706 closest distance to " O   HOH Z 423 " =    1.815
peak=    3.704 closest distance to " O   HOH Z 158 " =    3.029
peak=    3.697 closest distance to " O   HOH Z  78 " =    1.666
peak=    3.696 closest distance to " O   HOH Z 193 " =    2.071
peak=    3.688 closest distance to " CA  THR A 221 " =    0.875
peak=    3.687 closest distance to " O   HOH Z 180 " =    2.115
peak=    3.681 closest distance to " CG  LEU A 167 " =    1.180
peak=    3.679 closest distance to " NZ  LYS A 117 " =    3.329
peak=    3.677 closest distance to " CA  SER A  87 " =    0.994
peak=    3.672 closest distance to " O   HOH Z 427 " =    3.203
peak=    3.671 closest distance to " CD2 LEU A 297 " =    0.925
peak=    3.667 closest distance to " CB  LEU A  83 " =    0.842
peak=    3.655 closest distance to " O   HOH Z 403 " =    1.754
peak=    3.654 closest distance to " CB  ASN A 142 " =    1.042
peak=    3.652 closest distance to " CG1 VAL A 153 " =    1.053
peak=    3.648 closest distance to " CA  GLU A 152 " =    0.941
peak=    3.635 closest distance to " O   HOH Z  98 " =    1.760
peak=    3.626 closest distance to " CE1 TYR A 186 " =    1.269
peak=    3.624 closest distance to " CG2BVAL A  41 " =    0.869
peak=    3.606 closest distance to " OD1 ASN A 217 " =    1.735
peak=    3.596 closest distance to " OE1 GLN A  11 " =    2.018
peak=    3.595 closest distance to " O   HOH Z  63 " =    1.549
peak=    3.590 closest distance to " CB  ALA A 291 " =    1.249
peak=    3.585 closest distance to " O   SER A  87 " =    2.368
peak=    3.583 closest distance to " CA  MET A  40 " =    1.164
peak=    3.575 closest distance to " ND2 ASN A 249 " =    2.027
peak=    3.573 closest distance to " O   HOH Z 403 " =    1.396
peak=    3.570 closest distance to " CB  ALA A 242 " =    0.837
peak=    3.560 closest distance to " CB  SER A 141 " =    1.056
peak=    3.560 closest distance to " O   HOH Z 368 " =    3.652
peak=    3.552 closest distance to " O   HOH Z  43 " =    1.792
peak=    3.551 closest distance to " CD2 LEU A 255 " =    1.636
peak=    3.550 closest distance to " NE2 GLN A  77 " =    3.473
peak=    3.545 closest distance to " O   HOH Z 391 " =    2.935
peak=    3.543 closest distance to " CE  LYS A  76 " =    0.837
peak=    3.543 closest distance to " CA  ALA A 154 " =    1.017
peak=    3.540 closest distance to " CD  ARG A  66 " =    2.381
peak=    3.537 closest distance to " OD2 ASP A 298 " =    4.022
peak=    3.533 closest distance to " O   HOH Z 359 " =    1.553
peak=    3.532 closest distance to " O   HOH Z 294 " =    1.581
peak=    3.530 closest distance to " O   HOH Z 213 " =    1.871
peak=    3.527 closest distance to " CA  MET A 105 " =    1.037
peak=    3.526 closest distance to " CD2 TRP A 179 " =    1.317
peak=    3.525 closest distance to " O   HOH Z  80 " =    1.778
peak=    3.523 closest distance to " O   HOH Z 176 " =    1.579
peak=    3.521 closest distance to " CZ  PHE A  38 " =    1.296
peak=    3.507 closest distance to " O   HOH Z  59 " =    2.242
peak=    3.506 closest distance to " CB  GLN A 103 " =    0.917
peak=    3.504 closest distance to " O   TYR A 116 " =    1.303
peak=    3.497 closest distance to " CB  TRP A 179 " =    1.499
peak=    3.489 closest distance to " O   HOH Z 406 " =    1.680
peak=    3.485 closest distance to " N   ASN A  39 " =    1.322
peak=    3.475 closest distance to " CB  ALA A 104 " =    0.757
peak=    3.470 closest distance to " CB  MET A  40 " =    0.796
peak=    3.468 closest distance to " CA  THR A 264 " =    0.851
peak=    3.468 closest distance to " O   HOH Z 147 " =    1.768
peak=    3.466 closest distance to " O   HOH Z  88 " =    3.512
peak=    3.464 closest distance to " CG AARG A 275 " =    1.166
peak=    3.462 closest distance to " O   HOH Z 203 " =    1.860
peak=    3.459 closest distance to " O   PRO A 213 " =    1.614
peak=    3.459 closest distance to " CZ3 TRP A 266 " =    1.107
peak=    3.450 closest distance to " O   HOH Z 344 " =    3.182
peak=    3.450 closest distance to " O   ASN A  74 " =    1.592
peak=    3.443 closest distance to " CA  GLY A 241 " =    0.775
peak=    3.440 closest distance to " CD1 LEU A  96 " =    0.742
peak=    3.439 closest distance to " O   ALA A 165 " =    1.423
peak=    3.439 closest distance to " ND1 HIS A  81 " =    1.658
peak=    3.436 closest distance to " CB  ASN A 187 " =    1.062
peak=    3.433 closest distance to " CA  ALA A  21 " =    1.215
peak=    3.432 closest distance to " OG BSER A 134 " =    2.897
peak=    3.432 closest distance to " CB  GLU A  46 " =    0.989
peak=    3.430 closest distance to " CA  ALA A 158 " =    1.126
peak=    3.427 closest distance to " CB  ILE A 120 " =    1.224
peak=    3.424 closest distance to " CB  GLN A  89 " =    1.175
peak=    3.423 closest distance to " O   HOH Z 357 " =    2.699
peak=    3.423 closest distance to " O   HOH Z 116 " =    1.824
peak=    3.414 closest distance to " CB  GLN A  88 " =    1.272
peak=    3.414 closest distance to " O   HOH Z 280 " =    2.977
peak=    3.412 closest distance to " O   HOH Z 171 " =    3.848
peak=    3.405 closest distance to " CG BARG A 275 " =    1.389
peak=    3.401 closest distance to " O   HOH Z 421 " =    1.596
peak=    3.398 closest distance to " CB  ALA A   1 " =    4.812
peak=    3.397 closest distance to " OG BSER A 164 " =    2.456
peak=    3.393 closest distance to " O   HOH Z 174 " =    2.373
peak=    3.385 closest distance to " O   ALA A 158 " =    1.295
peak=    3.384 closest distance to " OD2 ASP A 200 " =    1.253
peak=    3.382 closest distance to " O   HOH Z 250 " =    1.398
peak=    3.378 closest distance to " O   HOH Z  47 " =    1.374
peak=    3.368 closest distance to " CD1 ILE A 106 " =    0.842
peak=    3.367 closest distance to " O  BHOH Z 338 " =    2.260
peak=    3.367 closest distance to " CA  ASP A 124 " =    0.767
peak=    3.363 closest distance to " O   HOH Z 135 " =    1.807
peak=    3.359 closest distance to " O   HOH Z 353 " =    2.754
peak=    3.355 closest distance to " N   ILE A  33 " =    1.027
peak=    3.355 closest distance to " N   VAL A 126 " =    1.517
peak=    3.354 closest distance to " O   HOH Z 346 " =    1.548
peak=    3.353 closest distance to " CD  ARG A 219 " =    1.067
peak=    3.352 closest distance to " O   HOH Z  61 " =    1.617
peak=    3.349 closest distance to " O   HOH Z 199 " =    1.605
peak=    3.349 closest distance to " CA  ILE A 106 " =    0.849
peak=    3.347 closest distance to " CB  ALA A   9 " =    1.625
peak=    3.346 closest distance to " O   HOH Z 422 " =    2.700
peak=    3.342 closest distance to " CB  SER A  62 " =    0.739
peak=    3.337 closest distance to " O   HOH Z  66 " =    2.121
peak=    3.330 closest distance to " O   HOH Z 402 " =    1.472
peak=    3.329 closest distance to " CB  MET A  47 " =    1.019
peak=    3.325 closest distance to " NZ  LYS A  48 " =    1.372
peak=    3.322 closest distance to " CA  ARG A 139 " =    1.303
peak=    3.320 closest distance to " O   HOH Z 102 " =    1.294
peak=    3.320 closest distance to " O   HOH Z 109 " =    2.669
peak=    3.318 closest distance to " O   HOH Z 114 " =    1.283
peak=    3.316 closest distance to " CB  PRO A 243 " =    1.413
peak=    3.309 closest distance to " CG  ARG A 159 " =    0.970
peak=    3.309 closest distance to " CA  GLU A  46 " =    0.801
peak=    3.308 closest distance to " O   HOH Z 285 " =    1.680
peak=    3.307 closest distance to " O   HOH Z 128 " =    2.451
peak=    3.307 closest distance to " NE2 HIS A 115 " =    1.030
peak=    3.306 closest distance to " O   HOH Z 193 " =    1.642
peak=    3.306 closest distance to " CA  ASP A 162 " =    1.165
peak=    3.303 closest distance to " CA  GLN A  88 " =    1.389
peak=    3.298 closest distance to " CD1 TRP A 266 " =    1.088
peak=    3.298 closest distance to " O   HOH Z 167 " =    1.702
peak=    3.297 closest distance to " N   CYS A 260 " =    0.818
peak=    3.297 closest distance to " NH2BARG A 145 " =    2.165
peak=    3.293 closest distance to " O   HOH Z 148 " =    3.359
peak=    3.289 closest distance to " CA  GLY A  98 " =    1.124
peak=    3.289 closest distance to " OG  SER A  22 " =    2.798
peak=    3.287 closest distance to " CA  VAL A 125 " =    1.159
peak=    3.285 closest distance to " O   HOH Z 433 " =    1.452
peak=    3.283 closest distance to " O   HOH Z 426 " =    1.563
peak=    3.282 closest distance to " O   HOH Z 291 " =    1.517
peak=    3.277 closest distance to " CZ3 TRP A  85 " =    0.940
peak=    3.277 closest distance to " O   HOH Z  48 " =    1.826
peak=    3.275 closest distance to " O   HOH Z 163 " =    1.636
peak=    3.274 closest distance to " CB  ALA A 248 " =    1.249
peak=    3.274 closest distance to " ND2 ASN A 249 " =    0.811
peak=    3.273 closest distance to " O   HOH Z 142 " =    1.591
peak=    3.271 closest distance to " O   HOH Z 247 " =    1.378
peak=    3.271 closest distance to " OE1 GLN A 278 " =    0.906
peak=    3.270 closest distance to " O   HOH Z 403 " =    2.190
peak=    3.267 closest distance to " O   HOH Z 325 " =    2.393
peak=    3.266 closest distance to " CB  ALA A 248 " =    1.097
peak=    3.266 closest distance to " O   HOH Z 432 " =    1.676
peak=    3.266 closest distance to " O   HOH Z 417 " =    3.252
peak=    3.258 closest distance to " CB  ALA A  34 " =    0.722
peak=    3.258 closest distance to " N   ARG A 156 " =    1.410
peak=    3.253 closest distance to " N   TYR A  15 " =    0.756
peak=    3.253 closest distance to " CB  PHE A 204 " =    0.888
peak=    3.251 closest distance to " O   HOH Z 193 " =    2.299
peak=    3.251 closest distance to " CA  ALA A 100 " =    1.121
peak=    3.244 closest distance to " CB  TYR A 116 " =    0.928
peak=    3.238 closest distance to " O   ASP A 124 " =    1.264
peak=    3.237 closest distance to " O   HOH Z 365 " =    2.905
peak=    3.230 closest distance to " CA  ARG A 102 " =    1.169
peak=    3.230 closest distance to " CG1 ILE A 151 " =    1.026
peak=    3.228 closest distance to " CG2 VAL A 197 " =    1.200
peak=    3.227 closest distance to " NE2 GLN A  58 " =    4.093
peak=    3.227 closest distance to " O   HOH Z 132 " =    2.731
peak=    3.225 closest distance to " O   HOH Z 371 " =    3.040
peak=    3.224 closest distance to " O   HOH Z  10 " =    1.815
peak=    3.223 closest distance to " O   HOH Z 258 " =    2.117
peak=    3.220 closest distance to " CB  ALA A  43 " =    0.906
peak=    3.219 closest distance to " CG2 THR A  29 " =    1.391
peak=    3.219 closest distance to " O   HOH Z 183 " =    1.419
peak=    3.215 closest distance to " OG  SER A  28 " =    1.502
peak=    3.211 closest distance to " CB  SER A 210 " =    0.871
peak=    3.201 closest distance to " O   HOH Z 197 " =    2.660
peak=    3.201 closest distance to " O   HOH Z 295 " =    1.496
peak=    3.200 closest distance to " CB  VAL A 257 " =    0.827
peak=    3.194 closest distance to " CA  THR A 221 " =    1.249
peak=    3.194 closest distance to " CA  GLY A 211 " =    1.236
peak=    3.190 closest distance to " CG  ARG A 138 " =    1.165
peak=    3.190 closest distance to " O   HOH Z  44 " =    3.291
peak=    3.186 closest distance to " O   GLN A 278 " =    1.263
peak=    3.182 closest distance to " O   HOH Z 201 " =    2.994
peak=    3.179 closest distance to " CB  SER A 212 " =    1.194
peak=    3.173 closest distance to " CA  TYR A 116 " =    1.362
peak=    3.172 closest distance to " O   HOH Z 327 " =    2.054
peak=    3.170 closest distance to " O   HOH Z 273 " =    2.838
peak=    3.169 closest distance to " O   HOH Z 329 " =    3.918
peak=    3.167 closest distance to " O   HOH Z 305 " =    3.749
peak=    3.167 closest distance to " ND2 ASN A 110 " =    1.476
peak=    3.160 closest distance to " O   HOH Z 134 " =    2.572
peak=    3.160 closest distance to " CG  MET A 185 " =    1.251
peak=    3.155 closest distance to " O   HOH Z  22 " =    2.747
peak=    3.155 closest distance to " CE2 TYR A  30 " =    0.804
peak=    3.152 closest distance to " CZ3 TRP A  92 " =    1.565
peak=    3.138 closest distance to " CB  ARG A 138 " =    1.063
peak=    3.136 closest distance to " O   HOH Z 272 " =    1.937
peak=    3.134 closest distance to " CB  SER A  26 " =    1.872
peak=    3.132 closest distance to " O   HOH Z   1 " =    2.445
peak=    3.128 closest distance to " O   HOH Z 271 " =    2.452
peak=    3.125 closest distance to " O   HOH Z 394 " =    1.823
peak=    3.123 closest distance to " CA  LEU A  83 " =    1.496
peak=    3.122 closest distance to " O   THR A 220 " =    1.158
peak=    3.120 closest distance to " O   HOH Z 327 " =    1.705
peak=    3.116 closest distance to " O   HOH Z  97 " =    2.349
peak=    3.112 closest distance to " CB  ALA A 100 " =    1.411
peak=    3.111 closest distance to " O   HOH Z 437 " =    1.161
peak=    3.109 closest distance to " CB  PHE A  61 " =    0.709
peak=    3.108 closest distance to " CG2AVAL A  72 " =    1.784
peak=    3.108 closest distance to " CA  ASN A 217 " =    1.341
peak=    3.108 closest distance to " CG2 ILE A 120 " =    0.799
peak=    3.103 closest distance to " O   ASP A 200 " =    1.620
peak=    3.095 closest distance to " O   ASN A 209 " =    1.301
peak=    3.095 closest distance to " CE2 TYR A 186 " =    0.900
peak=    3.091 closest distance to " CA  ALA A 291 " =    0.813
peak=    3.088 closest distance to " CG  ARG A 219 " =    1.167
peak=    3.088 closest distance to " CB  SER A 216 " =    0.858
peak=    3.084 closest distance to " O   TRP A 274 " =    1.763
peak=    3.083 closest distance to " NE2 HIS A 207 " =    1.190
peak=    3.072 closest distance to " CB  ARG A 156 " =    1.056
peak=    3.065 closest distance to " O   HOH Z 248 " =    1.843
peak=    3.064 closest distance to " CB  ASP A 140 " =    0.704
peak=    3.061 closest distance to " CZ3 TRP A 274 " =    4.526
peak=    3.049 closest distance to " O   HOH Z 302 " =    1.983
peak=    3.043 closest distance to " O   HOH Z 196 " =    0.918
peak=    3.038 closest distance to " CA  GLN A 223 " =    0.880
peak=    3.025 closest distance to " O   HOH Z 124 " =    1.858

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 215         
Filter by distance & map next to the model:
   mapped sites are within: 0.807 - 5.974
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 215 from: 215
   mapped sites are within: 0.807 - 5.974

peak=   -4.348 closest distance to " CG1 VAL A 112 " =    2.563
peak=   -4.309 closest distance to " CB  PRO A 243 " =    2.675
peak=   -4.268 closest distance to " O   HOH Z  10 " =    1.581
peak=   -4.266 closest distance to " CD  ARG A 156 " =    2.151
peak=   -4.257 closest distance to " CD  GLN A 223 " =    1.326
peak=   -4.255 closest distance to " CG1 VAL A 250 " =    2.686
peak=   -4.222 closest distance to " O   HOH Z 266 " =    5.354
peak=   -4.096 closest distance to " O   PRO A 198 " =    1.282
peak=   -4.053 closest distance to " CE2 TYR A  30 " =    2.757
peak=   -4.032 closest distance to " O   VAL A  67 " =    2.595
peak=   -4.018 closest distance to " C   ASN A 285 " =    2.573
peak=   -4.013 closest distance to " CD  ARG A  14 " =    3.313
peak=   -3.997 closest distance to " O   HOH Z  73 " =    2.284
peak=   -3.977 closest distance to " CA  GLY A 241 " =    3.175
peak=   -3.973 closest distance to " CZ3 TRP A 179 " =    1.118
peak=   -3.966 closest distance to " CD1 LEU A 101 " =    2.494
peak=   -3.947 closest distance to " O   PRO A 163 " =    2.242
peak=   -3.905 closest distance to " O   HOH Z 377 " =    1.839
peak=   -3.898 closest distance to " CD1 PHE A 130 " =    2.359
peak=   -3.892 closest distance to " O   HOH Z 290 " =    1.243
peak=   -3.885 closest distance to " O   HOH Z 394 " =    1.541
peak=   -3.867 closest distance to " C   HIS A 108 " =    1.090
peak=   -3.864 closest distance to " OE1 GLN A 223 " =    1.862
peak=   -3.856 closest distance to " O   HOH Z 196 " =    2.385
peak=   -3.835 closest distance to " CG  MET A 105 " =    0.932
peak=   -3.833 closest distance to " ND2 ASN A  45 " =    1.984
peak=   -3.833 closest distance to " OXT GLY A 302 " =    3.036
peak=   -3.814 closest distance to " OG  SER A  97 " =    2.267
peak=   -3.806 closest distance to " CD  GLN A  58 " =    0.954
peak=   -3.804 closest distance to " O   HOH Z  52 " =    1.617
peak=   -3.803 closest distance to " O   HOH Z 185 " =    2.499
peak=   -3.783 closest distance to " CD2 TYR A 293 " =    2.045
peak=   -3.769 closest distance to " CD1 PHE A  59 " =    1.981
peak=   -3.729 closest distance to " O   HOH Z 111 " =    1.968
peak=   -3.701 closest distance to " OD1 ASN A 148 " =    1.499
peak=   -3.700 closest distance to " O   HOH Z 150 " =    2.167
peak=   -3.693 closest distance to " CB  ALA A  10 " =    2.185
peak=   -3.680 closest distance to " OD1 ASP A 191 " =    1.601
peak=   -3.680 closest distance to " CA  ASP A 298 " =    1.112
peak=   -3.678 closest distance to " N   ALA A  43 " =    2.526
peak=   -3.676 closest distance to " CD1 ILE A 151 " =    2.441
peak=   -3.672 closest distance to " O   HOH Z 114 " =    1.326
peak=   -3.672 closest distance to " O   HOH Z 198 " =    2.436
peak=   -3.667 closest distance to " CG  ARG A 269 " =    2.464
peak=   -3.654 closest distance to " O   HOH Z 166 " =    1.749
peak=   -3.650 closest distance to " O   HOH Z  38 " =    1.146
peak=   -3.641 closest distance to " NH2 ARG A  66 " =    1.977
peak=   -3.616 closest distance to " CE2 PHE A  61 " =    2.602
peak=   -3.610 closest distance to " O   HOH Z 351 " =    1.564
peak=   -3.604 closest distance to " CB  ALA A 161 " =    2.730
peak=   -3.596 closest distance to " NH2 ARG A  79 " =    1.522
peak=   -3.593 closest distance to " CA  GLY A 133 " =    2.309
peak=   -3.590 closest distance to " CG2 ILE A  49 " =    2.804
peak=   -3.585 closest distance to " O   VAL A 189 " =    2.606
peak=   -3.577 closest distance to " O   HOH Z 234 " =    4.570
peak=   -3.576 closest distance to " O   HOH Z 393 " =    1.372
peak=   -3.569 closest distance to " C   LEU A 143 " =    1.217
peak=   -3.565 closest distance to " CG  ARG A  66 " =    2.462
peak=   -3.564 closest distance to " O   HOH Z 372 " =    2.612
peak=   -3.557 closest distance to " O   HOH Z 275 " =    1.648
peak=   -3.543 closest distance to " ND2 ASN A  45 " =    1.150
peak=   -3.542 closest distance to " CG1 VAL A 125 " =    1.998
peak=   -3.538 closest distance to " O   HOH Z  19 " =    2.143
peak=   -3.533 closest distance to " NH2AARG A 275 " =    5.523
peak=   -3.523 closest distance to " CG2 VAL A 189 " =    2.209
peak=   -3.517 closest distance to " CG  GLU A  53 " =    1.524
peak=   -3.516 closest distance to " CA  GLY A 241 " =    2.368
peak=   -3.515 closest distance to " CB  ALA A 291 " =    2.425
peak=   -3.503 closest distance to " O   ALA A  10 " =    1.715
peak=   -3.497 closest distance to " O   HOH Z 353 " =    2.275
peak=   -3.496 closest distance to " O   HOH Z  43 " =    1.500
peak=   -3.495 closest distance to " O   HOH Z  13 " =    1.727
peak=   -3.493 closest distance to " O   HOH Z 292 " =    4.705
peak=   -3.485 closest distance to " NE2 GLN A  88 " =    1.008
peak=   -3.479 closest distance to " CE3 TRP A 150 " =    2.056
peak=   -3.475 closest distance to " O   HOH Z 348 " =    2.237
peak=   -3.474 closest distance to " ND2 ASN A 187 " =    1.719
peak=   -3.470 closest distance to " O   HOH Z 106 " =    1.991
peak=   -3.470 closest distance to " NE2 GLN A 103 " =    1.844
peak=   -3.469 closest distance to " CD  GLN A  88 " =    0.807
peak=   -3.465 closest distance to " CD2 PHE A  59 " =    2.553
peak=   -3.464 closest distance to " CE3 TRP A  70 " =    1.938
peak=   -3.462 closest distance to " ND2 ASN A  69 " =    1.675
peak=   -3.459 closest distance to " O   HOH Z 177 " =    1.705
peak=   -3.449 closest distance to " O   HOH Z   6 " =    1.483
peak=   -3.449 closest distance to " CG1 VAL A 112 " =    2.850
peak=   -3.448 closest distance to " OE1 GLN A  88 " =    1.162
peak=   -3.443 closest distance to " O   SER A 276 " =    1.743
peak=   -3.440 closest distance to " CB  ALA A  43 " =    2.763
peak=   -3.436 closest distance to " O   HOH Z 350 " =    1.821
peak=   -3.435 closest distance to " O   HOH Z 128 " =    2.516
peak=   -3.435 closest distance to " C   SER A 206 " =    1.448
peak=   -3.433 closest distance to " N   THR A  18 " =    1.285
peak=   -3.423 closest distance to " CD  ARG A  79 " =    1.173
peak=   -3.423 closest distance to " ND2 ASN A  60 " =    1.371
peak=   -3.421 closest distance to " OD2 ASP A 171 " =    1.910
peak=   -3.417 closest distance to " O   HOH Z 275 " =    1.902
peak=   -3.413 closest distance to " O   VAL A  67 " =    2.991
peak=   -3.412 closest distance to " O   HOH Z 216 " =    1.831
peak=   -3.411 closest distance to " CG  GLU A 277 " =    1.221
peak=   -3.411 closest distance to " O   HOH Z 128 " =    4.295
peak=   -3.409 closest distance to " O   SER A 210 " =    2.019
peak=   -3.405 closest distance to " CD  ARG A 139 " =    1.633
peak=   -3.402 closest distance to " O   SER A 271 " =    2.104
peak=   -3.400 closest distance to " CG2 ILE A 263 " =    2.365
peak=   -3.390 closest distance to " CA  GLY A 203 " =    2.435
peak=   -3.386 closest distance to " CE BMET A  47 " =    2.135
peak=   -3.385 closest distance to " O   HOH Z  51 " =    1.665
peak=   -3.383 closest distance to " O   HOH Z 166 " =    1.759
peak=   -3.376 closest distance to " O   HOH Z 264 " =    1.784
peak=   -3.376 closest distance to " NE2 GLN A 194 " =    1.925
peak=   -3.373 closest distance to " C   ALA A 158 " =    1.414
peak=   -3.369 closest distance to " CD1 LEU A   5 " =    2.600
peak=   -3.368 closest distance to " CA  GLY A 241 " =    2.869
peak=   -3.367 closest distance to " CB  TRP A  85 " =    2.463
peak=   -3.364 closest distance to " CZ  PHE A  38 " =    2.675
peak=   -3.364 closest distance to " O   HOH Z  78 " =    1.902
peak=   -3.358 closest distance to " O   HOH Z 426 " =    1.762
peak=   -3.357 closest distance to " ND2BASN A 224 " =    1.839
peak=   -3.352 closest distance to " O   HOH Z  37 " =    1.946
peak=   -3.346 closest distance to " N   ALA A 226 " =    2.169
peak=   -3.339 closest distance to " O   HOH Z 118 " =    3.855
peak=   -3.335 closest distance to " CB  ALA A 131 " =    2.180
peak=   -3.330 closest distance to " O   HOH Z 232 " =    1.699
peak=   -3.329 closest distance to " CG  PRO A 163 " =    2.312
peak=   -3.324 closest distance to " CD1 LEU A 228 " =    2.440
peak=   -3.321 closest distance to " O   HOH Z 396 " =    1.850
peak=   -3.319 closest distance to " O   HOH Z 298 " =    2.602
peak=   -3.318 closest distance to " O   PRO A 243 " =    1.806
peak=   -3.317 closest distance to " O   HOH Z  11 " =    2.337
peak=   -3.315 closest distance to " N   THR A 157 " =    1.610
peak=   -3.302 closest distance to " O   HOH Z  70 " =    2.230
peak=   -3.302 closest distance to " CE  MET A  93 " =    1.592
peak=   -3.302 closest distance to " O   HOH Z  60 " =    2.373
peak=   -3.300 closest distance to " CG  PRO A 243 " =    1.738
peak=   -3.292 closest distance to " O   HOH Z 421 " =    3.588
peak=   -3.290 closest distance to " O   HOH Z 150 " =    1.280
peak=   -3.288 closest distance to " OG BSER A 134 " =    1.446
peak=   -3.285 closest distance to " O   ASP A  27 " =    2.137
peak=   -3.285 closest distance to " O   HOH Z 102 " =    1.590
peak=   -3.278 closest distance to " C   ASN A 187 " =    1.881
peak=   -3.275 closest distance to " CG2 THR A 221 " =    2.245
peak=   -3.271 closest distance to " O   HOH Z 211 " =    1.522
peak=   -3.270 closest distance to " O   HOH Z 312 " =    1.452
peak=   -3.269 closest distance to " CB  PRO A  54 " =    2.563
peak=   -3.263 closest distance to " O   VAL A 125 " =    2.218
peak=   -3.263 closest distance to " OD1 ASP A 171 " =    1.538
peak=   -3.259 closest distance to " O   HOH Z  90 " =    1.823
peak=   -3.257 closest distance to " O   HOH Z 357 " =    2.180
peak=   -3.257 closest distance to " N   SER A 276 " =    1.441
peak=   -3.251 closest distance to " O   HOH Z 292 " =    1.816
peak=   -3.248 closest distance to " O   HOH Z 236 " =    1.434
peak=   -3.247 closest distance to " CB  ASP A 132 " =    2.375
peak=   -3.245 closest distance to " O   HOH Z 377 " =    1.331
peak=   -3.241 closest distance to " O   HOH Z 183 " =    1.758
peak=   -3.241 closest distance to " CG  ASP A 231 " =    0.814
peak=   -3.239 closest distance to " CG  LEU A  83 " =    2.065
peak=   -3.238 closest distance to " CG  LEU A 281 " =    1.920
peak=   -3.234 closest distance to " O   HOH Z 241 " =    1.273
peak=   -3.229 closest distance to " CB  ASP A 286 " =    2.151
peak=   -3.224 closest distance to " O   HOH Z 371 " =    1.662
peak=   -3.219 closest distance to " OG BSER A 134 " =    1.987
peak=   -3.206 closest distance to " O   HOH Z 422 " =    1.484
peak=   -3.203 closest distance to " CD2 TYR A 293 " =    2.169
peak=   -3.202 closest distance to " CB  ARG A  79 " =    2.571
peak=   -3.199 closest distance to " O   HOH Z 283 " =    5.974
peak=   -3.199 closest distance to " O   HOH Z 156 " =    3.528
peak=   -3.198 closest distance to " CD2 LEU A 222 " =    2.093
peak=   -3.190 closest distance to " CG2BVAL A  41 " =    1.747
peak=   -3.189 closest distance to " O   HOH Z 113 " =    2.214
peak=   -3.183 closest distance to " CD  LYS A 289 " =    2.383
peak=   -3.178 closest distance to " O   HOH Z 189 " =    1.984
peak=   -3.176 closest distance to " O   HOH Z 407 " =    3.572
peak=   -3.174 closest distance to " NH2 ARG A 159 " =    2.294
peak=   -3.174 closest distance to " CD1 PHE A  16 " =    2.592
peak=   -3.170 closest distance to " NE1 TRP A 266 " =    2.308
peak=   -3.167 closest distance to " O   HOH Z 139 " =    3.032
peak=   -3.166 closest distance to " CE  MET A 105 " =    2.302
peak=   -3.164 closest distance to " CG  TRP A 266 " =    1.816
peak=   -3.163 closest distance to " N   THR A 235 " =    1.205
peak=   -3.163 closest distance to " CB  ALA A   9 " =    2.495
peak=   -3.158 closest distance to " CD1 TRP A 179 " =    1.049
peak=   -3.157 closest distance to " CG1 VAL A  78 " =    2.751
peak=   -3.156 closest distance to " C   ALA A 165 " =    2.004
peak=   -3.155 closest distance to " N   ALA A 248 " =    1.807
peak=   -3.154 closest distance to " O   GLY A 196 " =    1.184
peak=   -3.154 closest distance to " O   HOH Z 174 " =    2.247
peak=   -3.149 closest distance to " NH2 ARG A  79 " =    2.018
peak=   -3.147 closest distance to " OD1 ASN A 173 " =    1.293
peak=   -3.147 closest distance to " O   HOH Z 317 " =    2.301
peak=   -3.146 closest distance to " OD1 ASN A 187 " =    1.612
peak=   -3.146 closest distance to " O   HOH Z 191 " =    5.801
peak=   -3.146 closest distance to " OG1 THR A  82 " =    2.331
peak=   -3.145 closest distance to " O   HOH Z 198 " =    1.523
peak=   -3.145 closest distance to " CH2 TRP A 177 " =    2.158
peak=   -3.144 closest distance to " OD1 ASN A 301 " =    2.005
peak=   -3.142 closest distance to " O   HOH Z 413 " =    5.121
peak=   -3.140 closest distance to " O   GLY A 203 " =    2.383
peak=   -3.134 closest distance to " CA  GLY A  98 " =    2.202
peak=   -3.128 closest distance to " ND2 ASN A  60 " =    4.104
peak=   -3.126 closest distance to " O   HOH Z 436 " =    1.553
peak=   -3.125 closest distance to " CB  ALA A 291 " =    2.015
peak=   -3.119 closest distance to " CB  GLN A  11 " =    1.709
peak=   -3.118 closest distance to " C   GLY A  13 " =    0.958
peak=   -3.107 closest distance to " O   HOH Z  44 " =    2.194
peak=   -3.106 closest distance to " O   PHE A 218 " =    1.407
peak=   -3.101 closest distance to " O   TYR A 247 " =    2.911
peak=   -3.099 closest distance to " CB  ALA A 291 " =    2.251
peak=   -3.098 closest distance to " O   HOH Z 259 " =    2.118
peak=   -3.089 closest distance to " CG1AVAL A  41 " =    2.965
peak=   -3.081 closest distance to " O   ALA A  34 " =    2.554
peak=   -3.072 closest distance to " O   HOH Z 325 " =    2.002
peak=   -3.071 closest distance to " CB  PRO A 163 " =    2.621
peak=   -3.070 closest distance to " CD  GLN A  58 " =    1.224
peak=   -3.060 closest distance to " CG  ARG A 219 " =    2.766

================= 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    :  0.4235 0.4114   6.218945e+00   6.202352e+00
   1_bss:  0.4161 0.4037   6.209687e+00   6.190551e+00
   1_xyz:  0.2605 0.2840   5.839727e+00   5.910040e+00
   1_adp:  0.2355 0.2884   5.774841e+00   5.926526e+00
   1_occ:  0.2351 0.2884   5.774240e+00   5.926478e+00
   2_bss:  0.2334 0.2862   5.772644e+00   5.923527e+00
   2_xyz:  0.1644 0.2076   5.459875e+00   5.656513e+00
   2_adp:  0.1480 0.1891   5.366284e+00   5.569698e+00
   2_occ:  0.1478 0.1886   5.365169e+00   5.568996e+00
   3_bss:  0.1475 0.1883   5.363214e+00   5.565369e+00
   3_xyz:  0.1329 0.1762   5.282401e+00   5.496523e+00
   3_adp:  0.1302 0.1752   5.267265e+00   5.487454e+00
   3_occ:  0.1301 0.1751   5.267132e+00   5.487428e+00
   4_bss:  0.1301 0.1752   5.266959e+00   5.487298e+00
   4_xyz:  0.1211 0.1682   5.211353e+00   5.447974e+00
   4_adp:  0.1190 0.1685   5.202831e+00   5.447635e+00
   4_occ:  0.1190 0.1685   5.202755e+00   5.447693e+00
   5_bss:  0.1193 0.1683   5.203127e+00   5.447397e+00
   5_xyz:  0.1167 0.1689   5.196244e+00   5.449171e+00
   5_adp:  0.1169 0.1658   5.188202e+00   5.433895e+00
   5_occ:  0.1168 0.1658   5.188139e+00   5.433883e+00
   5_bss:  0.1168 0.1658   5.188113e+00   5.433924e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  67.975   0.517   2.137  -0.076   0.000  -0.000  -0.000
   1_xyz:  0.300  67.975   0.517   2.137  -0.076   0.000  -0.000  -0.000
   1_adp:  0.300  67.975   0.517   2.137  -0.076   0.000  -0.000  -0.000
   1_occ:  0.300  67.975   0.517   2.137  -0.076   0.000  -0.000  -0.000
   2_bss:  0.335  88.337  -1.138  -0.170  -0.790  -0.000  -0.000  -0.000
   2_xyz:  0.335  88.337  -1.138  -0.170  -0.790  -0.000  -0.000  -0.000
   2_adp:  0.335  88.337  -1.138  -0.170  -0.790  -0.000  -0.000  -0.000
   2_occ:  0.335  88.337  -1.138  -0.170  -0.790  -0.000  -0.000  -0.000
   3_bss:  0.333  80.001  -1.601  -1.108  -0.684  -0.000  -0.000  -0.000
   3_xyz:  0.333  80.001  -1.601  -1.108  -0.684  -0.000  -0.000  -0.000
   3_adp:  0.333  80.001  -1.601  -1.108  -0.684  -0.000  -0.000  -0.000
   3_occ:  0.333  80.001  -1.601  -1.108  -0.684  -0.000  -0.000  -0.000
   4_bss:  0.325  74.565  -1.607  -1.267  -0.532  -0.000  -0.000  -0.000
   4_xyz:  0.325  74.565  -1.607  -1.267  -0.532  -0.000  -0.000  -0.000
   4_adp:  0.325  74.565  -1.607  -1.267  -0.532  -0.000  -0.000  -0.000
   4_occ:  0.325  74.565  -1.607  -1.267  -0.532  -0.000  -0.000  -0.000
   5_bss:  0.325  74.565  -1.492  -1.259  -0.429  -0.000  -0.000  -0.000
   5_xyz:  0.325  74.565  -1.492  -1.259  -0.429  -0.000  -0.000  -0.000
   5_adp:  0.325  74.565  -1.492  -1.259  -0.429  -0.000  -0.000  -0.000
   5_occ:  0.325  74.565  -1.492  -1.259  -0.429  -0.000  -0.000  -0.000
   5_bss:  0.318  70.198  -1.332  -1.150  -0.233  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.880 0.5474  0.6905    51108.516
   1_bss:  47.195 0.5546  0.7263    49111.456
   1_xyz:  28.748 0.7724  0.9629    20922.567
   1_adp:  29.288 0.7660  0.9501    21824.315
   1_occ:  29.302 0.7658  0.9494    21817.494
   2_bss:  29.184 0.7670  0.9011    21639.382
   2_xyz:  20.493 0.8560  0.9721    11099.830
   2_adp:  18.043 0.8801  0.9752     9260.636
   2_occ:  18.023 0.8802  0.9752     9242.503
   3_bss:  17.942 0.8809  0.9609     9141.244
   3_xyz:  16.252 0.8962  0.9679     7828.571
   3_adp:  15.923 0.8994  0.9611     7708.888
   3_occ:  15.918 0.8994  0.9610     7705.498
   4_bss:  15.916 0.8994  0.9610     7701.745
   4_xyz:  15.113 0.9061  0.9650     7100.023
   4_adp:  15.057 0.9066  0.9560     7091.658
   4_occ:  15.056 0.9067  0.9559     7089.656
   5_bss:  15.072 0.9065  0.9582     7088.389
   5_xyz:  15.096 0.9064  0.9583     7121.446
   5_adp:  14.760 0.9092  0.9520     6923.732
   5_occ:  14.760 0.9092  0.9520     6922.861
   5_bss:  14.758 0.9092  0.9573     6920.800
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6528e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6528e-01
   1_xyz:   1.407  0.011  0.085 15.345  0.006  4.123   1.1253e-01
   1_adp:   1.407  0.011  0.085 15.345  0.006  4.123   1.1253e-01
   1_occ:   1.407  0.011  0.085 15.345  0.006  4.123   1.1253e-01
   2_bss:   1.407  0.011  0.085 15.345  0.006  4.123   1.1253e-01
   2_xyz:   1.186  0.010  0.084 15.047  0.005  4.146   7.9673e-02
   2_adp:   1.186  0.010  0.084 15.047  0.005  4.146   7.9673e-02
   2_occ:   1.186  0.010  0.084 15.047  0.005  4.146   7.9673e-02
   3_bss:   1.186  0.010  0.084 15.047  0.005  4.146   7.9673e-02
   3_xyz:   0.982  0.008  0.072 14.693  0.003  4.132   5.9061e-02
   3_adp:   0.982  0.008  0.072 14.693  0.003  4.132   5.9061e-02
   3_occ:   0.982  0.008  0.072 14.693  0.003  4.132   5.9061e-02
   4_bss:   0.982  0.008  0.072 14.693  0.003  4.132   5.9061e-02
   4_xyz:   1.107  0.010  0.082 14.872  0.004  4.140   7.1863e-02
   4_adp:   1.107  0.010  0.082 14.872  0.004  4.140   7.1863e-02
   4_occ:   1.107  0.010  0.082 14.872  0.004  4.140   7.1863e-02
   5_bss:   1.107  0.010  0.082 14.872  0.004  4.140   7.1863e-02
   5_xyz:   1.076  0.011  0.080 14.838  0.004  4.144   7.0975e-02
   5_adp:   1.076  0.011  0.080 14.838  0.004  4.144   7.0975e-02
   5_occ:   1.076  0.011  0.080 14.838  0.004  4.144   7.0975e-02
   5_bss:   1.076  0.011  0.080 14.838  0.004  4.144   7.0975e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.413   2.4509e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.413   2.4509e-01
   1_xyz:   9.595  0.091  0.262 85.118  0.048  1.992   2.1824e-01
   1_adp:   9.595  0.091  0.262 85.118  0.048  1.992   2.1824e-01
   1_occ:   9.595  0.091  0.262 85.118  0.048  1.992   2.1824e-01
   2_bss:   9.595  0.091  0.262 85.118  0.048  1.992   2.1824e-01
   2_xyz:   7.983  0.051  0.280 89.575  0.046  2.297   8.7489e-02
   2_adp:   7.983  0.051  0.280 89.575  0.046  2.297   8.7489e-02
   2_occ:   7.983  0.051  0.280 89.575  0.046  2.297   8.7489e-02
   3_bss:   7.983  0.051  0.280 89.575  0.046  2.297   8.7489e-02
   3_xyz:   8.315  0.043  0.229 80.159  0.042  2.325   6.9610e-02
   3_adp:   8.315  0.043  0.229 80.159  0.042  2.325   6.9610e-02
   3_occ:   8.315  0.043  0.229 80.159  0.042  2.325   6.9610e-02
   4_bss:   8.315  0.043  0.229 80.159  0.042  2.325   6.9610e-02
   4_xyz:   7.909  0.046  0.251 83.446  0.042  2.355   4.3945e-02
   4_adp:   7.909  0.046  0.251 83.446  0.042  2.355   4.3945e-02
   4_occ:   7.909  0.046  0.251 83.446  0.042  2.355   4.3945e-02
   5_bss:   7.909  0.046  0.251 83.446  0.042  2.355   4.3945e-02
   5_xyz:   8.139  0.050  0.247 81.214  0.039  2.367   5.2043e-02
   5_adp:   8.139  0.050  0.247 81.214  0.039  2.367   5.2043e-02
   5_occ:   8.139  0.050  0.247 81.214  0.039  2.367   5.2043e-02
   5_bss:   8.139  0.050  0.247 81.214  0.039  2.367   5.2043e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  98.93   0.00  18.36  88.43   0.00  13.67  98.93   2.81  43.91
   1_occ:  98.93   0.00  18.36  88.43   0.00  13.67  98.93   2.81  43.91
   2_bss:  98.93   0.00  18.36  88.43   0.00  13.67  98.93   2.81  43.91
   2_xyz:  98.93   0.00  18.36  88.43   0.00  13.67  98.93   2.81  43.91
   2_adp:  97.74   1.31  17.81  91.39   1.31  13.04  97.74   4.64  43.79
   2_occ:  97.74   1.31  17.81  91.39   1.31  13.04  97.74   4.64  43.79
   3_bss:  97.74   1.31  17.81  91.39   1.31  13.04  97.74   4.64  43.79
   3_xyz:  97.74   1.31  17.81  91.39   1.31  13.04  97.74   4.64  43.79
   3_adp:  97.34   0.00  17.60  91.89   0.00  12.81  97.34   5.23  43.69
   3_occ:  97.34   0.00  17.60  91.89   0.00  12.81  97.34   5.23  43.69
   4_bss:  97.34   0.00  17.60  91.89   0.00  12.81  97.34   5.23  43.69
   4_xyz:  97.34   0.00  17.60  91.89   0.00  12.81  97.34   5.23  43.69
   4_adp: 100.95   0.00  17.48 100.95   0.00  12.62 100.31   5.17  43.96
   4_occ: 100.95   0.00  17.48 100.95   0.00  12.62 100.31   5.17  43.96
   5_bss: 100.95   0.00  17.48 100.95   0.00  12.62 100.31   5.17  43.96
   5_xyz: 100.95   0.00  17.48 100.95   0.00  12.62 100.31   5.17  43.96
   5_adp:  99.94   0.00  17.01  99.94   0.00  12.29  98.53   5.30  42.69
   5_occ:  99.94   0.00  17.01  99.94   0.00  12.29  98.53   5.30  42.69
   5_bss:  99.94   0.00  17.01  99.94   0.00  12.30  98.53   5.30  42.70
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.648    0.026    0.444
   1_adp:    1.648    0.026    0.444
   1_occ:    1.648    0.026    0.444
   2_bss:    1.648    0.026    0.444
   2_xyz:    1.245    0.040    0.555
   2_adp:    1.245    0.040    0.555
   2_occ:    1.245    0.040    0.555
   3_bss:    1.245    0.040    0.555
   3_xyz:    1.158    0.035    0.594
   3_adp:    1.158    0.035    0.594
   3_occ:    1.158    0.035    0.594
   4_bss:    1.158    0.035    0.594
   4_xyz:    1.122    0.064    0.620
   4_adp:    1.122    0.064    0.620
   4_occ:    1.122    0.064    0.620
   5_bss:    1.122    0.064    0.620
   5_xyz:    1.200    0.057    0.634
   5_adp:    1.200    0.057    0.634
   5_occ:    1.200    0.057    0.634
   5_bss:    1.200    0.057    0.634
------------------------------------------------------------------------

CPU time actual refinement: 335.09


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1184/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_1184/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1184/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1184/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1184/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.95 
  Macro-tasks:
    bulk solvent and scale       = 49.62  
    individual site refinement   = 128.43 
    weights calculation          = 29.68  
    collect and process          = 6.70   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 214.56 
  Micro-tasks:
    mask                            = 1.75   
    f_calc                          = 103.06 
    alpha_beta                      = 8.23   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 110.80 
    fmodel                         = 8.21   
    r_factors                      = 0.24   
    phase_errors                   = 10.97  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 244.67 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.796 micro seconds
Total CPU time: 5.81 minutes
from_scatterers_fft:    634 calls, 102.67 s
gradients_fft:          579 calls,  98.25 s

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

# Date 2008-01-16 Time 06:37:26 PST -0800 (1200494246.44 s)
Start R-work = 0.4235, R-free = 0.4114 (no bulk solvent and anisotropic scale)
Final R-work = 0.1343, R-free = 0.1807 (no bulk solvent and anisotropic scale)

Start R-work = 0.4161, R-free = 0.4037
Final R-work = 0.1168, R-free = 0.1658