# Date 2008-01-16 Time 04:45:00 PST -0800 (1200487500.45 s)
#phil __OFF__

Command line arguments: "../450.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28410
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 450

-------------------------------------------------------------------------------
  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: (69.5475, 47.3993, 88.5498, 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: 3.29, per 1000 atoms: 1.17


================================== 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: (69.5475, 47.3993, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.981 1.98085
Completeness in resolution range: 0.935572
Completeness with d_max=infinity: 0.932721

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9810
                             d_min =   1.9809

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: (69.5475, 47.3993, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.981 1.98085
Completeness in resolution range: 0.935572
Completeness with d_max=infinity: 0.932721

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9814 -  4.2384 [2201/2229]  1980   221  10.0%
  bin  2:  4.2384 -  3.3768 [2109/2128]  1895   214  10.1%
  bin  3:  3.3768 -  2.9537 [2082/2102]  1880   202   9.7%
  bin  4:  2.9537 -  2.6853 [2064/2089]  1857   207  10.0%
  bin  5:  2.6853 -  2.4938 [2047/2066]  1838   209  10.2%
  bin  6:  2.4938 -  2.3474 [2030/2078]  1825   205  10.1%
  bin  7:  2.3474 -  2.2302 [2037/2069]  1844   193   9.5%
  bin  8:  2.2302 -  2.1334 [2033/2068]  1817   216  10.6%
  bin  9:  2.1334 -  2.0515 [2024/2054]  1827   197   9.7%
  bin 10:  2.0515 -  1.9809 [ 962/2055]   867    95   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_450/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: 0.15 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: 12
        2.11 -     2.80: 755
        2.80 -     3.50: 4390
        3.50 -     4.20: 9235
        4.20 -     4.90: 13586
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.408 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.496 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.661 3.040 -x+1,y+1/2,-z+1/2
  " NH2 ARG A  24 " - " OG  SER A  95 "  1.732 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.776 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27973 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_450/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_450/model_refine_001.geo

CPU time processing inputs: 9.16


============================ 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 = 69.5475 47.3993 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4229   r_free= 0.4172   ksol= 0.00   Bsol= 0.00   scale= 0.911    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.225309                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7272 0.99   1430  158 0.3289 0.3352      6.4786      6.4304|
|  2:  4.7272 -  3.7719 0.99   1375  153 0.3467 0.3736      6.6908      6.7923|
|  3:  3.7719 -  3.3009 0.99   1342  151 0.3993 0.3302      6.6055      6.5233|
|  4:  3.3009 -  3.0017 0.99   1351  142 0.4074 0.4157      6.4334      6.4321|
|  5:  3.0017 -  2.7881 0.99   1309  155 0.4498 0.4108      6.3045      6.3108|
|  6:  2.7881 -  2.6246 0.98   1334  144 0.4530 0.4916      6.2146      6.1619|
|  7:  2.6246 -  2.4938 0.99   1309  150 0.4433 0.4153      6.1699      6.0618|
|  8:  2.4938 -  2.3857 0.98   1324  142 0.4755 0.4477      6.1419      6.1192|
|  9:  2.3857 -  2.2942 0.98   1312  145 0.4697 0.4556      6.0803       6.119|
| 10:  2.2942 -  2.2153 0.98   1295  143 0.4943 0.4989      6.0662      6.0609|
| 11:  2.2153 -  2.1462 0.99   1313  156 0.4818 0.4746      5.9916      5.9818|
| 12:  2.1462 -  2.0850 0.98   1295  140 0.4855 0.4986       5.922      5.9566|
| 13:  2.0850 -  2.0303 0.93   1240  128 0.4884 0.4979      5.8621      5.8309|
| 14:  2.0303 -  1.9809 0.31    401   52 0.4516 0.4135      5.8419      5.7007|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9814 -  4.7272  1430   158  0.76  28.87   0.84     0.77      52298.75|
|  2:  4.7272 -  3.7719  1375   153  0.77  29.38   0.93     0.85      78368.03|
|  3:  3.7719 -  3.3009  1342   151  0.68  36.82   0.91     0.84      82396.15|
|  4:  3.3009 -  3.0017  1351   142  0.61  42.92   0.93     0.77      73390.72|
|  5:  3.0017 -  2.7881  1309   155  0.55  47.76   0.92     0.71      58983.10|
|  6:  2.7881 -  2.6246  1334   144  0.52  50.68   0.91     0.68      53577.82|
|  7:  2.6246 -  2.4938  1309   150  0.53  49.51   0.94     0.70      47582.87|
|  8:  2.4938 -  2.3857  1324   142  0.53  49.85   0.92     0.71      42401.47|
|  9:  2.3857 -  2.2942  1312   145  0.53  49.77   0.94     0.73      38991.69|
| 10:  2.2942 -  2.2153  1295   143  0.50  52.02   0.94     0.70      36680.72|
| 11:  2.2153 -  2.1462  1313   156  0.46  55.75   0.93     0.68      38673.34|
| 12:  2.1462 -  2.0850  1295   140  0.42  58.85   0.96     0.63      37210.01|
| 13:  2.0850 -  2.0303  1240   128  0.39  60.70   0.92     0.60      34159.32|
| 14:  2.0303 -  1.9809   401    52  0.42  58.40   1.01     0.55      26670.03|
|alpha:            min =        0.55 max =            0.85 mean =         0.72|
|beta:             min =    26670.03 max =        82396.15 mean =     51619.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.56|
|phase err.(work): min =        0.00 max =           90.00 mean =        47.12|
|phase err.(test): min =        0.00 max =           89.93 mean =        47.24|
|-----------------------------------------------------------------------------|

============================== 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 = 6.702236              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.773   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.329433              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.114   (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 |  1.408 -  1.757:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.757 -  2.106:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.106 -  2.456:       18 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.456 -  2.805:      737 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.805 -  3.154:     2049 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.154 -  3.503:     2341 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.503 -  3.852:     4529 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.852 -  4.202:     4706 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.202 -  4.551:     6141 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.551 -  4.900:     7445 |
|-----------------------------------------------------------------------------|
|-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 |        0.179 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.408 |       0.398 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.086)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4229   r_free= 0.4172   ksol= 0.00   Bsol= 0.00   scale= 0.911    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.225309                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4115   r_free= 0.4034   ksol= 0.31   Bsol= 44.04   scale= 0.954   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.67,-0.38,5.38,-0.00,0.00,0.00); trace/3= 0.78                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.211600                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.660368              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.476   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.735412              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.857   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4115      final r-factor (work) = 0.2953          |
| start r-factor (free) = 0.4034      final r-factor (free) = 0.3153          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.7548 = 5.66 * 0.50 * 6.2101 + 1.00 * 0.1791                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.1770 = 5.66 * 0.50 * 6.0332 + 1.00 * 0.1021                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2953      final r-factor (work) = 0.2678          |
| start r-factor (free) = 0.3153      final r-factor (free) = 0.3243          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4430 = 0.74 * 1.00 * 6.0332 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3408 = 0.74 * 1.00 * 5.8834 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.086)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.32   18.08    None  None   None       |
|    all(noH): 2823   0      0.00    93.32   18.08    None  None   None       |
|    Sol.    : 438    0      1.45    93.32   39.31    None  None   None       |
|    Mac.    : 2385   0      0.00    74.77   14.19    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:     0.000 -   9.332:  883   |   5:    46.661 -  55.993:   91        |
|      1:     9.332 -  18.664:  991   |   6:    55.993 -  65.326:   61        |
|      2:    18.664 -  27.997:  410   |   7:    65.326 -  74.658:   27        |
|      3:    27.997 -  37.329:  216   |   8:    74.658 -  83.990:    5        |
|      4:    37.329 -  46.661:  136   |   9:    83.990 -  93.322:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2678 r_free = 0.3243             target_work(ml) = 5.890         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2675 r_free = 0.3252             target_work(ml) = 5.890         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2675   r_free= 0.3252   ksol= 0.31   Bsol= 44.04   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.67,-0.38,5.38,-0.00,0.00,0.00); trace/3= 0.78                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.890311                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2656   r_free= 0.3242   ksol= 0.33   Bsol= 65.64   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-0.87,2.15,-0.00,0.00,0.00); trace/3= -0.41                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.888657                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.833011              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.676   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.356700              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.112  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2656      final r-factor (work) = 0.1821          |
| start r-factor (free) = 0.3242      final r-factor (free) = 0.2331          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.2041 = 6.83 * 0.50 * 5.8838 + 1.00 * 0.1021                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.7277 = 6.83 * 0.50 * 5.7499 + 1.00 * 0.0833                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1821      final r-factor (work) = 0.1624          |
| start r-factor (free) = 0.2331      final r-factor (free) = 0.2122          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0650 = 0.36 * 1.00 * 5.7499 + 1.00 * 0.0141                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9740 = 0.36 * 1.00 * 5.5056 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.086)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.70    92.45   17.36    None  None   None       |
|    all(noH): 2823   0      0.70    92.45   17.36    None  None   None       |
|    Sol.    : 438    0      5.37    92.45   40.76    None  None   None       |
|    Mac.    : 2385   0      0.70    73.66   13.06    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:     0.703 -   9.877: 1033   |   5:    46.575 -  55.749:  110        |
|      1:     9.877 -  19.051: 1050   |   6:    55.749 -  64.923:   55        |
|      2:    19.051 -  28.226:  270   |   7:    64.923 -  74.098:   27        |
|      3:    28.226 -  37.400:  137   |   8:    74.098 -  83.272:    5        |
|      4:    37.400 -  46.575:  134   |   9:    83.272 -  92.447:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1624 r_free = 0.2122             target_work(ml) = 5.458         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1623 r_free = 0.2122             target_work(ml) = 5.458         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1623   r_free= 0.2122   ksol= 0.33   Bsol= 65.64   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-0.87,2.15,-0.00,0.00,0.00); trace/3= -0.41                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.457695                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1622   r_free= 0.2104   ksol= 0.34   Bsol= 74.40   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-1.44,0.60,-0.00,0.00,0.00); trace/3= -1.15                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.453969                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.576068              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.108   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.968617              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.025  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1622      final r-factor (work) = 0.1306          |
| start r-factor (free) = 0.2104      final r-factor (free) = 0.1751          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.6884 = 4.58 * 0.50 * 5.5091 + 1.00 * 0.0833                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.3607 = 4.58 * 0.50 * 5.3677 + 1.00 * 0.0793                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1306      final r-factor (work) = 0.1233          |
| start r-factor (free) = 0.1751      final r-factor (free) = 0.1731          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.9445 = 2.97 * 1.00 * 5.3677 + 1.00 * 0.0100                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.5808 = 2.97 * 1.00 * 5.2444 + 1.00 * 0.0122                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.086)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.57    98.48   17.57    None  None   None       |
|    all(noH): 2823   0      0.57    98.48   17.57    None  None   None       |
|    Sol.    : 438    0      4.68    98.48   43.45    None  None   None       |
|    Mac.    : 2385   0      0.57    88.05   12.82    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:     0.570 -  10.361: 1204   |   5:    49.525 -  59.315:  102        |
|      1:    10.361 -  20.152:  966   |   6:    59.315 -  69.106:   75        |
|      2:    20.152 -  29.943:  216   |   7:    69.106 -  78.897:   24        |
|      3:    29.943 -  39.734:  116   |   8:    78.897 -  88.688:   14        |
|      4:    39.734 -  49.525:  104   |   9:    88.688 -  98.479:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1233 r_free = 0.1731             target_work(ml) = 5.239         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1232 r_free = 0.1730             target_work(ml) = 5.239         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1232   r_free= 0.1730   ksol= 0.34   Bsol= 74.40   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-1.44,0.60,-0.00,0.00,0.00); trace/3= -1.15                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.238525                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1233   r_free= 0.1729   ksol= 0.33   Bsol= 71.89   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.56,-1.55,0.15,-0.00,0.00,0.00); trace/3= -1.32                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.238290                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.170940              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.925  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.579073              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 103.108  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1233      final r-factor (work) = 0.1205          |
| start r-factor (free) = 0.1729      final r-factor (free) = 0.1678          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7721 = 2.17 * 0.50 * 5.2445 + 1.00 * 0.0793                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7370 = 2.17 * 0.50 * 5.2291 + 1.00 * 0.0610                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1205      final r-factor (work) = 0.1192          |
| start r-factor (free) = 0.1678      final r-factor (free) = 0.1678          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.4981 = 2.58 * 1.00 * 5.2291 + 1.00 * 0.0120                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.4505 = 2.58 * 1.00 * 5.2104 + 1.00 * 0.0124                              |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.086)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.59  17.36    None  None   None       |
|    all(noH): 2823   0      0.00    103.59  17.36    None  None   None       |
|    Sol.    : 438    0      0.00    103.59  43.10    None  None   None       |
|    Mac.    : 2385   0      0.00    91.95   12.63    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 -  10.359: 1223   |   5:    51.795 -  62.154:   91        |
|      1:    10.359 -  20.718:  973   |   6:    62.154 -  72.513:   58        |
|      2:    20.718 -  31.077:  216   |   7:    72.513 -  82.872:   23        |
|      3:    31.077 -  41.436:  121   |   8:    82.872 -  93.231:   11        |
|      4:    41.436 -  51.795:  106   |   9:    93.231 - 103.590:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1192 r_free = 0.1678             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1191 r_free = 0.1677             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1191   r_free= 0.1677   ksol= 0.33   Bsol= 71.89   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.56,-1.55,0.15,-0.00,0.00,0.00); trace/3= -1.32                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.210345                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1676   ksol= 0.33   Bsol= 66.49   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,-1.37,0.23,-0.00,0.00,0.00); trace/3= -1.15                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.210373                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.197632              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.684  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.023445              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.624  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1190      final r-factor (work) = 0.1190          |
| start r-factor (free) = 0.1676      final r-factor (free) = 0.1676          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7866 = 2.20 * 0.50 * 5.2107 + 1.00 * 0.0610                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7867 = 2.20 * 0.50 * 5.2104 + 1.00 * 0.0614                               |
|-----------------------------------------------------------------------------|
| number of iterations = 1       |    number of function evaluations = 1      |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1190      final r-factor (work) = 0.1190          |
| start r-factor (free) = 0.1676      final r-factor (free) = 0.1673          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.5553 = 2.02 * 1.00 * 5.2104 + 1.00 * 0.0124                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.5523 = 2.02 * 1.00 * 5.2088 + 1.00 * 0.0126                              |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.086)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.89  17.13    None  None   None       |
|    all(noH): 2823   0      0.00    110.89  17.13    None  None   None       |
|    Sol.    : 438    0      3.08    110.89  42.85    None  None   None       |
|    Mac.    : 2385   0      0.00    98.51   12.41    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.089: 1404   |   5:    55.444 -  66.533:   78        |
|      1:    11.089 -  22.178:  848   |   6:    66.533 -  77.622:   37        |
|      2:    22.178 -  33.267:  193   |   7:    77.622 -  88.711:   20        |
|      3:    33.267 -  44.356:  129   |   8:    88.711 -  99.800:    7        |
|      4:    44.356 -  55.444:  105   |   9:    99.800 - 110.889:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1190 r_free = 0.1673             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1189 r_free = 0.1673             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1189   r_free= 0.1673   ksol= 0.33   Bsol= 66.49   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,-1.37,0.23,-0.00,0.00,0.00); trace/3= -1.15                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.208348                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7272 0.99   1430  158 0.0982 0.1312       5.392       5.569|
|  2:  4.7272 -  3.7719 0.99   1375  153 0.0843 0.1058      5.4318       5.626|
|  3:  3.7719 -  3.3009 0.99   1342  151 0.1126 0.1533      5.5116      5.8357|
|  4:  3.3009 -  3.0017 0.99   1351  142 0.1310 0.1763      5.4995      5.6786|
|  5:  3.0017 -  2.7881 0.99   1309  155 0.1409 0.1672      5.3856       5.553|
|  6:  2.7881 -  2.6246 0.98   1334  144 0.1353 0.2182      5.2781      5.5672|
|  7:  2.6246 -  2.4938 0.99   1309  150 0.1375 0.1797      5.2434      5.4133|
|  8:  2.4938 -  2.3857 0.98   1324  142 0.1249 0.1781      5.1617      5.3838|
|  9:  2.3857 -  2.2942 0.98   1312  145 0.1265 0.2123      5.0993      5.4341|
| 10:  2.2942 -  2.2153 0.98   1295  143 0.1236 0.1731      5.0289      5.2106|
| 11:  2.2153 -  2.1462 0.99   1313  156 0.1259 0.2010      4.9939       5.364|
| 12:  2.1462 -  2.0850 0.98   1295  140 0.1230 0.1751      4.9495      5.1887|
| 13:  2.0850 -  2.0303 0.93   1240  128 0.1147 0.1765      4.8231      5.0262|
| 14:  2.0303 -  1.9809 0.31    401   52 0.0971 0.1919      4.6862      5.0638|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9814 -  4.7272  1430   158  0.94   9.45   0.96     0.93       7524.99|
|  2:  4.7272 -  3.7719  1375   153  0.95   8.11   1.01     0.99       9210.23|
|  3:  3.7719 -  3.3009  1342   151  0.93  11.87   1.02     1.02      10937.87|
|  4:  3.3009 -  3.0017  1351   142  0.91  14.49   1.01     1.00      11115.16|
|  5:  3.0017 -  2.7881  1309   155  0.89  17.13   0.99     0.97       9476.82|
|  6:  2.7881 -  2.6246  1334   144  0.88  18.02   0.97     0.95       8165.35|
|  7:  2.6246 -  2.4938  1309   150  0.89  17.20   0.98     0.95       7317.08|
|  8:  2.4938 -  2.3857  1324   142  0.89  17.15   0.99     0.94       6595.76|
|  9:  2.3857 -  2.2942  1312   145  0.89  17.63   0.99     0.94       5881.70|
| 10:  2.2942 -  2.2153  1295   143  0.89  17.37   0.97     0.93       5145.08|
| 11:  2.2153 -  2.1462  1313   156  0.89  17.64   0.97     0.93       4880.88|
| 12:  2.1462 -  2.0850  1295   140  0.89  17.55   0.99     0.98       4666.87|
| 13:  2.0850 -  2.0303  1240   128  0.89  17.23   0.97     0.95       3707.43|
| 14:  2.0303 -  1.9809   401    52  0.92  13.98   0.95     0.91       2683.49|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     2683.49 max =        11115.16 mean =      7216.89|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.33|
|phase err.(test): min =        0.00 max =           89.25 mean =        14.77|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1672   ksol= 0.33   Bsol= 66.49   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-1.13,0.44,-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: 5.208533                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1672   ksol= 0.33   Bsol= 66.49   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-1.13,0.44,-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: 5.208533                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7272 0.99   1430  158 0.0982 0.1314      5.3929      5.5706|
|  2:  4.7272 -  3.7719 0.99   1375  153 0.0843 0.1059      5.4325      5.6259|
|  3:  3.7719 -  3.3009 0.99   1342  151 0.1126 0.1534      5.5116      5.8361|
|  4:  3.3009 -  3.0017 0.99   1351  142 0.1310 0.1763      5.4995      5.6787|
|  5:  3.0017 -  2.7881 0.99   1309  155 0.1409 0.1672      5.3856      5.5527|
|  6:  2.7881 -  2.6246 0.98   1334  144 0.1353 0.2182      5.2781      5.5673|
|  7:  2.6246 -  2.4938 0.99   1309  150 0.1375 0.1797      5.2435      5.4133|
|  8:  2.4938 -  2.3857 0.98   1324  142 0.1249 0.1782       5.162       5.384|
|  9:  2.3857 -  2.2942 0.98   1312  145 0.1265 0.2123      5.0995      5.4342|
| 10:  2.2942 -  2.2153 0.98   1295  143 0.1236 0.1730      5.0291      5.2106|
| 11:  2.2153 -  2.1462 0.99   1313  156 0.1259 0.2009       4.994       5.364|
| 12:  2.1462 -  2.0850 0.98   1295  140 0.1230 0.1751      4.9493      5.1886|
| 13:  2.0850 -  2.0303 0.93   1240  128 0.1147 0.1765       4.823      5.0259|
| 14:  2.0303 -  1.9809 0.31    401   52 0.0971 0.1919      4.6866      5.0641|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9814 -  4.7272  1430   158  0.94   9.47   0.96     0.94       7539.75|
|  2:  4.7272 -  3.7719  1375   153  0.95   8.12   1.01     0.99       9220.16|
|  3:  3.7719 -  3.3009  1342   151  0.93  11.87   1.03     1.02      10941.64|
|  4:  3.3009 -  3.0017  1351   142  0.91  14.50   1.01     1.00      11116.59|
|  5:  3.0017 -  2.7881  1309   155  0.89  17.13   1.00     0.97       9478.10|
|  6:  2.7881 -  2.6246  1334   144  0.88  18.02   0.98     0.96       8165.30|
|  7:  2.6246 -  2.4938  1309   150  0.89  17.21   0.99     0.96       7318.62|
|  8:  2.4938 -  2.3857  1324   142  0.89  17.16   1.00     0.95       6598.51|
|  9:  2.3857 -  2.2942  1312   145  0.89  17.64   1.00     0.95       5882.57|
| 10:  2.2942 -  2.2153  1295   143  0.89  17.37   0.99     0.94       5143.84|
| 11:  2.2153 -  2.1462  1313   156  0.89  17.64   0.98     0.94       4877.17|
| 12:  2.1462 -  2.0850  1295   140  0.89  17.56   1.00     1.00       4666.19|
| 13:  2.0850 -  2.0303  1240   128  0.89  17.23   0.98     0.96       3706.30|
| 14:  2.0303 -  1.9809   401    52  0.92  13.99   0.96     0.92       2683.06|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2683.06 max =        11116.59 mean =      7219.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.34|
|phase err.(test): min =        0.00 max =           89.25 mean =        14.77|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.086)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.89  17.14    None  None   None       |
|    all(noH): 2823   0      0.00    110.89  17.14    None  None   None       |
|    Sol.    : 438    0      3.08    110.89  42.85    None  None   None       |
|    Mac.    : 2385   0      0.00    98.51   12.41    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 -  11.092: 1404   |   5:    55.447 -  66.536:   78        |
|      1:    11.092 -  22.181:  848   |   6:    66.536 -  77.625:   37        |
|      2:    22.181 -  33.270:  193   |   7:    77.625 -  88.714:   20        |
|      3:    33.270 -  44.359:  129   |   8:    88.714 -  99.803:    7        |
|      4:    44.359 -  55.447:  105   |   9:    99.803 - 110.892:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 310         
Filter by distance & map next to the model:
   mapped sites are within: 0.547 - 4.744
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 306 from: 310
   mapped sites are within: 0.705 - 4.744

peak=    7.409 closest distance to " O  BHOH Z  74 " =    1.137
peak=    5.298 closest distance to " CG  PRO A  54 " =    1.440
peak=    5.003 closest distance to " CB  GLN A 223 " =    1.456
peak=    4.874 closest distance to " O   HOH Z 113 " =    1.891
peak=    4.807 closest distance to " CG  PRO A  90 " =    1.233
peak=    4.753 closest distance to " O   HOH Z 287 " =    1.782
peak=    4.734 closest distance to " O   HOH Z 369 " =    2.277
peak=    4.719 closest distance to " CB  ARG A 190 " =    1.659
peak=    4.663 closest distance to " CZ  PHE A 218 " =    1.145
peak=    4.653 closest distance to " CB  ARG A 275 " =    0.974
peak=    4.580 closest distance to " CZ3 TRP A 266 " =    1.087
peak=    4.546 closest distance to " CD2 TRP A 179 " =    1.283
peak=    4.503 closest distance to " CA  ARG A  36 " =    1.080
peak=    4.433 closest distance to " O   HOH Z  49 " =    1.218
peak=    4.404 closest distance to " CA  TYR A  30 " =    0.952
peak=    4.328 closest distance to " CB  GLU A 277 " =    3.796
peak=    4.313 closest distance to " O   HOH Z 232 " =    2.360
peak=    4.302 closest distance to " CG  GLN A  58 " =    0.982
peak=    4.293 closest distance to " O   PRO A 198 " =    1.546
peak=    4.291 closest distance to " O   HOH Z 126 " =    1.615
peak=    4.278 closest distance to " O   HOH Z 188 " =    2.796
peak=    4.271 closest distance to " O   HOH Z 210 " =    1.047
peak=    4.266 closest distance to " CG  PRO A 243 " =    1.063
peak=    4.261 closest distance to " CB  ARG A  79 " =    1.480
peak=    4.253 closest distance to " CB  PRO A  54 " =    1.028
peak=    4.233 closest distance to " CB  GLN A 183 " =    1.244
peak=    4.225 closest distance to " CG  PRO A 213 " =    1.183
peak=    4.199 closest distance to " O   HOH Z 248 " =    1.278
peak=    4.185 closest distance to " CG  PRO A 198 " =    1.214
peak=    4.174 closest distance to " CB  SER A  63 " =    1.184
peak=    4.149 closest distance to " CA  ALA A 160 " =    0.931
peak=    4.140 closest distance to " CA  ALA A  51 " =    0.954
peak=    4.139 closest distance to " O   HOH Z 214 " =    1.277
peak=    4.134 closest distance to " CD1 LEU A  96 " =    0.833
peak=    4.088 closest distance to " O   SER A  87 " =    2.311
peak=    4.085 closest distance to " O   HOH Z 402 " =    1.416
peak=    4.074 closest distance to " O   HOH Z 346 " =    1.671
peak=    4.051 closest distance to " ND2 ASN A 249 " =    0.905
peak=    4.047 closest distance to " O   HOH Z 368 " =    3.637
peak=    4.030 closest distance to " CB  VAL A 202 " =    1.509
peak=    4.018 closest distance to " O   HOH Z 298 " =    1.963
peak=    4.014 closest distance to " NE2 GLN A  11 " =    1.088
peak=    4.013 closest distance to " CG  ARG A  66 " =    2.531
peak=    4.001 closest distance to " O   HOH Z  76 " =    1.073
peak=    3.985 closest distance to " O   HOH Z 406 " =    1.639
peak=    3.980 closest distance to " CB  ASN A 148 " =    1.449
peak=    3.971 closest distance to " NZ  LYS A 117 " =    2.914
peak=    3.963 closest distance to " ND2 ASN A 187 " =    1.616
peak=    3.957 closest distance to " CZ  PHE A  38 " =    1.212
peak=    3.935 closest distance to " CA  ARG A 195 " =    1.254
peak=    3.934 closest distance to " O   HOH Z 142 " =    1.577
peak=    3.930 closest distance to " O   HOH Z 412 " =    3.781
peak=    3.930 closest distance to " CB  VAL A 265 " =    1.259
peak=    3.923 closest distance to " CB  TYR A 169 " =    0.825
peak=    3.914 closest distance to " O   HOH Z 313 " =    1.984
peak=    3.910 closest distance to " CD  ARG A 269 " =    0.971
peak=    3.900 closest distance to " CB  GLU A 152 " =    1.219
peak=    3.886 closest distance to " CE  LYS A  76 " =    0.911
peak=    3.885 closest distance to " CB  ARG A  79 " =    0.960
peak=    3.868 closest distance to " CB  LYS A 117 " =    1.147
peak=    3.865 closest distance to " CB  PRO A  90 " =    1.126
peak=    3.847 closest distance to " O   HOH Z  63 " =    1.869
peak=    3.845 closest distance to " CA  VAL A 125 " =    1.125
peak=    3.842 closest distance to " O   HOH Z 126 " =    1.865
peak=    3.840 closest distance to " O   HOH Z 234 " =    3.791
peak=    3.823 closest distance to " O   HOH Z 368 " =    2.228
peak=    3.821 closest distance to " O   HOH Z  19 " =    1.807
peak=    3.798 closest distance to " O   HOH Z 251 " =    1.603
peak=    3.792 closest distance to " O   HOH Z 353 " =    2.755
peak=    3.791 closest distance to " CG2AVAL A 121 " =    2.235
peak=    3.791 closest distance to " O   HOH Z  43 " =    2.022
peak=    3.789 closest distance to " O   HOH Z 265 " =    2.091
peak=    3.789 closest distance to " CG2 ILE A 120 " =    1.326
peak=    3.784 closest distance to " CG  GLU A  37 " =    1.078
peak=    3.779 closest distance to " O   HOH Z 280 " =    2.921
peak=    3.762 closest distance to " O   HOH Z 359 " =    1.747
peak=    3.755 closest distance to " O   HOH Z 403 " =    1.601
peak=    3.746 closest distance to " O   HOH Z 423 " =    1.885
peak=    3.738 closest distance to " O  BHOH Z 338 " =    2.258
peak=    3.737 closest distance to " O   HOH Z  15 " =    2.316
peak=    3.731 closest distance to " O   HOH Z 303 " =    2.296
peak=    3.726 closest distance to " CD  LYS A  76 " =    1.980
peak=    3.724 closest distance to " O   HOH Z 427 " =    3.117
peak=    3.707 closest distance to " O   HOH Z 261 " =    2.363
peak=    3.704 closest distance to " CD1 ILE A 199 " =    1.178
peak=    3.704 closest distance to " O   HOH Z  80 " =    1.851
peak=    3.703 closest distance to " O   HOH Z 290 " =    1.013
peak=    3.695 closest distance to " O   HOH Z 361 " =    2.582
peak=    3.691 closest distance to " O   HOH Z 316 " =    3.139
peak=    3.688 closest distance to " OG BSER A 164 " =    2.347
peak=    3.682 closest distance to " CB  TRP A 179 " =    1.457
peak=    3.681 closest distance to " O   HOH Z  78 " =    1.645
peak=    3.680 closest distance to " O   HOH Z 193 " =    1.780
peak=    3.678 closest distance to " CB  ASN A 142 " =    1.134
peak=    3.664 closest distance to " OD1 ASN A  69 " =    2.373
peak=    3.663 closest distance to " N   TYR A 116 " =    1.577
peak=    3.651 closest distance to " CB  ASN A 187 " =    1.453
peak=    3.646 closest distance to " O   HOH Z 132 " =    2.890
peak=    3.644 closest distance to " CB  ASN A  39 " =    0.877
peak=    3.636 closest distance to " O   HOH Z 199 " =    1.594
peak=    3.614 closest distance to " O   THR A 220 " =    1.195
peak=    3.612 closest distance to " CB  ASN A 285 " =    1.000
peak=    3.594 closest distance to " CG2 VAL A 257 " =    0.782
peak=    3.592 closest distance to " CB  ASN A 215 " =    1.199
peak=    3.591 closest distance to " O   HOH Z 214 " =    3.104
peak=    3.586 closest distance to " CB  GLU A 128 " =    1.012
peak=    3.574 closest distance to " O   HOH Z  40 " =    1.936
peak=    3.571 closest distance to " CA  TYR A 116 " =    1.311
peak=    3.570 closest distance to " CG  MET A 185 " =    1.166
peak=    3.568 closest distance to " O   HOH Z 148 " =    3.553
peak=    3.566 closest distance to " CA  MET A 105 " =    1.182
peak=    3.565 closest distance to " O   HOH Z 193 " =    1.279
peak=    3.562 closest distance to " CB  SER A 210 " =    0.837
peak=    3.556 closest distance to " O   HOH Z 365 " =    2.793
peak=    3.549 closest distance to " CB  THR A  31 " =    1.574
peak=    3.548 closest distance to " CG  LEU A 167 " =    1.173
peak=    3.545 closest distance to " N   CYS A 260 " =    0.856
peak=    3.535 closest distance to " O   HOH Z 357 " =    2.131
peak=    3.535 closest distance to " O   HOH Z 371 " =    3.078
peak=    3.534 closest distance to " O   THR A 182 " =    1.439
peak=    3.525 closest distance to " CG2AVAL A  72 " =    1.878
peak=    3.519 closest distance to " O   HOH Z 180 " =    2.167
peak=    3.517 closest distance to " O   ALA A 165 " =    1.459
peak=    3.516 closest distance to " CD  LYS A 166 " =    1.334
peak=    3.510 closest distance to " O   HOH Z 250 " =    1.369
peak=    3.510 closest distance to " O   HOH Z 393 " =    3.026
peak=    3.506 closest distance to " O   TYR A 116 " =    1.443
peak=    3.506 closest distance to " CG  GLN A  11 " =    1.589
peak=    3.505 closest distance to " NE2 HIS A 207 " =    1.089
peak=    3.503 closest distance to " O   HOH Z 368 " =    4.248
peak=    3.493 closest distance to " CG  ARG A 138 " =    1.351
peak=    3.492 closest distance to " NH1AARG A 145 " =    1.434
peak=    3.477 closest distance to " N   ASN A  39 " =    1.308
peak=    3.476 closest distance to " CB  MET A  40 " =    0.976
peak=    3.476 closest distance to " O   HOH Z 325 " =    2.214
peak=    3.475 closest distance to " CB  TRP A 266 " =    1.115
peak=    3.474 closest distance to " O   HOH Z 117 " =    2.065
peak=    3.474 closest distance to " CD  ARG A 159 " =    0.786
peak=    3.468 closest distance to " O   HOH Z 380 " =    2.157
peak=    3.466 closest distance to " CA  GLU A 152 " =    0.799
peak=    3.465 closest distance to " CA  ASP A 162 " =    1.062
peak=    3.465 closest distance to " NE2 GLN A  77 " =    3.140
peak=    3.464 closest distance to " N   ARG A 156 " =    1.572
peak=    3.464 closest distance to " O   HOH Z 394 " =    3.863
peak=    3.464 closest distance to " CB  ALA A 299 " =    0.915
peak=    3.460 closest distance to " O   HOH Z  62 " =    2.207
peak=    3.452 closest distance to " O   HOH Z 285 " =    2.299
peak=    3.448 closest distance to " O   HOH Z 209 " =    2.277
peak=    3.445 closest distance to " O   HOH Z 422 " =    2.662
peak=    3.445 closest distance to " CG AARG A 275 " =    1.248
peak=    3.443 closest distance to " O   HOH Z 383 " =    1.962
peak=    3.443 closest distance to " O   HOH Z 214 " =    2.319
peak=    3.440 closest distance to " CB  LEU A  83 " =    0.733
peak=    3.439 closest distance to " CA  ILE A 234 " =    0.984
peak=    3.438 closest distance to " O   HOH Z  80 " =    1.927
peak=    3.436 closest distance to " O   ASP A 124 " =    1.241
peak=    3.435 closest distance to " CB  ASP A 124 " =    0.888
peak=    3.435 closest distance to " O   HOH Z  21 " =    1.860
peak=    3.427 closest distance to " CA  SER A  87 " =    1.044
peak=    3.426 closest distance to " CB  ASP A 298 " =    1.183
peak=    3.424 closest distance to " CA  ALA A 158 " =    1.403
peak=    3.423 closest distance to " CB  GLU A  46 " =    1.017
peak=    3.422 closest distance to " CA  ASN A 127 " =    1.272
peak=    3.420 closest distance to " OE2 GLU A  53 " =    1.227
peak=    3.418 closest distance to " CG2 VAL A 197 " =    1.140
peak=    3.415 closest distance to " O   HOH Z  35 " =    2.460
peak=    3.411 closest distance to " O   HOH Z 419 " =    1.917
peak=    3.410 closest distance to " CB  ASP A 140 " =    1.250
peak=    3.406 closest distance to " CB  ALA A 291 " =    0.889
peak=    3.395 closest distance to " O   HOH Z 298 " =    2.357
peak=    3.395 closest distance to " O   HOH Z 227 " =    1.501
peak=    3.390 closest distance to " O   HOH Z 425 " =    1.350
peak=    3.390 closest distance to " CB  LEU A 228 " =    1.139
peak=    3.385 closest distance to " O   HOH Z 246 " =    1.379
peak=    3.384 closest distance to " O   HOH Z 183 " =    1.657
peak=    3.381 closest distance to " OE2 GLU A  53 " =    1.873
peak=    3.380 closest distance to " CB  PHE A 204 " =    0.912
peak=    3.379 closest distance to " O   HOH Z 207 " =    1.097
peak=    3.378 closest distance to " O   ASP A 191 " =    1.581
peak=    3.374 closest distance to " CA  ALA A 154 " =    1.040
peak=    3.372 closest distance to " O   HOH Z 291 " =    1.399
peak=    3.370 closest distance to " OG  SER A 245 " =    1.590
peak=    3.369 closest distance to " CA  ASN A 215 " =    0.949
peak=    3.363 closest distance to " CB  SER A  26 " =    1.903
peak=    3.362 closest distance to " CB  SER A  62 " =    0.812
peak=    3.354 closest distance to " CE1 HIS A  81 " =    1.493
peak=    3.353 closest distance to " CA  GLN A  94 " =    0.797
peak=    3.351 closest distance to " O   HOH Z  59 " =    2.304
peak=    3.350 closest distance to " CB  SER A  62 " =    1.113
peak=    3.343 closest distance to " CG2 VAL A 268 " =    1.100
peak=    3.342 closest distance to " O   HOH Z  40 " =    1.774
peak=    3.341 closest distance to " CA  ILE A 106 " =    0.841
peak=    3.339 closest distance to " CE  LYS A 119 " =    1.090
peak=    3.336 closest distance to " O   HOH Z  88 " =    3.210
peak=    3.336 closest distance to " O   HOH Z 305 " =    3.636
peak=    3.335 closest distance to " CG1 ILE A  33 " =    1.221
peak=    3.334 closest distance to " O   HOH Z 156 " =    3.269
peak=    3.332 closest distance to " CB  THR A  52 " =    0.706
peak=    3.329 closest distance to " OE1 GLN A  55 " =    1.409
peak=    3.326 closest distance to " CA  ALA A 100 " =    0.926
peak=    3.326 closest distance to " O   HOH Z 139 " =    4.744
peak=    3.325 closest distance to " O   HOH Z 299 " =    4.454
peak=    3.322 closest distance to " O   HOH Z 293 " =    2.072
peak=    3.321 closest distance to " CD2 LEU A  83 " =    1.435
peak=    3.319 closest distance to " CB  GLN A  89 " =    1.338
peak=    3.316 closest distance to " O   HOH Z  85 " =    1.777
peak=    3.314 closest distance to " CG2 ILE A  20 " =    1.321
peak=    3.313 closest distance to " CG1 ILE A  20 " =    1.292
peak=    3.311 closest distance to " CA  ALA A 295 " =    1.028
peak=    3.308 closest distance to " O   HOH Z 203 " =    1.641
peak=    3.304 closest distance to " CD1 LEU A 300 " =    1.129
peak=    3.303 closest distance to " O   HOH Z  63 " =    2.301
peak=    3.303 closest distance to " CA  PHE A  59 " =    0.932
peak=    3.300 closest distance to " O   HOH Z  88 " =    1.718
peak=    3.300 closest distance to " NZ  LYS A 117 " =    1.318
peak=    3.300 closest distance to " O   HOH Z 417 " =    3.031
peak=    3.296 closest distance to " CB  PRO A 198 " =    1.273
peak=    3.295 closest distance to " O   HOH Z 144 " =    1.573
peak=    3.291 closest distance to " O   CYS A 168 " =    1.146
peak=    3.288 closest distance to " O   HOH Z 345 " =    3.950
peak=    3.288 closest distance to " O   HOH Z 102 " =    1.223
peak=    3.286 closest distance to " CA  LEU A  83 " =    1.222
peak=    3.285 closest distance to " CG1 VAL A 153 " =    1.081
peak=    3.282 closest distance to " OG  SER A  22 " =    2.528
peak=    3.282 closest distance to " CA  ASP A 140 " =    1.350
peak=    3.272 closest distance to " O   PHE A 192 " =    1.397
peak=    3.272 closest distance to " CD  PRO A  54 " =    0.962
peak=    3.270 closest distance to " CE1 TYR A 186 " =    1.307
peak=    3.268 closest distance to " CG2 THR A  29 " =    1.328
peak=    3.267 closest distance to " CA  THR A 264 " =    0.894
peak=    3.265 closest distance to " O   HOH Z   1 " =    2.124
peak=    3.261 closest distance to " OG1 THR A  82 " =    0.880
peak=    3.259 closest distance to " CA  THR A 221 " =    1.137
peak=    3.258 closest distance to " OG1 THR A 264 " =    0.705
peak=    3.258 closest distance to " OG BSER A 134 " =    2.774
peak=    3.245 closest distance to " CA  VAL A 153 " =    1.033
peak=    3.240 closest distance to " O   HOH Z 272 " =    1.803
peak=    3.240 closest distance to " CB  ASN A 110 " =    1.065
peak=    3.237 closest distance to " O   HOH Z 130 " =    2.222
peak=    3.231 closest distance to " N   HIS A 108 " =    1.808
peak=    3.230 closest distance to " CB  SER A 141 " =    1.130
peak=    3.229 closest distance to " O   THR A 251 " =    1.115
peak=    3.227 closest distance to " O   HOH Z 273 " =    1.104
peak=    3.226 closest distance to " O   HOH Z 132 " =    2.751
peak=    3.221 closest distance to " O   HOH Z 220 " =    1.504
peak=    3.219 closest distance to " O   HOH Z  54 " =    1.651
peak=    3.217 closest distance to " O   HOH Z  47 " =    1.835
peak=    3.215 closest distance to " OG  SER A  28 " =    1.605
peak=    3.215 closest distance to " CB  ARG A 138 " =    0.840
peak=    3.209 closest distance to " CB  ALA A 114 " =    0.715
peak=    3.209 closest distance to " O   LEU A 228 " =    1.861
peak=    3.207 closest distance to " CA  LEU A   5 " =    0.797
peak=    3.205 closest distance to " OD2 ASP A 298 " =    3.844
peak=    3.200 closest distance to " CB  ALA A 248 " =    1.464
peak=    3.194 closest distance to " CA  ASP A 124 " =    0.828
peak=    3.194 closest distance to " N   VAL A 265 " =    1.496
peak=    3.190 closest distance to " O   HOH Z 403 " =    2.023
peak=    3.184 closest distance to " NE2 GLN A  58 " =    4.674
peak=    3.182 closest distance to " O   HOH Z 258 " =    1.675
peak=    3.182 closest distance to " CD1 LEU A 167 " =    0.791
peak=    3.180 closest distance to " NH2AARG A 275 " =    3.473
peak=    3.176 closest distance to " O   HOH Z 193 " =    1.098
peak=    3.175 closest distance to " O   HOH Z 392 " =    2.533
peak=    3.169 closest distance to " OD2 ASP A  50 " =    2.904
peak=    3.168 closest distance to " CA  SER A  32 " =    1.610
peak=    3.167 closest distance to " NH2BARG A 145 " =    2.254
peak=    3.166 closest distance to " CE  LYS A  48 " =    1.130
peak=    3.166 closest distance to " CA  ASN A 217 " =    1.216
peak=    3.166 closest distance to " O   HOH Z 141 " =    1.576
peak=    3.165 closest distance to " CB  ASN A 148 " =    1.987
peak=    3.162 closest distance to " CG2 ILE A 239 " =    0.932
peak=    3.151 closest distance to " N   SER A 164 " =    1.008
peak=    3.150 closest distance to " O   HOH Z 162 " =    1.767
peak=    3.137 closest distance to " CA  ALA A  21 " =    1.296
peak=    3.137 closest distance to " ND2 ASN A 217 " =    1.173
peak=    3.134 closest distance to " O   HOH Z   4 " =    1.595
peak=    3.129 closest distance to " CB  ALA A  43 " =    0.831
peak=    3.128 closest distance to " CD  ARG A  66 " =    2.348
peak=    3.123 closest distance to " CD2 TYR A 186 " =    1.083
peak=    3.117 closest distance to " CB  ASN A 173 " =    1.111
peak=    3.116 closest distance to " CE3 TRP A 150 " =    1.136
peak=    3.116 closest distance to " CB  MET A 105 " =    0.827
peak=    3.112 closest distance to " O   HOH Z 128 " =    2.127
peak=    3.108 closest distance to " CG2 THR A 220 " =    0.860
peak=    3.108 closest distance to " N   PHE A 130 " =    1.294
peak=    3.106 closest distance to " CB  TYR A 247 " =    0.964
peak=    3.105 closest distance to " CG2 ILE A 234 " =    1.032
peak=    3.102 closest distance to " O   HOH Z 343 " =    2.593
peak=    3.100 closest distance to " O   HOH Z 371 " =    1.542
peak=    3.095 closest distance to " O   HOH Z 389 " =    1.926
peak=    3.090 closest distance to " NH1 ARG A 138 " =    0.990
peak=    3.087 closest distance to " O   HOH Z 162 " =    1.361
peak=    3.087 closest distance to " OG BSER A  99 " =    2.325
peak=    3.082 closest distance to " CB  ARG A 219 " =    1.010
peak=    3.082 closest distance to " CB  ARG A 139 " =    0.991
peak=    3.076 closest distance to " O   HOH Z 213 " =    1.916
peak=    3.068 closest distance to " CE1 HIS A  81 " =    1.440
peak=    3.065 closest distance to " O   HOH Z 327 " =    2.247
peak=    3.062 closest distance to " CG1AVAL A 121 " =    0.821
peak=    3.056 closest distance to " CE1 TYR A  30 " =    1.096
peak=    3.055 closest distance to " O   HOH Z  97 " =    1.276
peak=    3.045 closest distance to " CA  ARG A 156 " =    1.170
peak=    3.043 closest distance to " CB  ARG A 156 " =    1.106
peak=    3.019 closest distance to " CB  ARG A 102 " =    0.920
peak=    3.010 closest distance to " O   HOH Z 357 " =    2.479
peak=    3.009 closest distance to " O   HOH Z 421 " =    2.536

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.739 - 5.875
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 205
   mapped sites are within: 0.739 - 5.875

peak=   -4.728 closest distance to " SG  CYS A 254 " =    3.418
peak=   -4.658 closest distance to " O   PRO A 198 " =    1.318
peak=   -4.552 closest distance to " CG  GLN A  58 " =    1.026
peak=   -4.540 closest distance to " CD2 TYR A 293 " =    1.891
peak=   -4.450 closest distance to " C   HIS A 108 " =    1.091
peak=   -4.440 closest distance to " CG2 ILE A  49 " =    2.785
peak=   -4.377 closest distance to " CE2 PHE A  61 " =    2.731
peak=   -4.260 closest distance to " O   HOH Z 377 " =    2.088
peak=   -4.221 closest distance to " O   VAL A  67 " =    2.780
peak=   -4.196 closest distance to " CB  PRO A 243 " =    2.758
peak=   -4.157 closest distance to " CD  ARG A 156 " =    2.169
peak=   -4.117 closest distance to " CG1 VAL A 250 " =    2.701
peak=   -4.117 closest distance to " CG2 ILE A  20 " =    2.969
peak=   -4.072 closest distance to " O  BHOH Z  74 " =    0.761
peak=   -4.000 closest distance to " O   HOH Z 278 " =    1.080
peak=   -3.994 closest distance to " O   HOH Z 196 " =    2.073
peak=   -3.991 closest distance to " OE1 GLN A 223 " =    2.231
peak=   -3.986 closest distance to " O   HOH Z 193 " =    0.979
peak=   -3.983 closest distance to " OG BSER A 134 " =    1.249
peak=   -3.977 closest distance to " O   HOH Z 166 " =    1.792
peak=   -3.973 closest distance to " CG  GLN A  11 " =    1.546
peak=   -3.960 closest distance to " O   HOH Z 198 " =    1.474
peak=   -3.933 closest distance to " O   HOH Z 283 " =    2.546
peak=   -3.933 closest distance to " O   HOH Z 150 " =    2.370
peak=   -3.879 closest distance to " O   SER A 210 " =    1.789
peak=   -3.872 closest distance to " OXT GLY A 302 " =    3.059
peak=   -3.870 closest distance to " O   HOH Z 267 " =    5.685
peak=   -3.842 closest distance to " CE3 TRP A 150 " =    2.319
peak=   -3.835 closest distance to " O   HOH Z 211 " =    1.212
peak=   -3.833 closest distance to " N   ALA A  43 " =    2.726
peak=   -3.832 closest distance to " CB  HIS A  86 " =    1.122
peak=   -3.771 closest distance to " O   HOH Z   6 " =    1.948
peak=   -3.763 closest distance to " CG  PRO A 243 " =    1.659
peak=   -3.761 closest distance to " CD  GLN A 223 " =    1.559
peak=   -3.752 closest distance to " O   HOH Z 348 " =    2.177
peak=   -3.749 closest distance to " O   HOH Z 154 " =    1.656
peak=   -3.743 closest distance to " CA  ASP A 298 " =    1.080
peak=   -3.742 closest distance to " CD1 LEU A 101 " =    2.266
peak=   -3.741 closest distance to " O   HOH Z 174 " =    2.525
peak=   -3.731 closest distance to " CA  GLY A 241 " =    2.388
peak=   -3.723 closest distance to " NH2 ARG A  79 " =    1.560
peak=   -3.722 closest distance to " O   HOH Z  10 " =    1.567
peak=   -3.718 closest distance to " CG1 VAL A 112 " =    2.713
peak=   -3.711 closest distance to " CG  ARG A 269 " =    2.289
peak=   -3.708 closest distance to " N   THR A  52 " =    1.654
peak=   -3.704 closest distance to " CG1 VAL A 112 " =    2.700
peak=   -3.697 closest distance to " CD  ARG A  79 " =    1.253
peak=   -3.696 closest distance to " OG  SER A  97 " =    2.248
peak=   -3.694 closest distance to " O   HOH Z 394 " =    1.640
peak=   -3.683 closest distance to " O   HOH Z 366 " =    1.677
peak=   -3.680 closest distance to " O   HOH Z 374 " =    1.943
peak=   -3.660 closest distance to " O   PRO A 163 " =    2.043
peak=   -3.646 closest distance to " O   ALA A  34 " =    2.589
peak=   -3.643 closest distance to " CB  ALA A  43 " =    2.642
peak=   -3.642 closest distance to " CH2 TRP A 179 " =    1.275
peak=   -3.637 closest distance to " CA  GLY A 241 " =    3.377
peak=   -3.636 closest distance to " O   HOH Z 149 " =    2.031
peak=   -3.623 closest distance to " CB  TRP A  85 " =    2.505
peak=   -3.622 closest distance to " CE  MET A 105 " =    2.499
peak=   -3.618 closest distance to " CB  ALA A 161 " =    2.615
peak=   -3.607 closest distance to " O   HOH Z 106 " =    1.981
peak=   -3.604 closest distance to " CE BMET A  47 " =    1.584
peak=   -3.601 closest distance to " CD2 HIS A 207 " =    2.172
peak=   -3.595 closest distance to " CG  ARG A  66 " =    2.474
peak=   -3.582 closest distance to " CD2 PHE A  61 " =    2.144
peak=   -3.581 closest distance to " CB  ALA A 184 " =    2.404
peak=   -3.580 closest distance to " O   HOH Z  64 " =    1.394
peak=   -3.576 closest distance to " OD1 ASP A 171 " =    1.508
peak=   -3.574 closest distance to " O   HOH Z 357 " =    2.256
peak=   -3.572 closest distance to " CB  PHE A 192 " =    2.151
peak=   -3.566 closest distance to " O   HOH Z 102 " =    1.515
peak=   -3.562 closest distance to " O   GLU A 152 " =    1.332
peak=   -3.550 closest distance to " ND2 ASN A  45 " =    1.268
peak=   -3.545 closest distance to " O   HOH Z 191 " =    5.875
peak=   -3.541 closest distance to " O   HOH Z 210 " =    1.010
peak=   -3.533 closest distance to " CZ  PHE A  38 " =    2.340
peak=   -3.532 closest distance to " CB  ALA A 129 " =    2.449
peak=   -3.531 closest distance to " C   ASN A 285 " =    2.318
peak=   -3.527 closest distance to " CD1 ILE A 199 " =    2.561
peak=   -3.524 closest distance to " O   ALA A  10 " =    1.756
peak=   -3.510 closest distance to " O   HOH Z 171 " =    2.288
peak=   -3.509 closest distance to " OD2 ASP A 191 " =    1.449
peak=   -3.501 closest distance to " ND2 ASN A  45 " =    1.961
peak=   -3.498 closest distance to " O   HOH Z  68 " =    1.295
peak=   -3.489 closest distance to " O   HOH Z  13 " =    1.882
peak=   -3.489 closest distance to " CG2 VAL A 189 " =    2.193
peak=   -3.482 closest distance to " NE  ARG A 156 " =    1.974
peak=   -3.481 closest distance to " O   HOH Z 421 " =    3.653
peak=   -3.480 closest distance to " O   HOH Z 252 " =    3.875
peak=   -3.476 closest distance to " CB  GLU A 277 " =    1.373
peak=   -3.472 closest distance to " O   HOH Z   6 " =    1.407
peak=   -3.470 closest distance to " CD1 PHE A  59 " =    2.017
peak=   -3.450 closest distance to " O   HOH Z 128 " =    2.662
peak=   -3.438 closest distance to " O   VAL A 174 " =    2.163
peak=   -3.438 closest distance to " O   HOH Z 285 " =    1.644
peak=   -3.429 closest distance to " O   TRP A  70 " =    1.667
peak=   -3.426 closest distance to " CE2 TYR A  30 " =    2.757
peak=   -3.425 closest distance to " O   HOH Z 216 " =    1.037
peak=   -3.425 closest distance to " CB  ALA A 248 " =    2.238
peak=   -3.423 closest distance to " NE2 GLN A  88 " =    1.146
peak=   -3.419 closest distance to " O   ILE A 106 " =    1.847
peak=   -3.408 closest distance to " CG  ASP A 132 " =    2.347
peak=   -3.404 closest distance to " CG  GLU A  53 " =    1.559
peak=   -3.404 closest distance to " CG  GLN A 103 " =    2.482
peak=   -3.403 closest distance to " O   HOH Z  19 " =    2.277
peak=   -3.395 closest distance to " O   SER A 276 " =    1.716
peak=   -3.394 closest distance to " OE1 GLN A  88 " =    1.109
peak=   -3.383 closest distance to " O   HOH Z 185 " =    2.406
peak=   -3.382 closest distance to " O   HOH Z  63 " =    1.410
peak=   -3.378 closest distance to " O   HOH Z 131 " =    4.222
peak=   -3.378 closest distance to " O   HOH Z 368 " =    1.843
peak=   -3.377 closest distance to " O   HOH Z 407 " =    2.874
peak=   -3.375 closest distance to " CD  GLU A 236 " =    1.171
peak=   -3.373 closest distance to " CG1AVAL A  41 " =    2.590
peak=   -3.362 closest distance to " O   HOH Z 174 " =    3.648
peak=   -3.356 closest distance to " NH2 ARG A  79 " =    2.370
peak=   -3.354 closest distance to " CD  PRO A 243 " =    1.984
peak=   -3.349 closest distance to " CG1 VAL A  78 " =    2.762
peak=   -3.347 closest distance to " CG  MET A 105 " =    1.054
peak=   -3.336 closest distance to " O   HOH Z 113 " =    1.631
peak=   -3.332 closest distance to " CZ  TYR A 169 " =    1.854
peak=   -3.331 closest distance to " CZ3 TRP A 274 " =    2.413
peak=   -3.330 closest distance to " O   HOH Z 281 " =    2.599
peak=   -3.330 closest distance to " O   HOH Z 133 " =    1.394
peak=   -3.329 closest distance to " O   HOH Z 393 " =    1.265
peak=   -3.329 closest distance to " CG1BVAL A  41 " =    2.680
peak=   -3.329 closest distance to " O   VAL A 257 " =    1.342
peak=   -3.321 closest distance to " O   HOH Z 156 " =    3.588
peak=   -3.320 closest distance to " O   VAL A 189 " =    1.793
peak=   -3.320 closest distance to " O   TRP A  92 " =    2.036
peak=   -3.317 closest distance to " O   HOH Z 275 " =    1.557
peak=   -3.312 closest distance to " O   HOH Z 114 " =    3.381
peak=   -3.312 closest distance to " CA  ASP A  65 " =    1.361
peak=   -3.309 closest distance to " CZ  ARG A 156 " =    2.918
peak=   -3.300 closest distance to " O   HOH Z 244 " =    1.429
peak=   -3.297 closest distance to " CD  ARG A 195 " =    5.117
peak=   -3.294 closest distance to " CE1 TYR A 247 " =    2.706
peak=   -3.289 closest distance to " CD2 LEU A 282 " =    2.126
peak=   -3.287 closest distance to " CG  GLN A  58 " =    1.346
peak=   -3.286 closest distance to " O   HOH Z 128 " =    1.199
peak=   -3.282 closest distance to " O   HOH Z 351 " =    1.764
peak=   -3.282 closest distance to " CA  GLY A 203 " =    2.388
peak=   -3.280 closest distance to " O   PHE A 218 " =    1.442
peak=   -3.267 closest distance to " O   HOH Z 111 " =    3.903
peak=   -3.266 closest distance to " O   HOH Z 295 " =    1.674
peak=   -3.265 closest distance to " CG2 ILE A 263 " =    2.295
peak=   -3.264 closest distance to " O   HOH Z 165 " =    1.931
peak=   -3.262 closest distance to " O   HOH Z 264 " =    1.735
peak=   -3.261 closest distance to " CB  ALA A  10 " =    2.237
peak=   -3.257 closest distance to " O   TYR A 186 " =    1.766
peak=   -3.257 closest distance to " OD1 ASP A 191 " =    1.444
peak=   -3.255 closest distance to " O   HOH Z  38 " =    1.690
peak=   -3.253 closest distance to " O   GLN A 240 " =    2.656
peak=   -3.253 closest distance to " CB  PHE A  16 " =    2.452
peak=   -3.252 closest distance to " O   HOH Z 215 " =    1.177
peak=   -3.249 closest distance to " SG ACYS A 201 " =    1.127
peak=   -3.246 closest distance to " O   HOH Z 150 " =    1.927
peak=   -3.246 closest distance to " O   HOH Z 265 " =    2.504
peak=   -3.245 closest distance to " NZ  LYS A 166 " =    1.489
peak=   -3.236 closest distance to " CB  ALA A 291 " =    2.385
peak=   -3.235 closest distance to " CG2AVAL A  72 " =    2.571
peak=   -3.226 closest distance to " O   HOH Z 256 " =    2.382
peak=   -3.222 closest distance to " NE2 GLN A  88 " =    1.933
peak=   -3.217 closest distance to " CD2 TYR A 247 " =    2.461
peak=   -3.207 closest distance to " O   HOH Z  71 " =    2.900
peak=   -3.204 closest distance to " O   HOH Z 418 " =    1.436
peak=   -3.200 closest distance to " CD1 LEU A   5 " =    2.480
peak=   -3.194 closest distance to " O   HOH Z 345 " =    2.983
peak=   -3.192 closest distance to " C   SER A 206 " =    1.503
peak=   -3.185 closest distance to " CA  GLY A 241 " =    3.165
peak=   -3.184 closest distance to " O   HOH Z 389 " =    1.666
peak=   -3.183 closest distance to " NH2AARG A 275 " =    5.162
peak=   -3.183 closest distance to " NE2 GLN A 278 " =    1.635
peak=   -3.182 closest distance to " OG  SER A  26 " =    1.516
peak=   -3.172 closest distance to " O   HOH Z  78 " =    1.972
peak=   -3.171 closest distance to " O   ASN A 252 " =    1.448
peak=   -3.170 closest distance to " ND2 ASN A 249 " =    2.294
peak=   -3.164 closest distance to " O   HOH Z 145 " =    3.123
peak=   -3.162 closest distance to " O   ILE A 263 " =    2.245
peak=   -3.157 closest distance to " OH  TYR A 172 " =    1.981
peak=   -3.155 closest distance to " O   HOH Z  37 " =    1.786
peak=   -3.155 closest distance to " CG  TRP A 266 " =    1.908
peak=   -3.154 closest distance to " O   HOH Z 428 " =    2.995
peak=   -3.152 closest distance to " CD2 PHE A 225 " =    1.253
peak=   -3.152 closest distance to " O   HOH Z 196 " =    1.989
peak=   -3.147 closest distance to " O   HOH Z 290 " =    1.120
peak=   -3.146 closest distance to " O   HOH Z 359 " =    2.966
peak=   -3.143 closest distance to " CH2 TRP A 150 " =    1.139
peak=   -3.142 closest distance to " CG  LYS A 166 " =    2.218
peak=   -3.142 closest distance to " O   HOH Z 166 " =    1.590
peak=   -3.141 closest distance to " O   HOH Z 365 " =    1.242
peak=   -3.135 closest distance to " O   HOH Z 126 " =    1.913
peak=   -3.130 closest distance to " O   HOH Z 423 " =    2.436
peak=   -3.123 closest distance to " CZ  PHE A  38 " =    2.068
peak=   -3.122 closest distance to " CG  PHE A 283 " =    2.611
peak=   -3.118 closest distance to " CD1 TRP A  70 " =    1.115
peak=   -3.112 closest distance to " O   HOH Z 210 " =    1.663
peak=   -3.108 closest distance to " OD1 ASN A 148 " =    1.431
peak=   -3.106 closest distance to " NH2BARG A 145 " =    2.058
peak=   -3.096 closest distance to " O   VAL A 189 " =    2.670
peak=   -3.084 closest distance to " O   HOH Z  65 " =    0.739
peak=   -3.079 closest distance to " O   HOH Z  69 " =    1.940
peak=   -3.075 closest distance to " OG BSER A 134 " =    1.984
peak=   -3.051 closest distance to " CB  ASN A  45 " =    2.094
peak=   -3.034 closest distance to " O   HOH Z 116 " =    1.774

================= 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    :  0.4229 0.4172   6.225309e+00   6.207821e+00
   1_bss:  0.4115 0.4034   6.211600e+00   6.191557e+00
   1_xyz:  0.2953 0.3153   5.944812e+00   6.016838e+00
   1_adp:  0.2678 0.3243   5.890303e+00   6.032482e+00
   1_occ:  0.2675 0.3252   5.890311e+00   6.034129e+00
   2_bss:  0.2656 0.3242   5.888657e+00   6.034825e+00
   2_xyz:  0.1821 0.2331   5.556267e+00   5.751237e+00
   2_adp:  0.1624 0.2122   5.458003e+00   5.659440e+00
   2_occ:  0.1623 0.2122   5.457695e+00   5.659582e+00
   3_bss:  0.1622 0.2104   5.453969e+00   5.653006e+00
   3_xyz:  0.1306 0.1751   5.270732e+00   5.490076e+00
   3_adp:  0.1233 0.1731   5.239036e+00   5.475011e+00
   3_occ:  0.1232 0.1730   5.238525e+00   5.474359e+00
   4_bss:  0.1233 0.1729   5.238290e+00   5.473755e+00
   4_xyz:  0.1205 0.1678   5.216182e+00   5.450509e+00
   4_adp:  0.1192 0.1678   5.210455e+00   5.449001e+00
   4_occ:  0.1191 0.1677   5.210345e+00   5.448919e+00
   5_bss:  0.1190 0.1676   5.210373e+00   5.449111e+00
   5_xyz:  0.1190 0.1676   5.210373e+00   5.449111e+00
   5_adp:  0.1190 0.1673   5.208407e+00   5.446677e+00
   5_occ:  0.1189 0.1673   5.208348e+00   5.446678e+00
   5_bss:  0.1188 0.1672   5.208533e+00   5.446822e+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:  0.308  44.041  -2.674  -0.380   5.379  -0.000   0.000   0.000
   1_xyz:  0.308  44.041  -2.674  -0.380   5.379  -0.000   0.000   0.000
   1_adp:  0.308  44.041  -2.674  -0.380   5.379  -0.000   0.000   0.000
   1_occ:  0.308  44.041  -2.674  -0.380   5.379  -0.000   0.000   0.000
   2_bss:  0.327  65.637  -2.510  -0.870   2.153  -0.000   0.000   0.000
   2_xyz:  0.327  65.637  -2.510  -0.870   2.153  -0.000   0.000   0.000
   2_adp:  0.327  65.637  -2.510  -0.870   2.153  -0.000   0.000   0.000
   2_occ:  0.327  65.637  -2.510  -0.870   2.153  -0.000   0.000   0.000
   3_bss:  0.335  74.400  -2.595  -1.444   0.601  -0.000   0.000   0.000
   3_xyz:  0.335  74.400  -2.595  -1.444   0.601  -0.000   0.000   0.000
   3_adp:  0.335  74.400  -2.595  -1.444   0.601  -0.000   0.000   0.000
   3_occ:  0.335  74.400  -2.595  -1.444   0.601  -0.000   0.000   0.000
   4_bss:  0.332  71.887  -2.561  -1.552   0.155  -0.000   0.000   0.000
   4_xyz:  0.332  71.887  -2.561  -1.552   0.155  -0.000   0.000   0.000
   4_adp:  0.332  71.887  -2.561  -1.552   0.155  -0.000   0.000   0.000
   4_occ:  0.332  71.887  -2.561  -1.552   0.155  -0.000   0.000   0.000
   5_bss:  0.325  66.490  -2.302  -1.366   0.229  -0.000   0.000   0.000
   5_xyz:  0.325  66.490  -2.302  -1.366   0.229  -0.000   0.000   0.000
   5_adp:  0.325  66.490  -2.302  -1.366   0.229  -0.000   0.000   0.000
   5_occ:  0.325  66.490  -2.302  -1.366   0.229  -0.000   0.000   0.000
   5_bss:  0.325  66.493  -2.043  -1.130   0.437  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.135 0.5574  0.7186    51615.015
   1_bss:  45.692 0.5737  0.7630    48180.537
   1_xyz:  33.464 0.7195  0.9217    27665.951
   1_adp:  34.434 0.7076  0.9062    28899.106
   1_occ:  34.511 0.7067  0.9052    29033.835
   2_bss:  34.167 0.7109  0.8764    28863.213
   2_xyz:  23.319 0.8280  0.9774    14047.575
   2_adp:  20.482 0.8573  0.9858    11683.298
   2_occ:  20.480 0.8573  0.9857    11674.802
   3_bss:  20.217 0.8596  0.9628    11434.584
   3_xyz:  16.431 0.8940  0.9794     7979.282
   3_adp:  16.009 0.8981  0.9708     7730.176
   3_occ:  15.992 0.8982  0.9709     7719.323
   4_bss:  15.977 0.8984  0.9652     7719.524
   4_xyz:  15.379 0.9037  0.9680     7248.931
   4_adp:  15.327 0.9043  0.9601     7247.453
   4_occ:  15.326 0.9043  0.9600     7246.788
   5_bss:  15.330 0.9043  0.9658     7248.438
   5_xyz:  15.330 0.9043  0.9658     7248.438
   5_adp:  15.280 0.9047  0.9579     7215.768
   5_occ:  15.277 0.9047  0.9578     7216.201
   5_bss:  15.282 0.9047  0.9658     7218.540
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.7905e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.7905e-01
   1_xyz:   1.399  0.010  0.084 15.249  0.006  4.111   1.0210e-01
   1_adp:   1.399  0.010  0.084 15.249  0.006  4.111   1.0210e-01
   1_occ:   1.399  0.010  0.084 15.249  0.006  4.111   1.0210e-01
   2_bss:   1.399  0.010  0.084 15.249  0.006  4.111   1.0210e-01
   2_xyz:   1.214  0.010  0.084 15.018  0.004  4.109   8.3263e-02
   2_adp:   1.214  0.010  0.084 15.018  0.004  4.109   8.3263e-02
   2_occ:   1.214  0.010  0.084 15.018  0.004  4.109   8.3263e-02
   3_bss:   1.214  0.010  0.084 15.018  0.004  4.109   8.3263e-02
   3_xyz:   1.170  0.011  0.082 14.974  0.005  4.124   7.9307e-02
   3_adp:   1.170  0.011  0.082 14.974  0.005  4.124   7.9307e-02
   3_occ:   1.170  0.011  0.082 14.974  0.005  4.124   7.9307e-02
   4_bss:   1.170  0.011  0.082 14.974  0.005  4.124   7.9307e-02
   4_xyz:   1.018  0.008  0.077 14.464  0.004  4.128   6.1007e-02
   4_adp:   1.018  0.008  0.077 14.464  0.004  4.128   6.1007e-02
   4_occ:   1.018  0.008  0.077 14.464  0.004  4.128   6.1007e-02
   5_bss:   1.018  0.008  0.077 14.464  0.004  4.128   6.1007e-02
   5_xyz:   1.018  0.008  0.077 14.464  0.004  4.114   6.1445e-02
   5_adp:   1.018  0.008  0.077 14.464  0.004  4.114   6.1445e-02
   5_occ:   1.018  0.008  0.077 14.464  0.004  4.114   6.1445e-02
   5_bss:   1.018  0.008  0.077 14.464  0.004  4.114   6.1445e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.408   2.4396e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.408   2.4396e-01
   1_xyz:   9.179  0.055  0.323 83.940  0.041  1.942   9.6696e-02
   1_adp:   9.179  0.055  0.323 83.940  0.041  1.942   9.6696e-02
   1_occ:   9.179  0.055  0.323 83.940  0.041  1.942   9.6696e-02
   2_bss:   9.179  0.055  0.323 83.940  0.041  1.942   9.6696e-02
   2_xyz:   7.765  0.062  0.308 83.306  0.041  2.265   1.2231e-01
   2_adp:   7.765  0.062  0.308 83.306  0.041  2.265   1.2231e-01
   2_occ:   7.765  0.062  0.308 83.306  0.041  2.265   1.2231e-01
   3_bss:   7.765  0.062  0.308 83.306  0.041  2.265   1.2231e-01
   3_xyz:   8.295  0.053  0.278 83.709  0.042  2.231   6.1446e-02
   3_adp:   8.295  0.053  0.278 83.709  0.042  2.231   6.1446e-02
   3_occ:   8.295  0.053  0.278 83.709  0.042  2.231   6.1446e-02
   4_bss:   8.295  0.053  0.278 83.709  0.042  2.231   6.1446e-02
   4_xyz:   7.278  0.048  0.253 81.927  0.036  2.334   3.9840e-02
   4_adp:   7.278  0.048  0.253 81.927  0.036  2.334   3.9840e-02
   4_occ:   7.278  0.048  0.253 81.927  0.036  2.334   3.9840e-02
   5_bss:   7.278  0.048  0.253 81.927  0.036  2.334   3.9840e-02
   5_xyz:   7.278  0.048  0.253 81.927  0.036  2.334   4.0126e-02
   5_adp:   7.278  0.048  0.253 81.927  0.036  2.334   4.0126e-02
   5_occ:   7.278  0.048  0.253 81.927  0.036  2.334   4.0126e-02
   5_bss:   7.278  0.048  0.253 81.927  0.036  2.334   4.0126e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  93.32   0.00  18.08  74.77   0.00  14.19  93.32   1.45  39.31
   1_occ:  93.32   0.00  18.08  74.77   0.00  14.19  93.32   1.45  39.31
   2_bss:  93.32   0.00  18.08  74.77   0.00  14.19  93.32   1.45  39.31
   2_xyz:  93.32   0.00  18.08  74.77   0.00  14.19  93.32   1.45  39.31
   2_adp:  92.45   0.70  17.36  73.66   0.70  13.06  92.45   5.37  40.76
   2_occ:  92.45   0.70  17.36  73.66   0.70  13.06  92.45   5.37  40.76
   3_bss:  92.45   0.70  17.36  73.66   0.70  13.06  92.45   5.37  40.76
   3_xyz:  92.45   0.70  17.36  73.66   0.70  13.06  92.45   5.37  40.76
   3_adp:  98.48   0.57  17.57  88.05   0.57  12.82  98.48   4.68  43.45
   3_occ:  98.48   0.57  17.57  88.05   0.57  12.82  98.48   4.68  43.45
   4_bss:  98.48   0.57  17.57  88.05   0.57  12.82  98.48   4.68  43.45
   4_xyz:  98.48   0.57  17.57  88.05   0.57  12.82  98.48   4.68  43.45
   4_adp: 103.59   0.00  17.36  91.95   0.00  12.63 103.59   0.00  43.10
   4_occ: 103.59   0.00  17.36  91.95   0.00  12.63 103.59   0.00  43.10
   5_bss: 103.59   0.00  17.36  91.95   0.00  12.63 103.59   0.00  43.10
   5_xyz: 103.59   0.00  17.36  91.95   0.00  12.63 103.59   0.00  43.10
   5_adp: 110.89   0.00  17.13  98.51   0.00  12.41 110.89   3.08  42.85
   5_occ: 110.89   0.00  17.13  98.51   0.00  12.41 110.89   3.08  42.85
   5_bss: 110.89   0.00  17.14  98.51   0.00  12.41 110.89   3.08  42.85
------------------------------------------------------------------------
 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:    1.686    0.015    0.337
   1_adp:    1.686    0.015    0.337
   1_occ:    1.686    0.015    0.337
   2_bss:    1.686    0.015    0.337
   2_xyz:    1.585    0.057    0.532
   2_adp:    1.585    0.057    0.532
   2_occ:    1.585    0.057    0.532
   3_bss:    1.585    0.057    0.532
   3_xyz:    1.427    0.038    0.594
   3_adp:    1.427    0.038    0.594
   3_occ:    1.427    0.038    0.594
   4_bss:    1.427    0.038    0.594
   4_xyz:    1.412    0.070    0.615
   4_adp:    1.412    0.070    0.615
   4_occ:    1.412    0.070    0.615
   5_bss:    1.412    0.070    0.615
   5_xyz:    1.412    0.070    0.615
   5_adp:    1.412    0.070    0.615
   5_occ:    1.412    0.070    0.615
   5_bss:    1.412    0.070    0.615
------------------------------------------------------------------------

CPU time actual refinement: 326.33


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_450/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_450/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_450/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_450/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_450/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 326.17 
  Macro-tasks:
    bulk solvent and scale       = 39.17  
    individual site refinement   = 130.23 
    weights calculation          = 28.33  
    collect and process          = 6.05   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 203.91 
  Micro-tasks:
    mask                            = 1.83   
    f_calc                          = 104.39 
    alpha_beta                      = 8.32   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 112.39 
    fmodel                         = 6.53   
    r_factors                      = 0.24   
    phase_errors                   = 10.79  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 245.96 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.677 micro seconds
Total CPU time: 5.66 minutes
from_scatterers_fft:    641 calls, 103.99 s
gradients_fft:          586 calls,  99.28 s

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

# Date 2008-01-16 Time 04:50:38 PST -0800 (1200487838.69 s)
Start R-work = 0.4229, R-free = 0.4172 (no bulk solvent and anisotropic scale)
Final R-work = 0.1384, R-free = 0.1827 (no bulk solvent and anisotropic scale)

Start R-work = 0.4115, R-free = 0.4034
Final R-work = 0.1188, R-free = 0.1672