# Date 2008-01-16 Time 05:04:20 PST -0800 (1200488660.38 s)
#phil __OFF__

Command line arguments: "../581.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 16534
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 581

-------------------------------------------------------------------------------
  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: (69.8988, 47.6339, 88.1178, 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: 3.32, per 1000 atoms: 1.18


================================== 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: (69.8988, 47.6339, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.99077
Completeness in resolution range: 0.944458
Completeness with d_max=infinity: 0.941553

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0179
                             d_min =   1.9908

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: (69.8988, 47.6339, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.99077
Completeness in resolution range: 0.944458
Completeness with d_max=infinity: 0.941553

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0183 -  4.2594 [2183/2211]  1962   221  10.1%
  bin  2:  4.2594 -  3.3937 [2078/2097]  1870   208  10.0%
  bin  3:  3.3937 -  2.9684 [2078/2098]  1874   204   9.8%
  bin  4:  2.9684 -  2.6987 [2040/2065]  1833   207  10.1%
  bin  5:  2.6987 -  2.5063 [2022/2041]  1822   200   9.9%
  bin  6:  2.5063 -  2.3591 [2015/2061]  1811   204  10.1%
  bin  7:  2.3591 -  2.2413 [2016/2050]  1819   197   9.8%
  bin  8:  2.2413 -  2.1441 [2009/2044]  1799   210  10.5%
  bin  9:  2.1441 -  2.0617 [2005/2035]  1812   193   9.6%
  bin 10:  2.0617 -  1.9908 [1143/2039]  1028   115  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_581/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: 0.13 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:
        1.58 -     2.25: 11
        2.25 -     2.91: 1411
        2.91 -     3.57: 4389
        3.57 -     4.24: 9047
        4.24 -     4.90: 13032
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.585 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.840 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.896 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.913 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27885 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_581/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_581/model_refine_001.geo

CPU time processing inputs: 8.87


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 47.63395 88.1178 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: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4220   r_free= 0.4149   ksol= 0.00   Bsol= 0.00   scale= 0.909    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.224722                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7506 0.99   1414  157 0.3268 0.3329      6.4632       6.423|
|  2:  4.7506 -  3.7906 0.99   1363  153 0.3466 0.3743      6.6955       6.781|
|  3:  3.7906 -  3.3173 0.99   1334  150 0.3936 0.3442      6.6024      6.5114|
|  4:  3.3173 -  3.0167 0.99   1327  138 0.4055 0.4200      6.4384      6.4198|
|  5:  3.0167 -  2.8020 0.99   1311  150 0.4439 0.3824      6.3094      6.2777|
|  6:  2.8020 -  2.6377 0.98   1307  147 0.4489 0.4892      6.2131      6.1551|
|  7:  2.6377 -  2.5063 0.99   1305  145 0.4383 0.4425      6.1702      6.0903|
|  8:  2.5063 -  2.3976 0.98   1303  146 0.4718 0.4583      6.1483      6.1277|
|  9:  2.3976 -  2.3057 0.98   1304  143 0.4777 0.4382      6.0783      6.0955|
| 10:  2.3057 -  2.2264 0.98   1279  141 0.4918 0.4609      6.0852      6.0239|
| 11:  2.2264 -  2.1569 0.99   1309  146 0.4849 0.4581      5.9989      6.0024|
| 12:  2.1569 -  2.0955 0.98   1279  145 0.4788 0.4963      5.9324      6.0113|
| 13:  2.0955 -  2.0404 0.97   1280  131 0.5116 0.5053      5.8732      5.8054|
| 14:  2.0404 -  1.9908 0.40    515   67 0.4469 0.4976      5.8309       5.759|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0183 -  4.7506  1414   157  0.76  29.25   0.84     0.77      53230.72|
|  2:  4.7506 -  3.7906  1363   153  0.77  29.45   0.93     0.84      77827.80|
|  3:  3.7906 -  3.3173  1334   150  0.69  36.06   0.91     0.84      80718.30|
|  4:  3.3173 -  3.0167  1327   138  0.63  41.25   0.92     0.78      70961.85|
|  5:  3.0167 -  2.8020  1311   150  0.57  46.18   0.92     0.73      56162.57|
|  6:  2.8020 -  2.6377  1307   147  0.53  49.91   0.92     0.69      51711.29|
|  7:  2.6377 -  2.5063  1305   145  0.53  49.56   0.95     0.69      47130.22|
|  8:  2.5063 -  2.3976  1303   146  0.53  49.76   0.92     0.70      42967.22|
|  9:  2.3976 -  2.3057  1304   143  0.53  49.77   0.93     0.74      38669.55|
| 10:  2.3057 -  2.2264  1279   141  0.52  50.58   0.94     0.73      36201.21|
| 11:  2.2264 -  2.1569  1309   146  0.47  54.69   0.94     0.68      37268.87|
| 12:  2.1569 -  2.0955  1279   145  0.41  59.51   0.95     0.60      38346.82|
| 13:  2.0955 -  2.0404  1280   131  0.34  64.53   0.90     0.51      35829.12|
| 14:  2.0404 -  1.9908   515    67  0.35  63.80   1.00     0.45      29084.14|
|alpha:            min =        0.45 max =            0.84 mean =         0.71|
|beta:             min =    29084.14 max =        80718.30 mean =     50895.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.56|
|phase err.(work): min =        0.00 max =           89.92 mean =        47.21|
|phase err.(test): min =        0.00 max =           89.96 mean =        47.62|
|-----------------------------------------------------------------------------|

============================== 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 = 5.512713              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.890   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.290229              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.294   (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 |  1.585 -  1.916:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.916 -  2.248:        5 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.248 -  2.579:       33 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.579 -  2.911:     1378 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.911 -  3.242:     1877 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.242 -  3.574:     2512 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.574 -  3.905:     4632 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.905 -  4.237:     4415 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.237 -  4.568:     5929 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.568 -  4.900:     7103 |
|-----------------------------------------------------------------------------|
|-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 |        0.168 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.585 |       0.238 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.179)------------------------------------------|
|    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: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4220   r_free= 0.4149   ksol= 0.00   Bsol= 0.00   scale= 0.909    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.224722                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4107   r_free= 0.4034   ksol= 0.30   Bsol= 48.96   scale= 0.953   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.36,2.29,3.66,0.00,0.00,0.00); trace/3= 0.86                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.211684                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.735642              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.516   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.732937              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.990   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4107      final r-factor (work) = 0.2920          |
| start r-factor (free) = 0.4034      final r-factor (free) = 0.3134          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.8751 = 4.74 * 0.50 * 6.2110 + 1.00 * 0.1685                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.3765 = 4.74 * 0.50 * 6.0294 + 1.00 * 0.0999                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2920      final r-factor (work) = 0.2650          |
| start r-factor (free) = 0.3134      final r-factor (free) = 0.3252          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4251 = 0.73 * 1.00 * 6.0294 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3217 = 0.73 * 1.00 * 5.8766 + 1.00 * 0.0145                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.179)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.13  17.82    None  None   None       |
|    all(noH): 2823   0      0.00    102.13  17.82    None  None   None       |
|    Sol.    : 438    0      1.77    102.13  39.37    None  None   None       |
|    Mac.    : 2385   0      0.00    84.26   13.86    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 -  10.214: 1028   |   5:    51.067 -  61.281:   83        |
|      1:    10.214 -  20.427: 1014   |   6:    61.281 -  71.494:   45        |
|      2:    20.427 -  30.640:  337   |   7:    71.494 -  81.708:   11        |
|      3:    30.640 -  40.854:  188   |   8:    81.708 -  91.921:    4        |
|      4:    40.854 -  51.067:  110   |   9:    91.921 - 102.135:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2650 r_free = 0.3252             target_work(ml) = 5.886         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2647 r_free = 0.3258             target_work(ml) = 5.886         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2647   r_free= 0.3258   ksol= 0.30   Bsol= 48.96   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.36,2.29,3.66,0.00,0.00,0.00); trace/3= 0.86                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.886298                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2624   r_free= 0.3234   ksol= 0.33   Bsol= 71.87   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,0.44,1.16,0.00,0.00,0.00); trace/3= -0.32                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.883353                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.295727              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.649   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.272718              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.242  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2624      final r-factor (work) = 0.1864          |
| start r-factor (free) = 0.3234      final r-factor (free) = 0.2346          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7224 = 4.30 * 0.50 * 5.8768 + 1.00 * 0.0999                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.4391 = 4.30 * 0.50 * 5.7561 + 1.00 * 0.0758                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1864      final r-factor (work) = 0.1734          |
| start r-factor (free) = 0.2346      final r-factor (free) = 0.2170          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5843 = 0.27 * 1.00 * 5.7561 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5212 = 0.27 * 1.00 * 5.5419 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.179)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.21    101.54  17.26    None  None   None       |
|    all(noH): 2823   0      1.21    101.54  17.26    None  None   None       |
|    Sol.    : 438    0      5.14    101.54  39.88    None  None   None       |
|    Mac.    : 2385   0      1.21    83.64   13.11    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.207 -  11.240: 1304   |   5:    51.373 -  61.407:   82        |
|      1:    11.240 -  21.273:  858   |   6:    61.407 -  71.440:   39        |
|      2:    21.273 -  31.307:  242   |   7:    71.440 -  81.473:    9        |
|      3:    31.307 -  41.340:  165   |   8:    81.473 -  91.507:    3        |
|      4:    41.340 -  51.373:  118   |   9:    91.507 - 101.540:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1734 r_free = 0.2170             target_work(ml) = 5.509         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1733 r_free = 0.2169             target_work(ml) = 5.508         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1733   r_free= 0.2169   ksol= 0.33   Bsol= 71.87   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,0.44,1.16,0.00,0.00,0.00); trace/3= -0.32                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.508498                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1733   r_free= 0.2159   ksol= 0.34   Bsol= 74.01   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-0.69,0.26,-0.00,0.00,0.00); trace/3= -0.96                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.506995                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.878099              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.336   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.785952              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 113.158  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1733      final r-factor (work) = 0.1464          |
| start r-factor (free) = 0.2159      final r-factor (free) = 0.1867          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2815 = 1.88 * 0.50 * 5.5436 + 1.00 * 0.0758                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1529 = 1.88 * 0.50 * 5.4325 + 1.00 * 0.0515                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1464      final r-factor (work) = 0.1377          |
| start r-factor (free) = 0.1867      final r-factor (free) = 0.1863          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.1445 = 2.79 * 1.00 * 5.4325 + 1.00 * 0.0099                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.8677 = 2.79 * 1.00 * 5.3318 + 1.00 * 0.0134                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.179)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.50  17.78    None  None   None       |
|    all(noH): 2823   0      0.00    101.50  17.78    None  None   None       |
|    Sol.    : 438    0      4.63    101.50  44.43    None  None   None       |
|    Mac.    : 2385   0      0.00    92.68   12.89    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 -  10.150: 1162   |   5:    50.750 -  60.900:   84        |
|      1:    10.150 -  20.300: 1003   |   6:    60.900 -  71.049:   67        |
|      2:    20.300 -  30.450:  218   |   7:    71.049 -  81.199:   39        |
|      3:    30.450 -  40.600:  130   |   8:    81.199 -  91.349:   11        |
|      4:    40.600 -  50.750:  101   |   9:    91.349 - 101.499:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1377 r_free = 0.1863             target_work(ml) = 5.327         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1376 r_free = 0.1863             target_work(ml) = 5.327         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1376   r_free= 0.1863   ksol= 0.34   Bsol= 74.01   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-0.69,0.26,-0.00,0.00,0.00); trace/3= -0.96                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.326654                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1380   r_free= 0.1865   ksol= 0.34   Bsol= 80.99   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-1.02,0.08,-0.00,0.00,0.00); trace/3= -1.08                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.328478                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.203643              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.699  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.294120              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.587  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1380      final r-factor (work) = 0.1192          |
| start r-factor (free) = 0.1865      final r-factor (free) = 0.1702          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2615 = 4.20 * 0.50 * 5.3333 + 1.00 * 0.0519                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1485 = 4.20 * 0.50 * 5.2654 + 1.00 * 0.0816                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1192      final r-factor (work) = 0.1165          |
| start r-factor (free) = 0.1702      final r-factor (free) = 0.1665          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8275 = 1.29 * 1.00 * 5.2654 + 1.00 * 0.0135                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7461 = 1.29 * 1.00 * 5.2030 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.179)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.90  17.30    None  None   None       |
|    all(noH): 2823   0      0.00    101.90  17.30    None  None   None       |
|    Sol.    : 438    0      3.13    101.90  43.63    None  None   None       |
|    Mac.    : 2385   0      0.00    99.13   12.47    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 -  10.190: 1221   |   5:    50.951 -  61.141:   80        |
|      1:    10.190 -  20.381:  978   |   6:    61.141 -  71.332:   57        |
|      2:    20.381 -  30.571:  207   |   7:    71.332 -  81.522:   37        |
|      3:    30.571 -  40.761:  121   |   8:    81.522 -  91.712:   13        |
|      4:    40.761 -  50.951:  101   |   9:    91.712 - 101.902:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1165 r_free = 0.1665             target_work(ml) = 5.192         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1164 r_free = 0.1664             target_work(ml) = 5.191         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1664   ksol= 0.34   Bsol= 80.99   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-1.02,0.08,-0.00,0.00,0.00); trace/3= -1.08                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.191400                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1162   r_free= 0.1662   ksol= 0.33   Bsol= 71.86   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-0.81,0.42,-0.00,0.00,0.00); trace/3= -0.73                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.191357                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.582577              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.625  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.371654              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.442  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1162      final r-factor (work) = 0.1200          |
| start r-factor (free) = 0.1662      final r-factor (free) = 0.1677          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2002 = 1.58 * 0.50 * 5.2050 + 1.00 * 0.0816                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1757 = 1.58 * 0.50 * 5.2073 + 1.00 * 0.0552                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1200      final r-factor (work) = 0.1200          |
| start r-factor (free) = 0.1677      final r-factor (free) = 0.1658          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9480 = 0.37 * 1.00 * 5.2073 + 1.00 * 0.0127                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9478 = 0.37 * 1.00 * 5.2126 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.179)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.09   16.49    None  None   None       |
|    all(noH): 2823   0      0.00    99.09   16.49    None  None   None       |
|    Sol.    : 438    0      1.50    99.09   40.53    None  None   None       |
|    Mac.    : 2385   0      0.00    97.47   12.07    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.909: 1202   |   5:    49.543 -  59.452:   84        |
|      1:     9.909 -  19.817: 1002   |   6:    59.452 -  69.361:   39        |
|      2:    19.817 -  29.726:  209   |   7:    69.361 -  79.269:   27        |
|      3:    29.726 -  39.635:  140   |   8:    79.269 -  89.178:    6        |
|      4:    39.635 -  49.543:  107   |   9:    89.178 -  99.087:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1200 r_free = 0.1658             target_work(ml) = 5.209         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1199 r_free = 0.1658             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1199   r_free= 0.1658   ksol= 0.33   Bsol= 71.86   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-0.81,0.42,-0.00,0.00,0.00); trace/3= -0.73                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.208314                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7506 0.99   1414  157 0.1017 0.1311      5.4174      5.5749|
|  2:  4.7506 -  3.7906 0.99   1363  153 0.0860 0.1074      5.4441      5.6393|
|  3:  3.7906 -  3.3173 0.99   1334  150 0.1115 0.1524      5.5091      5.8307|
|  4:  3.3173 -  3.0167 0.99   1327  138 0.1303 0.1782      5.5055      5.6835|
|  5:  3.0167 -  2.8020 0.99   1311  150 0.1443 0.1728      5.4022      5.5723|
|  6:  2.8020 -  2.6377 0.98   1307  147 0.1377 0.2230      5.2934      5.5701|
|  7:  2.6377 -  2.5063 0.99   1305  145 0.1378 0.1761      5.2482       5.394|
|  8:  2.5063 -  2.3976 0.98   1303  146 0.1254 0.1802      5.1618      5.3824|
|  9:  2.3976 -  2.3057 0.98   1304  143 0.1293 0.2058      5.0987      5.4191|
| 10:  2.3057 -  2.2264 0.98   1279  141 0.1257 0.1681       5.032      5.1663|
| 11:  2.2264 -  2.1569 0.99   1309  146 0.1257 0.1852      4.9766       5.283|
| 12:  2.1569 -  2.0955 0.98   1279  145 0.1210 0.1833      4.9244      5.2403|
| 13:  2.0955 -  2.0404 0.97   1280  131 0.1217 0.1716      4.8331      5.0204|
| 14:  2.0404 -  1.9908 0.40    515   67 0.1046 0.1870       4.715      5.0049|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0183 -  4.7506  1414   157  0.94   9.49   0.96     0.93       7644.06|
|  2:  4.7506 -  3.7906  1363   153  0.95   8.21   1.00     0.99       9271.48|
|  3:  3.7906 -  3.3173  1334   150  0.93  11.75   1.02     1.02      10906.81|
|  4:  3.3173 -  3.0167  1327   138  0.91  14.42   1.00     0.99      11249.38|
|  5:  3.0167 -  2.8020  1311   150  0.89  17.33   1.00     0.97       9493.42|
|  6:  2.8020 -  2.6377  1307   147  0.88  17.91   0.98     0.96       8312.52|
|  7:  2.6377 -  2.5063  1305   145  0.89  16.89   0.99     0.96       7172.54|
|  8:  2.5063 -  2.3976  1303   146  0.89  17.00   0.99     0.95       6540.11|
|  9:  2.3976 -  2.3057  1304   143  0.89  17.18   1.00     0.96       5720.42|
| 10:  2.3057 -  2.2264  1279   141  0.89  16.95   0.99     0.94       4973.53|
| 11:  2.2264 -  2.1569  1309   146  0.89  16.97   0.99     0.95       4577.26|
| 12:  2.1569 -  2.0955  1279   145  0.90  16.30   1.00     0.99       4261.36|
| 13:  2.0955 -  2.0404  1280   131  0.90  16.83   0.98     0.97       3594.74|
| 14:  2.0404 -  1.9908   515    67  0.91  14.87   0.96     0.91       2772.71|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     2772.71 max =        11249.38 mean =      7113.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.09|
|phase err.(test): min =        0.00 max =           88.87 mean =        14.56|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1199   r_free= 0.1658   ksol= 0.32   Bsol= 66.41   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-0.81,0.42,-0.00,0.00,0.00); trace/3= -0.73                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.208248                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1199   r_free= 0.1658   ksol= 0.32   Bsol= 66.41   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-0.81,0.42,-0.00,0.00,0.00); trace/3= -0.73                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.208248                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7506 0.99   1414  157 0.1014 0.1308      5.4151      5.5718|
|  2:  4.7506 -  3.7906 0.99   1363  153 0.0857 0.1071      5.4415       5.637|
|  3:  3.7906 -  3.3173 0.99   1334  150 0.1115 0.1524      5.5079      5.8313|
|  4:  3.3173 -  3.0167 0.99   1327  138 0.1305 0.1785      5.5066      5.6841|
|  5:  3.0167 -  2.8020 0.99   1311  150 0.1445 0.1730      5.4036      5.5736|
|  6:  2.8020 -  2.6377 0.98   1307  147 0.1378 0.2234      5.2943      5.5715|
|  7:  2.6377 -  2.5063 0.99   1305  145 0.1379 0.1762       5.249      5.3946|
|  8:  2.5063 -  2.3976 0.98   1303  146 0.1254 0.1802      5.1622      5.3827|
|  9:  2.3976 -  2.3057 0.98   1304  143 0.1293 0.2058      5.0989      5.4191|
| 10:  2.3057 -  2.2264 0.98   1279  141 0.1258 0.1681      5.0321      5.1664|
| 11:  2.2264 -  2.1569 0.99   1309  146 0.1258 0.1852      4.9768      5.2831|
| 12:  2.1569 -  2.0955 0.98   1279  145 0.1210 0.1833      4.9245      5.2405|
| 13:  2.0955 -  2.0404 0.97   1280  131 0.1217 0.1717      4.8332      5.0203|
| 14:  2.0404 -  1.9908 0.40    515   67 0.1047 0.1870      4.7152      5.0051|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0183 -  4.7506  1414   157  0.94   9.47   0.96     0.93       7613.41|
|  2:  4.7506 -  3.7906  1363   153  0.95   8.19   1.00     0.99       9229.53|
|  3:  3.7906 -  3.3173  1334   150  0.93  11.72   1.02     1.02      10867.51|
|  4:  3.3173 -  3.0167  1327   138  0.91  14.43   1.00     0.99      11266.41|
|  5:  3.0167 -  2.8020  1311   150  0.89  17.35   1.00     0.97       9517.66|
|  6:  2.8020 -  2.6377  1307   147  0.88  17.93   0.98     0.96       8331.93|
|  7:  2.6377 -  2.5063  1305   145  0.89  16.91   0.99     0.96       7185.01|
|  8:  2.5063 -  2.3976  1303   146  0.89  17.00   0.99     0.95       6544.91|
|  9:  2.3976 -  2.3057  1304   143  0.89  17.18   1.00     0.96       5722.99|
| 10:  2.3057 -  2.2264  1279   141  0.89  16.95   0.99     0.94       4974.64|
| 11:  2.2264 -  2.1569  1309   146  0.89  16.97   0.99     0.95       4578.81|
| 12:  2.1569 -  2.0955  1279   145  0.90  16.31   1.00     0.99       4262.78|
| 13:  2.0955 -  2.0404  1280   131  0.90  16.84   0.98     0.97       3595.53|
| 14:  2.0404 -  1.9908   515    67  0.91  14.87   0.96     0.91       2773.23|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     2773.23 max =        11266.41 mean =      7110.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.09|
|phase err.(test): min =        0.00 max =           88.98 mean =        14.56|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.179)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.09   16.49    None  None   None       |
|    all(noH): 2823   0      0.00    99.09   16.49    None  None   None       |
|    Sol.    : 438    0      1.50    99.09   40.54    None  None   None       |
|    Mac.    : 2385   0      0.00    97.47   12.07    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.912: 1202   |   5:    49.546 -  59.455:   84        |
|      1:     9.912 -  19.820: 1002   |   6:    59.455 -  69.364:   39        |
|      2:    19.820 -  29.729:  209   |   7:    69.364 -  79.272:   27        |
|      3:    29.729 -  39.638:  140   |   8:    79.272 -  89.181:    6        |
|      4:    39.638 -  49.546:  107   |   9:    89.181 -  99.090:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 308         
Filter by distance & map next to the model:
   mapped sites are within: 0.495 - 5.922
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 306 from: 308
   mapped sites are within: 0.711 - 5.922

peak=    5.770 closest distance to " O   HOH Z 210 " =    1.307
peak=    5.386 closest distance to " CB  GLN A 223 " =    1.471
peak=    5.360 closest distance to " O   HOH Z 113 " =    2.072
peak=    5.150 closest distance to " CG  PRO A  54 " =    1.438
peak=    4.925 closest distance to " CB  ARG A 190 " =    1.720
peak=    4.751 closest distance to " CZ  PHE A 218 " =    1.110
peak=    4.706 closest distance to " CG  PRO A  90 " =    1.269
peak=    4.603 closest distance to " CB  GLN A 183 " =    1.253
peak=    4.573 closest distance to " CB  SER A  63 " =    1.150
peak=    4.565 closest distance to " CD2 TRP A 179 " =    1.286
peak=    4.497 closest distance to " CG  PRO A 198 " =    1.265
peak=    4.456 closest distance to " O   HOH Z 232 " =    2.338
peak=    4.404 closest distance to " CB  PRO A  54 " =    0.978
peak=    4.378 closest distance to " O   HOH Z 298 " =    1.888
peak=    4.366 closest distance to " O   HOH Z 369 " =    2.209
peak=    4.360 closest distance to " CA  ARG A  36 " =    1.107
peak=    4.324 closest distance to " CB  ARG A 275 " =    0.932
peak=    4.311 closest distance to " O   HOH Z  49 " =    1.127
peak=    4.308 closest distance to " CA  TYR A  30 " =    0.938
peak=    4.300 closest distance to " CZ3 TRP A 266 " =    1.109
peak=    4.283 closest distance to " O   PRO A 198 " =    1.536
peak=    4.265 closest distance to " CD  ARG A 269 " =    1.020
peak=    4.264 closest distance to " O   HOH Z 234 " =    3.868
peak=    4.218 closest distance to " CG  PRO A 213 " =    1.229
peak=    4.196 closest distance to " O   HOH Z 402 " =    1.527
peak=    4.194 closest distance to " O   HOH Z 189 " =    2.843
peak=    4.188 closest distance to " CB  GLU A 277 " =    3.803
peak=    4.161 closest distance to " CB  ARG A  79 " =    1.475
peak=    4.147 closest distance to " CB  TYR A 169 " =    0.808
peak=    4.116 closest distance to " O   HOH Z 248 " =    1.438
peak=    4.110 closest distance to " CZ  PHE A  38 " =    1.216
peak=    4.107 closest distance to " O   HOH Z 265 " =    2.063
peak=    4.074 closest distance to " O   HOH Z  43 " =    2.018
peak=    4.050 closest distance to " CG  PRO A 243 " =    1.089
peak=    4.042 closest distance to " O   HOH Z 368 " =    2.157
peak=    4.041 closest distance to " CB  GLU A 152 " =    1.199
peak=    4.028 closest distance to " ND2 ASN A 187 " =    1.568
peak=    4.022 closest distance to " CA  ALA A  51 " =    0.958
peak=    4.010 closest distance to " O   SER A  87 " =    2.252
peak=    4.001 closest distance to " O   ASN A  74 " =    1.488
peak=    3.997 closest distance to " O  BHOH Z  74 " =    1.158
peak=    3.994 closest distance to " CB  ASN A  39 " =    0.863
peak=    3.993 closest distance to " ND2 ASN A 249 " =    0.900
peak=    3.972 closest distance to " CB  GLU A 128 " =    1.104
peak=    3.968 closest distance to " O   HOH Z 287 " =    1.841
peak=    3.956 closest distance to " CA  ARG A 195 " =    1.224
peak=    3.924 closest distance to " CB  VAL A 202 " =    1.525
peak=    3.915 closest distance to " O   HOH Z 251 " =    1.624
peak=    3.909 closest distance to " O   HOH Z 403 " =    1.626
peak=    3.903 closest distance to " O   HOH Z 362 " =    3.591
peak=    3.901 closest distance to " O   HOH Z 316 " =    3.088
peak=    3.899 closest distance to " CD  LYS A 166 " =    1.304
peak=    3.896 closest distance to " O   HOH Z  19 " =    1.759
peak=    3.893 closest distance to " CG2 ILE A 120 " =    1.196
peak=    3.885 closest distance to " CB  ASN A 148 " =    1.479
peak=    3.843 closest distance to " O   HOH Z 412 " =    3.728
peak=    3.839 closest distance to " CD1 LEU A  96 " =    0.782
peak=    3.837 closest distance to " CB  TRP A 266 " =    1.040
peak=    3.831 closest distance to " O   HOH Z 126 " =    1.928
peak=    3.814 closest distance to " CA  ALA A 160 " =    0.937
peak=    3.813 closest distance to " O   HOH Z  97 " =    2.099
peak=    3.810 closest distance to " O   HOH Z  63 " =    1.916
peak=    3.801 closest distance to " O   ALA A 165 " =    1.453
peak=    3.795 closest distance to " NZ  LYS A 117 " =    2.935
peak=    3.790 closest distance to " CG  ARG A  66 " =    2.694
peak=    3.783 closest distance to " O   TYR A 116 " =    1.397
peak=    3.778 closest distance to " O   HOH Z 291 " =    1.453
peak=    3.756 closest distance to " O   HOH Z 346 " =    1.599
peak=    3.755 closest distance to " CB  ASN A 187 " =    1.305
peak=    3.752 closest distance to " CB  VAL A 265 " =    1.248
peak=    3.750 closest distance to " NH1AARG A 145 " =    1.353
peak=    3.747 closest distance to " O   HOH Z  40 " =    1.883
peak=    3.745 closest distance to " NE2 GLN A  77 " =    3.293
peak=    3.741 closest distance to " O   HOH Z 423 " =    1.900
peak=    3.736 closest distance to " CB  ASP A 124 " =    0.820
peak=    3.734 closest distance to " CG  GLN A  11 " =    1.410
peak=    3.732 closest distance to " O   THR A 220 " =    1.233
peak=    3.732 closest distance to " O   HOH Z  80 " =    1.981
peak=    3.728 closest distance to " O   HOH Z 406 " =    1.654
peak=    3.727 closest distance to " CB  GLU A  46 " =    0.989
peak=    3.726 closest distance to " O   HOH Z 133 " =    2.798
peak=    3.721 closest distance to " CA  ALA A 295 " =    1.051
peak=    3.711 closest distance to " CB  SER A  62 " =    0.884
peak=    3.709 closest distance to " O   HOH Z 214 " =    1.595
peak=    3.702 closest distance to " O   HOH Z 246 " =    1.439
peak=    3.698 closest distance to " CG  MET A 185 " =    1.167
peak=    3.694 closest distance to " O   HOH Z 261 " =    2.125
peak=    3.693 closest distance to " O   HOH Z 285 " =    2.544
peak=    3.685 closest distance to " CA  GLU A 152 " =    0.884
peak=    3.685 closest distance to " CB  LEU A  83 " =    0.794
peak=    3.681 closest distance to " O   HOH Z 383 " =    2.085
peak=    3.677 closest distance to " O   HOH Z  78 " =    1.690
peak=    3.676 closest distance to " CA  SER A  87 " =    1.059
peak=    3.673 closest distance to " CA  MET A 105 " =    1.096
peak=    3.673 closest distance to " CB  ALA A 291 " =    1.058
peak=    3.664 closest distance to " CB  TRP A 179 " =    1.434
peak=    3.663 closest distance to " CB  PRO A  90 " =    1.094
peak=    3.660 closest distance to " O   HOH Z 353 " =    2.677
peak=    3.658 closest distance to " O   HOH Z  21 " =    1.858
peak=    3.658 closest distance to " O   HOH Z  15 " =    2.270
peak=    3.655 closest distance to " CA  VAL A 125 " =    1.276
peak=    3.640 closest distance to " O   HOH Z 393 " =    3.153
peak=    3.640 closest distance to " O   HOH Z  48 " =    1.687
peak=    3.640 closest distance to " CG1 ILE A  20 " =    1.241
peak=    3.636 closest distance to " CG2AVAL A 121 " =    2.206
peak=    3.625 closest distance to " O   HOH Z 303 " =    2.290
peak=    3.617 closest distance to " CG  GLN A  58 " =    0.857
peak=    3.615 closest distance to " N   ASN A  39 " =    1.303
peak=    3.613 closest distance to " CE  LYS A  76 " =    0.893
peak=    3.609 closest distance to " OE1 GLN A  55 " =    1.471
peak=    3.608 closest distance to " O   HOH Z 258 " =    2.059
peak=    3.605 closest distance to " CB  ASN A 142 " =    1.105
peak=    3.601 closest distance to " O   HOH Z 313 " =    1.885
peak=    3.598 closest distance to " NE2 GLN A  11 " =    1.236
peak=    3.596 closest distance to " O   HOH Z 250 " =    1.350
peak=    3.596 closest distance to " CG AARG A 275 " =    1.233
peak=    3.596 closest distance to " CA  ALA A 154 " =    1.014
peak=    3.586 closest distance to " CA  ILE A 106 " =    0.798
peak=    3.584 closest distance to " O   HOH Z 361 " =    2.665
peak=    3.581 closest distance to " O   HOH Z 298 " =    2.420
peak=    3.577 closest distance to " CB  SER A 141 " =    1.097
peak=    3.576 closest distance to " CG  ARG A 138 " =    1.265
peak=    3.575 closest distance to " O   HOH Z 142 " =    1.590
peak=    3.574 closest distance to " CD1 ILE A 199 " =    1.189
peak=    3.572 closest distance to " CB  GLN A  89 " =    1.303
peak=    3.571 closest distance to " N   ARG A 156 " =    1.572
peak=    3.567 closest distance to " O   HOH Z 427 " =    3.175
peak=    3.558 closest distance to " O   ASN A  74 " =    1.804
peak=    3.555 closest distance to " O   HOH Z 359 " =    1.645
peak=    3.545 closest distance to " O   HOH Z 214 " =    2.371
peak=    3.540 closest distance to " O   THR A 251 " =    1.152
peak=    3.540 closest distance to " CD  ARG A 159 " =    0.804
peak=    3.539 closest distance to " O   HOH Z 209 " =    2.278
peak=    3.535 closest distance to " O   HOH Z 128 " =    2.119
peak=    3.533 closest distance to " CB  LEU A 228 " =    1.087
peak=    3.529 closest distance to " OG BSER A 164 " =    2.331
peak=    3.528 closest distance to " O   THR A 182 " =    1.455
peak=    3.524 closest distance to " CG2 VAL A 257 " =    0.810
peak=    3.523 closest distance to " O   HOH Z 193 " =    1.810
peak=    3.516 closest distance to " NH2 ARG A 156 " =    1.137
peak=    3.515 closest distance to " O  BHOH Z 338 " =    2.154
peak=    3.515 closest distance to " O   HOH Z 280 " =    2.950
peak=    3.514 closest distance to " OH  TYR A 116 " =    1.083
peak=    3.513 closest distance to " CB  PRO A 198 " =    1.130
peak=    3.508 closest distance to " O   HOH Z 148 " =    3.408
peak=    3.500 closest distance to " CB  ASP A 140 " =    1.014
peak=    3.496 closest distance to " CA  ASN A 176 " =    1.232
peak=    3.493 closest distance to " O   HOH Z  88 " =    1.603
peak=    3.493 closest distance to " O   HOH Z 294 " =    1.529
peak=    3.481 closest distance to " O   ASP A 124 " =    1.278
peak=    3.468 closest distance to " CG  GLU A  37 " =    0.964
peak=    3.466 closest distance to " CG  LEU A 167 " =    1.118
peak=    3.464 closest distance to " O   HOH Z 102 " =    1.216
peak=    3.460 closest distance to " CD1 LEU A 300 " =    1.203
peak=    3.459 closest distance to " OD1 ASN A 217 " =    1.767
peak=    3.459 closest distance to " O   HOH Z 185 " =    1.785
peak=    3.458 closest distance to " CA  ASN A 215 " =    0.970
peak=    3.456 closest distance to " OG1 THR A  82 " =    0.934
peak=    3.454 closest distance to " CG1 VAL A 153 " =    1.042
peak=    3.453 closest distance to " CA  ASP A 162 " =    1.065
peak=    3.452 closest distance to " OG BSER A 134 " =    2.778
peak=    3.447 closest distance to " OG  SER A  28 " =    1.543
peak=    3.444 closest distance to " NH2BARG A 145 " =    2.163
peak=    3.444 closest distance to " CD  PRO A  54 " =    0.933
peak=    3.435 closest distance to " O   HOH Z 146 " =    2.264
peak=    3.433 closest distance to " O   HOH Z 365 " =    2.758
peak=    3.427 closest distance to " CA  ALA A  21 " =    1.258
peak=    3.425 closest distance to " CD2 LEU A 297 " =    1.009
peak=    3.411 closest distance to " OD2 ASP A 298 " =    3.879
peak=    3.405 closest distance to " O   HOH Z 141 " =    1.675
peak=    3.405 closest distance to " CB  THR A  31 " =    1.517
peak=    3.403 closest distance to " CB  GLN A  88 " =    1.158
peak=    3.402 closest distance to " CB  PHE A 204 " =    0.834
peak=    3.399 closest distance to " O   HOH Z 411 " =    1.735
peak=    3.393 closest distance to " O   HOH Z 425 " =    1.360
peak=    3.393 closest distance to " O   HOH Z 327 " =    1.571
peak=    3.391 closest distance to " O   HOH Z 126 " =    1.553
peak=    3.391 closest distance to " O   LEU A 228 " =    1.887
peak=    3.383 closest distance to " O   HOH Z 290 " =    1.095
peak=    3.381 closest distance to " O   HOH Z 357 " =    2.161
peak=    3.381 closest distance to " O   HOH Z 389 " =    1.938
peak=    3.378 closest distance to " CA  TYR A 116 " =    1.305
peak=    3.378 closest distance to " N   HIS A 108 " =    1.867
peak=    3.377 closest distance to " O   PRO A 213 " =    1.415
peak=    3.371 closest distance to " CA  ASN A 217 " =    1.341
peak=    3.370 closest distance to " O   HOH Z 394 " =    3.984
peak=    3.370 closest distance to " CG2 VAL A 197 " =    1.150
peak=    3.368 closest distance to " CA  THR A 264 " =    0.885
peak=    3.368 closest distance to " O   HOH Z 183 " =    1.668
peak=    3.365 closest distance to " O   HOH Z 422 " =    2.679
peak=    3.365 closest distance to " O   HOH Z  59 " =    2.340
peak=    3.361 closest distance to " O   HOH Z 180 " =    2.115
peak=    3.349 closest distance to " O   HOH Z 285 " =    1.855
peak=    3.345 closest distance to " O   HOH Z 158 " =    3.105
peak=    3.341 closest distance to " O   HOH Z 325 " =    2.210
peak=    3.341 closest distance to " CB  ASP A 298 " =    1.184
peak=    3.336 closest distance to " CB  PHE A  16 " =    1.033
peak=    3.335 closest distance to " CB  MET A  40 " =    0.960
peak=    3.335 closest distance to " N   SER A 164 " =    1.058
peak=    3.335 closest distance to " N   TYR A 116 " =    1.585
peak=    3.325 closest distance to " OG  SER A 276 " =    1.456
peak=    3.320 closest distance to " CB  PRO A 243 " =    1.392
peak=    3.320 closest distance to " CG2AVAL A  72 " =    1.867
peak=    3.319 closest distance to " O   HOH Z 203 " =    1.762
peak=    3.318 closest distance to " CG2BVAL A  41 " =    0.855
peak=    3.317 closest distance to " O   HOH Z 371 " =    2.997
peak=    3.313 closest distance to " CD  LYS A 166 " =    1.776
peak=    3.310 closest distance to " CG2 THR A 221 " =    1.142
peak=    3.310 closest distance to " O   HOH Z  63 " =    2.199
peak=    3.309 closest distance to " O   HOH Z 124 " =    2.245
peak=    3.309 closest distance to " CB  ALA A 299 " =    0.815
peak=    3.309 closest distance to " O   HOH Z 139 " =    4.765
peak=    3.308 closest distance to " CG1 ILE A  33 " =    1.237
peak=    3.305 closest distance to " CB  MET A  47 " =    0.896
peak=    3.302 closest distance to " CA  GLY A 241 " =    0.971
peak=    3.301 closest distance to " O   HOH Z 271 " =    2.525
peak=    3.299 closest distance to " O   HOH Z 305 " =    3.808
peak=    3.297 closest distance to " CA  GLU A  46 " =    1.059
peak=    3.296 closest distance to " O   HOH Z 299 " =    4.502
peak=    3.285 closest distance to " N   CYS A 260 " =    0.813
peak=    3.282 closest distance to " O   HOH Z 336 " =    1.813
peak=    3.280 closest distance to " OE2 GLU A  53 " =    1.202
peak=    3.278 closest distance to " CE1 TYR A  30 " =    1.033
peak=    3.278 closest distance to " O   HOH Z 345 " =    1.733
peak=    3.278 closest distance to " O   ALA A 158 " =    1.152
peak=    3.277 closest distance to " CA  ARG A 156 " =    1.120
peak=    3.277 closest distance to " CG2 THR A 220 " =    0.794
peak=    3.273 closest distance to " CA  ASN A 127 " =    1.262
peak=    3.271 closest distance to " CA  ALA A 100 " =    0.915
peak=    3.271 closest distance to " OG  SER A  22 " =    2.688
peak=    3.269 closest distance to " N   ASP A 132 " =    1.145
peak=    3.268 closest distance to " CB  SER A 210 " =    0.886
peak=    3.264 closest distance to " CB  ASN A 215 " =    1.210
peak=    3.261 closest distance to " CB  SER A   3 " =    1.458
peak=    3.259 closest distance to " O   HOH Z  20 " =    1.305
peak=    3.258 closest distance to " O   HOH Z 199 " =    1.642
peak=    3.256 closest distance to " O   HOH Z 287 " =    2.089
peak=    3.256 closest distance to " CZ3 TRP A  85 " =    0.897
peak=    3.249 closest distance to " O   HOH Z  35 " =    2.388
peak=    3.245 closest distance to " CB  ASN A 285 " =    0.957
peak=    3.239 closest distance to " CB  ASP A 191 " =    1.215
peak=    3.239 closest distance to " OG  SER A 245 " =    1.596
peak=    3.237 closest distance to " NZ  LYS A  48 " =    1.209
peak=    3.225 closest distance to " O   HOH Z 417 " =    2.980
peak=    3.224 closest distance to " O   HOH Z 227 " =    1.562
peak=    3.218 closest distance to " O   HOH Z  44 " =    1.905
peak=    3.215 closest distance to " OE2 GLU A  53 " =    1.888
peak=    3.214 closest distance to " O   HOH Z 421 " =    1.869
peak=    3.212 closest distance to " O   HOH Z   1 " =    2.481
peak=    3.211 closest distance to " N   GLY A  98 " =    1.186
peak=    3.206 closest distance to " CG2 THR A  29 " =    1.265
peak=    3.206 closest distance to " N   VAL A 265 " =    1.343
peak=    3.205 closest distance to " OD1 ASN A  69 " =    2.478
peak=    3.204 closest distance to " NE2 HIS A 207 " =    1.095
peak=    3.200 closest distance to " CE3 TRP A  85 " =    1.053
peak=    3.200 closest distance to " NH1 ARG A 269 " =    0.757
peak=    3.197 closest distance to " CB  ALA A 104 " =    0.766
peak=    3.189 closest distance to " O   ALA A 242 " =    1.319
peak=    3.188 closest distance to " OG BSER A 212 " =    2.685
peak=    3.187 closest distance to " O   HOH Z 394 " =    1.678
peak=    3.185 closest distance to " CA  GLN A  94 " =    0.793
peak=    3.183 closest distance to " O   HOH Z 366 " =    2.585
peak=    3.182 closest distance to " NH2AARG A 275 " =    3.541
peak=    3.181 closest distance to " O   HOH Z 258 " =    2.076
peak=    3.180 closest distance to " CA  THR A 178 " =    1.485
peak=    3.180 closest distance to " CA  MET A 188 " =    0.958
peak=    3.179 closest distance to " CB  ALA A 292 " =    1.072
peak=    3.177 closest distance to " O   HOH Z 132 " =    2.844
peak=    3.176 closest distance to " O   HOH Z 293 " =    2.036
peak=    3.171 closest distance to " CB  TYR A 247 " =    0.966
peak=    3.163 closest distance to " CD2 TYR A 186 " =    1.013
peak=    3.159 closest distance to " NE2 GLN A  58 " =    3.624
peak=    3.159 closest distance to " O   HOH Z 109 " =    2.682
peak=    3.159 closest distance to " CA  ALA A 233 " =    1.607
peak=    3.158 closest distance to " O   HOH Z 147 " =    1.822
peak=    3.156 closest distance to " CG2 VAL A 126 " =    0.807
peak=    3.154 closest distance to " CG2BVAL A 121 " =    0.838
peak=    3.148 closest distance to " O   HOH Z 240 " =    2.610
peak=    3.144 closest distance to " CG  ARG A 219 " =    1.135
peak=    3.141 closest distance to " CD  PRO A 213 " =    1.453
peak=    3.137 closest distance to " CA  ASP A 191 " =    0.911
peak=    3.137 closest distance to " CB  MET A 105 " =    0.830
peak=    3.133 closest distance to " OD2 ASP A  50 " =    2.939
peak=    3.126 closest distance to " O   HOH Z  61 " =    1.637
peak=    3.124 closest distance to " CB  THR A  52 " =    0.761
peak=    3.116 closest distance to " O   HOH Z 173 " =    2.114
peak=    3.115 closest distance to " O   HOH Z 134 " =    1.204
peak=    3.115 closest distance to " CB  LYS A 117 " =    1.158
peak=    3.113 closest distance to " O   HOH Z 380 " =    2.068
peak=    3.106 closest distance to " CD  ARG A 219 " =    1.197
peak=    3.105 closest distance to " CB  ALA A  43 " =    0.837
peak=    3.103 closest distance to " CD  ARG A  66 " =    2.401
peak=    3.101 closest distance to " CE3 TRP A 150 " =    1.161
peak=    3.091 closest distance to " CA  ILE A 234 " =    0.880
peak=    3.090 closest distance to " OG1 THR A 264 " =    0.711
peak=    3.090 closest distance to " O   HOH Z 420 " =    5.922
peak=    3.090 closest distance to " CB  ALA A 248 " =    1.666
peak=    3.083 closest distance to " CA  SER A  32 " =    1.581
peak=    3.078 closest distance to " CG1 ILE A 120 " =    1.053
peak=    3.078 closest distance to " CB  GLN A 103 " =    0.836
peak=    3.074 closest distance to " CB  GLN A 240 " =    1.457
peak=    3.063 closest distance to " CA  ARG A 139 " =    1.082
peak=    3.058 closest distance to " O   HOH Z 142 " =    2.089
peak=    3.057 closest distance to " CE  LYS A 119 " =    1.079
peak=    3.037 closest distance to " CA  SER A  12 " =    1.598
peak=    3.031 closest distance to " CB  ALA A 114 " =    0.735

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.628 - 5.939
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 200
   mapped sites are within: 0.716 - 5.939

peak=   -4.606 closest distance to " CD  GLN A  58 " =    0.955
peak=   -4.467 closest distance to " O   PRO A 198 " =    1.299
peak=   -4.407 closest distance to " CE2 PHE A  61 " =    2.690
peak=   -4.405 closest distance to " CB  PRO A 243 " =    2.763
peak=   -4.329 closest distance to " CD  ARG A  14 " =    3.454
peak=   -4.318 closest distance to " CG1 VAL A 250 " =    2.738
peak=   -4.309 closest distance to " CG1 VAL A 112 " =    2.621
peak=   -4.251 closest distance to " O   HOH Z 266 " =    5.580
peak=   -4.222 closest distance to " O   HOH Z  10 " =    1.627
peak=   -4.184 closest distance to " C   HIS A 108 " =    1.076
peak=   -4.121 closest distance to " CD2 TYR A 293 " =    1.931
peak=   -4.060 closest distance to " CD  ARG A 156 " =    2.214
peak=   -4.049 closest distance to " O   HOH Z 210 " =    0.810
peak=   -4.013 closest distance to " CG2 ILE A  49 " =    2.794
peak=   -4.008 closest distance to " CG  ARG A  66 " =    2.497
peak=   -3.972 closest distance to " CG2 ILE A  20 " =    3.020
peak=   -3.955 closest distance to " O   HOH Z 193 " =    1.147
peak=   -3.951 closest distance to " O   HOH Z 196 " =    2.188
peak=   -3.943 closest distance to " N   ALA A  43 " =    2.625
peak=   -3.936 closest distance to " O   HOH Z 394 " =    1.623
peak=   -3.930 closest distance to " OXT GLY A 302 " =    3.015
peak=   -3.924 closest distance to " O   HOH Z 166 " =    1.647
peak=   -3.913 closest distance to " CD  GLN A 223 " =    1.369
peak=   -3.912 closest distance to " CH2 TRP A 179 " =    1.217
peak=   -3.908 closest distance to " O   HOH Z 211 " =    1.340
peak=   -3.901 closest distance to " CD  ARG A  79 " =    1.179
peak=   -3.899 closest distance to " O   VAL A  67 " =    2.685
peak=   -3.895 closest distance to " OG  SER A  97 " =    2.275
peak=   -3.877 closest distance to " CA  GLY A 241 " =    2.375
peak=   -3.874 closest distance to " O   HOH Z 283 " =    2.410
peak=   -3.856 closest distance to " CD1 LEU A 101 " =    2.419
peak=   -3.842 closest distance to " CG  GLN A  11 " =    1.467
peak=   -3.842 closest distance to " O   HOH Z 374 " =    1.966
peak=   -3.836 closest distance to " ND2BASN A 224 " =    1.870
peak=   -3.809 closest distance to " O   HOH Z 377 " =    2.095
peak=   -3.798 closest distance to " O   HOH Z 290 " =    1.019
peak=   -3.791 closest distance to " CA  GLY A 241 " =    3.310
peak=   -3.789 closest distance to " CE2 TYR A  30 " =    2.767
peak=   -3.785 closest distance to " CA  ASP A 298 " =    1.081
peak=   -3.779 closest distance to " O   HOH Z 231 " =    2.416
peak=   -3.760 closest distance to " OD1 ASN A 148 " =    1.346
peak=   -3.744 closest distance to " CD1 PHE A  59 " =    2.073
peak=   -3.743 closest distance to " NH2 ARG A  79 " =    1.600
peak=   -3.723 closest distance to " O   ALA A  34 " =    2.527
peak=   -3.718 closest distance to " CB  ALA A  10 " =    2.235
peak=   -3.713 closest distance to " O   SER A 210 " =    1.977
peak=   -3.700 closest distance to " CD1 ILE A 151 " =    2.457
peak=   -3.675 closest distance to " ND2 ASN A  45 " =    1.930
peak=   -3.659 closest distance to " O   HOH Z 106 " =    1.976
peak=   -3.646 closest distance to " CD2 PHE A 192 " =    2.145
peak=   -3.644 closest distance to " O   HOH Z 264 " =    1.775
peak=   -3.637 closest distance to " O   HOH Z 351 " =    1.646
peak=   -3.631 closest distance to " CZ  PHE A 155 " =    1.102
peak=   -3.630 closest distance to " CB  TRP A  85 " =    2.504
peak=   -3.626 closest distance to " O   HOH Z 171 " =    2.308
peak=   -3.625 closest distance to " O   HOH Z 348 " =    2.253
peak=   -3.623 closest distance to " CZ  TYR A 169 " =    1.830
peak=   -3.607 closest distance to " O   HOH Z 366 " =    1.650
peak=   -3.597 closest distance to " CB  ALA A 161 " =    2.594
peak=   -3.596 closest distance to " O   PRO A 163 " =    2.034
peak=   -3.585 closest distance to " CE3 TRP A 150 " =    2.233
peak=   -3.580 closest distance to " CG  PRO A 243 " =    1.714
peak=   -3.571 closest distance to " O   HOH Z 128 " =    2.673
peak=   -3.570 closest distance to " O   ALA A  10 " =    1.715
peak=   -3.569 closest distance to " CG1AVAL A  41 " =    2.576
peak=   -3.567 closest distance to " N   THR A  52 " =    1.646
peak=   -3.566 closest distance to " CE BMET A  47 " =    1.793
peak=   -3.535 closest distance to " CG  GLN A 103 " =    2.491
peak=   -3.530 closest distance to " CD  GLU A 236 " =    1.120
peak=   -3.524 closest distance to " O   SER A 276 " =    1.789
peak=   -3.518 closest distance to " O   HOH Z   6 " =    1.370
peak=   -3.516 closest distance to " CG  ARG A 269 " =    2.323
peak=   -3.511 closest distance to " CG  MET A 105 " =    1.011
peak=   -3.508 closest distance to " CD2 PHE A  61 " =    2.130
peak=   -3.506 closest distance to " NE  ARG A 156 " =    2.011
peak=   -3.505 closest distance to " O   HOH Z 285 " =    1.502
peak=   -3.494 closest distance to " O   HOH Z 185 " =    2.466
peak=   -3.488 closest distance to " OG BSER A 134 " =    1.230
peak=   -3.481 closest distance to " O   HOH Z 150 " =    2.073
peak=   -3.480 closest distance to " CD  GLN A  88 " =    0.855
peak=   -3.473 closest distance to " CG  GLU A  53 " =    1.402
peak=   -3.471 closest distance to " O   HOH Z  65 " =    0.716
peak=   -3.466 closest distance to " CB  ASP A 132 " =    2.395
peak=   -3.463 closest distance to " CB  ALA A 248 " =    2.279
peak=   -3.443 closest distance to " CD  PRO A 243 " =    2.022
peak=   -3.443 closest distance to " O   HOH Z  68 " =    1.576
peak=   -3.429 closest distance to " O   HOH Z 421 " =    3.873
peak=   -3.414 closest distance to " O   HOH Z 156 " =    3.541
peak=   -3.409 closest distance to " CB  ALA A 291 " =    2.452
peak=   -3.405 closest distance to " CB  HIS A  86 " =    1.179
peak=   -3.402 closest distance to " CH2 TRP A 150 " =    1.145
peak=   -3.402 closest distance to " O   HOH Z 174 " =    2.315
peak=   -3.398 closest distance to " CG2 VAL A 189 " =    2.211
peak=   -3.397 closest distance to " CG  GLN A  58 " =    1.153
peak=   -3.392 closest distance to " CG  GLU A 277 " =    1.355
peak=   -3.387 closest distance to " O   HOH Z 133 " =    1.331
peak=   -3.386 closest distance to " O   HOH Z   6 " =    1.794
peak=   -3.378 closest distance to " O   HOH Z  71 " =    2.510
peak=   -3.376 closest distance to " O   HOH Z  64 " =    1.652
peak=   -3.372 closest distance to " O   HOH Z 198 " =    1.754
peak=   -3.372 closest distance to " CG1 VAL A 112 " =    2.803
peak=   -3.371 closest distance to " O   SER A 206 " =    1.497
peak=   -3.369 closest distance to " O   HOH Z 407 " =    3.213
peak=   -3.366 closest distance to " O   HOH Z 102 " =    1.550
peak=   -3.366 closest distance to " O   HOH Z 357 " =    2.202
peak=   -3.365 closest distance to " O   HOH Z 418 " =    1.159
peak=   -3.362 closest distance to " O   HOH Z 154 " =    1.579
peak=   -3.360 closest distance to " CB  PHE A  16 " =    2.440
peak=   -3.359 closest distance to " CB  ALA A  43 " =    2.595
peak=   -3.358 closest distance to " O   HOH Z 113 " =    1.979
peak=   -3.354 closest distance to " O   HOH Z 150 " =    1.217
peak=   -3.352 closest distance to " O   TRP A  92 " =    2.007
peak=   -3.349 closest distance to " C   THR A 279 " =    1.132
peak=   -3.348 closest distance to " O   HOH Z 252 " =    3.807
peak=   -3.347 closest distance to " C   ASN A 285 " =    2.350
peak=   -3.342 closest distance to " O   HOH Z  37 " =    1.918
peak=   -3.339 closest distance to " O   HOH Z  63 " =    1.307
peak=   -3.336 closest distance to " CZ  PHE A  38 " =    2.421
peak=   -3.334 closest distance to " O   PHE A 218 " =    1.511
peak=   -3.331 closest distance to " CG1 VAL A 265 " =    2.276
peak=   -3.331 closest distance to " O   HOH Z 197 " =    2.030
peak=   -3.327 closest distance to " CG1 VAL A  78 " =    2.718
peak=   -3.325 closest distance to " CG  TRP A 266 " =    1.892
peak=   -3.323 closest distance to " NE2 GLN A  88 " =    1.830
peak=   -3.316 closest distance to " NE  ARG A  66 " =    4.387
peak=   -3.316 closest distance to " OD1 ASP A 171 " =    1.489
peak=   -3.313 closest distance to " NH2 ARG A 159 " =    2.254
peak=   -3.310 closest distance to " CA  GLY A 241 " =    2.897
peak=   -3.306 closest distance to " O   HOH Z  13 " =    1.851
peak=   -3.306 closest distance to " O   HOH Z 149 " =    2.035
peak=   -3.305 closest distance to " O   GLN A 240 " =    2.607
peak=   -3.304 closest distance to " NE2 GLN A 103 " =    1.869
peak=   -3.301 closest distance to " CA  GLY A 133 " =    2.439
peak=   -3.299 closest distance to " O   HOH Z 174 " =    3.619
peak=   -3.294 closest distance to " O   HOH Z 287 " =    1.987
peak=   -3.285 closest distance to " O   HOH Z 216 " =    1.265
peak=   -3.281 closest distance to " O   VAL A 189 " =    2.615
peak=   -3.277 closest distance to " CD2 LEU A 300 " =    2.668
peak=   -3.274 closest distance to " O   VAL A 189 " =    1.814
peak=   -3.273 closest distance to " OG BSER A 210 " =    1.470
peak=   -3.266 closest distance to " ND2 ASN A  45 " =    1.168
peak=   -3.265 closest distance to " O   HOH Z 177 " =    1.932
peak=   -3.256 closest distance to " O   HOH Z 396 " =    2.004
peak=   -3.241 closest distance to " O   HOH Z 191 " =    5.939
peak=   -3.240 closest distance to " CG  LEU A  83 " =    2.075
peak=   -3.237 closest distance to " CZ  PHE A  38 " =    2.032
peak=   -3.235 closest distance to " O   HOH Z  38 " =    1.516
peak=   -3.235 closest distance to " O   GLY A  17 " =    1.174
peak=   -3.234 closest distance to " CZ  TYR A 172 " =    1.878
peak=   -3.231 closest distance to " OG1 THR A  82 " =    1.289
peak=   -3.228 closest distance to " O   HOH Z  52 " =    1.847
peak=   -3.226 closest distance to " NH2 ARG A  79 " =    2.294
peak=   -3.225 closest distance to " CG1 VAL A 125 " =    1.965
peak=   -3.221 closest distance to " CG  ASP A 298 " =    0.876
peak=   -3.218 closest distance to " CG1BVAL A  41 " =    2.782
peak=   -3.215 closest distance to " O   HOH Z 372 " =    2.419
peak=   -3.210 closest distance to " O   HOH Z 165 " =    1.863
peak=   -3.208 closest distance to " NE2 GLN A 278 " =    1.448
peak=   -3.203 closest distance to " CD  ARG A 139 " =    1.061
peak=   -3.203 closest distance to " O   HOH Z  19 " =    2.203
peak=   -3.200 closest distance to " CD2 TYR A 247 " =    2.389
peak=   -3.197 closest distance to " ND2 ASN A 187 " =    1.661
peak=   -3.196 closest distance to " O   HOH Z 256 " =    2.363
peak=   -3.195 closest distance to " CZ3 TRP A 274 " =    2.434
peak=   -3.191 closest distance to " ND2 ASN A 249 " =    2.217
peak=   -3.191 closest distance to " CD  LYS A 289 " =    2.418
peak=   -3.188 closest distance to " O   HOH Z 292 " =    4.656
peak=   -3.187 closest distance to " O   HOH Z 136 " =    2.247
peak=   -3.187 closest distance to " CD2 HIS A 207 " =    2.273
peak=   -3.187 closest distance to " OD1 ASP A 191 " =    1.361
peak=   -3.187 closest distance to " O   HOH Z 393 " =    1.360
peak=   -3.184 closest distance to " O   HOH Z 351 " =    1.554
peak=   -3.181 closest distance to " O   HOH Z  78 " =    1.864
peak=   -3.178 closest distance to " O   SER A 271 " =    2.178
peak=   -3.175 closest distance to " O   HOH Z 145 " =    2.916
peak=   -3.174 closest distance to " O   HOH Z 340 " =    1.761
peak=   -3.165 closest distance to " C   GLY A 262 " =    2.019
peak=   -3.163 closest distance to " OD2 ASP A 270 " =    1.126
peak=   -3.152 closest distance to " N   ALA A 226 " =    1.985
peak=   -3.147 closest distance to " CB  ALA A   9 " =    2.377
peak=   -3.145 closest distance to " O   HOH Z 377 " =    1.309
peak=   -3.144 closest distance to " CD  ARG A 195 " =    5.058
peak=   -3.140 closest distance to " O   TYR A 186 " =    1.752
peak=   -3.135 closest distance to " CE1 TYR A 247 " =    2.723
peak=   -3.133 closest distance to " CE3 TRP A  70 " =    1.901
peak=   -3.124 closest distance to " OG BSER A 210 " =    2.190
peak=   -3.122 closest distance to " O   HOH Z 278 " =    1.245
peak=   -3.113 closest distance to " CD1 TRP A  70 " =    1.093
peak=   -3.105 closest distance to " CA  LYS A 166 " =    2.256
peak=   -3.100 closest distance to " O   HOH Z 139 " =    5.076
peak=   -3.094 closest distance to " O   GLY A  80 " =    2.568
peak=   -3.089 closest distance to " O   GLU A 152 " =    1.416
peak=   -3.067 closest distance to " O   HOH Z 351 " =    1.444
peak=   -3.067 closest distance to " O   SER A  62 " =    2.168
peak=   -3.063 closest distance to " O   HOH Z 331 " =    1.154
peak=   -3.044 closest distance to " N   ASP A 191 " =    1.060
peak=   -3.040 closest distance to " OG1 THR A 157 " =    2.899
peak=   -3.023 closest distance to " N   GLN A 223 " =    0.986
peak=   -3.011 closest distance to " O   HOH Z 426 " =    1.732

================= 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    :  0.4220 0.4149   6.224722e+00   6.201186e+00
   1_bss:  0.4107 0.4034   6.211684e+00   6.186014e+00
   1_xyz:  0.2920 0.3134   5.937536e+00   5.998360e+00
   1_adp:  0.2650 0.3252   5.886362e+00   6.020263e+00
   1_occ:  0.2647 0.3258   5.886298e+00   6.021223e+00
   2_bss:  0.2624 0.3234   5.883353e+00   6.019251e+00
   2_xyz:  0.1864 0.2346   5.576009e+00   5.758486e+00
   2_adp:  0.1734 0.2170   5.509157e+00   5.694068e+00
   2_occ:  0.1733 0.2169   5.508498e+00   5.693844e+00
   3_bss:  0.1733 0.2159   5.506995e+00   5.690548e+00
   3_xyz:  0.1464 0.1867   5.363559e+00   5.557599e+00
   3_adp:  0.1377 0.1863   5.327004e+00   5.541363e+00
   3_occ:  0.1376 0.1863   5.326654e+00   5.540818e+00
   4_bss:  0.1380 0.1865   5.328478e+00   5.541744e+00
   4_xyz:  0.1192 0.1702   5.213504e+00   5.454938e+00
   4_adp:  0.1165 0.1665   5.191633e+00   5.434095e+00
   4_occ:  0.1164 0.1664   5.191400e+00   5.433813e+00
   5_bss:  0.1162 0.1662   5.191357e+00   5.433841e+00
   5_xyz:  0.1200 0.1677   5.211525e+00   5.442431e+00
   5_adp:  0.1200 0.1658   5.208590e+00   5.435181e+00
   5_occ:  0.1199 0.1658   5.208314e+00   5.434979e+00
   5_bss:  0.1199 0.1658   5.208248e+00   5.434956e+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:  0.303  48.956  -3.358   2.286   3.661   0.000   0.000   0.000
   1_xyz:  0.303  48.956  -3.358   2.286   3.661   0.000   0.000   0.000
   1_adp:  0.303  48.956  -3.358   2.286   3.661   0.000   0.000   0.000
   1_occ:  0.303  48.956  -3.358   2.286   3.661   0.000   0.000   0.000
   2_bss:  0.327  71.867  -2.552   0.441   1.161   0.000   0.000   0.000
   2_xyz:  0.327  71.867  -2.552   0.441   1.161   0.000   0.000   0.000
   2_adp:  0.327  71.867  -2.552   0.441   1.161   0.000   0.000   0.000
   2_occ:  0.327  71.867  -2.552   0.441   1.161   0.000   0.000   0.000
   3_bss:  0.336  74.009  -2.453  -0.686   0.263  -0.000   0.000   0.000
   3_xyz:  0.336  74.009  -2.453  -0.686   0.263  -0.000   0.000   0.000
   3_adp:  0.336  74.009  -2.453  -0.686   0.263  -0.000   0.000   0.000
   3_occ:  0.336  74.009  -2.453  -0.686   0.263  -0.000   0.000   0.000
   4_bss:  0.336  80.994  -2.317  -1.017   0.085  -0.000   0.000   0.000
   4_xyz:  0.336  80.994  -2.317  -1.017   0.085  -0.000   0.000   0.000
   4_adp:  0.336  80.994  -2.317  -1.017   0.085  -0.000   0.000   0.000
   4_occ:  0.336  80.994  -2.317  -1.017   0.085  -0.000   0.000   0.000
   5_bss:  0.328  71.860  -1.797  -0.811   0.423  -0.000   0.000   0.000
   5_xyz:  0.328  71.860  -1.797  -0.811   0.423  -0.000   0.000   0.000
   5_adp:  0.328  71.860  -1.797  -0.811   0.423  -0.000   0.000   0.000
   5_occ:  0.328  71.860  -1.797  -0.811   0.423  -0.000   0.000   0.000
   5_bss:  0.323  66.414  -1.800  -0.814   0.420  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.254 0.5555  0.7099    50889.379
   1_bss:  46.098 0.5681  0.7508    47771.860
   1_xyz:  33.216 0.7221  0.9176    26788.678
   1_adp:  34.475 0.7071  0.8945    28642.597
   1_occ:  34.534 0.7065  0.8934    28734.435
   2_bss:  34.083 0.7119  0.8675    28395.672
   2_xyz:  23.622 0.8249  0.9661    14322.575
   2_adp:  21.271 0.8496  0.9728    12315.195
   2_occ:  21.261 0.8497  0.9726    12307.692
   3_bss:  21.099 0.8512  0.9527    12163.802
   3_xyz:  17.792 0.8825  0.9704     9097.076
   3_adp:  17.385 0.8862  0.9605     8816.762
   3_occ:  17.371 0.8863  0.9605     8806.697
   4_bss:  17.374 0.8864  0.9568     8832.800
   4_xyz:  15.673 0.9008  0.9659     7374.398
   4_adp:  15.165 0.9054  0.9588     7094.581
   4_occ:  15.158 0.9055  0.9587     7090.685
   5_bss:  15.162 0.9055  0.9710     7089.837
   5_xyz:  15.217 0.9053  0.9707     7173.374
   5_adp:  15.046 0.9069  0.9644     7113.932
   5_occ:  15.040 0.9069  0.9644     7112.022
   5_bss:  15.041 0.9069  0.9644     7109.699
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6847e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6847e-01
   1_xyz:   1.401  0.010  0.085 15.077  0.006  4.111   9.9916e-02
   1_adp:   1.401  0.010  0.085 15.077  0.006  4.111   9.9916e-02
   1_occ:   1.401  0.010  0.085 15.077  0.006  4.111   9.9916e-02
   2_bss:   1.401  0.010  0.085 15.077  0.006  4.111   9.9916e-02
   2_xyz:   1.146  0.009  0.079 14.547  0.005  4.129   7.5824e-02
   2_adp:   1.146  0.009  0.079 14.547  0.005  4.129   7.5824e-02
   2_occ:   1.146  0.009  0.079 14.547  0.005  4.129   7.5824e-02
   3_bss:   1.146  0.009  0.079 14.547  0.005  4.129   7.5824e-02
   3_xyz:   0.917  0.006  0.065 14.439  0.003  4.135   5.1528e-02
   3_adp:   0.917  0.006  0.065 14.439  0.003  4.135   5.1528e-02
   3_occ:   0.917  0.006  0.065 14.439  0.003  4.135   5.1528e-02
   4_bss:   0.917  0.006  0.065 14.439  0.003  4.135   5.1528e-02
   4_xyz:   1.181  0.011  0.086 14.860  0.005  4.133   8.1559e-02
   4_adp:   1.181  0.011  0.086 14.860  0.005  4.133   8.1559e-02
   4_occ:   1.181  0.011  0.086 14.860  0.005  4.133   8.1559e-02
   5_bss:   1.181  0.011  0.086 14.860  0.005  4.133   8.1559e-02
   5_xyz:   0.950  0.007  0.074 14.426  0.004  4.115   5.5234e-02
   5_adp:   0.950  0.007  0.074 14.426  0.004  4.115   5.5234e-02
   5_occ:   0.950  0.007  0.074 14.426  0.004  4.115   5.5234e-02
   5_bss:   0.950  0.007  0.074 14.426  0.004  4.115   5.5234e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.585   2.4389e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.585   2.4389e-01
   1_xyz:   8.691  0.062  0.352 85.485  0.044  2.011   1.1963e-01
   1_adp:   8.691  0.062  0.352 85.485  0.044  2.011   1.1963e-01
   1_occ:   8.691  0.062  0.352 85.485  0.044  2.011   1.1963e-01
   2_bss:   8.691  0.062  0.352 85.485  0.044  2.011   1.1963e-01
   2_xyz:   7.636  0.064  0.267 80.568  0.042  2.344   1.5379e-01
   2_adp:   7.636  0.064  0.267 80.568  0.042  2.344   1.5379e-01
   2_occ:   7.636  0.064  0.267 80.568  0.042  2.344   1.5379e-01
   3_bss:   7.636  0.064  0.267 80.568  0.042  2.344   1.5379e-01
   3_xyz:   7.004  0.039  0.217 80.214  0.037  2.213   3.3267e-02
   3_adp:   7.004  0.039  0.217 80.214  0.037  2.213   3.3267e-02
   3_occ:   7.004  0.039  0.217 80.214  0.037  2.213   3.3267e-02
   4_bss:   7.004  0.039  0.217 80.214  0.037  2.213   3.3267e-02
   4_xyz:   8.389  0.057  0.310 83.837  0.044  2.276   6.3069e-02
   4_adp:   8.389  0.057  0.310 83.837  0.044  2.276   6.3069e-02
   4_occ:   8.389  0.057  0.310 83.837  0.044  2.276   6.3069e-02
   5_bss:   8.389  0.057  0.310 83.837  0.044  2.276   6.3069e-02
   5_xyz:   7.011  0.045  0.241 81.088  0.036  2.320   3.4307e-02
   5_adp:   7.011  0.045  0.241 81.088  0.036  2.320   3.4307e-02
   5_occ:   7.011  0.045  0.241 81.088  0.036  2.320   3.4307e-02
   5_bss:   7.011  0.045  0.241 81.088  0.036  2.320   3.4307e-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: 102.13   0.00  17.82  84.26   0.00  13.86 102.13   1.77  39.37
   1_occ: 102.13   0.00  17.82  84.26   0.00  13.86 102.13   1.77  39.37
   2_bss: 102.13   0.00  17.82  84.26   0.00  13.86 102.13   1.77  39.37
   2_xyz: 102.13   0.00  17.82  84.26   0.00  13.86 102.13   1.77  39.37
   2_adp: 101.54   1.21  17.26  83.64   1.21  13.11 101.54   5.14  39.88
   2_occ: 101.54   1.21  17.26  83.64   1.21  13.11 101.54   5.14  39.88
   3_bss: 101.54   1.21  17.26  83.64   1.21  13.11 101.54   5.14  39.88
   3_xyz: 101.54   1.21  17.26  83.64   1.21  13.11 101.54   5.14  39.88
   3_adp: 101.50   0.00  17.78  92.68   0.00  12.89 101.50   4.63  44.43
   3_occ: 101.50   0.00  17.78  92.68   0.00  12.89 101.50   4.63  44.43
   4_bss: 101.50   0.00  17.78  92.68   0.00  12.89 101.50   4.63  44.43
   4_xyz: 101.50   0.00  17.78  92.68   0.00  12.89 101.50   4.63  44.43
   4_adp: 101.90   0.00  17.30  99.13   0.00  12.47 101.90   3.13  43.63
   4_occ: 101.90   0.00  17.30  99.13   0.00  12.47 101.90   3.13  43.63
   5_bss: 101.90   0.00  17.30  99.13   0.00  12.47 101.90   3.13  43.63
   5_xyz: 101.90   0.00  17.30  99.13   0.00  12.47 101.90   3.13  43.63
   5_adp:  99.09   0.00  16.49  97.47   0.00  12.07  99.09   1.50  40.53
   5_occ:  99.09   0.00  16.49  97.47   0.00  12.07  99.09   1.50  40.53
   5_bss:  99.09   0.00  16.49  97.47   0.00  12.07  99.09   1.50  40.54
------------------------------------------------------------------------
 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:    1.789    0.007    0.344
   1_adp:    1.789    0.007    0.344
   1_occ:    1.789    0.007    0.344
   2_bss:    1.789    0.007    0.344
   2_xyz:    1.381    0.062    0.494
   2_adp:    1.381    0.062    0.494
   2_occ:    1.381    0.062    0.494
   3_bss:    1.381    0.062    0.494
   3_xyz:    1.352    0.047    0.572
   3_adp:    1.352    0.047    0.572
   3_occ:    1.352    0.047    0.572
   4_bss:    1.352    0.047    0.572
   4_xyz:    1.311    0.057    0.619
   4_adp:    1.311    0.057    0.619
   4_occ:    1.311    0.057    0.619
   5_bss:    1.311    0.057    0.619
   5_xyz:    1.282    0.051    0.623
   5_adp:    1.282    0.051    0.623
   5_occ:    1.282    0.051    0.623
   5_bss:    1.282    0.051    0.623
------------------------------------------------------------------------

CPU time actual refinement: 337.17


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_581/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_581/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_581/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_581/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_581/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 337.02 
  Macro-tasks:
    bulk solvent and scale       = 47.05  
    individual site refinement   = 136.46 
    weights calculation          = 29.78  
    collect and process          = 6.60   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 219.98 
  Micro-tasks:
    mask                            = 1.67   
    f_calc                          = 105.98 
    alpha_beta                      = 8.26   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 110.46 
    fmodel                         = 7.66   
    r_factors                      = 0.07   
    phase_errors                   = 11.82  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 247.33 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.755 micro seconds
Total CPU time: 5.84 minutes
from_scatterers_fft:    644 calls, 105.52 s
gradients_fft:          589 calls,  98.58 s

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

# Date 2008-01-16 Time 05:10:10 PST -0800 (1200489010.53 s)
Start R-work = 0.4220, R-free = 0.4149 (no bulk solvent and anisotropic scale)
Final R-work = 0.1387, R-free = 0.1812 (no bulk solvent and anisotropic scale)

Start R-work = 0.4107, R-free = 0.4034
Final R-work = 0.1199, R-free = 0.1658