# Date 2008-01-16 Time 06:11:32 PST -0800 (1200492692.51 s)
#phil __OFF__

Command line arguments: "../1045.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2325
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1045

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 47.3993, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.33, 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: (71.3037, 47.3993, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.049 1.95145
Completeness in resolution range: 0.91726
Completeness with d_max=infinity: 0.914562

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0490
                             d_min =   1.9515

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.3993, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.049 1.95145
Completeness in resolution range: 0.91726
Completeness with d_max=infinity: 0.914562

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0495 -  4.1771 [2246/2275]  2023   223   9.9%
  bin  2:  4.1771 -  3.3273 [2145/2168]  1930   215  10.0%
  bin  3:  3.3273 -  2.9102 [2119/2144]  1902   217  10.2%
  bin  4:  2.9102 -  2.6456 [2107/2123]  1902   205   9.7%
  bin  5:  2.6456 -  2.4569 [2082/2126]  1877   205   9.8%
  bin  6:  2.4569 -  2.3126 [2082/2110]  1871   211  10.1%
  bin  7:  2.3126 -  2.1971 [2074/2110]  1863   211  10.2%
  bin  8:  2.1971 -  2.1018 [2055/2097]  1852   203   9.9%
  bin  9:  2.1018 -  2.0210 [2031/2105]  1826   205  10.1%
  bin 10:  2.0210 -  1.9515 [ 648/2098]   584    64   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1045/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:
        1.49 -     2.17: 22
        2.17 -     2.85: 1143
        2.85 -     3.54: 4422
        3.54 -     4.22: 9276
        4.22 -     4.90: 13519
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.492 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.533 3.040 -x+1/2,-y+1,z+1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.793 3.120 -x+1/2,-y+1,z-1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 324 " - " O   HOH Z 396 "  1.829 3.040 -x,y-1/2,-z+1/2
  ... (remaining 28377 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_1045/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1045/model_refine_001.geo

CPU time processing inputs: 8.93


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 47.3993 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4350   r_free= 0.4372   ksol= 0.00   Bsol= 0.00   scale= 0.915    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.238798                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0495 -  4.6597 0.99   1458  165 0.3370 0.3422      6.4856      6.4864|
|  2:  4.6597 -  3.7169 0.99   1393  151 0.3565 0.3418      6.7099      6.7091|
|  3:  3.7169 -  3.2524 0.99   1372  152 0.3932 0.3962      6.5831      6.6374|
|  4:  3.2524 -  2.9575 0.99   1364  150 0.4254 0.4131      6.4438      6.4466|
|  5:  2.9575 -  2.7469 0.98   1357  150 0.4441 0.4338      6.2963      6.2913|
|  6:  2.7469 -  2.5858 0.99   1351  156 0.4695 0.4815      6.2302      6.1664|
|  7:  2.5858 -  2.4569 0.98   1339  141 0.4720 0.4354       6.201      6.1666|
|  8:  2.4569 -  2.3504 0.99   1338  153 0.4826 0.5021      6.1234      6.1744|
|  9:  2.3504 -  2.2602 0.99   1339  152 0.5043 0.4873      6.1279      6.0794|
| 10:  2.2602 -  2.1824 0.98   1323  149 0.5005 0.5285      6.0481      6.1394|
| 11:  2.1824 -  2.1144 0.97   1331  136 0.4989 0.6004      6.0192      5.9927|
| 12:  2.1144 -  2.0541 0.99   1317  157 0.5066 0.5242      5.9228      5.9612|
| 13:  2.0541 -  2.0001 0.79   1068  122 0.5136 0.4735      5.8635      5.8304|
| 14:  2.0001 -  1.9515 0.20    280   25 0.5853 0.4836      5.8124      5.8263|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0495 -  4.6597  1458   165  0.75  30.16   0.85     0.77      55237.30|
|  2:  4.6597 -  3.7169  1393   151  0.75  30.64   0.94     0.84      80944.84|
|  3:  3.7169 -  3.2524  1372   152  0.66  38.64   0.93     0.83      89582.22|
|  4:  3.2524 -  2.9575  1364   150  0.57  46.50   0.94     0.78      83669.49|
|  5:  2.9575 -  2.7469  1357   150  0.51  51.25   0.90     0.70      67830.92|
|  6:  2.7469 -  2.5858  1351   156  0.48  53.22   0.92     0.68      58621.96|
|  7:  2.5858 -  2.4569  1339   141  0.48  53.32   0.94     0.65      51967.30|
|  8:  2.4569 -  2.3504  1338   153  0.44  56.59   0.91     0.64      51390.79|
|  9:  2.3504 -  2.2602  1339   152  0.41  59.27   0.95     0.59      48728.61|
| 10:  2.2602 -  2.1824  1323   149  0.34  64.36   0.95     0.51      50646.21|
| 11:  2.1824 -  2.1144  1331   136  0.28  68.96   0.95     0.42      48816.93|
| 12:  2.1144 -  2.0541  1317   157  0.23  73.23   0.94     0.38      47726.42|
| 13:  2.0541 -  2.0001  1068   122  0.25  71.75   0.93     0.40      39933.08|
| 14:  2.0001 -  1.9515   280    25  0.29  68.50   0.87     0.45      31021.76|
|alpha:            min =        0.38 max =            0.84 mean =         0.63|
|beta:             min =    31021.76 max =        89582.22 mean =     59633.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           90.00 mean =        53.33|
|phase err.(test): min =        0.00 max =           89.83 mean =        53.35|
|-----------------------------------------------------------------------------|

============================== 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 = 11.335938             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.880   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.238870              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.669   (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 |  1.492 -  1.832:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.832 -  2.173:       17 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.173 -  2.514:       26 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.514 -  2.855:     1117 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.855 -  3.196:     1952 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.196 -  3.537:     2470 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.537 -  3.877:     4629 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.877 -  4.218:     4647 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.218 -  4.559:     6137 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.559 -  4.900:     7382 |
|-----------------------------------------------------------------------------|
|-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 |        0.184 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.492 |       0.494 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.884)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4350   r_free= 0.4372   ksol= 0.00   Bsol= 0.00   scale= 0.915    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.238798                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4266   r_free= 0.4295   ksol= 0.30   Bsol= 50.00   scale= 0.952   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.70,-0.17,2.43,-0.00,0.00,0.00); trace/3= 0.52                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.233794                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.873339              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.039   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.003122              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.410   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4266      final r-factor (work) = 0.2897          |
| start r-factor (free) = 0.4295      final r-factor (free) = 0.3256          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.8220 = 8.87 * 0.50 * 6.2295 + 1.00 * 0.1836                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.0309 = 8.87 * 0.50 * 6.0674 + 1.00 * 0.1121                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2897      final r-factor (work) = 0.2629          |
| start r-factor (free) = 0.3256      final r-factor (free) = 0.3297          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0927 = 1.00 * 1.00 * 6.0674 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9191 = 1.00 * 1.00 * 5.8824 + 1.00 * 0.0183                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.884)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.19  18.59    None  None   None       |
|    all(noH): 2823   0      0.00    101.19  18.59    None  None   None       |
|    Sol.    : 438    0      3.88    101.19  42.83    None  None   None       |
|    Mac.    : 2385   0      0.00    98.46   14.14    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 -  10.119:  979   |   5:    50.593 -  60.711:   79        |
|      1:    10.119 -  20.237: 1014   |   6:    60.711 -  70.830:   63        |
|      2:    20.237 -  30.356:  356   |   7:    70.830 -  80.948:   23        |
|      3:    30.356 -  40.474:  177   |   8:    80.948 -  91.067:    8        |
|      4:    40.474 -  50.593:  121   |   9:    91.067 - 101.186:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2629 r_free = 0.3297             target_work(ml) = 5.888         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2627 r_free = 0.3295             target_work(ml) = 5.887         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2627   r_free= 0.3295   ksol= 0.30   Bsol= 50.00   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.70,-0.17,2.43,-0.00,0.00,0.00); trace/3= 0.52                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.886822                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2605   r_free= 0.3271   ksol= 0.33   Bsol= 62.69   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.75,-1.29,-0.15,-0.00,-0.00,-0.00); trace/3= -1.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.884297                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.537874              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.347   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.487591              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 104.270  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2605      final r-factor (work) = 0.1865          |
| start r-factor (free) = 0.3271      final r-factor (free) = 0.2413          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.4107 = 5.54 * 0.50 * 5.8862 + 1.00 * 0.1121                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.0353 = 5.54 * 0.50 * 5.7659 + 1.00 * 0.0697                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1865      final r-factor (work) = 0.1676          |
| start r-factor (free) = 0.2413      final r-factor (free) = 0.2203          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8322 = 0.49 * 1.00 * 5.7659 + 1.00 * 0.0207                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7128 = 0.49 * 1.00 * 5.5419 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.884)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.12    91.94   18.29    None  None   None       |
|    all(noH): 2823   0      1.12    91.94   18.29    None  None   None       |
|    Sol.    : 438    0      5.43    88.45   43.81    None  None   None       |
|    Mac.    : 2385   0      1.12    91.94   13.61    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:     1.119 -  10.200: 1025   |   5:    46.528 -  55.610:  113        |
|      1:    10.200 -  19.282: 1039   |   6:    55.610 -  64.691:   70        |
|      2:    19.282 -  28.364:  270   |   7:    64.691 -  73.773:   32        |
|      3:    28.364 -  37.446:  128   |   8:    73.773 -  82.855:   21        |
|      4:    37.446 -  46.528:  115   |   9:    82.855 -  91.937:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1676 r_free = 0.2203             target_work(ml) = 5.496         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1674 r_free = 0.2201             target_work(ml) = 5.496         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1674   r_free= 0.2201   ksol= 0.33   Bsol= 62.69   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.75,-1.29,-0.15,-0.00,-0.00,-0.00); trace/3= -1.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.495504                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1671   r_free= 0.2192   ksol= 0.32   Bsol= 57.20   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-1.93,-1.57,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.494008                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.595373              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.812   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.524966              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.041  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1671      final r-factor (work) = 0.1344          |
| start r-factor (free) = 0.2192      final r-factor (free) = 0.1804          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0383 = 3.60 * 0.50 * 5.5450 + 1.00 * 0.0701                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7867 = 3.60 * 0.50 * 5.4095 + 1.00 * 0.0620                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1344      final r-factor (work) = 0.1262          |
| start r-factor (free) = 0.1804      final r-factor (free) = 0.1726          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8504 = 0.52 * 1.00 * 5.4095 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7783 = 0.52 * 1.00 * 5.2732 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.884)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.78   18.00    None  None   None       |
|    all(noH): 2823   0      0.00    96.78   18.00    None  None   None       |
|    Sol.    : 438    0      5.61    85.87   43.52    None  None   None       |
|    Mac.    : 2385   0      0.00    96.78   13.32    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 -   9.678:  923   |   5:    48.388 -  58.065:  105        |
|      1:     9.678 -  19.355: 1201   |   6:    58.065 -  67.743:   59        |
|      2:    19.355 -  29.033:  249   |   7:    67.743 -  77.420:   31        |
|      3:    29.033 -  38.710:  118   |   8:    77.420 -  87.098:   17        |
|      4:    38.710 -  48.388:  115   |   9:    87.098 -  96.776:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1262 r_free = 0.1726             target_work(ml) = 5.250         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1261 r_free = 0.1726             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1261   r_free= 0.1726   ksol= 0.32   Bsol= 57.20   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-1.93,-1.57,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.249401                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1264   r_free= 0.1727   ksol= 0.32   Bsol= 52.55   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.21,-2.09,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.251110                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.840064              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.279  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.622472              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.902  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1264      final r-factor (work) = 0.1200          |
| start r-factor (free) = 0.1727      final r-factor (free) = 0.1652          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9152 = 1.84 * 0.50 * 5.2750 + 1.00 * 0.0620                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8671 = 1.84 * 0.50 * 5.2316 + 1.00 * 0.0538                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1200      final r-factor (work) = 0.1181          |
| start r-factor (free) = 0.1652      final r-factor (free) = 0.1648          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2665 = 0.62 * 1.00 * 5.2316 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2481 = 0.62 * 1.00 * 5.2021 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.884)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.33    102.01  17.80    None  None   None       |
|    all(noH): 2823   0      1.33    102.01  17.80    None  None   None       |
|    Sol.    : 438    0      5.49    86.43   42.74    None  None   None       |
|    Mac.    : 2385   0      1.33    102.01  13.22    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:     1.329 -  11.397: 1313   |   5:    51.670 -  61.739:   91        |
|      1:    11.397 -  21.465:  909   |   6:    61.739 -  71.807:   45        |
|      2:    21.465 -  31.534:  194   |   7:    71.807 -  81.875:   27        |
|      3:    31.534 -  41.602:  122   |   8:    81.875 -  91.944:    8        |
|      4:    41.602 -  51.670:  109   |   9:    91.944 - 102.012:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1181 r_free = 0.1648             target_work(ml) = 5.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1180 r_free = 0.1647             target_work(ml) = 5.198         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1647   ksol= 0.32   Bsol= 52.55   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.21,-2.09,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.198276                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1647   ksol= 0.32   Bsol= 52.55   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-2.14,-2.15,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.198229                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.511300              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.026  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.823477              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.274  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1180      final r-factor (work) = 0.1159          |
| start r-factor (free) = 0.1647      final r-factor (free) = 0.1628          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9846 = 1.51 * 0.50 * 5.2018 + 1.00 * 0.0538                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9743 = 1.51 * 0.50 * 5.1913 + 1.00 * 0.0515                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1159      final r-factor (work) = 0.1153          |
| start r-factor (free) = 0.1628      final r-factor (free) = 0.1628          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2848 = 0.82 * 1.00 * 5.1913 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2790 = 0.82 * 1.00 * 5.1840 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.884)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.14    108.17  17.61    None  None   None       |
|    all(noH): 2823   0      1.14    108.17  17.61    None  None   None       |
|    Sol.    : 438    0      5.71    90.31   42.24    None  None   None       |
|    Mac.    : 2385   0      1.14    108.17  13.08    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:     1.142 -  11.845: 1437   |   5:    54.655 -  65.357:   75        |
|      1:    11.845 -  22.547:  824   |   6:    65.357 -  76.060:   29        |
|      2:    22.547 -  33.250:  187   |   7:    76.060 -  86.762:   20        |
|      3:    33.250 -  43.952:  120   |   8:    86.762 -  97.465:    3        |
|      4:    43.952 -  54.655:  124   |   9:    97.465 - 108.167:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1153 r_free = 0.1628             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1153 r_free = 0.1628             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1153   r_free= 0.1628   ksol= 0.32   Bsol= 52.55   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-2.14,-2.15,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.185172                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0495 -  4.6597 0.99   1458  165 0.0956 0.1275      5.3581      5.5358|
|  2:  4.6597 -  3.7169 0.99   1393  151 0.0835 0.1030      5.4114      5.6134|
|  3:  3.7169 -  3.2524 0.99   1372  152 0.1069 0.1692      5.4727      5.9131|
|  4:  3.2524 -  2.9575 0.99   1364  150 0.1317 0.1549      5.4953      5.6195|
|  5:  2.9575 -  2.7469 0.98   1357  150 0.1379 0.1846      5.3636      5.5313|
|  6:  2.7469 -  2.5858 0.99   1351  156 0.1301 0.1966      5.2472      5.4871|
|  7:  2.5858 -  2.4569 0.98   1339  141 0.1275 0.1758      5.1943      5.4135|
|  8:  2.4569 -  2.3504 0.99   1338  153 0.1240 0.1671      5.0961      5.2832|
|  9:  2.3504 -  2.2602 0.99   1339  152 0.1226 0.2055      5.0616      5.3547|
| 10:  2.2602 -  2.1824 0.98   1323  149 0.1164 0.1720      4.9957        5.29|
| 11:  2.1824 -  2.1144 0.97   1331  136 0.1191 0.1940      4.9635      5.2521|
| 12:  2.1144 -  2.0541 0.99   1317  157 0.1194 0.1864      4.9053      5.1585|
| 13:  2.0541 -  2.0001 0.79   1068  122 0.1212 0.1755      4.8219      5.0256|
| 14:  2.0001 -  1.9515 0.20    280   25 0.1148 0.1785      4.6997      5.0027|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0495 -  4.6597  1458   165  0.94   8.78   0.97     0.95       6752.05|
|  2:  4.6597 -  3.7169  1393   151  0.96   7.64   1.01     0.99       8537.14|
|  3:  3.7169 -  3.2524  1372   152  0.93  11.49   1.03     1.02      10372.49|
|  4:  3.2524 -  2.9575  1364   150  0.91  15.35   1.01     0.98      11254.51|
|  5:  2.9575 -  2.7469  1357   150  0.89  16.91   0.99     0.97       9104.21|
|  6:  2.7469 -  2.5858  1351   156  0.89  16.91   0.98     0.96       7614.27|
|  7:  2.5858 -  2.4569  1339   141  0.90  16.12   0.99     0.96       6699.64|
|  8:  2.4569 -  2.3504  1338   153  0.90  16.53   0.99     0.95       5743.85|
|  9:  2.3504 -  2.2602  1339   152  0.89  17.12   0.99     0.96       5394.25|
| 10:  2.2602 -  2.1824  1323   149  0.90  15.99   0.98     0.94       4803.09|
| 11:  2.1824 -  2.1144  1331   136  0.89  16.99   0.98     0.94       4618.33|
| 12:  2.1144 -  2.0541  1317   157  0.90  17.02   0.99     0.98       4333.50|
| 13:  2.0541 -  2.0001  1068   122  0.89  17.59   0.98     0.96       3655.80|
| 14:  2.0001 -  1.9515   280    25  0.89  17.19   0.97     0.94       2871.16|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2871.16 max =        11254.51 mean =      6849.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.88|
|phase err.(test): min =        0.00 max =           88.99 mean =        14.26|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1153   r_free= 0.1628   ksol= 0.32   Bsol= 52.51   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,-1.95,-1.96,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.185270                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1153   r_free= 0.1628   ksol= 0.32   Bsol= 52.51   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,-1.95,-1.96,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.185270                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0495 -  4.6597 0.99   1458  165 0.0957 0.1275      5.3585      5.5375|
|  2:  4.6597 -  3.7169 0.99   1393  151 0.0836 0.1031      5.4124      5.6141|
|  3:  3.7169 -  3.2524 0.99   1372  152 0.1069 0.1692      5.4728       5.913|
|  4:  3.2524 -  2.9575 0.99   1364  150 0.1317 0.1550      5.4953      5.6195|
|  5:  2.9575 -  2.7469 0.98   1357  150 0.1379 0.1846      5.3634       5.531|
|  6:  2.7469 -  2.5858 0.99   1351  156 0.1301 0.1967      5.2471       5.487|
|  7:  2.5858 -  2.4569 0.98   1339  141 0.1276 0.1758      5.1943      5.4135|
|  8:  2.4569 -  2.3504 0.99   1338  153 0.1240 0.1671      5.0962      5.2833|
|  9:  2.3504 -  2.2602 0.99   1339  152 0.1226 0.2055      5.0618      5.3546|
| 10:  2.2602 -  2.1824 0.98   1323  149 0.1164 0.1720      4.9958      5.2899|
| 11:  2.1824 -  2.1144 0.97   1331  136 0.1191 0.1940      4.9635       5.252|
| 12:  2.1144 -  2.0541 0.99   1317  157 0.1194 0.1863       4.905       5.158|
| 13:  2.0541 -  2.0001 0.79   1068  122 0.1212 0.1753      4.8218      5.0251|
| 14:  2.0001 -  1.9515 0.20    280   25 0.1148 0.1786      4.6996       5.003|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0495 -  4.6597  1458   165  0.94   8.81   0.97     0.95       6767.85|
|  2:  4.6597 -  3.7169  1393   151  0.96   7.65   1.01     1.00       8552.58|
|  3:  3.7169 -  3.2524  1372   152  0.93  11.50   1.03     1.03      10381.65|
|  4:  3.2524 -  2.9575  1364   150  0.91  15.35   1.01     0.98      11253.31|
|  5:  2.9575 -  2.7469  1357   150  0.89  16.92   0.99     0.97       9102.35|
|  6:  2.7469 -  2.5858  1351   156  0.89  16.91   0.99     0.96       7613.11|
|  7:  2.5858 -  2.4569  1339   141  0.90  16.12   0.99     0.97       6700.13|
|  8:  2.4569 -  2.3504  1338   153  0.90  16.54   0.99     0.96       5744.27|
|  9:  2.3504 -  2.2602  1339   152  0.89  17.13   1.00     0.97       5394.17|
| 10:  2.2602 -  2.1824  1323   149  0.90  15.99   0.99     0.95       4802.87|
| 11:  2.1824 -  2.1144  1331   136  0.89  16.99   0.99     0.95       4617.36|
| 12:  2.1144 -  2.0541  1317   157  0.90  17.02   1.00     0.99       4330.89|
| 13:  2.0541 -  2.0001  1068   122  0.89  17.59   0.99     0.97       3654.22|
| 14:  2.0001 -  1.9515   280    25  0.89  17.19   0.98     0.94       2870.70|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     2870.70 max =        11253.31 mean =      6852.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.89|
|phase err.(test): min =        0.00 max =           88.99 mean =        14.27|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.884)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.10    108.13  17.57    None  None   None       |
|    all(noH): 2823   0      1.10    108.13  17.57    None  None   None       |
|    Sol.    : 438    0      5.67    90.27   42.20    None  None   None       |
|    Mac.    : 2385   0      1.10    108.13  13.04    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.102 -  11.805: 1437   |   5:    54.615 -  65.317:   75        |
|      1:    11.805 -  22.507:  824   |   6:    65.317 -  76.020:   29        |
|      2:    22.507 -  33.210:  187   |   7:    76.020 -  86.722:   20        |
|      3:    33.210 -  43.912:  120   |   8:    86.722 -  97.425:    3        |
|      4:    43.912 -  54.615:  124   |   9:    97.425 - 108.127:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 340         
Filter by distance & map next to the model:
   mapped sites are within: 0.595 - 5.769
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 334 from: 340
   mapped sites are within: 0.706 - 5.769

peak=    5.828 closest distance to " NH2 ARG A  56 " =    2.255
peak=    5.713 closest distance to " CG  PRO A  54 " =    1.216
peak=    5.709 closest distance to " CB  GLN A 223 " =    1.479
peak=    5.525 closest distance to " CB  SER A  63 " =    1.329
peak=    5.238 closest distance to " CG  PRO A 213 " =    1.262
peak=    5.135 closest distance to " CG  PRO A  90 " =    1.114
peak=    5.097 closest distance to " CG  PRO A 198 " =    1.316
peak=    4.964 closest distance to " CB  ARG A 275 " =    0.928
peak=    4.838 closest distance to " CB  GLU A 128 " =    1.170
peak=    4.826 closest distance to " CB  PRO A  54 " =    0.866
peak=    4.708 closest distance to " O   HOH Z 193 " =    1.933
peak=    4.694 closest distance to " O   HOH Z 232 " =    2.217
peak=    4.667 closest distance to " NH2BARG A 102 " =    1.040
peak=    4.633 closest distance to " O   HOH Z 134 " =    1.568
peak=    4.610 closest distance to " CB  LEU A 228 " =    1.140
peak=    4.580 closest distance to " O   PRO A 198 " =    1.534
peak=    4.575 closest distance to " O   HOH Z  15 " =    2.125
peak=    4.558 closest distance to " O   HOH Z 214 " =    1.067
peak=    4.543 closest distance to " O   HOH Z 247 " =    1.379
peak=    4.506 closest distance to " CB  SER A   3 " =    1.363
peak=    4.478 closest distance to " OD2 ASP A 286 " =    2.880
peak=    4.469 closest distance to " O   HOH Z 298 " =    1.817
peak=    4.445 closest distance to " CA  TYR A  30 " =    0.955
peak=    4.437 closest distance to " CB  GLN A 183 " =    1.267
peak=    4.429 closest distance to " O   HOH Z 207 " =    1.855
peak=    4.384 closest distance to " O   HOH Z 132 " =    1.119
peak=    4.383 closest distance to " CB  VAL A 202 " =    1.648
peak=    4.382 closest distance to " O   HOH Z 368 " =    2.017
peak=    4.381 closest distance to " O   HOH Z 108 " =    1.647
peak=    4.373 closest distance to " CB  ASN A 148 " =    1.377
peak=    4.369 closest distance to " CA  ALA A  21 " =    1.223
peak=    4.330 closest distance to " O   HOH Z 234 " =    3.823
peak=    4.289 closest distance to " CB  TYR A 169 " =    0.761
peak=    4.285 closest distance to " CG  PRO A 280 " =    0.774
peak=    4.283 closest distance to " O   HOH Z 126 " =    1.581
peak=    4.265 closest distance to " OD1 ASN A  69 " =    2.492
peak=    4.262 closest distance to " NH2 ARG A 156 " =    1.231
peak=    4.244 closest distance to " O   HOH Z 180 " =    2.184
peak=    4.232 closest distance to " CA  THR A 221 " =    0.947
peak=    4.226 closest distance to " O   HOH Z 260 " =    1.189
peak=    4.223 closest distance to " O   HOH Z  78 " =    2.036
peak=    4.215 closest distance to " O   HOH Z 316 " =    3.021
peak=    4.189 closest distance to " O   HOH Z  67 " =    1.853
peak=    4.173 closest distance to " O   HOH Z 426 " =    1.531
peak=    4.169 closest distance to " O   HOH Z 389 " =    1.932
peak=    4.158 closest distance to " O   HOH Z 142 " =    1.646
peak=    4.143 closest distance to " O   HOH Z 209 " =    2.355
peak=    4.141 closest distance to " O   HOH Z 156 " =    3.459
peak=    4.119 closest distance to " CD  LYS A 119 " =    1.241
peak=    4.101 closest distance to " O   HOH Z  20 " =    1.866
peak=    4.096 closest distance to " CB  TRP A 179 " =    1.382
peak=    4.071 closest distance to " CD BLYS A 290 " =    1.025
peak=    4.070 closest distance to " CG  PRO A 243 " =    1.109
peak=    4.060 closest distance to " O   HOH Z 287 " =    1.987
peak=    4.029 closest distance to " NE2 GLN A  11 " =    1.067
peak=    4.023 closest distance to " O   HOH Z  80 " =    1.743
peak=    4.023 closest distance to " O   HOH Z 124 " =    1.384
peak=    4.015 closest distance to " O   SER A  87 " =    2.184
peak=    4.000 closest distance to " O   HOH Z 135 " =    1.889
peak=    3.999 closest distance to " O   HOH Z 374 " =    2.518
peak=    3.987 closest distance to " O   HOH Z  48 " =    1.429
peak=    3.987 closest distance to " O   HOH Z 427 " =    2.908
peak=    3.983 closest distance to " O   HOH Z 282 " =    1.541
peak=    3.980 closest distance to " CG1 ILE A  33 " =    1.240
peak=    3.977 closest distance to " CD1 LEU A 300 " =    1.229
peak=    3.972 closest distance to " CB  GLU A 152 " =    1.140
peak=    3.970 closest distance to " O   HOH Z 126 " =    1.805
peak=    3.969 closest distance to " CB  GLU A 277 " =    3.671
peak=    3.968 closest distance to " O   HOH Z 344 " =    2.986
peak=    3.965 closest distance to " O   HOH Z 352 " =    1.871
peak=    3.961 closest distance to " O   HOH Z 132 " =    2.083
peak=    3.955 closest distance to " CB  PRO A 198 " =    1.003
peak=    3.951 closest distance to " CB  GLU A 152 " =    1.579
peak=    3.935 closest distance to " O   HOH Z 411 " =    3.581
peak=    3.933 closest distance to " CB  TRP A 266 " =    0.951
peak=    3.930 closest distance to " O   HOH Z 132 " =    2.614
peak=    3.882 closest distance to " O   ALA A 165 " =    1.402
peak=    3.877 closest distance to " N   ASN A  39 " =    1.323
peak=    3.872 closest distance to " CB  PRO A  54 " =    1.361
peak=    3.871 closest distance to " O   HOH Z  40 " =    1.595
peak=    3.870 closest distance to " CG2 THR A 221 " =    0.984
peak=    3.859 closest distance to " O   HOH Z  97 " =    1.886
peak=    3.856 closest distance to " O   HOH Z 369 " =    2.070
peak=    3.852 closest distance to " O   HOH Z  54 " =    1.751
peak=    3.852 closest distance to " O   HOH Z 278 " =    0.985
peak=    3.833 closest distance to " O   HOH Z  49 " =    2.291
peak=    3.826 closest distance to " O   HOH Z  21 " =    1.692
peak=    3.822 closest distance to " O   HOH Z 261 " =    2.011
peak=    3.820 closest distance to " CA  ALA A  51 " =    0.977
peak=    3.818 closest distance to " NH2BARG A 145 " =    2.120
peak=    3.815 closest distance to " O   HOH Z 279 " =    2.308
peak=    3.813 closest distance to " CB  MET A  47 " =    1.031
peak=    3.807 closest distance to " O   HOH Z 272 " =    1.882
peak=    3.803 closest distance to " C   ILE A 106 " =    1.930
peak=    3.788 closest distance to " NZ  LYS A 117 " =    3.267
peak=    3.787 closest distance to " CA  ASP A 124 " =    0.739
peak=    3.786 closest distance to " OD1 ASP A 238 " =    0.864
peak=    3.786 closest distance to " CD  ARG A 159 " =    0.834
peak=    3.782 closest distance to " O   HOH Z 284 " =    2.971
peak=    3.778 closest distance to " O   HOH Z 189 " =    2.141
peak=    3.771 closest distance to " CA  MET A  40 " =    1.057
peak=    3.770 closest distance to " O   HOH Z 183 " =    1.554
peak=    3.764 closest distance to " O   HOH Z  88 " =    3.520
peak=    3.760 closest distance to " CB  ARG A 190 " =    1.697
peak=    3.756 closest distance to " O   HOH Z 403 " =    1.704
peak=    3.752 closest distance to " ND2 ASN A 187 " =    1.560
peak=    3.746 closest distance to " CB  ARG A  79 " =    1.338
peak=    3.744 closest distance to " O   HOH Z 295 " =    1.463
peak=    3.719 closest distance to " O   HOH Z 133 " =    1.699
peak=    3.706 closest distance to " O   HOH Z 326 " =    1.473
peak=    3.705 closest distance to " CD  PRO A 280 " =    0.950
peak=    3.704 closest distance to " CG  ARG A  66 " =    2.513
peak=    3.704 closest distance to " O   HOH Z 108 " =    1.869
peak=    3.690 closest distance to " CA  GLU A 152 " =    0.865
peak=    3.688 closest distance to " O   HOH Z 193 " =    2.171
peak=    3.680 closest distance to " O   HOH Z 313 " =    1.826
peak=    3.662 closest distance to " NH1AARG A 145 " =    1.039
peak=    3.662 closest distance to " O   HOH Z  93 " =    2.470
peak=    3.660 closest distance to " O   HOH Z  19 " =    2.382
peak=    3.650 closest distance to " CD  LYS A 166 " =    1.380
peak=    3.646 closest distance to " CA  ARG A  36 " =    1.174
peak=    3.644 closest distance to " CB  SER A 216 " =    0.827
peak=    3.637 closest distance to " CA  ASP A 140 " =    1.170
peak=    3.634 closest distance to " CD  ARG A 269 " =    0.931
peak=    3.632 closest distance to " CA  ASN A 176 " =    1.775
peak=    3.631 closest distance to " CA  ALA A 160 " =    0.822
peak=    3.630 closest distance to " O   HOH Z 112 " =    1.439
peak=    3.627 closest distance to " O   HOH Z   6 " =    2.135
peak=    3.620 closest distance to " O   HOH Z 163 " =    1.536
peak=    3.616 closest distance to " O   HOH Z  59 " =    2.360
peak=    3.614 closest distance to " CD2 LEU A 255 " =    1.368
peak=    3.608 closest distance to " O   HOH Z 128 " =    2.192
peak=    3.605 closest distance to " O   HOH Z  43 " =    2.096
peak=    3.603 closest distance to " CB  VAL A 265 " =    1.213
peak=    3.596 closest distance to " CB  SER A 141 " =    1.000
peak=    3.596 closest distance to " O   HOH Z 394 " =    1.630
peak=    3.591 closest distance to " CB  PHE A  16 " =    0.989
peak=    3.589 closest distance to " O   HOH Z 425 " =    1.432
peak=    3.588 closest distance to " CD1 TRP A 266 " =    1.217
peak=    3.583 closest distance to " CG2BVAL A  41 " =    0.797
peak=    3.581 closest distance to " CA  ASP A 191 " =    0.849
peak=    3.575 closest distance to " O   HOH Z 102 " =    1.228
peak=    3.570 closest distance to " O   HOH Z  11 " =    1.193
peak=    3.562 closest distance to " CB  ALA A 291 " =    1.398
peak=    3.560 closest distance to " O   HOH Z 345 " =    3.326
peak=    3.558 closest distance to " O   HOH Z 227 " =    1.643
peak=    3.556 closest distance to " CG2 VAL A  78 " =    0.960
peak=    3.529 closest distance to " O   HOH Z 128 " =    2.345
peak=    3.528 closest distance to " O   THR A 251 " =    1.227
peak=    3.524 closest distance to " O   HOH Z 215 " =    1.472
peak=    3.515 closest distance to " O   HOH Z 423 " =    1.894
peak=    3.507 closest distance to " NZ  LYS A  76 " =    1.228
peak=    3.500 closest distance to " O   HOH Z 116 " =    1.820
peak=    3.500 closest distance to " O   HOH Z 346 " =    1.562
peak=    3.498 closest distance to " O   HOH Z 345 " =    1.704
peak=    3.495 closest distance to " CG1 VAL A 153 " =    1.017
peak=    3.493 closest distance to " O   HOH Z  61 " =    1.633
peak=    3.478 closest distance to " O   HOH Z 211 " =    1.074
peak=    3.478 closest distance to " CG  LEU A 167 " =    1.135
peak=    3.477 closest distance to " OE1 GLN A  11 " =    1.868
peak=    3.475 closest distance to " CA  ASN A 215 " =    1.177
peak=    3.475 closest distance to " CG2 ILE A 120 " =    1.146
peak=    3.471 closest distance to " O   HOH Z  10 " =    1.840
peak=    3.466 closest distance to " O   TRP A 274 " =    1.782
peak=    3.465 closest distance to " O   HOH Z 387 " =    2.661
peak=    3.459 closest distance to " N   ASN A 127 " =    1.247
peak=    3.455 closest distance to " O   HOH Z 166 " =    1.561
peak=    3.455 closest distance to " CA  LEU A 282 " =    1.088
peak=    3.452 closest distance to " O   HOH Z 303 " =    2.163
peak=    3.452 closest distance to " CG  GLN A  88 " =    1.053
peak=    3.451 closest distance to " CG1 ILE A 151 " =    0.890
peak=    3.444 closest distance to " CE  LYS A  76 " =    0.848
peak=    3.439 closest distance to " O   THR A 220 " =    1.380
peak=    3.436 closest distance to " CG BARG A 102 " =    1.952
peak=    3.428 closest distance to " OG BSER A 164 " =    2.573
peak=    3.425 closest distance to " CZ  PHE A 218 " =    1.035
peak=    3.424 closest distance to " O   HOH Z 199 " =    1.014
peak=    3.415 closest distance to " OE1 GLN A  58 " =    5.769
peak=    3.414 closest distance to " O   HOH Z 215 " =    1.482
peak=    3.414 closest distance to " CE1 TYR A 186 " =    1.162
peak=    3.405 closest distance to " CZ  PHE A 192 " =    0.880
peak=    3.403 closest distance to " CG2 VAL A 197 " =    1.192
peak=    3.400 closest distance to " O   HOH Z 281 " =    4.067
peak=    3.398 closest distance to " O   HOH Z 118 " =    1.604
peak=    3.397 closest distance to " CG  MET A  93 " =    1.037
peak=    3.394 closest distance to " O   HOH Z 437 " =    1.487
peak=    3.388 closest distance to " CA  THR A 264 " =    0.876
peak=    3.388 closest distance to " O   HOH Z  40 " =    2.005
peak=    3.388 closest distance to " ND1 HIS A  81 " =    1.591
peak=    3.386 closest distance to " O   HOH Z  30 " =    1.475
peak=    3.383 closest distance to " CB  SER A 273 " =    0.898
peak=    3.375 closest distance to " O   ALA A 158 " =    1.247
peak=    3.372 closest distance to " CB  ASN A 285 " =    0.930
peak=    3.367 closest distance to " CG1BVAL A  72 " =    1.594
peak=    3.366 closest distance to " CB  ALA A 248 " =    0.982
peak=    3.363 closest distance to " CB  ILE A 199 " =    0.954
peak=    3.363 closest distance to " CZ  PHE A 208 " =    1.115
peak=    3.363 closest distance to " O   HOH Z 243 " =    1.660
peak=    3.363 closest distance to " O   HOH Z  44 " =    1.839
peak=    3.362 closest distance to " CA  LYS A 117 " =    1.217
peak=    3.360 closest distance to " O   HOH Z 193 " =    1.507
peak=    3.360 closest distance to " O   HOH Z 276 " =    1.309
peak=    3.359 closest distance to " O   HOH Z 368 " =    2.559
peak=    3.353 closest distance to " CB  TYR A  30 " =    1.455
peak=    3.352 closest distance to " O   HOH Z 171 " =    3.800
peak=    3.352 closest distance to " C   GLY A  80 " =    1.100
peak=    3.350 closest distance to " O   HOH Z 263 " =    2.241
peak=    3.346 closest distance to " O   HOH Z 147 " =    1.671
peak=    3.345 closest distance to " O   HOH Z 411 " =    1.802
peak=    3.337 closest distance to " CB  ASP A 140 " =    0.706
peak=    3.332 closest distance to " CD2 LEU A 297 " =    0.866
peak=    3.329 closest distance to " CD  GLU A 152 " =    0.885
peak=    3.329 closest distance to " CD2 HIS A  81 " =    1.209
peak=    3.326 closest distance to " CB  MET A  40 " =    0.845
peak=    3.325 closest distance to " O   HOH Z 173 " =    1.882
peak=    3.321 closest distance to " NH2AARG A 190 " =    1.502
peak=    3.320 closest distance to " CA  GLN A 223 " =    0.980
peak=    3.320 closest distance to " O   HOH Z 211 " =    2.271
peak=    3.320 closest distance to " C   SER A  32 " =    1.045
peak=    3.318 closest distance to " CG1 VAL A 202 " =    2.163
peak=    3.315 closest distance to " O   HOH Z 427 " =    3.092
peak=    3.314 closest distance to " O   GLY A  57 " =    2.522
peak=    3.313 closest distance to " O   HOH Z 114 " =    1.481
peak=    3.309 closest distance to " O   HOH Z 214 " =    1.978
peak=    3.308 closest distance to " C   LYS A 290 " =    1.259
peak=    3.306 closest distance to " CB  SER A  62 " =    1.219
peak=    3.303 closest distance to " O   HOH Z 172 " =    4.178
peak=    3.302 closest distance to " O   HOH Z 174 " =    2.497
peak=    3.299 closest distance to " N   ARG A 156 " =    1.410
peak=    3.293 closest distance to " CA  ASN A  74 " =    1.229
peak=    3.293 closest distance to " O   HOH Z 403 " =    1.379
peak=    3.290 closest distance to " O   HOH Z  63 " =    2.037
peak=    3.287 closest distance to " CA  ALA A 248 " =    1.166
peak=    3.285 closest distance to " CB  ARG A 139 " =    0.905
peak=    3.283 closest distance to " CG2 THR A 220 " =    1.010
peak=    3.282 closest distance to " O   HOH Z 422 " =    2.651
peak=    3.281 closest distance to " CG2 VAL A 257 " =    0.876
peak=    3.280 closest distance to " NZ ALYS A 290 " =    1.189
peak=    3.275 closest distance to " OG  SER A  22 " =    2.823
peak=    3.272 closest distance to " CG2 VAL A 112 " =    1.391
peak=    3.268 closest distance to " NE AARG A 275 " =    1.423
peak=    3.268 closest distance to " CB  ASN A 187 " =    1.325
peak=    3.261 closest distance to " O   HOH Z 152 " =    1.290
peak=    3.258 closest distance to " O   HOH Z 353 " =    2.700
peak=    3.255 closest distance to " O   HOH Z 334 " =    1.392
peak=    3.254 closest distance to " O   HOH Z 261 " =    1.504
peak=    3.253 closest distance to " OD1 ASP A 231 " =    1.883
peak=    3.253 closest distance to " CG  GLN A  58 " =    2.456
peak=    3.252 closest distance to " O   HOH Z  61 " =    1.526
peak=    3.251 closest distance to " O   HOH Z 271 " =    2.177
peak=    3.249 closest distance to " O   HOH Z  54 " =    2.344
peak=    3.247 closest distance to " O   HOH Z 368 " =    3.631
peak=    3.245 closest distance to " O   HOH Z 329 " =    3.406
peak=    3.245 closest distance to " CD  ARG A 195 " =    3.555
peak=    3.243 closest distance to " O   HOH Z   4 " =    1.945
peak=    3.242 closest distance to " CB  LEU A 143 " =    1.119
peak=    3.237 closest distance to " O   HOH Z 383 " =    2.046
peak=    3.235 closest distance to " O   HOH Z 197 " =    2.465
peak=    3.235 closest distance to " CB  SER A 212 " =    1.057
peak=    3.231 closest distance to " CB  TYR A 116 " =    1.005
peak=    3.226 closest distance to " CB  ALA A  43 " =    0.859
peak=    3.224 closest distance to " CA  GLY A 267 " =    1.129
peak=    3.224 closest distance to " CB  TRP A 123 " =    1.069
peak=    3.223 closest distance to " O   HOH Z 357 " =    1.997
peak=    3.222 closest distance to " O   HOH Z 409 " =    3.288
peak=    3.222 closest distance to " CA  ALA A 158 " =    1.065
peak=    3.221 closest distance to " O   HOH Z 214 " =    2.195
peak=    3.220 closest distance to " O   HOH Z 273 " =    2.776
peak=    3.216 closest distance to " O   HOH Z 189 " =    1.431
peak=    3.215 closest distance to " O   HOH Z 217 " =    1.287
peak=    3.214 closest distance to " O   ALA A   1 " =    1.475
peak=    3.211 closest distance to " C   ALA A 299 " =    0.950
peak=    3.202 closest distance to " OH  TYR A  30 " =    1.325
peak=    3.201 closest distance to " NH1 ARG A  56 " =    1.190
peak=    3.200 closest distance to " O   HOH Z 327 " =    2.196
peak=    3.198 closest distance to " O   HOH Z 286 " =    2.132
peak=    3.194 closest distance to " NE2 HIS A 115 " =    0.953
peak=    3.192 closest distance to " O   HOH Z 337 " =    3.790
peak=    3.187 closest distance to " CG1 ILE A 120 " =    1.051
peak=    3.187 closest distance to " O   HOH Z 152 " =    3.281
peak=    3.186 closest distance to " O   HOH Z 236 " =    1.564
peak=    3.185 closest distance to " CA  ALA A 154 " =    1.015
peak=    3.182 closest distance to " ND1 HIS A  86 " =    1.890
peak=    3.179 closest distance to " O   HOH Z 185 " =    1.828
peak=    3.171 closest distance to " CD1AILE A 234 " =    0.991
peak=    3.170 closest distance to " O   THR A  31 " =    1.553
peak=    3.169 closest distance to " O   HOH Z 355 " =    1.553
peak=    3.167 closest distance to " CD  ARG A 219 " =    0.954
peak=    3.165 closest distance to " O   HOH Z 139 " =    3.126
peak=    3.165 closest distance to " CA  ALA A 295 " =    1.144
peak=    3.165 closest distance to " OG  SER A  97 " =    3.535
peak=    3.161 closest distance to " O   HOH Z 285 " =    1.980
peak=    3.160 closest distance to " O   HOH Z 343 " =    2.423
peak=    3.160 closest distance to " CA  GLY A 196 " =    1.091
peak=    3.157 closest distance to " O   HOH Z 332 " =    1.577
peak=    3.157 closest distance to " O   HOH Z 261 " =    2.009
peak=    3.154 closest distance to " O   HOH Z  50 " =    3.503
peak=    3.153 closest distance to " O   HOH Z 419 " =    3.053
peak=    3.148 closest distance to " O   HOH Z 166 " =    3.186
peak=    3.148 closest distance to " O   HOH Z 156 " =    2.874
peak=    3.146 closest distance to " O   HOH Z  44 " =    3.407
peak=    3.143 closest distance to " CA  MET A 105 " =    1.039
peak=    3.140 closest distance to " O   HOH Z  22 " =    2.524
peak=    3.140 closest distance to " NH1BARG A 145 " =    1.051
peak=    3.139 closest distance to " NE BARG A 102 " =    1.314
peak=    3.130 closest distance to " O   HOH Z 425 " =    2.199
peak=    3.129 closest distance to " O   HOH Z  71 " =    1.011
peak=    3.122 closest distance to " O   HOH Z 438 " =    2.291
peak=    3.122 closest distance to " O   HOH Z 109 " =    2.832
peak=    3.121 closest distance to " NZ  LYS A 166 " =    3.011
peak=    3.118 closest distance to " C   PRO A 163 " =    1.710
peak=    3.113 closest distance to " CG  MET A 113 " =    1.311
peak=    3.106 closest distance to " CG2 VAL A 112 " =    0.780
peak=    3.099 closest distance to " O   HOH Z 406 " =    1.535
peak=    3.093 closest distance to " CA  LEU A 101 " =    1.534
peak=    3.087 closest distance to " O   HOH Z 421 " =    1.718
peak=    3.083 closest distance to " CB  SER A  28 " =    0.955
peak=    3.082 closest distance to " CD1 LEU A 222 " =    0.830
peak=    3.080 closest distance to " O   HOH Z  47 " =    1.239
peak=    3.073 closest distance to " CB  ASN A 215 " =    1.098
peak=    3.071 closest distance to " NH1 ARG A  14 " =    1.200
peak=    3.071 closest distance to " OG1 THR A 294 " =    1.616
peak=    3.069 closest distance to " O   HOH Z 305 " =    3.620
peak=    3.066 closest distance to " O   HOH Z 248 " =    1.548
peak=    3.064 closest distance to " CB  MET A 105 " =    1.200
peak=    3.057 closest distance to " CG2 ILE A 106 " =    1.062
peak=    3.053 closest distance to " OG ASER A  99 " =    2.041
peak=    3.041 closest distance to " CZ  PHE A  38 " =    1.435
peak=    3.035 closest distance to " O   HOH Z 280 " =    2.333
peak=    3.034 closest distance to " O   HOH Z 407 " =    2.807
peak=    3.032 closest distance to " O   HOH Z  20 " =    1.686
peak=    3.030 closest distance to " O   HOH Z 197 " =    2.117
peak=    3.020 closest distance to " O   HOH Z 128 " =    2.969
peak=    3.017 closest distance to " O   HOH Z 280 " =    2.712

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.872 - 5.425
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 205
   mapped sites are within: 0.872 - 5.425

peak=   -4.529 closest distance to " O   HOH Z 266 " =    4.255
peak=   -4.224 closest distance to " O   HOH Z 274 " =    2.969
peak=   -4.217 closest distance to " O   HOH Z 198 " =    2.539
peak=   -4.146 closest distance to " O   HOH Z  92 " =    1.520
peak=   -4.143 closest distance to " CD  ARG A 156 " =    1.906
peak=   -4.139 closest distance to " NH2 ARG A  66 " =    1.840
peak=   -4.134 closest distance to " O   HOH Z 290 " =    1.045
peak=   -4.133 closest distance to " O   HOH Z 377 " =    1.940
peak=   -4.071 closest distance to " O   HOH Z 388 " =    1.973
peak=   -4.047 closest distance to " O   HOH Z  13 " =    1.429
peak=   -4.040 closest distance to " O   HOH Z  43 " =    1.496
peak=   -4.028 closest distance to " O   HOH Z  19 " =    2.025
peak=   -4.014 closest distance to " N   ALA A  43 " =    2.459
peak=   -4.006 closest distance to " OG  SER A  97 " =    2.187
peak=   -4.002 closest distance to " CB  TYR A  15 " =    2.223
peak=   -3.979 closest distance to " CG  LYS A 193 " =    2.496
peak=   -3.969 closest distance to " O   HOH Z 407 " =    3.437
peak=   -3.966 closest distance to " O   HOH Z  11 " =    1.766
peak=   -3.956 closest distance to " O   HOH Z  52 " =    1.525
peak=   -3.910 closest distance to " O   HOH Z  93 " =    1.599
peak=   -3.891 closest distance to " O   HOH Z 231 " =    2.062
peak=   -3.888 closest distance to " OG ASER A 134 " =    1.262
peak=   -3.887 closest distance to " O   HOH Z 292 " =    4.469
peak=   -3.875 closest distance to " O   PRO A 163 " =    2.120
peak=   -3.874 closest distance to " C   ASN A 187 " =    1.840
peak=   -3.873 closest distance to " CD2 LEU A 300 " =    2.932
peak=   -3.866 closest distance to " CB  PRO A 243 " =    2.639
peak=   -3.858 closest distance to " C   ALA A 158 " =    1.205
peak=   -3.855 closest distance to " O   PRO A 198 " =    1.301
peak=   -3.853 closest distance to " CD1 LEU A 228 " =    2.374
peak=   -3.835 closest distance to " ND2 ASN A  45 " =    0.914
peak=   -3.826 closest distance to " O   ILE A 109 " =    2.630
peak=   -3.826 closest distance to " O   VAL A  67 " =    2.840
peak=   -3.823 closest distance to " O   HOH Z  98 " =    1.830
peak=   -3.787 closest distance to " CE  MET A  93 " =    1.294
peak=   -3.786 closest distance to " C   ASN A 285 " =    2.566
peak=   -3.781 closest distance to " CD2 LEU A 237 " =    2.665
peak=   -3.779 closest distance to " CH2 TRP A 179 " =    1.228
peak=   -3.769 closest distance to " O   HOH Z 166 " =    1.819
peak=   -3.769 closest distance to " CG  GLU A  53 " =    1.390
peak=   -3.745 closest distance to " N   GLN A  58 " =    1.712
peak=   -3.743 closest distance to " O   HOH Z  10 " =    1.626
peak=   -3.742 closest distance to " CD2 PHE A  59 " =    2.509
peak=   -3.734 closest distance to " N   SER A 276 " =    1.352
peak=   -3.709 closest distance to " CG2 THR A   4 " =    1.931
peak=   -3.693 closest distance to " CG  ASP A 231 " =    0.893
peak=   -3.684 closest distance to " O   HOH Z  17 " =    1.400
peak=   -3.684 closest distance to " CD  LYS A 289 " =    2.507
peak=   -3.679 closest distance to " O   HOH Z 353 " =    2.177
peak=   -3.672 closest distance to " CG  GLN A  58 " =    1.272
peak=   -3.667 closest distance to " O   HOH Z 283 " =    1.808
peak=   -3.656 closest distance to " O   HOH Z  97 " =    1.768
peak=   -3.634 closest distance to " CD  GLN A  88 " =    2.124
peak=   -3.633 closest distance to " C   HIS A 108 " =    1.053
peak=   -3.626 closest distance to " CE2 TYR A  30 " =    2.812
peak=   -3.612 closest distance to " O   HOH Z  38 " =    1.354
peak=   -3.612 closest distance to " CD  ARG A 139 " =    1.687
peak=   -3.598 closest distance to " O   HOH Z 266 " =    4.696
peak=   -3.588 closest distance to " CZ  TYR A 169 " =    1.808
peak=   -3.573 closest distance to " N   ALA A 226 " =    2.120
peak=   -3.554 closest distance to " O   GLY A 118 " =    2.220
peak=   -3.551 closest distance to " CB  ASN A  39 " =    2.207
peak=   -3.546 closest distance to " CD  GLN A  88 " =    0.872
peak=   -3.546 closest distance to " O   HOH Z 377 " =    1.170
peak=   -3.544 closest distance to " O   HOH Z 185 " =    2.226
peak=   -3.542 closest distance to " OG  SER A  62 " =    1.568
peak=   -3.534 closest distance to " CB  ALA A 291 " =    2.370
peak=   -3.532 closest distance to " O   GLY A 196 " =    1.093
peak=   -3.526 closest distance to " CB  LEU A 167 " =    2.125
peak=   -3.525 closest distance to " O   HOH Z  71 " =    1.107
peak=   -3.518 closest distance to " CG  GLU A 277 " =    1.140
peak=   -3.517 closest distance to " OD1 ASP A 191 " =    1.593
peak=   -3.516 closest distance to " OE2 GLU A   2 " =    1.535
peak=   -3.515 closest distance to " CD  ARG A 195 " =    5.107
peak=   -3.512 closest distance to " OD1 ASN A 148 " =    1.667
peak=   -3.499 closest distance to " CB  CYS A 254 " =    2.292
peak=   -3.486 closest distance to " O   HOH Z 234 " =    4.221
peak=   -3.486 closest distance to " O   HOH Z 166 " =    1.478
peak=   -3.485 closest distance to " O   HOH Z 213 " =    1.322
peak=   -3.484 closest distance to " O   HOH Z  98 " =    1.375
peak=   -3.482 closest distance to " N   SER A 212 " =    1.979
peak=   -3.471 closest distance to " ND2 ASN A  45 " =    1.172
peak=   -3.456 closest distance to " OD2 ASP A 171 " =    2.361
peak=   -3.452 closest distance to " OE1 GLN A  88 " =    1.089
peak=   -3.445 closest distance to " O   HOH Z 385 " =    3.821
peak=   -3.445 closest distance to " CD2 LEU A 167 " =    1.710
peak=   -3.438 closest distance to " CD  PRO A 198 " =    1.370
peak=   -3.433 closest distance to " CD1 LEU A 101 " =    2.554
peak=   -3.429 closest distance to " O   HOH Z 418 " =    1.509
peak=   -3.411 closest distance to " O   HOH Z 151 " =    1.369
peak=   -3.411 closest distance to " O   HOH Z  76 " =    1.929
peak=   -3.409 closest distance to " CD1 PHE A  59 " =    1.820
peak=   -3.400 closest distance to " ND2 ASN A 187 " =    1.623
peak=   -3.400 closest distance to " CG  MET A 105 " =    0.930
peak=   -3.398 closest distance to " NH1 ARG A 195 " =    2.632
peak=   -3.398 closest distance to " O   HOH Z 275 " =    1.563
peak=   -3.395 closest distance to " CD2 TYR A 293 " =    2.133
peak=   -3.390 closest distance to " CB  PHE A  16 " =    2.630
peak=   -3.387 closest distance to " O   HOH Z 396 " =    1.495
peak=   -3.386 closest distance to " CA  ASP A 298 " =    1.053
peak=   -3.385 closest distance to " O   GLY A 211 " =    1.407
peak=   -3.385 closest distance to " OD1 ASP A 200 " =    1.419
peak=   -3.382 closest distance to " CG  ASP A  50 " =    2.590
peak=   -3.380 closest distance to " OD2 ASP A 171 " =    1.699
peak=   -3.378 closest distance to " CD1 LEU A  25 " =    2.437
peak=   -3.378 closest distance to " CB  SER A 134 " =    1.831
peak=   -3.377 closest distance to " CB  ALA A 248 " =    1.892
peak=   -3.364 closest distance to " OH  TYR A 169 " =    1.013
peak=   -3.363 closest distance to " CA  SER A 245 " =    2.432
peak=   -3.353 closest distance to " OE1 GLN A 223 " =    1.980
peak=   -3.351 closest distance to " O   HOH Z 128 " =    2.525
peak=   -3.351 closest distance to " CA  GLY A 203 " =    2.161
peak=   -3.350 closest distance to " N   THR A 157 " =    1.670
peak=   -3.346 closest distance to " O   HOH Z  15 " =    1.690
peak=   -3.346 closest distance to " CA  VAL A 197 " =    1.056
peak=   -3.341 closest distance to " CE  MET A 105 " =    2.057
peak=   -3.339 closest distance to " CD1 ILE A 263 " =    2.385
peak=   -3.333 closest distance to " O   HOH Z 243 " =    1.844
peak=   -3.328 closest distance to " OG  SER A  87 " =    1.405
peak=   -3.324 closest distance to " O   HOH Z 411 " =    3.327
peak=   -3.323 closest distance to " OG  SER A 245 " =    0.959
peak=   -3.323 closest distance to " O   VAL A 174 " =    2.044
peak=   -3.319 closest distance to " OG BSER A 134 " =    1.195
peak=   -3.313 closest distance to " SG ACYS A 201 " =    2.343
peak=   -3.313 closest distance to " O   HOH Z  60 " =    1.998
peak=   -3.305 closest distance to " O   HOH Z 385 " =    2.060
peak=   -3.303 closest distance to " N   GLN A 122 " =    1.629
peak=   -3.296 closest distance to " O   HOH Z 118 " =    2.681
peak=   -3.295 closest distance to " O   HOH Z 165 " =    2.008
peak=   -3.294 closest distance to " O   HOH Z 399 " =    2.203
peak=   -3.293 closest distance to " CB  ALA A 291 " =    2.258
peak=   -3.293 closest distance to " O   LEU A 167 " =    1.546
peak=   -3.290 closest distance to " O   HOH Z  98 " =    2.319
peak=   -3.290 closest distance to " NH1 ARG A 195 " =    2.272
peak=   -3.287 closest distance to " O   HOH Z 184 " =    1.507
peak=   -3.286 closest distance to " NH2 ARG A  66 " =    5.074
peak=   -3.284 closest distance to " CA  VAL A 232 " =    2.463
peak=   -3.282 closest distance to " O   ALA A 256 " =    1.466
peak=   -3.280 closest distance to " CD  ARG A  14 " =    3.297
peak=   -3.278 closest distance to " NH2 ARG A 159 " =    2.437
peak=   -3.272 closest distance to " ND2 ASN A 249 " =    2.016
peak=   -3.271 closest distance to " NH2AARG A 275 " =    5.425
peak=   -3.267 closest distance to " O   HOH Z   9 " =    2.061
peak=   -3.267 closest distance to " SG  CYS A 254 " =    3.045
peak=   -3.266 closest distance to " O   ALA A 160 " =    1.525
peak=   -3.266 closest distance to " N   GLY A 133 " =    1.820
peak=   -3.255 closest distance to " NH2 ARG A  79 " =    1.867
peak=   -3.251 closest distance to " O   HOH Z 252 " =    4.255
peak=   -3.248 closest distance to " CB  ALA A  43 " =    2.467
peak=   -3.247 closest distance to " CD  GLN A 223 " =    1.410
peak=   -3.246 closest distance to " CG  ARG A 269 " =    2.389
peak=   -3.244 closest distance to " ND2 ASN A  60 " =    1.491
peak=   -3.241 closest distance to " CD  GLU A 236 " =    1.064
peak=   -3.239 closest distance to " CB  ASP A 286 " =    2.089
peak=   -3.234 closest distance to " O   ALA A 161 " =    1.515
peak=   -3.234 closest distance to " CB  SER A 258 " =    2.073
peak=   -3.230 closest distance to " CG2 ILE A  49 " =    2.694
peak=   -3.220 closest distance to " O   ASN A 301 " =    1.667
peak=   -3.220 closest distance to " CE3 TRP A 150 " =    1.583
peak=   -3.216 closest distance to " O   HOH Z 423 " =    2.253
peak=   -3.204 closest distance to " CD  ARG A 159 " =    1.182
peak=   -3.199 closest distance to " O   HOH Z 221 " =    1.439
peak=   -3.199 closest distance to " C   LEU A 143 " =    1.414
peak=   -3.196 closest distance to " O   HOH Z 148 " =    3.369
peak=   -3.196 closest distance to " CD2 HIS A  86 " =    1.192
peak=   -3.196 closest distance to " O   ASP A  50 " =    1.524
peak=   -3.194 closest distance to " CG  TRP A 266 " =    1.658
peak=   -3.187 closest distance to " CE  MET A 105 " =    1.906
peak=   -3.187 closest distance to " O   HOH Z 241 " =    1.314
peak=   -3.185 closest distance to " CE3 TRP A  70 " =    1.763
peak=   -3.185 closest distance to " CB  PRO A 163 " =    2.608
peak=   -3.183 closest distance to " OD1 ASN A 187 " =    1.502
peak=   -3.180 closest distance to " O   HOH Z 108 " =    2.446
peak=   -3.179 closest distance to " O   HOH Z 409 " =    4.689
peak=   -3.179 closest distance to " O   HOH Z 117 " =    4.271
peak=   -3.179 closest distance to " O   VAL A 153 " =    2.277
peak=   -3.171 closest distance to " CB  ASP A 132 " =    2.258
peak=   -3.169 closest distance to " O   HOH Z  61 " =    1.491
peak=   -3.163 closest distance to " O   HOH Z 313 " =    1.077
peak=   -3.162 closest distance to " OD1 ASN A 249 " =    1.181
peak=   -3.162 closest distance to " O   ALA A  34 " =    2.597
peak=   -3.159 closest distance to " CA  ARG A 139 " =    0.974
peak=   -3.149 closest distance to " CZ  PHE A  59 " =    1.773
peak=   -3.142 closest distance to " O   HOH Z 350 " =    1.813
peak=   -3.138 closest distance to " O   PHE A 218 " =    1.427
peak=   -3.130 closest distance to " CG  ARG A 259 " =    2.854
peak=   -3.125 closest distance to " O   HOH Z 222 " =    1.270
peak=   -3.124 closest distance to " O   HOH Z 265 " =    1.929
peak=   -3.122 closest distance to " CG1 VAL A 112 " =    2.560
peak=   -3.121 closest distance to " CE3 TRP A 150 " =    2.302
peak=   -3.118 closest distance to " OD2 ASP A 140 " =    1.441
peak=   -3.116 closest distance to " ND2 ASN A 215 " =    2.112
peak=   -3.116 closest distance to " SG  CYS A 168 " =    1.085
peak=   -3.098 closest distance to " OG ASER A 216 " =    0.997
peak=   -3.088 closest distance to " O   MET A  40 " =    2.747
peak=   -3.082 closest distance to " O   HOH Z 389 " =    1.760
peak=   -3.080 closest distance to " CG2 VAL A 189 " =    2.178
peak=   -3.074 closest distance to " CB  PHE A 208 " =    2.226
peak=   -3.072 closest distance to " O   PRO A 198 " =    2.094
peak=   -3.072 closest distance to " CB  SER A 271 " =    1.764
peak=   -3.069 closest distance to " O   HOH Z 417 " =    2.659
peak=   -3.069 closest distance to " O   HOH Z  90 " =    1.800
peak=   -3.050 closest distance to " O   HOH Z 280 " =    2.204
peak=   -3.023 closest distance to " CD  GLN A  88 " =    1.017

================= 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    :  0.4350 0.4372   6.238798e+00   6.240819e+00
   1_bss:  0.4266 0.4295   6.233794e+00   6.230396e+00
   1_xyz:  0.2897 0.3256   5.941474e+00   6.032462e+00
   1_adp:  0.2629 0.3297   5.888097e+00   6.045960e+00
   1_occ:  0.2627 0.3295   5.886822e+00   6.045082e+00
   2_bss:  0.2605 0.3271   5.884297e+00   6.041114e+00
   2_xyz:  0.1865 0.2413   5.587268e+00   5.792763e+00
   2_adp:  0.1676 0.2203   5.496239e+00   5.709840e+00
   2_occ:  0.1674 0.2201   5.495504e+00   5.709253e+00
   3_bss:  0.1671 0.2192   5.494008e+00   5.705687e+00
   3_xyz:  0.1344 0.1804   5.298161e+00   5.522311e+00
   3_adp:  0.1262 0.1726   5.249627e+00   5.478418e+00
   3_occ:  0.1261 0.1726   5.249401e+00   5.478465e+00
   4_bss:  0.1264 0.1727   5.251110e+00   5.480046e+00
   4_xyz:  0.1200 0.1652   5.207978e+00   5.437166e+00
   4_adp:  0.1181 0.1648   5.198589e+00   5.431077e+00
   4_occ:  0.1180 0.1647   5.198276e+00   5.430975e+00
   5_bss:  0.1180 0.1647   5.198229e+00   5.430916e+00
   5_xyz:  0.1159 0.1628   5.186208e+00   5.421935e+00
   5_adp:  0.1153 0.1628   5.185356e+00   5.423468e+00
   5_occ:  0.1153 0.1628   5.185172e+00   5.423439e+00
   5_bss:  0.1153 0.1628   5.185270e+00   5.423542e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  50.000  -0.702  -0.168   2.427  -0.000   0.000   0.000
   1_xyz:  0.300  50.000  -0.702  -0.168   2.427  -0.000   0.000   0.000
   1_adp:  0.300  50.000  -0.702  -0.168   2.427  -0.000   0.000   0.000
   1_occ:  0.300  50.000  -0.702  -0.168   2.427  -0.000   0.000   0.000
   2_bss:  0.328  62.691  -1.747  -1.292  -0.152  -0.000  -0.000  -0.000
   2_xyz:  0.328  62.691  -1.747  -1.292  -0.152  -0.000  -0.000  -0.000
   2_adp:  0.328  62.691  -1.747  -1.292  -0.152  -0.000  -0.000  -0.000
   2_occ:  0.328  62.691  -1.747  -1.292  -0.152  -0.000  -0.000  -0.000
   3_bss:  0.325  57.205  -2.193  -1.927  -1.575  -0.000  -0.000  -0.000
   3_xyz:  0.325  57.205  -2.193  -1.927  -1.575  -0.000  -0.000  -0.000
   3_adp:  0.325  57.205  -2.193  -1.927  -1.575  -0.000  -0.000  -0.000
   3_occ:  0.325  57.205  -2.193  -1.927  -1.575  -0.000  -0.000  -0.000
   4_bss:  0.322  52.554  -2.400  -2.210  -2.091  -0.000  -0.000  -0.000
   4_xyz:  0.322  52.554  -2.400  -2.210  -2.091  -0.000  -0.000  -0.000
   4_adp:  0.322  52.554  -2.400  -2.210  -2.091  -0.000  -0.000  -0.000
   4_occ:  0.322  52.554  -2.400  -2.210  -2.091  -0.000  -0.000  -0.000
   5_bss:  0.322  52.554  -2.308  -2.145  -2.147  -0.000  -0.000  -0.000
   5_xyz:  0.322  52.554  -2.308  -2.145  -2.147  -0.000  -0.000  -0.000
   5_adp:  0.322  52.554  -2.308  -2.145  -2.147  -0.000  -0.000  -0.000
   5_occ:  0.322  52.554  -2.308  -2.145  -2.147  -0.000  -0.000  -0.000
   5_bss:  0.320  52.514  -2.088  -1.948  -1.960  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.332 0.4775  0.6342    59629.302
   1_bss:  52.259 0.4888  0.6632    56319.726
   1_xyz:  34.273 0.7100  0.9329    28985.319
   1_adp:  35.311 0.6969  0.9244    30283.947
   1_occ:  35.264 0.6974  0.9243    30159.703
   2_bss:  34.998 0.7003  0.8788    29825.672
   2_xyz:  24.575 0.8143  0.9787    15405.983
   2_adp:  21.777 0.8438  0.9916    12801.917
   2_occ:  21.763 0.8439  0.9915    12778.476
   3_bss:  21.656 0.8449  0.9627    12674.377
   3_xyz:  17.236 0.8866  0.9846     8461.963
   3_adp:  16.125 0.8970  0.9846     7789.294
   3_occ:  16.117 0.8971  0.9845     7787.281
   4_bss:  16.152 0.8969  0.9723     7838.594
   4_xyz:  15.187 0.9051  0.9755     7072.883
   4_adp:  15.001 0.9069  0.9711     7000.391
   4_occ:  14.993 0.9070  0.9709     6999.514
   5_bss:  14.993 0.9070  0.9721     7000.974
   5_xyz:  14.816 0.9084  0.9721     6838.233
   5_adp:  14.823 0.9084  0.9668     6847.441
   5_occ:  14.818 0.9085  0.9667     6848.893
   5_bss:  14.824 0.9084  0.9722     6851.481
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.8358e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.8358e-01
   1_xyz:   1.389  0.011  0.086 15.875  0.005  4.117   1.1209e-01
   1_adp:   1.389  0.011  0.086 15.875  0.005  4.117   1.1209e-01
   1_occ:   1.389  0.011  0.086 15.875  0.005  4.117   1.1209e-01
   2_bss:   1.389  0.011  0.086 15.875  0.005  4.117   1.1209e-01
   2_xyz:   1.112  0.008  0.077 14.483  0.005  4.134   6.9742e-02
   2_adp:   1.112  0.008  0.077 14.483  0.005  4.134   6.9742e-02
   2_occ:   1.112  0.008  0.077 14.483  0.005  4.134   6.9742e-02
   3_bss:   1.112  0.008  0.077 14.483  0.005  4.134   6.9742e-02
   3_xyz:   1.046  0.007  0.072 14.478  0.004  4.119   6.2047e-02
   3_adp:   1.046  0.007  0.072 14.478  0.004  4.119   6.2047e-02
   3_occ:   1.046  0.007  0.072 14.478  0.004  4.119   6.2047e-02
   4_bss:   1.046  0.007  0.072 14.478  0.004  4.119   6.2047e-02
   4_xyz:   0.959  0.006  0.069 14.317  0.004  4.121   5.3841e-02
   4_adp:   0.959  0.006  0.069 14.317  0.004  4.121   5.3841e-02
   4_occ:   0.959  0.006  0.069 14.317  0.004  4.121   5.3841e-02
   5_bss:   0.959  0.006  0.069 14.317  0.004  4.121   5.3841e-02
   5_xyz:   0.945  0.006  0.068 14.192  0.003  4.123   5.1451e-02
   5_adp:   0.945  0.006  0.068 14.192  0.003  4.123   5.1451e-02
   5_occ:   0.945  0.006  0.068 14.192  0.003  4.123   5.1451e-02
   5_bss:   0.945  0.006  0.068 14.192  0.003  4.123   5.1451e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.492   2.4148e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.492   2.4148e-01
   1_xyz:   8.975  0.096  0.314 87.962  0.032  2.117   9.0609e-02
   1_adp:   8.975  0.096  0.314 87.962  0.032  2.117   9.0609e-02
   1_occ:   8.975  0.096  0.314 87.962  0.032  2.117   9.0609e-02
   2_bss:   8.975  0.096  0.314 87.962  0.032  2.117   9.0609e-02
   2_xyz:   7.354  0.041  0.287 88.507  0.045  2.280   9.0136e-02
   2_adp:   7.354  0.041  0.287 88.507  0.045  2.280   9.0136e-02
   2_occ:   7.354  0.041  0.287 88.507  0.045  2.280   9.0136e-02
   3_bss:   7.354  0.041  0.287 88.507  0.045  2.280   9.0136e-02
   3_xyz:   7.711  0.045  0.271 81.600  0.039  2.271   4.3911e-02
   3_adp:   7.711  0.045  0.271 81.600  0.039  2.271   4.3911e-02
   3_occ:   7.711  0.045  0.271 81.600  0.039  2.271   4.3911e-02
   4_bss:   7.711  0.045  0.271 81.600  0.039  2.271   4.3911e-02
   4_xyz:   7.321  0.038  0.228 83.429  0.032  2.380   4.5123e-02
   4_adp:   7.321  0.038  0.228 83.429  0.032  2.380   4.5123e-02
   4_occ:   7.321  0.038  0.228 83.429  0.032  2.380   4.5123e-02
   5_bss:   7.321  0.038  0.228 83.429  0.032  2.380   4.5123e-02
   5_xyz:   7.544  0.045  0.209 81.976  0.030  2.325   2.9448e-02
   5_adp:   7.544  0.045  0.209 81.976  0.030  2.325   2.9448e-02
   5_occ:   7.544  0.045  0.209 81.976  0.030  2.325   2.9448e-02
   5_bss:   7.544  0.045  0.209 81.976  0.030  2.325   2.9448e-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: 101.19   0.00  18.59  98.46   0.00  14.14 101.19   3.88  42.83
   1_occ: 101.19   0.00  18.59  98.46   0.00  14.14 101.19   3.88  42.83
   2_bss: 101.19   0.00  18.59  98.46   0.00  14.14 101.19   3.88  42.83
   2_xyz: 101.19   0.00  18.59  98.46   0.00  14.14 101.19   3.88  42.83
   2_adp:  91.94   1.12  18.29  91.94   1.12  13.61  88.45   5.43  43.81
   2_occ:  91.94   1.12  18.29  91.94   1.12  13.61  88.45   5.43  43.81
   3_bss:  91.94   1.12  18.29  91.94   1.12  13.61  88.45   5.43  43.81
   3_xyz:  91.94   1.12  18.29  91.94   1.12  13.61  88.45   5.43  43.81
   3_adp:  96.78   0.00  18.00  96.78   0.00  13.32  85.87   5.61  43.52
   3_occ:  96.78   0.00  18.00  96.78   0.00  13.32  85.87   5.61  43.52
   4_bss:  96.78   0.00  18.00  96.78   0.00  13.32  85.87   5.61  43.52
   4_xyz:  96.78   0.00  18.00  96.78   0.00  13.32  85.87   5.61  43.52
   4_adp: 102.01   1.33  17.80 102.01   1.33  13.22  86.43   5.49  42.74
   4_occ: 102.01   1.33  17.80 102.01   1.33  13.22  86.43   5.49  42.74
   5_bss: 102.01   1.33  17.80 102.01   1.33  13.22  86.43   5.49  42.74
   5_xyz: 102.01   1.33  17.80 102.01   1.33  13.22  86.43   5.49  42.74
   5_adp: 108.17   1.14  17.61 108.17   1.14  13.08  90.31   5.71  42.24
   5_occ: 108.17   1.14  17.61 108.17   1.14  13.08  90.31   5.71  42.24
   5_bss: 108.13   1.10  17.57 108.13   1.10  13.04  90.27   5.67  42.20
------------------------------------------------------------------------
 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:    1.936    0.010    0.413
   1_adp:    1.936    0.010    0.413
   1_occ:    1.936    0.010    0.413
   2_bss:    1.936    0.010    0.413
   2_xyz:    1.561    0.053    0.553
   2_adp:    1.561    0.053    0.553
   2_occ:    1.561    0.053    0.553
   3_bss:    1.561    0.053    0.553
   3_xyz:    1.603    0.055    0.630
   3_adp:    1.603    0.055    0.630
   3_occ:    1.603    0.055    0.630
   4_bss:    1.603    0.055    0.630
   4_xyz:    1.654    0.021    0.647
   4_adp:    1.654    0.021    0.647
   4_occ:    1.654    0.021    0.647
   5_bss:    1.654    0.021    0.647
   5_xyz:    1.739    0.050    0.660
   5_adp:    1.739    0.050    0.660
   5_occ:    1.739    0.050    0.660
   5_bss:    1.739    0.050    0.660
------------------------------------------------------------------------

CPU time actual refinement: 353.06


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1045/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_1045/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1045/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1045/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1045/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 352.93 
  Macro-tasks:
    bulk solvent and scale       = 41.13  
    individual site refinement   = 146.90 
    weights calculation          = 30.89  
    collect and process          = 6.75   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 225.76 
  Micro-tasks:
    mask                            = 1.77   
    f_calc                          = 118.03 
    alpha_beta                      = 8.66   
    target                          = 1.26   
    gradients_wrt_atomic_parameters = 120.48 
    fmodel                         = 6.65   
    r_factors                      = 0.12   
    phase_errors                   = 11.66  
    foms                           = 0.20   
    TOTAL for micro-tasks          = 268.83 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 5.016 micro seconds
Total CPU time: 6.11 minutes
from_scatterers_fft:    631 calls, 117.64 s
gradients_fft:          576 calls, 109.08 s

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

# Date 2008-01-16 Time 06:17:39 PST -0800 (1200493059.19 s)
Start R-work = 0.4350, R-free = 0.4372 (no bulk solvent and anisotropic scale)
Final R-work = 0.1386, R-free = 0.1832 (no bulk solvent and anisotropic scale)

Start R-work = 0.4266, R-free = 0.4295
Final R-work = 0.1153, R-free = 0.1628