# Date 2008-01-16 Time 05:55:07 PST -0800 (1200491707.64 s)
#phil __OFF__

Command line arguments: "../935.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 32563
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 935

-------------------------------------------------------------------------------
  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: (70.9525, 47.6339, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.29, per 1000 atoms: 1.17


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

F-obs:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA

R-free flags:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9961 1.95151
Completeness in resolution range: 0.916916
Completeness with d_max=infinity: 0.91422

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9961
                             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: (70.9525, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9961 1.95151
Completeness in resolution range: 0.916916
Completeness with d_max=infinity: 0.91422

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9965 -  4.1770 [2243/2272]  2020   223   9.9%
  bin  2:  4.1770 -  3.3273 [2147/2170]  1931   216  10.1%
  bin  3:  3.3273 -  2.9102 [2114/2139]  1901   213  10.1%
  bin  4:  2.9102 -  2.6457 [2104/2121]  1897   207   9.8%
  bin  5:  2.6457 -  2.4569 [2088/2131]  1883   205   9.8%
  bin  6:  2.4569 -  2.3126 [2086/2114]  1878   208  10.0%
  bin  7:  2.3126 -  2.1972 [2071/2107]  1859   212  10.2%
  bin  8:  2.1972 -  2.1018 [2054/2096]  1850   204   9.9%
  bin  9:  2.1018 -  2.0211 [2037/2106]  1831   206  10.1%
  bin 10:  2.0211 -  1.9515 [ 645/2108]   580    65  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_935/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.47 -     2.15: 20
        2.15 -     2.84: 1046
        2.84 -     3.53: 4404
        3.53 -     4.21: 9309
        4.21 -     4.90: 13580
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.465 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.580 3.040 -x+1/2,-y+1,z+1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.674 3.120 -x+1/2,-y+1,z-1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.682 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.686 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28354 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_935/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_935/model_refine_001.geo

CPU time processing inputs: 9.37


============================ 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 = 70.9525 47.63395 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4478   r_free= 0.4445   ksol= 0.00   Bsol= 0.00   scale= 0.907    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.256111                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6593 0.99   1458  165 0.3463 0.3527      6.5094      6.4971|
|  2:  4.6593 -  3.7168 0.99   1393  151 0.3718 0.3629      6.7507      6.7614|
|  3:  3.7168 -  3.2524 0.99   1376  152 0.4092 0.3991        6.61      6.6446|
|  4:  3.2524 -  2.9575 0.99   1360  151 0.4374 0.4211        6.47      6.4574|
|  5:  2.9575 -  2.7470 0.99   1357  152 0.4591 0.4447      6.3146       6.302|
|  6:  2.7470 -  2.5859 0.99   1348  156 0.4817 0.4742      6.2516      6.1591|
|  7:  2.5859 -  2.4569 0.98   1340  137 0.4796 0.4474      6.2183      6.1749|
|  8:  2.4569 -  2.3504 0.98   1336  149 0.5092 0.5202      6.1386      6.1975|
|  9:  2.3504 -  2.2602 0.99   1332  154 0.5206 0.4988      6.1324      6.1075|
| 10:  2.2602 -  2.1825 0.98   1342  149 0.5043 0.5316      6.0644      6.1235|
| 11:  2.1825 -  2.1144 0.97   1318  141 0.5145 0.5843      6.0209       5.994|
| 12:  2.1144 -  2.0542 0.98   1318  147 0.5143 0.5405      5.9297      5.9882|
| 13:  2.0542 -  2.0002 0.80   1070  127 0.5185 0.4534      5.8747      5.8265|
| 14:  2.0002 -  1.9515 0.20    282   28 0.5787 0.4618      5.7915      5.7702|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9965 -  4.6593  1458   165  0.73  31.51   0.84     0.75      61007.30|
|  2:  4.6593 -  3.7168  1393   151  0.74  32.19   0.93     0.82      88338.89|
|  3:  3.7168 -  3.2524  1376   152  0.64  40.25   0.92     0.82      95925.13|
|  4:  3.2524 -  2.9575  1360   151  0.55  47.56   0.93     0.76      87889.42|
|  5:  2.9575 -  2.7470  1357   152  0.50  52.24   0.89     0.70      70170.28|
|  6:  2.7470 -  2.5859  1348   156  0.47  54.57   0.91     0.66      60945.05|
|  7:  2.5859 -  2.4569  1340   137  0.45  55.70   0.93     0.62      56134.05|
|  8:  2.4569 -  2.3504  1336   149  0.39  60.74   0.89     0.58      56157.41|
|  9:  2.3504 -  2.2602  1332   154  0.35  63.46   0.93     0.53      53416.88|
| 10:  2.2602 -  2.1825  1342   149  0.30  67.83   0.96     0.45      53238.46|
| 11:  2.1825 -  2.1144  1318   141  0.24  71.92   0.94     0.37      50830.01|
| 12:  2.1144 -  2.0542  1318   147  0.20  75.54   0.93     0.33      48765.56|
| 13:  2.0542 -  2.0002  1070   127  0.21  74.04   0.93     0.35      40935.41|
| 14:  2.0002 -  1.9515   282    28  0.25  71.08   0.86     0.41      32808.89|
|alpha:            min =        0.33 max =            0.82 mean =         0.60|
|beta:             min =    32808.89 max =        95925.13 mean =     63418.35|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           90.00 mean =        55.60|
|phase err.(test): min =        0.00 max =           89.99 mean =        55.68|
|-----------------------------------------------------------------------------|

============================== 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 = 11.352991             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.895   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.572834              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.529   (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 |  1.465 -  1.809:        8 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.809 -  2.152:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.152 -  2.496:       33 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.496 -  2.839:     1013 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.839 -  3.183:     1979 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.183 -  3.526:     2425 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.526 -  3.870:     4632 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.870 -  4.213:     4677 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.213 -  4.556:     6156 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.556 -  4.900:     7424 |
|-----------------------------------------------------------------------------|
|-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 |        0.188 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.465 |       0.563 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.871)------------------------------------------|
|    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 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4478   r_free= 0.4445   ksol= 0.00   Bsol= 0.00   scale= 0.907    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.256111                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4390   r_free= 0.4357   ksol= 0.30   Bsol= 50.00   scale= 0.946   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,1.96,2.12,0.00,0.00,0.00); trace/3= 0.70                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.250112                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.877526              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.874   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.092601              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.274   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4390      final r-factor (work) = 0.3196          |
| start r-factor (free) = 0.4357      final r-factor (free) = 0.3527          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.9178 = 8.88 * 0.50 * 6.2471 + 1.00 * 0.1884                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.2292 = 8.88 * 0.50 * 6.1047 + 1.00 * 0.1319                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3196      final r-factor (work) = 0.2909          |
| start r-factor (free) = 0.3527      final r-factor (free) = 0.3616          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6762 = 1.09 * 1.00 * 6.1047 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5289 = 1.09 * 1.00 * 5.9589 + 1.00 * 0.0183                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.871)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.26  18.82    None  None   None       |
|    all(noH): 2823   0      0.00    104.26  18.82    None  None   None       |
|    Sol.    : 438    0      3.12    100.88  41.50    None  None   None       |
|    Mac.    : 2385   0      0.00    104.26  14.66    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 -  10.426:  974   |   5:    52.131 -  62.557:   77        |
|      1:    10.426 -  20.852:  987   |   6:    62.557 -  72.983:   38        |
|      2:    20.852 -  31.279:  387   |   7:    72.983 -  83.409:   27        |
|      3:    31.279 -  41.705:  196   |   8:    83.409 -  93.836:    3        |
|      4:    41.705 -  52.131:  129   |   9:    93.836 - 104.262:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2909 r_free = 0.3616             target_work(ml) = 5.965         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2906 r_free = 0.3619             target_work(ml) = 5.964         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2906   r_free= 0.3619   ksol= 0.30   Bsol= 50.00   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,1.96,2.12,0.00,0.00,0.00); trace/3= 0.70                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.964076                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2882   r_free= 0.3593   ksol= 0.33   Bsol= 62.54   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,0.04,-0.09,0.00,-0.00,-0.00); trace/3= -0.68                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.961986                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.729170              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.341   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.521225              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 108.673  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2882      final r-factor (work) = 0.2146          |
| start r-factor (free) = 0.3593      final r-factor (free) = 0.2700          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.2018 = 5.73 * 0.50 * 5.9590 + 1.00 * 0.1319                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.8583 = 5.73 * 0.50 * 5.8586 + 1.00 * 0.0760                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2146      final r-factor (work) = 0.2001          |
| start r-factor (free) = 0.2700      final r-factor (free) = 0.2553          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0719 = 0.52 * 1.00 * 5.8586 + 1.00 * 0.0183                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9934 = 0.52 * 1.00 * 5.6798 + 1.00 * 0.0329                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.871)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    205.36  18.74    None  None   None       |
|    all(noH): 2823   0      0.00    205.36  18.74    None  None   None       |
|    Sol.    : 438    0      4.75    100.24  42.04    None  None   None       |
|    Mac.    : 2385   0      0.00    205.36  14.46    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 -  20.536: 2020   |   5:   102.679 - 123.215:    1        |
|      1:    20.536 -  41.072:  517   |   6:   123.215 - 143.751:    0        |
|      2:    41.072 -  61.607:  207   |   7:   143.751 - 164.286:    0        |
|      3:    61.607 -  82.143:   70   |   8:   164.286 - 184.822:    0        |
|      4:    82.143 - 102.679:    7   |   9:   184.822 - 205.358:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2001 r_free = 0.2553             target_work(ml) = 5.654         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1997 r_free = 0.2555             target_work(ml) = 5.654         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1997   r_free= 0.2555   ksol= 0.33   Bsol= 62.54   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,0.04,-0.09,0.00,-0.00,-0.00); trace/3= -0.68                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.654328                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1996   r_free= 0.2550   ksol= 0.32   Bsol= 54.72   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-0.77,-1.24,-0.00,-0.00,-0.00); trace/3= -1.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.652644                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.784025              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.760   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 12.017859             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.103   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1996      final r-factor (work) = 0.1641          |
| start r-factor (free) = 0.2550      final r-factor (free) = 0.2137          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9833 = 2.78 * 0.50 * 5.6805 + 1.00 * 0.0760                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8112 = 2.78 * 0.50 * 5.5733 + 1.00 * 0.0531                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1641      final r-factor (work) = 0.1482          |
| start r-factor (free) = 0.2137      final r-factor (free) = 0.2017          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 67.1014 = 12.02 * 1.00 * 5.5733 + 1.00 * 0.1223                             |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 65.2833 = 12.02 * 1.00 * 5.4310 + 1.00 * 0.0148                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.871)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    127.81  19.10    None  None   None       |
|    all(noH): 2823   0      0.00    127.81  19.10    None  None   None       |
|    Sol.    : 438    0      5.63    102.08  47.27    None  None   None       |
|    Mac.    : 2385   0      0.00    127.81  13.92    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 -  12.781: 1473   |   5:    63.903 -  76.684:   69        |
|      1:    12.781 -  25.561:  795   |   6:    76.684 -  89.464:   34        |
|      2:    25.561 -  38.342:  176   |   7:    89.464 - 102.245:   13        |
|      3:    38.342 -  51.123:  143   |   8:   102.245 - 115.026:    4        |
|      4:    51.123 -  63.903:  114   |   9:   115.026 - 127.806:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1482 r_free = 0.2017             target_work(ml) = 5.394         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1482 r_free = 0.2017             target_work(ml) = 5.394         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1482   r_free= 0.2017   ksol= 0.32   Bsol= 54.72   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-0.77,-1.24,-0.00,-0.00,-0.00); trace/3= -1.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.393995                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1484   r_free= 0.2022   ksol= 0.32   Bsol= 60.43   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-1.50,-1.80,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.396238                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.359782              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.830  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.843300              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.169  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1484      final r-factor (work) = 0.1306          |
| start r-factor (free) = 0.2022      final r-factor (free) = 0.1809          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4649 = 2.36 * 0.50 * 5.4342 + 1.00 * 0.0531                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3594 = 2.36 * 0.50 * 5.3429 + 1.00 * 0.0553                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1306      final r-factor (work) = 0.1258          |
| start r-factor (free) = 0.1809      final r-factor (free) = 0.1744          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5204 = 0.84 * 1.00 * 5.3429 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4574 = 0.84 * 1.00 * 5.2712 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.871)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.21    117.43  18.42    None  None   None       |
|    all(noH): 2823   0      1.21    117.43  18.42    None  None   None       |
|    Sol.    : 438    0      5.14    98.30   45.48    None  None   None       |
|    Mac.    : 2385   0      1.21    117.43  13.44    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:     1.214 -  12.835: 1566   |   5:    59.322 -  70.944:   62        |
|      1:    12.835 -  24.457:  715   |   6:    70.944 -  82.565:   43        |
|      2:    24.457 -  36.079:  170   |   7:    82.565 -  94.187:   17        |
|      3:    36.079 -  47.700:  130   |   8:    94.187 - 105.808:    6        |
|      4:    47.700 -  59.322:  109   |   9:   105.808 - 117.430:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1258 r_free = 0.1744             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1258 r_free = 0.1745             target_work(ml) = 5.250         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1258   r_free= 0.1745   ksol= 0.32   Bsol= 60.43   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-1.50,-1.80,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.249567                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1257   r_free= 0.1743   ksol= 0.32   Bsol= 55.54   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-1.50,-1.80,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.249342                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.295735              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.222  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.129360              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.009  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1257      final r-factor (work) = 0.1181          |
| start r-factor (free) = 0.1743      final r-factor (free) = 0.1671          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1058 = 2.30 * 0.50 * 5.2711 + 1.00 * 0.0553                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0567 = 2.30 * 0.50 * 5.2259 + 1.00 * 0.0581                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1181      final r-factor (work) = 0.1196          |
| start r-factor (free) = 0.1671      final r-factor (free) = 0.1631          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6882 = 0.13 * 1.00 * 5.2259 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6813 = 0.13 * 1.00 * 5.2099 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.871)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.76    101.42  16.95    None  None   None       |
|    all(noH): 2823   0      2.76    101.42  16.95    None  None   None       |
|    Sol.    : 438    0      5.24    86.65   39.09    None  None   None       |
|    Mac.    : 2385   0      2.76    101.42  12.88    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.762 -  12.628: 1581   |   5:    52.091 -  61.957:   48        |
|      1:    12.628 -  22.494:  716   |   6:    61.957 -  71.823:   33        |
|      2:    22.494 -  32.360:  171   |   7:    71.823 -  81.689:   12        |
|      3:    32.360 -  42.225:  149   |   8:    81.689 -  91.554:    6        |
|      4:    42.225 -  52.091:  102   |   9:    91.554 - 101.420:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1196 r_free = 0.1631             target_work(ml) = 5.198         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1194 r_free = 0.1629             target_work(ml) = 5.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1194   r_free= 0.1629   ksol= 0.32   Bsol= 55.54   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-1.50,-1.80,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.197121                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6593 0.99   1458  165 0.0985 0.1282      5.3679      5.5429|
|  2:  4.6593 -  3.7168 0.99   1393  151 0.0887 0.1062      5.4442      5.6379|
|  3:  3.7168 -  3.2524 0.99   1376  152 0.1109 0.1772      5.5061      5.9291|
|  4:  3.2524 -  2.9575 0.99   1360  151 0.1366 0.1608      5.5229      5.6435|
|  5:  2.9575 -  2.7470 0.99   1357  152 0.1435 0.1911      5.3824      5.5568|
|  6:  2.7470 -  2.5859 0.99   1348  156 0.1352 0.1966      5.2654      5.4671|
|  7:  2.5859 -  2.4569 0.98   1340  137 0.1316 0.1734       5.208      5.4146|
|  8:  2.4569 -  2.3504 0.98   1336  149 0.1311 0.1719      5.1227      5.3113|
|  9:  2.3504 -  2.2602 0.99   1332  154 0.1246 0.1920      5.0548      5.3053|
| 10:  2.2602 -  2.1825 0.98   1342  149 0.1231 0.1697      5.0011      5.2789|
| 11:  2.1825 -  2.1144 0.97   1318  141 0.1190 0.1909      4.9437      5.2296|
| 12:  2.1144 -  2.0542 0.98   1318  147 0.1240 0.1748      4.9049      5.1267|
| 13:  2.0542 -  2.0002 0.80   1070  127 0.1234 0.1769      4.8149      5.0243|
| 14:  2.0002 -  1.9515 0.20    282   28 0.1290 0.1381      4.7029      4.8664|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9965 -  4.6593  1458   165  0.94   8.65   0.98     0.95       6642.42|
|  2:  4.6593 -  3.7168  1393   151  0.95   7.96   1.01     1.00       8805.62|
|  3:  3.7168 -  3.2524  1376   152  0.93  12.13   1.02     1.02      11130.95|
|  4:  3.2524 -  2.9575  1360   151  0.90  15.63   1.01     0.98      11745.75|
|  5:  2.9575 -  2.7470  1357   152  0.88  17.67   1.00     0.96       9307.33|
|  6:  2.7470 -  2.5859  1348   156  0.89  16.92   0.99     0.97       7634.50|
|  7:  2.5859 -  2.4569  1340   137  0.90  15.94   0.99     0.97       6559.70|
|  8:  2.4569 -  2.3504  1336   149  0.89  17.11   1.01     0.98       5984.86|
|  9:  2.3504 -  2.2602  1332   154  0.90  16.59   1.01     0.98       5185.83|
| 10:  2.2602 -  2.1825  1342   149  0.90  15.71   1.00     0.96       4570.26|
| 11:  2.1825 -  2.1144  1318   141  0.90  16.31   1.00     0.96       4285.38|
| 12:  2.1144 -  2.0542  1318   147  0.90  16.58   1.01     1.01       4127.04|
| 13:  2.0542 -  2.0002  1070   127  0.90  16.72   1.00     0.99       3381.95|
| 14:  2.0002 -  1.9515   282    28  0.89  16.72   0.99     0.96       2608.82|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2608.82 max =        11745.75 mean =      6887.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.68 mean =        14.85|
|phase err.(test): min =        0.00 max =           87.30 mean =        14.21|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1197   r_free= 0.1627   ksol= 0.32   Bsol= 49.47   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-1.71,-1.92,-0.00,-0.00,-0.00); trace/3= -1.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.199856                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1197   r_free= 0.1627   ksol= 0.32   Bsol= 49.47   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-1.71,-1.92,-0.00,-0.00,-0.00); trace/3= -1.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.199856                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6593 0.99   1458  165 0.0992 0.1257      5.3815      5.5508|
|  2:  4.6593 -  3.7168 0.99   1393  151 0.0891 0.1070      5.4528      5.6533|
|  3:  3.7168 -  3.2524 0.99   1376  152 0.1110 0.1749      5.5107      5.9209|
|  4:  3.2524 -  2.9575 0.99   1360  151 0.1370 0.1594      5.5225      5.6394|
|  5:  2.9575 -  2.7470 0.99   1357  152 0.1439 0.1915      5.3839       5.555|
|  6:  2.7470 -  2.5859 0.99   1348  156 0.1354 0.1970      5.2675      5.4716|
|  7:  2.5859 -  2.4569 0.98   1340  137 0.1317 0.1742        5.21      5.4174|
|  8:  2.4569 -  2.3504 0.98   1336  149 0.1312 0.1723      5.1241       5.313|
|  9:  2.3504 -  2.2602 0.99   1332  154 0.1242 0.1919      5.0543      5.3065|
| 10:  2.2602 -  2.1825 0.98   1342  149 0.1232 0.1700      5.0014      5.2798|
| 11:  2.1825 -  2.1144 0.97   1318  141 0.1189 0.1910      4.9432      5.2293|
| 12:  2.1144 -  2.0542 0.98   1318  147 0.1241 0.1755       4.906      5.1295|
| 13:  2.0542 -  2.0002 0.80   1070  127 0.1232 0.1764      4.8156      5.0241|
| 14:  2.0002 -  1.9515 0.20    282   28 0.1290 0.1380      4.7029      4.8665|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9965 -  4.6593  1458   165  0.94   8.81   0.97     0.95       6903.00|
|  2:  4.6593 -  3.7168  1393   151  0.95   8.21   1.01     0.99       9077.01|
|  3:  3.7168 -  3.2524  1376   152  0.93  12.20   1.02     1.02      11320.22|
|  4:  3.2524 -  2.9575  1360   151  0.90  15.50   1.00     0.97      11647.37|
|  5:  2.9575 -  2.7470  1357   152  0.88  17.66   0.99     0.95       9292.81|
|  6:  2.7470 -  2.5859  1348   156  0.89  16.95   0.98     0.96       7675.06|
|  7:  2.5859 -  2.4569  1340   137  0.90  16.01   0.98     0.96       6606.24|
|  8:  2.4569 -  2.3504  1336   149  0.89  17.14   1.00     0.97       6012.47|
|  9:  2.3504 -  2.2602  1332   154  0.90  16.61   1.00     0.97       5198.65|
| 10:  2.2602 -  2.1825  1342   149  0.90  15.72   0.98     0.95       4575.51|
| 11:  2.1825 -  2.1144  1318   141  0.90  16.31   0.99     0.95       4289.68|
| 12:  2.1144 -  2.0542  1318   147  0.90  16.59   0.99     1.00       4136.32|
| 13:  2.0542 -  2.0002  1070   127  0.90  16.72   0.99     0.98       3387.83|
| 14:  2.0002 -  1.9515   282    28  0.89  16.72   0.98     0.95       2607.05|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2607.05 max =        11647.37 mean =      6948.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.89 mean =        14.89|
|phase err.(test): min =        0.00 max =           88.52 mean =        14.28|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.871)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.66    101.32  16.85    None  None   None       |
|    all(noH): 2823   0      2.66    101.32  16.85    None  None   None       |
|    Sol.    : 438    0      5.14    86.55   38.99    None  None   None       |
|    Mac.    : 2385   0      2.66    101.32  12.78    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.662 -  12.527: 1581   |   5:    51.991 -  61.856:   48        |
|      1:    12.527 -  22.393:  716   |   6:    61.856 -  71.722:   33        |
|      2:    22.393 -  32.259:  171   |   7:    71.722 -  81.588:   12        |
|      3:    32.259 -  42.125:  149   |   8:    81.588 -  91.454:    6        |
|      4:    42.125 -  51.991:  102   |   9:    91.454 - 101.320:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 318         
Filter by distance & map next to the model:
   mapped sites are within: 0.572 - 5.895
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 314 from: 318
   mapped sites are within: 0.727 - 5.895

peak=    5.607 closest distance to " CB  SER A  63 " =    1.256
peak=    5.559 closest distance to " O   HOH Z 113 " =    2.306
peak=    5.318 closest distance to " CB  GLN A 223 " =    1.443
peak=    5.246 closest distance to " CG  PRO A  54 " =    1.261
peak=    4.973 closest distance to " O   HOH Z  11 " =    1.370
peak=    4.943 closest distance to " CG  PRO A 198 " =    1.318
peak=    4.941 closest distance to " O   HOH Z  15 " =    1.997
peak=    4.928 closest distance to " O   HOH Z 132 " =    1.289
peak=    4.870 closest distance to " O   HOH Z 214 " =    1.300
peak=    4.812 closest distance to " NH2BARG A 102 " =    0.989
peak=    4.810 closest distance to " CG  PRO A 213 " =    1.249
peak=    4.733 closest distance to " CB  ARG A 275 " =    0.901
peak=    4.681 closest distance to " CG  PRO A  90 " =    1.158
peak=    4.610 closest distance to " NH2 ARG A 156 " =    1.246
peak=    4.597 closest distance to " O   HOH Z 124 " =    1.441
peak=    4.575 closest distance to " O   HOH Z 134 " =    1.677
peak=    4.564 closest distance to " O   HOH Z 368 " =    2.074
peak=    4.540 closest distance to " O   HOH Z 234 " =    3.818
peak=    4.506 closest distance to " CB  SER A   3 " =    1.473
peak=    4.484 closest distance to " O   SER A  87 " =    2.078
peak=    4.473 closest distance to " O   HOH Z 193 " =    1.947
peak=    4.458 closest distance to " O   HOH Z  80 " =    1.817
peak=    4.430 closest distance to " O   HOH Z 246 " =    1.471
peak=    4.376 closest distance to " CB  GLU A 277 " =    3.611
peak=    4.368 closest distance to " CG  PRO A 280 " =    0.731
peak=    4.352 closest distance to " O   HOH Z 108 " =    1.607
peak=    4.351 closest distance to " O   HOH Z 403 " =    1.737
peak=    4.317 closest distance to " O   HOH Z 154 " =    1.494
peak=    4.308 closest distance to " O   HOH Z 260 " =    1.376
peak=    4.306 closest distance to " CB  GLN A 183 " =    1.233
peak=    4.303 closest distance to " O   HOH Z 272 " =    1.982
peak=    4.270 closest distance to " CB  TYR A 169 " =    0.979
peak=    4.249 closest distance to " CB  GLU A 152 " =    1.169
peak=    4.226 closest distance to " CB  LEU A 228 " =    1.138
peak=    4.226 closest distance to " O   HOH Z 298 " =    1.818
peak=    4.212 closest distance to " O   HOH Z  40 " =    1.872
peak=    4.200 closest distance to " CG1 ILE A  33 " =    1.277
peak=    4.165 closest distance to " O   HOH Z 411 " =    3.343
peak=    4.163 closest distance to " CA  ALA A  21 " =    1.286
peak=    4.163 closest distance to " O   HOH Z  63 " =    1.950
peak=    4.156 closest distance to " O   HOH Z 282 " =    1.650
peak=    4.154 closest distance to " NH1BARG A 145 " =    0.790
peak=    4.146 closest distance to " O   HOH Z  97 " =    1.912
peak=    4.136 closest distance to " CG  PRO A 243 " =    1.179
peak=    4.113 closest distance to " O   HOH Z 389 " =    1.935
peak=    4.111 closest distance to " CB  GLU A 128 " =    1.140
peak=    4.108 closest distance to " CA  TYR A  30 " =    1.020
peak=    4.103 closest distance to " O   HOH Z  61 " =    1.687
peak=    4.098 closest distance to " CB  PRO A  54 " =    0.820
peak=    4.094 closest distance to " O   HOH Z 215 " =    1.462
peak=    4.092 closest distance to " OE1 GLN A  11 " =    1.912
peak=    4.089 closest distance to " CB  VAL A 202 " =    1.539
peak=    4.085 closest distance to " O   HOH Z 126 " =    1.720
peak=    4.079 closest distance to " O   HOH Z 236 " =    1.886
peak=    4.078 closest distance to " OD2 ASP A 286 " =    2.917
peak=    4.070 closest distance to " O   HOH Z  67 " =    1.885
peak=    4.069 closest distance to " O   HOH Z 215 " =    1.521
peak=    4.063 closest distance to " O   PRO A 198 " =    1.542
peak=    4.057 closest distance to " N   ASN A  39 " =    1.341
peak=    4.056 closest distance to " CB  PRO A 198 " =    0.979
peak=    4.056 closest distance to " O   HOH Z  43 " =    1.421
peak=    4.043 closest distance to " O   HOH Z  59 " =    2.404
peak=    4.035 closest distance to " CB  TRP A 179 " =    1.295
peak=    4.032 closest distance to " CG1BVAL A  72 " =    1.648
peak=    4.032 closest distance to " CB  SER A 141 " =    1.011
peak=    4.015 closest distance to " O   HOH Z 316 " =    3.033
peak=    4.015 closest distance to " O   HOH Z 426 " =    1.435
peak=    4.014 closest distance to " O   HOH Z 156 " =    3.392
peak=    4.013 closest distance to " CG  ARG A  66 " =    2.553
peak=    4.013 closest distance to " CG2 THR A 221 " =    1.001
peak=    3.995 closest distance to " O   HOH Z 207 " =    1.826
peak=    3.973 closest distance to " O   ALA A 165 " =    1.268
peak=    3.972 closest distance to " O   HOH Z 313 " =    1.977
peak=    3.966 closest distance to " CA  ASP A 191 " =    0.827
peak=    3.959 closest distance to " ND2 ASN A 187 " =    1.643
peak=    3.947 closest distance to " O   HOH Z 232 " =    2.246
peak=    3.946 closest distance to " O   HOH Z 189 " =    1.986
peak=    3.939 closest distance to " O   HOH Z 211 " =    1.262
peak=    3.911 closest distance to " O   HOH Z 133 " =    1.656
peak=    3.906 closest distance to " O   HOH Z 135 " =    1.886
peak=    3.903 closest distance to " O   HOH Z 374 " =    2.546
peak=    3.896 closest distance to " O   HOH Z 132 " =    2.728
peak=    3.891 closest distance to " O   HOH Z 128 " =    2.135
peak=    3.881 closest distance to " O   HOH Z 326 " =    1.564
peak=    3.869 closest distance to " O   HOH Z 344 " =    2.948
peak=    3.867 closest distance to " O   HOH Z 394 " =    1.724
peak=    3.863 closest distance to " O   HOH Z  88 " =    3.488
peak=    3.858 closest distance to " O   HOH Z  30 " =    1.562
peak=    3.844 closest distance to " O   HOH Z 369 " =    2.031
peak=    3.835 closest distance to " CB  ARG A 190 " =    1.730
peak=    3.818 closest distance to " CG AARG A 275 " =    0.989
peak=    3.811 closest distance to " O   HOH Z 128 " =    2.208
peak=    3.810 closest distance to " O   HOH Z 102 " =    1.304
peak=    3.807 closest distance to " O   HOH Z 163 " =    1.673
peak=    3.807 closest distance to " O   HOH Z  54 " =    1.649
peak=    3.806 closest distance to " CB  PHE A  16 " =    1.096
peak=    3.789 closest distance to " NZ  LYS A 117 " =    3.255
peak=    3.786 closest distance to " O   HOH Z 142 " =    1.548
peak=    3.768 closest distance to " CD  LYS A 119 " =    1.482
peak=    3.767 closest distance to " OD1 ASN A  69 " =    2.561
peak=    3.764 closest distance to " O   HOH Z 108 " =    2.015
peak=    3.763 closest distance to " O   HOH Z 234 " =    1.864
peak=    3.760 closest distance to " O   HOH Z 180 " =    2.142
peak=    3.759 closest distance to " CA  THR A 221 " =    0.958
peak=    3.756 closest distance to " O   HOH Z 133 " =    1.975
peak=    3.753 closest distance to " OE1 GLN A  58 " =    5.895
peak=    3.753 closest distance to " O   HOH Z 193 " =    2.230
peak=    3.752 closest distance to " O   HOH Z  48 " =    1.524
peak=    3.740 closest distance to " O   HOH Z 406 " =    1.628
peak=    3.738 closest distance to " O   HOH Z 209 " =    2.387
peak=    3.736 closest distance to " CB  ASN A 187 " =    1.046
peak=    3.735 closest distance to " O   HOH Z 265 " =    2.278
peak=    3.734 closest distance to " O   HOH Z 147 " =    1.722
peak=    3.707 closest distance to " O   HOH Z 261 " =    2.197
peak=    3.707 closest distance to " NH2AARG A 190 " =    1.431
peak=    3.705 closest distance to " O   HOH Z 387 " =    2.509
peak=    3.705 closest distance to " O   HOH Z 183 " =    1.482
peak=    3.700 closest distance to " O   HOH Z 248 " =    1.600
peak=    3.697 closest distance to " O   HOH Z 279 " =    2.274
peak=    3.679 closest distance to " CB  ARG A  79 " =    1.341
peak=    3.673 closest distance to " CD  ARG A 269 " =    0.884
peak=    3.653 closest distance to " CA  LEU A 282 " =    1.135
peak=    3.649 closest distance to " CG1 VAL A 153 " =    1.013
peak=    3.645 closest distance to " O   HOH Z  20 " =    1.774
peak=    3.641 closest distance to " NZ  LYS A  76 " =    1.205
peak=    3.638 closest distance to " O   HOH Z  78 " =    2.363
peak=    3.634 closest distance to " O   HOH Z  39 " =    1.283
peak=    3.628 closest distance to " CB  ASN A 148 " =    1.075
peak=    3.612 closest distance to " OD1 ASN A 217 " =    1.797
peak=    3.603 closest distance to " CB  TRP A 266 " =    0.921
peak=    3.597 closest distance to " O   HOH Z 278 " =    1.005
peak=    3.570 closest distance to " O   HOH Z 427 " =    3.040
peak=    3.562 closest distance to " CD2 LEU A 297 " =    0.884
peak=    3.561 closest distance to " NZ  LYS A 117 " =    1.210
peak=    3.559 closest distance to " O   HOH Z 227 " =    1.756
peak=    3.559 closest distance to " CB  ASN A 148 " =    1.914
peak=    3.553 closest distance to " CD  PRO A  54 " =    1.140
peak=    3.551 closest distance to " O   HOH Z 118 " =    1.543
peak=    3.550 closest distance to " CB  ALA A 291 " =    1.198
peak=    3.547 closest distance to " O   HOH Z 358 " =    2.170
peak=    3.546 closest distance to " O   HOH Z  14 " =    2.300
peak=    3.544 closest distance to " CA  ARG A  36 " =    1.152
peak=    3.543 closest distance to " NE AARG A 275 " =    1.363
peak=    3.540 closest distance to " O   HOH Z 434 " =    1.444
peak=    3.535 closest distance to " O   HOH Z 332 " =    1.510
peak=    3.534 closest distance to " O   HOH Z 276 " =    1.372
peak=    3.534 closest distance to " O   HOH Z 126 " =    1.642
peak=    3.534 closest distance to " CA  MET A  40 " =    1.041
peak=    3.526 closest distance to " CA  GLN A 223 " =    0.886
peak=    3.526 closest distance to " CA  ASP A 140 " =    1.212
peak=    3.521 closest distance to " O   HOH Z 427 " =    2.803
peak=    3.513 closest distance to " CB  ARG A 139 " =    1.054
peak=    3.512 closest distance to " OG BSER A 258 " =    3.557
peak=    3.511 closest distance to " NH2BARG A 145 " =    1.962
peak=    3.504 closest distance to " OD1 ASP A 238 " =    0.852
peak=    3.503 closest distance to " O   HOH Z  49 " =    2.387
peak=    3.501 closest distance to " O   HOH Z 295 " =    1.455
peak=    3.490 closest distance to " C   SER A  32 " =    1.029
peak=    3.488 closest distance to " O   HOH Z  43 " =    2.107
peak=    3.474 closest distance to " O   HOH Z 423 " =    1.970
peak=    3.471 closest distance to " O   HOH Z  44 " =    1.876
peak=    3.467 closest distance to " O   HOH Z 368 " =    2.531
peak=    3.463 closest distance to " O   HOH Z 291 " =    1.678
peak=    3.463 closest distance to " CG2AVAL A 121 " =    2.201
peak=    3.462 closest distance to " O   HOH Z  21 " =    1.849
peak=    3.457 closest distance to " CA  GLU A 152 " =    0.885
peak=    3.449 closest distance to " O   HOH Z 173 " =    2.016
peak=    3.448 closest distance to " O   HOH Z  93 " =    2.455
peak=    3.441 closest distance to " O   HOH Z 156 " =    2.461
peak=    3.439 closest distance to " O   HOH Z 207 " =    1.971
peak=    3.437 closest distance to " CB  ILE A 199 " =    1.091
peak=    3.432 closest distance to " O   HOH Z 217 " =    1.312
peak=    3.432 closest distance to " O   HOH Z 292 " =    1.724
peak=    3.431 closest distance to " CD  LYS A 166 " =    1.382
peak=    3.429 closest distance to " O   HOH Z  78 " =    1.751
peak=    3.428 closest distance to " O   HOH Z  59 " =    1.847
peak=    3.426 closest distance to " O   HOH Z 284 " =    2.964
peak=    3.422 closest distance to " O   HOH Z 112 " =    1.498
peak=    3.421 closest distance to " CA  ASP A 162 " =    1.210
peak=    3.420 closest distance to " O   HOH Z 281 " =    4.026
peak=    3.420 closest distance to " CA  GLY A 196 " =    1.034
peak=    3.416 closest distance to " CG  GLN A  11 " =    0.998
peak=    3.416 closest distance to " O   HOH Z 127 " =    1.226
peak=    3.415 closest distance to " CB  MET A  47 " =    0.965
peak=    3.413 closest distance to " O   HOH Z   6 " =    2.151
peak=    3.409 closest distance to " O   HOH Z   4 " =    1.948
peak=    3.399 closest distance to " NE2 GLN A  11 " =    1.103
peak=    3.396 closest distance to " O   ALA A   1 " =    1.442
peak=    3.393 closest distance to " CA  ARG A 195 " =    1.288
peak=    3.392 closest distance to " CB  ASN A 285 " =    0.930
peak=    3.385 closest distance to " CD  ARG A 159 " =    0.770
peak=    3.380 closest distance to " CD1 LEU A 300 " =    1.223
peak=    3.379 closest distance to " O   HOH Z 346 " =    1.483
peak=    3.379 closest distance to " CA  ILE A 263 " =    0.974
peak=    3.378 closest distance to " O   HOH Z 287 " =    1.803
peak=    3.378 closest distance to " CB  ASN A  39 " =    0.896
peak=    3.377 closest distance to " CB  SER A 216 " =    0.727
peak=    3.375 closest distance to " OD1 ASP A 231 " =    1.891
peak=    3.374 closest distance to " O   HOH Z 336 " =    1.682
peak=    3.372 closest distance to " CB  SER A  62 " =    0.834
peak=    3.369 closest distance to " O   HOH Z 203 " =    1.789
peak=    3.358 closest distance to " CG  GLN A  58 " =    2.330
peak=    3.358 closest distance to " O   HOH Z 345 " =    3.122
peak=    3.357 closest distance to " O   HOH Z 174 " =    2.402
peak=    3.353 closest distance to " O   ALA A 158 " =    1.199
peak=    3.349 closest distance to " CB  ALA A 100 " =    1.343
peak=    3.347 closest distance to " O   HOH Z  61 " =    1.577
peak=    3.346 closest distance to " O   HOH Z 116 " =    1.760
peak=    3.345 closest distance to " O   HOH Z 362 " =    3.577
peak=    3.340 closest distance to " O   HOH Z 210 " =    1.242
peak=    3.336 closest distance to " CA  ASP A 124 " =    0.744
peak=    3.335 closest distance to " O   HOH Z  19 " =    1.858
peak=    3.329 closest distance to " CB  LEU A 143 " =    1.128
peak=    3.327 closest distance to " CD2 HIS A  81 " =    1.308
peak=    3.323 closest distance to " O   HOH Z 214 " =    1.996
peak=    3.310 closest distance to " O   HOH Z 433 " =    1.527
peak=    3.304 closest distance to " O   HOH Z 416 " =    2.836
peak=    3.298 closest distance to " O   HOH Z 227 " =    1.724
peak=    3.298 closest distance to " O   HOH Z 197 " =    1.930
peak=    3.298 closest distance to " O   HOH Z 337 " =    3.869
peak=    3.297 closest distance to " CD  ARG A  66 " =    3.180
peak=    3.293 closest distance to " O   HOH Z 266 " =    1.615
peak=    3.286 closest distance to " O   HOH Z 128 " =    1.709
peak=    3.279 closest distance to " CG2AVAL A  41 " =    0.804
peak=    3.276 closest distance to " O   HOH Z 299 " =    2.270
peak=    3.275 closest distance to " CH2 TRP A 274 " =    2.057
peak=    3.263 closest distance to " O   GLY A  57 " =    2.504
peak=    3.258 closest distance to " O   HOH Z 104 " =    3.056
peak=    3.257 closest distance to " O   HOH Z  87 " =    2.482
peak=    3.254 closest distance to " CB  ALA A 244 " =    0.885
peak=    3.248 closest distance to " O   HOH Z 402 " =    1.480
peak=    3.248 closest distance to " CB  ALA A 256 " =    1.130
peak=    3.247 closest distance to " O   HOH Z 263 " =    2.158
peak=    3.245 closest distance to " O   MET A 105 " =    1.789
peak=    3.241 closest distance to " O   HOH Z 438 " =    2.443
peak=    3.239 closest distance to " O   HOH Z 303 " =    2.118
peak=    3.235 closest distance to " CD BLYS A 290 " =    1.090
peak=    3.235 closest distance to " O   HOH Z 345 " =    1.892
peak=    3.235 closest distance to " O   GLN A  58 " =    1.645
peak=    3.235 closest distance to " O   HOH Z 388 " =    1.767
peak=    3.234 closest distance to " O   HOH Z 280 " =    2.371
peak=    3.233 closest distance to " N   ARG A 156 " =    1.466
peak=    3.233 closest distance to " O   HOH Z 425 " =    1.430
peak=    3.228 closest distance to " CG BARG A 102 " =    1.805
peak=    3.227 closest distance to " O   HOH Z 166 " =    3.055
peak=    3.226 closest distance to " O   HOH Z 352 " =    1.189
peak=    3.225 closest distance to " O   HOH Z  47 " =    1.399
peak=    3.221 closest distance to " CZ  PHE A 208 " =    1.142
peak=    3.221 closest distance to " O   HOH Z 366 " =    2.958
peak=    3.217 closest distance to " CA  GLY A 211 " =    1.068
peak=    3.212 closest distance to " CA  GLU A 152 " =    1.508
peak=    3.211 closest distance to " O   HOH Z 357 " =    1.925
peak=    3.208 closest distance to " O   HOH Z 125 " =    2.270
peak=    3.207 closest distance to " O   TRP A 274 " =    1.687
peak=    3.207 closest distance to " CE1 PHE A 155 " =    1.359
peak=    3.207 closest distance to " O   HOH Z 196 " =    0.934
peak=    3.207 closest distance to " NH1 ARG A 138 " =    1.150
peak=    3.204 closest distance to " O   HOH Z 420 " =    1.994
peak=    3.203 closest distance to " O   HOH Z 250 " =    1.755
peak=    3.202 closest distance to " O   SER A  26 " =    1.700
peak=    3.199 closest distance to " CZ  PHE A 192 " =    1.075
peak=    3.198 closest distance to " OG BSER A 164 " =    2.407
peak=    3.198 closest distance to " OH  TYR A  30 " =    1.325
peak=    3.196 closest distance to " CA  VAL A  41 " =    0.799
peak=    3.184 closest distance to " C   PRO A 163 " =    1.689
peak=    3.183 closest distance to " CB  TYR A  30 " =    1.352
peak=    3.183 closest distance to " CD1 TRP A 266 " =    1.178
peak=    3.181 closest distance to " O   HOH Z 261 " =    2.025
peak=    3.181 closest distance to " O   HOH Z 409 " =    2.959
peak=    3.177 closest distance to " ND1 HIS A  81 " =    1.611
peak=    3.174 closest distance to " CA  LYS A 117 " =    1.267
peak=    3.173 closest distance to " CG2 VAL A 197 " =    1.209
peak=    3.173 closest distance to " O   THR A  31 " =    1.533
peak=    3.171 closest distance to " O   HOH Z  50 " =    2.045
peak=    3.170 closest distance to " O   HOH Z 361 " =    2.469
peak=    3.168 closest distance to " CG2 VAL A  78 " =    0.954
peak=    3.165 closest distance to " CA  ASN A  74 " =    1.072
peak=    3.164 closest distance to " O   HOH Z 238 " =    5.392
peak=    3.161 closest distance to " O   HOH Z 106 " =    2.266
peak=    3.161 closest distance to " O   HOH Z  88 " =    1.622
peak=    3.160 closest distance to " CG  MET A 113 " =    1.536
peak=    3.156 closest distance to " CG2 VAL A 257 " =    0.834
peak=    3.154 closest distance to " CG  MET A  93 " =    1.092
peak=    3.152 closest distance to " CG  ASP A 231 " =    0.956
peak=    3.149 closest distance to " C   GLY A  80 " =    1.166
peak=    3.139 closest distance to " CB  TYR A 116 " =    1.184
peak=    3.139 closest distance to " O   HOH Z 261 " =    1.545
peak=    3.139 closest distance to " O   HOH Z 273 " =    2.569
peak=    3.133 closest distance to " O   HOH Z 130 " =    2.261
peak=    3.130 closest distance to " O   HOH Z 166 " =    1.562
peak=    3.129 closest distance to " CA  SER A  87 " =    0.850
peak=    3.128 closest distance to " O   HOH Z 395 " =    1.474
peak=    3.123 closest distance to " CB  GLN A  58 " =    0.763
peak=    3.119 closest distance to " CD1 LEU A 222 " =    0.877
peak=    3.119 closest distance to " CG  GLN A  77 " =    0.806
peak=    3.115 closest distance to " O   HOH Z 145 " =    2.092
peak=    3.106 closest distance to " NE2 GLN A  58 " =    4.415
peak=    3.100 closest distance to " O   HOH Z 285 " =    1.790
peak=    3.096 closest distance to " O   HOH Z  22 " =    2.365
peak=    3.093 closest distance to " CA  ALA A 160 " =    0.869
peak=    3.093 closest distance to " O   HOH Z 171 " =    2.653
peak=    3.089 closest distance to " CD2 TRP A 179 " =    1.292
peak=    3.085 closest distance to " CB  GLN A 194 " =    0.856
peak=    3.085 closest distance to " O   HOH Z  98 " =    2.137
peak=    3.083 closest distance to " O   HOH Z 383 " =    1.983
peak=    3.072 closest distance to " CB  THR A  31 " =    1.704
peak=    3.071 closest distance to " O   HOH Z 329 " =    3.368
peak=    3.070 closest distance to " CA  ILE A  33 " =    1.600
peak=    3.067 closest distance to " CB  ALA A  71 " =    1.253
peak=    3.063 closest distance to " CD  ARG A 195 " =    0.978
peak=    3.062 closest distance to " CG2 ILE A 120 " =    1.181
peak=    3.062 closest distance to " O   HOH Z 162 " =    1.886
peak=    3.061 closest distance to " CA  GLY A 241 " =    0.881
peak=    3.046 closest distance to " CA  ALA A 158 " =    1.074

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.347 - 5.239
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 210
   mapped sites are within: 0.756 - 5.239

peak=   -5.198 closest distance to " O   HOH Z 290 " =    0.841
peak=   -4.840 closest distance to " O   HOH Z 377 " =    0.763
peak=   -4.685 closest distance to " O   HOH Z 221 " =    0.987
peak=   -4.347 closest distance to " O   VAL A  67 " =    2.696
peak=   -4.259 closest distance to " O   HOH Z 266 " =    4.187
peak=   -4.173 closest distance to " OXT GLY A 302 " =    3.058
peak=   -4.165 closest distance to " OG ASER A 134 " =    1.376
peak=   -4.151 closest distance to " N   ALA A  43 " =    2.524
peak=   -4.066 closest distance to " NH2 ARG A  66 " =    1.509
peak=   -4.064 closest distance to " CE2 TYR A  30 " =    2.810
peak=   -4.027 closest distance to " O   HOH Z 407 " =    3.493
peak=   -4.019 closest distance to " O   HOH Z  17 " =    1.056
peak=   -4.011 closest distance to " O   HOH Z  52 " =    1.898
peak=   -4.008 closest distance to " CD  ARG A 156 " =    1.977
peak=   -3.983 closest distance to " O   HOH Z  71 " =    1.100
peak=   -3.976 closest distance to " O   HOH Z  92 " =    1.208
peak=   -3.949 closest distance to " CD2 LEU A 300 " =    2.901
peak=   -3.929 closest distance to " C   ALA A 158 " =    1.192
peak=   -3.918 closest distance to " OE2 GLU A   2 " =    1.319
peak=   -3.906 closest distance to " O   HOH Z  11 " =    1.637
peak=   -3.889 closest distance to " O   HOH Z  13 " =    1.300
peak=   -3.865 closest distance to " OG  SER A  97 " =    2.198
peak=   -3.838 closest distance to " O   HOH Z  93 " =    1.255
peak=   -3.832 closest distance to " CD  GLU A 152 " =    0.849
peak=   -3.811 closest distance to " C   ASN A 285 " =    2.539
peak=   -3.806 closest distance to " O   HOH Z  58 " =    0.779
peak=   -3.801 closest distance to " O   HOH Z 418 " =    1.223
peak=   -3.794 closest distance to " O   HOH Z 166 " =    1.837
peak=   -3.768 closest distance to " O   HOH Z  98 " =    1.727
peak=   -3.766 closest distance to " CB  ALA A 161 " =    2.653
peak=   -3.764 closest distance to " C   HIS A 108 " =    1.070
peak=   -3.754 closest distance to " CE  MET A  93 " =    1.354
peak=   -3.752 closest distance to " CD2 LEU A 237 " =    2.413
peak=   -3.751 closest distance to " CE  MET A 105 " =    1.970
peak=   -3.738 closest distance to " O   GLY A 196 " =    1.129
peak=   -3.732 closest distance to " O   PRO A 198 " =    1.224
peak=   -3.729 closest distance to " N   GLN A  58 " =    1.731
peak=   -3.726 closest distance to " O   HOH Z 151 " =    1.359
peak=   -3.716 closest distance to " O   HOH Z  19 " =    2.080
peak=   -3.715 closest distance to " O   HOH Z   5 " =    1.526
peak=   -3.692 closest distance to " CB  PRO A 243 " =    2.620
peak=   -3.685 closest distance to " CA  SER A 164 " =    2.034
peak=   -3.683 closest distance to " CG  GLU A  53 " =    1.488
peak=   -3.680 closest distance to " NE2 GLN A  58 " =    0.913
peak=   -3.678 closest distance to " O   HOH Z 313 " =    0.985
peak=   -3.665 closest distance to " OG1 THR A   4 " =    1.900
peak=   -3.662 closest distance to " O   HOH Z 150 " =    1.317
peak=   -3.658 closest distance to " CG  ASP A 231 " =    0.773
peak=   -3.643 closest distance to " CG  ASP A  50 " =    2.365
peak=   -3.640 closest distance to " CB  LEU A 167 " =    2.168
peak=   -3.638 closest distance to " CB  CYS A 254 " =    2.485
peak=   -3.631 closest distance to " OD1 ASP A 191 " =    1.592
peak=   -3.628 closest distance to " O   HOH Z 292 " =    4.435
peak=   -3.624 closest distance to " CD2 PHE A  59 " =    2.442
peak=   -3.621 closest distance to " CD1 LEU A 228 " =    2.435
peak=   -3.618 closest distance to " N   SER A 276 " =    1.454
peak=   -3.618 closest distance to " O   HOH Z 353 " =    2.285
peak=   -3.607 closest distance to " NH1 ARG A 195 " =    2.592
peak=   -3.605 closest distance to " O   GLY A 118 " =    2.206
peak=   -3.596 closest distance to " CA  ASN A 148 " =    1.742
peak=   -3.593 closest distance to " CH2 TRP A 179 " =    1.098
peak=   -3.591 closest distance to " CG  GLN A  58 " =    1.223
peak=   -3.588 closest distance to " O   HOH Z 283 " =    1.798
peak=   -3.587 closest distance to " O   HOH Z 259 " =    1.068
peak=   -3.571 closest distance to " SG ACYS A 201 " =    2.327
peak=   -3.568 closest distance to " CB  TYR A  15 " =    2.233
peak=   -3.563 closest distance to " O   HOH Z  43 " =    1.607
peak=   -3.555 closest distance to " CB  ALA A 291 " =    2.403
peak=   -3.543 closest distance to " CA  VAL A  67 " =    2.955
peak=   -3.540 closest distance to " CD1 LEU A 101 " =    2.927
peak=   -3.535 closest distance to " N   ALA A 226 " =    2.104
peak=   -3.529 closest distance to " OG BSER A 134 " =    1.778
peak=   -3.525 closest distance to " O   HOH Z  63 " =    0.970
peak=   -3.522 closest distance to " CZ  TYR A 169 " =    1.858
peak=   -3.511 closest distance to " O   HOH Z  38 " =    1.263
peak=   -3.504 closest distance to " ND2 ASN A  45 " =    0.958
peak=   -3.502 closest distance to " CD  GLN A 223 " =    0.756
peak=   -3.501 closest distance to " CD1 PHE A  59 " =    1.885
peak=   -3.500 closest distance to " O   HOH Z 423 " =    2.334
peak=   -3.499 closest distance to " CG  LYS A 193 " =    2.558
peak=   -3.492 closest distance to " O   HOH Z 231 " =    2.254
peak=   -3.478 closest distance to " ND2 ASN A 187 " =    1.714
peak=   -3.476 closest distance to " O   HOH Z 234 " =    4.389
peak=   -3.475 closest distance to " O   HOH Z 241 " =    1.189
peak=   -3.474 closest distance to " CG  TRP A 266 " =    1.628
peak=   -3.452 closest distance to " CZ  ARG A  66 " =    0.991
peak=   -3.442 closest distance to " O   HOH Z  15 " =    1.633
peak=   -3.439 closest distance to " OG  SER A 245 " =    0.870
peak=   -3.437 closest distance to " O   HOH Z 213 " =    1.232
peak=   -3.434 closest distance to " NH2 ARG A  66 " =    5.038
peak=   -3.433 closest distance to " O   HOH Z 176 " =    0.827
peak=   -3.430 closest distance to " O   HOH Z 236 " =    1.590
peak=   -3.428 closest distance to " O   TRP A  92 " =    1.878
peak=   -3.422 closest distance to " O   HOH Z 388 " =    2.069
peak=   -3.407 closest distance to " OD2 ASP A 171 " =    2.234
peak=   -3.407 closest distance to " O   HOH Z 165 " =    2.088
peak=   -3.406 closest distance to " CD  LYS A 119 " =    0.989
peak=   -3.404 closest distance to " CD1 LEU A 101 " =    2.631
peak=   -3.399 closest distance to " N   GLN A  77 " =    1.394
peak=   -3.398 closest distance to " O   HOH Z 265 " =    1.886
peak=   -3.393 closest distance to " O   HOH Z 196 " =    2.457
peak=   -3.389 closest distance to " ND2 ASN A  60 " =    1.399
peak=   -3.388 closest distance to " O   SER A 210 " =    1.838
peak=   -3.386 closest distance to " CB  PRO A 163 " =    2.638
peak=   -3.384 closest distance to " CB  ASN A  39 " =    2.175
peak=   -3.379 closest distance to " CG  MET A 105 " =    0.921
peak=   -3.374 closest distance to " OG  SER A  62 " =    1.357
peak=   -3.363 closest distance to " ND2 ASN A 249 " =    1.935
peak=   -3.361 closest distance to " O   HOH Z 396 " =    1.751
peak=   -3.360 closest distance to " C   LEU A 143 " =    1.769
peak=   -3.359 closest distance to " CD  LYS A 289 " =    2.583
peak=   -3.359 closest distance to " CD1 TRP A 274 " =    1.716
peak=   -3.355 closest distance to " CD1 TYR A 247 " =    2.384
peak=   -3.354 closest distance to " O   HOH Z 377 " =    2.046
peak=   -3.334 closest distance to " CG  ARG A 269 " =    2.309
peak=   -3.334 closest distance to " NH2 ARG A  79 " =    1.916
peak=   -3.332 closest distance to " CB  SER A 146 " =    2.225
peak=   -3.331 closest distance to " O   HOH Z 184 " =    1.492
peak=   -3.330 closest distance to " CD2 LEU A 167 " =    1.688
peak=   -3.325 closest distance to " O   HOH Z 384 " =    2.296
peak=   -3.324 closest distance to " CB  PRO A 163 " =    2.767
peak=   -3.321 closest distance to " O   HOH Z 185 " =    2.354
peak=   -3.316 closest distance to " OH  TYR A 172 " =    1.652
peak=   -3.315 closest distance to " CD2 TYR A 293 " =    2.082
peak=   -3.312 closest distance to " O   HOH Z 435 " =    2.492
peak=   -3.309 closest distance to " CD2 TRP A 274 " =    1.051
peak=   -3.308 closest distance to " CG1 VAL A 112 " =    2.565
peak=   -3.306 closest distance to " ND2 ASN A  45 " =    1.158
peak=   -3.304 closest distance to " CD  ARG A 195 " =    5.075
peak=   -3.301 closest distance to " NZ  LYS A 117 " =    1.541
peak=   -3.299 closest distance to " O   ASN A 187 " =    1.515
peak=   -3.297 closest distance to " CG  LEU A  83 " =    1.997
peak=   -3.296 closest distance to " OG  SER A  32 " =    1.097
peak=   -3.294 closest distance to " CB  ALA A 248 " =    1.912
peak=   -3.264 closest distance to " O   HOH Z 266 " =    4.782
peak=   -3.259 closest distance to " CD  PRO A 198 " =    1.282
peak=   -3.256 closest distance to " CA  GLY A 241 " =    2.304
peak=   -3.256 closest distance to " N   GLY A 133 " =    1.796
peak=   -3.254 closest distance to " NH2AARG A 275 " =    5.239
peak=   -3.251 closest distance to " CA  GLY A 203 " =    2.100
peak=   -3.250 closest distance to " O   HOH Z 426 " =    1.649
peak=   -3.247 closest distance to " CA  VAL A 232 " =    2.404
peak=   -3.246 closest distance to " OD1 ASN A 249 " =    1.062
peak=   -3.246 closest distance to " O   HOH Z 298 " =    2.708
peak=   -3.242 closest distance to " O   SER A 146 " =    0.864
peak=   -3.241 closest distance to " O   HOH Z 409 " =    4.773
peak=   -3.241 closest distance to " CZ3 TRP A 274 " =    1.120
peak=   -3.240 closest distance to " C   SER A 206 " =    1.665
peak=   -3.239 closest distance to " O   HOH Z  42 " =    0.768
peak=   -3.238 closest distance to " CA  VAL A 197 " =    0.962
peak=   -3.237 closest distance to " O   HOH Z 252 " =    4.236
peak=   -3.235 closest distance to " O   HOH Z 118 " =    2.989
peak=   -3.232 closest distance to " O   HOH Z  91 " =    2.177
peak=   -3.230 closest distance to " N   MET A 188 " =    1.913
peak=   -3.229 closest distance to " CE3 TRP A 150 " =    1.941
peak=   -3.227 closest distance to " O   HOH Z 140 " =    0.831
peak=   -3.223 closest distance to " O   ALA A 256 " =    1.508
peak=   -3.213 closest distance to " OH  TYR A 169 " =    0.978
peak=   -3.210 closest distance to " O   ASP A 191 " =    1.360
peak=   -3.207 closest distance to " O   HOH Z  76 " =    2.066
peak=   -3.204 closest distance to " O   HOH Z 322 " =    1.090
peak=   -3.204 closest distance to " C   THR A 279 " =    1.149
peak=   -3.202 closest distance to " CB  ALA A 291 " =    2.112
peak=   -3.198 closest distance to " O   HOH Z 166 " =    1.626
peak=   -3.197 closest distance to " O   HOH Z 385 " =    3.815
peak=   -3.182 closest distance to " CD  GLN A  58 " =    1.310
peak=   -3.168 closest distance to " O   HOH Z 385 " =    2.093
peak=   -3.168 closest distance to " O   LEU A 167 " =    1.567
peak=   -3.160 closest distance to " CD  ARG A 139 " =    1.622
peak=   -3.158 closest distance to " O   ARG A 275 " =    2.216
peak=   -3.157 closest distance to " CG1 VAL A 153 " =    2.141
peak=   -3.157 closest distance to " CG  PRO A 163 " =    2.386
peak=   -3.154 closest distance to " CA  ASP A 298 " =    1.121
peak=   -3.151 closest distance to " CD2 LEU A 237 " =    2.428
peak=   -3.147 closest distance to " O   PRO A 198 " =    1.309
peak=   -3.142 closest distance to " O   HOH Z  97 " =    1.826
peak=   -3.141 closest distance to " CH2 TRP A 177 " =    2.036
peak=   -3.140 closest distance to " O   VAL A 125 " =    2.033
peak=   -3.140 closest distance to " O   HOH Z 163 " =    4.862
peak=   -3.135 closest distance to " O   HOH Z 132 " =    1.088
peak=   -3.134 closest distance to " O   HOH Z 148 " =    3.523
peak=   -3.132 closest distance to " CB  ASP A 286 " =    2.256
peak=   -3.120 closest distance to " O   HOH Z 264 " =    1.862
peak=   -3.118 closest distance to " O   HOH Z 414 " =    1.381
peak=   -3.112 closest distance to " ND2 ASN A  60 " =    1.623
peak=   -3.108 closest distance to " CB  SER A 258 " =    1.999
peak=   -3.107 closest distance to " CG  GLU A 277 " =    1.113
peak=   -3.107 closest distance to " CD  GLU A 236 " =    1.106
peak=   -3.103 closest distance to " O   HOH Z 424 " =    2.913
peak=   -3.091 closest distance to " N   GLY A 262 " =    2.065
peak=   -3.084 closest distance to " O   GLN A 194 " =    1.270
peak=   -3.077 closest distance to " O   HOH Z 437 " =    1.766
peak=   -3.072 closest distance to " CB  PHE A 283 " =    2.831
peak=   -3.069 closest distance to " N   LEU A 261 " =    1.356
peak=   -3.056 closest distance to " CB  THR A  82 " =    2.143
peak=   -3.048 closest distance to " O   HOH Z 417 " =    2.681
peak=   -3.038 closest distance to " O   ALA A 160 " =    1.471
peak=   -3.035 closest distance to " O   HOH Z  20 " =    1.353
peak=   -3.033 closest distance to " CE2 TRP A 274 " =    0.979

================= 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    :  0.4478 0.4445   6.256111e+00   6.251183e+00
   1_bss:  0.4390 0.4357   6.250112e+00   6.237571e+00
   1_xyz:  0.3196 0.3527   6.015804e+00   6.091199e+00
   1_adp:  0.2909 0.3616   5.965155e+00   6.109768e+00
   1_occ:  0.2906 0.3619   5.964076e+00   6.109146e+00
   2_bss:  0.2882 0.3593   5.961986e+00   6.107205e+00
   2_xyz:  0.2146 0.2700   5.709321e+00   5.900479e+00
   2_adp:  0.2001 0.2553   5.654486e+00   5.853202e+00
   2_occ:  0.1997 0.2555   5.654328e+00   5.853181e+00
   3_bss:  0.1996 0.2550   5.652644e+00   5.850196e+00
   3_xyz:  0.1641 0.2137   5.476923e+00   5.690449e+00
   3_adp:  0.1482 0.2017   5.394220e+00   5.617904e+00
   3_occ:  0.1482 0.2017   5.393995e+00   5.617610e+00
   4_bss:  0.1484 0.2022   5.396238e+00   5.619958e+00
   4_xyz:  0.1306 0.1809   5.283489e+00   5.519724e+00
   4_adp:  0.1258 0.1744   5.249465e+00   5.482173e+00
   4_occ:  0.1258 0.1745   5.249567e+00   5.482546e+00
   5_bss:  0.1257 0.1743   5.249342e+00   5.481989e+00
   5_xyz:  0.1181 0.1671   5.200979e+00   5.439650e+00
   5_adp:  0.1196 0.1631   5.197578e+00   5.420570e+00
   5_occ:  0.1194 0.1629   5.197121e+00   5.420569e+00
   5_bss:  0.1197 0.1627   5.199856e+00   5.422354e+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  -1.994   1.963   2.123   0.000   0.000   0.000
   1_xyz:  0.300  50.000  -1.994   1.963   2.123   0.000   0.000   0.000
   1_adp:  0.300  50.000  -1.994   1.963   2.123   0.000   0.000   0.000
   1_occ:  0.300  50.000  -1.994   1.963   2.123   0.000   0.000   0.000
   2_bss:  0.327  62.538  -1.990   0.038  -0.090   0.000  -0.000  -0.000
   2_xyz:  0.327  62.538  -1.990   0.038  -0.090   0.000  -0.000  -0.000
   2_adp:  0.327  62.538  -1.990   0.038  -0.090   0.000  -0.000  -0.000
   2_occ:  0.327  62.538  -1.990   0.038  -0.090   0.000  -0.000  -0.000
   3_bss:  0.321  54.724  -2.072  -0.767  -1.242  -0.000  -0.000  -0.000
   3_xyz:  0.321  54.724  -2.072  -0.767  -1.242  -0.000  -0.000  -0.000
   3_adp:  0.321  54.724  -2.072  -0.767  -1.242  -0.000  -0.000  -0.000
   3_occ:  0.321  54.724  -2.072  -0.767  -1.242  -0.000  -0.000  -0.000
   4_bss:  0.322  60.434  -2.265  -1.501  -1.802  -0.000  -0.000  -0.000
   4_xyz:  0.322  60.434  -2.265  -1.501  -1.802  -0.000  -0.000  -0.000
   4_adp:  0.322  60.434  -2.265  -1.501  -1.802  -0.000  -0.000  -0.000
   4_occ:  0.322  60.434  -2.265  -1.501  -1.802  -0.000  -0.000  -0.000
   5_bss:  0.321  55.543  -2.265  -1.501  -1.802  -0.000  -0.000  -0.000
   5_xyz:  0.321  55.543  -2.265  -1.501  -1.802  -0.000  -0.000  -0.000
   5_adp:  0.321  55.543  -2.265  -1.501  -1.802  -0.000  -0.000  -0.000
   5_occ:  0.321  55.543  -2.265  -1.501  -1.802  -0.000  -0.000  -0.000
   5_bss:  0.318  49.470  -2.294  -1.707  -1.918  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.611 0.4484  0.5984    63411.386
   1_bss:  54.219 0.4642  0.6358    59684.727
   1_xyz:  38.118 0.6648  0.8899    34567.990
   1_adp:  39.399 0.6486  0.8798    36389.519
   1_occ:  39.346 0.6492  0.8796    36284.607
   2_bss:  39.059 0.6526  0.8447    35963.619
   2_xyz:  28.454 0.7732  0.9616    20027.278
   2_adp:  26.279 0.7976  0.9759    17845.153
   2_occ:  26.310 0.7972  0.9752    17883.571
   3_bss:  26.180 0.7985  0.9529    17709.692
   3_xyz:  21.221 0.8488  0.9856    12054.726
   3_adp:  19.354 0.8674  0.9845    10447.346
   3_occ:  19.349 0.8674  0.9845    10440.353
   4_bss:  19.384 0.8672  0.9674    10518.218
   4_xyz:  17.141 0.8876  0.9791     8463.838
   4_adp:  16.200 0.8963  0.9779     7837.869
   4_occ:  16.206 0.8963  0.9778     7844.121
   5_bss:  16.200 0.8963  0.9777     7827.884
   5_xyz:  15.273 0.9042  0.9800     7098.123
   5_adp:  14.788 0.9086  0.9778     6883.268
   5_occ:  14.786 0.9087  0.9777     6887.104
   5_bss:  14.830 0.9084  0.9702     6947.577
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.8840e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.8840e-01
   1_xyz:   1.541  0.012  0.092 15.988  0.006  4.117   1.3188e-01
   1_adp:   1.541  0.012  0.092 15.988  0.006  4.117   1.3188e-01
   1_occ:   1.541  0.012  0.092 15.988  0.006  4.117   1.3188e-01
   2_bss:   1.541  0.012  0.092 15.988  0.006  4.117   1.3188e-01
   2_xyz:   1.210  0.008  0.081 14.421  0.005  4.112   7.5999e-02
   2_adp:   1.210  0.008  0.081 14.421  0.005  4.112   7.5999e-02
   2_occ:   1.210  0.008  0.081 14.421  0.005  4.112   7.5999e-02
   3_bss:   1.210  0.008  0.081 14.421  0.005  4.112   7.5999e-02
   3_xyz:   0.918  0.006  0.063 14.241  0.004  4.119   5.3092e-02
   3_adp:   0.918  0.006  0.063 14.241  0.004  4.119   5.3092e-02
   3_occ:   0.918  0.006  0.063 14.241  0.004  4.119   5.3092e-02
   4_bss:   0.918  0.006  0.063 14.241  0.004  4.119   5.3092e-02
   4_xyz:   0.979  0.006  0.070 14.253  0.004  4.124   5.5350e-02
   4_adp:   0.979  0.006  0.070 14.253  0.004  4.124   5.5350e-02
   4_occ:   0.979  0.006  0.070 14.253  0.004  4.124   5.5350e-02
   5_bss:   0.979  0.006  0.070 14.253  0.004  4.124   5.5350e-02
   5_xyz:   1.009  0.007  0.073 14.438  0.004  4.114   5.8086e-02
   5_adp:   1.009  0.007  0.073 14.438  0.004  4.114   5.8086e-02
   5_occ:   1.009  0.007  0.073 14.438  0.004  4.114   5.8086e-02
   5_bss:   1.009  0.007  0.073 14.438  0.004  4.114   5.8086e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.465   2.4198e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.465   2.4198e-01
   1_xyz:   8.907  0.107  0.401 88.234  0.026  1.959   1.5711e-01
   1_adp:   8.907  0.107  0.401 88.234  0.026  1.959   1.5711e-01
   1_occ:   8.907  0.107  0.401 88.234  0.026  1.959   1.5711e-01
   2_bss:   8.907  0.107  0.401 88.234  0.026  1.959   1.5711e-01
   2_xyz:   7.735  0.049  0.241 85.940  0.054  2.236   8.3039e-02
   2_adp:   7.735  0.049  0.241 85.940  0.054  2.236   8.3039e-02
   2_occ:   7.735  0.049  0.241 85.940  0.054  2.236   8.3039e-02
   3_bss:   7.735  0.049  0.241 85.940  0.054  2.236   8.3039e-02
   3_xyz:   7.610  0.055  0.240 88.102  0.033  2.343   4.0024e-02
   3_adp:   7.610  0.055  0.240 88.102  0.033  2.343   4.0024e-02
   3_occ:   7.610  0.055  0.240 88.102  0.033  2.343   4.0024e-02
   4_bss:   7.610  0.055  0.240 88.102  0.033  2.343   4.0024e-02
   4_xyz:   6.900  0.035  0.225 80.329  0.032  2.344   4.0519e-02
   4_adp:   6.900  0.035  0.225 80.329  0.032  2.344   4.0519e-02
   4_occ:   6.900  0.035  0.225 80.329  0.032  2.344   4.0519e-02
   5_bss:   6.900  0.035  0.225 80.329  0.032  2.344   4.0519e-02
   5_xyz:   7.610  0.041  0.227 83.168  0.031  2.290   4.3295e-02
   5_adp:   7.610  0.041  0.227 83.168  0.031  2.290   4.3295e-02
   5_occ:   7.610  0.041  0.227 83.168  0.031  2.290   4.3295e-02
   5_bss:   7.610  0.041  0.227 83.168  0.031  2.290   4.3295e-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: 104.26   0.00  18.82 104.26   0.00  14.66 100.88   3.12  41.50
   1_occ: 104.26   0.00  18.82 104.26   0.00  14.66 100.88   3.12  41.50
   2_bss: 104.26   0.00  18.82 104.26   0.00  14.66 100.88   3.12  41.50
   2_xyz: 104.26   0.00  18.82 104.26   0.00  14.66 100.88   3.12  41.50
   2_adp: 205.36   0.00  18.74 205.36   0.00  14.46 100.24   4.75  42.04
   2_occ: 205.36   0.00  18.74 205.36   0.00  14.46 100.24   4.75  42.04
   3_bss: 205.36   0.00  18.74 205.36   0.00  14.46 100.24   4.75  42.04
   3_xyz: 205.36   0.00  18.74 205.36   0.00  14.46 100.24   4.75  42.04
   3_adp: 127.81   0.00  19.10 127.81   0.00  13.92 102.08   5.63  47.27
   3_occ: 127.81   0.00  19.10 127.81   0.00  13.92 102.08   5.63  47.27
   4_bss: 127.81   0.00  19.10 127.81   0.00  13.92 102.08   5.63  47.27
   4_xyz: 127.81   0.00  19.10 127.81   0.00  13.92 102.08   5.63  47.27
   4_adp: 117.43   1.21  18.42 117.43   1.21  13.44  98.30   5.14  45.48
   4_occ: 117.43   1.21  18.42 117.43   1.21  13.44  98.30   5.14  45.48
   5_bss: 117.43   1.21  18.42 117.43   1.21  13.44  98.30   5.14  45.48
   5_xyz: 117.43   1.21  18.42 117.43   1.21  13.44  98.30   5.14  45.48
   5_adp: 101.42   2.76  16.95 101.42   2.76  12.88  86.65   5.24  39.09
   5_occ: 101.42   2.76  16.95 101.42   2.76  12.88  86.65   5.24  39.09
   5_bss: 101.32   2.66  16.85 101.32   2.66  12.78  86.55   5.14  38.99
------------------------------------------------------------------------
 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:    1.987    0.034    0.409
   1_adp:    1.987    0.034    0.409
   1_occ:    1.987    0.034    0.409
   2_bss:    1.987    0.034    0.409
   2_xyz:    1.595    0.043    0.550
   2_adp:    1.595    0.043    0.550
   2_occ:    1.595    0.043    0.550
   3_bss:    1.595    0.043    0.550
   3_xyz:    1.617    0.017    0.648
   3_adp:    1.617    0.017    0.648
   3_occ:    1.617    0.017    0.648
   4_bss:    1.617    0.017    0.648
   4_xyz:    1.665    0.043    0.691
   4_adp:    1.665    0.043    0.691
   4_occ:    1.665    0.043    0.691
   5_bss:    1.665    0.043    0.691
   5_xyz:    1.773    0.074    0.715
   5_adp:    1.773    0.074    0.715
   5_occ:    1.773    0.074    0.715
   5_bss:    1.773    0.074    0.715
------------------------------------------------------------------------

CPU time actual refinement: 353.92


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_935/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_935/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_935/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_935/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_935/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 353.78 
  Macro-tasks:
    bulk solvent and scale       = 37.26  
    individual site refinement   = 148.33 
    weights calculation          = 29.51  
    collect and process          = 5.98   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 221.18 
  Micro-tasks:
    mask                            = 2.63   
    f_calc                          = 119.71 
    alpha_beta                      = 8.10   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 126.22 
    fmodel                         = 6.36   
    r_factors                      = 0.22   
    phase_errors                   = 10.40  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 275.03 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.057 micro seconds
Total CPU time: 6.13 minutes
from_scatterers_fft:    637 calls, 119.40 s
gradients_fft:          582 calls, 113.34 s

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

# Date 2008-01-16 Time 06:01:15 PST -0800 (1200492075.25 s)
Start R-work = 0.4478, R-free = 0.4445 (no bulk solvent and anisotropic scale)
Final R-work = 0.1427, R-free = 0.1839 (no bulk solvent and anisotropic scale)

Start R-work = 0.4390, R-free = 0.4357
Final R-work = 0.1197, R-free = 0.1627