# Date 2008-01-16 Time 05:23:56 PST -0800 (1200489836.38 s)
#phil __OFF__

Command line arguments: "../716.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 20498
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 716

-------------------------------------------------------------------------------
  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: (70.25, 48.1033, 84.6622, 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: 3.25, per 1000 atoms: 1.15


================================== 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: (70.25, 48.1033, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9947 1.96156
Completeness in resolution range: 0.926807
Completeness with d_max=infinity: 0.924053

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9947
                             d_min =   1.9616

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: (70.25, 48.1033, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9947 1.96156
Completeness in resolution range: 0.926807
Completeness with d_max=infinity: 0.924053

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9952 -  4.1980 [2221/2250]  1998   223  10.0%
  bin  2:  4.1980 -  3.3443 [2122/2145]  1912   210   9.9%
  bin  3:  3.3443 -  2.9251 [2090/2115]  1880   210  10.0%
  bin  4:  2.9251 -  2.6593 [2082/2108]  1877   205   9.8%
  bin  5:  2.6593 -  2.4696 [2092/2126]  1882   210  10.0%
  bin  6:  2.4696 -  2.3245 [2043/2071]  1844   199   9.7%
  bin  7:  2.3245 -  2.2085 [2040/2076]  1832   208  10.2%
  bin  8:  2.2085 -  2.1126 [2042/2084]  1832   210  10.3%
  bin  9:  2.1126 -  2.0315 [1993/2074]  1795   198   9.9%
  bin 10:  2.0315 -  1.9616 [ 864/2087]   778    86  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_716/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:
        1.44 -     2.13: 14
        2.13 -     2.83: 935
        2.83 -     3.52: 4406
        3.52 -     4.21: 9327
        4.21 -     4.90: 13637
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.443 3.040 -x+1/2,-y+1,z-1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.475 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.500 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.595 3.040 -x+1/2,-y+1,z+1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.713 3.120 -x+1/2,-y+1,z-1/2
  ... (remaining 28314 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_716/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_716/model_refine_001.geo

CPU time processing inputs: 9.16


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 48.10325 84.6622 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: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4621   r_free= 0.4504   ksol= 0.00   Bsol= 0.00   scale= 0.892    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.278378                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9952 -  4.6826 0.99   1443  163 0.3770 0.3948      6.5744      6.5944|
|  2:  4.6826 -  3.7357 0.99   1383  148 0.4069 0.4100      6.8317      6.7881|
|  3:  3.7357 -  3.2690 0.99   1358  152 0.4353 0.4032      6.6637      6.6975|
|  4:  3.2690 -  2.9727 0.98   1339  152 0.4457 0.4284      6.5016       6.455|
|  5:  2.9727 -  2.7610 0.99   1352  150 0.4812 0.4464      6.3658      6.3118|
|  6:  2.7610 -  2.5991 0.99   1331  149 0.5029 0.4371      6.2703      6.1421|
|  7:  2.5991 -  2.4696 0.98   1343  144 0.4862 0.4332      6.2375      6.1898|
|  8:  2.4696 -  2.3625 0.98   1305  147 0.5031 0.5493      6.1378      6.1956|
|  9:  2.3625 -  2.2719 0.99   1328  139 0.5379 0.5000      6.1464      6.1066|
| 10:  2.2719 -  2.1937 0.99   1315  153 0.4855 0.5159      6.0782      6.1116|
| 11:  2.1937 -  2.1253 0.97   1295  141 0.5147 0.5233      6.0183       6.019|
| 12:  2.1253 -  2.0647 0.98   1307  152 0.4873 0.5111      5.9253      5.9731|
| 13:  2.0647 -  2.0105 0.87   1150  131 0.5125 0.4632       5.865      5.8415|
| 14:  2.0105 -  1.9616 0.28    381   38 0.5477 0.4724      5.8287      5.6681|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9952 -  4.6826  1443   163  0.67  37.09   0.82     0.70      81757.89|
|  2:  4.6826 -  3.7357  1383   148  0.70  35.55   0.90     0.79     104641.03|
|  3:  3.7357 -  3.2690  1358   152  0.61  42.88   0.91     0.79     107098.68|
|  4:  3.2690 -  2.9727  1339   152  0.55  47.83   0.91     0.75      90437.26|
|  5:  2.9727 -  2.7610  1352   150  0.50  52.00   0.88     0.70      72087.08|
|  6:  2.7610 -  2.5991  1331   149  0.47  54.32   0.89     0.66      60413.54|
|  7:  2.5991 -  2.4696  1343   144  0.46  55.22   0.92     0.62      56439.96|
|  8:  2.4696 -  2.3625  1305   147  0.39  61.06   0.89     0.57      56564.21|
|  9:  2.3625 -  2.2719  1328   139  0.36  62.82   0.91     0.54      53080.96|
| 10:  2.2719 -  2.1937  1315   153  0.35  64.11   0.96     0.51      50884.60|
| 11:  2.1937 -  2.1253  1295   141  0.33  65.61   0.92     0.49      46658.77|
| 12:  2.1253 -  2.0647  1307   152  0.30  67.60   0.96     0.48      44280.18|
| 13:  2.0647 -  2.0105  1150   131  0.33  65.65   0.94     0.51      36019.95|
| 14:  2.0105 -  1.9616   381    38  0.39  60.66   0.90     0.59      27882.89|
|alpha:            min =        0.48 max =            0.79 mean =         0.63|
|beta:             min =    27882.89 max =       107098.68 mean =     66050.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.46|
|phase err.(work): min =        0.00 max =           90.00 mean =        54.51|
|phase err.(test): min =        0.00 max =           89.94 mean =        54.59|
|-----------------------------------------------------------------------------|

============================== 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 = 11.226555             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.559   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.541997              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.028   (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 |  1.443 -  1.789:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.789 -  2.135:        7 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.135 -  2.480:       39 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.480 -  2.826:      896 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.826 -  3.172:     2020 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.172 -  3.517:     2386 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.517 -  3.863:     4611 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.863 -  4.209:     4716 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.209 -  4.554:     6181 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.554 -  4.900:     7456 |
|-----------------------------------------------------------------------------|
|-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 |        0.190 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.443 |       0.578 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.901)------------------------------------------|
|    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: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4621   r_free= 0.4504   ksol= 0.00   Bsol= 0.00   scale= 0.892    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.278378                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4509   r_free= 0.4370   ksol= 0.30   Bsol= 20.00   scale= 0.930   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.35,4.65,0.89,0.00,0.00,0.00); trace/3= 0.73                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.269627                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.693238              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.168   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.228524              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.882   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4509      final r-factor (work) = 0.3718          |
| start r-factor (free) = 0.4370      final r-factor (free) = 0.4029          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.5708 = 9.69 * 0.50 * 6.2685 + 1.00 * 0.1897                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.0144 = 9.69 * 0.50 * 6.1662 + 1.00 * 0.1292                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3718      final r-factor (work) = 0.3405          |
| start r-factor (free) = 0.4029      final r-factor (free) = 0.4154          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5813 = 1.23 * 1.00 * 6.1662 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5052 = 1.23 * 1.00 * 6.0935 + 1.00 * 0.0192                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.901)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.31  19.34    None  None   None       |
|    all(noH): 2823   0      0.00    100.31  19.34    None  None   None       |
|    Sol.    : 438    0      1.90    100.31  36.78    None  None   None       |
|    Mac.    : 2385   0      0.00    91.63   16.14    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.031:  868   |   5:    50.157 -  60.188:   96        |
|      1:    10.031 -  20.063:  909   |   6:    60.188 -  70.220:   41        |
|      2:    20.063 -  30.094:  512   |   7:    70.220 -  80.251:   12        |
|      3:    30.094 -  40.126:  255   |   8:    80.251 -  90.282:    6        |
|      4:    40.126 -  50.157:  120   |   9:    90.282 - 100.314:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3405 r_free = 0.4154             target_work(ml) = 6.100         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3404 r_free = 0.4158             target_work(ml) = 6.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3404   r_free= 0.4158   ksol= 0.30   Bsol= 20.00   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.35,4.65,0.89,0.00,0.00,0.00); trace/3= 0.73                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.099913                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3394   r_free= 0.4124   ksol= 0.31   Bsol= 50.00   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.84,2.72,-0.04,0.00,-0.00,-0.00); trace/3= 0.28                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.101015                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.137029             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.112  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.652791              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.100  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3394      final r-factor (work) = 0.2753          |
| start r-factor (free) = 0.4124      final r-factor (free) = 0.3425          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.0690 = 11.14 * 0.50 * 6.0949 + 1.00 * 0.1292                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.6453 = 11.14 * 0.50 * 6.0205 + 1.00 * 0.1202                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2753      final r-factor (work) = 0.2566          |
| start r-factor (free) = 0.3425      final r-factor (free) = 0.3277          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9494 = 0.65 * 1.00 * 6.0205 + 1.00 * 0.0193                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8605 = 0.65 * 1.00 * 5.8944 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.901)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.36  18.34    None  None   None       |
|    all(noH): 2823   0      0.00    100.36  18.34    None  None   None       |
|    Sol.    : 438    0      3.44    100.36  37.97    None  None   None       |
|    Mac.    : 2385   0      0.00    91.13   14.73    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 -  10.037: 1012   |   5:    50.182 -  60.219:   83        |
|      1:    10.037 -  20.073:  913   |   6:    60.219 -  70.255:   27        |
|      2:    20.073 -  30.109:  395   |   7:    70.255 -  80.292:   20        |
|      3:    30.109 -  40.146:  226   |   8:    80.292 -  90.328:    7        |
|      4:    40.146 -  50.182:  137   |   9:    90.328 - 100.365:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2566 r_free = 0.3277             target_work(ml) = 5.878         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2564 r_free = 0.3275             target_work(ml) = 5.877         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2564   r_free= 0.3275   ksol= 0.31   Bsol= 50.00   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.84,2.72,-0.04,0.00,-0.00,-0.00); trace/3= 0.28                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.877236                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2560   r_free= 0.3263   ksol= 0.32   Bsol= 52.85   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.38,1.53,-0.45,0.00,-0.00,-0.00); trace/3= -0.10                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.876403                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.184312              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.842   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.382874              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.041  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2560      final r-factor (work) = 0.2023          |
| start r-factor (free) = 0.3263      final r-factor (free) = 0.2598          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.3464 = 6.18 * 0.50 * 5.8943 + 1.00 * 0.1202                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.9747 = 6.18 * 0.50 * 5.7881 + 1.00 * 0.0769                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2023      final r-factor (work) = 0.1861          |
| start r-factor (free) = 0.2598      final r-factor (free) = 0.2368          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2289 = 0.38 * 1.00 * 5.7881 + 1.00 * 0.0128                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1621 = 0.38 * 1.00 * 5.6198 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.901)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.52   17.74    None  None   None       |
|    all(noH): 2823   0      0.00    94.52   17.74    None  None   None       |
|    Sol.    : 438    0      4.86    94.52   40.72    None  None   None       |
|    Mac.    : 2385   0      0.00    85.20   13.52    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.452: 1003   |   5:    47.261 -  56.713:  101        |
|      1:     9.452 -  18.904: 1020   |   6:    56.713 -  66.165:   53        |
|      2:    18.904 -  28.357:  305   |   7:    66.165 -  75.618:   21        |
|      3:    28.357 -  37.809:  161   |   8:    75.618 -  85.070:   17        |
|      4:    37.809 -  47.261:  139   |   9:    85.070 -  94.522:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1861 r_free = 0.2368             target_work(ml) = 5.581         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1858 r_free = 0.2364             target_work(ml) = 5.580         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1858   r_free= 0.2364   ksol= 0.32   Bsol= 52.85   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.38,1.53,-0.45,0.00,-0.00,-0.00); trace/3= -0.10                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.579986                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1857   r_free= 0.2350   ksol= 0.32   Bsol= 58.22   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,-0.01,-1.31,-0.00,-0.00,-0.00); trace/3= -1.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.578908                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.000063              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.676  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.508223              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.987  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1857      final r-factor (work) = 0.1437          |
| start r-factor (free) = 0.2350      final r-factor (free) = 0.1904          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.1400 = 5.00 * 0.50 * 5.6251 + 1.00 * 0.0769                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.7506 = 5.00 * 0.50 * 5.4695 + 1.00 * 0.0767                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1437      final r-factor (work) = 0.1320          |
| start r-factor (free) = 0.1904      final r-factor (free) = 0.1801          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7901 = 0.51 * 1.00 * 5.4695 + 1.00 * 0.0104                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7120 = 0.51 * 1.00 * 5.3151 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.901)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.07    96.53   17.61    None  None   None       |
|    all(noH): 2823   0      1.07    96.53   17.61    None  None   None       |
|    Sol.    : 438    0      3.28    96.53   43.23    None  None   None       |
|    Mac.    : 2385   0      1.07    92.50   12.90    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:     1.068 -  10.614: 1231   |   5:    48.797 -  58.342:  100        |
|      1:    10.614 -  20.159:  944   |   6:    58.342 -  67.888:   64        |
|      2:    20.159 -  29.705:  208   |   7:    67.888 -  77.434:   33        |
|      3:    29.705 -  39.251:  118   |   8:    77.434 -  86.980:   12        |
|      4:    39.251 -  48.797:  104   |   9:    86.980 -  96.525:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1320 r_free = 0.1801             target_work(ml) = 5.286         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1319 r_free = 0.1799             target_work(ml) = 5.285         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1319   r_free= 0.1799   ksol= 0.32   Bsol= 58.22   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,-0.01,-1.31,-0.00,-0.00,-0.00); trace/3= -1.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.285145                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1322   r_free= 0.1802   ksol= 0.33   Bsol= 59.52   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-0.78,-1.48,-0.00,-0.00,-0.00); trace/3= -1.51                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.288547                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.712956              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.568  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.240247              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.452  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1322      final r-factor (work) = 0.1227          |
| start r-factor (free) = 0.1802      final r-factor (free) = 0.1713          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2898 = 2.71 * 0.50 * 5.3175 + 1.00 * 0.0767                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1993 = 2.71 * 0.50 * 5.2600 + 1.00 * 0.0642                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1227      final r-factor (work) = 0.1215          |
| start r-factor (free) = 0.1713      final r-factor (free) = 0.1684          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2743 = 0.24 * 1.00 * 5.2600 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2647 = 0.24 * 1.00 * 5.2256 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.901)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.43    92.80   17.07    None  None   None       |
|    all(noH): 2823   0      1.43    92.80   17.07    None  None   None       |
|    Sol.    : 438    0      4.22    92.80   41.41    None  None   None       |
|    Mac.    : 2385   0      1.43    91.27   12.60    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:     1.431 -  10.569: 1232   |   5:    47.117 -  56.254:   87        |
|      1:    10.569 -  19.706:  960   |   6:    56.254 -  65.391:   60        |
|      2:    19.706 -  28.843:  205   |   7:    65.391 -  74.528:   30        |
|      3:    28.843 -  37.980:  120   |   8:    74.528 -  83.665:   12        |
|      4:    37.980 -  47.117:  106   |   9:    83.665 -  92.802:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1215 r_free = 0.1684             target_work(ml) = 5.219         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1214 r_free = 0.1683             target_work(ml) = 5.218         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1214   r_free= 0.1683   ksol= 0.33   Bsol= 59.52   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-0.78,-1.48,-0.00,-0.00,-0.00); trace/3= -1.51                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.218391                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9952 -  4.6826 0.99   1443  163 0.0993 0.1322      5.3909      5.5664|
|  2:  4.6826 -  3.7357 0.99   1383  148 0.0888 0.1155      5.4669      5.6834|
|  3:  3.7357 -  3.2690 0.99   1358  152 0.1140 0.1630      5.5354      5.8914|
|  4:  3.2690 -  2.9727 0.98   1339  152 0.1380 0.1694       5.532      5.6827|
|  5:  2.9727 -  2.7610 0.99   1352  150 0.1462 0.1967      5.4161      5.5854|
|  6:  2.7610 -  2.5991 0.99   1331  149 0.1406 0.2080      5.3075      5.5184|
|  7:  2.5991 -  2.4696 0.98   1343  144 0.1341 0.1822      5.2412       5.458|
|  8:  2.4696 -  2.3625 0.98   1305  147 0.1364 0.1900      5.1636      5.3856|
|  9:  2.3625 -  2.2719 0.99   1328  139 0.1249 0.1822      5.0782      5.3077|
| 10:  2.2719 -  2.1937 0.99   1315  153 0.1237 0.1803      5.0318      5.2816|
| 11:  2.1937 -  2.1253 0.97   1295  141 0.1219 0.1852      4.9671      5.2583|
| 12:  2.1253 -  2.0647 0.98   1307  152 0.1225 0.1864      4.9109      5.1605|
| 13:  2.0647 -  2.0105 0.87   1150  131 0.1220 0.1757      4.8319      5.0658|
| 14:  2.0105 -  1.9616 0.28    381   38 0.1218 0.1871      4.7336      4.9786|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9952 -  4.6826  1443   163  0.94   9.56   0.97     0.95       7427.56|
|  2:  4.6826 -  3.7357  1383   148  0.95   8.51   1.01     1.00       9785.47|
|  3:  3.7357 -  3.2690  1358   152  0.92  12.64   1.02     1.01      11841.74|
|  4:  3.2690 -  2.9727  1339   152  0.91  15.39   1.01     0.99      11915.21|
|  5:  2.9727 -  2.7610  1352   150  0.88  18.20   1.00     0.98      10179.33|
|  6:  2.7610 -  2.5991  1331   149  0.89  17.79   0.98     0.95       8403.75|
|  7:  2.5991 -  2.4696  1343   144  0.89  17.32   0.99     0.95       7422.21|
|  8:  2.4696 -  2.3625  1305   147  0.89  17.95   1.00     0.96       6588.86|
|  9:  2.3625 -  2.2719  1328   139  0.89  17.35   1.00     0.96       5634.96|
| 10:  2.2719 -  2.1937  1315   153  0.90  16.44   0.99     0.95       5035.18|
| 11:  2.1937 -  2.1253  1295   141  0.89  17.20   1.00     0.96       4602.88|
| 12:  2.1253 -  2.0647  1307   152  0.90  16.43   0.99     0.97       4198.61|
| 13:  2.0647 -  2.0105  1150   131  0.89  17.51   0.99     0.99       3649.36|
| 14:  2.0105 -  1.9616   381    38  0.89  17.19   0.97     0.93       2958.60|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2958.60 max =        11915.21 mean =      7412.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.51|
|phase err.(test): min =        0.00 max =           88.44 mean =        14.94|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1214   r_free= 0.1682   ksol= 0.32   Bsol= 56.15   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-0.89,-1.37,-0.00,-0.00,-0.00); trace/3= -1.48                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.218344                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1214   r_free= 0.1682   ksol= 0.32   Bsol= 56.15   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-0.89,-1.37,-0.00,-0.00,-0.00); trace/3= -1.48                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.218344                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9952 -  4.6826 0.99   1443  163 0.0992 0.1319      5.3896      5.5643|
|  2:  4.6826 -  3.7357 0.99   1383  148 0.0886 0.1153      5.4651      5.6812|
|  3:  3.7357 -  3.2690 0.99   1358  152 0.1140 0.1629      5.5345      5.8914|
|  4:  3.2690 -  2.9727 0.98   1339  152 0.1381 0.1693      5.5323      5.6824|
|  5:  2.9727 -  2.7610 0.99   1352  150 0.1462 0.1967      5.4162      5.5851|
|  6:  2.7610 -  2.5991 0.99   1331  149 0.1406 0.2078      5.3075      5.5183|
|  7:  2.5991 -  2.4696 0.98   1343  144 0.1342 0.1824      5.2414      5.4579|
|  8:  2.4696 -  2.3625 0.98   1305  147 0.1363 0.1900      5.1641      5.3871|
|  9:  2.3625 -  2.2719 0.99   1328  139 0.1247 0.1823      5.0785      5.3081|
| 10:  2.2719 -  2.1937 0.99   1315  153 0.1237 0.1804      5.0325      5.2829|
| 11:  2.1937 -  2.1253 0.97   1295  141 0.1218 0.1852      4.9672      5.2578|
| 12:  2.1253 -  2.0647 0.98   1307  152 0.1225 0.1868      4.9119      5.1625|
| 13:  2.0647 -  2.0105 0.87   1150  131 0.1218 0.1756      4.8322      5.0648|
| 14:  2.0105 -  1.9616 0.28    381   38 0.1220 0.1870       4.734      4.9782|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9952 -  4.6826  1443   163  0.94   9.54   0.97     0.95       7398.76|
|  2:  4.6826 -  3.7357  1383   148  0.95   8.49   1.01     1.00       9746.03|
|  3:  3.7357 -  3.2690  1358   152  0.92  12.61   1.02     1.01      11806.20|
|  4:  3.2690 -  2.9727  1339   152  0.91  15.38   1.01     0.99      11914.01|
|  5:  2.9727 -  2.7610  1352   150  0.88  18.18   1.00     0.98      10164.86|
|  6:  2.7610 -  2.5991  1331   149  0.89  17.77   0.98     0.95       8397.19|
|  7:  2.5991 -  2.4696  1343   144  0.89  17.31   0.99     0.95       7423.25|
|  8:  2.4696 -  2.3625  1305   147  0.89  17.97   1.00     0.96       6598.45|
|  9:  2.3625 -  2.2719  1328   139  0.89  17.37   1.00     0.96       5650.31|
| 10:  2.2719 -  2.1937  1315   153  0.90  16.46   0.99     0.95       5043.71|
| 11:  2.1937 -  2.1253  1295   141  0.89  17.20   0.99     0.96       4608.41|
| 12:  2.1253 -  2.0647  1307   152  0.90  16.46   0.99     0.97       4209.61|
| 13:  2.0647 -  2.0105  1150   131  0.89  17.52   0.99     0.99       3652.11|
| 14:  2.0105 -  1.9616   381    38  0.89  17.20   0.97     0.93       2953.56|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2953.56 max =        11914.01 mean =      7406.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        15.51|
|phase err.(test): min =        0.00 max =           88.45 mean =        14.94|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.901)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.38    92.75   17.02    None  None   None       |
|    all(noH): 2823   0      1.38    92.75   17.02    None  None   None       |
|    Sol.    : 438    0      4.17    92.75   41.36    None  None   None       |
|    Mac.    : 2385   0      1.38    91.22   12.55    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:     1.381 -  10.518: 1232   |   5:    47.066 -  56.203:   87        |
|      1:    10.518 -  19.655:  960   |   6:    56.203 -  65.340:   60        |
|      2:    19.655 -  28.792:  205   |   7:    65.340 -  74.477:   30        |
|      3:    28.792 -  37.929:  120   |   8:    74.477 -  83.615:   12        |
|      4:    37.929 -  47.066:  106   |   9:    83.615 -  92.752:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 341         
Filter by distance & map next to the model:
   mapped sites are within: 0.714 - 5.545
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 340 from: 341
   mapped sites are within: 0.714 - 5.545

peak=    5.651 closest distance to " O   HOH Z 210 " =    1.487
peak=    5.502 closest distance to " CB  SER A  63 " =    1.202
peak=    5.358 closest distance to " NH2 ARG A  56 " =    2.456
peak=    5.312 closest distance to " O   HOH Z 142 " =    1.669
peak=    5.118 closest distance to " C   PRO A 198 " =    1.602
peak=    5.063 closest distance to " O   HOH Z  15 " =    2.173
peak=    5.062 closest distance to " CG  PRO A  54 " =    1.213
peak=    4.972 closest distance to " O   HOH Z 120 " =    1.053
peak=    4.938 closest distance to " O   HOH Z 134 " =    2.094
peak=    4.849 closest distance to " CB  GLN A 223 " =    1.399
peak=    4.837 closest distance to " O   HOH Z 433 " =    1.790
peak=    4.835 closest distance to " O   HOH Z 422 " =    0.962
peak=    4.790 closest distance to " O   HOH Z 132 " =    1.441
peak=    4.757 closest distance to " CA  TYR A  30 " =    0.982
peak=    4.662 closest distance to " O   HOH Z  80 " =    2.001
peak=    4.639 closest distance to " O   HOH Z 133 " =    1.896
peak=    4.609 closest distance to " O   HOH Z 209 " =    2.426
peak=    4.603 closest distance to " O   HOH Z 126 " =    1.814
peak=    4.590 closest distance to " O   HOH Z 124 " =    1.470
peak=    4.531 closest distance to " O   HOH Z  97 " =    1.922
peak=    4.503 closest distance to " CG  PRO A 198 " =    1.262
peak=    4.492 closest distance to " CB  ARG A 275 " =    0.871
peak=    4.487 closest distance to " CG  PRO A 213 " =    1.280
peak=    4.468 closest distance to " CG  PRO A 280 " =    0.714
peak=    4.462 closest distance to " O   HOH Z 247 " =    1.441
peak=    4.451 closest distance to " O   HOH Z 352 " =    1.291
peak=    4.435 closest distance to " O   HOH Z 196 " =    1.780
peak=    4.428 closest distance to " CB  PRO A  54 " =    0.787
peak=    4.418 closest distance to " CG  PRO A  90 " =    1.217
peak=    4.335 closest distance to " O   HOH Z 389 " =    2.023
peak=    4.311 closest distance to " O   HOH Z 357 " =    2.053
peak=    4.308 closest distance to " O   HOH Z 234 " =    3.745
peak=    4.305 closest distance to " O   HOH Z  49 " =    1.268
peak=    4.303 closest distance to " O   HOH Z 272 " =    1.213
peak=    4.254 closest distance to " CB  GLN A 183 " =    1.335
peak=    4.248 closest distance to " O   HOH Z 189 " =    2.027
peak=    4.224 closest distance to " CB  SER A   3 " =    1.346
peak=    4.185 closest distance to " CB  ARG A  79 " =    1.324
peak=    4.181 closest distance to " O   HOH Z  61 " =    1.574
peak=    4.181 closest distance to " CB  TRP A 179 " =    1.207
peak=    4.152 closest distance to " O   HOH Z  44 " =    1.833
peak=    4.135 closest distance to " O   HOH Z  40 " =    1.995
peak=    4.128 closest distance to " O   HOH Z 271 " =    1.296
peak=    4.117 closest distance to " O   HOH Z 250 " =    2.393
peak=    4.110 closest distance to " CB  SER A 141 " =    1.038
peak=    4.084 closest distance to " O   HOH Z 428 " =    1.226
peak=    4.079 closest distance to " OE1 GLN A  11 " =    1.967
peak=    4.078 closest distance to " O   HOH Z 402 " =    1.625
peak=    4.071 closest distance to " O   HOH Z 203 " =    1.735
peak=    4.050 closest distance to " O   HOH Z 130 " =    2.743
peak=    4.023 closest distance to " O   HOH Z  67 " =    1.931
peak=    4.018 closest distance to " CB  ARG A 190 " =    1.720
peak=    4.001 closest distance to " O   HOH Z 412 " =    3.103
peak=    4.000 closest distance to " O   HOH Z  43 " =    1.743
peak=    3.999 closest distance to " O   SER A  87 " =    2.233
peak=    3.999 closest distance to " O   HOH Z 102 " =    1.297
peak=    3.997 closest distance to " N   ASN A  39 " =    1.274
peak=    3.959 closest distance to " O   HOH Z  63 " =    2.144
peak=    3.958 closest distance to " O   HOH Z 132 " =    2.354
peak=    3.948 closest distance to " O   HOH Z 406 " =    1.518
peak=    3.941 closest distance to " CG  GLN A  77 " =    0.866
peak=    3.940 closest distance to " O   HOH Z  48 " =    1.561
peak=    3.939 closest distance to " CB  SER A  62 " =    0.905
peak=    3.929 closest distance to " O   HOH Z 298 " =    1.985
peak=    3.929 closest distance to " CB  GLU A 128 " =    1.133
peak=    3.915 closest distance to " O   HOH Z 362 " =    3.464
peak=    3.914 closest distance to " O   HOH Z 374 " =    2.526
peak=    3.902 closest distance to " O   HOH Z 163 " =    1.590
peak=    3.892 closest distance to " O   HOH Z  20 " =    1.729
peak=    3.886 closest distance to " O   HOH Z 193 " =    1.762
peak=    3.884 closest distance to " CG1 ILE A  33 " =    1.281
peak=    3.880 closest distance to " CB  LEU A 228 " =    1.191
peak=    3.866 closest distance to " O   HOH Z 245 " =    1.347
peak=    3.863 closest distance to " O   HOH Z 271 " =    2.276
peak=    3.861 closest distance to " O   HOH Z 369 " =    2.188
peak=    3.859 closest distance to " NE2 GLN A  11 " =    1.055
peak=    3.850 closest distance to " NH2BARG A 145 " =    1.974
peak=    3.849 closest distance to " CH2 TRP A 274 " =    1.953
peak=    3.841 closest distance to " C   SER A  32 " =    1.106
peak=    3.833 closest distance to " O   HOH Z 394 " =    1.659
peak=    3.830 closest distance to " O   HOH Z 265 " =    2.247
peak=    3.820 closest distance to " CB  TYR A 169 " =    0.833
peak=    3.818 closest distance to " NH2 ARG A 156 " =    1.236
peak=    3.803 closest distance to " O   HOH Z 142 " =    1.550
peak=    3.799 closest distance to " CE  LYS A 119 " =    1.109
peak=    3.799 closest distance to " O   HOH Z 437 " =    1.867
peak=    3.798 closest distance to " CD1 LEU A 300 " =    1.270
peak=    3.787 closest distance to " OG  SER A  62 " =    3.113
peak=    3.783 closest distance to " O   HOH Z   7 " =    0.963
peak=    3.783 closest distance to " CA  ASN A 176 " =    1.521
peak=    3.781 closest distance to " NZ  LYS A 117 " =    3.155
peak=    3.779 closest distance to " O   HOH Z 326 " =    1.492
peak=    3.774 closest distance to " O   GLY A  91 " =    1.203
peak=    3.769 closest distance to " O   HOH Z  39 " =    1.897
peak=    3.769 closest distance to " CG2BVAL A  41 " =    0.936
peak=    3.765 closest distance to " O   GLY A  23 " =    2.380
peak=    3.760 closest distance to " O   HOH Z 118 " =    1.578
peak=    3.757 closest distance to " CD  PRO A  54 " =    1.086
peak=    3.752 closest distance to " O   HOH Z 346 " =    1.549
peak=    3.749 closest distance to " O   HOH Z 141 " =    1.759
peak=    3.743 closest distance to " CB  GLU A 152 " =    1.119
peak=    3.741 closest distance to " CB  GLN A  58 " =    0.901
peak=    3.735 closest distance to " CG2 VAL A 197 " =    1.209
peak=    3.733 closest distance to " CB  GLU A 277 " =    3.663
peak=    3.728 closest distance to " O   HOH Z 403 " =    1.781
peak=    3.725 closest distance to " CB  ALA A 100 " =    1.413
peak=    3.721 closest distance to " CD  LYS A 166 " =    1.472
peak=    3.721 closest distance to " OE1 GLU A   2 " =    2.067
peak=    3.715 closest distance to " O   HOH Z 395 " =    1.509
peak=    3.711 closest distance to " CA  ASP A 191 " =    0.870
peak=    3.709 closest distance to " CG  ARG A  66 " =    0.903
peak=    3.703 closest distance to " CB  VAL A 202 " =    1.496
peak=    3.698 closest distance to " O   HOH Z 128 " =    2.246
peak=    3.691 closest distance to " O   HOH Z  35 " =    2.232
peak=    3.687 closest distance to " O   HOH Z 133 " =    1.867
peak=    3.681 closest distance to " CG2 THR A 221 " =    1.099
peak=    3.679 closest distance to " O   HOH Z 435 " =    1.846
peak=    3.679 closest distance to " CB  ASN A 148 " =    1.277
peak=    3.678 closest distance to " O   HOH Z 423 " =    1.941
peak=    3.678 closest distance to " O   HOH Z 334 " =    1.592
peak=    3.673 closest distance to " O   HOH Z 408 " =    1.889
peak=    3.671 closest distance to " CA  GLU A 152 " =    0.913
peak=    3.671 closest distance to " O   HOH Z  47 " =    1.420
peak=    3.663 closest distance to " O   HOH Z  30 " =    1.698
peak=    3.654 closest distance to " CB  PRO A  54 " =    1.309
peak=    3.651 closest distance to " O   HOH Z  66 " =    2.254
peak=    3.650 closest distance to " ND2 ASN A 187 " =    1.549
peak=    3.647 closest distance to " O   HOH Z 431 " =    1.328
peak=    3.633 closest distance to " OD2 ASP A 286 " =    2.831
peak=    3.631 closest distance to " CA  ALA A  21 " =    1.371
peak=    3.621 closest distance to " O   HOH Z 339 " =    1.315
peak=    3.615 closest distance to " O   HOH Z 255 " =    1.771
peak=    3.614 closest distance to " CB  ARG A 139 " =    0.957
peak=    3.614 closest distance to " CB  ASN A 285 " =    0.864
peak=    3.613 closest distance to " CD  LYS A 119 " =    1.725
peak=    3.601 closest distance to " CD  ARG A 159 " =    0.849
peak=    3.599 closest distance to " O   HOH Z 279 " =    2.050
peak=    3.594 closest distance to " O   HOH Z 336 " =    1.606
peak=    3.593 closest distance to " OG1 THR A 294 " =    2.467
peak=    3.588 closest distance to " O   HOH Z 404 " =    1.579
peak=    3.585 closest distance to " NZ  LYS A 119 " =    1.534
peak=    3.573 closest distance to " CD2 LEU A 297 " =    0.879
peak=    3.573 closest distance to " O   HOH Z  11 " =    1.374
peak=    3.559 closest distance to " CB  PHE A 283 " =    0.911
peak=    3.557 closest distance to " O   HOH Z  88 " =    3.245
peak=    3.554 closest distance to " O   HOH Z 195 " =    1.227
peak=    3.545 closest distance to " OD1 ASN A  69 " =    2.400
peak=    3.545 closest distance to " CB  GLN A 194 " =    0.892
peak=    3.544 closest distance to " O   HOH Z 345 " =    1.751
peak=    3.541 closest distance to " CG2 THR A 220 " =    0.802
peak=    3.534 closest distance to " O   THR A 251 " =    1.334
peak=    3.523 closest distance to " O   HOH Z 438 " =    2.510
peak=    3.523 closest distance to " O   HOH Z 345 " =    2.731
peak=    3.519 closest distance to " CD2 LEU A 255 " =    1.085
peak=    3.515 closest distance to " O   HOH Z 250 " =    1.496
peak=    3.510 closest distance to " NH2AARG A 145 " =    2.176
peak=    3.509 closest distance to " N   SER A 164 " =    1.041
peak=    3.501 closest distance to " O   SER A  26 " =    1.701
peak=    3.498 closest distance to " O   HOH Z 386 " =    2.276
peak=    3.489 closest distance to " CA  ARG A  36 " =    1.056
peak=    3.482 closest distance to " CA  VAL A  41 " =    0.788
peak=    3.477 closest distance to " O   HOH Z 208 " =    1.697
peak=    3.474 closest distance to " O   HOH Z 371 " =    3.359
peak=    3.469 closest distance to " O   HOH Z 344 " =    2.886
peak=    3.468 closest distance to " O   HOH Z 316 " =    3.012
peak=    3.468 closest distance to " CA  ALA A 158 " =    1.156
peak=    3.467 closest distance to " CG AARG A 275 " =    1.386
peak=    3.462 closest distance to " O   HOH Z  59 " =    2.365
peak=    3.461 closest distance to " CD  ARG A 269 " =    0.980
peak=    3.460 closest distance to " CB  TRP A 179 " =    1.750
peak=    3.457 closest distance to " CB  ALA A  71 " =    1.282
peak=    3.456 closest distance to " CG1 ILE A 120 " =    1.075
peak=    3.455 closest distance to " O   HOH Z 368 " =    2.124
peak=    3.454 closest distance to " O   HOH Z 166 " =    1.590
peak=    3.453 closest distance to " C   ILE A 106 " =    1.847
peak=    3.452 closest distance to " O   HOH Z 287 " =    1.876
peak=    3.450 closest distance to " CA  ALA A  51 " =    0.960
peak=    3.443 closest distance to " O   HOH Z  59 " =    1.897
peak=    3.442 closest distance to " O   HOH Z  22 " =    2.582
peak=    3.441 closest distance to " CB  PRO A 198 " =    0.943
peak=    3.440 closest distance to " O   HOH Z 123 " =    2.037
peak=    3.438 closest distance to " O   HOH Z 109 " =    2.451
peak=    3.437 closest distance to " CG  GLN A  11 " =    1.368
peak=    3.436 closest distance to " O   HOH Z 227 " =    1.816
peak=    3.436 closest distance to " CB  PHE A  16 " =    1.265
peak=    3.436 closest distance to " O   HOH Z 332 " =    1.646
peak=    3.434 closest distance to " O   HOH Z 291 " =    1.486
peak=    3.433 closest distance to " CD  ARG A 195 " =    1.073
peak=    3.431 closest distance to " O   HOH Z 301 " =    1.548
peak=    3.429 closest distance to " CA  LEU A  83 " =    1.413
peak=    3.428 closest distance to " CB  TRP A 266 " =    0.957
peak=    3.428 closest distance to " ND1 HIS A  81 " =    1.461
peak=    3.423 closest distance to " O   HOH Z 150 " =    1.764
peak=    3.423 closest distance to " O   HOH Z  48 " =    1.924
peak=    3.422 closest distance to " O   HOH Z  78 " =    2.230
peak=    3.421 closest distance to " OD1 ASN A  60 " =    1.210
peak=    3.420 closest distance to " O   HOH Z 363 " =    1.190
peak=    3.416 closest distance to " O   ALA A 165 " =    1.212
peak=    3.404 closest distance to " O   HOH Z 383 " =    2.008
peak=    3.403 closest distance to " O   HOH Z 358 " =    2.001
peak=    3.400 closest distance to " CB  ASP A 140 " =    0.718
peak=    3.399 closest distance to " C   GLY A  80 " =    1.190
peak=    3.396 closest distance to " O   HOH Z 426 " =    1.434
peak=    3.394 closest distance to " CG  GLN A  58 " =    2.232
peak=    3.386 closest distance to " O   HOH Z 417 " =    3.066
peak=    3.384 closest distance to " O   GLY A 211 " =    1.389
peak=    3.382 closest distance to " CB  MET A 105 " =    1.216
peak=    3.381 closest distance to " O   HOH Z 139 " =    4.249
peak=    3.381 closest distance to " O   HOH Z 130 " =    1.232
peak=    3.380 closest distance to " O   HOH Z 284 " =    2.920
peak=    3.378 closest distance to " CG2 VAL A  78 " =    0.991
peak=    3.372 closest distance to " OG  SER A 245 " =    1.523
peak=    3.372 closest distance to " O   HOH Z 263 " =    2.172
peak=    3.366 closest distance to " O   HOH Z 173 " =    2.134
peak=    3.359 closest distance to " CA  ARG A 195 " =    1.078
peak=    3.357 closest distance to " CB  MET A  47 " =    1.048
peak=    3.353 closest distance to " CA  ALA A 295 " =    1.092
peak=    3.350 closest distance to " CA  GLY A 196 " =    1.173
peak=    3.349 closest distance to " O   HOH Z  78 " =    1.808
peak=    3.348 closest distance to " O   HOH Z 106 " =    1.532
peak=    3.346 closest distance to " O   HOH Z 315 " =    1.898
peak=    3.346 closest distance to " O   HOH Z  26 " =    1.331
peak=    3.345 closest distance to " O   HOH Z 421 " =    1.720
peak=    3.338 closest distance to " CA  THR A 221 " =    1.570
peak=    3.335 closest distance to " O   HOH Z 108 " =    1.084
peak=    3.331 closest distance to " CB  ALA A  51 " =    0.867
peak=    3.330 closest distance to " CD BLYS A 290 " =    1.069
peak=    3.328 closest distance to " O   HOH Z 387 " =    2.479
peak=    3.322 closest distance to " O   HOH Z   1 " =    3.214
peak=    3.321 closest distance to " CA  GLN A 223 " =    0.844
peak=    3.320 closest distance to " CD2 TRP A 179 " =    1.344
peak=    3.318 closest distance to " CB  GLN A  73 " =    1.074
peak=    3.315 closest distance to " O   HOH Z 380 " =    2.119
peak=    3.314 closest distance to " O   HOH Z 327 " =    1.775
peak=    3.310 closest distance to " CG2 ILE A  20 " =    1.369
peak=    3.301 closest distance to " CG  PRO A 243 " =    1.193
peak=    3.300 closest distance to " CB  ASN A 148 " =    1.752
peak=    3.299 closest distance to " O   HOH Z 358 " =    1.347
peak=    3.298 closest distance to " O   HOH Z 409 " =    3.431
peak=    3.297 closest distance to " O   HOH Z 432 " =    1.962
peak=    3.294 closest distance to " CA  ILE A 106 " =    0.768
peak=    3.294 closest distance to " O   HOH Z 112 " =    1.582
peak=    3.293 closest distance to " O   HOH Z 427 " =    3.157
peak=    3.289 closest distance to " O   ASN A  74 " =    1.612
peak=    3.289 closest distance to " O   HOH Z 250 " =    1.800
peak=    3.288 closest distance to " O   HOH Z 145 " =    1.984
peak=    3.286 closest distance to " O   HOH Z 377 " =    1.263
peak=    3.284 closest distance to " CE3 TRP A 274 " =    2.421
peak=    3.282 closest distance to " O   HOH Z 426 " =    3.391
peak=    3.280 closest distance to " CD1 LEU A  96 " =    0.761
peak=    3.280 closest distance to " O   HOH Z 189 " =    2.849
peak=    3.279 closest distance to " CB  LEU A 261 " =    1.293
peak=    3.276 closest distance to " O   HOH Z 280 " =    2.375
peak=    3.276 closest distance to " O   HOH Z 128 " =    2.162
peak=    3.275 closest distance to " O   HOH Z 423 " =    3.257
peak=    3.268 closest distance to " O   HOH Z 147 " =    1.769
peak=    3.265 closest distance to " O   HOH Z 152 " =    1.796
peak=    3.262 closest distance to " CA  ARG A  66 " =    1.125
peak=    3.262 closest distance to " CB  ASN A 187 " =    1.131
peak=    3.259 closest distance to " CB  THR A  52 " =    1.151
peak=    3.257 closest distance to " O   HOH Z 313 " =    2.053
peak=    3.254 closest distance to " CG1BVAL A  72 " =    1.686
peak=    3.254 closest distance to " O   HOH Z 219 " =    5.114
peak=    3.247 closest distance to " OG BSER A 210 " =    1.110
peak=    3.246 closest distance to " NH1 ARG A 269 " =    0.776
peak=    3.242 closest distance to " O   HOH Z 272 " =    1.903
peak=    3.241 closest distance to " CA  PRO A  90 " =    1.012
peak=    3.236 closest distance to " CG2 ILE A 120 " =    1.175
peak=    3.236 closest distance to " O   HOH Z 403 " =    1.493
peak=    3.233 closest distance to " CB  ALA A 256 " =    1.025
peak=    3.233 closest distance to " O   HOH Z 261 " =    1.878
peak=    3.232 closest distance to " O   HOH Z 155 " =    3.017
peak=    3.231 closest distance to " CD1 LEU A 222 " =    0.821
peak=    3.229 closest distance to " NH2AARG A 275 " =    3.504
peak=    3.229 closest distance to " O   HOH Z 257 " =    2.254
peak=    3.224 closest distance to " CB  GLU A 277 " =    0.986
peak=    3.223 closest distance to " CB  PHE A 218 " =    1.869
peak=    3.223 closest distance to " O   HOH Z 124 " =    3.130
peak=    3.221 closest distance to " O   HOH Z 402 " =    2.900
peak=    3.218 closest distance to " CG2 THR A  42 " =    0.917
peak=    3.218 closest distance to " N   CYS A 260 " =    0.796
peak=    3.213 closest distance to " O   HOH Z 142 " =    1.856
peak=    3.212 closest distance to " CA  GLU A  46 " =    0.778
peak=    3.211 closest distance to " CA  ALA A 100 " =    1.495
peak=    3.209 closest distance to " CA  SER A  87 " =    0.937
peak=    3.209 closest distance to " CG  MET A  40 " =    2.248
peak=    3.204 closest distance to " CA  ASN A 215 " =    1.146
peak=    3.202 closest distance to " OH  TYR A  30 " =    1.345
peak=    3.202 closest distance to " O   HOH Z 192 " =    1.776
peak=    3.200 closest distance to " CA  VAL A 125 " =    1.172
peak=    3.199 closest distance to " CB  ILE A 199 " =    1.027
peak=    3.197 closest distance to " O   HOH Z  63 " =    1.945
peak=    3.195 closest distance to " NE AARG A 275 " =    1.361
peak=    3.195 closest distance to " O   HOH Z 282 " =    2.245
peak=    3.183 closest distance to " CA  LYS A  48 " =    1.374
peak=    3.182 closest distance to " CD2 HIS A  81 " =    1.245
peak=    3.182 closest distance to " O   HOH Z  88 " =    3.260
peak=    3.181 closest distance to " O   HOH Z 217 " =    2.140
peak=    3.175 closest distance to " O   HOH Z  38 " =    3.460
peak=    3.174 closest distance to " CG  GLN A  89 " =    1.412
peak=    3.173 closest distance to " OG BSER A 164 " =    2.521
peak=    3.173 closest distance to " O   HOH Z 156 " =    2.542
peak=    3.172 closest distance to " O   HOH Z  51 " =    1.580
peak=    3.171 closest distance to " O   HOH Z 155 " =    1.331
peak=    3.171 closest distance to " CG2AVAL A 121 " =    2.021
peak=    3.170 closest distance to " CB  THR A 157 " =    1.187
peak=    3.163 closest distance to " N   GLY A  75 " =    1.235
peak=    3.162 closest distance to " O   HOH Z 197 " =    1.939
peak=    3.162 closest distance to " O   HOH Z 353 " =    2.695
peak=    3.161 closest distance to " NH2AARG A 275 " =    2.699
peak=    3.157 closest distance to " CB  ARG A 269 " =    1.100
peak=    3.156 closest distance to " OG  SER A  97 " =    3.559
peak=    3.153 closest distance to " O   HOH Z 293 " =    1.838
peak=    3.150 closest distance to " O   HOH Z 227 " =    1.870
peak=    3.144 closest distance to " O   ASP A 124 " =    1.692
peak=    3.142 closest distance to " O   HOH Z 214 " =    1.133
peak=    3.141 closest distance to " CA  ASP A 162 " =    1.222
peak=    3.137 closest distance to " CA  VAL A 126 " =    0.918
peak=    3.135 closest distance to " O   HOH Z 343 " =    2.313
peak=    3.134 closest distance to " CB  THR A  31 " =    1.824
peak=    3.131 closest distance to " O   HOH Z 238 " =    5.545
peak=    3.130 closest distance to " CA  ALA A 160 " =    0.928
peak=    3.128 closest distance to " O   HOH Z 303 " =    2.303
peak=    3.123 closest distance to " O   HOH Z 162 " =    1.885
peak=    3.114 closest distance to " O   HOH Z  50 " =    3.448
peak=    3.111 closest distance to " O   HOH Z 126 " =    2.147
peak=    3.096 closest distance to " NE2 HIS A 115 " =    0.971
peak=    3.093 closest distance to " OD1 ASP A 238 " =    0.925
peak=    3.092 closest distance to " CE BMET A  47 " =    1.599
peak=    3.085 closest distance to " O   HOH Z 425 " =    1.424
peak=    3.084 closest distance to " O   HOH Z 287 " =    2.085
peak=    3.078 closest distance to " CB  ALA A   1 " =    1.129
peak=    3.075 closest distance to " N   PHE A 130 " =    1.401
peak=    3.059 closest distance to " O   HOH Z  88 " =    2.584
peak=    3.056 closest distance to " CB  SER A 273 " =    0.764
peak=    3.041 closest distance to " CZ3 TRP A  85 " =    1.009
peak=    3.031 closest distance to " O   HOH Z 273 " =    2.701
peak=    3.030 closest distance to " CA  TRP A 150 " =    0.858
peak=    3.018 closest distance to " NH2AARG A 275 " =    3.956
peak=    3.005 closest distance to " O   HOH Z 264 " =    1.616

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 208         
Filter by distance & map next to the model:
   mapped sites are within: 0.430 - 5.085
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 208
   mapped sites are within: 0.715 - 5.085

peak=   -4.376 closest distance to " O   HOH Z 350 " =    0.861
peak=   -4.335 closest distance to " O   PRO A 163 " =    2.117
peak=   -4.317 closest distance to " OG  SER A  97 " =    2.225
peak=   -4.294 closest distance to " O   HOH Z 196 " =    1.753
peak=   -4.270 closest distance to " O   HOH Z 266 " =    4.520
peak=   -4.264 closest distance to " O   HOH Z 120 " =    0.882
peak=   -4.261 closest distance to " O   HOH Z 155 " =    1.560
peak=   -4.211 closest distance to " CG2BVAL A  41 " =    2.682
peak=   -4.199 closest distance to " NH2 ARG A  66 " =    1.210
peak=   -4.178 closest distance to " OXT GLY A 302 " =    2.625
peak=   -4.171 closest distance to " O   HOH Z 221 " =    1.134
peak=   -4.124 closest distance to " CD1 PHE A  59 " =    1.994
peak=   -4.109 closest distance to " CA  VAL A  67 " =    2.880
peak=   -4.017 closest distance to " O   HOH Z  52 " =    1.975
peak=   -4.011 closest distance to " CB  LEU A 167 " =    2.136
peak=   -4.009 closest distance to " O   HOH Z 348 " =    2.346
peak=   -3.981 closest distance to " O   HOH Z 290 " =    0.867
peak=   -3.960 closest distance to " O   HOH Z 377 " =    0.884
peak=   -3.931 closest distance to " CD2 LEU A 300 " =    2.732
peak=   -3.914 closest distance to " C   HIS A 108 " =    1.054
peak=   -3.879 closest distance to " CE2 TYR A  30 " =    2.699
peak=   -3.863 closest distance to " NH2 ARG A  66 " =    1.179
peak=   -3.855 closest distance to " N   ALA A  43 " =    2.724
peak=   -3.817 closest distance to " O   PRO A 198 " =    1.349
peak=   -3.811 closest distance to " NH2 ARG A  79 " =    1.925
peak=   -3.811 closest distance to " SG  CYS A 254 " =    3.317
peak=   -3.797 closest distance to " CA  SER A 276 " =    1.398
peak=   -3.796 closest distance to " O   HOH Z 234 " =    4.147
peak=   -3.795 closest distance to " C   ASN A 285 " =    2.365
peak=   -3.769 closest distance to " O   HOH Z 313 " =    1.245
peak=   -3.763 closest distance to " O   ALA A   1 " =    2.107
peak=   -3.763 closest distance to " CA  GLY A 203 " =    2.348
peak=   -3.750 closest distance to " C   SER A 206 " =    1.522
peak=   -3.743 closest distance to " ND2 ASN A  60 " =    1.401
peak=   -3.732 closest distance to " O   HOH Z 423 " =    2.442
peak=   -3.716 closest distance to " CA  TYR A  68 " =    2.673
peak=   -3.698 closest distance to " O   HOH Z 165 " =    2.062
peak=   -3.698 closest distance to " O   HOH Z 210 " =    0.720
peak=   -3.694 closest distance to " OD1 ASP A 191 " =    1.734
peak=   -3.693 closest distance to " CA  VAL A 197 " =    0.975
peak=   -3.684 closest distance to " NE  ARG A 156 " =    1.847
peak=   -3.674 closest distance to " CD1 LEU A  25 " =    2.516
peak=   -3.673 closest distance to " O   HOH Z 396 " =    1.653
peak=   -3.671 closest distance to " CD1 LEU A 101 " =    2.566
peak=   -3.651 closest distance to " ND2 ASN A  45 " =    1.070
peak=   -3.651 closest distance to " C   THR A 279 " =    1.181
peak=   -3.633 closest distance to " CD  GLN A 223 " =    0.884
peak=   -3.621 closest distance to " OD2 ASP A 171 " =    1.834
peak=   -3.621 closest distance to " CG  ASP A 231 " =    0.766
peak=   -3.616 closest distance to " O   HOH Z 422 " =    1.400
peak=   -3.598 closest distance to " O   HOH Z 185 " =    2.358
peak=   -3.596 closest distance to " CH2 TRP A 179 " =    1.187
peak=   -3.590 closest distance to " O   HOH Z 388 " =    2.078
peak=   -3.588 closest distance to " CG  GLN A  58 " =    1.220
peak=   -3.583 closest distance to " O   PHE A 218 " =    1.395
peak=   -3.569 closest distance to " O   HOH Z 150 " =    1.424
peak=   -3.569 closest distance to " O   HOH Z   7 " =    1.145
peak=   -3.554 closest distance to " CD2 PHE A  59 " =    2.342
peak=   -3.545 closest distance to " O   HOH Z  93 " =    1.181
peak=   -3.540 closest distance to " CA  GLY A  98 " =    2.194
peak=   -3.534 closest distance to " O   GLY A 196 " =    2.402
peak=   -3.532 closest distance to " OG BSER A 210 " =    2.295
peak=   -3.512 closest distance to " OG  SER A  62 " =    1.303
peak=   -3.511 closest distance to " CE  MET A  93 " =    1.202
peak=   -3.509 closest distance to " CD2 LEU A 237 " =    2.440
peak=   -3.507 closest distance to " O   HOH Z 109 " =    3.392
peak=   -3.502 closest distance to " O   HOH Z  19 " =    2.346
peak=   -3.498 closest distance to " O   HOH Z 103 " =    1.850
peak=   -3.495 closest distance to " OG  SER A  32 " =    1.246
peak=   -3.493 closest distance to " CG2 THR A 221 " =    2.336
peak=   -3.492 closest distance to " CD1 TRP A 179 " =    1.098
peak=   -3.486 closest distance to " OG ASER A 134 " =    1.219
peak=   -3.477 closest distance to " O   HOH Z 210 " =    2.572
peak=   -3.472 closest distance to " CD  GLN A  58 " =    0.887
peak=   -3.470 closest distance to " O   HOH Z  71 " =    1.563
peak=   -3.467 closest distance to " CG  GLU A  53 " =    1.309
peak=   -3.464 closest distance to " ND2 ASN A 187 " =    1.641
peak=   -3.463 closest distance to " O   HOH Z   6 " =    1.617
peak=   -3.462 closest distance to " N   GLN A  58 " =    1.797
peak=   -3.462 closest distance to " OG BSER A 210 " =    1.219
peak=   -3.462 closest distance to " CB  ALA A 131 " =    2.305
peak=   -3.459 closest distance to " CA  ASP A 298 " =    1.057
peak=   -3.457 closest distance to " CB  ALA A 291 " =    2.510
peak=   -3.455 closest distance to " O   HOH Z  39 " =    0.956
peak=   -3.449 closest distance to " O   HOH Z 407 " =    0.804
peak=   -3.447 closest distance to " CD  GLN A  88 " =    0.715
peak=   -3.432 closest distance to " CG  PRO A 243 " =    1.609
peak=   -3.419 closest distance to " O  BHOH Z 338 " =    1.487
peak=   -3.418 closest distance to " CE  MET A 105 " =    1.936
peak=   -3.411 closest distance to " O   HOH Z 377 " =    2.169
peak=   -3.408 closest distance to " O   TRP A  92 " =    1.957
peak=   -3.406 closest distance to " CE  MET A 105 " =    2.110
peak=   -3.406 closest distance to " CD1 LEU A 101 " =    2.802
peak=   -3.404 closest distance to " OE2 GLU A 152 " =    2.233
peak=   -3.400 closest distance to " CD  GLN A 223 " =    1.523
peak=   -3.396 closest distance to " O   HOH Z 151 " =    1.513
peak=   -3.394 closest distance to " O   ALA A 161 " =    1.853
peak=   -3.391 closest distance to " O   HOH Z  78 " =    1.765
peak=   -3.382 closest distance to " ND2 ASN A  39 " =    1.214
peak=   -3.381 closest distance to " O   HOH Z 392 " =    1.260
peak=   -3.381 closest distance to " O   HOH Z  15 " =    1.602
peak=   -3.373 closest distance to " CD1 TYR A 247 " =    2.217
peak=   -3.372 closest distance to " CB  ALA A 161 " =    2.523
peak=   -3.372 closest distance to " CG2 THR A   4 " =    1.799
peak=   -3.360 closest distance to " O   HOH Z 118 " =    3.428
peak=   -3.354 closest distance to " O   GLY A 196 " =    0.998
peak=   -3.353 closest distance to " C   ALA A   8 " =    1.581
peak=   -3.343 closest distance to " CD1 LEU A 228 " =    2.426
peak=   -3.341 closest distance to " O   HOH Z 378 " =    1.195
peak=   -3.340 closest distance to " O   HOH Z 380 " =    4.356
peak=   -3.334 closest distance to " O   HOH Z  39 " =    1.581
peak=   -3.332 closest distance to " OD1 ASP A 298 " =    1.948
peak=   -3.331 closest distance to " O   HOH Z 275 " =    1.457
peak=   -3.330 closest distance to " CD1 PHE A 130 " =    2.305
peak=   -3.329 closest distance to " NE2 GLN A 103 " =    1.627
peak=   -3.328 closest distance to " O   HOH Z   7 " =    1.612
peak=   -3.327 closest distance to " O   HOH Z 150 " =    2.254
peak=   -3.326 closest distance to " CG2AVAL A  41 " =    2.912
peak=   -3.319 closest distance to " CG2 ILE A  49 " =    2.557
peak=   -3.317 closest distance to " CD  GLN A  73 " =    0.807
peak=   -3.309 closest distance to " O   ALA A  10 " =    1.785
peak=   -3.288 closest distance to " O   HOH Z 136 " =    1.551
peak=   -3.287 closest distance to " O   HOH Z 422 " =    1.860
peak=   -3.285 closest distance to " CB  ALA A 291 " =    2.163
peak=   -3.284 closest distance to " CD  PRO A 198 " =    1.093
peak=   -3.284 closest distance to " O   VAL A 174 " =    1.990
peak=   -3.280 closest distance to " C   GLY A 133 " =    1.297
peak=   -3.280 closest distance to " O   HOH Z  10 " =    1.529
peak=   -3.279 closest distance to " OG BSER A 134 " =    1.804
peak=   -3.276 closest distance to " O   HOH Z 407 " =    1.573
peak=   -3.276 closest distance to " OE2 GLU A   2 " =    1.289
peak=   -3.275 closest distance to " O   TYR A  15 " =    1.543
peak=   -3.273 closest distance to " O   HOH Z  91 " =    2.213
peak=   -3.273 closest distance to " NH1 ARG A 195 " =    2.665
peak=   -3.272 closest distance to " CB  ASP A  50 " =    2.495
peak=   -3.270 closest distance to " O   HOH Z  37 " =    1.565
peak=   -3.267 closest distance to " O   HOH Z 171 " =    2.329
peak=   -3.267 closest distance to " ND2 ASN A  60 " =    1.451
peak=   -3.266 closest distance to " O   HOH Z  11 " =    1.513
peak=   -3.265 closest distance to " O   ALA A 256 " =    1.515
peak=   -3.258 closest distance to " NH2 ARG A 159 " =    2.338
peak=   -3.258 closest distance to " O   ASN A 187 " =    1.625
peak=   -3.256 closest distance to " CD  GLN A  88 " =    0.907
peak=   -3.243 closest distance to " O   HOH Z 417 " =    2.843
peak=   -3.242 closest distance to " CB  ALA A 100 " =    1.830
peak=   -3.242 closest distance to " CZ  TYR A 169 " =    1.921
peak=   -3.242 closest distance to " CB  ALA A   9 " =    2.608
peak=   -3.235 closest distance to " CB  ALA A 244 " =    2.515
peak=   -3.230 closest distance to " CD2 LEU A 237 " =    2.622
peak=   -3.229 closest distance to " CD  ARG A 195 " =    5.085
peak=   -3.229 closest distance to " C   ALA A 158 " =    1.159
peak=   -3.226 closest distance to " O   HOH Z 137 " =    1.298
peak=   -3.225 closest distance to " CD  GLN A  77 " =    1.117
peak=   -3.221 closest distance to " O   HOH Z 385 " =    3.671
peak=   -3.219 closest distance to " O   HOH Z 360 " =    2.434
peak=   -3.219 closest distance to " NH2BARG A 145 " =    2.313
peak=   -3.212 closest distance to " O   HOH Z 313 " =    1.715
peak=   -3.211 closest distance to " CB  PRO A 163 " =    2.830
peak=   -3.207 closest distance to " OH  TYR A 169 " =    0.931
peak=   -3.202 closest distance to " N   ALA A 226 " =    1.989
peak=   -3.197 closest distance to " CE2 TRP A 274 " =    1.197
peak=   -3.195 closest distance to " O   HOH Z 368 " =    2.112
peak=   -3.195 closest distance to " O   HOH Z 198 " =    1.446
peak=   -3.193 closest distance to " CE3 TRP A 274 " =    2.412
peak=   -3.193 closest distance to " O   HOH Z 196 " =    2.199
peak=   -3.190 closest distance to " ND2 ASN A  45 " =    1.031
peak=   -3.187 closest distance to " O   HOH Z 424 " =    2.984
peak=   -3.176 closest distance to " O   ALA A  34 " =    2.424
peak=   -3.174 closest distance to " CG  ARG A 219 " =    2.395
peak=   -3.173 closest distance to " C   ASN A 187 " =    1.988
peak=   -3.172 closest distance to " O   HOH Z 145 " =    1.920
peak=   -3.170 closest distance to " O   HOH Z  40 " =    3.050
peak=   -3.168 closest distance to " O   SER A 146 " =    0.936
peak=   -3.162 closest distance to " CA  GLY A 241 " =    2.203
peak=   -3.159 closest distance to " CB  CYS A 254 " =    2.462
peak=   -3.159 closest distance to " O   HOH Z 428 " =    1.030
peak=   -3.156 closest distance to " C   TRP A 274 " =    1.484
peak=   -3.155 closest distance to " CG1 VAL A 112 " =    2.614
peak=   -3.153 closest distance to " CG  ARG A 269 " =    2.428
peak=   -3.151 closest distance to " O   HOH Z 351 " =    1.506
peak=   -3.150 closest distance to " O   HOH Z 292 " =    3.003
peak=   -3.138 closest distance to " OG  SER A 273 " =    2.161
peak=   -3.134 closest distance to " CD2 HIS A 115 " =    1.003
peak=   -3.132 closest distance to " CB  ALA A  43 " =    2.465
peak=   -3.125 closest distance to " CD2 PHE A  61 " =    1.915
peak=   -3.125 closest distance to " O   HOH Z 176 " =    1.689
peak=   -3.125 closest distance to " OD1 ASN A 148 " =    1.639
peak=   -3.124 closest distance to " O   HOH Z  17 " =    0.965
peak=   -3.123 closest distance to " NH2BARG A 275 " =    1.570
peak=   -3.123 closest distance to " CA  GLN A  73 " =    1.160
peak=   -3.119 closest distance to " O   HOH Z 405 " =    2.358
peak=   -3.116 closest distance to " O   VAL A 125 " =    2.135
peak=   -3.115 closest distance to " O   HOH Z  25 " =    2.154
peak=   -3.114 closest distance to " CE2 TRP A  85 " =    0.930
peak=   -3.113 closest distance to " CH2 TRP A 150 " =    1.151
peak=   -3.108 closest distance to " NH1 ARG A  66 " =    3.924
peak=   -3.101 closest distance to " CA  GLY A 133 " =    2.092
peak=   -3.099 closest distance to " CD  ARG A 139 " =    1.535
peak=   -3.099 closest distance to " O   HOH Z 397 " =    1.211
peak=   -3.095 closest distance to " O   HOH Z 283 " =    1.675
peak=   -3.092 closest distance to " O   HOH Z 418 " =    1.416
peak=   -3.089 closest distance to " NE2 GLN A  88 " =    2.024
peak=   -3.084 closest distance to " CB  ALA A 244 " =    2.109
peak=   -3.061 closest distance to " CG2 VAL A 296 " =    2.058
peak=   -3.055 closest distance to " O   HOH Z 100 " =    0.873
peak=   -3.037 closest distance to " O   HOH Z 427 " =    1.476

================= 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    :  0.4621 0.4504   6.278378e+00   6.260269e+00
   1_bss:  0.4509 0.4370   6.269627e+00   6.246708e+00
   1_xyz:  0.3718 0.4029   6.141777e+00   6.187752e+00
   1_adp:  0.3405 0.4154   6.100252e+00   6.201083e+00
   1_occ:  0.3404 0.4158   6.099913e+00   6.201389e+00
   2_bss:  0.3394 0.4124   6.101015e+00   6.200595e+00
   2_xyz:  0.2753 0.3425   5.923262e+00   6.072719e+00
   2_adp:  0.2566 0.3277   5.877618e+00   6.043959e+00
   2_occ:  0.2564 0.3275   5.877236e+00   6.043744e+00
   3_bss:  0.2560 0.3263   5.876403e+00   6.042076e+00
   3_xyz:  0.2023 0.2598   5.655260e+00   5.841817e+00
   3_adp:  0.1861 0.2368   5.580539e+00   5.765599e+00
   3_occ:  0.1858 0.2364   5.579986e+00   5.764817e+00
   4_bss:  0.1857 0.2350   5.578908e+00   5.762212e+00
   4_xyz:  0.1437 0.1904   5.351842e+00   5.565141e+00
   4_adp:  0.1320 0.1801   5.285999e+00   5.510848e+00
   4_occ:  0.1319 0.1799   5.285145e+00   5.510046e+00
   5_bss:  0.1322 0.1802   5.288547e+00   5.512437e+00
   5_xyz:  0.1227 0.1713   5.228947e+00   5.459415e+00
   5_adp:  0.1215 0.1684   5.218943e+00   5.446808e+00
   5_occ:  0.1214 0.1683   5.218391e+00   5.446602e+00
   5_bss:  0.1214 0.1682   5.218344e+00   5.446486e+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:  0.296  20.001  -3.347   4.650   0.887   0.000   0.000   0.000
   1_xyz:  0.296  20.001  -3.347   4.650   0.887   0.000   0.000   0.000
   1_adp:  0.296  20.001  -3.347   4.650   0.887   0.000   0.000   0.000
   1_occ:  0.296  20.001  -3.347   4.650   0.887   0.000   0.000   0.000
   2_bss:  0.314  50.000  -1.836   2.718  -0.037   0.000  -0.000  -0.000
   2_xyz:  0.314  50.000  -1.836   2.718  -0.037   0.000  -0.000  -0.000
   2_adp:  0.314  50.000  -1.836   2.718  -0.037   0.000  -0.000  -0.000
   2_occ:  0.314  50.000  -1.836   2.718  -0.037   0.000  -0.000  -0.000
   3_bss:  0.318  52.855  -1.382   1.527  -0.448   0.000  -0.000  -0.000
   3_xyz:  0.318  52.855  -1.382   1.527  -0.448   0.000  -0.000  -0.000
   3_adp:  0.318  52.855  -1.382   1.527  -0.448   0.000  -0.000  -0.000
   3_occ:  0.318  52.855  -1.382   1.527  -0.448   0.000  -0.000  -0.000
   4_bss:  0.323  58.218  -2.090  -0.010  -1.313  -0.000  -0.000  -0.000
   4_xyz:  0.323  58.218  -2.090  -0.010  -1.313  -0.000  -0.000  -0.000
   4_adp:  0.323  58.218  -2.090  -0.010  -1.313  -0.000  -0.000  -0.000
   4_occ:  0.323  58.218  -2.090  -0.010  -1.313  -0.000  -0.000  -0.000
   5_bss:  0.327  59.519  -2.268  -0.777  -1.479  -0.000  -0.000  -0.000
   5_xyz:  0.327  59.519  -2.268  -0.777  -1.479  -0.000  -0.000  -0.000
   5_adp:  0.327  59.519  -2.268  -0.777  -1.479  -0.000  -0.000  -0.000
   5_occ:  0.327  59.519  -2.268  -0.777  -1.479  -0.000  -0.000  -0.000
   5_bss:  0.323  56.150  -2.191  -0.888  -1.375  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.521 0.4645  0.6262    66047.958
   1_bss:  53.124 0.4809  0.6616    61974.009
   1_xyz:  46.094 0.5685  0.7707    48703.498
   1_adp:  47.519 0.5502  0.7569    50724.856
   1_occ:  47.566 0.5496  0.7547    50727.782
   2_bss:  47.240 0.5537  0.7535    50373.260
   2_xyz:  37.657 0.6686  0.8891    32915.594
   2_adp:  35.490 0.6946  0.8920    30068.500
   2_occ:  35.491 0.6946  0.8914    30061.413
   3_bss:  35.313 0.6966  0.8829    29839.978
   3_xyz:  26.407 0.7958  0.9750    17549.768
   3_adp:  23.457 0.8276  0.9899    14774.430
   3_occ:  23.429 0.8279  0.9901    14760.590
   4_bss:  23.243 0.8296  0.9564    14539.560
   4_xyz:  18.276 0.8772  0.9830     9293.546
   4_adp:  16.974 0.8894  0.9815     8379.244
   4_occ:  16.954 0.8896  0.9816     8368.478
   5_bss:  17.006 0.8892  0.9695     8448.843
   5_xyz:  15.761 0.9003  0.9748     7545.696
   5_adp:  15.460 0.9031  0.9711     7415.453
   5_occ:  15.451 0.9032  0.9711     7412.105
   5_bss:  15.449 0.9032  0.9704     7406.099
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.8968e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.8968e-01
   1_xyz:   1.563  0.012  0.092 15.938  0.006  4.106   1.2917e-01
   1_adp:   1.563  0.012  0.092 15.938  0.006  4.106   1.2917e-01
   1_occ:   1.563  0.012  0.092 15.938  0.006  4.106   1.2917e-01
   2_bss:   1.563  0.012  0.092 15.938  0.006  4.106   1.2917e-01
   2_xyz:   1.499  0.011  0.092 15.318  0.006  4.111   1.2016e-01
   2_adp:   1.499  0.011  0.092 15.318  0.006  4.111   1.2016e-01
   2_occ:   1.499  0.011  0.092 15.318  0.006  4.111   1.2016e-01
   3_bss:   1.499  0.011  0.092 15.318  0.006  4.111   1.2016e-01
   3_xyz:   1.193  0.009  0.069 14.728  0.005  4.123   7.6942e-02
   3_adp:   1.193  0.009  0.069 14.728  0.005  4.123   7.6942e-02
   3_occ:   1.193  0.009  0.069 14.728  0.005  4.123   7.6942e-02
   4_bss:   1.193  0.009  0.069 14.728  0.005  4.123   7.6942e-02
   4_xyz:   1.149  0.009  0.079 14.900  0.005  4.122   7.6675e-02
   4_adp:   1.149  0.009  0.079 14.900  0.005  4.122   7.6675e-02
   4_occ:   1.149  0.009  0.079 14.900  0.005  4.122   7.6675e-02
   5_bss:   1.149  0.009  0.079 14.900  0.005  4.122   7.6675e-02
   5_xyz:   1.053  0.008  0.074 14.709  0.004  4.113   6.4225e-02
   5_adp:   1.053  0.008  0.074 14.709  0.004  4.113   6.4225e-02
   5_occ:   1.053  0.008  0.074 14.709  0.004  4.113   6.4225e-02
   5_bss:   1.053  0.008  0.074 14.709  0.004  4.113   6.4225e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.443   2.4249e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.443   2.4249e-01
   1_xyz:   9.240  0.066  0.430 86.852  0.020  2.004   1.0460e-01
   1_adp:   9.240  0.066  0.430 86.852  0.020  2.004   1.0460e-01
   1_occ:   9.240  0.066  0.430 86.852  0.020  2.004   1.0460e-01
   2_bss:   9.240  0.066  0.430 86.852  0.020  2.004   1.0460e-01
   2_xyz:   7.894  0.071  0.283 82.427  0.039  1.996   1.7952e-01
   2_adp:   7.894  0.071  0.283 82.427  0.039  1.996   1.7952e-01
   2_occ:   7.894  0.071  0.283 82.427  0.039  1.996   1.7952e-01
   3_bss:   7.894  0.071  0.283 82.427  0.039  1.996   1.7952e-01
   3_xyz:   7.496  0.049  0.232 89.109  0.052  2.274   7.0067e-02
   3_adp:   7.496  0.049  0.232 89.109  0.052  2.274   7.0067e-02
   3_occ:   7.496  0.049  0.232 89.109  0.052  2.274   7.0067e-02
   4_bss:   7.496  0.049  0.232 89.109  0.052  2.274   7.0067e-02
   4_xyz:   8.163  0.074  0.259 81.307  0.034  2.225   6.1420e-02
   4_adp:   8.163  0.074  0.259 81.307  0.034  2.225   6.1420e-02
   4_occ:   8.163  0.074  0.259 81.307  0.034  2.225   6.1420e-02
   5_bss:   8.163  0.074  0.259 81.307  0.034  2.225   6.1420e-02
   5_xyz:   7.647  0.040  0.243 82.894  0.036  2.354   4.5365e-02
   5_adp:   7.647  0.040  0.243 82.894  0.036  2.354   4.5365e-02
   5_occ:   7.647  0.040  0.243 82.894  0.036  2.354   4.5365e-02
   5_bss:   7.647  0.040  0.243 82.894  0.036  2.354   4.5365e-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: 100.31   0.00  19.34  91.63   0.00  16.14 100.31   1.90  36.78
   1_occ: 100.31   0.00  19.34  91.63   0.00  16.14 100.31   1.90  36.78
   2_bss: 100.31   0.00  19.34  91.63   0.00  16.14 100.31   1.90  36.78
   2_xyz: 100.31   0.00  19.34  91.63   0.00  16.14 100.31   1.90  36.78
   2_adp: 100.36   0.00  18.34  91.13   0.00  14.73 100.36   3.44  37.97
   2_occ: 100.36   0.00  18.34  91.13   0.00  14.73 100.36   3.44  37.97
   3_bss: 100.36   0.00  18.34  91.13   0.00  14.73 100.36   3.44  37.97
   3_xyz: 100.36   0.00  18.34  91.13   0.00  14.73 100.36   3.44  37.97
   3_adp:  94.52   0.00  17.74  85.20   0.00  13.52  94.52   4.86  40.72
   3_occ:  94.52   0.00  17.74  85.20   0.00  13.52  94.52   4.86  40.72
   4_bss:  94.52   0.00  17.74  85.20   0.00  13.52  94.52   4.86  40.72
   4_xyz:  94.52   0.00  17.74  85.20   0.00  13.52  94.52   4.86  40.72
   4_adp:  96.53   1.07  17.61  92.50   1.07  12.90  96.53   3.28  43.23
   4_occ:  96.53   1.07  17.61  92.50   1.07  12.90  96.53   3.28  43.23
   5_bss:  96.53   1.07  17.61  92.50   1.07  12.90  96.53   3.28  43.23
   5_xyz:  96.53   1.07  17.61  92.50   1.07  12.90  96.53   3.28  43.23
   5_adp:  92.80   1.43  17.07  91.27   1.43  12.60  92.80   4.22  41.41
   5_occ:  92.80   1.43  17.07  91.27   1.43  12.60  92.80   4.22  41.41
   5_bss:  92.75   1.38  17.02  91.22   1.38  12.55  92.75   4.17  41.36
------------------------------------------------------------------------
 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:    2.222    0.017    0.327
   1_adp:    2.222    0.017    0.327
   1_occ:    2.222    0.017    0.327
   2_bss:    2.222    0.017    0.327
   2_xyz:    1.733    0.049    0.587
   2_adp:    1.733    0.049    0.587
   2_occ:    1.733    0.049    0.587
   3_bss:    1.733    0.049    0.587
   3_xyz:    1.500    0.052    0.726
   3_adp:    1.500    0.052    0.726
   3_occ:    1.500    0.052    0.726
   4_bss:    1.500    0.052    0.726
   4_xyz:    1.540    0.078    0.833
   4_adp:    1.540    0.078    0.833
   4_occ:    1.540    0.078    0.833
   5_bss:    1.540    0.078    0.833
   5_xyz:    1.616    0.129    0.856
   5_adp:    1.616    0.129    0.856
   5_occ:    1.616    0.129    0.856
   5_bss:    1.616    0.129    0.856
------------------------------------------------------------------------

CPU time actual refinement: 340.52


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_716/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_716/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_716/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_716/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_716/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 340.36 
  Macro-tasks:
    bulk solvent and scale       = 45.30  
    individual site refinement   = 132.36 
    weights calculation          = 29.36  
    collect and process          = 6.38   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 213.50 
  Micro-tasks:
    mask                            = 2.39   
    f_calc                          = 108.30 
    alpha_beta                      = 8.12   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 115.24 
    fmodel                         = 7.03   
    r_factors                      = 0.25   
    phase_errors                   = 10.49  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 253.21 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.884 micro seconds
Total CPU time: 5.90 minutes
from_scatterers_fft:    645 calls, 107.92 s
gradients_fft:          590 calls, 102.66 s

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

# Date 2008-01-16 Time 05:29:50 PST -0800 (1200490190.09 s)
Start R-work = 0.4621, R-free = 0.4504 (no bulk solvent and anisotropic scale)
Final R-work = 0.1425, R-free = 0.1872 (no bulk solvent and anisotropic scale)

Start R-work = 0.4509, R-free = 0.4370
Final R-work = 0.1214, R-free = 0.1682