# Date 2008-01-16 Time 05:26:11 PST -0800 (1200489971.31 s)
#phil __OFF__

Command line arguments: "../736.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4615
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 736

-------------------------------------------------------------------------------
  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: (70.6012, 45.7567, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, 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: (70.6012, 45.7567, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1485 1.95393
Completeness in resolution range: 0.91623
Completeness with d_max=infinity: 0.913623

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1485
                             d_min =   1.9539

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: (70.6012, 45.7567, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1485 1.95393
Completeness in resolution range: 0.91623
Completeness with d_max=infinity: 0.913623

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1490 -  4.1829 [2244/2270]  2018   226  10.1%
  bin  2:  4.1829 -  3.3317 [2160/2180]  1949   211   9.8%
  bin  3:  3.3317 -  2.9139 [2128/2147]  1913   215  10.1%
  bin  4:  2.9139 -  2.6491 [2104/2134]  1885   219  10.4%
  bin  5:  2.6491 -  2.4600 [2112/2131]  1902   210   9.9%
  bin  6:  2.4600 -  2.3155 [2076/2101]  1869   207  10.0%
  bin  7:  2.3155 -  2.1999 [2103/2131]  1894   209   9.9%
  bin  8:  2.1999 -  2.1044 [2049/2085]  1842   207  10.1%
  bin  9:  2.1044 -  2.0236 [1977/2102]  1789   188   9.5%
  bin 10:  2.0236 -  1.9539 [ 636/2099]   569    67  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_736/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.68 -     2.32: 34
        2.32 -     2.97: 1782
        2.97 -     3.61: 4571
        3.61 -     4.26: 9145
        4.26 -     4.90: 12738
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.704 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.740 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.774 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28265 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_736/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_736/model_refine_001.geo

CPU time processing inputs: 9.11


============================ 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 = 70.60125 45.75675 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4861   r_free= 0.4894   ksol= 0.00   Bsol= 0.00   scale= 0.871    |
|                                                                             |
| 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:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.301572                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1490 -  4.6663 0.99   1457  160 0.4052 0.3953      6.6442      6.6092|
|  2:  4.6663 -  3.7218 0.99   1401  158 0.4370 0.4375      6.8558      6.8505|
|  3:  3.7218 -  3.2567 0.99   1381  154 0.4588 0.4433      6.6925      6.6798|
|  4:  3.2567 -  2.9614 0.99   1370  153 0.4892 0.5138      6.5467      6.5435|
|  5:  2.9614 -  2.7504 0.99   1360  152 0.5235 0.5159      6.3726      6.3985|
|  6:  2.7504 -  2.5891 0.99   1369  147 0.5158 0.5436      6.2836      6.2216|
|  7:  2.5891 -  2.4600 0.99   1329  157 0.5169 0.5445      6.2341      6.1949|
|  8:  2.4600 -  2.3534 0.98   1338  147 0.5291 0.5190      6.1708      6.1409|
|  9:  2.3534 -  2.2631 0.98   1332  144 0.5152 0.5451      6.1258      6.2208|
| 10:  2.2631 -  2.1852 1.00   1358  151 0.5288 0.5440      6.0693      6.0797|
| 11:  2.1852 -  2.1171 0.98   1314  150 0.5098 0.4873      6.0119      6.0352|
| 12:  2.1171 -  2.0567 0.98   1331  136 0.5244 0.5248      5.9356      5.9197|
| 13:  2.0567 -  2.0027 0.78   1040  122 0.5157 0.5122      5.8912      5.7955|
| 14:  2.0027 -  1.9539 0.19    250   28 0.5361 0.4952      5.8434      5.8952|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1490 -  4.6663  1457   160  0.70  34.09   0.80     0.76      74492.78|
|  2:  4.6663 -  3.7218  1401   158  0.65  39.96   0.87     0.75     133269.36|
|  3:  3.7218 -  3.2567  1381   154  0.48  53.44   0.90     0.66     147702.45|
|  4:  3.2567 -  2.9614  1370   153  0.34  64.48   0.87     0.50     139539.16|
|  5:  2.9614 -  2.7504  1360   152  0.29  68.27   0.85     0.43      99371.97|
|  6:  2.7504 -  2.5891  1369   147  0.27  69.86   0.88     0.40      83904.03|
|  7:  2.5891 -  2.4600  1329   157  0.29  68.37   0.89     0.41      71191.81|
|  8:  2.4600 -  2.3534  1338   147  0.26  70.55   0.89     0.39      66920.95|
|  9:  2.3534 -  2.2631  1332   144  0.23  72.64   0.91     0.35      62964.86|
| 10:  2.2631 -  2.1852  1358   151  0.23  73.16   0.90     0.35      56063.92|
| 11:  2.1852 -  2.1171  1314   150  0.23  73.01   0.96     0.36      52875.45|
| 12:  2.1171 -  2.0567  1331   136  0.27  70.14   0.90     0.44      45539.98|
| 13:  2.0567 -  2.0027  1040   122  0.29  68.63   0.93     0.48      39477.04|
| 14:  2.0027 -  1.9539   250    28  0.35  63.78   1.01     0.52      29711.46|
|alpha:            min =        0.35 max =            0.76 mean =         0.49|
|beta:             min =    29711.46 max =       147702.45 mean =     82991.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.35|
|phase err.(work): min =        0.00 max =           89.99 mean =        63.20|
|phase err.(test): min =        0.00 max =           89.94 mean =        63.62|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.500922             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.729   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.094177              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.870   (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 |  1.681 -  2.003:       18 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.003 -  2.325:       16 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.325 -  2.647:       78 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.647 -  2.969:     1704 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.969 -  3.290:     1909 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.290 -  3.612:     2662 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.612 -  3.934:     4725 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.934 -  4.256:     4420 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.256 -  4.578:     5795 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.578 -  4.900:     6943 |
|-----------------------------------------------------------------------------|
|-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 |   4.108    4.900  1.681 |       0.586 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.827)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4861   r_free= 0.4894   ksol= 0.00   Bsol= 0.00   scale= 0.871    |
|                                                                             |
| 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:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.301572                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4760   r_free= 0.4834   ksol= 0.34   Bsol= 50.00   scale= 0.908   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.12,1.08,3.54,0.00,0.00,0.00); trace/3= 0.50                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.297163                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.975851             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.550   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.650935              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.480   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4760      final r-factor (work) = 0.4183          |
| start r-factor (free) = 0.4834      final r-factor (free) = 0.4614          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.8672 = 11.98 * 0.50 * 6.2921 + 1.00 * 0.1905                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.4469 = 11.98 * 0.50 * 6.2337 + 1.00 * 0.1199                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4183      final r-factor (work) = 0.3885          |
| start r-factor (free) = 0.4614      final r-factor (free) = 0.4661          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2975 = 1.65 * 1.00 * 6.2337 + 1.00 * 0.0060                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2281 = 1.65 * 1.00 * 6.1832 + 1.00 * 0.0199                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.827)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.49   19.78    None  None   None       |
|    all(noH): 2823   0      0.00    99.49   19.78    None  None   None       |
|    Sol.    : 438    0      0.00    99.49   34.10    None  None   None       |
|    Mac.    : 2385   0      0.00    87.16   17.16    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 -   9.949:  762   |   5:    49.743 -  59.692:   75        |
|      1:     9.949 -  19.897:  932   |   6:    59.692 -  69.640:   36        |
|      2:    19.897 -  29.846:  576   |   7:    69.640 -  79.589:   20        |
|      3:    29.846 -  39.794:  295   |   8:    79.589 -  89.537:    6        |
|      4:    39.794 -  49.743:  117   |   9:    89.537 -  99.486:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3885 r_free = 0.4661             target_work(ml) = 6.185         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3883 r_free = 0.4681             target_work(ml) = 6.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3883   r_free= 0.4681   ksol= 0.34   Bsol= 50.00   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.12,1.08,3.54,0.00,0.00,0.00); trace/3= 0.50                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.185198                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3887   r_free= 0.4666   ksol= 0.36   Bsol= 72.47   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.02,0.34,2.24,0.00,0.00,0.00); trace/3= 0.52                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.189106                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.373602             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.282  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.847494              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.335  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3887      final r-factor (work) = 0.3303          |
| start r-factor (free) = 0.4666      final r-factor (free) = 0.4185          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 53.8564 = 17.37 * 0.50 * 6.1860 + 1.00 * 0.1199                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 53.4465 = 17.37 * 0.50 * 6.1386 + 1.00 * 0.1216                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3303      final r-factor (work) = 0.3152          |
| start r-factor (free) = 0.4185      final r-factor (free) = 0.4097          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2224 = 0.85 * 1.00 * 6.1386 + 1.00 * 0.0200                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1520 = 0.85 * 1.00 * 6.0618 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.827)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.72   19.33    None  None   None       |
|    all(noH): 2823   0      0.00    98.72   19.33    None  None   None       |
|    Sol.    : 438    0      0.00    98.72   34.96    None  None   None       |
|    Mac.    : 2385   0      0.00    81.17   16.46    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.873:  788   |   5:    49.362 -  59.235:   70        |
|      1:     9.873 -  19.745:  942   |   6:    59.235 -  69.107:   37        |
|      2:    19.745 -  29.617:  576   |   7:    69.107 -  78.980:   16        |
|      3:    29.617 -  39.490:  269   |   8:    78.980 -  88.852:    3        |
|      4:    39.490 -  49.362:  118   |   9:    88.852 -  98.724:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3152 r_free = 0.4097             target_work(ml) = 6.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3151 r_free = 0.4098             target_work(ml) = 6.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3151   r_free= 0.4098   ksol= 0.36   Bsol= 72.47   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.02,0.34,2.24,0.00,0.00,0.00); trace/3= 0.52                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.052203                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3154   r_free= 0.4084   ksol= 0.37   Bsol= 87.91   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.73,-0.27,1.43,-0.00,0.00,0.00); trace/3= 0.14                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.051097                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.473341              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.823   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 11.099559             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.628  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3154      final r-factor (work) = 0.2657          |
| start r-factor (free) = 0.4084      final r-factor (free) = 0.3465          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.8059 = 8.47 * 0.50 * 6.0624 + 1.00 * 0.1214                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.5067 = 8.47 * 0.50 * 5.9988 + 1.00 * 0.0917                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2657      final r-factor (work) = 0.2399          |
| start r-factor (free) = 0.3465      final r-factor (free) = 0.3390          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 66.5991 = 11.10 * 1.00 * 5.9988 + 1.00 * 0.0147                             |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 65.1290 = 11.10 * 1.00 * 5.8651 + 1.00 * 0.0287                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.827)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    117.12  21.73    None  None   None       |
|    all(noH): 2823   0      0.00    117.12  21.73    None  None   None       |
|    Sol.    : 438    0      0.27    117.12  49.62    None  None   None       |
|    Mac.    : 2385   0      0.00    110.08  16.61    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.712: 1136   |   5:    58.562 -  70.274:   97        |
|      1:    11.712 -  23.425:  805   |   6:    70.274 -  81.987:   61        |
|      2:    23.425 -  35.137:  349   |   7:    81.987 -  93.699:   35        |
|      3:    35.137 -  46.850:  196   |   8:    93.699 - 105.411:   19        |
|      4:    46.850 -  58.562:  114   |   9:   105.411 - 117.124:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2399 r_free = 0.3390             target_work(ml) = 5.852         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2398 r_free = 0.3388             target_work(ml) = 5.851         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2398   r_free= 0.3388   ksol= 0.37   Bsol= 87.91   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.73,-0.27,1.43,-0.00,0.00,0.00); trace/3= 0.14                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.851384                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2400   r_free= 0.3386   ksol= 0.36   Bsol= 98.21   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.93,-0.79,0.98,-0.00,0.00,0.00); trace/3= -0.24                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.851068                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.294738              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.515   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.236870              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.017  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2400      final r-factor (work) = 0.1981          |
| start r-factor (free) = 0.3386      final r-factor (free) = 0.2791          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.4163 = 8.29 * 0.50 * 5.8651 + 1.00 * 0.0917                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.0746 = 8.29 * 0.50 * 5.7851 + 1.00 * 0.0817                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1981      final r-factor (work) = 0.1830          |
| start r-factor (free) = 0.2791      final r-factor (free) = 0.2383          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3987 = 0.24 * 1.00 * 5.7851 + 1.00 * 0.0284                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3498 = 0.24 * 1.00 * 5.6513 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.827)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.73   18.05    None  None   None       |
|    all(noH): 2823   0      0.00    98.73   18.05    None  None   None       |
|    Sol.    : 438    0      4.75    97.47   42.58    None  None   None       |
|    Mac.    : 2385   0      0.00    98.73   13.54    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 -   9.873:  973   |   5:    49.367 -  59.240:   92        |
|      1:     9.873 -  19.747: 1085   |   6:    59.240 -  69.113:   40        |
|      2:    19.747 -  29.620:  303   |   7:    69.113 -  78.986:   23        |
|      3:    29.620 -  39.493:  156   |   8:    78.986 -  88.860:   13        |
|      4:    39.493 -  49.367:  133   |   9:    88.860 -  98.733:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1830 r_free = 0.2383             target_work(ml) = 5.572         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1828 r_free = 0.2379             target_work(ml) = 5.570         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1828   r_free= 0.2379   ksol= 0.36   Bsol= 98.21   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.93,-0.79,0.98,-0.00,0.00,0.00); trace/3= -0.24                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.570212                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1820   r_free= 0.2366   ksol= 0.34   Bsol= 80.00   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.84,-2.14,0.14,-0.00,0.00,0.00); trace/3= -1.28                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.567681                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.801453              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.695  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.202000              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.904   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1820      final r-factor (work) = 0.1492          |
| start r-factor (free) = 0.2366      final r-factor (free) = 0.1985          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8253 = 3.80 * 0.50 * 5.6524 + 1.00 * 0.0817                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4954 = 3.80 * 0.50 * 5.4873 + 1.00 * 0.0655                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1492      final r-factor (work) = 0.1468          |
| start r-factor (free) = 0.1985      final r-factor (free) = 0.1965          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1198 = 0.20 * 1.00 * 5.4873 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1048 = 0.20 * 1.00 * 5.3794 + 1.00 * 0.0182                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.827)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.72   18.07    None  None   None       |
|    all(noH): 2823   0      0.00    98.72   18.07    None  None   None       |
|    Sol.    : 438    0      5.62    97.37   42.63    None  None   None       |
|    Mac.    : 2385   0      0.00    98.72   13.55    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:     0.000 -   9.872:  962   |   5:    49.362 -  59.234:   92        |
|      1:     9.872 -  19.745: 1113   |   6:    59.234 -  69.107:   40        |
|      2:    19.745 -  29.617:  287   |   7:    69.107 -  78.979:   24        |
|      3:    29.617 -  39.490:  153   |   8:    78.979 -  88.852:   13        |
|      4:    39.490 -  49.362:  134   |   9:    88.852 -  98.724:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1468 r_free = 0.1965             target_work(ml) = 5.373         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1464 r_free = 0.1960             target_work(ml) = 5.371         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1464   r_free= 0.1960   ksol= 0.34   Bsol= 80.00   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.84,-2.14,0.14,-0.00,0.00,0.00); trace/3= -1.28                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.370874                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1490 -  4.6663 0.99   1457  160 0.1022 0.1416        5.43      5.6748|
|  2:  4.6663 -  3.7218 0.99   1401  158 0.0999 0.1413      5.5844      5.8655|
|  3:  3.7218 -  3.2567 0.99   1381  154 0.1359 0.1855      5.6816       5.947|
|  4:  3.2567 -  2.9614 0.99   1370  153 0.1721 0.2185      5.7147      5.8875|
|  5:  2.9614 -  2.7504 0.99   1360  152 0.1763 0.2233      5.5719      5.7815|
|  6:  2.7504 -  2.5891 0.99   1369  147 0.1685 0.2474      5.4489      5.6744|
|  7:  2.5891 -  2.4600 0.99   1329  157 0.1625 0.2172      5.3801      5.5794|
|  8:  2.4600 -  2.3534 0.98   1338  147 0.1701 0.2268      5.3522       5.577|
|  9:  2.3534 -  2.2631 0.98   1332  144 0.1679 0.2179      5.2923      5.4977|
| 10:  2.2631 -  2.1852 1.00   1358  151 0.1557 0.1995      5.1694      5.3272|
| 11:  2.1852 -  2.1171 0.98   1314  150 0.1501 0.2228      5.1288      5.4885|
| 12:  2.1171 -  2.0567 0.98   1331  136 0.1539 0.1911      5.0434      5.2102|
| 13:  2.0567 -  2.0027 0.78   1040  122 0.1478 0.1981      4.9758      5.1285|
| 14:  2.0027 -  1.9539 0.19    250   28 0.1482 0.1993       4.931      5.2276|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1490 -  4.6663  1457   160  0.93  10.16   0.97     0.95       8531.42|
|  2:  4.6663 -  3.7218  1401   158  0.94  10.13   1.03     1.02      12289.90|
|  3:  3.7218 -  3.2567  1381   154  0.90  15.79   1.05     1.04      16178.02|
|  4:  3.2567 -  2.9614  1370   153  0.86  20.26   1.02     0.99      17969.31|
|  5:  2.9614 -  2.7504  1360   152  0.85  21.56   1.01     0.97      14035.71|
|  6:  2.7504 -  2.5891  1369   147  0.84  22.23   1.00     0.94      11419.16|
|  7:  2.5891 -  2.4600  1329   157  0.85  21.10   1.03     0.98       9982.30|
|  8:  2.4600 -  2.3534  1338   147  0.85  22.04   1.03     0.99       9538.13|
|  9:  2.3534 -  2.2631  1332   144  0.84  22.21   1.03     0.97       8459.38|
| 10:  2.2631 -  2.1852  1358   151  0.86  20.96   1.02     0.99       6711.59|
| 11:  2.1852 -  2.1171  1314   150  0.86  20.38   1.03     0.97       6261.67|
| 12:  2.1171 -  2.0567  1331   136  0.86  20.37   1.03     1.03       5374.41|
| 13:  2.0567 -  2.0027  1040   122  0.86  20.46   1.02     1.00       4775.30|
| 14:  2.0027 -  1.9539   250    28  0.90  16.64   1.00     0.98       3877.14|
|alpha:            min =        0.94 max =            1.04 mean =         0.99|
|beta:             min =     3877.14 max =        17969.31 mean =     10156.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.98 mean =        18.90|
|phase err.(test): min =        0.00 max =           89.44 mean =        17.84|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1462   r_free= 0.1952   ksol= 0.32   Bsol= 55.69   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.66,-0.36,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.368180                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1462   r_free= 0.1952   ksol= 0.32   Bsol= 55.69   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.66,-0.36,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.368180                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1490 -  4.6663 0.99   1457  160 0.1017 0.1358      5.4083      5.6435|
|  2:  4.6663 -  3.7218 0.99   1401  158 0.0989 0.1398        5.57      5.8591|
|  3:  3.7218 -  3.2567 0.99   1381  154 0.1353 0.1846      5.6758      5.9386|
|  4:  3.2567 -  2.9614 0.99   1370  153 0.1721 0.2180      5.7127      5.8847|
|  5:  2.9614 -  2.7504 0.99   1360  152 0.1762 0.2235      5.5716      5.7844|
|  6:  2.7504 -  2.5891 0.99   1369  147 0.1690 0.2477      5.4509      5.6759|
|  7:  2.5891 -  2.4600 0.99   1329  157 0.1627 0.2184      5.3825       5.582|
|  8:  2.4600 -  2.3534 0.98   1338  147 0.1703 0.2280      5.3542      5.5803|
|  9:  2.3534 -  2.2631 0.98   1332  144 0.1680 0.2177      5.2932      5.4964|
| 10:  2.2631 -  2.1852 1.00   1358  151 0.1560 0.2000      5.1707      5.3295|
| 11:  2.1852 -  2.1171 0.98   1314  150 0.1501 0.2231       5.129       5.489|
| 12:  2.1171 -  2.0567 0.98   1331  136 0.1539 0.1912       5.045      5.2111|
| 13:  2.0567 -  2.0027 0.78   1040  122 0.1479 0.1982       4.977      5.1305|
| 14:  2.0027 -  1.9539 0.19    250   28 0.1483 0.1997      4.9319      5.2291|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1490 -  4.6663  1457   160  0.93   9.80   0.97     0.94       7867.67|
|  2:  4.6663 -  3.7218  1401   158  0.94   9.85   1.03     1.02      11765.22|
|  3:  3.7218 -  3.2567  1381   154  0.90  15.62   1.04     1.03      15927.90|
|  4:  3.2567 -  2.9614  1370   153  0.86  20.13   1.01     0.98      17763.88|
|  5:  2.9614 -  2.7504  1360   152  0.85  21.54   0.99     0.96      14042.13|
|  6:  2.7504 -  2.5891  1369   147  0.84  22.28   0.98     0.93      11480.04|
|  7:  2.5891 -  2.4600  1329   157  0.85  21.16   1.00     0.96      10051.88|
|  8:  2.4600 -  2.3534  1338   147  0.85  22.10   1.00     0.96       9597.79|
|  9:  2.3534 -  2.2631  1332   144  0.84  22.23   1.00     0.95       8486.72|
| 10:  2.2631 -  2.1852  1358   151  0.86  20.96   1.00     0.96       6724.81|
| 11:  2.1852 -  2.1171  1314   150  0.86  20.40   1.00     0.94       6279.78|
| 12:  2.1171 -  2.0567  1331   136  0.86  20.38   1.00     1.00       5389.56|
| 13:  2.0567 -  2.0027  1040   122  0.86  20.47   0.99     0.97       4789.85|
| 14:  2.0027 -  1.9539   250    28  0.90  16.66   0.97     0.95       3890.94|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     3890.94 max =        17763.88 mean =     10045.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           90.00 mean =        18.84|
|phase err.(test): min =        0.00 max =           89.61 mean =        17.81|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.827)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.73   18.07    None  None   None       |
|    all(noH): 2823   0      0.00    98.73   18.07    None  None   None       |
|    Sol.    : 438    0      5.63    97.37   42.63    None  None   None       |
|    Mac.    : 2385   0      0.00    98.73   13.56    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.875:  962   |   5:    49.365 -  59.237:   92        |
|      1:     9.875 -  19.748: 1113   |   6:    59.237 -  69.110:   40        |
|      2:    19.748 -  29.620:  287   |   7:    69.110 -  78.982:   24        |
|      3:    29.620 -  39.493:  153   |   8:    78.982 -  88.855:   13        |
|      4:    39.493 -  49.365:  134   |   9:    88.855 -  98.727:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 343         
Filter by distance & map next to the model:
   mapped sites are within: 0.393 - 4.489
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 325 from: 343
   mapped sites are within: 0.745 - 4.489

peak=    7.026 closest distance to " O   HOH Z 103 " =    1.062
peak=    6.666 closest distance to " O   HOH Z 387 " =    1.932
peak=    6.315 closest distance to " O   HOH Z 390 " =    1.086
peak=    6.186 closest distance to " O   HOH Z 245 " =    1.371
peak=    6.139 closest distance to " O   HOH Z 381 " =    1.086
peak=    5.885 closest distance to " O   HOH Z 431 " =    2.123
peak=    5.736 closest distance to " O   HOH Z 131 " =    1.442
peak=    5.501 closest distance to " O   HOH Z 130 " =    1.061
peak=    5.465 closest distance to " O   HOH Z 424 " =    1.988
peak=    5.462 closest distance to " O   VAL A  72 " =    0.888
peak=    5.369 closest distance to " O   HOH Z  77 " =    1.320
peak=    5.257 closest distance to " O   HOH Z  29 " =    1.905
peak=    5.064 closest distance to " O   HOH Z 287 " =    1.993
peak=    4.991 closest distance to " O   HOH Z  69 " =    2.205
peak=    4.899 closest distance to " O   HOH Z 417 " =    2.856
peak=    4.842 closest distance to " O   HOH Z  66 " =    1.359
peak=    4.830 closest distance to " O   HOH Z  63 " =    1.645
peak=    4.804 closest distance to " O   HOH Z 126 " =    1.972
peak=    4.771 closest distance to " O   HOH Z  46 " =    1.545
peak=    4.761 closest distance to " O   HOH Z 359 " =    1.869
peak=    4.749 closest distance to " O   HOH Z 105 " =    1.479
peak=    4.732 closest distance to " O   HOH Z 396 " =    0.849
peak=    4.708 closest distance to " O   HOH Z  49 " =    2.199
peak=    4.704 closest distance to " CG  PRO A  90 " =    1.343
peak=    4.693 closest distance to " O   HOH Z 222 " =    1.979
peak=    4.665 closest distance to " CB  ARG A 275 " =    1.019
peak=    4.623 closest distance to " O   HOH Z 143 " =    1.989
peak=    4.621 closest distance to " O   HOH Z  65 " =    1.897
peak=    4.565 closest distance to " CB  SER A  63 " =    1.453
peak=    4.565 closest distance to " O   HOH Z 139 " =    1.166
peak=    4.485 closest distance to " CZ3 TRP A 266 " =    1.092
peak=    4.465 closest distance to " O   HOH Z 403 " =    1.777
peak=    4.459 closest distance to " NE2 GLN A  11 " =    1.407
peak=    4.453 closest distance to " O   ASP A 286 " =    2.617
peak=    4.433 closest distance to " O   HOH Z 414 " =    1.848
peak=    4.418 closest distance to " O   HOH Z 418 " =    1.295
peak=    4.381 closest distance to " C   GLN A  73 " =    1.014
peak=    4.379 closest distance to " O   HOH Z 298 " =    2.014
peak=    4.376 closest distance to " O   PRO A 198 " =    1.438
peak=    4.357 closest distance to " CG  PRO A  54 " =    1.539
peak=    4.353 closest distance to " O   HOH Z 295 " =    1.475
peak=    4.329 closest distance to " CA  PRO A  54 " =    0.949
peak=    4.329 closest distance to " O   HOH Z 232 " =    2.260
peak=    4.303 closest distance to " O   HOH Z  67 " =    1.662
peak=    4.266 closest distance to " O   HOH Z 415 " =    1.067
peak=    4.258 closest distance to " O   HOH Z  70 " =    1.044
peak=    4.257 closest distance to " O   HOH Z 427 " =    1.334
peak=    4.241 closest distance to " O   HOH Z  39 " =    1.497
peak=    4.239 closest distance to " CA  SER A  87 " =    0.878
peak=    4.237 closest distance to " O   HOH Z 422 " =    1.145
peak=    4.231 closest distance to " NH1AARG A 145 " =    1.127
peak=    4.220 closest distance to " O   HOH Z 427 " =    2.096
peak=    4.202 closest distance to " O   HOH Z 119 " =    1.583
peak=    4.178 closest distance to " O   HOH Z  92 " =    1.497
peak=    4.172 closest distance to " O   HOH Z 154 " =    2.304
peak=    4.167 closest distance to " O   HOH Z  21 " =    1.308
peak=    4.158 closest distance to " O   HOH Z  97 " =    1.541
peak=    4.135 closest distance to " N   GLN A 278 " =    1.146
peak=    4.096 closest distance to " O   HOH Z   7 " =    2.475
peak=    4.093 closest distance to " O   HOH Z  30 " =    1.914
peak=    4.091 closest distance to " O   HOH Z 147 " =    1.403
peak=    4.085 closest distance to " OG ASER A 212 " =    1.446
peak=    4.083 closest distance to " N   ALA A   1 " =    1.600
peak=    4.075 closest distance to " O   HOH Z  57 " =    1.559
peak=    4.067 closest distance to " CB  PRO A  90 " =    1.088
peak=    4.064 closest distance to " CE3 TRP A 274 " =    1.393
peak=    4.058 closest distance to " O   HOH Z  91 " =    2.480
peak=    4.039 closest distance to " O   HOH Z 410 " =    1.440
peak=    4.018 closest distance to " O   HOH Z 181 " =    1.604
peak=    3.990 closest distance to " CE  LYS A 119 " =    1.283
peak=    3.979 closest distance to " OG ASER A 258 " =    3.106
peak=    3.979 closest distance to " O   HOH Z 244 " =    1.796
peak=    3.968 closest distance to " CE  MET A  93 " =    1.483
peak=    3.964 closest distance to " NH2 ARG A  56 " =    1.988
peak=    3.952 closest distance to " O   HOH Z 411 " =    3.572
peak=    3.927 closest distance to " O   HOH Z 350 " =    1.349
peak=    3.924 closest distance to " NH2AARG A 145 " =    1.215
peak=    3.922 closest distance to " CB  ASN A 187 " =    0.763
peak=    3.914 closest distance to " N   GLN A  73 " =    0.891
peak=    3.914 closest distance to " CD  LYS A  76 " =    1.874
peak=    3.912 closest distance to " O   HOH Z 112 " =    1.427
peak=    3.907 closest distance to " O   HOH Z 132 " =    1.099
peak=    3.902 closest distance to " O   HOH Z 225 " =    1.871
peak=    3.887 closest distance to " O   HOH Z  51 " =    2.029
peak=    3.880 closest distance to " CA  ALA A  51 " =    0.952
peak=    3.844 closest distance to " CG  LYS A 119 " =    0.842
peak=    3.831 closest distance to " CB  GLN A 223 " =    1.554
peak=    3.825 closest distance to " O   HOH Z  11 " =    1.365
peak=    3.824 closest distance to " CB  SER A  62 " =    0.904
peak=    3.822 closest distance to " O  BHOH Z  74 " =    1.175
peak=    3.819 closest distance to " O   HOH Z 207 " =    1.354
peak=    3.816 closest distance to " O   HOH Z 126 " =    1.509
peak=    3.813 closest distance to " CB  SER A 276 " =    1.208
peak=    3.810 closest distance to " NZ  LYS A 117 " =    3.053
peak=    3.805 closest distance to " CB  ALA A 114 " =    1.091
peak=    3.798 closest distance to " O   HOH Z 153 " =    3.617
peak=    3.789 closest distance to " O   HOH Z 258 " =    2.189
peak=    3.783 closest distance to " O   HOH Z 128 " =    2.007
peak=    3.779 closest distance to " O   HOH Z  27 " =    1.018
peak=    3.768 closest distance to " CZ  PHE A  16 " =    0.884
peak=    3.763 closest distance to " O   HOH Z  68 " =    1.819
peak=    3.762 closest distance to " O   HOH Z 368 " =    3.431
peak=    3.761 closest distance to " ND2AASN A 224 " =    0.999
peak=    3.756 closest distance to " O   HOH Z 278 " =    1.338
peak=    3.755 closest distance to " CA  LEU A 282 " =    0.966
peak=    3.754 closest distance to " CB  ASP A 124 " =    0.955
peak=    3.754 closest distance to " CB  THR A 294 " =    1.220
peak=    3.752 closest distance to " CB  SER A 216 " =    1.109
peak=    3.748 closest distance to " CG2 THR A 221 " =    1.175
peak=    3.743 closest distance to " CB  ASN A 148 " =    1.326
peak=    3.740 closest distance to " ND2 ASN A  60 " =    2.852
peak=    3.735 closest distance to " O   HOH Z 380 " =    2.051
peak=    3.732 closest distance to " O   HOH Z 124 " =    1.161
peak=    3.730 closest distance to " NE2 HIS A 207 " =    1.013
peak=    3.729 closest distance to " CB  ILE A 120 " =    1.283
peak=    3.728 closest distance to " CB  TRP A 179 " =    1.266
peak=    3.711 closest distance to " O   HOH Z 296 " =    1.268
peak=    3.710 closest distance to " O   HOH Z 120 " =    0.844
peak=    3.705 closest distance to " CB  SER A   3 " =    1.568
peak=    3.703 closest distance to " O   HOH Z 219 " =    4.021
peak=    3.702 closest distance to " O   HOH Z 374 " =    1.328
peak=    3.686 closest distance to " O   HOH Z 133 " =    0.993
peak=    3.677 closest distance to " CG  PRO A 198 " =    1.246
peak=    3.676 closest distance to " O   HOH Z 434 " =    1.645
peak=    3.674 closest distance to " O   HOH Z 286 " =    1.742
peak=    3.669 closest distance to " CA  VAL A 125 " =    1.179
peak=    3.669 closest distance to " CG AARG A 275 " =    1.248
peak=    3.659 closest distance to " O   HOH Z 371 " =    1.727
peak=    3.659 closest distance to " CG1 VAL A 296 " =    1.142
peak=    3.657 closest distance to " O   HOH Z 363 " =    1.085
peak=    3.653 closest distance to " O   HOH Z 248 " =    1.789
peak=    3.640 closest distance to " O   HOH Z 368 " =    1.827
peak=    3.640 closest distance to " O   HOH Z 362 " =    1.999
peak=    3.637 closest distance to " CG2 VAL A 257 " =    0.945
peak=    3.634 closest distance to " CG  GLN A  58 " =    1.248
peak=    3.628 closest distance to " NH2 ARG A  56 " =    1.157
peak=    3.628 closest distance to " CB  VAL A 202 " =    1.514
peak=    3.627 closest distance to " O   HOH Z 424 " =    1.252
peak=    3.624 closest distance to " OD1 ASP A  65 " =    1.987
peak=    3.615 closest distance to " CD  GLN A  77 " =    1.435
peak=    3.613 closest distance to " O   HOH Z 158 " =    1.535
peak=    3.613 closest distance to " CA  ILE A 234 " =    1.078
peak=    3.612 closest distance to " O   HOH Z 361 " =    1.623
peak=    3.609 closest distance to " CG2 ILE A 239 " =    0.929
peak=    3.607 closest distance to " CB  LYS A 166 " =    0.872
peak=    3.600 closest distance to " O   HOH Z 365 " =    2.404
peak=    3.600 closest distance to " CZ  PHE A  38 " =    1.216
peak=    3.595 closest distance to " O   TYR A 116 " =    1.256
peak=    3.592 closest distance to " CB  GLU A 152 " =    1.137
peak=    3.589 closest distance to " O   HOH Z 389 " =    1.851
peak=    3.580 closest distance to " O   HOH Z 127 " =    0.930
peak=    3.569 closest distance to " O   HOH Z 424 " =    3.275
peak=    3.567 closest distance to " CD2 LEU A 300 " =    1.519
peak=    3.561 closest distance to " CB  ARG A 138 " =    0.992
peak=    3.561 closest distance to " CB  GLU A 175 " =    0.846
peak=    3.555 closest distance to " O   HOH Z 155 " =    1.900
peak=    3.551 closest distance to " O   HOH Z 146 " =    1.498
peak=    3.544 closest distance to " O   HOH Z 211 " =    1.642
peak=    3.542 closest distance to " O   HOH Z 293 " =    1.423
peak=    3.539 closest distance to " O   HOH Z 143 " =    1.430
peak=    3.537 closest distance to " O   HOH Z 330 " =    0.921
peak=    3.536 closest distance to " O   HOH Z 276 " =    1.278
peak=    3.536 closest distance to " O   HOH Z  43 " =    1.408
peak=    3.535 closest distance to " O   HOH Z  58 " =    1.812
peak=    3.535 closest distance to " CB  ASN A  39 " =    0.898
peak=    3.526 closest distance to " O   HOH Z 180 " =    2.230
peak=    3.518 closest distance to " O   HOH Z 240 " =    2.028
peak=    3.518 closest distance to " CG  LEU A 101 " =    1.039
peak=    3.513 closest distance to " NZ  LYS A 119 " =    2.148
peak=    3.512 closest distance to " CE3 TRP A 150 " =    1.160
peak=    3.510 closest distance to " O   HOH Z 171 " =    2.005
peak=    3.507 closest distance to " NH2 ARG A 269 " =    1.096
peak=    3.506 closest distance to " O   HOH Z  76 " =    1.532
peak=    3.498 closest distance to " O   HOH Z  53 " =    2.292
peak=    3.483 closest distance to " O   ALA A 165 " =    1.520
peak=    3.482 closest distance to " O   HOH Z 303 " =    2.084
peak=    3.481 closest distance to " CG1AVAL A 121 " =    0.886
peak=    3.477 closest distance to " CB  ALA A  43 " =    0.963
peak=    3.474 closest distance to " CB  LYS A 290 " =    0.877
peak=    3.468 closest distance to " CD  ARG A 195 " =    3.611
peak=    3.464 closest distance to " O   HOH Z 213 " =    2.031
peak=    3.463 closest distance to " CB  GLU A 277 " =    3.526
peak=    3.461 closest distance to " O   HOH Z 430 " =    2.110
peak=    3.459 closest distance to " O   HOH Z 400 " =    0.745
peak=    3.457 closest distance to " O   HOH Z  40 " =    2.225
peak=    3.456 closest distance to " O   HOH Z 326 " =    1.309
peak=    3.456 closest distance to " O   HOH Z 181 " =    2.290
peak=    3.455 closest distance to " CB  MET A  40 " =    0.965
peak=    3.454 closest distance to " CB  SER A 210 " =    0.944
peak=    3.448 closest distance to " O   HOH Z 358 " =    1.467
peak=    3.445 closest distance to " CB  SER A  99 " =    0.966
peak=    3.443 closest distance to " N   PHE A 130 " =    1.327
peak=    3.441 closest distance to " CE1 PHE A  61 " =    1.588
peak=    3.435 closest distance to " O   HOH Z  78 " =    1.886
peak=    3.427 closest distance to " CB  THR A  31 " =    1.470
peak=    3.426 closest distance to " O   HOH Z 423 " =    1.710
peak=    3.426 closest distance to " N   GLN A  11 " =    0.957
peak=    3.426 closest distance to " O   HOH Z 298 " =    4.038
peak=    3.426 closest distance to " O   HOH Z 422 " =    2.114
peak=    3.425 closest distance to " O   HOH Z 201 " =    1.947
peak=    3.416 closest distance to " N   ALA A 292 " =    1.211
peak=    3.411 closest distance to " OE1 GLU A  53 " =    0.999
peak=    3.411 closest distance to " O   HOH Z  26 " =    1.693
peak=    3.409 closest distance to " O   HOH Z 425 " =    1.523
peak=    3.404 closest distance to " CA  ALA A   7 " =    0.988
peak=    3.401 closest distance to " NE2 GLN A 278 " =    3.323
peak=    3.401 closest distance to " CA  TYR A  30 " =    1.316
peak=    3.400 closest distance to " O   HOH Z  61 " =    1.641
peak=    3.397 closest distance to " OE1 GLN A 240 " =    1.610
peak=    3.396 closest distance to " O   ASN A 142 " =    1.043
peak=    3.393 closest distance to " O   HOH Z 153 " =    4.088
peak=    3.389 closest distance to " O   HOH Z 352 " =    1.749
peak=    3.386 closest distance to " O   HOH Z 218 " =    1.864
peak=    3.385 closest distance to " CB  SER A  26 " =    1.525
peak=    3.384 closest distance to " O   HOH Z 357 " =    2.150
peak=    3.382 closest distance to " CA  ARG A 195 " =    1.348
peak=    3.380 closest distance to " O   HOH Z  88 " =    3.605
peak=    3.376 closest distance to " O   HOH Z 351 " =    0.854
peak=    3.373 closest distance to " OG BSER A  12 " =    0.978
peak=    3.373 closest distance to " SD BMET A  47 " =    1.118
peak=    3.371 closest distance to " N   ALA A 165 " =    1.159
peak=    3.369 closest distance to " O   HOH Z   1 " =    1.698
peak=    3.367 closest distance to " C   GLU A 277 " =    1.383
peak=    3.366 closest distance to " O   HOH Z 375 " =    1.142
peak=    3.365 closest distance to " N   TYR A  15 " =    1.148
peak=    3.361 closest distance to " CB  ASN A 176 " =    1.041
peak=    3.359 closest distance to " CE3 TRP A  85 " =    1.177
peak=    3.358 closest distance to " O   HOH Z 365 " =    1.599
peak=    3.358 closest distance to " CG2BVAL A  41 " =    1.231
peak=    3.356 closest distance to " CB  GLN A  88 " =    1.372
peak=    3.354 closest distance to " O   HOH Z   6 " =    1.790
peak=    3.350 closest distance to " O   HOH Z 117 " =    0.877
peak=    3.347 closest distance to " O   HIS A 115 " =    0.844
peak=    3.346 closest distance to " CG  LEU A 167 " =    1.413
peak=    3.343 closest distance to " O   HOH Z  33 " =    1.822
peak=    3.342 closest distance to " CG1AVAL A  72 " =    1.376
peak=    3.335 closest distance to " N   SER A  97 " =    0.798
peak=    3.328 closest distance to " O   HOH Z 214 " =    2.517
peak=    3.319 closest distance to " O   HOH Z 185 " =    2.129
peak=    3.308 closest distance to " CD  ARG A 259 " =    1.594
peak=    3.306 closest distance to " CB  ASN A 142 " =    0.981
peak=    3.306 closest distance to " CB  ALA A 131 " =    1.656
peak=    3.303 closest distance to " CG  PRO A 243 " =    1.182
peak=    3.303 closest distance to " CD  LYS A 166 " =    1.595
peak=    3.300 closest distance to " N   GLU A   2 " =    1.336
peak=    3.296 closest distance to " CB  ALA A  10 " =    0.898
peak=    3.295 closest distance to " O   HOH Z 368 " =    4.489
peak=    3.295 closest distance to " O   HOH Z 271 " =    1.918
peak=    3.293 closest distance to " O   HOH Z 171 " =    1.716
peak=    3.292 closest distance to " CG2 VAL A 202 " =    1.568
peak=    3.288 closest distance to " OD1 ASP A 238 " =    1.069
peak=    3.282 closest distance to " O   HOH Z 217 " =    1.345
peak=    3.277 closest distance to " CG  ARG A 159 " =    0.763
peak=    3.276 closest distance to " CZ  PHE A 218 " =    1.200
peak=    3.271 closest distance to " O   HOH Z 327 " =    2.206
peak=    3.269 closest distance to " O   HOH Z 280 " =    1.525
peak=    3.266 closest distance to " CD2 TYR A 186 " =    1.024
peak=    3.265 closest distance to " CE  LYS A  76 " =    0.984
peak=    3.264 closest distance to " CB  ILE A 263 " =    1.130
peak=    3.261 closest distance to " N   ARG A 156 " =    1.134
peak=    3.260 closest distance to " O   HOH Z 239 " =    1.666
peak=    3.251 closest distance to " CB  LEU A 300 " =    1.132
peak=    3.250 closest distance to " CD  LYS A  76 " =    1.421
peak=    3.246 closest distance to " O   HOH Z 393 " =    1.361
peak=    3.245 closest distance to " N   GLY A 302 " =    1.073
peak=    3.239 closest distance to " OD1 ASN A 301 " =    1.311
peak=    3.238 closest distance to " CB  TRP A 150 " =    1.232
peak=    3.237 closest distance to " O   HOH Z   9 " =    2.013
peak=    3.231 closest distance to " OG1 THR A 294 " =    2.380
peak=    3.229 closest distance to " O   HOH Z  20 " =    1.512
peak=    3.225 closest distance to " CZ3 TRP A 123 " =    1.681
peak=    3.225 closest distance to " OG  SER A 276 " =    1.071
peak=    3.221 closest distance to " CA  SER A  12 " =    1.644
peak=    3.219 closest distance to " O   HOH Z  29 " =    1.654
peak=    3.216 closest distance to " CB  ARG A  79 " =    0.852
peak=    3.215 closest distance to " O   HOH Z 426 " =    1.343
peak=    3.211 closest distance to " CB  ALA A 242 " =    1.523
peak=    3.210 closest distance to " O   HOH Z 212 " =    1.788
peak=    3.206 closest distance to " OE2 GLU A  53 " =    1.914
peak=    3.206 closest distance to " CA  ARG A 159 " =    1.250
peak=    3.199 closest distance to " CB  PHE A 130 " =    1.258
peak=    3.197 closest distance to " CA  VAL A 121 " =    0.849
peak=    3.197 closest distance to " CG  GLN A  89 " =    1.637
peak=    3.195 closest distance to " OG BSER A  99 " =    2.332
peak=    3.191 closest distance to " O   HOH Z 220 " =    1.565
peak=    3.191 closest distance to " O   HOH Z  17 " =    2.041
peak=    3.187 closest distance to " CA  LEU A  83 " =    1.784
peak=    3.183 closest distance to " CD  ARG A  66 " =    1.915
peak=    3.182 closest distance to " O   HOH Z 194 " =    2.345
peak=    3.173 closest distance to " CB  PHE A  16 " =    0.997
peak=    3.163 closest distance to " O   HOH Z 158 " =    2.683
peak=    3.163 closest distance to " CB  MET A 105 " =    1.410
peak=    3.163 closest distance to " CB  ALA A 184 " =    1.422
peak=    3.161 closest distance to " CB  ASP A 140 " =    0.745
peak=    3.154 closest distance to " O   HOH Z 173 " =    1.985
peak=    3.151 closest distance to " CD2 LEU A   5 " =    1.385
peak=    3.149 closest distance to " OG BSER A 212 " =    2.683
peak=    3.147 closest distance to " O   HOH Z 283 " =    1.826
peak=    3.145 closest distance to " OG  SER A 271 " =    1.462
peak=    3.143 closest distance to " NH2BARG A 190 " =    1.221
peak=    3.142 closest distance to " CB  VAL A 265 " =    1.372
peak=    3.138 closest distance to " O   HOH Z 171 " =    2.475
peak=    3.136 closest distance to " CB  TYR A  30 " =    1.156
peak=    3.134 closest distance to " O   HOH Z  44 " =    1.960
peak=    3.134 closest distance to " CB  TRP A 266 " =    0.973
peak=    3.119 closest distance to " O   HOH Z 437 " =    2.096
peak=    3.112 closest distance to " CA  ARG A 219 " =    2.074
peak=    3.108 closest distance to " N   PHE A 208 " =    0.981
peak=    3.108 closest distance to " O   MET A 105 " =    1.568
peak=    3.108 closest distance to " O   HOH Z 186 " =    3.570
peak=    3.089 closest distance to " O   HOH Z 162 " =    3.200
peak=    3.085 closest distance to " CD1 LEU A 228 " =    1.794
peak=    3.082 closest distance to " CB  ASN A  74 " =    1.035
peak=    3.078 closest distance to " O   HOH Z 343 " =    2.932
peak=    3.077 closest distance to " NZ BLYS A 290 " =    1.009
peak=    3.066 closest distance to " O   GLY A 136 " =    1.087
peak=    3.066 closest distance to " CA  ALA A 161 " =    0.888
peak=    3.062 closest distance to " O   HOH Z 236 " =    1.872
peak=    3.054 closest distance to " CB  ARG A 145 " =    1.088
peak=    3.053 closest distance to " O   HOH Z 378 " =    1.342
peak=    3.053 closest distance to " O   HOH Z 145 " =    1.819
peak=    3.048 closest distance to " N   GLU A 152 " =    1.448
peak=    3.046 closest distance to " N   VAL A 125 " =    1.487
peak=    3.040 closest distance to " CB  THR A  52 " =    0.844
peak=    3.013 closest distance to " O   GLY A 302 " =    1.795

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.168 - 5.789
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 179 from: 199
   mapped sites are within: 0.713 - 5.789

peak=   -4.773 closest distance to " O   PRO A 198 " =    1.007
peak=   -4.548 closest distance to " O   HOH Z  60 " =    1.418
peak=   -4.398 closest distance to " OE1 GLU A  44 " =    1.975
peak=   -4.362 closest distance to " O   HOH Z  69 " =    1.233
peak=   -4.323 closest distance to " O   HOH Z 216 " =    1.221
peak=   -4.277 closest distance to " O   HOH Z 415 " =    0.966
peak=   -4.275 closest distance to " O   HOH Z  28 " =    0.957
peak=   -4.266 closest distance to " O   GLY A 203 " =    2.534
peak=   -4.256 closest distance to " CD  ARG A  14 " =    3.184
peak=   -4.216 closest distance to " O   HOH Z 313 " =    1.304
peak=   -4.189 closest distance to " O   ALA A  10 " =    1.665
peak=   -4.188 closest distance to " O   HOH Z 385 " =    1.327
peak=   -4.112 closest distance to " O   HOH Z 100 " =    0.769
peak=   -4.072 closest distance to " CG  MET A 105 " =    0.931
peak=   -4.057 closest distance to " O   SER A  22 " =    2.699
peak=   -4.019 closest distance to " OG  SER A  97 " =    2.079
peak=   -3.953 closest distance to " O   PRO A 163 " =    1.841
peak=   -3.949 closest distance to " O   HOH Z  24 " =    0.908
peak=   -3.920 closest distance to " CB  ALA A 291 " =    2.210
peak=   -3.918 closest distance to " O   HOH Z 377 " =    0.733
peak=   -3.897 closest distance to " O   HOH Z 198 " =    0.842
peak=   -3.844 closest distance to " O   SER A 135 " =    1.525
peak=   -3.832 closest distance to " O   HOH Z 275 " =    1.697
peak=   -3.801 closest distance to " O   HOH Z  39 " =    0.713
peak=   -3.780 closest distance to " CG1 VAL A 265 " =    2.466
peak=   -3.758 closest distance to " CE3 TRP A 179 " =    1.237
peak=   -3.747 closest distance to " CG  ARG A 259 " =    2.379
peak=   -3.710 closest distance to " CA  GLY A 241 " =    2.378
peak=   -3.702 closest distance to " O   HOH Z   5 " =    0.940
peak=   -3.695 closest distance to " N   GLN A 122 " =    1.436
peak=   -3.688 closest distance to " CG1BVAL A  41 " =    2.867
peak=   -3.687 closest distance to " CB  ALA A  43 " =    2.430
peak=   -3.682 closest distance to " O   ASP A 191 " =    1.967
peak=   -3.672 closest distance to " CB  ALA A 291 " =    2.023
peak=   -3.671 closest distance to " CG1 VAL A 125 " =    2.393
peak=   -3.670 closest distance to " CB  ASP A 171 " =    2.378
peak=   -3.666 closest distance to " CB  ASP A 132 " =    2.502
peak=   -3.665 closest distance to " O   HOH Z  70 " =    1.954
peak=   -3.655 closest distance to " O   HOH Z 181 " =    1.206
peak=   -3.652 closest distance to " CG  GLN A  88 " =    0.937
peak=   -3.648 closest distance to " CB  PRO A 243 " =    2.594
peak=   -3.648 closest distance to " CD2 TYR A 293 " =    1.916
peak=   -3.642 closest distance to " O   HOH Z 139 " =    1.003
peak=   -3.642 closest distance to " C   ASN A 285 " =    2.080
peak=   -3.624 closest distance to " CZ2 TRP A  92 " =    2.826
peak=   -3.614 closest distance to " O   HOH Z 111 " =    1.414
peak=   -3.611 closest distance to " O   HOH Z 251 " =    0.844
peak=   -3.611 closest distance to " NE2 GLN A  55 " =    1.116
peak=   -3.606 closest distance to " CB  TYR A  68 " =    1.490
peak=   -3.604 closest distance to " O   HOH Z 129 " =    3.681
peak=   -3.603 closest distance to " NE2 GLN A  58 " =    3.517
peak=   -3.603 closest distance to " O   HOH Z  26 " =    0.923
peak=   -3.600 closest distance to " O   HOH Z  49 " =    1.065
peak=   -3.596 closest distance to " OE1 GLU A 277 " =    2.295
peak=   -3.586 closest distance to " OD2 ASP A 272 " =    1.597
peak=   -3.583 closest distance to " O   HOH Z 140 " =    0.847
peak=   -3.572 closest distance to " O   HOH Z 412 " =    3.907
peak=   -3.557 closest distance to " O   HOH Z 285 " =    1.486
peak=   -3.553 closest distance to " O   HOH Z  25 " =    1.545
peak=   -3.551 closest distance to " O   HOH Z 151 " =    0.930
peak=   -3.549 closest distance to " NE1 TRP A 179 " =    1.206
peak=   -3.542 closest distance to " CB  PRO A  54 " =    2.269
peak=   -3.541 closest distance to " C   VAL A  72 " =    0.977
peak=   -3.533 closest distance to " OE1 GLN A  11 " =    0.778
peak=   -3.526 closest distance to " SG ACYS A 201 " =    2.483
peak=   -3.523 closest distance to " O   HOH Z 389 " =    2.497
peak=   -3.512 closest distance to " O   HOH Z 298 " =    2.541
peak=   -3.508 closest distance to " O   GLN A 240 " =    3.171
peak=   -3.497 closest distance to " O   HOH Z  35 " =    2.917
peak=   -3.487 closest distance to " CB  ALA A 161 " =    1.820
peak=   -3.465 closest distance to " CG  GLN A  55 " =    1.441
peak=   -3.462 closest distance to " ND2 ASN A 209 " =    1.684
peak=   -3.457 closest distance to " N   ALA A  43 " =    2.735
peak=   -3.443 closest distance to " CA  GLY A 133 " =    1.985
peak=   -3.439 closest distance to " CG1 VAL A 126 " =    2.342
peak=   -3.430 closest distance to " CB  ALA A   7 " =    1.887
peak=   -3.428 closest distance to " CD2 HIS A 207 " =    1.359
peak=   -3.417 closest distance to " CB  ASN A 110 " =    1.028
peak=   -3.416 closest distance to " CB  ASN A  45 " =    2.127
peak=   -3.415 closest distance to " CB  ALA A   9 " =    2.474
peak=   -3.410 closest distance to " O   HOH Z 103 " =    1.202
peak=   -3.408 closest distance to " ND2 ASN A 285 " =    2.228
peak=   -3.404 closest distance to " OG  SER A  62 " =    1.327
peak=   -3.403 closest distance to " CG  TRP A 266 " =    1.764
peak=   -3.398 closest distance to " C   GLU A   2 " =    1.874
peak=   -3.396 closest distance to " O   LYS A  76 " =    2.000
peak=   -3.393 closest distance to " O   HOH Z  29 " =    0.799
peak=   -3.387 closest distance to " O   HOH Z 414 " =    1.990
peak=   -3.383 closest distance to " CB  ALA A 248 " =    2.024
peak=   -3.375 closest distance to " O   HOH Z 139 " =    3.113
peak=   -3.370 closest distance to " O   GLY A  80 " =    2.731
peak=   -3.364 closest distance to " O   HOH Z 323 " =    2.065
peak=   -3.364 closest distance to " OG  SER A  63 " =    1.260
peak=   -3.359 closest distance to " CA  GLY A  98 " =    1.644
peak=   -3.358 closest distance to " O   HOH Z  68 " =    1.494
peak=   -3.357 closest distance to " CG1BVAL A  41 " =    3.102
peak=   -3.355 closest distance to " O   HOH Z 259 " =    0.873
peak=   -3.348 closest distance to " NZ  LYS A 166 " =    1.645
peak=   -3.344 closest distance to " CE BMET A  47 " =    1.386
peak=   -3.340 closest distance to " CD  GLU A 236 " =    1.015
peak=   -3.337 closest distance to " NE2 GLN A 223 " =    1.233
peak=   -3.330 closest distance to " OG1 THR A 157 " =    1.512
peak=   -3.320 closest distance to " CB  ASP A  27 " =    2.457
peak=   -3.318 closest distance to " CB  ALA A 160 " =    2.053
peak=   -3.313 closest distance to " C   HIS A 108 " =    1.252
peak=   -3.312 closest distance to " CE3 TRP A 274 " =    2.159
peak=   -3.303 closest distance to " O   HOH Z 189 " =    3.652
peak=   -3.300 closest distance to " O   HOH Z 426 " =    1.679
peak=   -3.289 closest distance to " O   HOH Z 219 " =    3.514
peak=   -3.289 closest distance to " CD  GLU A 277 " =    1.045
peak=   -3.284 closest distance to " O   HOH Z  37 " =    1.411
peak=   -3.281 closest distance to " CD  GLN A  77 " =    1.060
peak=   -3.279 closest distance to " OD2 ASP A  27 " =    1.209
peak=   -3.278 closest distance to " NH2 ARG A  79 " =    1.503
peak=   -3.270 closest distance to " O   HOH Z 163 " =    1.941
peak=   -3.269 closest distance to " O   TRP A  70 " =    1.477
peak=   -3.260 closest distance to " N   HIS A  81 " =    1.229
peak=   -3.258 closest distance to " O   HOH Z 128 " =    2.741
peak=   -3.255 closest distance to " O   SER A  28 " =    1.374
peak=   -3.251 closest distance to " O   HOH Z 389 " =    0.848
peak=   -3.249 closest distance to " O   HOH Z 100 " =    1.181
peak=   -3.248 closest distance to " O   HOH Z 280 " =    0.757
peak=   -3.245 closest distance to " CA  ARG A 156 " =    1.317
peak=   -3.245 closest distance to " NH2AARG A 275 " =    5.322
peak=   -3.239 closest distance to " O   HOH Z  12 " =    0.735
peak=   -3.238 closest distance to " O   HOH Z 241 " =    1.102
peak=   -3.236 closest distance to " O   ASN A 170 " =    2.051
peak=   -3.228 closest distance to " O   HOH Z 278 " =    1.853
peak=   -3.226 closest distance to " N   ALA A   1 " =    1.770
peak=   -3.224 closest distance to " O   HOH Z 292 " =    1.423
peak=   -3.222 closest distance to " O   HOH Z 103 " =    1.375
peak=   -3.222 closest distance to " N   PRO A 163 " =    1.574
peak=   -3.221 closest distance to " CB  ALA A 227 " =    2.350
peak=   -3.203 closest distance to " O   HOH Z 244 " =    1.344
peak=   -3.201 closest distance to " O   HOH Z 108 " =    0.886
peak=   -3.193 closest distance to " C   SER A 273 " =    1.278
peak=   -3.190 closest distance to " CZ  ARG A 259 " =    0.930
peak=   -3.189 closest distance to " CB  SER A 210 " =    1.246
peak=   -3.188 closest distance to " N   GLN A  58 " =    1.270
peak=   -3.187 closest distance to " O   HOH Z 168 " =    2.865
peak=   -3.186 closest distance to " O   HOH Z 407 " =    5.789
peak=   -3.186 closest distance to " CD1 LEU A 101 " =    2.366
peak=   -3.183 closest distance to " O   HOH Z 231 " =    1.287
peak=   -3.181 closest distance to " OD1 ASP A 107 " =    1.017
peak=   -3.181 closest distance to " O   HOH Z 403 " =    1.577
peak=   -3.176 closest distance to " O   HOH Z 165 " =    2.382
peak=   -3.175 closest distance to " OG  SER A  63 " =    1.577
peak=   -3.170 closest distance to " CD2 TYR A 169 " =    2.597
peak=   -3.165 closest distance to " CB  ASP A 200 " =    2.649
peak=   -3.163 closest distance to " O   HOH Z 278 " =    0.761
peak=   -3.162 closest distance to " ND2 ASN A  45 " =    2.854
peak=   -3.162 closest distance to " O   HOH Z 134 " =    4.169
peak=   -3.155 closest distance to " CD1 TYR A 247 " =    2.437
peak=   -3.147 closest distance to " O   HOH Z  66 " =    0.882
peak=   -3.141 closest distance to " O   HOH Z  54 " =    1.656
peak=   -3.136 closest distance to " O   HOH Z 256 " =    1.219
peak=   -3.135 closest distance to " O   HOH Z 245 " =    1.697
peak=   -3.134 closest distance to " O   HOH Z 434 " =    4.303
peak=   -3.133 closest distance to " O   HOH Z 290 " =    0.822
peak=   -3.130 closest distance to " C   LEU A 101 " =    1.345
peak=   -3.119 closest distance to " C   ALA A 299 " =    1.388
peak=   -3.118 closest distance to " CH2 TRP A 266 " =    1.084
peak=   -3.118 closest distance to " CD  GLN A  55 " =    1.458
peak=   -3.115 closest distance to " O   HOH Z 297 " =    1.476
peak=   -3.105 closest distance to " N   VAL A 125 " =    1.087
peak=   -3.100 closest distance to " CG  GLN A  73 " =    1.499
peak=   -3.098 closest distance to " O   HOH Z 270 " =    2.813
peak=   -3.094 closest distance to " N   GLN A 223 " =    1.510
peak=   -3.090 closest distance to " CG2 ILE A 120 " =    1.585
peak=   -3.088 closest distance to " OG  SER A 245 " =    1.666
peak=   -3.085 closest distance to " O   HOH Z   2 " =    0.767
peak=   -3.084 closest distance to " O   HOH Z 100 " =    1.699
peak=   -3.068 closest distance to " O   HOH Z  76 " =    0.777
peak=   -3.063 closest distance to " SG  CYS A 254 " =    2.715
peak=   -3.060 closest distance to " O   HOH Z 284 " =    1.451
peak=   -3.053 closest distance to " O   HOH Z 149 " =    0.829
peak=   -3.039 closest distance to " O   HOH Z 181 " =    2.050
peak=   -3.016 closest distance to " O   HOH Z  71 " =    1.359
peak=   -2.996 closest distance to " O   HOH Z  60 " =    0.770

================= 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    :  0.4861 0.4894   6.301572e+00   6.293244e+00
   1_bss:  0.4760 0.4834   6.297163e+00   6.287940e+00
   1_xyz:  0.4183 0.4614   6.215176e+00   6.259515e+00
   1_adp:  0.3885 0.4661   6.185286e+00   6.264637e+00
   1_occ:  0.3883 0.4681   6.185198e+00   6.265254e+00
   2_bss:  0.3887 0.4666   6.189106e+00   6.266679e+00
   2_xyz:  0.3303 0.4185   6.074736e+00   6.201256e+00
   2_adp:  0.3152 0.4097   6.052587e+00   6.187867e+00
   2_occ:  0.3151 0.4098   6.052203e+00   6.187860e+00
   3_bss:  0.3154 0.4084   6.051097e+00   6.186272e+00
   3_xyz:  0.2657 0.3465   5.904955e+00   6.073958e+00
   3_adp:  0.2399 0.3390   5.851616e+00   6.052340e+00
   3_occ:  0.2398 0.3388   5.851384e+00   6.052444e+00
   4_bss:  0.2400 0.3386   5.851068e+00   6.052336e+00
   4_xyz:  0.1981 0.2791   5.669945e+00   5.902162e+00
   4_adp:  0.1830 0.2383   5.571765e+00   5.776047e+00
   4_occ:  0.1828 0.2379   5.570212e+00   5.774667e+00
   5_bss:  0.1820 0.2366   5.567681e+00   5.771868e+00
   5_xyz:  0.1492 0.1985   5.387093e+00   5.608727e+00
   5_adp:  0.1468 0.1965   5.372746e+00   5.596482e+00
   5_occ:  0.1464 0.1960   5.370874e+00   5.594712e+00
   5_bss:  0.1462 0.1952   5.368180e+00   5.591899e+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:  0.343  50.000  -3.120   1.077   3.542   0.000   0.000   0.000
   1_xyz:  0.343  50.000  -3.120   1.077   3.542   0.000   0.000   0.000
   1_adp:  0.343  50.000  -3.120   1.077   3.542   0.000   0.000   0.000
   1_occ:  0.343  50.000  -3.120   1.077   3.542   0.000   0.000   0.000
   2_bss:  0.360  72.474  -1.019   0.344   2.242   0.000   0.000   0.000
   2_xyz:  0.360  72.474  -1.019   0.344   2.242   0.000   0.000   0.000
   2_adp:  0.360  72.474  -1.019   0.344   2.242   0.000   0.000   0.000
   2_occ:  0.360  72.474  -1.019   0.344   2.242   0.000   0.000   0.000
   3_bss:  0.367  87.910  -0.725  -0.270   1.430  -0.000   0.000   0.000
   3_xyz:  0.367  87.910  -0.725  -0.270   1.430  -0.000   0.000   0.000
   3_adp:  0.367  87.910  -0.725  -0.270   1.430  -0.000   0.000   0.000
   3_occ:  0.367  87.910  -0.725  -0.270   1.430  -0.000   0.000   0.000
   4_bss:  0.358  98.213  -0.926  -0.786   0.977  -0.000   0.000   0.000
   4_xyz:  0.358  98.213  -0.926  -0.786   0.977  -0.000   0.000   0.000
   4_adp:  0.358  98.213  -0.926  -0.786   0.977  -0.000   0.000   0.000
   4_occ:  0.358  98.213  -0.926  -0.786   0.977  -0.000   0.000   0.000
   5_bss:  0.344  80.000  -1.842  -2.136   0.141  -0.000   0.000   0.000
   5_xyz:  0.344  80.000  -1.842  -2.136   0.141  -0.000   0.000   0.000
   5_adp:  0.344  80.000  -1.842  -2.136   0.141  -0.000   0.000   0.000
   5_occ:  0.344  80.000  -1.842  -2.136   0.141  -0.000   0.000   0.000
   5_bss:  0.318  55.687  -2.375  -2.656  -0.362  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  63.244 0.3513  0.4862    83004.045
   1_bss:  61.587 0.3721  0.5315    80338.439
   1_xyz:  56.085 0.4424  0.6210    68316.202
   1_adp:  56.836 0.4324  0.6221    70149.843
   1_occ:  56.936 0.4311  0.6199    70402.460
   2_bss:  57.043 0.4297  0.6196    70800.394
   2_xyz:  48.419 0.5381  0.7695    52347.411
   2_adp:  46.673 0.5602  0.7906    50111.435
   2_occ:  46.682 0.5601  0.7903    50076.133
   3_bss:  46.507 0.5620  0.7823    49596.120
   3_xyz:  37.221 0.6741  0.9127    33307.018
   3_adp:  35.770 0.6911  0.9040    31304.991
   3_occ:  35.759 0.6912  0.9040    31296.685
   4_bss:  35.733 0.6915  0.8921    31264.244
   4_xyz:  28.910 0.7674  0.9634    20537.799
   4_adp:  23.894 0.8226  0.9951    15287.876
   4_occ:  23.856 0.8229  0.9950    15208.150
   5_bss:  23.735 0.8240  0.9604    15056.774
   5_xyz:  19.167 0.8691  0.9824    10435.645
   5_adp:  18.837 0.8724  0.9878    10201.822
   5_occ:  18.795 0.8727  0.9883    10157.689
   5_bss:  18.739 0.8731  0.9703    10047.204
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.9046e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.9046e-01
   1_xyz:   1.478  0.010  0.100 15.764  0.007  4.104   1.1985e-01
   1_adp:   1.478  0.010  0.100 15.764  0.007  4.104   1.1985e-01
   1_occ:   1.478  0.010  0.100 15.764  0.007  4.104   1.1985e-01
   2_bss:   1.478  0.010  0.100 15.764  0.007  4.104   1.1985e-01
   2_xyz:   1.436  0.010  0.100 16.293  0.005  4.103   1.2162e-01
   2_adp:   1.436  0.010  0.100 16.293  0.005  4.103   1.2162e-01
   2_occ:   1.436  0.010  0.100 16.293  0.005  4.103   1.2162e-01
   3_bss:   1.436  0.010  0.100 16.293  0.005  4.103   1.2162e-01
   3_xyz:   1.182  0.010  0.084 15.090  0.005  4.117   9.1658e-02
   3_adp:   1.182  0.010  0.084 15.090  0.005  4.117   9.1658e-02
   3_occ:   1.182  0.010  0.084 15.090  0.005  4.117   9.1658e-02
   4_bss:   1.182  0.010  0.084 15.090  0.005  4.117   9.1658e-02
   4_xyz:   1.219  0.009  0.086 15.075  0.004  4.109   8.1698e-02
   4_adp:   1.219  0.009  0.086 15.075  0.004  4.109   8.1698e-02
   4_occ:   1.219  0.009  0.086 15.075  0.004  4.109   8.1698e-02
   5_bss:   1.219  0.009  0.086 15.075  0.004  4.109   8.1698e-02
   5_xyz:   1.045  0.008  0.075 14.662  0.004  4.120   6.5532e-02
   5_adp:   1.045  0.008  0.075 14.662  0.004  4.120   6.5532e-02
   5_occ:   1.045  0.008  0.075 14.662  0.004  4.120   6.5532e-02
   5_bss:   1.045  0.008  0.075 14.662  0.004  4.120   6.5532e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.681   2.4227e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.681   2.4227e-01
   1_xyz:   8.334  0.059  0.354 82.358  0.056  2.007   8.1996e-02
   1_adp:   8.334  0.059  0.354 82.358  0.056  2.007   8.1996e-02
   1_occ:   8.334  0.059  0.354 82.358  0.056  2.007   8.1996e-02
   2_bss:   8.334  0.059  0.354 82.358  0.056  2.007   8.1996e-02
   2_xyz:   8.848  0.071  0.394 80.133  0.048  1.874   1.3523e-01
   2_adp:   8.848  0.071  0.394 80.133  0.048  1.874   1.3523e-01
   2_occ:   8.848  0.071  0.394 80.133  0.048  1.874   1.3523e-01
   3_bss:   8.848  0.071  0.394 80.133  0.048  1.874   1.3523e-01
   3_xyz:   8.087  0.079  0.315 87.132  0.027  2.198   1.9705e-01
   3_adp:   8.087  0.079  0.315 87.132  0.027  2.198   1.9705e-01
   3_occ:   8.087  0.079  0.315 87.132  0.027  2.198   1.9705e-01
   4_bss:   8.087  0.079  0.315 87.132  0.027  2.198   1.9705e-01
   4_xyz:  11.425  0.069  0.246 87.816  0.038  2.318   6.5847e-02
   4_adp:  11.425  0.069  0.246 87.816  0.038  2.318   6.5847e-02
   4_occ:  11.425  0.069  0.246 87.816  0.038  2.318   6.5847e-02
   5_bss:  11.425  0.069  0.246 87.816  0.038  2.318   6.5847e-02
   5_xyz:   6.744  0.048  0.275 82.025  0.033  2.284   7.7779e-02
   5_adp:   6.744  0.048  0.275 82.025  0.033  2.284   7.7779e-02
   5_occ:   6.744  0.048  0.275 82.025  0.033  2.284   7.7779e-02
   5_bss:   6.744  0.048  0.275 82.025  0.033  2.284   7.7779e-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:  99.49   0.00  19.78  87.16   0.00  17.16  99.49   0.00  34.10
   1_occ:  99.49   0.00  19.78  87.16   0.00  17.16  99.49   0.00  34.10
   2_bss:  99.49   0.00  19.78  87.16   0.00  17.16  99.49   0.00  34.10
   2_xyz:  99.49   0.00  19.78  87.16   0.00  17.16  99.49   0.00  34.10
   2_adp:  98.72   0.00  19.33  81.17   0.00  16.46  98.72   0.00  34.96
   2_occ:  98.72   0.00  19.33  81.17   0.00  16.46  98.72   0.00  34.96
   3_bss:  98.72   0.00  19.33  81.17   0.00  16.46  98.72   0.00  34.96
   3_xyz:  98.72   0.00  19.33  81.17   0.00  16.46  98.72   0.00  34.96
   3_adp: 117.12   0.00  21.73 110.08   0.00  16.61 117.12   0.27  49.62
   3_occ: 117.12   0.00  21.73 110.08   0.00  16.61 117.12   0.27  49.62
   4_bss: 117.12   0.00  21.73 110.08   0.00  16.61 117.12   0.27  49.62
   4_xyz: 117.12   0.00  21.73 110.08   0.00  16.61 117.12   0.27  49.62
   4_adp:  98.73   0.00  18.05  98.73   0.00  13.54  97.47   4.75  42.58
   4_occ:  98.73   0.00  18.05  98.73   0.00  13.54  97.47   4.75  42.58
   5_bss:  98.73   0.00  18.05  98.73   0.00  13.54  97.47   4.75  42.58
   5_xyz:  98.73   0.00  18.05  98.73   0.00  13.54  97.47   4.75  42.58
   5_adp:  98.72   0.00  18.07  98.72   0.00  13.55  97.37   5.62  42.63
   5_occ:  98.72   0.00  18.07  98.72   0.00  13.55  97.37   5.62  42.63
   5_bss:  98.73   0.00  18.07  98.73   0.00  13.56  97.37   5.63  42.63
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.730    0.019    0.297
   1_adp:    1.730    0.019    0.297
   1_occ:    1.730    0.019    0.297
   2_bss:    1.730    0.019    0.297
   2_xyz:    1.632    0.034    0.551
   2_adp:    1.632    0.034    0.551
   2_occ:    1.632    0.034    0.551
   3_bss:    1.632    0.034    0.551
   3_xyz:    1.694    0.023    0.712
   3_adp:    1.694    0.023    0.712
   3_occ:    1.694    0.023    0.712
   4_bss:    1.694    0.023    0.712
   4_xyz:    1.738    0.097    0.836
   4_adp:    1.738    0.097    0.836
   4_occ:    1.738    0.097    0.836
   5_bss:    1.738    0.097    0.836
   5_xyz:    1.730    0.089    0.902
   5_adp:    1.730    0.089    0.902
   5_occ:    1.730    0.089    0.902
   5_bss:    1.730    0.089    0.902
------------------------------------------------------------------------

CPU time actual refinement: 367.98


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_736/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_736/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_736/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_736/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_736/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 367.83 
  Macro-tasks:
    bulk solvent and scale       = 55.02  
    individual site refinement   = 146.38 
    weights calculation          = 29.74  
    collect and process          = 6.15   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 237.40 
  Micro-tasks:
    mask                            = 3.08   
    f_calc                          = 117.44 
    alpha_beta                      = 8.07   
    target                          = 1.11   
    gradients_wrt_atomic_parameters = 124.37 
    fmodel                         = 8.55   
    r_factors                      = 0.30   
    phase_errors                   = 9.86   
    foms                           = 0.33   
    TOTAL for micro-tasks          = 273.11 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.202 micro seconds
Total CPU time: 6.36 minutes
from_scatterers_fft:    645 calls, 117.14 s
gradients_fft:          590 calls, 111.61 s

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

# Date 2008-01-16 Time 05:32:31 PST -0800 (1200490351.13 s)
Start R-work = 0.4861, R-free = 0.4894 (no bulk solvent and anisotropic scale)
Final R-work = 0.1675, R-free = 0.2146 (no bulk solvent and anisotropic scale)

Start R-work = 0.4760, R-free = 0.4834
Final R-work = 0.1462, R-free = 0.1952