# Date 2008-01-16 Time 06:12:54 PST -0800 (1200492774.18 s)
#phil __OFF__

Command line arguments: "../1057.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30800
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1057

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 47.6339, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.24, 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: (71.3037, 47.6339, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0711 1.96145
Completeness in resolution range: 0.921835
Completeness with d_max=infinity: 0.91911

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0711
                             d_min =   1.9615

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.6339, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0711 1.96145
Completeness in resolution range: 0.921835
Completeness with d_max=infinity: 0.91911

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0715 -  4.1982 [2234/2263]  2012   222   9.9%
  bin  2:  4.1982 -  3.3442 [2135/2158]  1921   214  10.0%
  bin  3:  3.3442 -  2.9250 [2109/2134]  1894   215  10.2%
  bin  4:  2.9250 -  2.6592 [2092/2108]  1890   202   9.7%
  bin  5:  2.6592 -  2.4695 [2079/2123]  1870   209  10.1%
  bin  6:  2.4695 -  2.3244 [2077/2105]  1869   208  10.0%
  bin  7:  2.3244 -  2.2084 [2050/2086]  1841   209  10.2%
  bin  8:  2.2084 -  2.1125 [2050/2092]  1845   205  10.0%
  bin  9:  2.1125 -  2.0314 [2047/2093]  1846   201   9.8%
  bin 10:  2.0314 -  1.9615 [ 716/2088]   642    74  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1057/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.71 -     2.34: 24
        2.34 -     2.98: 1832
        2.98 -     3.62: 4560
        3.62 -     4.26: 9138
        4.26 -     4.90: 12682
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.706 3.040 -x+1/2,-y+1,z+1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.741 3.120 -x+1/2,-y+1,z-1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.778 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.779 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.783 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28231 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_1057/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1057/model_refine_001.geo

CPU time processing inputs: 9.08


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 47.63395 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4405   r_free= 0.4386   ksol= 0.00   Bsol= 0.00   scale= 0.908    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.244889                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6831 0.99   1451  163 0.3383 0.3473      6.4869      6.4725|
|  2:  4.6831 -  3.7357 0.99   1386  150 0.3593 0.3545      6.7285      6.7397|
|  3:  3.7357 -  3.2690 0.99   1369  155 0.4012 0.3771      6.5946      6.5902|
|  4:  3.2690 -  2.9726 0.99   1355  148 0.4318 0.4145      6.4515      6.4387|
|  5:  2.9726 -  2.7609 0.98   1339  147 0.4478 0.4518      6.3047      6.3093|
|  6:  2.7609 -  2.5990 0.99   1347  157 0.4806 0.4807      6.2441      6.1638|
|  7:  2.5990 -  2.4695 0.98   1340  142 0.4795 0.4317      6.2078       6.154|
|  8:  2.4695 -  2.3624 0.99   1330  149 0.4999 0.5129      6.1363      6.1947|
|  9:  2.3624 -  2.2718 0.99   1336  151 0.5142 0.4895      6.1304      6.0885|
| 10:  2.2718 -  2.1936 0.98   1323  148 0.5006 0.5507      6.0558      6.1251|
| 11:  2.1936 -  2.1252 0.97   1301  135 0.5049 0.5789      6.0185      5.9955|
| 12:  2.1252 -  2.0646 0.99   1339  154 0.5104 0.5374      5.9363      5.9901|
| 13:  2.0646 -  2.0104 0.84   1111  131 0.5018 0.4406      5.8631      5.8152|
| 14:  2.0104 -  1.9615 0.22    303   29 0.5733 0.4875       5.815      5.8139|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0715 -  4.6831  1451   163  0.74  30.42   0.84     0.76      57957.97|
|  2:  4.6831 -  3.7357  1386   150  0.75  30.68   0.94     0.83      80437.93|
|  3:  3.7357 -  3.2690  1369   155  0.66  38.42   0.92     0.83      88353.58|
|  4:  3.2690 -  2.9726  1355   148  0.58  45.76   0.93     0.77      81835.73|
|  5:  2.9726 -  2.7609  1339   147  0.50  51.57   0.90     0.70      68806.40|
|  6:  2.7609 -  2.5990  1347   157  0.48  53.64   0.92     0.66      58627.50|
|  7:  2.5990 -  2.4695  1340   142  0.48  53.86   0.92     0.64      53185.46|
|  8:  2.4695 -  2.3624  1330   149  0.43  57.44   0.89     0.62      51947.40|
|  9:  2.3624 -  2.2718  1336   151  0.39  60.57   0.93     0.58      50806.29|
| 10:  2.2718 -  2.1936  1323   148  0.33  65.37   0.94     0.49      51872.96|
| 11:  2.1936 -  2.1252  1301   135  0.27  69.59   0.93     0.42      49880.62|
| 12:  2.1252 -  2.0646  1339   154  0.23  72.58   0.93     0.39      47551.71|
| 13:  2.0646 -  2.0104  1111   131  0.27  70.05   0.94     0.42      38899.93|
| 14:  2.0104 -  1.9615   303    29  0.32  66.23   0.87     0.50      29980.42|
|alpha:            min =        0.39 max =            0.83 mean =         0.63|
|beta:             min =    29980.42 max =        88353.58 mean =     59912.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           89.98 mean =        53.55|
|phase err.(test): min =        0.00 max =           89.98 mean =        53.69|
|-----------------------------------------------------------------------------|

============================== 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 = 10.066024             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.223   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.338685              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.647   (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 |  1.706 -  2.025:       11 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.025 -  2.345:       13 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.345 -  2.664:       77 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.664 -  2.983:     1755 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.983 -  3.303:     1891 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.303 -  3.622:     2669 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.622 -  3.942:     4693 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.942 -  4.261:     4445 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.261 -  4.581:     5770 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.581 -  4.900:     6912 |
|-----------------------------------------------------------------------------|
|-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 |        0.177 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.706 |       0.391 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.005)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4405   r_free= 0.4386   ksol= 0.00   Bsol= 0.00   scale= 0.908    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.244889                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4326   r_free= 0.4315   ksol= 0.30   Bsol= 38.27   scale= 0.951   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.92,2.00,1.23,0.00,0.00,0.00); trace/3= 0.77                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.238879                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.031232              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.273   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.055841              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.307   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4326      final r-factor (work) = 0.3007          |
| start r-factor (free) = 0.4315      final r-factor (free) = 0.3369          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.2202 = 8.03 * 0.50 * 6.2364 + 1.00 * 0.1773                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.5175 = 8.03 * 0.50 * 6.0763 + 1.00 * 0.1174                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3007      final r-factor (work) = 0.2738          |
| start r-factor (free) = 0.3369      final r-factor (free) = 0.3448          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4218 = 1.06 * 1.00 * 6.0763 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2573 = 1.06 * 1.00 * 5.9109 + 1.00 * 0.0163                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.005)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.95  18.43    None  None   None       |
|    all(noH): 2823   0      0.00    101.95  18.43    None  None   None       |
|    Sol.    : 438    0      1.64    101.95  41.20    None  None   None       |
|    Mac.    : 2385   0      0.00    92.45   14.25    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.195:  984   |   5:    50.976 -  61.171:   84        |
|      1:    10.195 -  20.390:  983   |   6:    61.171 -  71.366:   48        |
|      2:    20.390 -  30.586:  387   |   7:    71.366 -  81.561:   20        |
|      3:    30.586 -  40.781:  196   |   8:    81.561 -  91.756:    5        |
|      4:    40.781 -  50.976:  113   |   9:    91.756 - 101.952:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2738 r_free = 0.3448             target_work(ml) = 5.919         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2734 r_free = 0.3453             target_work(ml) = 5.918         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2734   r_free= 0.3453   ksol= 0.30   Bsol= 38.27   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.92,2.00,1.23,0.00,0.00,0.00); trace/3= 0.77                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.918172                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2712   r_free= 0.3430   ksol= 0.33   Bsol= 67.22   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.60,0.03,-0.62,0.00,-0.00,-0.00); trace/3= -0.73                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.916147                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.852914              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.463   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.454193              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.897  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2712      final r-factor (work) = 0.1978          |
| start r-factor (free) = 0.3430      final r-factor (free) = 0.2496          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.4215 = 5.85 * 0.50 * 5.9130 + 1.00 * 0.1174                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.0614 = 5.85 * 0.50 * 5.8054 + 1.00 * 0.0722                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1978      final r-factor (work) = 0.1788          |
| start r-factor (free) = 0.2496      final r-factor (free) = 0.2269          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6529 = 0.45 * 1.00 * 5.8054 + 1.00 * 0.0161                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5487 = 0.45 * 1.00 * 5.5878 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.005)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.26   18.05    None  None   None       |
|    all(noH): 2823   0      0.00    97.26   18.05    None  None   None       |
|    Sol.    : 438    0      6.12    97.26   42.40    None  None   None       |
|    Mac.    : 2385   0      0.00    89.28   13.57    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 -   9.726:  974   |   5:    48.631 -  58.357:  103        |
|      1:     9.726 -  19.452: 1072   |   6:    58.357 -  68.083:   58        |
|      2:    19.452 -  29.178:  295   |   7:    68.083 -  77.809:   23        |
|      3:    29.178 -  38.905:  156   |   8:    77.809 -  87.535:   11        |
|      4:    38.905 -  48.631:  128   |   9:    87.535 -  97.261:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1788 r_free = 0.2269             target_work(ml) = 5.545         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1785 r_free = 0.2269             target_work(ml) = 5.544         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1785   r_free= 0.2269   ksol= 0.33   Bsol= 67.22   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.60,0.03,-0.62,0.00,-0.00,-0.00); trace/3= -0.73                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.544283                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1784   r_free= 0.2270   ksol= 0.33   Bsol= 61.20   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-1.02,-1.53,-0.00,-0.00,-0.00); trace/3= -1.52                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.543648                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.686769              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.955  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.968431              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.451  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1784      final r-factor (work) = 0.1394          |
| start r-factor (free) = 0.2270      final r-factor (free) = 0.1829          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3777 = 3.69 * 0.50 * 5.5905 + 1.00 * 0.0722                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0995 = 3.69 * 0.50 * 5.4437 + 1.00 * 0.0648                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1394      final r-factor (work) = 0.1283          |
| start r-factor (free) = 0.1829      final r-factor (free) = 0.1752          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.7263 = 1.97 * 1.00 * 5.4437 + 1.00 * 0.0108                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.4219 = 1.97 * 1.00 * 5.2884 + 1.00 * 0.0121                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.005)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.37    104.78  18.29    None  None   None       |
|    all(noH): 2823   0      1.37    104.78  18.29    None  None   None       |
|    Sol.    : 438    0      5.50    104.32  45.30    None  None   None       |
|    Mac.    : 2385   0      1.37    104.78  13.33    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.366 -  11.708: 1352   |   5:    53.075 -  63.417:   83        |
|      1:    11.708 -  22.049:  870   |   6:    63.417 -  73.759:   59        |
|      2:    22.049 -  32.391:  176   |   7:    73.759 -  84.101:   32        |
|      3:    32.391 -  42.733:  123   |   8:    84.101 -  94.443:   11        |
|      4:    42.733 -  53.075:  112   |   9:    94.443 - 104.784:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1283 r_free = 0.1752             target_work(ml) = 5.268         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1283 r_free = 0.1751             target_work(ml) = 5.268         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1283   r_free= 0.1751   ksol= 0.33   Bsol= 61.20   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-1.02,-1.53,-0.00,-0.00,-0.00); trace/3= -1.52                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.268094                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1286   r_free= 0.1756   ksol= 0.32   Bsol= 60.23   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-1.60,-1.84,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.270433                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.696648              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.773  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.289595              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.493  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1286      final r-factor (work) = 0.1235          |
| start r-factor (free) = 0.1756      final r-factor (free) = 0.1704          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5532 = 1.70 * 0.50 * 5.2910 + 1.00 * 0.0648                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5092 = 1.70 * 0.50 * 5.2538 + 1.00 * 0.0523                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1235      final r-factor (work) = 0.1225          |
| start r-factor (free) = 0.1704      final r-factor (free) = 0.1679          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5335 = 0.29 * 1.00 * 5.2538 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5250 = 0.29 * 1.00 * 5.2336 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.005)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.06    104.01  17.41    None  None   None       |
|    all(noH): 2823   0      2.06    104.01  17.41    None  None   None       |
|    Sol.    : 438    0      5.21    87.39   41.63    None  None   None       |
|    Mac.    : 2385   0      2.06    104.01  12.97    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.063 -  12.258: 1502   |   5:    53.035 -  63.229:   66        |
|      1:    12.258 -  22.452:  760   |   6:    63.229 -  73.423:   40        |
|      2:    22.452 -  32.646:  174   |   7:    73.423 -  83.617:   13        |
|      3:    32.646 -  42.840:  135   |   8:    83.617 -  93.812:    7        |
|      4:    42.840 -  53.035:  122   |   9:    93.812 - 104.006:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1225 r_free = 0.1679             target_work(ml) = 5.224         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1224 r_free = 0.1678             target_work(ml) = 5.224         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1224   r_free= 0.1678   ksol= 0.32   Bsol= 60.23   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-1.60,-1.84,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.223937                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1224   r_free= 0.1677   ksol= 0.33   Bsol= 60.23   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-1.60,-1.84,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.223956                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.988166              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.704  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.314452              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.839  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1224      final r-factor (work) = 0.1130          |
| start r-factor (free) = 0.1677      final r-factor (free) = 0.1614          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8716 = 2.99 * 0.50 * 5.2335 + 1.00 * 0.0523                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8272 = 2.99 * 0.50 * 5.1904 + 1.00 * 0.0723                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1130      final r-factor (work) = 0.1123          |
| start r-factor (free) = 0.1614      final r-factor (free) = 0.1605          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6414 = 0.31 * 1.00 * 5.1904 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6328 = 0.31 * 1.00 * 5.1646 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.005)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.71    103.75  17.05    None  None   None       |
|    all(noH): 2823   0      1.71    103.75  17.05    None  None   None       |
|    Sol.    : 438    0      5.34    82.74   40.40    None  None   None       |
|    Mac.    : 2385   0      1.71    103.75  12.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.710 -  11.915: 1493   |   5:    52.732 -  62.936:   66        |
|      1:    11.915 -  22.119:  769   |   6:    62.936 -  73.141:   37        |
|      2:    22.119 -  32.323:  191   |   7:    73.141 -  83.345:   13        |
|      3:    32.323 -  42.528:  131   |   8:    83.345 -  93.549:    2        |
|      4:    42.528 -  52.732:  117   |   9:    93.549 - 103.754:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1123 r_free = 0.1605             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1123 r_free = 0.1605             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1123   r_free= 0.1605   ksol= 0.33   Bsol= 60.23   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-1.60,-1.84,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.162841                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6831 0.99   1451  163 0.0962 0.1289      5.3584      5.5343|
|  2:  4.6831 -  3.7357 0.99   1386  150 0.0840 0.1041      5.4088      5.6177|
|  3:  3.7357 -  3.2690 0.99   1369  155 0.1058 0.1677       5.466      5.8891|
|  4:  3.2690 -  2.9726 0.99   1355  148 0.1288 0.1532      5.4799      5.6091|
|  5:  2.9726 -  2.7609 0.98   1339  147 0.1361 0.1887      5.3494       5.545|
|  6:  2.7609 -  2.5990 0.99   1347  157 0.1257 0.1879      5.2235      5.4458|
|  7:  2.5990 -  2.4695 0.98   1340  142 0.1236 0.1717      5.1677      5.3954|
|  8:  2.4695 -  2.3624 0.99   1330  149 0.1179 0.1751      5.0599      5.3035|
|  9:  2.3624 -  2.2718 0.99   1336  151 0.1169 0.1916      5.0368      5.3211|
| 10:  2.2718 -  2.1936 0.98   1323  148 0.1122 0.1704      4.9721      5.2541|
| 11:  2.1936 -  2.1252 0.97   1301  135 0.1137 0.1912      4.9371      5.2579|
| 12:  2.1252 -  2.0646 0.99   1339  154 0.1115 0.1686      4.8675      5.0946|
| 13:  2.0646 -  2.0104 0.84   1111  131 0.1166 0.1800      4.7926      5.0296|
| 14:  2.0104 -  1.9615 0.22    303   29 0.1154 0.1530      4.6704       4.894|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0715 -  4.6831  1451   163  0.94   8.80   0.97     0.95       6872.51|
|  2:  4.6831 -  3.7357  1386   150  0.95   7.77   1.01     0.99       8522.33|
|  3:  3.7357 -  3.2690  1369   155  0.93  11.44   1.02     1.02      10292.89|
|  4:  3.2690 -  2.9726  1355   148  0.91  15.14   1.00     0.98      11176.95|
|  5:  2.9726 -  2.7609  1339   147  0.89  17.21   0.99     0.96       8998.56|
|  6:  2.7609 -  2.5990  1347   157  0.90  16.53   0.99     0.96       7327.31|
|  7:  2.5990 -  2.4695  1340   142  0.91  15.52   0.99     0.96       6328.86|
|  8:  2.4695 -  2.3624  1330   149  0.90  16.20   0.99     0.96       5473.42|
|  9:  2.3624 -  2.2718  1336   151  0.90  16.59   0.99     0.95       5130.52|
| 10:  2.2718 -  2.1936  1323   148  0.91  15.48   0.99     0.95       4621.71|
| 11:  2.1936 -  2.1252  1301   135  0.89  16.84   0.99     0.95       4495.26|
| 12:  2.1252 -  2.0646  1339   154  0.90  16.27   0.99     0.98       4061.04|
| 13:  2.0646 -  2.0104  1111   131  0.90  16.64   0.98     0.97       3397.76|
| 14:  2.0104 -  1.9615   303    29  0.89  16.76   0.97     0.95       2669.73|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2669.73 max =        11176.95 mean =      6666.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.64 mean =        14.59|
|phase err.(test): min =        0.00 max =           89.33 mean =        13.96|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1123   r_free= 0.1604   ksol= 0.33   Bsol= 60.17   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,-1.62,-1.70,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.162853                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1123   r_free= 0.1604   ksol= 0.33   Bsol= 60.17   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,-1.62,-1.70,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.162853                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6831 0.99   1451  163 0.0962 0.1289      5.3587      5.5349|
|  2:  4.6831 -  3.7357 0.99   1386  150 0.0841 0.1041      5.4094      5.6184|
|  3:  3.7357 -  3.2690 0.99   1369  155 0.1059 0.1678      5.4665      5.8896|
|  4:  3.2690 -  2.9726 0.99   1355  148 0.1288 0.1532      5.4799      5.6088|
|  5:  2.9726 -  2.7609 0.98   1339  147 0.1361 0.1887       5.349      5.5444|
|  6:  2.7609 -  2.5990 0.99   1347  157 0.1257 0.1877       5.223       5.445|
|  7:  2.5990 -  2.4695 0.98   1340  142 0.1237 0.1719      5.1676      5.3955|
|  8:  2.4695 -  2.3624 0.99   1330  149 0.1178 0.1749      5.0598      5.3031|
|  9:  2.3624 -  2.2718 0.99   1336  151 0.1169 0.1921      5.0367      5.3222|
| 10:  2.2718 -  2.1936 0.98   1323  148 0.1122 0.1703      4.9723      5.2545|
| 11:  2.1936 -  2.1252 0.97   1301  135 0.1137 0.1907      4.9367      5.2566|
| 12:  2.1252 -  2.0646 0.99   1339  154 0.1115 0.1691      4.8677      5.0961|
| 13:  2.0646 -  2.0104 0.84   1111  131 0.1166 0.1798      4.7926      5.0284|
| 14:  2.0104 -  1.9615 0.22    303   29 0.1155 0.1523      4.6699      4.8921|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0715 -  4.6831  1451   163  0.94   8.81   0.97     0.95       6877.56|
|  2:  4.6831 -  3.7357  1386   150  0.95   7.78   1.01     0.99       8530.54|
|  3:  3.7357 -  3.2690  1369   155  0.93  11.44   1.02     1.02      10308.62|
|  4:  3.2690 -  2.9726  1355   148  0.91  15.15   1.00     0.98      11178.79|
|  5:  2.9726 -  2.7609  1339   147  0.89  17.20   0.99     0.96       8988.64|
|  6:  2.7609 -  2.5990  1347   157  0.90  16.51   0.99     0.96       7315.82|
|  7:  2.5990 -  2.4695  1340   142  0.91  15.51   0.99     0.96       6323.86|
|  8:  2.4695 -  2.3624  1330   149  0.90  16.20   0.99     0.96       5473.75|
|  9:  2.3624 -  2.2718  1336   151  0.90  16.59   1.00     0.95       5135.53|
| 10:  2.2718 -  2.1936  1323   148  0.91  15.49   0.99     0.95       4624.89|
| 11:  2.1936 -  2.1252  1301   135  0.90  16.83   0.99     0.95       4493.70|
| 12:  2.1252 -  2.0646  1339   154  0.90  16.27   1.00     0.99       4063.41|
| 13:  2.0646 -  2.0104  1111   131  0.90  16.63   0.99     0.97       3395.12|
| 14:  2.0104 -  1.9615   303    29  0.89  16.74   0.98     0.95       2662.73|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2662.73 max =        11178.79 mean =      6667.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.65 mean =        14.59|
|phase err.(test): min =        0.00 max =           89.33 mean =        13.96|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.005)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.65    103.69  16.99    None  None   None       |
|    all(noH): 2823   0      1.65    103.69  16.99    None  None   None       |
|    Sol.    : 438    0      5.28    82.67   40.34    None  None   None       |
|    Mac.    : 2385   0      1.65    103.69  12.71    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.649 -  11.853: 1493   |   5:    52.671 -  62.875:   66        |
|      1:    11.853 -  22.058:  769   |   6:    62.875 -  73.080:   37        |
|      2:    22.058 -  32.262:  191   |   7:    73.080 -  83.284:   13        |
|      3:    32.262 -  42.467:  131   |   8:    83.284 -  93.488:    2        |
|      4:    42.467 -  52.671:  117   |   9:    93.488 - 103.693:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 320         
Filter by distance & map next to the model:
   mapped sites are within: 0.735 - 5.910
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 320 from: 320
   mapped sites are within: 0.735 - 5.910

peak=    5.865 closest distance to " O   HOH Z 111 " =    2.270
peak=    5.683 closest distance to " CB  SER A  63 " =    1.262
peak=    5.652 closest distance to " CB  GLN A 223 " =    1.456
peak=    5.302 closest distance to " CG  PRO A  54 " =    1.164
peak=    4.952 closest distance to " O   HOH Z  15 " =    2.066
peak=    4.786 closest distance to " O   HOH Z 403 " =    1.869
peak=    4.744 closest distance to " O   HOH Z 232 " =    2.282
peak=    4.682 closest distance to " O   HOH Z 193 " =    1.977
peak=    4.624 closest distance to " CB  GLN A 183 " =    1.255
peak=    4.602 closest distance to " O   HOH Z 298 " =    1.920
peak=    4.597 closest distance to " CB  ARG A 275 " =    0.889
peak=    4.515 closest distance to " NH2 ARG A 156 " =    1.222
peak=    4.480 closest distance to " CB  GLU A 152 " =    1.164
peak=    4.454 closest distance to " CG  PRO A 213 " =    1.192
peak=    4.405 closest distance to " O   HOH Z 234 " =    3.794
peak=    4.374 closest distance to " O   PRO A 198 " =    1.522
peak=    4.362 closest distance to " OD2 ASP A 286 " =    2.910
peak=    4.362 closest distance to " CB  LEU A 228 " =    1.137
peak=    4.348 closest distance to " O   SER A  87 " =    2.143
peak=    4.345 closest distance to " CG  PRO A 198 " =    1.342
peak=    4.325 closest distance to " CB  TYR A 169 " =    0.869
peak=    4.317 closest distance to " O   HOH Z 133 " =    2.187
peak=    4.304 closest distance to " O   HOH Z 134 " =    1.534
peak=    4.303 closest distance to " CB  GLU A 277 " =    3.639
peak=    4.301 closest distance to " OD1 ASN A  69 " =    2.565
peak=    4.275 closest distance to " CA  TYR A  30 " =    0.946
peak=    4.260 closest distance to " CB  ARG A  79 " =    1.353
peak=    4.246 closest distance to " O   HOH Z  80 " =    1.749
peak=    4.246 closest distance to " CB  GLU A 128 " =    1.206
peak=    4.241 closest distance to " O   HOH Z  40 " =    1.835
peak=    4.238 closest distance to " CB  PRO A  54 " =    0.805
peak=    4.231 closest distance to " O   HOH Z 369 " =    2.234
peak=    4.230 closest distance to " O   HOH Z 368 " =    2.152
peak=    4.224 closest distance to " CB  VAL A 202 " =    1.600
peak=    4.209 closest distance to " CG1 ILE A  33 " =    1.188
peak=    4.192 closest distance to " CB  SER A   3 " =    1.362
peak=    4.184 closest distance to " O   HOH Z  68 " =    1.954
peak=    4.161 closest distance to " O   HOH Z 163 " =    1.693
peak=    4.150 closest distance to " NH2BARG A 145 " =    2.094
peak=    4.144 closest distance to " O   HOH Z  20 " =    1.955
peak=    4.122 closest distance to " O   HOH Z 214 " =    0.954
peak=    4.118 closest distance to " CA  THR A 221 " =    0.920
peak=    4.115 closest distance to " O   HOH Z 425 " =    1.418
peak=    4.111 closest distance to " CG2 THR A 221 " =    0.984
peak=    4.102 closest distance to " CA  ALA A  21 " =    1.317
peak=    4.096 closest distance to " O   HOH Z 180 " =    2.224
peak=    4.093 closest distance to " O   HOH Z 247 " =    1.387
peak=    4.082 closest distance to " O   HOH Z 126 " =    1.618
peak=    4.070 closest distance to " O   HOH Z 236 " =    1.888
peak=    4.067 closest distance to " O   HOH Z  78 " =    2.082
peak=    4.045 closest distance to " O   HOH Z 316 " =    3.040
peak=    4.031 closest distance to " O   HOH Z 132 " =    2.695
peak=    4.028 closest distance to " O   HOH Z 374 " =    2.706
peak=    4.021 closest distance to " NZ  LYS A 117 " =    3.209
peak=    4.020 closest distance to " O   HOH Z 193 " =    2.251
peak=    4.013 closest distance to " O   HOH Z 371 " =    3.437
peak=    4.006 closest distance to " CG  ARG A  66 " =    2.623
peak=    4.000 closest distance to " O   HOH Z 108 " =    2.122
peak=    3.990 closest distance to " CG  PRO A  90 " =    1.092
peak=    3.985 closest distance to " O   HOH Z  59 " =    2.407
peak=    3.979 closest distance to " O   HOH Z 284 " =    2.938
peak=    3.964 closest distance to " O   HOH Z 426 " =    1.530
peak=    3.956 closest distance to " CB  ASN A 148 " =    1.230
peak=    3.947 closest distance to " O   HOH Z  49 " =    2.419
peak=    3.939 closest distance to " CB  SER A 141 " =    0.990
peak=    3.931 closest distance to " O   HOH Z 352 " =    1.935
peak=    3.926 closest distance to " O   HOH Z  97 " =    1.909
peak=    3.915 closest distance to " O   HOH Z 261 " =    2.097
peak=    3.911 closest distance to " O   HOH Z 389 " =    1.925
peak=    3.904 closest distance to " ND2 ASN A 110 " =    1.758
peak=    3.899 closest distance to " O   HOH Z 108 " =    1.346
peak=    3.897 closest distance to " CB  ARG A 190 " =    1.692
peak=    3.893 closest distance to " O   HOH Z 279 " =    2.248
peak=    3.889 closest distance to " NE2 GLN A  11 " =    1.055
peak=    3.869 closest distance to " O   HOH Z 135 " =    1.817
peak=    3.865 closest distance to " CG  PRO A 243 " =    1.157
peak=    3.860 closest distance to " O   ALA A 165 " =    1.352
peak=    3.857 closest distance to " O   HOH Z 411 " =    3.420
peak=    3.846 closest distance to " CD1 LEU A 300 " =    1.233
peak=    3.822 closest distance to " O   HOH Z  54 " =    2.275
peak=    3.822 closest distance to " O   HOH Z  61 " =    1.595
peak=    3.808 closest distance to " O   HOH Z 272 " =    1.956
peak=    3.803 closest distance to " N   ASN A  39 " =    1.336
peak=    3.803 closest distance to " CG  PRO A 280 " =    0.743
peak=    3.799 closest distance to " NH2BARG A 102 " =    0.992
peak=    3.788 closest distance to " O   HOH Z 174 " =    2.448
peak=    3.777 closest distance to " O   HOH Z 142 " =    1.544
peak=    3.777 closest distance to " O   HOH Z 189 " =    2.220
peak=    3.774 closest distance to " CA  ASP A 191 " =    0.779
peak=    3.767 closest distance to " O   HOH Z 132 " =    1.030
peak=    3.766 closest distance to " O   MET A 105 " =    1.899
peak=    3.766 closest distance to " CB  ASN A 148 " =    1.751
peak=    3.765 closest distance to " O   HOH Z 344 " =    3.058
peak=    3.765 closest distance to " CA  ALA A  51 " =    0.971
peak=    3.764 closest distance to " O   HOH Z 313 " =    2.001
peak=    3.754 closest distance to " O   HOH Z 102 " =    1.300
peak=    3.750 closest distance to " CB  TRP A 179 " =    1.407
peak=    3.737 closest distance to " O   HOH Z  48 " =    1.513
peak=    3.725 closest distance to " CA  MET A  40 " =    1.087
peak=    3.719 closest distance to " O   HOH Z 124 " =    1.418
peak=    3.711 closest distance to " O   HOH Z  47 " =    1.361
peak=    3.708 closest distance to " O   HOH Z 345 " =    3.305
peak=    3.700 closest distance to " ND1 HIS A  81 " =    1.589
peak=    3.696 closest distance to " O   HOH Z 126 " =    1.827
peak=    3.695 closest distance to " O   HOH Z 295 " =    1.505
peak=    3.687 closest distance to " OE1 GLN A  11 " =    1.970
peak=    3.681 closest distance to " ND2 ASN A 187 " =    1.562
peak=    3.674 closest distance to " CA  ASN A 176 " =    1.843
peak=    3.663 closest distance to " O   HOH Z  88 " =    3.510
peak=    3.662 closest distance to " O   HOH Z  19 " =    2.135
peak=    3.658 closest distance to " O   HOH Z 209 " =    2.334
peak=    3.654 closest distance to " CB  TRP A 266 " =    0.900
peak=    3.652 closest distance to " O   HOH Z 214 " =    2.224
peak=    3.648 closest distance to " O   HOH Z 326 " =    1.523
peak=    3.637 closest distance to " O   HOH Z 133 " =    1.711
peak=    3.637 closest distance to " O   HOH Z 423 " =    1.926
peak=    3.634 closest distance to " O   HOH Z 394 " =    1.650
peak=    3.624 closest distance to " O   HOH Z 128 " =    2.128
peak=    3.623 closest distance to " OG BSER A 164 " =    2.512
peak=    3.622 closest distance to " CB  ASP A 140 " =    0.825
peak=    3.616 closest distance to " O   HOH Z  54 " =    1.683
peak=    3.616 closest distance to " O   HOH Z 147 " =    1.738
peak=    3.613 closest distance to " CB  ASN A 187 " =    1.065
peak=    3.600 closest distance to " O   HOH Z 368 " =    2.536
peak=    3.595 closest distance to " CB  ARG A 139 " =    0.960
peak=    3.590 closest distance to " CG BARG A 102 " =    1.914
peak=    3.588 closest distance to " O   HOH Z  30 " =    1.476
peak=    3.577 closest distance to " CB  VAL A 265 " =    1.240
peak=    3.573 closest distance to " NH1AARG A 145 " =    1.065
peak=    3.566 closest distance to " CG AARG A 275 " =    1.111
peak=    3.565 closest distance to " O   HOH Z 427 " =    2.798
peak=    3.564 closest distance to " CG  GLN A  58 " =    2.571
peak=    3.559 closest distance to " CA  ARG A 195 " =    1.273
peak=    3.556 closest distance to " O   HOH Z 260 " =    1.291
peak=    3.555 closest distance to " O   HOH Z  93 " =    2.604
peak=    3.552 closest distance to " O   HOH Z  43 " =    2.140
peak=    3.551 closest distance to " O   HOH Z 118 " =    1.598
peak=    3.543 closest distance to " CA  ARG A  36 " =    1.264
peak=    3.541 closest distance to " CD  PRO A  54 " =    1.224
peak=    3.535 closest distance to " O   HOH Z 227 " =    1.689
peak=    3.533 closest distance to " CD  ARG A 269 " =    0.892
peak=    3.531 closest distance to " CB  ALA A 100 " =    1.311
peak=    3.528 closest distance to " CG1BVAL A  72 " =    1.659
peak=    3.527 closest distance to " CB  MET A  40 " =    0.867
peak=    3.525 closest distance to " O   HOH Z 303 " =    2.149
peak=    3.522 closest distance to " CA  GLU A 152 " =    0.877
peak=    3.513 closest distance to " O   THR A 251 " =    1.261
peak=    3.507 closest distance to " O   HOH Z  21 " =    1.727
peak=    3.505 closest distance to " O   HOH Z   6 " =    2.108
peak=    3.498 closest distance to " CD  ARG A 159 " =    0.842
peak=    3.496 closest distance to " O   HOH Z 197 " =    2.147
peak=    3.491 closest distance to " CA  ALA A 160 " =    0.869
peak=    3.490 closest distance to " O   HOH Z 406 " =    1.635
peak=    3.486 closest distance to " O   HOH Z  63 " =    1.855
peak=    3.478 closest distance to " O   HOH Z 437 " =    1.467
peak=    3.469 closest distance to " CG2 VAL A 197 " =    1.179
peak=    3.468 closest distance to " CA  LYS A 117 " =    1.273
peak=    3.457 closest distance to " O   HOH Z  44 " =    1.939
peak=    3.457 closest distance to " O   HOH Z 387 " =    2.618
peak=    3.456 closest distance to " O   HOH Z 286 " =    2.199
peak=    3.451 closest distance to " CD1 TRP A 266 " =    1.196
peak=    3.443 closest distance to " O   HOH Z 263 " =    2.277
peak=    3.442 closest distance to " O   HOH Z 281 " =    4.136
peak=    3.441 closest distance to " CG2BVAL A  41 " =    0.888
peak=    3.434 closest distance to " CB  TYR A 169 " =    0.786
peak=    3.425 closest distance to " CD BLYS A 290 " =    1.075
peak=    3.419 closest distance to " O   HOH Z 183 " =    1.557
peak=    3.414 closest distance to " NH1 ARG A  56 " =    1.244
peak=    3.413 closest distance to " CB  SER A 216 " =    0.796
peak=    3.413 closest distance to " OG  SER A  62 " =    3.073
peak=    3.412 closest distance to " CD  LYS A 166 " =    1.394
peak=    3.410 closest distance to " CD  ARG A  66 " =    2.973
peak=    3.408 closest distance to " CE1 HIS A 115 " =    0.977
peak=    3.406 closest distance to " CD2 LEU A 255 " =    1.375
peak=    3.400 closest distance to " CA  TYR A 116 " =    1.531
peak=    3.397 closest distance to " O   HOH Z 427 " =    3.098
peak=    3.397 closest distance to " CB  ARG A 259 " =    1.884
peak=    3.391 closest distance to " O   HOH Z 116 " =    1.813
peak=    3.390 closest distance to " CA  ASN A 215 " =    1.166
peak=    3.389 closest distance to " O   HOH Z 207 " =    2.048
peak=    3.388 closest distance to " O   HOH Z 234 " =    1.865
peak=    3.386 closest distance to " CB  ALA A 291 " =    1.320
peak=    3.383 closest distance to " O   HOH Z 128 " =    2.255
peak=    3.382 closest distance to " O   HOH Z 154 " =    1.310
peak=    3.378 closest distance to " O   HOH Z 383 " =    2.015
peak=    3.378 closest distance to " O   HOH Z  61 " =    1.588
peak=    3.378 closest distance to " CA  ASP A 162 " =    1.214
peak=    3.372 closest distance to " NH2AARG A 190 " =    1.413
peak=    3.366 closest distance to " O   HOH Z  10 " =    1.828
peak=    3.366 closest distance to " O   HOH Z 438 " =    2.244
peak=    3.366 closest distance to " CZ  PHE A 218 " =    1.069
peak=    3.365 closest distance to " CB  ILE A 120 " =    1.333
peak=    3.365 closest distance to " NE AARG A 275 " =    1.419
peak=    3.359 closest distance to " CA  ASP A 124 " =    0.735
peak=    3.358 closest distance to " O   HOH Z 112 " =    1.539
peak=    3.357 closest distance to " O   HOH Z 327 " =    2.471
peak=    3.357 closest distance to " CG2 VAL A  78 " =    0.956
peak=    3.357 closest distance to " O   HOH Z 292 " =    1.657
peak=    3.353 closest distance to " CB  MET A  47 " =    0.994
peak=    3.345 closest distance to " O   HOH Z 357 " =    1.996
peak=    3.344 closest distance to " O   HOH Z 197 " =    2.469
peak=    3.333 closest distance to " CG  ARG A 219 " =    1.283
peak=    3.333 closest distance to " NH1BARG A 145 " =    1.179
peak=    3.332 closest distance to " CA  GLU A 152 " =    1.564
peak=    3.330 closest distance to " CG1 VAL A 153 " =    1.027
peak=    3.325 closest distance to " CB  TYR A 116 " =    1.050
peak=    3.321 closest distance to " CD  LYS A 119 " =    1.639
peak=    3.319 closest distance to " O   HOH Z  87 " =    2.506
peak=    3.319 closest distance to " O   HOH Z  11 " =    1.188
peak=    3.318 closest distance to " O   HOH Z 345 " =    1.743
peak=    3.315 closest distance to " CA  GLN A 223 " =    0.922
peak=    3.314 closest distance to " O   HOH Z 368 " =    3.650
peak=    3.314 closest distance to " O   HOH Z 409 " =    2.889
peak=    3.306 closest distance to " N   ASN A 127 " =    1.242
peak=    3.306 closest distance to " O   HOH Z 173 " =    1.992
peak=    3.301 closest distance to " CD2 TRP A 179 " =    1.338
peak=    3.298 closest distance to " CB  ASN A  39 " =    0.824
peak=    3.297 closest distance to " O   HOH Z 215 " =    1.535
peak=    3.295 closest distance to " O   ALA A 158 " =    1.273
peak=    3.295 closest distance to " O   HOH Z 365 " =    3.016
peak=    3.291 closest distance to " O   HOH Z   4 " =    1.884
peak=    3.289 closest distance to " CA  ASP A 140 " =    1.181
peak=    3.289 closest distance to " O   HOH Z 185 " =    1.791
peak=    3.288 closest distance to " CD1 ILE A 106 " =    0.883
peak=    3.284 closest distance to " CB  TYR A  30 " =    1.385
peak=    3.282 closest distance to " O   ALA A   1 " =    1.494
peak=    3.282 closest distance to " O   HOH Z 337 " =    3.831
peak=    3.271 closest distance to " CD2 HIS A  81 " =    1.137
peak=    3.271 closest distance to " O   HOH Z 214 " =    2.121
peak=    3.269 closest distance to " CG BARG A 275 " =    1.504
peak=    3.268 closest distance to " CB  TRP A 150 " =    1.567
peak=    3.266 closest distance to " O   HOH Z 255 " =    1.621
peak=    3.264 closest distance to " C   SER A  32 " =    0.996
peak=    3.261 closest distance to " CA  ARG A 195 " =    1.243
peak=    3.259 closest distance to " CZ  PHE A 192 " =    1.018
peak=    3.258 closest distance to " CB  ASN A 285 " =    0.880
peak=    3.256 closest distance to " O   HOH Z 156 " =    2.568
peak=    3.253 closest distance to " NZ  LYS A  76 " =    1.231
peak=    3.245 closest distance to " CG1 VAL A 202 " =    2.147
peak=    3.245 closest distance to " O   HOH Z  85 " =    2.074
peak=    3.242 closest distance to " CD2 LEU A 297 " =    0.881
peak=    3.238 closest distance to " O   HOH Z 139 " =    3.204
peak=    3.237 closest distance to " OD2 ASP A 298 " =    4.138
peak=    3.236 closest distance to " O   HOH Z 166 " =    1.545
peak=    3.236 closest distance to " CA  ALA A 158 " =    1.081
peak=    3.235 closest distance to " CE1 TYR A 186 " =    1.134
peak=    3.234 closest distance to " O   HOH Z 355 " =    1.616
peak=    3.234 closest distance to " O   HOH Z 417 " =    3.332
peak=    3.234 closest distance to " O   HOH Z 245 " =    1.332
peak=    3.234 closest distance to " O   HOH Z 158 " =    2.903
peak=    3.228 closest distance to " O   GLY A  57 " =    2.556
peak=    3.221 closest distance to " CD  PRO A 280 " =    1.056
peak=    3.220 closest distance to " O   HOH Z 189 " =    1.438
peak=    3.218 closest distance to " CA  GLY A 196 " =    1.028
peak=    3.214 closest distance to " OG  SER A  97 " =    3.533
peak=    3.214 closest distance to " CG  MET A 185 " =    1.195
peak=    3.213 closest distance to " O   HOH Z 341 " =    1.778
peak=    3.212 closest distance to " O   HOH Z 167 " =    1.861
peak=    3.211 closest distance to " CA  GLY A 267 " =    1.044
peak=    3.208 closest distance to " CA  ALA A 295 " =    1.102
peak=    3.208 closest distance to " CB  ASN A 127 " =    1.031
peak=    3.207 closest distance to " CB  LEU A 143 " =    1.094
peak=    3.207 closest distance to " CG  LEU A 167 " =    1.207
peak=    3.206 closest distance to " O   HOH Z 114 " =    1.553
peak=    3.204 closest distance to " O   HOH Z 211 " =    2.588
peak=    3.204 closest distance to " O   HOH Z 388 " =    1.812
peak=    3.196 closest distance to " O   HOH Z  44 " =    3.274
peak=    3.194 closest distance to " O   HOH Z 343 " =    2.532
peak=    3.194 closest distance to " CB  ILE A 199 " =    0.989
peak=    3.194 closest distance to " O   HOH Z 423 " =    3.344
peak=    3.192 closest distance to " O   HOH Z 411 " =    1.774
peak=    3.189 closest distance to " CD  ARG A 195 " =    0.926
peak=    3.186 closest distance to " CB  SER A 212 " =    1.169
peak=    3.184 closest distance to " CG1 ILE A 151 " =    0.899
peak=    3.181 closest distance to " O   HOH Z  59 " =    1.709
peak=    3.177 closest distance to " O   HOH Z 287 " =    1.683
peak=    3.177 closest distance to " CE  LYS A 193 " =    1.896
peak=    3.177 closest distance to " CB  MET A 105 " =    1.184
peak=    3.175 closest distance to " O   HOH Z 305 " =    3.766
peak=    3.173 closest distance to " CA  LEU A  83 " =    1.515
peak=    3.170 closest distance to " CG2 VAL A 112 " =    1.494
peak=    3.169 closest distance to " O   GLN A 278 " =    1.219
peak=    3.167 closest distance to " O   HOH Z 425 " =    2.214
peak=    3.167 closest distance to " CB  PRO A 198 " =    1.011
peak=    3.166 closest distance to " OE1 GLN A  58 " =    5.910
peak=    3.166 closest distance to " O   TRP A 274 " =    1.809
peak=    3.164 closest distance to " OG  SER A  22 " =    2.914
peak=    3.160 closest distance to " NH1 ARG A 138 " =    1.137
peak=    3.160 closest distance to " O   HOH Z 227 " =    1.712
peak=    3.160 closest distance to " NE2 GLN A  58 " =    4.429
peak=    3.158 closest distance to " O   HOH Z 329 " =    3.541
peak=    3.155 closest distance to " O   TRP A  70 " =    1.311
peak=    3.154 closest distance to " CG2 VAL A 257 " =    0.896
peak=    3.152 closest distance to " O   HOH Z 410 " =    1.801
peak=    3.149 closest distance to " CB  ALA A  71 " =    1.240
peak=    3.148 closest distance to " O   HOH Z 250 " =    1.796
peak=    3.148 closest distance to " CG  MET A  93 " =    1.011
peak=    3.144 closest distance to " O   HOH Z 215 " =    1.394
peak=    3.143 closest distance to " O   HOH Z 346 " =    1.511
peak=    3.141 closest distance to " O   HOH Z  50 " =    3.518
peak=    3.138 closest distance to " O   HOH Z 171 " =    3.855
peak=    3.133 closest distance to " O   HOH Z   1 " =    2.569
peak=    3.131 closest distance to " O   HOH Z 422 " =    2.635
peak=    3.128 closest distance to " NZ  LYS A 117 " =    1.692
peak=    3.126 closest distance to " O   HOH Z 299 " =    2.358
peak=    3.125 closest distance to " NZ ALYS A 290 " =    1.108
peak=    3.124 closest distance to " O   HOH Z  22 " =    2.503
peak=    3.121 closest distance to " O   HOH Z 421 " =    1.789
peak=    3.115 closest distance to " NZ  LYS A 166 " =    3.029
peak=    3.108 closest distance to " O   HOH Z 109 " =    2.755
peak=    3.107 closest distance to " CA  MET A 105 " =    1.106
peak=    3.106 closest distance to " O   HOH Z 128 " =    1.625
peak=    3.099 closest distance to " CB  PHE A  16 " =    1.036
peak=    3.092 closest distance to " O   HOH Z 244 " =    1.741
peak=    3.092 closest distance to " O   HOH Z 106 " =    2.360
peak=    3.083 closest distance to " O   HOH Z 420 " =    1.866
peak=    3.073 closest distance to " O   HOH Z 285 " =    1.857
peak=    3.066 closest distance to " CG  GLN A  77 " =    1.901
peak=    3.036 closest distance to " C   GLY A  80 " =    1.145
peak=    3.032 closest distance to " O   HOH Z 248 " =    1.548

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 208         
Filter by distance & map next to the model:
   mapped sites are within: 0.820 - 5.361
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 208
   mapped sites are within: 0.820 - 5.361

peak=   -4.755 closest distance to " O   HOH Z 266 " =    4.282
peak=   -4.448 closest distance to " CD  ARG A 156 " =    1.938
peak=   -4.233 closest distance to " O   HOH Z  17 " =    1.289
peak=   -4.216 closest distance to " O   HOH Z  52 " =    1.547
peak=   -4.173 closest distance to " O   HOH Z 377 " =    1.011
peak=   -4.168 closest distance to " O   HOH Z 290 " =    1.058
peak=   -4.142 closest distance to " N   ALA A  43 " =    2.517
peak=   -4.066 closest distance to " CD1 LEU A 228 " =    2.384
peak=   -4.041 closest distance to " OXT GLY A 302 " =    2.914
peak=   -4.005 closest distance to " O   HOH Z 353 " =    2.247
peak=   -3.994 closest distance to " O   VAL A  67 " =    2.773
peak=   -3.979 closest distance to " O   HOH Z 407 " =    3.573
peak=   -3.960 closest distance to " O   HOH Z   5 " =    1.601
peak=   -3.949 closest distance to " OG  SER A  97 " =    2.227
peak=   -3.948 closest distance to " NH2 ARG A  66 " =    1.658
peak=   -3.941 closest distance to " CD2 LEU A 300 " =    2.944
peak=   -3.933 closest distance to " O   HOH Z 377 " =    2.057
peak=   -3.933 closest distance to " O   HOH Z 292 " =    4.522
peak=   -3.932 closest distance to " CG  LEU A 101 " =    2.603
peak=   -3.923 closest distance to " O   ILE A 109 " =    2.670
peak=   -3.895 closest distance to " O   PRO A 163 " =    2.106
peak=   -3.895 closest distance to " OD1 ASN A 148 " =    1.657
peak=   -3.887 closest distance to " O   HOH Z 283 " =    1.860
peak=   -3.884 closest distance to " CD2 LEU A 237 " =    2.617
peak=   -3.840 closest distance to " O   HOH Z  13 " =    1.505
peak=   -3.834 closest distance to " CG1 VAL A 112 " =    2.584
peak=   -3.824 closest distance to " CG  GLU A  53 " =    1.420
peak=   -3.824 closest distance to " CB  PRO A 243 " =    2.595
peak=   -3.816 closest distance to " OG ASER A 134 " =    1.328
peak=   -3.814 closest distance to " CH2 TRP A 179 " =    1.163
peak=   -3.808 closest distance to " O   HOH Z  11 " =    1.796
peak=   -3.797 closest distance to " CD  ARG A 139 " =    1.638
peak=   -3.788 closest distance to " O   SER A 210 " =    1.923
peak=   -3.781 closest distance to " O   HOH Z  43 " =    1.536
peak=   -3.766 closest distance to " O   HOH Z  19 " =    2.098
peak=   -3.750 closest distance to " CD1 PHE A  59 " =    1.906
peak=   -3.736 closest distance to " OG  SER A  62 " =    1.418
peak=   -3.729 closest distance to " CE2 TYR A  30 " =    2.738
peak=   -3.725 closest distance to " N   SER A 276 " =    1.421
peak=   -3.697 closest distance to " C   ALA A 158 " =    1.216
peak=   -3.694 closest distance to " O   HOH Z  38 " =    1.285
peak=   -3.691 closest distance to " CD2 PHE A  59 " =    2.434
peak=   -3.691 closest distance to " CG  MET A  93 " =    2.467
peak=   -3.688 closest distance to " OE2 GLU A   2 " =    1.454
peak=   -3.678 closest distance to " CB  ALA A 291 " =    2.394
peak=   -3.677 closest distance to " CB  TYR A  15 " =    2.262
peak=   -3.662 closest distance to " O   HOH Z 234 " =    4.313
peak=   -3.654 closest distance to " CD  ARG A  14 " =    3.430
peak=   -3.654 closest distance to " ND2 ASN A  45 " =    1.173
peak=   -3.642 closest distance to " O   GLY A 196 " =    1.151
peak=   -3.640 closest distance to " N   GLN A  58 " =    1.672
peak=   -3.632 closest distance to " OE1 GLN A 223 " =    2.094
peak=   -3.629 closest distance to " O   HOH Z 231 " =    2.207
peak=   -3.627 closest distance to " CB  CYS A 254 " =    2.397
peak=   -3.626 closest distance to " O   PRO A 198 " =    1.321
peak=   -3.615 closest distance to " O   HOH Z 372 " =    2.656
peak=   -3.610 closest distance to " O   GLY A 118 " =    2.243
peak=   -3.609 closest distance to " CE  MET A  93 " =    1.196
peak=   -3.605 closest distance to " ND2 ASN A 187 " =    1.636
peak=   -3.602 closest distance to " N   MET A 188 " =    1.886
peak=   -3.602 closest distance to " O   HOH Z 388 " =    2.089
peak=   -3.594 closest distance to " OD1 ASP A 191 " =    1.697
peak=   -3.593 closest distance to " CD2 TYR A 293 " =    2.101
peak=   -3.584 closest distance to " SG ACYS A 201 " =    2.164
peak=   -3.569 closest distance to " C   ASN A 285 " =    2.530
peak=   -3.565 closest distance to " O   HOH Z 166 " =    1.696
peak=   -3.562 closest distance to " C   HIS A 108 " =    1.095
peak=   -3.555 closest distance to " CD  LYS A 289 " =    2.486
peak=   -3.552 closest distance to " OG BSER A 134 " =    1.821
peak=   -3.550 closest distance to " CG  ARG A  66 " =    2.361
peak=   -3.546 closest distance to " O   HOH Z  97 " =    1.763
peak=   -3.541 closest distance to " CG  ASP A 231 " =    0.860
peak=   -3.537 closest distance to " O   HOH Z  71 " =    1.336
peak=   -3.531 closest distance to " O   HOH Z  92 " =    1.624
peak=   -3.531 closest distance to " O   HOH Z 311 " =    3.597
peak=   -3.530 closest distance to " O   HOH Z 426 " =    1.708
peak=   -3.529 closest distance to " O   HOH Z  93 " =    1.483
peak=   -3.523 closest distance to " CG2 THR A   4 " =    1.958
peak=   -3.521 closest distance to " O   HOH Z 165 " =    2.056
peak=   -3.515 closest distance to " CZ  PHE A  59 " =    1.841
peak=   -3.507 closest distance to " CD  GLN A  88 " =    0.820
peak=   -3.499 closest distance to " CA  ASP A 298 " =    1.088
peak=   -3.490 closest distance to " O   HOH Z 151 " =    1.489
peak=   -3.467 closest distance to " NE2 GLN A  88 " =    2.048
peak=   -3.461 closest distance to " CE  MET A 105 " =    1.977
peak=   -3.460 closest distance to " O   HOH Z  15 " =    1.594
peak=   -3.460 closest distance to " O   LEU A 167 " =    1.594
peak=   -3.445 closest distance to " CG  ASP A  50 " =    2.235
peak=   -3.444 closest distance to " O   HOH Z 176 " =    0.888
peak=   -3.439 closest distance to " CG  GLN A  58 " =    1.155
peak=   -3.439 closest distance to " OH  TYR A 169 " =    1.050
peak=   -3.435 closest distance to " O   ALA A 256 " =    1.517
peak=   -3.435 closest distance to " NH2 ARG A  66 " =    5.327
peak=   -3.435 closest distance to " O   VAL A 125 " =    2.164
peak=   -3.434 closest distance to " O   TRP A  92 " =    1.871
peak=   -3.416 closest distance to " O   HOH Z 275 " =    1.474
peak=   -3.414 closest distance to " OG BSER A 134 " =    1.225
peak=   -3.405 closest distance to " O   HOH Z 241 " =    1.169
peak=   -3.398 closest distance to " O   ASN A 301 " =    1.446
peak=   -3.397 closest distance to " CB  ALA A 248 " =    1.944
peak=   -3.396 closest distance to " O   HOH Z 118 " =    2.988
peak=   -3.391 closest distance to " O   HOH Z 385 " =    3.912
peak=   -3.388 closest distance to " NH2 ARG A  79 " =    1.900
peak=   -3.385 closest distance to " CB  ASP A 132 " =    2.351
peak=   -3.384 closest distance to " CB  LEU A 167 " =    2.176
peak=   -3.380 closest distance to " CG  LEU A  83 " =    1.996
peak=   -3.377 closest distance to " O   HOH Z  37 " =    1.871
peak=   -3.377 closest distance to " CA  GLY A 133 " =    2.318
peak=   -3.376 closest distance to " O   HOH Z 399 " =    2.248
peak=   -3.373 closest distance to " O   HOH Z 414 " =    1.416
peak=   -3.370 closest distance to " N   ALA A 226 " =    2.075
peak=   -3.368 closest distance to " O   HOH Z 128 " =    2.517
peak=   -3.360 closest distance to " O   HOH Z 111 " =    1.370
peak=   -3.360 closest distance to " CA  VAL A 232 " =    2.375
peak=   -3.358 closest distance to " CB  ASN A  39 " =    2.203
peak=   -3.358 closest distance to " CD  GLN A 223 " =    1.379
peak=   -3.355 closest distance to " O   HOH Z 389 " =    1.832
peak=   -3.354 closest distance to " O   HOH Z 236 " =    1.282
peak=   -3.353 closest distance to " NH1 ARG A 195 " =    2.582
peak=   -3.352 closest distance to " O   HOH Z 196 " =    2.253
peak=   -3.352 closest distance to " O   HOH Z 221 " =    1.248
peak=   -3.350 closest distance to " N   THR A 235 " =    1.373
peak=   -3.342 closest distance to " OG  SER A  26 " =    1.319
peak=   -3.340 closest distance to " CA  VAL A  67 " =    2.754
peak=   -3.334 closest distance to " O   ASN A 187 " =    1.517
peak=   -3.332 closest distance to " O   HOH Z 266 " =    4.849
peak=   -3.332 closest distance to " CG  PRO A 163 " =    2.493
peak=   -3.331 closest distance to " CA  VAL A 197 " =    1.000
peak=   -3.328 closest distance to " CB  ASP A 286 " =    2.256
peak=   -3.327 closest distance to " CD  ARG A 195 " =    5.109
peak=   -3.324 closest distance to " CZ  ARG A  66 " =    0.952
peak=   -3.324 closest distance to " O   HOH Z 385 " =    2.008
peak=   -3.319 closest distance to " CA  GLY A  98 " =    2.206
peak=   -3.316 closest distance to " OG  SER A 245 " =    0.980
peak=   -3.310 closest distance to " CA  GLY A 203 " =    2.104
peak=   -3.309 closest distance to " O   HOH Z 418 " =    1.399
peak=   -3.308 closest distance to " O   HOH Z 166 " =    1.573
peak=   -3.305 closest distance to " OD2 ASP A 171 " =    2.343
peak=   -3.298 closest distance to " CG2 THR A 221 " =    2.280
peak=   -3.287 closest distance to " ND2 ASN A  60 " =    1.522
peak=   -3.282 closest distance to " NH2AARG A 275 " =    5.361
peak=   -3.280 closest distance to " ND2BASN A 224 " =    1.831
peak=   -3.277 closest distance to " O   HOH Z  98 " =    2.070
peak=   -3.276 closest distance to " CA  GLY A 241 " =    3.067
peak=   -3.275 closest distance to " CD1 LEU A 101 " =    2.801
peak=   -3.271 closest distance to " CB  TRP A  85 " =    2.414
peak=   -3.266 closest distance to " NE2 GLN A  58 " =    0.926
peak=   -3.265 closest distance to " CG  MET A 105 " =    0.923
peak=   -3.263 closest distance to " CB  PRO A 163 " =    2.738
peak=   -3.250 closest distance to " O   HOH Z 184 " =    1.597
peak=   -3.250 closest distance to " CE3 TRP A  70 " =    1.709
peak=   -3.249 closest distance to " OD2 ASP A 171 " =    1.813
peak=   -3.247 closest distance to " O   HOH Z 313 " =    1.036
peak=   -3.247 closest distance to " O   ALA A 160 " =    1.463
peak=   -3.244 closest distance to " OD1 ASN A 187 " =    1.766
peak=   -3.242 closest distance to " OG  SER A  87 " =    1.475
peak=   -3.239 closest distance to " CG  GLU A 277 " =    1.088
peak=   -3.239 closest distance to " O   HOH Z 417 " =    2.738
peak=   -3.238 closest distance to " O   PHE A 218 " =    1.512
peak=   -3.236 closest distance to " O   HOH Z 259 " =    1.224
peak=   -3.235 closest distance to " O   HOH Z  76 " =    1.987
peak=   -3.231 closest distance to " O   PRO A 198 " =    1.875
peak=   -3.228 closest distance to " ND2 ASN A 249 " =    2.006
peak=   -3.218 closest distance to " CZ  TYR A 169 " =    1.842
peak=   -3.216 closest distance to " O   HOH Z  90 " =    1.884
peak=   -3.213 closest distance to " CD2 LEU A 167 " =    1.706
peak=   -3.213 closest distance to " O   HOH Z 252 " =    4.065
peak=   -3.212 closest distance to " O   HOH Z 396 " =    1.725
peak=   -3.210 closest distance to " CE3 TRP A 150 " =    2.025
peak=   -3.199 closest distance to " CG  TRP A 266 " =    1.751
peak=   -3.198 closest distance to " O   VAL A 174 " =    2.118
peak=   -3.196 closest distance to " O   HOH Z 185 " =    2.415
peak=   -3.194 closest distance to " NE  ARG A 259 " =    1.098
peak=   -3.193 closest distance to " O   GLY A 211 " =    1.521
peak=   -3.189 closest distance to " O   HOH Z  61 " =    1.558
peak=   -3.188 closest distance to " CD2 LEU A 237 " =    2.630
peak=   -3.186 closest distance to " CB  PHE A  16 " =    2.706
peak=   -3.186 closest distance to " O   HOH Z 393 " =    1.608
peak=   -3.186 closest distance to " O   HOH Z 189 " =    1.866
peak=   -3.183 closest distance to " CE1 TYR A 169 " =    2.388
peak=   -3.177 closest distance to " CB  SER A 258 " =    2.040
peak=   -3.172 closest distance to " N   ALA A 248 " =    2.003
peak=   -3.172 closest distance to " CB  SER A 245 " =    2.401
peak=   -3.171 closest distance to " CG2 ILE A 263 " =    2.347
peak=   -3.165 closest distance to " NH1 ARG A 195 " =    2.312
peak=   -3.164 closest distance to " O   HOH Z 108 " =    2.274
peak=   -3.159 closest distance to " O   ALA A  34 " =    2.512
peak=   -3.157 closest distance to " CG  LYS A 119 " =    2.957
peak=   -3.155 closest distance to " OG1 THR A 246 " =    1.450
peak=   -3.154 closest distance to " O   PRO A 198 " =    1.336
peak=   -3.150 closest distance to " O   VAL A 189 " =    2.588
peak=   -3.146 closest distance to " N   VAL A 189 " =    1.736
peak=   -3.143 closest distance to " CG  ARG A 269 " =    2.315
peak=   -3.135 closest distance to " CB  PHE A 208 " =    2.238
peak=   -3.133 closest distance to " O   HOH Z 323 " =    1.403
peak=   -3.130 closest distance to " O   HOH Z 265 " =    1.935
peak=   -3.126 closest distance to " OD2 ASP A  65 " =    1.840
peak=   -3.118 closest distance to " O   HOH Z 242 " =    1.573
peak=   -3.117 closest distance to " CD1 TYR A 247 " =    2.261
peak=   -3.111 closest distance to " C   LEU A 143 " =    1.299
peak=   -3.098 closest distance to " O   HOH Z 423 " =    2.336
peak=   -3.088 closest distance to " CB  ALA A 291 " =    2.263
peak=   -3.080 closest distance to " O   HOH Z  98 " =    1.431
peak=   -3.061 closest distance to " O   HOH Z  25 " =    2.124
peak=   -3.059 closest distance to " O   HOH Z 163 " =    4.732
peak=   -3.046 closest distance to " O   VAL A 153 " =    2.322
peak=   -3.038 closest distance to " CB  PHE A 192 " =    1.905
peak=   -3.035 closest distance to " SD  MET A 188 " =    2.289

================= 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    :  0.4405 0.4386   6.244889e+00   6.238163e+00
   1_bss:  0.4326 0.4315   6.238879e+00   6.225920e+00
   1_xyz:  0.3007 0.3369   5.968008e+00   6.048970e+00
   1_adp:  0.2738 0.3448   5.919114e+00   6.070233e+00
   1_occ:  0.2734 0.3453   5.918172e+00   6.069986e+00
   2_bss:  0.2712 0.3430   5.916147e+00   6.067109e+00
   2_xyz:  0.1978 0.2496   5.629407e+00   5.825916e+00
   2_adp:  0.1788 0.2269   5.544828e+00   5.742713e+00
   2_occ:  0.1785 0.2269   5.544283e+00   5.742457e+00
   3_bss:  0.1784 0.2270   5.543648e+00   5.740602e+00
   3_xyz:  0.1394 0.1829   5.323443e+00   5.540455e+00
   3_adp:  0.1283 0.1752   5.268184e+00   5.498976e+00
   3_occ:  0.1283 0.1751   5.268094e+00   5.498929e+00
   4_bss:  0.1286 0.1756   5.270433e+00   5.500452e+00
   4_xyz:  0.1235 0.1704   5.234651e+00   5.465547e+00
   4_adp:  0.1225 0.1679   5.224080e+00   5.449005e+00
   4_occ:  0.1224 0.1678   5.223937e+00   5.448939e+00
   5_bss:  0.1224 0.1677   5.223956e+00   5.448853e+00
   5_xyz:  0.1130 0.1614   5.166660e+00   5.409120e+00
   5_adp:  0.1123 0.1605   5.162724e+00   5.405714e+00
   5_occ:  0.1123 0.1605   5.162841e+00   5.406050e+00
   5_bss:  0.1123 0.1604   5.162853e+00   5.406091e+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:  0.302  38.273  -0.925   2.004   1.229   0.000   0.000   0.000
   1_xyz:  0.302  38.273  -0.925   2.004   1.229   0.000   0.000   0.000
   1_adp:  0.302  38.273  -0.925   2.004   1.229   0.000   0.000   0.000
   1_occ:  0.302  38.273  -0.925   2.004   1.229   0.000   0.000   0.000
   2_bss:  0.330  67.221  -1.604   0.031  -0.621   0.000  -0.000  -0.000
   2_xyz:  0.330  67.221  -1.604   0.031  -0.621   0.000  -0.000  -0.000
   2_adp:  0.330  67.221  -1.604   0.031  -0.621   0.000  -0.000  -0.000
   2_occ:  0.330  67.221  -1.604   0.031  -0.621   0.000  -0.000  -0.000
   3_bss:  0.325  61.198  -1.998  -1.019  -1.530  -0.000  -0.000  -0.000
   3_xyz:  0.325  61.198  -1.998  -1.019  -1.530  -0.000  -0.000  -0.000
   3_adp:  0.325  61.198  -1.998  -1.019  -1.530  -0.000  -0.000  -0.000
   3_occ:  0.325  61.198  -1.998  -1.019  -1.530  -0.000  -0.000  -0.000
   4_bss:  0.323  60.233  -2.179  -1.602  -1.835  -0.000  -0.000  -0.000
   4_xyz:  0.323  60.233  -2.179  -1.602  -1.835  -0.000  -0.000  -0.000
   4_adp:  0.323  60.233  -2.179  -1.602  -1.835  -0.000  -0.000  -0.000
   4_occ:  0.323  60.233  -2.179  -1.602  -1.835  -0.000  -0.000  -0.000
   5_bss:  0.326  60.233  -2.179  -1.602  -1.835  -0.000  -0.000  -0.000
   5_xyz:  0.326  60.233  -2.179  -1.602  -1.835  -0.000  -0.000  -0.000
   5_adp:  0.326  60.233  -2.179  -1.602  -1.835  -0.000  -0.000  -0.000
   5_occ:  0.326  60.233  -2.179  -1.602  -1.835  -0.000  -0.000  -0.000
   5_bss:  0.326  60.172  -2.015  -1.620  -1.704  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.567 0.4746  0.6276    59909.361
   1_bss:  52.270 0.4890  0.6667    56428.048
   1_xyz:  35.696 0.6933  0.9166    30860.633
   1_adp:  37.067 0.6763  0.9020    32763.853
   1_occ:  37.023 0.6768  0.9020    32711.266
   2_bss:  36.784 0.6795  0.8612    32405.896
   2_xyz:  25.643 0.8035  0.9712    16674.013
   2_adp:  22.585 0.8362  0.9837    13791.437
   2_occ:  22.585 0.8362  0.9835    13777.066
   3_bss:  22.517 0.8368  0.9572    13696.793
   3_xyz:  17.508 0.8843  0.9844     8694.017
   3_adp:  16.550 0.8933  0.9812     8066.132
   3_occ:  16.543 0.8934  0.9810     8060.097
   4_bss:  16.583 0.8931  0.9687     8115.201
   4_xyz:  15.795 0.8999  0.9721     7495.756
   4_adp:  15.404 0.9035  0.9693     7305.884
   4_occ:  15.401 0.9036  0.9692     7305.704
   5_bss:  15.400 0.9036  0.9692     7304.119
   5_xyz:  14.643 0.9096  0.9727     6711.205
   5_adp:  14.525 0.9107  0.9687     6663.523
   5_occ:  14.529 0.9107  0.9686     6666.335
   5_bss:  14.528 0.9107  0.9698     6667.172
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.7733e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.7733e-01
   1_xyz:   1.486  0.011  0.091 15.762  0.006  4.118   1.1741e-01
   1_adp:   1.486  0.011  0.091 15.762  0.006  4.118   1.1741e-01
   1_occ:   1.486  0.011  0.091 15.762  0.006  4.118   1.1741e-01
   2_bss:   1.486  0.011  0.091 15.762  0.006  4.118   1.1741e-01
   2_xyz:   1.168  0.008  0.081 14.341  0.005  4.111   7.2229e-02
   2_adp:   1.168  0.008  0.081 14.341  0.005  4.111   7.2229e-02
   2_occ:   1.168  0.008  0.081 14.341  0.005  4.111   7.2229e-02
   3_bss:   1.168  0.008  0.081 14.341  0.005  4.111   7.2229e-02
   3_xyz:   1.047  0.008  0.072 14.532  0.004  4.121   6.4761e-02
   3_adp:   1.047  0.008  0.072 14.532  0.004  4.121   6.4761e-02
   3_occ:   1.047  0.008  0.072 14.532  0.004  4.121   6.4761e-02
   4_bss:   1.047  0.008  0.072 14.532  0.004  4.121   6.4761e-02
   4_xyz:   0.943  0.006  0.069 14.267  0.003  4.115   5.2300e-02
   4_adp:   0.943  0.006  0.069 14.267  0.003  4.115   5.2300e-02
   4_occ:   0.943  0.006  0.069 14.267  0.003  4.115   5.2300e-02
   5_bss:   0.943  0.006  0.069 14.267  0.003  4.115   5.2300e-02
   5_xyz:   1.125  0.010  0.081 14.715  0.004  4.118   7.2295e-02
   5_adp:   1.125  0.010  0.081 14.715  0.004  4.118   7.2295e-02
   5_occ:   1.125  0.010  0.081 14.715  0.004  4.118   7.2295e-02
   5_bss:   1.125  0.010  0.081 14.715  0.004  4.118   7.2295e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.706   2.4209e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.706   2.4209e-01
   1_xyz:   9.775  0.069  0.358 85.835  0.029  1.981   8.2458e-02
   1_adp:   9.775  0.069  0.358 85.835  0.029  1.981   8.2458e-02
   1_occ:   9.775  0.069  0.358 85.835  0.029  1.981   8.2458e-02
   2_bss:   9.775  0.069  0.358 85.835  0.029  1.981   8.2458e-02
   2_xyz:   7.464  0.045  0.257 83.977  0.042  2.321   8.2702e-02
   2_adp:   7.464  0.045  0.257 83.977  0.042  2.321   8.2702e-02
   2_occ:   7.464  0.045  0.257 83.977  0.042  2.321   8.2702e-02
   3_bss:   7.464  0.045  0.257 83.977  0.042  2.321   8.2702e-02
   3_xyz:   7.410  0.051  0.241 82.077  0.035  2.289   6.5907e-02
   3_adp:   7.410  0.051  0.241 82.077  0.035  2.289   6.5907e-02
   3_occ:   7.410  0.051  0.241 82.077  0.035  2.289   6.5907e-02
   4_bss:   7.410  0.051  0.241 82.077  0.035  2.289   6.5907e-02
   4_xyz:   7.165  0.033  0.208 82.843  0.033  2.411   3.2288e-02
   4_adp:   7.165  0.033  0.208 82.843  0.033  2.411   3.2288e-02
   4_occ:   7.165  0.033  0.208 82.843  0.033  2.411   3.2288e-02
   5_bss:   7.165  0.033  0.208 82.843  0.033  2.411   3.2288e-02
   5_xyz:   7.545  0.046  0.253 82.594  0.034  2.243   5.4839e-02
   5_adp:   7.545  0.046  0.253 82.594  0.034  2.243   5.4839e-02
   5_occ:   7.545  0.046  0.253 82.594  0.034  2.243   5.4839e-02
   5_bss:   7.545  0.046  0.253 82.594  0.034  2.243   5.4839e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp: 101.95   0.00  18.43  92.45   0.00  14.25 101.95   1.64  41.20
   1_occ: 101.95   0.00  18.43  92.45   0.00  14.25 101.95   1.64  41.20
   2_bss: 101.95   0.00  18.43  92.45   0.00  14.25 101.95   1.64  41.20
   2_xyz: 101.95   0.00  18.43  92.45   0.00  14.25 101.95   1.64  41.20
   2_adp:  97.26   0.00  18.05  89.28   0.00  13.57  97.26   6.12  42.40
   2_occ:  97.26   0.00  18.05  89.28   0.00  13.57  97.26   6.12  42.40
   3_bss:  97.26   0.00  18.05  89.28   0.00  13.57  97.26   6.12  42.40
   3_xyz:  97.26   0.00  18.05  89.28   0.00  13.57  97.26   6.12  42.40
   3_adp: 104.78   1.37  18.29 104.78   1.37  13.33 104.32   5.50  45.30
   3_occ: 104.78   1.37  18.29 104.78   1.37  13.33 104.32   5.50  45.30
   4_bss: 104.78   1.37  18.29 104.78   1.37  13.33 104.32   5.50  45.30
   4_xyz: 104.78   1.37  18.29 104.78   1.37  13.33 104.32   5.50  45.30
   4_adp: 104.01   2.06  17.41 104.01   2.06  12.97  87.39   5.21  41.63
   4_occ: 104.01   2.06  17.41 104.01   2.06  12.97  87.39   5.21  41.63
   5_bss: 104.01   2.06  17.41 104.01   2.06  12.97  87.39   5.21  41.63
   5_xyz: 104.01   2.06  17.41 104.01   2.06  12.97  87.39   5.21  41.63
   5_adp: 103.75   1.71  17.05 103.75   1.71  12.77  82.74   5.34  40.40
   5_occ: 103.75   1.71  17.05 103.75   1.71  12.77  82.74   5.34  40.40
   5_bss: 103.69   1.65  16.99 103.69   1.65  12.71  82.67   5.28  40.34
------------------------------------------------------------------------
 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:    1.960    0.021    0.401
   1_adp:    1.960    0.021    0.401
   1_occ:    1.960    0.021    0.401
   2_bss:    1.960    0.021    0.401
   2_xyz:    1.204    0.051    0.542
   2_adp:    1.204    0.051    0.542
   2_occ:    1.204    0.051    0.542
   3_bss:    1.204    0.051    0.542
   3_xyz:    1.334    0.008    0.646
   3_adp:    1.334    0.008    0.646
   3_occ:    1.334    0.008    0.646
   4_bss:    1.334    0.008    0.646
   4_xyz:    1.354    0.055    0.664
   4_adp:    1.354    0.055    0.664
   4_occ:    1.354    0.055    0.664
   5_bss:    1.354    0.055    0.664
   5_xyz:    1.394    0.095    0.689
   5_adp:    1.394    0.095    0.689
   5_occ:    1.394    0.095    0.689
   5_bss:    1.394    0.095    0.689
------------------------------------------------------------------------

CPU time actual refinement: 336.92


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1057/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_1057/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1057/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1057/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1057/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.77 
  Macro-tasks:
    bulk solvent and scale       = 39.21  
    individual site refinement   = 137.87 
    weights calculation          = 29.35  
    collect and process          = 6.50   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 213.03 
  Micro-tasks:
    mask                            = 1.86   
    f_calc                          = 110.24 
    alpha_beta                      = 8.45   
    target                          = 1.22   
    gradients_wrt_atomic_parameters = 117.24 
    fmodel                         = 5.99   
    r_factors                      = 0.20   
    phase_errors                   = 10.80  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 256.28 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.855 micro seconds
Total CPU time: 5.84 minutes
from_scatterers_fft:    618 calls, 109.93 s
gradients_fft:          563 calls, 104.52 s

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

# Date 2008-01-16 Time 06:18:43 PST -0800 (1200493123.33 s)
Start R-work = 0.4405, R-free = 0.4386 (no bulk solvent and anisotropic scale)
Final R-work = 0.1347, R-free = 0.1797 (no bulk solvent and anisotropic scale)

Start R-work = 0.4326, R-free = 0.4315
Final R-work = 0.1123, R-free = 0.1604