# Date 2008-01-16 Time 05:36:15 PST -0800 (1200490575.36 s)
#phil __OFF__

Command line arguments: "../801.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8117
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 801

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.1647, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.1647, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1289 2.01025
Completeness in resolution range: 0.972014
Completeness with d_max=infinity: 0.968985

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1289
                             d_min =   2.0103

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.1647, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1289 2.01025
Completeness in resolution range: 0.972014
Completeness with d_max=infinity: 0.968985

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1294 -  4.3009 [2124/2148]  1909   215  10.1%
  bin  2:  4.3009 -  3.4268 [2031/2051]  1832   199   9.8%
  bin  3:  3.4268 -  2.9975 [2011/2030]  1810   201  10.0%
  bin  4:  2.9975 -  2.7251 [1967/1997]  1766   201  10.2%
  bin  5:  2.7251 -  2.5308 [1991/2010]  1792   199  10.0%
  bin  6:  2.5308 -  2.3822 [1966/1991]  1771   195   9.9%
  bin  7:  2.3822 -  2.2633 [1946/1974]  1751   195  10.0%
  bin  8:  2.2633 -  2.1651 [1960/1996]  1765   195   9.9%
  bin  9:  2.1651 -  2.0819 [1931/1973]  1736   195  10.1%
  bin 10:  2.0819 -  2.0103 [1662/1983]  1498   164   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_801/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:
        1.73 -     2.37: 10
        2.37 -     3.00: 1893
        3.00 -     3.63: 4502
        3.63 -     4.27: 8963
        4.27 -     4.90: 12481
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.734 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.923 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.923 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.984 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27844 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_801/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_801/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 = 70.60125 47.16465 88.1178 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: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3472   r_free= 0.3382   ksol= 0.00   Bsol= 0.00   scale= 0.945    |
|                                                                             |
| 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:   0.44 A                  |
| x-ray target function (ml) for work reflections: 6.102321                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1294 -  4.7967 0.99   1382  152 0.2917 0.2833      6.3733      6.2785|
|  2:  4.7967 -  3.8276 0.99   1312  151 0.2674 0.2698      6.5047      6.5565|
|  3:  3.8276 -  3.3498 0.99   1299  141 0.3133 0.2674      6.4628      6.3787|
|  4:  3.3498 -  3.0462 0.99   1295  141 0.3212 0.3491      6.3168      6.3112|
|  5:  3.0462 -  2.8294 0.99   1267  144 0.3567 0.3038      6.1808      6.1046|
|  6:  2.8294 -  2.6635 0.99   1289  144 0.3566 0.3989      6.0823      6.0832|
|  7:  2.6635 -  2.5308 0.99   1265  142 0.3737 0.3504      6.0637      6.0607|
|  8:  2.5308 -  2.4211 0.98   1271  137 0.3892 0.3541       6.052      6.0038|
|  9:  2.4211 -  2.3282 0.98   1248  142 0.3804 0.3663      5.9649      5.9633|
| 10:  2.3282 -  2.2481 1.00   1271  139 0.4080 0.3644      6.0016      5.9091|
| 11:  2.2481 -  2.1781 0.97   1252  138 0.4127 0.4321      5.9264      5.9781|
| 12:  2.1781 -  2.1160 0.98   1250  138 0.3997 0.3966      5.8645       5.958|
| 13:  2.1160 -  2.0604 0.99   1253  140 0.4077 0.3906      5.7854      5.7213|
| 14:  2.0604 -  2.0103 0.77    976  110 0.3763 0.4048      5.6976      5.6858|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1294 -  4.7967  1382   152  0.80  25.49   0.85     0.81      41243.86|
|  2:  4.7967 -  3.8276  1312   151  0.83  23.01   0.95     0.90      51052.50|
|  3:  3.8276 -  3.3498  1299   141  0.79  27.58   0.96     0.91      50228.48|
|  4:  3.3498 -  3.0462  1295   141  0.75  30.89   0.96     0.87      44394.87|
|  5:  3.0462 -  2.8294  1267   144  0.70  35.70   0.98     0.84      35666.60|
|  6:  2.8294 -  2.6635  1289   144  0.67  38.14   0.95     0.82      34002.47|
|  7:  2.6635 -  2.5308  1265   142  0.65  39.52   0.98     0.82      32075.06|
|  8:  2.5308 -  2.4211  1271   137  0.66  38.83   0.96     0.84      29679.90|
|  9:  2.4211 -  2.3282  1248   142  0.66  38.91   0.99     0.86      26515.47|
| 10:  2.3282 -  2.2481  1271   139  0.66  39.54   1.02     0.85      24341.07|
| 11:  2.2481 -  2.1781  1252   138  0.63  41.39   0.98     0.84      24977.54|
| 12:  2.1781 -  2.1160  1250   138  0.62  42.81   1.00     0.84      24235.60|
| 13:  2.1160 -  2.0604  1253   140  0.60  44.06   0.99     0.83      21960.59|
| 14:  2.0604 -  2.0103   976   110  0.62  42.65   1.02     0.81      17840.39|
|alpha:            min =        0.81 max =            0.91 mean =         0.84|
|beta:             min =    17840.39 max =        51052.50 mean =     33157.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.69|
|phase err.(work): min =        0.00 max =           89.95 mean =        36.07|
|phase err.(test): min =        0.00 max =           89.92 mean =        35.75|
|-----------------------------------------------------------------------------|

============================== 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 = 7.753558              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.282   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.764444              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.227   (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 |  1.734 -  2.051:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.051 -  2.367:        5 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.367 -  2.684:       82 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.684 -  3.000:     1811 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.000 -  3.317:     1846 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.317 -  3.634:     2656 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.634 -  3.950:     4645 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.950 -  4.267:     4318 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.267 -  4.583:     5688 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.583 -  4.900:     6793 |
|-----------------------------------------------------------------------------|
|-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 |        0.165 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.734 |       0.178 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.230)------------------------------------------|
|    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: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3472   r_free= 0.3382   ksol= 0.00   Bsol= 0.00   scale= 0.945    |
|                                                                             |
| 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:   0.44 A                  |
| x-ray target function (ml) for work reflections: 6.102321                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3322   r_free= 0.3236   ksol= 0.32   Bsol= 68.72   scale= 0.964   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-2.21,4.36,-0.00,0.00,0.00); trace/3= -0.32                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 6.076853                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.873972              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.042   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.440162              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.915   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3322      final r-factor (work) = 0.1827          |
| start r-factor (free) = 0.3236      final r-factor (free) = 0.2071          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.0559 = 6.87 * 0.50 * 6.0784 + 1.00 * 0.1645                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.9564 = 6.87 * 0.50 * 5.7809 + 1.00 * 0.0875                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1827      final r-factor (work) = 0.1670          |
| start r-factor (free) = 0.2071      final r-factor (free) = 0.2100          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5514 = 0.44 * 1.00 * 5.7809 + 1.00 * 0.0069                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4802 = 0.44 * 1.00 * 5.4616 + 1.00 * 0.0762                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.230)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.60   16.84    None  None   None       |
|    all(noH): 2823   0      0.00    92.60   16.84    None  None   None       |
|    Sol.    : 438    0      5.62    65.78   38.52    None  None   None       |
|    Mac.    : 2385   0      0.00    92.60   12.86    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 -   9.260:  812   |   5:    46.298 -  55.557:  110        |
|      1:     9.260 -  18.519: 1239   |   6:    55.557 -  64.817:   37        |
|      2:    18.519 -  27.779:  333   |   7:    64.817 -  74.076:    1        |
|      3:    27.779 -  37.038:  149   |   8:    74.076 -  83.336:    0        |
|      4:    37.038 -  46.298:  141   |   9:    83.336 -  92.595:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1670 r_free = 0.2100             target_work(ml) = 5.469         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1666 r_free = 0.2101             target_work(ml) = 5.468         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1666   r_free= 0.2101   ksol= 0.32   Bsol= 68.72   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-2.21,4.36,-0.00,0.00,0.00); trace/3= -0.32                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.468152                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1627   r_free= 0.2057   ksol= 0.34   Bsol= 73.55   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.01,-2.39,0.54,-0.00,0.00,0.00); trace/3= -1.62                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.449651                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.825679              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.222  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.491519              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.180   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1627      final r-factor (work) = 0.1306          |
| start r-factor (free) = 0.2057      final r-factor (free) = 0.1701          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8067 = 2.83 * 0.50 * 5.4636 + 1.00 * 0.0875                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6300 = 2.83 * 0.50 * 5.3549 + 1.00 * 0.0643                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1306      final r-factor (work) = 0.1236          |
| start r-factor (free) = 0.1701      final r-factor (free) = 0.1662          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6613 = 0.49 * 1.00 * 5.3549 + 1.00 * 0.0293                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5798 = 0.49 * 1.00 * 5.2287 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.230)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.71    79.85   17.21    None  None   None       |
|    all(noH): 2823   0      0.71    79.85   17.21    None  None   None       |
|    Sol.    : 438    0      5.84    78.40   40.88    None  None   None       |
|    Mac.    : 2385   0      0.71    79.85   12.86    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:     0.710 -   8.624:  737   |   5:    40.278 -  48.192:   97        |
|      1:     8.624 -  16.538: 1231   |   6:    48.192 -  56.106:   80        |
|      2:    16.538 -  24.451:  336   |   7:    56.106 -  64.019:   70        |
|      3:    24.451 -  32.365:  131   |   8:    64.019 -  71.933:   31        |
|      4:    32.365 -  40.278:  105   |   9:    71.933 -  79.847:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1236 r_free = 0.1662             target_work(ml) = 5.215         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1235 r_free = 0.1662             target_work(ml) = 5.215         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1235   r_free= 0.1662   ksol= 0.34   Bsol= 73.55   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.01,-2.39,0.54,-0.00,0.00,0.00); trace/3= -1.62                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.214727                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1230   r_free= 0.1658   ksol= 0.34   Bsol= 73.55   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,-2.17,-0.15,-0.00,-0.00,-0.00); trace/3= -1.65                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.211252                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.615657              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.787  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.284609              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.759  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1230      final r-factor (work) = 0.1150          |
| start r-factor (free) = 0.1658      final r-factor (free) = 0.1608          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9005 = 2.62 * 0.50 * 5.2271 + 1.00 * 0.0643                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8511 = 2.62 * 0.50 * 5.1819 + 1.00 * 0.0741                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1150      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1608      final r-factor (free) = 0.1591          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4846 = 0.28 * 1.00 * 5.1819 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4783 = 0.28 * 1.00 * 5.1624 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.230)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.87    80.58   16.84    None  None   None       |
|    all(noH): 2823   0      0.87    80.58   16.84    None  None   None       |
|    Sol.    : 438    0      4.33    80.50   39.78    None  None   None       |
|    Mac.    : 2385   0      0.87    80.58   12.63    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:     0.869 -   8.840:  814   |   5:    40.725 -  48.697:   78        |
|      1:     8.840 -  16.811: 1211   |   6:    48.697 -  56.668:   92        |
|      2:    16.811 -  24.783:  298   |   7:    56.668 -  64.639:   52        |
|      3:    24.783 -  32.754:  130   |   8:    64.639 -  72.610:   24        |
|      4:    32.754 -  40.725:  118   |   9:    72.610 -  80.582:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1142 r_free = 0.1591             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1141 r_free = 0.1590             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1590   ksol= 0.34   Bsol= 73.55   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,-2.17,-0.15,-0.00,-0.00,-0.00); trace/3= -1.65                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.156109                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1140   r_free= 0.1589   ksol= 0.33   Bsol= 63.87   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-1.90,-0.20,-0.00,-0.00,-0.00); trace/3= -1.46                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.155913                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.198250              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.529  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.292577              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.857  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1140      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1589      final r-factor (free) = 0.1593          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7487 = 2.20 * 0.50 * 5.1629 + 1.00 * 0.0741                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7313 = 2.20 * 0.50 * 5.1540 + 1.00 * 0.0664                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1134      final r-factor (work) = 0.1133          |
| start r-factor (free) = 0.1593      final r-factor (free) = 0.1589          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5169 = 0.29 * 1.00 * 5.1540 + 1.00 * 0.0089                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5172 = 0.29 * 1.00 * 5.1555 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.230)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.84    80.72   16.52    None  None   None       |
|    all(noH): 2823   0      0.84    80.72   16.52    None  None   None       |
|    Sol.    : 438    0      5.18    80.33   38.98    None  None   None       |
|    Mac.    : 2385   0      0.84    80.72   12.40    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:     0.843 -   8.831:  865   |   5:    40.784 -  48.772:   79        |
|      1:     8.831 -  16.820: 1183   |   6:    48.772 -  56.760:   91        |
|      2:    16.820 -  24.808:  285   |   7:    56.760 -  64.749:   40        |
|      3:    24.808 -  32.796:  127   |   8:    64.749 -  72.737:   23        |
|      4:    32.796 -  40.784:  125   |   9:    72.737 -  80.725:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1133 r_free = 0.1589             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1132 r_free = 0.1588             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1588   ksol= 0.33   Bsol= 63.87   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-1.90,-0.20,-0.00,-0.00,-0.00); trace/3= -1.46                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.155310                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1588   ksol= 0.33   Bsol= 63.87   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-1.76,-0.15,-0.00,-0.00,-0.00); trace/3= -1.35                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.155353                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.802791              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 163.121  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.662331              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.625  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1132      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1588      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2917 = 2.80 * 0.50 * 5.1558 + 1.00 * 0.0664                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2862 = 2.80 * 0.50 * 5.1454 + 1.00 * 0.0755                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1107      final r-factor (work) = 0.1105          |
| start r-factor (free) = 0.1588      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4167 = 0.66 * 1.00 * 5.1454 + 1.00 * 0.0087                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4145 = 0.66 * 1.00 * 5.1411 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.230)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.17    80.99   16.37    None  None   None       |
|    all(noH): 2823   0      0.17    80.99   16.37    None  None   None       |
|    Sol.    : 438    0      5.25    80.43   39.06    None  None   None       |
|    Mac.    : 2385   0      0.17    80.99   12.21    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:     0.169 -   8.251:  784   |   5:    40.578 -  48.659:   86        |
|      1:     8.251 -  16.333: 1228   |   6:    48.659 -  56.741:   91        |
|      2:    16.333 -  24.414:  311   |   7:    56.741 -  64.823:   44        |
|      3:    24.414 -  32.496:  132   |   8:    64.823 -  72.904:   23        |
|      4:    32.496 -  40.578:  119   |   9:    72.904 -  80.986:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1105 r_free = 0.1596             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1105 r_free = 0.1596             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1105   r_free= 0.1596   ksol= 0.33   Bsol= 63.87   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-1.76,-0.15,-0.00,-0.00,-0.00); trace/3= -1.35                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.143863                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1294 -  4.7967 0.99   1382  152 0.1006 0.1354      5.4142      5.5535|
|  2:  4.7967 -  3.8276 0.99   1312  151 0.0852 0.1137      5.4454      5.6592|
|  3:  3.8276 -  3.3498 0.99   1299  141 0.1033 0.1470      5.4702      5.8364|
|  4:  3.3498 -  3.0462 0.99   1295  141 0.1182 0.1565      5.4383      5.5817|
|  5:  3.0462 -  2.8294 0.99   1267  144 0.1315 0.1729       5.325      5.5649|
|  6:  2.8294 -  2.6635 0.99   1289  144 0.1197 0.2032      5.2216      5.5349|
|  7:  2.6635 -  2.5308 0.99   1265  142 0.1256 0.1611      5.1711      5.3365|
|  8:  2.5308 -  2.4211 0.98   1271  137 0.1144 0.1673      5.0779      5.3388|
|  9:  2.4211 -  2.3282 0.98   1248  142 0.1126 0.1785      5.0217      5.2976|
| 10:  2.3282 -  2.2481 1.00   1271  139 0.1124 0.1769      4.9681      5.2521|
| 11:  2.2481 -  2.1781 0.97   1252  138 0.1127 0.1720      4.9478      5.1982|
| 12:  2.1781 -  2.1160 0.98   1250  138 0.1141 0.1754       4.893       5.247|
| 13:  2.1160 -  2.0604 0.99   1253  140 0.1078 0.1829      4.7942      5.1042|
| 14:  2.0604 -  2.0103 0.77    976  110 0.0991 0.1672      4.6504      4.9168|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1294 -  4.7967  1382   152  0.94   9.76   0.97     0.94       7974.73|
|  2:  4.7967 -  3.8276  1312   151  0.95   8.22   1.00     0.98       9504.92|
|  3:  3.8276 -  3.3498  1299   141  0.93  11.12   1.01     1.01      10352.46|
|  4:  3.3498 -  3.0462  1295   141  0.92  13.30   0.99     0.97      10017.24|
|  5:  3.0462 -  2.8294  1267   144  0.90  15.50   0.99     0.96       8279.96|
|  6:  2.8294 -  2.6635  1289   144  0.90  16.35   0.98     0.95       7350.45|
|  7:  2.6635 -  2.5308  1265   142  0.90  15.85   0.97     0.95       6376.10|
|  8:  2.5308 -  2.4211  1271   137  0.91  15.02   0.98     0.95       5420.42|
|  9:  2.4211 -  2.3282  1248   142  0.91  15.30   0.99     0.95       5040.45|
| 10:  2.3282 -  2.2481  1271   139  0.90  15.80   0.98     0.93       4423.92|
| 11:  2.2481 -  2.1781  1252   138  0.90  16.18   0.98     0.94       4523.80|
| 12:  2.1781 -  2.1160  1250   138  0.90  16.09   0.99     0.97       4119.86|
| 13:  2.1160 -  2.0604  1253   140  0.91  15.76   0.97     0.95       3425.16|
| 14:  2.0604 -  2.0103   976   110  0.92  13.88   0.95     0.91       2487.07|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2487.07 max =        10352.46 mean =      6482.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.10|
|phase err.(test): min =        0.00 max =           89.50 mean =        13.58|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1594   ksol= 0.33   Bsol= 63.87   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.84,-1.49,0.09,-0.00,0.00,0.00); trace/3= -1.08                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.143979                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1594   ksol= 0.33   Bsol= 63.87   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.84,-1.49,0.09,-0.00,0.00,0.00); trace/3= -1.08                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.143979                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1294 -  4.7967 0.99   1382  152 0.1006 0.1355      5.4149      5.5547|
|  2:  4.7967 -  3.8276 0.99   1312  151 0.0853 0.1137      5.4459      5.6591|
|  3:  3.8276 -  3.3498 0.99   1299  141 0.1033 0.1471      5.4702       5.837|
|  4:  3.3498 -  3.0462 0.99   1295  141 0.1182 0.1565      5.4383       5.582|
|  5:  3.0462 -  2.8294 0.99   1267  144 0.1315 0.1728      5.3249      5.5647|
|  6:  2.8294 -  2.6635 0.99   1289  144 0.1196 0.2033      5.2217      5.5351|
|  7:  2.6635 -  2.5308 0.99   1265  142 0.1256 0.1611      5.1712      5.3366|
|  8:  2.5308 -  2.4211 0.98   1271  137 0.1144 0.1673      5.0781      5.3386|
|  9:  2.4211 -  2.3282 0.98   1248  142 0.1126 0.1786      5.0217      5.2977|
| 10:  2.3282 -  2.2481 1.00   1271  139 0.1125 0.1769      4.9681      5.2519|
| 11:  2.2481 -  2.1781 0.97   1252  138 0.1127 0.1719      4.9477      5.1977|
| 12:  2.1781 -  2.1160 0.98   1250  138 0.1141 0.1752      4.8929      5.2465|
| 13:  2.1160 -  2.0604 0.99   1253  140 0.1077 0.1830      4.7942      5.1046|
| 14:  2.0604 -  2.0103 0.77    976  110 0.0991 0.1671      4.6507      4.9168|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1294 -  4.7967  1382   152  0.94   9.77   0.97     0.94       7991.26|
|  2:  4.7967 -  3.8276  1312   151  0.95   8.23   1.00     0.99       9514.94|
|  3:  3.8276 -  3.3498  1299   141  0.93  11.12   1.02     1.01      10353.24|
|  4:  3.3498 -  3.0462  1295   141  0.92  13.30   1.00     0.98      10016.60|
|  5:  3.0462 -  2.8294  1267   144  0.90  15.50   1.00     0.97       8280.12|
|  6:  2.8294 -  2.6635  1289   144  0.90  16.36   0.98     0.96       7349.62|
|  7:  2.6635 -  2.5308  1265   142  0.90  15.85   0.98     0.96       6377.34|
|  8:  2.5308 -  2.4211  1271   137  0.91  15.02   0.99     0.96       5421.43|
|  9:  2.4211 -  2.3282  1248   142  0.91  15.30   1.00     0.96       5041.85|
| 10:  2.3282 -  2.2481  1271   139  0.90  15.79   0.99     0.95       4422.47|
| 11:  2.2481 -  2.1781  1252   138  0.90  16.17   0.99     0.95       4521.40|
| 12:  2.1781 -  2.1160  1250   138  0.90  16.09   1.00     0.98       4118.21|
| 13:  2.1160 -  2.0604  1253   140  0.91  15.76   0.99     0.96       3425.23|
| 14:  2.0604 -  2.0103   976   110  0.92  13.88   0.96     0.93       2488.79|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2488.79 max =        10353.24 mean =      6484.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.11|
|phase err.(test): min =        0.00 max =           89.50 mean =        13.58|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.230)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.17    80.98   16.37    None  None   None       |
|    all(noH): 2823   0      0.17    80.98   16.37    None  None   None       |
|    Sol.    : 438    0      5.24    80.43   39.06    None  None   None       |
|    Mac.    : 2385   0      0.17    80.98   12.20    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:     0.166 -   8.248:  784   |   5:    40.574 -  48.656:   86        |
|      1:     8.248 -  16.329: 1228   |   6:    48.656 -  56.738:   91        |
|      2:    16.329 -  24.411:  311   |   7:    56.738 -  64.819:   44        |
|      3:    24.411 -  32.493:  132   |   8:    64.819 -  72.901:   23        |
|      4:    32.493 -  40.574:  119   |   9:    72.901 -  80.983:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 292         
Filter by distance & map next to the model:
   mapped sites are within: 0.436 - 4.939
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 285 from: 292
   mapped sites are within: 0.726 - 4.939

peak=    5.746 closest distance to " NH2 ARG A  56 " =    2.256
peak=    5.295 closest distance to " CB  GLN A 223 " =    1.453
peak=    4.993 closest distance to " CG  PRO A  54 " =    1.335
peak=    4.796 closest distance to " CB  ARG A  79 " =    1.342
peak=    4.737 closest distance to " CB  GLN A 183 " =    1.242
peak=    4.728 closest distance to " NE2 GLN A  11 " =    1.115
peak=    4.707 closest distance to " CB  ARG A 190 " =    1.675
peak=    4.697 closest distance to " O   HOH Z 126 " =    1.747
peak=    4.641 closest distance to " CB  SER A  63 " =    1.171
peak=    4.562 closest distance to " CB  ARG A 275 " =    0.922
peak=    4.539 closest distance to " CZ  PHE A 218 " =    1.106
peak=    4.525 closest distance to " O   HOH Z 298 " =    1.956
peak=    4.478 closest distance to " O   HOH Z  53 " =    2.509
peak=    4.440 closest distance to " O   HOH Z 232 " =    2.355
peak=    4.439 closest distance to " CG  PRO A 213 " =    1.147
peak=    4.421 closest distance to " O   HOH Z 369 " =    2.134
peak=    4.387 closest distance to " O   HOH Z 142 " =    1.617
peak=    4.386 closest distance to " CG  PRO A 198 " =    1.291
peak=    4.290 closest distance to " CB  GLU A 152 " =    1.173
peak=    4.267 closest distance to " CB  PRO A  54 " =    0.915
peak=    4.237 closest distance to " O   HOH Z 189 " =    2.916
peak=    4.231 closest distance to " CA  TYR A  30 " =    0.977
peak=    4.205 closest distance to " O   HOH Z  15 " =    2.119
peak=    4.202 closest distance to " O   HOH Z  78 " =    1.658
peak=    4.183 closest distance to " O   HOH Z 158 " =    3.181
peak=    4.170 closest distance to " CB  LEU A 228 " =    1.097
peak=    4.142 closest distance to " O   HOH Z 287 " =    2.185
peak=    4.103 closest distance to " CB  ASN A 148 " =    1.405
peak=    4.080 closest distance to " C   PRO A 198 " =    1.456
peak=    4.067 closest distance to " CD  ARG A 159 " =    0.784
peak=    4.062 closest distance to " CD2 TRP A 179 " =    1.327
peak=    4.046 closest distance to " CE  LYS A  76 " =    0.866
peak=    4.038 closest distance to " CB  GLU A  46 " =    0.954
peak=    4.032 closest distance to " O   HOH Z 368 " =    2.139
peak=    4.023 closest distance to " O   HOH Z 313 " =    1.986
peak=    4.022 closest distance to " CB  VAL A 265 " =    1.304
peak=    4.016 closest distance to " O   HOH Z 406 " =    1.674
peak=    4.013 closest distance to " CG2 VAL A 257 " =    0.838
peak=    4.007 closest distance to " NH1AARG A 145 " =    1.402
peak=    4.007 closest distance to " CG  PRO A 280 " =    0.813
peak=    4.002 closest distance to " O   HOH Z 303 " =    2.127
peak=    3.999 closest distance to " O   HOH Z 423 " =    1.950
peak=    3.998 closest distance to " CB  TYR A 169 " =    0.778
peak=    3.990 closest distance to " O   HOH Z 126 " =    1.968
peak=    3.987 closest distance to " CA  ALA A  51 " =    0.950
peak=    3.968 closest distance to " O   HOH Z 234 " =    3.835
peak=    3.967 closest distance to " O   SER A  87 " =    2.215
peak=    3.961 closest distance to " CB  GLU A 277 " =    3.688
peak=    3.958 closest distance to " O   HOH Z 427 " =    3.110
peak=    3.936 closest distance to " ND2 ASN A 187 " =    1.488
peak=    3.928 closest distance to " CB  ASN A 142 " =    1.054
peak=    3.928 closest distance to " CA  ARG A 195 " =    1.243
peak=    3.923 closest distance to " CB  VAL A 202 " =    1.596
peak=    3.901 closest distance to " O   HOH Z 346 " =    1.698
peak=    3.899 closest distance to " O  BHOH Z 338 " =    2.330
peak=    3.885 closest distance to " CB  TRP A 266 " =    1.022
peak=    3.880 closest distance to " O   HOH Z  40 " =    1.766
peak=    3.819 closest distance to " CB  ASN A  39 " =    0.909
peak=    3.817 closest distance to " CD  ARG A 269 " =    0.902
peak=    3.805 closest distance to " O   HOH Z 392 " =    2.885
peak=    3.798 closest distance to " O   HOH Z 180 " =    2.122
peak=    3.790 closest distance to " CA  ARG A  36 " =    1.077
peak=    3.790 closest distance to " O   HOH Z 265 " =    2.172
peak=    3.784 closest distance to " CB  ASP A 140 " =    1.069
peak=    3.775 closest distance to " CA  ASN A 215 " =    1.128
peak=    3.772 closest distance to " CD  LYS A 166 " =    1.296
peak=    3.767 closest distance to " O   HOH Z 272 " =    1.864
peak=    3.753 closest distance to " O   HOH Z  21 " =    1.866
peak=    3.753 closest distance to " CD1 LEU A 300 " =    1.195
peak=    3.753 closest distance to " O   HOH Z 403 " =    1.515
peak=    3.747 closest distance to " O   HOH Z 250 " =    1.464
peak=    3.737 closest distance to " O   HOH Z 148 " =    3.358
peak=    3.731 closest distance to " CG  PRO A 243 " =    1.063
peak=    3.725 closest distance to " OD1 ASN A  69 " =    2.590
peak=    3.714 closest distance to " CG  LEU A 167 " =    1.259
peak=    3.712 closest distance to " O   HOH Z 193 " =    1.948
peak=    3.706 closest distance to " CD2 LEU A 297 " =    0.882
peak=    3.701 closest distance to " O   HOH Z 316 " =    3.138
peak=    3.696 closest distance to " CG  MET A 185 " =    1.145
peak=    3.682 closest distance to " CB  ASN A 187 " =    1.410
peak=    3.674 closest distance to " CA  PRO A  54 " =    1.373
peak=    3.669 closest distance to " CB  GLU A 128 " =    0.966
peak=    3.668 closest distance to " O   HOH Z 214 " =    2.193
peak=    3.663 closest distance to " O   HOH Z  10 " =    1.782
peak=    3.657 closest distance to " O   HOH Z 209 " =    2.298
peak=    3.648 closest distance to " CB  PRO A  90 " =    1.170
peak=    3.623 closest distance to " NH2 ARG A 156 " =    1.190
peak=    3.622 closest distance to " CG2 ILE A 120 " =    1.092
peak=    3.621 closest distance to " O   HOH Z  43 " =    1.956
peak=    3.620 closest distance to " NZ  LYS A 117 " =    3.232
peak=    3.618 closest distance to " O   ASN A  74 " =    1.447
peak=    3.617 closest distance to " O   HOH Z 248 " =    1.634
peak=    3.617 closest distance to " CD1 LEU A  96 " =    0.726
peak=    3.613 closest distance to " O   HOH Z 280 " =    2.947
peak=    3.612 closest distance to " O   HOH Z  61 " =    1.598
peak=    3.606 closest distance to " O   HOH Z 389 " =    1.923
peak=    3.604 closest distance to " ND2 ASN A 249 " =    0.838
peak=    3.604 closest distance to " O   HOH Z 147 " =    1.872
peak=    3.596 closest distance to " CA  SER A  87 " =    1.023
peak=    3.595 closest distance to " O   HOH Z 294 " =    1.526
peak=    3.589 closest distance to " CZ3 TRP A 266 " =    1.139
peak=    3.584 closest distance to " CB  LEU A  83 " =    0.762
peak=    3.582 closest distance to " CB  ASN A 110 " =    1.115
peak=    3.580 closest distance to " CG1 VAL A 153 " =    0.985
peak=    3.575 closest distance to " O   HOH Z  59 " =    2.215
peak=    3.572 closest distance to " O   HOH Z 368 " =    3.581
peak=    3.569 closest distance to " O   HOH Z 172 " =    3.602
peak=    3.569 closest distance to " O   HOH Z   1 " =    2.156
peak=    3.568 closest distance to " CA  ALA A 158 " =    1.239
peak=    3.567 closest distance to " O   HOH Z 411 " =    3.912
peak=    3.566 closest distance to " O   HOH Z 371 " =    3.023
peak=    3.563 closest distance to " CA  THR A 264 " =    0.900
peak=    3.560 closest distance to " O   HOH Z 185 " =    1.897
peak=    3.542 closest distance to " O   HOH Z 291 " =    1.559
peak=    3.542 closest distance to " O   HOH Z 417 " =    3.419
peak=    3.541 closest distance to " NZ  LYS A  48 " =    1.271
peak=    3.537 closest distance to " OG BSER A 164 " =    2.420
peak=    3.533 closest distance to " CG2 ILE A 234 " =    0.843
peak=    3.533 closest distance to " O   HOH Z 359 " =    1.551
peak=    3.532 closest distance to " O   HOH Z 353 " =    2.621
peak=    3.520 closest distance to " CE1 PHE A  38 " =    1.266
peak=    3.509 closest distance to " CG2AVAL A  72 " =    1.751
peak=    3.508 closest distance to " O   HOH Z  62 " =    2.151
peak=    3.506 closest distance to " O   HOH Z 273 " =    2.777
peak=    3.500 closest distance to " CB  TYR A 116 " =    0.798
peak=    3.495 closest distance to " CB  THR A  31 " =    1.571
peak=    3.493 closest distance to " N   ASN A 127 " =    1.290
peak=    3.489 closest distance to " N   ARG A 156 " =    1.378
peak=    3.483 closest distance to " O   HOH Z 133 " =    2.611
peak=    3.480 closest distance to " O   HOH Z 425 " =    1.895
peak=    3.478 closest distance to " CB  GLN A  88 " =    1.192
peak=    3.478 closest distance to " CA  VAL A 125 " =    1.155
peak=    3.472 closest distance to " CA  GLY A 241 " =    0.821
peak=    3.471 closest distance to " CB  ARG A 138 " =    0.997
peak=    3.453 closest distance to " O   HOH Z 299 " =    4.436
peak=    3.452 closest distance to " O   HOH Z 285 " =    2.403
peak=    3.447 closest distance to " CB  SER A 212 " =    1.221
peak=    3.446 closest distance to " CA  ALA A 154 " =    1.006
peak=    3.442 closest distance to " CA  MET A 105 " =    1.002
peak=    3.437 closest distance to " O   HOH Z 422 " =    2.714
peak=    3.437 closest distance to " O   HOH Z 128 " =    2.304
peak=    3.437 closest distance to " CA  ASP A 162 " =    1.010
peak=    3.436 closest distance to " N   ASN A  39 " =    1.307
peak=    3.435 closest distance to " O   HOH Z 203 " =    1.673
peak=    3.433 closest distance to " CD  ARG A  66 " =    2.442
peak=    3.426 closest distance to " O   HOH Z 419 " =    1.997
peak=    3.425 closest distance to " CA  TYR A 116 " =    1.360
peak=    3.425 closest distance to " O   HOH Z 213 " =    2.051
peak=    3.424 closest distance to " CG2 ILE A  20 " =    1.294
peak=    3.424 closest distance to " CA  TYR A  30 " =    1.052
peak=    3.423 closest distance to " NH2AARG A 275 " =    3.621
peak=    3.423 closest distance to " O   HOH Z 394 " =    4.050
peak=    3.421 closest distance to " O   THR A 220 " =    1.256
peak=    3.417 closest distance to " CB  SER A   3 " =    1.342
peak=    3.410 closest distance to " O   HOH Z 421 " =    2.086
peak=    3.406 closest distance to " CZ2 TRP A 179 " =    1.748
peak=    3.401 closest distance to " O   HOH Z 325 " =    2.295
peak=    3.401 closest distance to " C   ILE A 106 " =    1.935
peak=    3.394 closest distance to " NH2BARG A 145 " =    2.222
peak=    3.393 closest distance to " O   HOH Z 166 " =    3.900
peak=    3.392 closest distance to " CA  THR A 221 " =    0.980
peak=    3.389 closest distance to " CB  MET A  40 " =    0.840
peak=    3.388 closest distance to " CB  ALA A   9 " =    1.599
peak=    3.388 closest distance to " CA  ALA A 160 " =    0.957
peak=    3.386 closest distance to " O   HOH Z 285 " =    1.968
peak=    3.386 closest distance to " O   TYR A 116 " =    1.339
peak=    3.386 closest distance to " O   HOH Z 383 " =    2.193
peak=    3.384 closest distance to " CB  ALA A 291 " =    1.200
peak=    3.381 closest distance to " O   HOH Z  66 " =    2.167
peak=    3.377 closest distance to " CB  ASP A 298 " =    1.196
peak=    3.372 closest distance to " CD BLYS A 290 " =    0.995
peak=    3.372 closest distance to " CB  ALA A   1 " =    4.939
peak=    3.368 closest distance to " O   HOH Z 163 " =    1.937
peak=    3.367 closest distance to " OG1 THR A 294 " =    2.473
peak=    3.365 closest distance to " CG  GLN A  11 " =    1.608
peak=    3.360 closest distance to " CB  GLN A 103 " =    0.841
peak=    3.353 closest distance to " O   HOH Z 126 " =    1.698
peak=    3.350 closest distance to " OG  SER A  22 " =    2.723
peak=    3.346 closest distance to " CB  TRP A 179 " =    1.441
peak=    3.341 closest distance to " O   HOH Z  88 " =    3.661
peak=    3.340 closest distance to " O   HOH Z 261 " =    1.777
peak=    3.337 closest distance to " O   ASP A 191 " =    1.459
peak=    3.329 closest distance to " O   HOH Z  80 " =    1.601
peak=    3.323 closest distance to " CG2 VAL A 197 " =    1.085
peak=    3.322 closest distance to " OG  SER A 245 " =    1.664
peak=    3.322 closest distance to " CB  SER A 216 " =    0.897
peak=    3.312 closest distance to " CG AARG A 275 " =    1.112
peak=    3.311 closest distance to " CB  ILE A 120 " =    1.250
peak=    3.310 closest distance to " CG  ARG A 138 " =    1.142
peak=    3.310 closest distance to " O   HOH Z 402 " =    1.362
peak=    3.305 closest distance to " CE1 TYR A 186 " =    1.345
peak=    3.302 closest distance to " O   HOH Z 128 " =    2.206
peak=    3.301 closest distance to " CA  ALA A 295 " =    1.041
peak=    3.301 closest distance to " OH  TYR A 116 " =    1.108
peak=    3.300 closest distance to " CB  GLN A  89 " =    1.274
peak=    3.299 closest distance to " CB  ALA A 291 " =    0.778
peak=    3.297 closest distance to " O   HOH Z 106 " =    4.197
peak=    3.289 closest distance to " CB  LYS A 117 " =    1.186
peak=    3.280 closest distance to " NE2 GLN A  77 " =    3.328
peak=    3.279 closest distance to " O   HOH Z 345 " =    1.721
peak=    3.278 closest distance to " O   HOH Z 390 " =    2.748
peak=    3.274 closest distance to " O   HOH Z 234 " =    1.824
peak=    3.274 closest distance to " CA  ASP A 124 " =    0.730
peak=    3.272 closest distance to " O   THR A 251 " =    1.144
peak=    3.270 closest distance to " CA  ASN A 217 " =    1.249
peak=    3.264 closest distance to " O   HOH Z  96 " =    1.933
peak=    3.264 closest distance to " CB  ALA A 248 " =    0.934
peak=    3.263 closest distance to " CB  ARG A 139 " =    0.980
peak=    3.259 closest distance to " NE  ARG A  79 " =    1.117
peak=    3.258 closest distance to " NE2 HIS A 207 " =    1.203
peak=    3.257 closest distance to " O   HOH Z 132 " =    2.775
peak=    3.257 closest distance to " CG  PHE A 204 " =    0.848
peak=    3.257 closest distance to " CB  PHE A 204 " =    0.910
peak=    3.256 closest distance to " OG BSER A 134 " =    2.891
peak=    3.253 closest distance to " O   HOH Z 271 " =    2.620
peak=    3.249 closest distance to " O   HOH Z  97 " =    1.904
peak=    3.248 closest distance to " O   HOH Z 305 " =    3.756
peak=    3.247 closest distance to " CA  ALA A 233 " =    1.483
peak=    3.243 closest distance to " O   HOH Z 193 " =    1.757
peak=    3.242 closest distance to " CD  ARG A  66 " =    2.517
peak=    3.232 closest distance to " C   TYR A 214 " =    1.580
peak=    3.228 closest distance to " CG2 THR A 221 " =    1.087
peak=    3.227 closest distance to " O   HOH Z 426 " =    1.760
peak=    3.227 closest distance to " CB  SER A  26 " =    1.753
peak=    3.224 closest distance to " O   HOH Z 251 " =    1.612
peak=    3.222 closest distance to " CD  LYS A  76 " =    2.086
peak=    3.222 closest distance to " O   HOH Z 171 " =    3.962
peak=    3.221 closest distance to " O   HOH Z 407 " =    2.557
peak=    3.220 closest distance to " O   HOH Z 403 " =    1.664
peak=    3.216 closest distance to " CG  GLU A  37 " =    0.866
peak=    3.213 closest distance to " CB  SER A 141 " =    1.044
peak=    3.212 closest distance to " CG1 ILE A  49 " =    1.544
peak=    3.208 closest distance to " CB  MET A  47 " =    0.996
peak=    3.206 closest distance to " CA  ALA A 291 " =    0.785
peak=    3.205 closest distance to " O   HOH Z 258 " =    1.600
peak=    3.201 closest distance to " OD1 ASN A 217 " =    1.775
peak=    3.200 closest distance to " CB  PHE A 204 " =    0.738
peak=    3.198 closest distance to " N   GLY A  98 " =    1.142
peak=    3.197 closest distance to " O   HOH Z  48 " =    1.631
peak=    3.189 closest distance to " CD1 ILE A 106 " =    0.781
peak=    3.180 closest distance to " O   HOH Z 245 " =    1.281
peak=    3.178 closest distance to " CG BARG A 102 " =    1.793
peak=    3.177 closest distance to " O   HOH Z 430 " =    1.514
peak=    3.175 closest distance to " OE1 GLU A   2 " =    2.029
peak=    3.174 closest distance to " O   HOH Z 213 " =    2.505
peak=    3.173 closest distance to " N   CYS A 260 " =    0.837
peak=    3.164 closest distance to " O   HOH Z  97 " =    2.417
peak=    3.159 closest distance to " CA  ILE A 234 " =    0.953
peak=    3.156 closest distance to " N   ALA A 158 " =    1.504
peak=    3.155 closest distance to " O   HOH Z 365 " =    2.883
peak=    3.154 closest distance to " CB  ASN A 215 " =    1.098
peak=    3.152 closest distance to " O   HOH Z 261 " =    1.804
peak=    3.149 closest distance to " CG BARG A 275 " =    1.367
peak=    3.143 closest distance to " CB  GLN A 205 " =    1.093
peak=    3.136 closest distance to " O   THR A 182 " =    1.403
peak=    3.130 closest distance to " O   HOH Z 425 " =    1.260
peak=    3.130 closest distance to " CB  PRO A 243 " =    1.736
peak=    3.122 closest distance to " CB  ALA A 227 " =    1.097
peak=    3.116 closest distance to " CE  LYS A  48 " =    1.087
peak=    3.112 closest distance to " CB  ALA A 100 " =    1.138
peak=    3.108 closest distance to " CA  GLU A  46 " =    1.068
peak=    3.108 closest distance to " N   PHE A 130 " =    1.280
peak=    3.107 closest distance to " ND1 HIS A  81 " =    1.720
peak=    3.103 closest distance to " CA  ALA A 129 " =    1.266
peak=    3.099 closest distance to " O   HOH Z 344 " =    3.220
peak=    3.096 closest distance to " O   HOH Z 409 " =    3.157
peak=    3.088 closest distance to " OG BSER A  99 " =    2.315
peak=    3.088 closest distance to " CG1 ILE A  33 " =    1.230
peak=    3.080 closest distance to " O   HOH Z 248 " =    1.595
peak=    3.079 closest distance to " OE2 GLU A  53 " =    2.091
peak=    3.073 closest distance to " CA  ASP A 191 " =    1.210
peak=    3.073 closest distance to " O   HOH Z 172 " =    3.095
peak=    3.070 closest distance to " O   HOH Z   9 " =    2.132
peak=    3.067 closest distance to " O   SER A 164 " =    1.446
peak=    3.066 closest distance to " CB  ASN A 173 " =    1.157
peak=    3.062 closest distance to " CA  ARG A 102 " =    1.112
peak=    3.062 closest distance to " CB  SER A 210 " =    0.767
peak=    3.055 closest distance to " CA  ILE A 106 " =    0.825
peak=    3.053 closest distance to " CG  ARG A 159 " =    0.847
peak=    3.050 closest distance to " CA  GLY A 211 " =    1.307
peak=    3.049 closest distance to " O   ALA A 158 " =    1.212
peak=    3.037 closest distance to " CD  ARG A 195 " =    3.466
peak=    3.033 closest distance to " ND2 ASN A 110 " =    1.523
peak=    3.031 closest distance to " N   ASP A 162 " =    1.229
peak=    3.018 closest distance to " O   HOH Z 361 " =    3.205

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 195         
Filter by distance & map next to the model:
   mapped sites are within: 0.471 - 5.481
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 195
   mapped sites are within: 0.799 - 5.481

peak=   -4.783 closest distance to " CD  ARG A  14 " =    3.479
peak=   -4.689 closest distance to " CD  GLN A  58 " =    0.913
peak=   -4.581 closest distance to " CG1 VAL A 112 " =    2.624
peak=   -4.482 closest distance to " CB  PRO A 243 " =    2.678
peak=   -4.464 closest distance to " O   VAL A  67 " =    2.748
peak=   -4.435 closest distance to " CD  ARG A 156 " =    2.111
peak=   -4.239 closest distance to " O   HOH Z 266 " =    5.481
peak=   -4.238 closest distance to " O   HOH Z 231 " =    2.299
peak=   -4.204 closest distance to " C   HIS A 108 " =    1.111
peak=   -4.200 closest distance to " O   HOH Z  73 " =    2.324
peak=   -4.194 closest distance to " CZ3 TRP A 179 " =    1.193
peak=   -4.156 closest distance to " O   HOH Z 377 " =    2.111
peak=   -4.151 closest distance to " OG BSER A 134 " =    1.345
peak=   -4.121 closest distance to " CA  VAL A  67 " =    2.935
peak=   -4.100 closest distance to " N   ALA A  43 " =    2.633
peak=   -4.080 closest distance to " O   PRO A 198 " =    1.316
peak=   -4.053 closest distance to " OG  SER A  97 " =    2.313
peak=   -4.008 closest distance to " CE2 PHE A  61 " =    2.695
peak=   -3.972 closest distance to " CD2 TYR A 293 " =    2.015
peak=   -3.952 closest distance to " OE1 GLN A 223 " =    2.101
peak=   -3.941 closest distance to " O   HOH Z  10 " =    1.514
peak=   -3.927 closest distance to " OXT GLY A 302 " =    2.934
peak=   -3.890 closest distance to " CG1 VAL A 250 " =    2.717
peak=   -3.880 closest distance to " CD1 PHE A  59 " =    2.045
peak=   -3.873 closest distance to " CB  ALA A 161 " =    2.561
peak=   -3.869 closest distance to " CG1 VAL A 112 " =    2.849
peak=   -3.864 closest distance to " O   HOH Z 198 " =    2.068
peak=   -3.845 closest distance to " CD1 LEU A 101 " =    2.386
peak=   -3.834 closest distance to " CE2 TYR A  30 " =    2.742
peak=   -3.823 closest distance to " CD2 PHE A 192 " =    2.068
peak=   -3.818 closest distance to " O   HOH Z 196 " =    1.969
peak=   -3.813 closest distance to " O   HOH Z 394 " =    1.522
peak=   -3.803 closest distance to " CA  ASP A 298 " =    1.095
peak=   -3.801 closest distance to " OD1 ASN A 148 " =    1.492
peak=   -3.790 closest distance to " CA  GLY A 241 " =    3.315
peak=   -3.782 closest distance to " O   HOH Z 211 " =    1.515
peak=   -3.771 closest distance to " O   HOH Z 290 " =    1.225
peak=   -3.771 closest distance to " NH2AARG A 275 " =    5.425
peak=   -3.702 closest distance to " O   HOH Z 185 " =    2.313
peak=   -3.701 closest distance to " O   HOH Z  51 " =    1.737
peak=   -3.666 closest distance to " NE2 GLN A 194 " =    1.873
peak=   -3.654 closest distance to " OD1 ASP A 171 " =    1.680
peak=   -3.630 closest distance to " CE  MET A 105 " =    2.491
peak=   -3.628 closest distance to " O   HOH Z  71 " =    2.159
peak=   -3.624 closest distance to " CG2 ILE A  49 " =    2.790
peak=   -3.620 closest distance to " CB  ALA A 129 " =    2.475
peak=   -3.618 closest distance to " O   HOH Z   6 " =    1.442
peak=   -3.610 closest distance to " O   HOH Z 313 " =    1.965
peak=   -3.605 closest distance to " CA  GLY A 241 " =    2.352
peak=   -3.595 closest distance to " CE BMET A  47 " =    1.633
peak=   -3.593 closest distance to " CB  ASN A  39 " =    2.329
peak=   -3.592 closest distance to " O   HOH Z 114 " =    3.138
peak=   -3.587 closest distance to " O   HOH Z 372 " =    2.401
peak=   -3.578 closest distance to " CG  PHE A 283 " =    2.653
peak=   -3.569 closest distance to " NE2 GLN A  11 " =    1.746
peak=   -3.567 closest distance to " N   THR A  52 " =    1.673
peak=   -3.566 closest distance to " CB  ALA A  43 " =    2.644
peak=   -3.564 closest distance to " O   HOH Z  38 " =    1.495
peak=   -3.563 closest distance to " NE2 GLN A  88 " =    1.910
peak=   -3.557 closest distance to " ND2 ASN A  45 " =    1.900
peak=   -3.553 closest distance to " CB  ALA A 291 " =    2.362
peak=   -3.553 closest distance to " CG2 ILE A 263 " =    2.344
peak=   -3.549 closest distance to " C   LEU A 143 " =    1.113
peak=   -3.547 closest distance to " N   ALA A 248 " =    1.733
peak=   -3.538 closest distance to " ND2 ASN A 249 " =    2.454
peak=   -3.527 closest distance to " O   PRO A 163 " =    2.135
peak=   -3.521 closest distance to " O   HOH Z 351 " =    1.443
peak=   -3.518 closest distance to " O   HOH Z 357 " =    2.133
peak=   -3.507 closest distance to " CG  ARG A 269 " =    2.457
peak=   -3.503 closest distance to " ND2 ASN A  45 " =    1.193
peak=   -3.490 closest distance to " O   HOH Z 128 " =    2.659
peak=   -3.484 closest distance to " CG  ARG A  66 " =    2.311
peak=   -3.483 closest distance to " CG1 VAL A 125 " =    1.940
peak=   -3.478 closest distance to " CE3 TRP A 150 " =    2.234
peak=   -3.471 closest distance to " CB  ALA A 291 " =    2.349
peak=   -3.467 closest distance to " O   HOH Z 407 " =    3.213
peak=   -3.464 closest distance to " O   ALA A  10 " =    1.695
peak=   -3.459 closest distance to " O   PHE A 218 " =    1.489
peak=   -3.455 closest distance to " NH2 ARG A  79 " =    1.532
peak=   -3.453 closest distance to " O   HOH Z 103 " =    1.852
peak=   -3.446 closest distance to " O   SER A 210 " =    1.931
peak=   -3.435 closest distance to " CB  ASP A 132 " =    2.346
peak=   -3.433 closest distance to " O   HOH Z 134 " =    3.078
peak=   -3.428 closest distance to " O   HOH Z 389 " =    2.000
peak=   -3.418 closest distance to " O   VAL A 189 " =    2.675
peak=   -3.415 closest distance to " CG  LEU A  83 " =    1.991
peak=   -3.413 closest distance to " O   HOH Z 166 " =    1.880
peak=   -3.412 closest distance to " NE2 GLN A 103 " =    1.705
peak=   -3.402 closest distance to " CA  GLY A 203 " =    2.451
peak=   -3.377 closest distance to " O   HOH Z 216 " =    1.350
peak=   -3.372 closest distance to " CD  GLN A 223 " =    0.799
peak=   -3.372 closest distance to " CB  TRP A  85 " =    2.596
peak=   -3.368 closest distance to " O   HOH Z   6 " =    2.388
peak=   -3.367 closest distance to " ND2BASN A 224 " =    1.799
peak=   -3.356 closest distance to " O   HOH Z 348 " =    2.208
peak=   -3.355 closest distance to " CZ  PHE A 155 " =    1.317
peak=   -3.350 closest distance to " C   SER A 206 " =    1.462
peak=   -3.345 closest distance to " CG2 VAL A 189 " =    2.176
peak=   -3.343 closest distance to " O   HOH Z  60 " =    1.818
peak=   -3.343 closest distance to " ND2 ASN A  60 " =    1.305
peak=   -3.342 closest distance to " O   HOH Z 426 " =    1.644
peak=   -3.341 closest distance to " NH2 ARG A 159 " =    2.387
peak=   -3.340 closest distance to " CB  ALA A 248 " =    2.381
peak=   -3.340 closest distance to " CB  ASP A 286 " =    2.092
peak=   -3.331 closest distance to " O   HOH Z 171 " =    1.966
peak=   -3.330 closest distance to " N   THR A 157 " =    1.585
peak=   -3.321 closest distance to " O   HOH Z 326 " =    5.151
peak=   -3.318 closest distance to " CG  GLU A 277 " =    1.156
peak=   -3.315 closest distance to " O   HOH Z 232 " =    1.649
peak=   -3.307 closest distance to " NE2 GLN A  88 " =    1.115
peak=   -3.306 closest distance to " O   HOH Z 311 " =    3.837
peak=   -3.300 closest distance to " O   HOH Z 429 " =    2.082
peak=   -3.294 closest distance to " O   VAL A 189 " =    1.607
peak=   -3.293 closest distance to " O   HOH Z  44 " =    2.346
peak=   -3.291 closest distance to " C   MET A 188 " =    1.366
peak=   -3.289 closest distance to " O   HOH Z 353 " =    2.205
peak=   -3.288 closest distance to " O   HOH Z 243 " =    1.959
peak=   -3.283 closest distance to " OD2 ASP A 191 " =    1.514
peak=   -3.283 closest distance to " CG1AVAL A  41 " =    2.786
peak=   -3.283 closest distance to " CE3 TRP A 274 " =    2.471
peak=   -3.278 closest distance to " O   HOH Z 435 " =    2.839
peak=   -3.276 closest distance to " CG  HIS A  86 " =    1.145
peak=   -3.275 closest distance to " O   GLN A 240 " =    2.495
peak=   -3.272 closest distance to " O   HOH Z  43 " =    1.634
peak=   -3.266 closest distance to " CZ  PHE A  38 " =    2.019
peak=   -3.261 closest distance to " O   HOH Z 174 " =    2.620
peak=   -3.255 closest distance to " CD2 PHE A  61 " =    2.073
peak=   -3.253 closest distance to " O   HOH Z 106 " =    1.869
peak=   -3.248 closest distance to " CD2 LEU A 237 " =    2.913
peak=   -3.245 closest distance to " CD  ARG A  79 " =    1.197
peak=   -3.245 closest distance to " O   HOH Z 265 " =    2.448
peak=   -3.244 closest distance to " OH  TYR A 247 " =    2.153
peak=   -3.244 closest distance to " O   SER A 135 " =    1.478
peak=   -3.239 closest distance to " CD1 TRP A  70 " =    1.081
peak=   -3.237 closest distance to " O   HOH Z 193 " =    1.637
peak=   -3.236 closest distance to " O   HOH Z 264 " =    1.733
peak=   -3.236 closest distance to " O   HOH Z 359 " =    3.101
peak=   -3.234 closest distance to " O   HOH Z  52 " =    1.469
peak=   -3.233 closest distance to " O   HOH Z 351 " =    1.432
peak=   -3.225 closest distance to " O   HOH Z 322 " =    1.279
peak=   -3.224 closest distance to " O   HOH Z 393 " =    1.354
peak=   -3.220 closest distance to " O   HOH Z 111 " =    1.822
peak=   -3.219 closest distance to " OG BSER A 134 " =    1.881
peak=   -3.219 closest distance to " C   GLY A  17 " =    1.162
peak=   -3.216 closest distance to " O   SER A 276 " =    1.739
peak=   -3.214 closest distance to " O   SER A  95 " =    1.663
peak=   -3.210 closest distance to " O   HOH Z 211 " =    1.779
peak=   -3.205 closest distance to " N   SER A 276 " =    1.369
peak=   -3.202 closest distance to " CD2 HIS A 207 " =    2.342
peak=   -3.201 closest distance to " O   HOH Z 177 " =    1.808
peak=   -3.198 closest distance to " CB  ALA A 100 " =    2.136
peak=   -3.190 closest distance to " SG ACYS A 201 " =    2.020
peak=   -3.184 closest distance to " O   GLN A 240 " =    2.182
peak=   -3.182 closest distance to " CG  MET A 105 " =    0.971
peak=   -3.180 closest distance to " CG  ASN A 252 " =    1.573
peak=   -3.178 closest distance to " CG1BVAL A  41 " =    2.865
peak=   -3.176 closest distance to " O   HOH Z 275 " =    1.554
peak=   -3.175 closest distance to " C   ALA A 158 " =    1.387
peak=   -3.173 closest distance to " O   HOH Z 322 " =    1.649
peak=   -3.170 closest distance to " O   HOH Z  47 " =    1.647
peak=   -3.170 closest distance to " CA  GLY A 241 " =    2.899
peak=   -3.168 closest distance to " CA  SER A 135 " =    1.291
peak=   -3.167 closest distance to " CB  ASP A 171 " =    2.464
peak=   -3.167 closest distance to " OE1 GLN A  88 " =    1.140
peak=   -3.160 closest distance to " N   ALA A 226 " =    2.126
peak=   -3.153 closest distance to " CG1BVAL A  72 " =    2.387
peak=   -3.152 closest distance to " CD1 LEU A   5 " =    2.582
peak=   -3.151 closest distance to " O   HOH Z 174 " =    4.011
peak=   -3.147 closest distance to " CE3 TRP A  70 " =    1.791
peak=   -3.145 closest distance to " O   HOH Z 421 " =    3.187
peak=   -3.143 closest distance to " O   PRO A 198 " =    1.377
peak=   -3.141 closest distance to " OD2 ASP A 171 " =    1.864
peak=   -3.139 closest distance to " OH  TYR A 247 " =    1.865
peak=   -3.137 closest distance to " CZ  TYR A 169 " =    1.781
peak=   -3.132 closest distance to " O   HOH Z 278 " =    1.697
peak=   -3.131 closest distance to " O   HOH Z 395 " =    1.434
peak=   -3.120 closest distance to " O   ALA A 161 " =    1.808
peak=   -3.120 closest distance to " O   GLY A  80 " =    2.511
peak=   -3.119 closest distance to " CD1 ILE A 239 " =    2.098
peak=   -3.111 closest distance to " NE2 GLN A 278 " =    1.607
peak=   -3.111 closest distance to " CD2 TYR A 247 " =    2.401
peak=   -3.104 closest distance to " CG1 VAL A  67 " =    3.054
peak=   -3.094 closest distance to " N   SER A   3 " =    2.074
peak=   -3.094 closest distance to " OD1 ASN A 187 " =    1.586
peak=   -3.090 closest distance to " CZ  PHE A 192 " =    2.857
peak=   -3.089 closest distance to " CG  PRO A 163 " =    2.354
peak=   -3.080 closest distance to " O   HOH Z 357 " =    2.229
peak=   -3.080 closest distance to " CA  GLY A 133 " =    2.298
peak=   -3.078 closest distance to " O   HOH Z  85 " =    2.251
peak=   -3.075 closest distance to " SD  MET A 188 " =    2.202
peak=   -3.063 closest distance to " ND2 ASN A 249 " =    2.218
peak=   -3.045 closest distance to " CD1 ILE A 199 " =    2.562
peak=   -3.044 closest distance to " O   HOH Z  13 " =    1.614
peak=   -3.022 closest distance to " CA  SER A  62 " =    2.490

================= 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    :  0.3472 0.3382   6.102321e+00   6.081461e+00
   1_bss:  0.3322 0.3236   6.076853e+00   6.055517e+00
   1_xyz:  0.1827 0.2071   5.522405e+00   5.626052e+00
   1_adp:  0.1670 0.2100   5.468570e+00   5.647470e+00
   1_occ:  0.1666 0.2101   5.468152e+00   5.648402e+00
   2_bss:  0.1627 0.2057   5.449651e+00   5.631639e+00
   2_xyz:  0.1306 0.1701   5.257684e+00   5.464634e+00
   2_adp:  0.1236 0.1662   5.214944e+00   5.435200e+00
   2_occ:  0.1235 0.1662   5.214727e+00   5.435287e+00
   3_bss:  0.1230 0.1658   5.211252e+00   5.431879e+00
   3_xyz:  0.1150 0.1608   5.165450e+00   5.403930e+00
   3_adp:  0.1142 0.1591   5.156363e+00   5.393361e+00
   3_occ:  0.1141 0.1590   5.156109e+00   5.393380e+00
   4_bss:  0.1140 0.1589   5.155913e+00   5.393670e+00
   4_xyz:  0.1134 0.1593   5.157482e+00   5.398531e+00
   4_adp:  0.1133 0.1589   5.155429e+00   5.396567e+00
   4_occ:  0.1132 0.1588   5.155310e+00   5.396702e+00
   5_bss:  0.1132 0.1588   5.155353e+00   5.396751e+00
   5_xyz:  0.1107 0.1588   5.143902e+00   5.395073e+00
   5_adp:  0.1105 0.1596   5.143901e+00   5.398307e+00
   5_occ:  0.1105 0.1596   5.143863e+00   5.398366e+00
   5_bss:  0.1103 0.1594   5.143979e+00   5.398445e+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:  0.320  68.716  -3.102  -2.205   4.357  -0.000   0.000   0.000
   1_xyz:  0.320  68.716  -3.102  -2.205   4.357  -0.000   0.000   0.000
   1_adp:  0.320  68.716  -3.102  -2.205   4.357  -0.000   0.000   0.000
   1_occ:  0.320  68.716  -3.102  -2.205   4.357  -0.000   0.000   0.000
   2_bss:  0.339  73.546  -3.015  -2.390   0.536  -0.000   0.000   0.000
   2_xyz:  0.339  73.546  -3.015  -2.390   0.536  -0.000   0.000   0.000
   2_adp:  0.339  73.546  -3.015  -2.390   0.536  -0.000   0.000   0.000
   2_occ:  0.339  73.546  -3.015  -2.390   0.536  -0.000   0.000   0.000
   3_bss:  0.336  73.546  -2.637  -2.167  -0.151  -0.000  -0.000  -0.000
   3_xyz:  0.336  73.546  -2.637  -2.167  -0.151  -0.000  -0.000  -0.000
   3_adp:  0.336  73.546  -2.637  -2.167  -0.151  -0.000  -0.000  -0.000
   3_occ:  0.336  73.546  -2.637  -2.167  -0.151  -0.000  -0.000  -0.000
   4_bss:  0.327  63.872  -2.286  -1.903  -0.199  -0.000  -0.000  -0.000
   4_xyz:  0.327  63.872  -2.286  -1.903  -0.199  -0.000  -0.000  -0.000
   4_adp:  0.327  63.872  -2.286  -1.903  -0.199  -0.000  -0.000  -0.000
   4_occ:  0.327  63.872  -2.286  -1.903  -0.199  -0.000  -0.000  -0.000
   5_bss:  0.327  63.872  -2.135  -1.765  -0.150  -0.000  -0.000  -0.000
   5_xyz:  0.327  63.872  -2.135  -1.765  -0.150  -0.000  -0.000  -0.000
   5_adp:  0.327  63.872  -2.135  -1.765  -0.150  -0.000  -0.000  -0.000
   5_occ:  0.327  63.872  -2.135  -1.765  -0.150  -0.000  -0.000  -0.000
   5_bss:  0.327  63.868  -1.839  -1.488   0.093  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  36.039 0.6922  0.8446    33156.818
   1_bss:  34.877 0.7042  0.8523    30309.537
   1_xyz:  19.516 0.8671  0.9974    10745.243
   1_adp:  20.122 0.8606  0.9938    11148.271
   1_occ:  20.155 0.8603  0.9930    11156.952
   2_bss:  19.549 0.8664  0.9559    10798.807
   2_xyz:  15.708 0.9005  0.9704     7379.296
   2_adp:  15.006 0.9067  0.9627     6956.903
   2_occ:  15.004 0.9067  0.9626     6953.986
   3_bss:  14.924 0.9074  0.9625     6901.035
   3_xyz:  14.272 0.9129  0.9672     6518.967
   3_adp:  14.005 0.9152  0.9616     6390.598
   3_occ:  14.000 0.9152  0.9616     6389.280
   4_bss:  14.006 0.9152  0.9681     6392.434
   4_xyz:  14.085 0.9147  0.9671     6466.635
   4_adp:  14.027 0.9152  0.9592     6446.643
   4_occ:  14.029 0.9152  0.9592     6446.654
   5_bss:  14.030 0.9152  0.9631     6448.079
   5_xyz:  14.000 0.9153  0.9644     6455.516
   5_adp:  14.051 0.9150  0.9562     6481.206
   5_occ:  14.050 0.9150  0.9562     6481.860
   5_bss:  14.053 0.9150  0.9654     6483.835
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6455e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6455e-01
   1_xyz:   1.273  0.011  0.080 15.400  0.005  4.121   8.7453e-02
   1_adp:   1.273  0.011  0.080 15.400  0.005  4.121   8.7453e-02
   1_occ:   1.273  0.011  0.080 15.400  0.005  4.121   8.7453e-02
   2_bss:   1.273  0.011  0.080 15.400  0.005  4.121   8.7453e-02
   2_xyz:   1.047  0.009  0.078 14.835  0.004  4.132   6.4310e-02
   2_adp:   1.047  0.009  0.078 14.835  0.004  4.132   6.4310e-02
   2_occ:   1.047  0.009  0.078 14.835  0.004  4.132   6.4310e-02
   3_bss:   1.047  0.009  0.078 14.835  0.004  4.132   6.4310e-02
   3_xyz:   1.105  0.010  0.084 14.883  0.004  4.114   7.4051e-02
   3_adp:   1.105  0.010  0.084 14.883  0.004  4.114   7.4051e-02
   3_occ:   1.105  0.010  0.084 14.883  0.004  4.114   7.4051e-02
   4_bss:   1.105  0.010  0.084 14.883  0.004  4.114   7.4051e-02
   4_xyz:   1.034  0.010  0.080 14.670  0.004  4.117   6.6369e-02
   4_adp:   1.034  0.010  0.080 14.670  0.004  4.117   6.6369e-02
   4_occ:   1.034  0.010  0.080 14.670  0.004  4.117   6.6369e-02
   5_bss:   1.034  0.010  0.080 14.670  0.004  4.117   6.6369e-02
   5_xyz:   1.103  0.011  0.085 14.823  0.004  4.118   7.5486e-02
   5_adp:   1.103  0.011  0.085 14.823  0.004  4.118   7.5486e-02
   5_occ:   1.103  0.011  0.085 14.823  0.004  4.118   7.5486e-02
   5_bss:   1.103  0.011  0.085 14.823  0.004  4.118   7.5486e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.734   2.4403e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.734   2.4403e-01
   1_xyz:  11.163  0.054  0.249 80.703  0.039  2.265   8.8541e-02
   1_adp:  11.163  0.054  0.249 80.703  0.039  2.265   8.8541e-02
   1_occ:  11.163  0.054  0.249 80.703  0.039  2.265   8.8541e-02
   2_bss:  11.163  0.054  0.249 80.703  0.039  2.265   8.8541e-02
   2_xyz:   7.187  0.051  0.242 83.848  0.038  2.367   4.7217e-02
   2_adp:   7.187  0.051  0.242 83.848  0.038  2.367   4.7217e-02
   2_occ:   7.187  0.051  0.242 83.848  0.038  2.367   4.7217e-02
   3_bss:   7.187  0.051  0.242 83.848  0.038  2.367   4.7217e-02
   3_xyz:   7.855  0.044  0.277 83.147  0.031  2.362   5.1413e-02
   3_adp:   7.855  0.044  0.277 83.147  0.031  2.362   5.1413e-02
   3_occ:   7.855  0.044  0.277 83.147  0.031  2.362   5.1413e-02
   4_bss:   7.855  0.044  0.277 83.147  0.031  2.362   5.1413e-02
   4_xyz:   7.060  0.047  0.263 81.727  0.030  2.355   4.6520e-02
   4_adp:   7.060  0.047  0.263 81.727  0.030  2.355   4.6520e-02
   4_occ:   7.060  0.047  0.263 81.727  0.030  2.355   4.6520e-02
   5_bss:   7.060  0.047  0.263 81.727  0.030  2.355   4.6520e-02
   5_xyz:   7.535  0.053  0.278 82.426  0.028  2.324   5.4938e-02
   5_adp:   7.535  0.053  0.278 82.426  0.028  2.324   5.4938e-02
   5_occ:   7.535  0.053  0.278 82.426  0.028  2.324   5.4938e-02
   5_bss:   7.535  0.053  0.278 82.426  0.028  2.324   5.4938e-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:  92.60   0.00  16.84  92.60   0.00  12.86  65.78   5.62  38.52
   1_occ:  92.60   0.00  16.84  92.60   0.00  12.86  65.78   5.62  38.52
   2_bss:  92.60   0.00  16.84  92.60   0.00  12.86  65.78   5.62  38.52
   2_xyz:  92.60   0.00  16.84  92.60   0.00  12.86  65.78   5.62  38.52
   2_adp:  79.85   0.71  17.21  79.85   0.71  12.86  78.40   5.84  40.88
   2_occ:  79.85   0.71  17.21  79.85   0.71  12.86  78.40   5.84  40.88
   3_bss:  79.85   0.71  17.21  79.85   0.71  12.86  78.40   5.84  40.88
   3_xyz:  79.85   0.71  17.21  79.85   0.71  12.86  78.40   5.84  40.88
   3_adp:  80.58   0.87  16.84  80.58   0.87  12.63  80.50   4.33  39.78
   3_occ:  80.58   0.87  16.84  80.58   0.87  12.63  80.50   4.33  39.78
   4_bss:  80.58   0.87  16.84  80.58   0.87  12.63  80.50   4.33  39.78
   4_xyz:  80.58   0.87  16.84  80.58   0.87  12.63  80.50   4.33  39.78
   4_adp:  80.72   0.84  16.52  80.72   0.84  12.40  80.33   5.18  38.98
   4_occ:  80.72   0.84  16.52  80.72   0.84  12.40  80.33   5.18  38.98
   5_bss:  80.72   0.84  16.52  80.72   0.84  12.40  80.33   5.18  38.98
   5_xyz:  80.72   0.84  16.52  80.72   0.84  12.40  80.33   5.18  38.98
   5_adp:  80.99   0.17  16.37  80.99   0.17  12.21  80.43   5.25  39.06
   5_occ:  80.99   0.17  16.37  80.99   0.17  12.21  80.43   5.25  39.06
   5_bss:  80.98   0.17  16.37  80.98   0.17  12.20  80.43   5.24  39.06
------------------------------------------------------------------------
 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:    1.123    0.024    0.378
   1_adp:    1.123    0.024    0.378
   1_occ:    1.123    0.024    0.378
   2_bss:    1.123    0.024    0.378
   2_xyz:    0.938    0.035    0.407
   2_adp:    0.938    0.035    0.407
   2_occ:    0.938    0.035    0.407
   3_bss:    0.938    0.035    0.407
   3_xyz:    1.094    0.046    0.431
   3_adp:    1.094    0.046    0.431
   3_occ:    1.094    0.046    0.431
   4_bss:    1.094    0.046    0.431
   4_xyz:    1.420    0.036    0.444
   4_adp:    1.420    0.036    0.444
   4_occ:    1.420    0.036    0.444
   5_bss:    1.420    0.036    0.444
   5_xyz:    1.465    0.034    0.450
   5_adp:    1.465    0.034    0.450
   5_occ:    1.465    0.034    0.450
   5_bss:    1.465    0.034    0.450
------------------------------------------------------------------------

CPU time actual refinement: 322.86


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_801/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_801/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_801/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_801/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_801/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 322.71 
  Macro-tasks:
    bulk solvent and scale       = 38.52  
    individual site refinement   = 136.49 
    weights calculation          = 28.83  
    collect and process          = 6.60   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 210.56 
  Micro-tasks:
    mask                            = 1.17   
    f_calc                          = 101.15 
    alpha_beta                      = 8.11   
    target                          = 1.24   
    gradients_wrt_atomic_parameters = 111.24 
    fmodel                         = 6.81   
    r_factors                      = 0.21   
    phase_errors                   = 11.27  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 241.45 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.536 micro seconds
Total CPU time: 5.60 minutes
from_scatterers_fft:    645 calls, 100.73 s
gradients_fft:          590 calls,  97.41 s

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

# Date 2008-01-16 Time 05:41:50 PST -0800 (1200490910.87 s)
Start R-work = 0.3472, R-free = 0.3382 (no bulk solvent and anisotropic scale)
Final R-work = 0.1308, R-free = 0.1756 (no bulk solvent and anisotropic scale)

Start R-work = 0.3322, R-free = 0.3236
Final R-work = 0.1103, R-free = 0.1594