# Date 2008-01-16 Time 03:54:08 PST -0800 (1200484448.66 s)
#phil __OFF__

Command line arguments: "../92.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 20421
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 92

-------------------------------------------------------------------------------
  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: (68.4938, 47.6339, 85.9581, 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: 2.75, per 1000 atoms: 0.97


================================== 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: (68.4938, 47.6339, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8941 1.95078
Completeness in resolution range: 0.929137
Completeness with d_max=infinity: 0.926369

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8941
                             d_min =   1.9508

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: (68.4938, 47.6339, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8941 1.95078
Completeness in resolution range: 0.929137
Completeness with d_max=infinity: 0.926369

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8945 -  4.1749 [2212/2241]  1986   226  10.2%
  bin  2:  4.1749 -  3.3258 [2122/2145]  1912   210   9.9%
  bin  3:  3.3258 -  2.9090 [2093/2118]  1885   208   9.9%
  bin  4:  2.9090 -  2.6446 [2066/2084]  1857   209  10.1%
  bin  5:  2.6446 -  2.4560 [2056/2098]  1852   204   9.9%
  bin  6:  2.4560 -  2.3117 [2060/2088]  1858   202   9.8%
  bin  7:  2.3117 -  2.1964 [2036/2072]  1835   201   9.9%
  bin  8:  2.1964 -  2.1010 [2024/2066]  1824   200   9.9%
  bin  9:  2.1010 -  2.0203 [2036/2096]  1832   204  10.0%
  bin 10:  2.0203 -  1.9508 [ 884/2075]   789    95  10.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_92/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: 0.12 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:
        0.94 -     1.73: 10
        1.73 -     2.52: 56
        2.52 -     3.32: 3861
        3.32 -     4.11: 9518
        4.11 -     4.90: 15182
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  0.938 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.279 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.468 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.539 3.040 -x+1,y-1/2,-z+1/2
  " C   GLY A  91 " - " O   HOH Z 401 "  1.548 3.270 -x+1,y-1/2,-z+1/2
  ... (remaining 28622 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_92/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_92/model_refine_001.geo

CPU time processing inputs: 8.10


============================ 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 = 68.49375 47.63395 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4283   r_free= 0.4265   ksol= 0.00   Bsol= 0.00   scale= 0.924    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.235535                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8945 -  4.6567 0.99   1434  159 0.3469 0.3644      6.5088      6.5706|
|  2:  4.6567 -  3.7151 0.99   1393  155 0.3572 0.3489      6.7041       6.698|
|  3:  3.7151 -  3.2510 0.99   1349  148 0.3862 0.3666      6.5748        6.64|
|  4:  3.2510 -  2.9563 0.99   1335  144 0.4092 0.3958      6.4392      6.3999|
|  5:  2.9563 -  2.7458 0.99   1339  152 0.4419 0.4171      6.3053      6.3094|
|  6:  2.7458 -  2.5848 0.99   1347  154 0.4532 0.4780      6.2275      6.1227|
|  7:  2.5848 -  2.4560 0.98   1295  145 0.4689 0.4050      6.1902      6.1115|
|  8:  2.4560 -  2.3495 0.98   1331  139 0.4734 0.4994      6.1434      6.1872|
|  9:  2.3495 -  2.2594 0.99   1314  150 0.4996 0.4996      6.1062      6.1546|
| 10:  2.2594 -  2.1817 0.98   1319  143 0.4733 0.4835      6.0678      6.0697|
| 11:  2.1817 -  2.1136 0.97   1310  147 0.4952 0.5235      6.0083      6.0221|
| 12:  2.1136 -  2.0534 0.98   1286  151 0.4952 0.4750       5.931       5.957|
| 13:  2.0534 -  1.9995 0.90   1193  125 0.4900 0.5092      5.8522       5.818|
| 14:  1.9995 -  1.9508 0.29    385   47 0.4919 0.5209      5.8783      5.7271|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8945 -  4.6567  1434   159  0.70  34.11   0.85     0.72      67906.51|
|  2:  4.6567 -  3.7151  1393   155  0.74  31.99   0.94     0.83      88827.49|
|  3:  3.7151 -  3.2510  1349   148  0.67  38.38   0.95     0.86      89893.83|
|  4:  3.2510 -  2.9563  1335   144  0.61  42.70   0.95     0.82      75753.32|
|  5:  2.9563 -  2.7458  1339   152  0.56  47.38   0.92     0.77      60966.75|
|  6:  2.7458 -  2.5848  1347   154  0.54  48.97   0.92     0.73      52677.36|
|  7:  2.5848 -  2.4560  1295   145  0.52  50.50   0.93     0.71      49529.67|
|  8:  2.4560 -  2.3495  1331   139  0.47  54.20   0.95     0.67      47950.53|
|  9:  2.3495 -  2.2594  1314   150  0.45  56.30   0.92     0.67      47428.28|
| 10:  2.2594 -  2.1817  1319   143  0.42  58.03   0.97     0.63      44640.18|
| 11:  2.1817 -  2.1136  1310   147  0.41  59.59   0.95     0.62      42767.46|
| 12:  2.1136 -  2.0534  1286   151  0.37  62.58   0.96     0.59      40443.95|
| 13:  2.0534 -  1.9995  1193   125  0.34  64.55   0.97     0.55      35719.06|
| 14:  1.9995 -  1.9508   385    47  0.35  63.38   0.96     0.45      28360.09|
|alpha:            min =        0.45 max =            0.86 mean =         0.70|
|beta:             min =    28360.09 max =        89893.83 mean =     57109.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           89.99 mean =        49.90|
|phase err.(test): min =        0.00 max =           89.97 mean =        50.15|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.390467             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.484   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.562196              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.438   (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 |  0.938 -  1.334:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.334 -  1.730:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.730 -  2.127:       15 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.127 -  2.523:       41 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.523 -  2.919:     1488 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.919 -  3.315:     2373 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.315 -  3.711:     3779 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.711 -  4.108:     5739 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.108 -  4.504:     6649 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.504 -  4.900:     8533 |
|-----------------------------------------------------------------------------|
|-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 |        0.223 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  0.938 |       1.092 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.606)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4283   r_free= 0.4265   ksol= 0.00   Bsol= 0.00   scale= 0.924    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.235535                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4196   r_free= 0.4145   ksol= 0.31   Bsol= 26.19   scale= 0.955   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.53,2.11,-1.54,0.00,-0.00,-0.00); trace/3= 0.37                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.225397                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.191657              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.304   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.819439              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.100   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4196      final r-factor (work) = 0.2720          |
| start r-factor (free) = 0.4145      final r-factor (free) = 0.2967          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.8472 = 9.19 * 0.50 * 6.2283 + 1.00 * 0.2229                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.8805 = 9.19 * 0.50 * 6.0400 + 1.00 * 0.1218                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2720      final r-factor (work) = 0.2435          |
| start r-factor (free) = 0.2967      final r-factor (free) = 0.3015          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9559 = 0.82 * 1.00 * 6.0400 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7793 = 0.82 * 1.00 * 5.8097 + 1.00 * 0.0186                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.606)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.87   18.47    None  None   None       |
|    all(noH): 2823   0      0.00    99.87   18.47    None  None   None       |
|    Sol.    : 438    0      5.69    99.87   41.02    None  None   None       |
|    Mac.    : 2385   0      0.00    89.63   14.33    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.987:  997   |   5:    49.933 -  59.920:   81        |
|      1:     9.987 -  19.973:  961   |   6:    59.920 -  69.907:   48        |
|      2:    19.973 -  29.960:  378   |   7:    69.907 -  79.893:   26        |
|      3:    29.960 -  39.947:  192   |   8:    79.893 -  89.880:    9        |
|      4:    39.947 -  49.933:  127   |   9:    89.880 -  99.867:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2435 r_free = 0.3015             target_work(ml) = 5.818         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2432 r_free = 0.3020             target_work(ml) = 5.818         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2432   r_free= 0.3020   ksol= 0.31   Bsol= 26.19   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.53,2.11,-1.54,0.00,-0.00,-0.00); trace/3= 0.37                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.818182                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2389   r_free= 0.2974   ksol= 0.31   Bsol= 41.06   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.95,-0.13,-1.38,-0.00,-0.00,-0.00); trace/3= -1.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.807429                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.087131              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.919   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.408651              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.375   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2389      final r-factor (work) = 0.1794          |
| start r-factor (free) = 0.2974      final r-factor (free) = 0.2288          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0898 = 3.09 * 0.50 * 5.8101 + 1.00 * 0.1215                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8514 = 3.09 * 0.50 * 5.6959 + 1.00 * 0.0595                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1794      final r-factor (work) = 0.1659          |
| start r-factor (free) = 0.2288      final r-factor (free) = 0.2125          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3452 = 0.41 * 1.00 * 5.6959 + 1.00 * 0.0176                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2694 = 0.41 * 1.00 * 5.5136 + 1.00 * 0.0162                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.606)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.57   17.94    None  None   None       |
|    all(noH): 2823   0      0.00    92.57   17.94    None  None   None       |
|    Sol.    : 438    0      4.81    88.22   41.28    None  None   None       |
|    Mac.    : 2385   0      0.00    92.57   13.65    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 -   9.257:  868   |   5:    46.284 -  55.541:  105        |
|      1:     9.257 -  18.514: 1161   |   6:    55.541 -  64.798:   65        |
|      2:    18.514 -  27.771:  296   |   7:    64.798 -  74.055:   32        |
|      3:    27.771 -  37.028:  148   |   8:    74.055 -  83.312:   12        |
|      4:    37.028 -  46.284:  127   |   9:    83.312 -  92.569:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1659 r_free = 0.2125             target_work(ml) = 5.482         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1657 r_free = 0.2124             target_work(ml) = 5.482         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1657   r_free= 0.2124   ksol= 0.31   Bsol= 41.06   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.95,-0.13,-1.38,-0.00,-0.00,-0.00); trace/3= -1.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.481598                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1659   r_free= 0.2122   ksol= 0.31   Bsol= 41.06   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.72,-0.94,-1.32,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.481598                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.133454              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.497  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.361663              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.113   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1659      final r-factor (work) = 0.1315          |
| start r-factor (free) = 0.2122      final r-factor (free) = 0.1769          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7010 = 3.13 * 0.50 * 5.5157 + 1.00 * 0.0595                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4933 = 3.13 * 0.50 * 5.3812 + 1.00 * 0.0625                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1315      final r-factor (work) = 0.1244          |
| start r-factor (free) = 0.1769      final r-factor (free) = 0.1708          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9581 = 0.36 * 1.00 * 5.3812 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9097 = 0.36 * 1.00 * 5.2547 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.606)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.63    93.40   17.56    None  None   None       |
|    all(noH): 2823   0      1.63    93.40   17.56    None  None   None       |
|    Sol.    : 438    0      6.07    84.91   41.32    None  None   None       |
|    Mac.    : 2385   0      1.63    93.40   13.19    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:     1.625 -  10.803: 1196   |   5:    47.513 -  56.691:  114        |
|      1:    10.803 -  19.980:  977   |   6:    56.691 -  65.868:   59        |
|      2:    19.980 -  29.158:  202   |   7:    65.868 -  75.046:   25        |
|      3:    29.158 -  38.336:  120   |   8:    75.046 -  84.223:   10        |
|      4:    38.336 -  47.513:  114   |   9:    84.223 -  93.401:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1244 r_free = 0.1708             target_work(ml) = 5.236         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1243 r_free = 0.1707             target_work(ml) = 5.236         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1243   r_free= 0.1707   ksol= 0.31   Bsol= 41.06   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.72,-0.94,-1.32,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.235806                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1246   r_free= 0.1705   ksol= 0.32   Bsol= 47.37   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.03,-1.44,-1.35,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.236549                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.613472              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.068  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.322792              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.038  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1246      final r-factor (work) = 0.1198          |
| start r-factor (free) = 0.1705      final r-factor (free) = 0.1645          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3032 = 1.61 * 0.50 * 5.2567 + 1.00 * 0.0625                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2630 = 1.61 * 0.50 * 5.2207 + 1.00 * 0.0513                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1198      final r-factor (work) = 0.1186          |
| start r-factor (free) = 0.1645      final r-factor (free) = 0.1638          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6945 = 0.32 * 1.00 * 5.2207 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6863 = 0.32 * 1.00 * 5.1966 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.606)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.36    94.35   17.19    None  None   None       |
|    all(noH): 2823   0      1.36    94.35   17.19    None  None   None       |
|    Sol.    : 438    0      1.36    80.12   40.34    None  None   None       |
|    Mac.    : 2385   0      1.57    94.35   12.94    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.361 -  10.660: 1189   |   5:    47.853 -  57.152:  105        |
|      1:    10.660 -  19.958: 1006   |   6:    57.152 -  66.450:   48        |
|      2:    19.958 -  29.256:  199   |   7:    66.450 -  75.749:   22        |
|      3:    29.256 -  38.555:  118   |   8:    75.749 -  85.047:    5        |
|      4:    38.555 -  47.853:  126   |   9:    85.047 -  94.346:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1186 r_free = 0.1638             target_work(ml) = 5.194         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1186 r_free = 0.1639             target_work(ml) = 5.194         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1186   r_free= 0.1639   ksol= 0.32   Bsol= 47.37   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.03,-1.44,-1.35,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.193649                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1185   r_free= 0.1639   ksol= 0.32   Bsol= 47.37   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.99,-1.45,-1.21,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.193726                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.365018              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.365  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.244742              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.167  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1185      final r-factor (work) = 0.1150          |
| start r-factor (free) = 0.1639      final r-factor (free) = 0.1605          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5979 = 1.37 * 0.50 * 5.1964 + 1.00 * 0.0513                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5883 = 1.37 * 0.50 * 5.1827 + 1.00 * 0.0510                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1150      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1605      final r-factor (free) = 0.1595          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2772 = 0.24 * 1.00 * 5.1827 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2740 = 0.24 * 1.00 * 5.1726 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.606)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.66    93.21   16.79    None  None   None       |
|    all(noH): 2823   0      1.66    93.21   16.79    None  None   None       |
|    Sol.    : 438    0      2.39    83.30   38.85    None  None   None       |
|    Mac.    : 2385   0      1.66    93.21   12.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.662 -  10.817: 1243   |   5:    47.436 -  56.591:  100        |
|      1:    10.817 -  19.972:  967   |   6:    56.591 -  65.746:   42        |
|      2:    19.972 -  29.127:  190   |   7:    65.746 -  74.901:   14        |
|      3:    29.127 -  38.282:  124   |   8:    74.901 -  84.056:    4        |
|      4:    38.282 -  47.436:  134   |   9:    84.056 -  93.211:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1151 r_free = 0.1595             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1151 r_free = 0.1595             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1151   r_free= 0.1595   ksol= 0.32   Bsol= 47.37   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.99,-1.45,-1.21,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.168780                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8945 -  4.6567 0.99   1434  159 0.1005 0.1320      5.3964      5.5681|
|  2:  4.6567 -  3.7151 0.99   1393  155 0.0868 0.1082      5.4393      5.6269|
|  3:  3.7151 -  3.2510 0.99   1349  148 0.1085 0.1478      5.4699       5.796|
|  4:  3.2510 -  2.9563 0.99   1335  144 0.1266 0.1632      5.4661      5.6412|
|  5:  2.9563 -  2.7458 0.99   1339  152 0.1343 0.1666      5.3311      5.5073|
|  6:  2.7458 -  2.5848 0.99   1347  154 0.1311 0.2131       5.243      5.4888|
|  7:  2.5848 -  2.4560 0.98   1295  145 0.1260 0.1612      5.1685      5.3673|
|  8:  2.4560 -  2.3495 0.98   1331  139 0.1228 0.1635       5.107      5.2787|
|  9:  2.3495 -  2.2594 0.99   1314  150 0.1201 0.1891      5.0367      5.3516|
| 10:  2.2594 -  2.1817 0.98   1319  143 0.1147 0.1709      4.9638      5.1766|
| 11:  2.1817 -  2.1136 0.97   1310  147 0.1165 0.1805      4.9268      5.2124|
| 12:  2.1136 -  2.0534 0.98   1286  151 0.1191 0.1604      4.8668      5.1172|
| 13:  2.0534 -  1.9995 0.90   1193  125 0.1192 0.1940      4.8123       5.116|
| 14:  1.9995 -  1.9508 0.29    385   47 0.1109 0.1680      4.7366      4.8742|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8945 -  4.6567  1434   159  0.94   9.32   0.98     0.96       7350.52|
|  2:  4.6567 -  3.7151  1393   155  0.95   8.02   1.02     1.01       9002.22|
|  3:  3.7151 -  3.2510  1349   148  0.93  11.49   1.03     1.02      10207.97|
|  4:  3.2510 -  2.9563  1335   144  0.92  13.82   1.01     1.01      10404.56|
|  5:  2.9563 -  2.7458  1339   152  0.90  16.12   1.00     0.97       8369.89|
|  6:  2.7458 -  2.5848  1347   154  0.89  16.81   0.98     0.94       7259.83|
|  7:  2.5848 -  2.4560  1295   145  0.90  15.78   0.99     0.95       6213.58|
|  8:  2.4560 -  2.3495  1331   139  0.90  15.93   1.00     0.98       5752.28|
|  9:  2.3495 -  2.2594  1314   150  0.90  15.90   1.00     0.97       5032.87|
| 10:  2.2594 -  2.1817  1319   143  0.90  15.92   1.00     0.97       4517.87|
| 11:  2.1817 -  2.1136  1310   147  0.90  15.95   1.00     0.96       4241.73|
| 12:  2.1136 -  2.0534  1286   151  0.91  15.58   1.00     0.99       3764.87|
| 13:  2.0534 -  1.9995  1193   125  0.90  16.69   1.00     1.00       3449.20|
| 14:  1.9995 -  1.9508   385    47  0.91  15.21   0.98     0.93       2789.29|
|alpha:            min =        0.93 max =            1.02 mean =         0.98|
|beta:             min =     2789.29 max =        10404.56 mean =      6556.43|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.35|
|phase err.(test): min =        0.00 max =           88.26 mean =        13.93|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1151   r_free= 0.1595   ksol= 0.32   Bsol= 47.31   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-1.39,-1.05,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.168839                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1151   r_free= 0.1595   ksol= 0.32   Bsol= 47.31   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-1.39,-1.05,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.168839                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8945 -  4.6567 0.99   1434  159 0.1005 0.1320      5.3969      5.5686|
|  2:  4.6567 -  3.7151 0.99   1393  155 0.0868 0.1083      5.4396      5.6269|
|  3:  3.7151 -  3.2510 0.99   1349  148 0.1085 0.1478      5.4699       5.796|
|  4:  3.2510 -  2.9563 0.99   1335  144 0.1265 0.1632      5.4661       5.641|
|  5:  2.9563 -  2.7458 0.99   1339  152 0.1343 0.1666       5.331      5.5073|
|  6:  2.7458 -  2.5848 0.99   1347  154 0.1311 0.2130      5.2427      5.4882|
|  7:  2.5848 -  2.4560 0.98   1295  145 0.1260 0.1612      5.1683      5.3674|
|  8:  2.4560 -  2.3495 0.98   1331  139 0.1227 0.1634      5.1068      5.2786|
|  9:  2.3495 -  2.2594 0.99   1314  150 0.1201 0.1892      5.0368      5.3519|
| 10:  2.2594 -  2.1817 0.98   1319  143 0.1146 0.1711       4.964      5.1775|
| 11:  2.1817 -  2.1136 0.97   1310  147 0.1165 0.1805      4.9271      5.2123|
| 12:  2.1136 -  2.0534 0.98   1286  151 0.1192 0.1605      4.8669      5.1178|
| 13:  2.0534 -  1.9995 0.90   1193  125 0.1193 0.1939      4.8124      5.1154|
| 14:  1.9995 -  1.9508 0.29    385   47 0.1108 0.1682      4.7362      4.8737|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8945 -  4.6567  1434   159  0.94   9.33   0.98     0.96       7356.42|
|  2:  4.6567 -  3.7151  1393   155  0.95   8.03   1.02     1.01       9005.04|
|  3:  3.7151 -  3.2510  1349   148  0.93  11.49   1.03     1.02      10207.89|
|  4:  3.2510 -  2.9563  1335   144  0.92  13.82   1.01     1.01      10405.16|
|  5:  2.9563 -  2.7458  1339   152  0.90  16.12   1.00     0.97       8362.88|
|  6:  2.7458 -  2.5848  1347   154  0.89  16.80   0.98     0.94       7256.19|
|  7:  2.5848 -  2.4560  1295   145  0.90  15.77   0.99     0.96       6210.08|
|  8:  2.4560 -  2.3495  1331   139  0.90  15.93   1.00     0.98       5751.94|
|  9:  2.3495 -  2.2594  1314   150  0.90  15.91   1.01     0.97       5035.54|
| 10:  2.2594 -  2.1817  1319   143  0.90  15.93   1.00     0.98       4522.13|
| 11:  2.1817 -  2.1136  1310   147  0.90  15.97   1.00     0.97       4246.72|
| 12:  2.1136 -  2.0534  1286   151  0.91  15.58   1.00     0.99       3766.67|
| 13:  2.0534 -  1.9995  1193   125  0.90  16.69   1.00     1.00       3448.06|
| 14:  1.9995 -  1.9508   385    47  0.91  15.20   0.98     0.93       2785.84|
|alpha:            min =        0.93 max =            1.02 mean =         0.98|
|beta:             min =     2785.84 max =        10405.16 mean =      6556.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.35|
|phase err.(test): min =        0.00 max =           88.27 mean =        13.93|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.606)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.60    93.15   16.73    None  None   None       |
|    all(noH): 2823   0      1.60    93.15   16.73    None  None   None       |
|    Sol.    : 438    0      2.33    83.24   38.79    None  None   None       |
|    Mac.    : 2385   0      1.60    93.15   12.67    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.602 -  10.757: 1243   |   5:    47.377 -  56.532:  100        |
|      1:    10.757 -  19.912:  967   |   6:    56.532 -  65.687:   42        |
|      2:    19.912 -  29.067:  190   |   7:    65.687 -  74.842:   14        |
|      3:    29.067 -  38.222:  124   |   8:    74.842 -  83.997:    4        |
|      4:    38.222 -  47.377:  134   |   9:    83.997 -  93.152:    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)= 312         
Filter by distance & map next to the model:
   mapped sites are within: 0.485 - 4.306
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 307 from: 312
   mapped sites are within: 0.720 - 4.306

peak=    6.762 closest distance to " O   HOH Z 102 " =    1.614
peak=    5.435 closest distance to " CB  ARG A 275 " =    0.929
peak=    5.226 closest distance to " CG  PRO A  90 " =    1.258
peak=    5.197 closest distance to " O   HOH Z 403 " =    1.925
peak=    5.174 closest distance to " CG  PRO A  54 " =    1.285
peak=    5.154 closest distance to " NH2 ARG A  56 " =    2.225
peak=    4.973 closest distance to " O   HOH Z 401 " =    1.268
peak=    4.887 closest distance to " CB  GLN A 223 " =    1.403
peak=    4.881 closest distance to " O   HOH Z  97 " =    1.949
peak=    4.797 closest distance to " O   HOH Z 234 " =    3.591
peak=    4.794 closest distance to " CA  TYR A  30 " =    0.920
peak=    4.784 closest distance to " O   HOH Z 402 " =    1.485
peak=    4.763 closest distance to " O   HOH Z 193 " =    1.776
peak=    4.721 closest distance to " CG  PRO A 198 " =    1.233
peak=    4.707 closest distance to " O   HOH Z 232 " =    2.293
peak=    4.678 closest distance to " O   SER A  87 " =    2.191
peak=    4.660 closest distance to " CB  PRO A 213 " =    1.342
peak=    4.654 closest distance to " CB  SER A  63 " =    1.124
peak=    4.652 closest distance to " O   HOH Z 298 " =    1.805
peak=    4.613 closest distance to " C   PRO A 198 " =    1.575
peak=    4.529 closest distance to " NH2BARG A 145 " =    2.071
peak=    4.474 closest distance to " O   HOH Z 128 " =    2.166
peak=    4.468 closest distance to " CB  GLN A 183 " =    1.270
peak=    4.463 closest distance to " CB  ASN A 187 " =    1.724
peak=    4.421 closest distance to " O   HOH Z  44 " =    2.044
peak=    4.388 closest distance to " O   HOH Z 142 " =    1.609
peak=    4.370 closest distance to " O   HOH Z 327 " =    1.753
peak=    4.369 closest distance to " CG  PRO A 243 " =    1.164
peak=    4.364 closest distance to " O   HOH Z 209 " =    2.222
peak=    4.348 closest distance to " O   HOH Z 227 " =    1.807
peak=    4.339 closest distance to " O   HOH Z 272 " =    1.861
peak=    4.325 closest distance to " O   HOH Z  63 " =    1.943
peak=    4.323 closest distance to " O  BHOH Z  74 " =    1.292
peak=    4.306 closest distance to " O   HOH Z 346 " =    1.586
peak=    4.294 closest distance to " O   HOH Z 389 " =    1.915
peak=    4.293 closest distance to " O   HOH Z 124 " =    1.366
peak=    4.250 closest distance to " O   HOH Z  80 " =    1.781
peak=    4.238 closest distance to " O   HOH Z 130 " =    2.646
peak=    4.217 closest distance to " NZ  LYS A 117 " =    3.014
peak=    4.206 closest distance to " O   HOH Z 406 " =    1.536
peak=    4.200 closest distance to " CB  GLU A 152 " =    1.156
peak=    4.130 closest distance to " CB  ARG A  79 " =    1.362
peak=    4.127 closest distance to " CB  ARG A 190 " =    1.758
peak=    4.126 closest distance to " N   ASN A  39 " =    1.199
peak=    4.115 closest distance to " O   HOH Z  59 " =    2.175
peak=    4.106 closest distance to " O   GLY A  23 " =    2.365
peak=    4.103 closest distance to " ND2 ASN A 187 " =    1.594
peak=    4.088 closest distance to " CD2 TRP A 179 " =    1.365
peak=    4.081 closest distance to " O   HOH Z  85 " =    1.509
peak=    4.080 closest distance to " CB  PRO A  54 " =    0.998
peak=    4.071 closest distance to " O   HOH Z  97 " =    2.223
peak=    4.063 closest distance to " O   HOH Z 128 " =    1.970
peak=    4.056 closest distance to " O   HOH Z 368 " =    2.024
peak=    4.040 closest distance to " O   HOH Z 369 " =    2.495
peak=    4.039 closest distance to " O   HOH Z  15 " =    2.081
peak=    4.037 closest distance to " CG  ARG A  66 " =    1.067
peak=    4.025 closest distance to " CB  SER A   3 " =    1.231
peak=    4.025 closest distance to " O   HOH Z 287 " =    1.884
peak=    3.986 closest distance to " O   HOH Z 109 " =    1.964
peak=    3.969 closest distance to " CG AARG A 275 " =    1.106
peak=    3.962 closest distance to " O   HOH Z 203 " =    1.786
peak=    3.931 closest distance to " O   HOH Z 426 " =    1.440
peak=    3.930 closest distance to " O   HOH Z 421 " =    1.903
peak=    3.925 closest distance to " CD  ARG A 269 " =    1.035
peak=    3.892 closest distance to " CB  ALA A 248 " =    1.415
peak=    3.892 closest distance to " O   HOH Z  54 " =    2.173
peak=    3.891 closest distance to " O   HOH Z 423 " =    1.862
peak=    3.880 closest distance to " O   HOH Z 250 " =    1.460
peak=    3.876 closest distance to " CG1 ILE A  33 " =    1.241
peak=    3.876 closest distance to " CA  ALA A  84 " =    1.147
peak=    3.875 closest distance to " CA  ALA A  21 " =    1.133
peak=    3.858 closest distance to " O   HOH Z 189 " =    2.150
peak=    3.846 closest distance to " CB  TRP A 179 " =    1.161
peak=    3.845 closest distance to " CB  SER A  62 " =    0.993
peak=    3.845 closest distance to " CA  ALA A  51 " =    0.908
peak=    3.844 closest distance to " CB  ASN A 148 " =    1.407
peak=    3.843 closest distance to " O   HOH Z 315 " =    1.868
peak=    3.817 closest distance to " OG BSER A 212 " =    2.534
peak=    3.814 closest distance to " NE2 GLN A  11 " =    1.048
peak=    3.813 closest distance to " O   HOH Z 298 " =    2.249
peak=    3.796 closest distance to " O   HOH Z 247 " =    1.402
peak=    3.787 closest distance to " O   HOH Z 316 " =    2.953
peak=    3.785 closest distance to " CA  ARG A  36 " =    0.990
peak=    3.785 closest distance to " O   HOH Z 357 " =    1.885
peak=    3.782 closest distance to " O   HOH Z 245 " =    1.426
peak=    3.779 closest distance to " CG2BVAL A  41 " =    0.840
peak=    3.777 closest distance to " O   HOH Z  40 " =    2.000
peak=    3.773 closest distance to " CA  ARG A 195 " =    1.264
peak=    3.766 closest distance to " CD2 LEU A 297 " =    1.068
peak=    3.765 closest distance to " O   HOH Z  43 " =    1.676
peak=    3.762 closest distance to " CB  GLU A 277 " =    3.551
peak=    3.751 closest distance to " O   HOH Z 134 " =    1.435
peak=    3.745 closest distance to " O   HOH Z 345 " =    1.825
peak=    3.741 closest distance to " CG2 ILE A 120 " =    1.274
peak=    3.736 closest distance to " CA  ASP A 162 " =    1.171
peak=    3.729 closest distance to " O   HOH Z 261 " =    1.814
peak=    3.720 closest distance to " O   HOH Z 408 " =    1.730
peak=    3.713 closest distance to " O   HOH Z 279 " =    2.096
peak=    3.708 closest distance to " CB  VAL A 265 " =    1.250
peak=    3.703 closest distance to " O   HOH Z 345 " =    2.500
peak=    3.701 closest distance to " CB  THR A  31 " =    1.628
peak=    3.699 closest distance to " CE  LYS A 119 " =    1.142
peak=    3.694 closest distance to " O   HOH Z  54 " =    1.646
peak=    3.694 closest distance to " N   TRP A 150 " =    1.606
peak=    3.693 closest distance to " O   HOH Z 154 " =    1.484
peak=    3.681 closest distance to " OE1 GLU A   2 " =    2.321
peak=    3.676 closest distance to " CA  ASN A 176 " =    1.192
peak=    3.675 closest distance to " O   HOH Z 334 " =    1.418
peak=    3.673 closest distance to " CG2 ILE A  20 " =    1.397
peak=    3.671 closest distance to " CZ  PHE A 218 " =    1.075
peak=    3.663 closest distance to " CB  GLU A 128 " =    1.148
peak=    3.659 closest distance to " O   HOH Z 132 " =    2.250
peak=    3.659 closest distance to " O   HOH Z 365 " =    2.552
peak=    3.651 closest distance to " NH1AARG A 275 " =    0.990
peak=    3.648 closest distance to " O   HOH Z 284 " =    2.944
peak=    3.639 closest distance to " O   HOH Z  35 " =    2.211
peak=    3.637 closest distance to " O   HOH Z 178 " =    0.942
peak=    3.629 closest distance to " NZ  LYS A 119 " =    1.546
peak=    3.629 closest distance to " O   HOH Z 173 " =    2.167
peak=    3.611 closest distance to " O   HOH Z 361 " =    3.237
peak=    3.604 closest distance to " CB  TRP A 266 " =    1.061
peak=    3.591 closest distance to " O   HOH Z  47 " =    1.644
peak=    3.591 closest distance to " CB  VAL A 202 " =    1.492
peak=    3.573 closest distance to " CB  ASN A  39 " =    0.841
peak=    3.564 closest distance to " O   HOH Z  63 " =    2.242
peak=    3.554 closest distance to " O   HOH Z 303 " =    2.088
peak=    3.548 closest distance to " O   HOH Z  49 " =    2.401
peak=    3.545 closest distance to " CB  SER A  26 " =    1.733
peak=    3.543 closest distance to " CB  TYR A 169 " =    0.720
peak=    3.540 closest distance to " CG2AVAL A 121 " =    2.125
peak=    3.540 closest distance to " CB  ARG A 139 " =    0.889
peak=    3.535 closest distance to " O   HOH Z 392 " =    2.404
peak=    3.534 closest distance to " CD  LYS A 166 " =    1.329
peak=    3.531 closest distance to " OD2 ASP A 286 " =    2.784
peak=    3.526 closest distance to " CG1BVAL A  72 " =    1.752
peak=    3.515 closest distance to " O   HOH Z 359 " =    1.589
peak=    3.511 closest distance to " CD1 LEU A  96 " =    0.772
peak=    3.510 closest distance to " O   ALA A 165 " =    1.389
peak=    3.510 closest distance to " O   HOH Z 305 " =    3.694
peak=    3.509 closest distance to " O   HOH Z 411 " =    3.632
peak=    3.502 closest distance to " O   HOH Z  78 " =    1.689
peak=    3.499 closest distance to " CZ  PHE A  38 " =    1.304
peak=    3.495 closest distance to " CG2 VAL A 257 " =    0.827
peak=    3.488 closest distance to " O   HOH Z 402 " =    2.889
peak=    3.487 closest distance to " CG  MET A 185 " =    1.129
peak=    3.483 closest distance to " O   HOH Z 380 " =    1.945
peak=    3.479 closest distance to " OH  TYR A  30 " =    1.208
peak=    3.477 closest distance to " CD  PRO A  54 " =    1.175
peak=    3.476 closest distance to " O   HOH Z 427 " =    2.865
peak=    3.471 closest distance to " CB  PRO A 198 " =    1.106
peak=    3.469 closest distance to " CD  GLN A 194 " =    1.626
peak=    3.468 closest distance to " O   HOH Z 158 " =    2.909
peak=    3.462 closest distance to " CB  SER A 141 " =    1.020
peak=    3.456 closest distance to " O   HOH Z 250 " =    1.758
peak=    3.453 closest distance to " O   THR A 220 " =    1.149
peak=    3.451 closest distance to " CA  THR A 221 " =    0.949
peak=    3.448 closest distance to " O   ASN A  74 " =    1.671
peak=    3.446 closest distance to " O   HOH Z 163 " =    1.546
peak=    3.446 closest distance to " O   HOH Z 427 " =    3.038
peak=    3.437 closest distance to " CB  LEU A 228 " =    1.159
peak=    3.433 closest distance to " O   HOH Z  48 " =    1.625
peak=    3.431 closest distance to " O   HOH Z 337 " =    3.568
peak=    3.428 closest distance to " CB  GLN A 278 " =    0.824
peak=    3.427 closest distance to " CA  ASN A 215 " =    1.032
peak=    3.424 closest distance to " CB  PRO A 163 " =    3.889
peak=    3.419 closest distance to " O   HOH Z 257 " =    2.124
peak=    3.419 closest distance to " NH1AARG A 145 " =    1.284
peak=    3.416 closest distance to " O   HOH Z 358 " =    2.138
peak=    3.415 closest distance to " N   CYS A 260 " =    0.940
peak=    3.414 closest distance to " O   HOH Z 371 " =    3.128
peak=    3.412 closest distance to " O   HOH Z 407 " =    1.468
peak=    3.410 closest distance to " O   THR A 182 " =    1.477
peak=    3.405 closest distance to " CB  ILE A 120 " =    1.236
peak=    3.402 closest distance to " CD  ARG A 159 " =    0.791
peak=    3.397 closest distance to " O   HOH Z 419 " =    1.568
peak=    3.391 closest distance to " O   HOH Z  61 " =    1.538
peak=    3.382 closest distance to " CG  GLN A  58 " =    2.597
peak=    3.382 closest distance to " O   HOH Z 185 " =    1.724
peak=    3.381 closest distance to " OD2 ASP A 298 " =    3.923
peak=    3.380 closest distance to " O   HOH Z 214 " =    2.447
peak=    3.366 closest distance to " O   HOH Z 438 " =    2.017
peak=    3.366 closest distance to " CB  ALA A 114 " =    1.000
peak=    3.364 closest distance to " O   HOH Z 422 " =    2.628
peak=    3.364 closest distance to " CG  GLN A  11 " =    1.533
peak=    3.361 closest distance to " CB  ASP A 191 " =    1.229
peak=    3.358 closest distance to " OH  TYR A 116 " =    1.055
peak=    3.354 closest distance to " O   HOH Z 108 " =    2.706
peak=    3.352 closest distance to " NE2 GLN A  77 " =    3.229
peak=    3.351 closest distance to " O   HOH Z 132 " =    1.033
peak=    3.350 closest distance to " NE  ARG A  24 " =    0.978
peak=    3.348 closest distance to " CG  LYS A 119 " =    1.112
peak=    3.343 closest distance to " CB  ARG A 269 " =    0.786
peak=    3.337 closest distance to " OG  SER A 276 " =    1.395
peak=    3.335 closest distance to " N   HIS A 108 " =    1.758
peak=    3.335 closest distance to " O   HOH Z 414 " =    1.572
peak=    3.325 closest distance to " CB  GLU A  46 " =    1.062
peak=    3.324 closest distance to " O   HOH Z 264 " =    1.552
peak=    3.318 closest distance to " OG BSER A 164 " =    2.284
peak=    3.309 closest distance to " O   HOH Z 217 " =    2.273
peak=    3.307 closest distance to " O   HOH Z 425 " =    1.939
peak=    3.307 closest distance to " NH2AARG A 145 " =    2.251
peak=    3.304 closest distance to " O   HOH Z 244 " =    1.746
peak=    3.300 closest distance to " O   HOH Z 404 " =    2.218
peak=    3.299 closest distance to " CE1 HIS A 108 " =    1.187
peak=    3.298 closest distance to " O   HOH Z  89 " =    1.739
peak=    3.290 closest distance to " OG  SER A  62 " =    2.744
peak=    3.285 closest distance to " O   HOH Z 415 " =    3.389
peak=    3.284 closest distance to " CB  ASN A  45 " =    1.064
peak=    3.279 closest distance to " O   HOH Z 248 " =    1.621
peak=    3.277 closest distance to " O   HOH Z  88 " =    3.024
peak=    3.274 closest distance to " ND2 ASN A 249 " =    0.884
peak=    3.274 closest distance to " O   HOH Z 162 " =    1.783
peak=    3.268 closest distance to " O   HOH Z 353 " =    2.654
peak=    3.267 closest distance to " CB  HIS A 108 " =    0.868
peak=    3.260 closest distance to " N   ARG A 156 " =    1.420
peak=    3.260 closest distance to " CA  TRP A  85 " =    1.067
peak=    3.259 closest distance to " O   HOH Z 236 " =    1.490
peak=    3.256 closest distance to " N   ASP A 162 " =    1.178
peak=    3.253 closest distance to " O   TRP A 274 " =    1.886
peak=    3.252 closest distance to " CD  ARG A 195 " =    0.851
peak=    3.250 closest distance to " O   HOH Z 148 " =    3.210
peak=    3.250 closest distance to " CB  ALA A 104 " =    0.763
peak=    3.245 closest distance to " CG1 ILE A 120 " =    1.118
peak=    3.245 closest distance to " CB  PRO A  90 " =    0.874
peak=    3.239 closest distance to " O   HOH Z   1 " =    2.275
peak=    3.236 closest distance to " O   HOH Z 412 " =    3.519
peak=    3.236 closest distance to " O   HOH Z 132 " =    2.563
peak=    3.236 closest distance to " CD  LYS A 119 " =    1.911
peak=    3.236 closest distance to " O   HOH Z 234 " =    1.838
peak=    3.233 closest distance to " CB  MET A  47 " =    1.193
peak=    3.232 closest distance to " O   HOH Z 291 " =    1.622
peak=    3.231 closest distance to " CB  ALA A 291 " =    1.159
peak=    3.230 closest distance to " O   HOH Z 293 " =    1.765
peak=    3.230 closest distance to " CA  LYS A 117 " =    1.270
peak=    3.229 closest distance to " CB  PHE A  16 " =    1.085
peak=    3.227 closest distance to " O   HOH Z 130 " =    2.592
peak=    3.222 closest distance to " O   HOH Z 291 " =    1.420
peak=    3.217 closest distance to " O   HOH Z 381 " =    1.375
peak=    3.216 closest distance to " O   HOH Z  30 " =    2.176
peak=    3.215 closest distance to " CA  ASP A 140 " =    1.115
peak=    3.211 closest distance to " O   HOH Z 147 " =    1.800
peak=    3.209 closest distance to " CE BLYS A 290 " =    1.127
peak=    3.207 closest distance to " CB  GLN A 205 " =    1.140
peak=    3.205 closest distance to " O   HOH Z  66 " =    2.125
peak=    3.203 closest distance to " O   HOH Z  88 " =    3.047
peak=    3.202 closest distance to " CB  ASN A 110 " =    0.982
peak=    3.199 closest distance to " O   HOH Z 374 " =    2.584
peak=    3.192 closest distance to " CB  GLN A 103 " =    0.843
peak=    3.191 closest distance to " O   HOH Z 380 " =    1.796
peak=    3.190 closest distance to " CA  ASP A 191 " =    0.923
peak=    3.188 closest distance to " CE1 TYR A 186 " =    1.310
peak=    3.187 closest distance to " CA  SER A 146 " =    1.919
peak=    3.184 closest distance to " CG2 VAL A 197 " =    1.072
peak=    3.178 closest distance to " O   GLY A  91 " =    1.403
peak=    3.177 closest distance to " CB  ASN A 285 " =    0.965
peak=    3.176 closest distance to " CG2 THR A 220 " =    0.765
peak=    3.175 closest distance to " O   HOH Z 273 " =    2.931
peak=    3.175 closest distance to " O   HOH Z 281 " =    4.306
peak=    3.172 closest distance to " CB  LYS A 289 " =    1.068
peak=    3.171 closest distance to " O   HOH Z 383 " =    2.090
peak=    3.169 closest distance to " O   HOH Z 216 " =    2.530
peak=    3.166 closest distance to " O   HOH Z 123 " =    2.177
peak=    3.160 closest distance to " OE1 GLN A  58 " =    1.613
peak=    3.156 closest distance to " CA  VAL A 126 " =    1.171
peak=    3.154 closest distance to " NH1 ARG A 138 " =    1.248
peak=    3.150 closest distance to " CB  THR A  52 " =    0.737
peak=    3.149 closest distance to " CB  GLU A 175 " =    1.353
peak=    3.149 closest distance to " O   HOH Z 425 " =    1.300
peak=    3.147 closest distance to " CA  MET A  40 " =    1.074
peak=    3.147 closest distance to " N   PHE A 130 " =    1.344
peak=    3.147 closest distance to " O   HOH Z 350 " =    1.950
peak=    3.145 closest distance to " CA  GLU A 152 " =    0.894
peak=    3.144 closest distance to " CD  GLN A 240 " =    1.477
peak=    3.143 closest distance to " O   HOH Z 173 " =    1.933
peak=    3.136 closest distance to " O   HOH Z 111 " =    1.451
peak=    3.135 closest distance to " O   HOH Z 152 " =    1.907
peak=    3.134 closest distance to " O   HOH Z 234 " =    2.371
peak=    3.134 closest distance to " CD  ARG A 139 " =    1.455
peak=    3.132 closest distance to " NH2 ARG A 156 " =    1.105
peak=    3.129 closest distance to " O   HOH Z 116 " =    2.540
peak=    3.128 closest distance to " CE1 TYR A  30 " =    0.914
peak=    3.127 closest distance to " CB  ASP A 140 " =    0.942
peak=    3.126 closest distance to " OG BSER A 258 " =    3.108
peak=    3.124 closest distance to " OG ASER A  99 " =    1.458
peak=    3.122 closest distance to " CG  GLN A  77 " =    2.004
peak=    3.122 closest distance to " OG1 THR A 221 " =    1.285
peak=    3.120 closest distance to " NH2 ARG A 219 " =    1.916
peak=    3.108 closest distance to " C   TYR A 214 " =    1.476
peak=    3.105 closest distance to " CG  GLU A 277 " =    2.278
peak=    3.102 closest distance to " O   HOH Z 375 " =    2.128
peak=    3.097 closest distance to " N   TYR A 116 " =    1.601
peak=    3.093 closest distance to " CA  ARG A 156 " =    1.124
peak=    3.092 closest distance to " CZ2 TRP A 150 " =    1.073
peak=    3.091 closest distance to " CA  LYS A 290 " =    1.072
peak=    3.090 closest distance to " OG BSER A 134 " =    2.879
peak=    3.089 closest distance to " CB  ALA A  84 " =    0.862
peak=    3.089 closest distance to " CB  LEU A  83 " =    0.840
peak=    3.087 closest distance to " CA  SER A  87 " =    1.013
peak=    3.085 closest distance to " CG  GLU A  37 " =    0.867
peak=    3.084 closest distance to " O   HOH Z 394 " =    1.625
peak=    3.074 closest distance to " CD1 LEU A 300 " =    1.307
peak=    3.073 closest distance to " CG2 VAL A 202 " =    1.315
peak=    3.069 closest distance to " O   HOH Z  78 " =    1.872
peak=    3.067 closest distance to " O   HOH Z 313 " =    1.817
peak=    3.064 closest distance to " OG  SER A 245 " =    1.494
peak=    3.028 closest distance to " O   HOH Z 434 " =    3.910
peak=    3.015 closest distance to " O   HOH Z  19 " =    1.438

                           ----------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: 0.683 - 5.467
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 191 from: 195
   mapped sites are within: 0.756 - 5.467

peak=   -4.753 closest distance to " C   HIS A 108 " =    1.093
peak=   -4.639 closest distance to " O   HOH Z 266 " =    4.674
peak=   -4.480 closest distance to " CD  GLN A  58 " =    1.105
peak=   -4.324 closest distance to " O   HOH Z 290 " =    0.868
peak=   -4.299 closest distance to " OXT GLY A 302 " =    2.911
peak=   -4.231 closest distance to " OG BSER A 134 " =    1.295
peak=   -4.214 closest distance to " CD  ARG A 156 " =    2.070
peak=   -4.133 closest distance to " O   HOH Z  13 " =    1.780
peak=   -4.127 closest distance to " CG  MET A  93 " =    2.392
peak=   -4.115 closest distance to " SG  CYS A 254 " =    3.325
peak=   -4.101 closest distance to " ND2 ASN A  45 " =    1.011
peak=   -4.095 closest distance to " CA  VAL A  67 " =    2.869
peak=   -4.095 closest distance to " O   HOH Z 401 " =    0.756
peak=   -4.092 closest distance to " C   THR A 279 " =    1.223
peak=   -4.012 closest distance to " O   PRO A 163 " =    2.054
peak=   -3.989 closest distance to " OD2 ASP A 171 " =    2.399
peak=   -3.987 closest distance to " CB  ALA A 161 " =    2.531
peak=   -3.925 closest distance to " CH2 TRP A 179 " =    1.315
peak=   -3.897 closest distance to " N   ALA A 248 " =    1.768
peak=   -3.877 closest distance to " CG2 ILE A  49 " =    2.635
peak=   -3.876 closest distance to " O   HOH Z 165 " =    1.894
peak=   -3.874 closest distance to " O   HOH Z 351 " =    1.496
peak=   -3.869 closest distance to " CZ  TYR A 169 " =    1.860
peak=   -3.833 closest distance to " O   TRP A  92 " =    1.958
peak=   -3.811 closest distance to " O   HOH Z 174 " =    3.941
peak=   -3.809 closest distance to " CZ  ARG A  66 " =    0.951
peak=   -3.789 closest distance to " ND2 ASN A  39 " =    1.093
peak=   -3.787 closest distance to " O   HOH Z  92 " =    1.755
peak=   -3.775 closest distance to " O   GLY A  80 " =    2.391
peak=   -3.774 closest distance to " O   PHE A 218 " =    1.598
peak=   -3.773 closest distance to " O   PRO A 198 " =    1.264
peak=   -3.743 closest distance to " CG  GLN A 223 " =    1.940
peak=   -3.739 closest distance to " O   HOH Z  11 " =    1.851
peak=   -3.736 closest distance to " OD2 ASP A 191 " =    1.417
peak=   -3.731 closest distance to " O   HOH Z 198 " =    1.534
peak=   -3.725 closest distance to " N   GLN A  58 " =    1.652
peak=   -3.722 closest distance to " OG  SER A  97 " =    2.119
peak=   -3.722 closest distance to " O   VAL A 174 " =    2.092
peak=   -3.715 closest distance to " N   THR A  52 " =    1.740
peak=   -3.705 closest distance to " O   HOH Z 234 " =    3.902
peak=   -3.697 closest distance to " CD2 LEU A 237 " =    2.414
peak=   -3.694 closest distance to " CD1 LEU A  25 " =    2.480
peak=   -3.689 closest distance to " CB  ALA A 291 " =    2.243
peak=   -3.688 closest distance to " CG  GLU A  53 " =    1.337
peak=   -3.688 closest distance to " CB  PHE A 192 " =    2.052
peak=   -3.687 closest distance to " CG  ASP A 132 " =    2.284
peak=   -3.682 closest distance to " O   VAL A  67 " =    2.604
peak=   -3.680 closest distance to " CD2 TYR A  30 " =    2.806
peak=   -3.649 closest distance to " CD  ARG A 139 " =    1.534
peak=   -3.644 closest distance to " O   HOH Z 377 " =    1.620
peak=   -3.639 closest distance to " O   HOH Z 102 " =    0.912
peak=   -3.627 closest distance to " ND2 ASN A 187 " =    1.495
peak=   -3.626 closest distance to " O   HOH Z 377 " =    2.101
peak=   -3.594 closest distance to " O   SER A 210 " =    1.970
peak=   -3.575 closest distance to " O   HOH Z 353 " =    2.197
peak=   -3.529 closest distance to " O   ALA A  34 " =    2.374
peak=   -3.527 closest distance to " NE2 GLN A  88 " =    0.999
peak=   -3.527 closest distance to " O   HOH Z 109 " =    2.668
peak=   -3.524 closest distance to " O   HOH Z 372 " =    2.253
peak=   -3.523 closest distance to " CA  ASP A 298 " =    1.085
peak=   -3.513 closest distance to " CA  GLY A 133 " =    1.839
peak=   -3.512 closest distance to " N   ALA A 226 " =    1.833
peak=   -3.503 closest distance to " CE1 TYR A 247 " =    2.648
peak=   -3.502 closest distance to " O   HOH Z  71 " =    1.697
peak=   -3.500 closest distance to " CG1 VAL A 112 " =    2.718
peak=   -3.499 closest distance to " O   GLY A 241 " =    2.283
peak=   -3.491 closest distance to " O   HOH Z 183 " =    1.491
peak=   -3.487 closest distance to " CZ3 TRP A 274 " =    1.144
peak=   -3.471 closest distance to " CD1 PHE A 130 " =    2.284
peak=   -3.458 closest distance to " O   GLN A  11 " =    1.322
peak=   -3.451 closest distance to " ND2 ASN A  69 " =    1.689
peak=   -3.444 closest distance to " N   ALA A  43 " =    2.575
peak=   -3.443 closest distance to " CB  PHE A 208 " =    2.264
peak=   -3.440 closest distance to " C   GLY A  91 " =    1.291
peak=   -3.439 closest distance to " NH2 ARG A  79 " =    2.136
peak=   -3.439 closest distance to " O   ALA A   1 " =    1.810
peak=   -3.436 closest distance to " O   HOH Z 369 " =    2.218
peak=   -3.434 closest distance to " CB  PRO A 243 " =    2.661
peak=   -3.427 closest distance to " CD  GLN A 223 " =    0.979
peak=   -3.427 closest distance to " NE2 GLN A 194 " =    1.883
peak=   -3.426 closest distance to " CA  TYR A  68 " =    2.943
peak=   -3.422 closest distance to " O   HOH Z  15 " =    1.552
peak=   -3.421 closest distance to " O   HOH Z 422 " =    1.432
peak=   -3.420 closest distance to " O   HOH Z 198 " =    1.288
peak=   -3.418 closest distance to " NE2 GLN A  88 " =    1.587
peak=   -3.415 closest distance to " CD1 PHE A  59 " =    2.014
peak=   -3.413 closest distance to " O  BHOH Z 338 " =    1.295
peak=   -3.412 closest distance to " O   HOH Z 395 " =    5.095
peak=   -3.409 closest distance to " OG  SER A  26 " =    1.163
peak=   -3.405 closest distance to " O   HOH Z  88 " =    4.350
peak=   -3.403 closest distance to " O   HOH Z 109 " =    5.357
peak=   -3.396 closest distance to " O   MET A 188 " =    1.901
peak=   -3.383 closest distance to " CG1AVAL A  41 " =    2.579
peak=   -3.382 closest distance to " C   GLN A 144 " =    0.841
peak=   -3.380 closest distance to " O   HOH Z 326 " =    1.709
peak=   -3.373 closest distance to " CB  ASP A 286 " =    1.904
peak=   -3.367 closest distance to " O   HOH Z 150 " =    2.233
peak=   -3.364 closest distance to " O   ALA A 256 " =    1.576
peak=   -3.356 closest distance to " CD2 LEU A 300 " =    2.688
peak=   -3.355 closest distance to " OD1 ASN A 148 " =    1.526
peak=   -3.355 closest distance to " O   HOH Z 171 " =    2.263
peak=   -3.353 closest distance to " O   SER A   3 " =    0.961
peak=   -3.352 closest distance to " O   HOH Z  10 " =    1.547
peak=   -3.352 closest distance to " OD1 ASN A  39 " =    2.183
peak=   -3.346 closest distance to " O   HOH Z 427 " =    1.469
peak=   -3.346 closest distance to " O   HOH Z  56 " =    0.866
peak=   -3.344 closest distance to " O   HOH Z 301 " =    2.253
peak=   -3.343 closest distance to " O   HOH Z 197 " =    1.954
peak=   -3.341 closest distance to " O   HOH Z 114 " =    3.459
peak=   -3.341 closest distance to " CD  LYS A 289 " =    2.428
peak=   -3.335 closest distance to " OG  SER A   3 " =    1.386
peak=   -3.328 closest distance to " O   GLU A 152 " =    1.464
peak=   -3.324 closest distance to " O   HOH Z 418 " =    1.390
peak=   -3.315 closest distance to " CB  PRO A 163 " =    2.592
peak=   -3.313 closest distance to " CB  ALA A 248 " =    2.249
peak=   -3.311 closest distance to " O   HOH Z 251 " =    1.429
peak=   -3.303 closest distance to " CG  ASP A 231 " =    0.861
peak=   -3.303 closest distance to " O   SER A 273 " =    1.299
peak=   -3.294 closest distance to " O   ASN A  45 " =    1.744
peak=   -3.294 closest distance to " CD1 LEU A 228 " =    2.094
peak=   -3.292 closest distance to " C   SER A 206 " =    1.625
peak=   -3.290 closest distance to " O   HOH Z 166 " =    1.960
peak=   -3.285 closest distance to " CG  TRP A 266 " =    2.078
peak=   -3.285 closest distance to " CE3 TRP A 150 " =    2.165
peak=   -3.283 closest distance to " N   ASP A 286 " =    2.182
peak=   -3.275 closest distance to " CD2 TRP A 274 " =    1.015
peak=   -3.274 closest distance to " OD1 ASP A 171 " =    1.432
peak=   -3.272 closest distance to " O   GLY A  75 " =    1.374
peak=   -3.271 closest distance to " O   LEU A 167 " =    1.562
peak=   -3.268 closest distance to " NH2 ARG A  66 " =    5.467
peak=   -3.268 closest distance to " CD2 TYR A 293 " =    1.938
peak=   -3.256 closest distance to " O   HOH Z 265 " =    2.342
peak=   -3.247 closest distance to " O   SER A 135 " =    1.536
peak=   -3.246 closest distance to " CZ  TYR A 172 " =    1.869
peak=   -3.246 closest distance to " OH  TYR A 169 " =    0.913
peak=   -3.242 closest distance to " OE2 GLU A   2 " =    1.548
peak=   -3.241 closest distance to " O   HOH Z 126 " =    1.900
peak=   -3.240 closest distance to " O   HOH Z 414 " =    1.317
peak=   -3.228 closest distance to " CG  GLN A  11 " =    1.639
peak=   -3.226 closest distance to " CZ  PHE A  38 " =    2.022
peak=   -3.224 closest distance to " CD2 TYR A 247 " =    2.329
peak=   -3.219 closest distance to " O   ALA A 161 " =    1.517
peak=   -3.219 closest distance to " O   HOH Z 281 " =    2.473
peak=   -3.218 closest distance to " CE  LYS A 166 " =    2.902
peak=   -3.216 closest distance to " O   HOH Z  19 " =    2.402
peak=   -3.215 closest distance to " CG2 ILE A 263 " =    2.217
peak=   -3.210 closest distance to " N   VAL A 189 " =    1.613
peak=   -3.210 closest distance to " OE1 GLN A 183 " =    1.424
peak=   -3.209 closest distance to " O   HOH Z 389 " =    1.663
peak=   -3.207 closest distance to " O   HOH Z  97 " =    1.144
peak=   -3.203 closest distance to " O   GLN A  94 " =    2.193
peak=   -3.196 closest distance to " O   HOH Z 154 " =    1.630
peak=   -3.196 closest distance to " NZ BLYS A 290 " =    1.151
peak=   -3.186 closest distance to " O   HOH Z 252 " =    4.234
peak=   -3.184 closest distance to " O   HOH Z 423 " =    2.334
peak=   -3.163 closest distance to " N   SER A 276 " =    1.262
peak=   -3.160 closest distance to " C   ALA A 158 " =    1.301
peak=   -3.156 closest distance to " O   HOH Z 364 " =    5.100
peak=   -3.150 closest distance to " O   GLY A 196 " =    0.959
peak=   -3.150 closest distance to " O   HOH Z 280 " =    2.273
peak=   -3.148 closest distance to " O   HOH Z 231 " =    1.034
peak=   -3.147 closest distance to " O   HOH Z 252 " =    3.152
peak=   -3.143 closest distance to " O   HOH Z 250 " =    1.401
peak=   -3.143 closest distance to " CG  PHE A 225 " =    1.391
peak=   -3.142 closest distance to " O   HOH Z  11 " =    1.805
peak=   -3.139 closest distance to " CA  GLY A 241 " =    3.220
peak=   -3.135 closest distance to " O   ALA A  10 " =    1.889
peak=   -3.134 closest distance to " O   HOH Z 193 " =    1.640
peak=   -3.132 closest distance to " OG BSER A  99 " =    1.088
peak=   -3.131 closest distance to " OD1 ASP A 191 " =    1.291
peak=   -3.126 closest distance to " CD  GLN A  88 " =    0.882
peak=   -3.123 closest distance to " O   PRO A 198 " =    1.230
peak=   -3.120 closest distance to " N   ALA A 248 " =    2.254
peak=   -3.115 closest distance to " CE  MET A  93 " =    1.107
peak=   -3.113 closest distance to " O   HOH Z 185 " =    2.457
peak=   -3.110 closest distance to " NH1 ARG A 195 " =    2.598
peak=   -3.102 closest distance to " CG  PRO A 243 " =    1.656
peak=   -3.091 closest distance to " O   HOH Z 166 " =    1.990
peak=   -3.088 closest distance to " NH2 ARG A  66 " =    5.194
peak=   -3.087 closest distance to " CD2 PHE A  61 " =    2.145
peak=   -3.081 closest distance to " O   HOH Z 174 " =    2.225
peak=   -3.081 closest distance to " O   HOH Z 219 " =    3.458
peak=   -3.080 closest distance to " O   HOH Z 128 " =    1.552
peak=   -3.077 closest distance to " CD  GLN A 223 " =    1.616
peak=   -3.074 closest distance to " N   HIS A 115 " =    2.145
peak=   -3.073 closest distance to " O   THR A 182 " =    1.306
peak=   -3.071 closest distance to " O   HOH Z 361 " =    3.436
peak=   -3.060 closest distance to " OG ASER A 134 " =    1.901
peak=   -3.046 closest distance to " CD2 LEU A 300 " =    2.667
peak=   -3.032 closest distance to " CG BARG A 275 " =    0.883
peak=   -3.012 closest distance to " O   HOH Z 139 " =    3.271

================= 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    :  0.4283 0.4265   6.235535e+00   6.231590e+00
   1_bss:  0.4196 0.4145   6.225397e+00   6.218446e+00
   1_xyz:  0.2720 0.2967   5.879994e+00   5.951835e+00
   1_adp:  0.2435 0.3015   5.818478e+00   5.972980e+00
   1_occ:  0.2432 0.3020   5.818182e+00   5.973198e+00
   2_bss:  0.2389 0.2974   5.807429e+00   5.965236e+00
   2_xyz:  0.1794 0.2288   5.548616e+00   5.738979e+00
   2_adp:  0.1659 0.2125   5.482232e+00   5.675781e+00
   2_occ:  0.1657 0.2124   5.481598e+00   5.675399e+00
   3_bss:  0.1659 0.2122   5.481598e+00   5.672674e+00
   3_xyz:  0.1315 0.1769   5.279866e+00   5.495754e+00
   3_adp:  0.1244 0.1708   5.236051e+00   5.458637e+00
   3_occ:  0.1243 0.1707   5.235806e+00   5.458498e+00
   4_bss:  0.1246 0.1705   5.236549e+00   5.456454e+00
   4_xyz:  0.1198 0.1645   5.200907e+00   5.423947e+00
   4_adp:  0.1186 0.1638   5.193895e+00   5.418884e+00
   4_occ:  0.1186 0.1639   5.193649e+00   5.418873e+00
   5_bss:  0.1185 0.1639   5.193726e+00   5.418940e+00
   5_xyz:  0.1150 0.1605   5.172635e+00   5.402288e+00
   5_adp:  0.1151 0.1595   5.169209e+00   5.397141e+00
   5_occ:  0.1151 0.1595   5.168780e+00   5.396897e+00
   5_bss:  0.1151 0.1595   5.168839e+00   5.396952e+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:  0.309  26.193   0.529   2.108  -1.537   0.000  -0.000  -0.000
   1_xyz:  0.309  26.193   0.529   2.108  -1.537   0.000  -0.000  -0.000
   1_adp:  0.309  26.193   0.529   2.108  -1.537   0.000  -0.000  -0.000
   1_occ:  0.309  26.193   0.529   2.108  -1.537   0.000  -0.000  -0.000
   2_bss:  0.312  41.056  -1.947  -0.133  -1.382  -0.000  -0.000  -0.000
   2_xyz:  0.312  41.056  -1.947  -0.133  -1.382  -0.000  -0.000  -0.000
   2_adp:  0.312  41.056  -1.947  -0.133  -1.382  -0.000  -0.000  -0.000
   2_occ:  0.312  41.056  -1.947  -0.133  -1.382  -0.000  -0.000  -0.000
   3_bss:  0.312  41.056  -2.717  -0.942  -1.315  -0.000  -0.000  -0.000
   3_xyz:  0.312  41.056  -2.717  -0.942  -1.315  -0.000  -0.000  -0.000
   3_adp:  0.312  41.056  -2.717  -0.942  -1.315  -0.000  -0.000  -0.000
   3_occ:  0.312  41.056  -2.717  -0.942  -1.315  -0.000  -0.000  -0.000
   4_bss:  0.320  47.368  -3.030  -1.438  -1.347  -0.000  -0.000  -0.000
   4_xyz:  0.320  47.368  -3.030  -1.438  -1.347  -0.000  -0.000  -0.000
   4_adp:  0.320  47.368  -3.030  -1.438  -1.347  -0.000  -0.000  -0.000
   4_occ:  0.320  47.368  -3.030  -1.438  -1.347  -0.000  -0.000  -0.000
   5_bss:  0.321  47.368  -2.990  -1.450  -1.214  -0.000  -0.000  -0.000
   5_xyz:  0.321  47.368  -2.990  -1.450  -1.214  -0.000  -0.000  -0.000
   5_adp:  0.321  47.368  -2.990  -1.450  -1.214  -0.000  -0.000  -0.000
   5_occ:  0.321  47.368  -2.990  -1.450  -1.214  -0.000  -0.000  -0.000
   5_bss:  0.321  47.308  -2.884  -1.388  -1.045  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.921 0.5226  0.7018    57099.841
   1_bss:  48.699 0.5364  0.7336    53557.065
   1_xyz:  30.514 0.7529  0.9652    23462.617
   1_adp:  31.618 0.7395  0.9520    24620.014
   1_occ:  31.656 0.7390  0.9510    24678.440
   2_bss:  31.156 0.7442  0.9080    23897.697
   2_xyz:  22.755 0.8334  0.9810    13415.666
   2_adp:  20.705 0.8547  0.9871    11671.495
   2_occ:  20.690 0.8549  0.9873    11659.609
   3_bss:  20.631 0.8554  0.9694    11583.348
   3_xyz:  16.691 0.8916  0.9902     7987.028
   3_adp:  15.860 0.8993  0.9878     7517.710
   3_occ:  15.860 0.8993  0.9876     7510.449
   4_bss:  15.806 0.8998  0.9782     7468.032
   4_xyz:  14.968 0.9070  0.9812     6896.199
   4_adp:  14.815 0.9085  0.9769     6860.741
   4_occ:  14.813 0.9085  0.9767     6854.845
   5_bss:  14.815 0.9085  0.9787     6856.177
   5_xyz:  14.454 0.9115  0.9805     6607.997
   5_adp:  14.316 0.9127  0.9777     6562.495
   5_occ:  14.306 0.9128  0.9777     6555.158
   5_bss:  14.308 0.9128  0.9796     6555.673
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   2.2286e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   2.2286e-01
   1_xyz:   1.473  0.013  0.089 15.730  0.006  4.107   1.2176e-01
   1_adp:   1.473  0.013  0.089 15.730  0.006  4.107   1.2176e-01
   1_occ:   1.473  0.013  0.089 15.730  0.006  4.107   1.2176e-01
   2_bss:   1.473  0.013  0.089 15.730  0.006  4.107   1.2176e-01
   2_xyz:   1.028  0.007  0.069 14.445  0.004  4.119   5.9454e-02
   2_adp:   1.028  0.007  0.069 14.445  0.004  4.119   5.9454e-02
   2_occ:   1.028  0.007  0.069 14.445  0.004  4.119   5.9454e-02
   3_bss:   1.028  0.007  0.069 14.445  0.004  4.119   5.9454e-02
   3_xyz:   1.058  0.007  0.071 14.701  0.004  4.108   6.2458e-02
   3_adp:   1.058  0.007  0.071 14.701  0.004  4.108   6.2458e-02
   3_occ:   1.058  0.007  0.071 14.701  0.004  4.108   6.2458e-02
   4_bss:   1.058  0.007  0.071 14.701  0.004  4.108   6.2458e-02
   4_xyz:   0.929  0.005  0.068 14.419  0.004  4.110   5.1262e-02
   4_adp:   0.929  0.005  0.068 14.419  0.004  4.110   5.1262e-02
   4_occ:   0.929  0.005  0.068 14.419  0.004  4.110   5.1262e-02
   5_bss:   0.929  0.005  0.068 14.419  0.004  4.110   5.1262e-02
   5_xyz:   0.928  0.005  0.068 14.308  0.004  4.111   5.1015e-02
   5_adp:   0.928  0.005  0.068 14.308  0.004  4.111   5.1015e-02
   5_occ:   0.928  0.005  0.068 14.308  0.004  4.111   5.1015e-02
   5_bss:   0.928  0.005  0.068 14.308  0.004  4.111   5.1015e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  0.938   2.4382e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  0.938   2.4382e-01
   1_xyz:   8.805  0.140  0.311 84.931  0.037  1.986   1.1569e-01
   1_adp:   8.805  0.140  0.311 84.931  0.037  1.986   1.1569e-01
   1_occ:   8.805  0.140  0.311 84.931  0.037  1.986   1.1569e-01
   2_bss:   8.805  0.140  0.311 84.931  0.037  1.986   1.1569e-01
   2_xyz:   8.508  0.045  0.265 80.032  0.046  2.238   5.6348e-02
   2_adp:   8.508  0.045  0.265 80.032  0.046  2.238   5.6348e-02
   2_occ:   8.508  0.045  0.265 80.032  0.046  2.238   5.6348e-02
   3_bss:   8.508  0.045  0.265 80.032  0.046  2.238   5.6348e-02
   3_xyz:   7.870  0.050  0.218 80.345  0.041  2.205   4.3050e-02
   3_adp:   7.870  0.050  0.218 80.345  0.041  2.205   4.3050e-02
   3_occ:   7.870  0.050  0.218 80.345  0.041  2.205   4.3050e-02
   4_bss:   7.870  0.050  0.218 80.345  0.041  2.205   4.3050e-02
   4_xyz:   6.638  0.037  0.219 82.352  0.033  2.338   3.1737e-02
   4_adp:   6.638  0.037  0.219 82.352  0.033  2.338   3.1737e-02
   4_occ:   6.638  0.037  0.219 82.352  0.033  2.338   3.1737e-02
   5_bss:   6.638  0.037  0.219 82.352  0.033  2.338   3.1737e-02
   5_xyz:   6.849  0.042  0.221 81.963  0.032  2.389   3.6893e-02
   5_adp:   6.849  0.042  0.221 81.963  0.032  2.389   3.6893e-02
   5_occ:   6.849  0.042  0.221 81.963  0.032  2.389   3.6893e-02
   5_bss:   6.849  0.042  0.221 81.963  0.032  2.389   3.6893e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  99.87   0.00  18.47  89.63   0.00  14.33  99.87   5.69  41.02
   1_occ:  99.87   0.00  18.47  89.63   0.00  14.33  99.87   5.69  41.02
   2_bss:  99.87   0.00  18.47  89.63   0.00  14.33  99.87   5.69  41.02
   2_xyz:  99.87   0.00  18.47  89.63   0.00  14.33  99.87   5.69  41.02
   2_adp:  92.57   0.00  17.94  92.57   0.00  13.65  88.22   4.81  41.28
   2_occ:  92.57   0.00  17.94  92.57   0.00  13.65  88.22   4.81  41.28
   3_bss:  92.57   0.00  17.94  92.57   0.00  13.65  88.22   4.81  41.28
   3_xyz:  92.57   0.00  17.94  92.57   0.00  13.65  88.22   4.81  41.28
   3_adp:  93.40   1.63  17.56  93.40   1.63  13.19  84.91   6.07  41.32
   3_occ:  93.40   1.63  17.56  93.40   1.63  13.19  84.91   6.07  41.32
   4_bss:  93.40   1.63  17.56  93.40   1.63  13.19  84.91   6.07  41.32
   4_xyz:  93.40   1.63  17.56  93.40   1.63  13.19  84.91   6.07  41.32
   4_adp:  94.35   1.36  17.19  94.35   1.57  12.94  80.12   1.36  40.34
   4_occ:  94.35   1.36  17.19  94.35   1.57  12.94  80.12   1.36  40.34
   5_bss:  94.35   1.36  17.19  94.35   1.57  12.94  80.12   1.36  40.34
   5_xyz:  94.35   1.36  17.19  94.35   1.57  12.94  80.12   1.36  40.34
   5_adp:  93.21   1.66  16.79  93.21   1.66  12.73  83.30   2.39  38.85
   5_occ:  93.21   1.66  16.79  93.21   1.66  12.73  83.30   2.39  38.85
   5_bss:  93.15   1.60  16.73  93.15   1.60  12.67  83.24   2.33  38.79
------------------------------------------------------------------------
 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:    3.248    0.032    0.437
   1_adp:    3.248    0.032    0.437
   1_occ:    3.248    0.032    0.437
   2_bss:    3.248    0.032    0.437
   2_xyz:    2.513    0.056    0.526
   2_adp:    2.513    0.056    0.526
   2_occ:    2.513    0.056    0.526
   3_bss:    2.513    0.056    0.526
   3_xyz:    2.395    0.046    0.626
   3_adp:    2.395    0.046    0.626
   3_occ:    2.395    0.046    0.626
   4_bss:    2.395    0.046    0.626
   4_xyz:    2.232    0.031    0.639
   4_adp:    2.232    0.031    0.639
   4_occ:    2.232    0.031    0.639
   5_bss:    2.232    0.031    0.639
   5_xyz:    1.968    0.049    0.659
   5_adp:    1.968    0.049    0.659
   5_occ:    1.968    0.049    0.659
   5_bss:    1.968    0.049    0.659
------------------------------------------------------------------------

CPU time actual refinement: 294.74


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_92/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_92/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_92/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_92/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_92/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 294.62 
  Macro-tasks:
    bulk solvent and scale       = 31.56  
    individual site refinement   = 128.51 
    weights calculation          = 25.07  
    collect and process          = 5.46   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 190.69 
  Micro-tasks:
    mask                            = 1.53   
    f_calc                          = 96.30  
    alpha_beta                      = 7.18   
    target                          = 1.00   
    gradients_wrt_atomic_parameters = 105.17 
    fmodel                         = 5.54   
    r_factors                      = 0.19   
    phase_errors                   = 8.90   
    foms                           = 0.25   
    TOTAL for micro-tasks          = 226.06 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.080 micro seconds
Total CPU time: 5.11 minutes
from_scatterers_fft:    678 calls, 95.95 s
gradients_fft:          623 calls, 92.73 s

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

# Date 2008-01-16 Time 03:59:14 PST -0800 (1200484754.03 s)
Start R-work = 0.4283, R-free = 0.4265 (no bulk solvent and anisotropic scale)
Final R-work = 0.1389, R-free = 0.1784 (no bulk solvent and anisotropic scale)

Start R-work = 0.4196, R-free = 0.4145
Final R-work = 0.1151, R-free = 0.1595