# Date 2008-01-16 Time 03:56:32 PST -0800 (1200484592.31 s)
#phil __OFF__

Command line arguments: "../111.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7652
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 111

-------------------------------------------------------------------------------
  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, 48.1033, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.29, per 1000 atoms: 1.17


================================== 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, 48.1033, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9947 1.95067
Completeness in resolution range: 0.935706
Completeness with d_max=infinity: 0.932898

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9947
                             d_min =   1.9507

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, 48.1033, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9947 1.95067
Completeness in resolution range: 0.935706
Completeness with d_max=infinity: 0.932898

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9952 -  4.1752 [2200/2229]  1978   222  10.1%
  bin  2:  4.1752 -  3.3259 [2116/2139]  1906   210   9.9%
  bin  3:  3.3259 -  2.9089 [2072/2097]  1868   204   9.8%
  bin  4:  2.9089 -  2.6446 [2048/2081]  1845   203   9.9%
  bin  5:  2.6446 -  2.4559 [2059/2086]  1846   213  10.3%
  bin  6:  2.4559 -  2.3116 [2047/2075]  1851   196   9.6%
  bin  7:  2.3116 -  2.1962 [2025/2061]  1817   208  10.3%
  bin  8:  2.1962 -  2.1009 [2015/2057]  1821   194   9.6%
  bin  9:  2.1009 -  2.0202 [1954/2063]  1757   197  10.1%
  bin 10:  2.0202 -  1.9507 [1053/2047]   941   112  10.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_111/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        0.96 -     1.74: 13
        1.74 -     2.53: 104
        2.53 -     3.32: 3926
        3.32 -     4.11: 9532
        4.11 -     4.90: 15169
  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 "  0.955 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.075 3.040 -x+1/2,-y+1,z+1/2
  " C   GLY A  91 " - " O   HOH Z 401 "  1.271 3.270 -x+1,y-1/2,-z+1/2
  " O   HOH Z  69 " - " O   HOH Z 357 "  1.387 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 183 " - " O   HOH Z  52 "  1.535 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28739 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_111/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_111/model_refine_001.geo

CPU time processing inputs: 9.16


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.49375 48.10325 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5057   r_free= 0.5047   ksol= 0.00   Bsol= 0.00   scale= 0.871    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.305681                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9952 -  4.6574 0.99   1429  159 0.4216 0.4369      6.6473      6.7022|
|  2:  4.6574 -  3.7152 0.99   1368  152 0.4588 0.4508      6.8718      6.8564|
|  3:  3.7152 -  3.2510 0.99   1356  149 0.4833 0.4804      6.7157      6.7965|
|  4:  3.2510 -  2.9563 0.98   1326  147 0.5008 0.4659       6.544      6.4883|
|  5:  2.9563 -  2.7458 0.99   1331  151 0.5293 0.5279      6.3896      6.3758|
|  6:  2.7458 -  2.5847 0.99   1317  146 0.5355 0.5387      6.2935      6.1855|
|  7:  2.5847 -  2.4559 0.98   1316  148 0.5445 0.5085      6.2694      6.2302|
|  8:  2.4559 -  2.3494 0.98   1323  135 0.5391 0.5940        6.18      6.2073|
|  9:  2.3494 -  2.2593 0.98   1299  147 0.5738 0.5525      6.1322      6.1462|
| 10:  2.2593 -  2.1816 0.99   1316  144 0.5358 0.5725      6.1166      6.1482|
| 11:  2.1816 -  2.1135 0.98   1303  151 0.5379 0.5560       6.018      6.0513|
| 12:  2.1135 -  2.0533 0.97   1267  145 0.5295 0.4773      5.9584      5.9778|
| 13:  2.0533 -  1.9993 0.86   1141  122 0.5274 0.5421      5.8844      5.8671|
| 14:  1.9993 -  1.9507 0.41    538   63 0.5532 0.5409      5.8479      5.7031|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9952 -  4.6574  1429   159  0.59  43.55   0.80     0.63     102699.76|
|  2:  4.6574 -  3.7152  1368   152  0.61  43.19   0.88     0.70     143780.42|
|  3:  3.7152 -  3.2510  1356   149  0.50  52.01   0.90     0.70     146245.23|
|  4:  3.2510 -  2.9563  1326   147  0.43  57.38   0.89     0.63     119094.52|
|  5:  2.9563 -  2.7458  1331   151  0.36  63.06   0.86     0.54      92962.87|
|  6:  2.7458 -  2.5847  1317   146  0.31  66.77   0.87     0.45      78650.10|
|  7:  2.5847 -  2.4559  1316   148  0.23  73.04   0.87     0.31      74524.92|
|  8:  2.4559 -  2.3494  1323   135  0.17  77.34   0.89     0.26      71493.65|
|  9:  2.3494 -  2.2593  1299   147  0.15  78.91   0.88     0.24      66910.73|
| 10:  2.2593 -  2.1816  1316   144  0.19  75.58   0.93     0.29      58856.88|
| 11:  2.1816 -  2.1135  1303   151  0.22  73.52   0.93     0.35      52076.23|
| 12:  2.1135 -  2.0533  1267   145  0.22  73.74   0.94     0.37      48970.69|
| 13:  2.0533 -  1.9993  1141   122  0.19  76.25   0.96     0.30      42304.69|
| 14:  1.9993 -  1.9507   538    63  0.11  81.83   0.90     0.15      34360.51|
|alpha:            min =        0.15 max =            0.70 mean =         0.44|
|beta:             min =    34360.51 max =       146245.23 mean =     83986.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.32|
|phase err.(work): min =        0.00 max =           90.00 mean =        65.82|
|phase err.(test): min =        0.00 max =           90.00 mean =        65.73|
|-----------------------------------------------------------------------------|

============================== 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 = 25.696249             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.627   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.560042              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.258   (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 |  0.955 -  1.350:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.350 -  1.744:       10 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.744 -  2.139:       35 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.139 -  2.533:       69 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.533 -  2.928:     1544 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.928 -  3.322:     2382 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.322 -  3.717:     3776 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.717 -  4.111:     5756 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.111 -  4.505:     6682 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.505 -  4.900:     8487 |
|-----------------------------------------------------------------------------|
|-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 |        0.258 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.106    4.900  0.955 |       1.629 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.504)------------------------------------------|
|    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 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5057   r_free= 0.5047   ksol= 0.00   Bsol= 0.00   scale= 0.871    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.305681                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4997   r_free= 0.4962   ksol= 0.30   Bsol= 20.00   scale= 0.903   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.23,2.65,-0.01,0.00,-0.00,-0.00); trace/3= 0.47                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.303392                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 21.442836             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.173   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.049847              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.839   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4997      final r-factor (work) = 0.4117          |
| start r-factor (free) = 0.4962      final r-factor (free) = 0.4364          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 67.8283 = 21.44 * 0.50 * 6.3023 + 1.00 * 0.2584                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 66.9932 = 21.44 * 0.50 * 6.2317 + 1.00 * 0.1801                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4117      final r-factor (work) = 0.3696          |
| start r-factor (free) = 0.4364      final r-factor (free) = 0.4425          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.7801 = 2.05 * 1.00 * 6.2317 + 1.00 * 0.0060                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.6342 = 2.05 * 1.00 * 6.1498 + 1.00 * 0.0280                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.504)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.15   21.80    None  None   None       |
|    all(noH): 2823   0      0.00    99.15   21.80    None  None   None       |
|    Sol.    : 438    0      0.00    99.15   39.09    None  None   None       |
|    Mac.    : 2385   0      0.00    91.73   18.62    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 -   9.915:  793   |   5:    49.573 -  59.488:  129        |
|      1:     9.915 -  19.829:  774   |   6:    59.488 -  69.402:   71        |
|      2:    19.829 -  29.744:  498   |   7:    69.402 -  79.317:   25        |
|      3:    29.744 -  39.658:  334   |   8:    79.317 -  89.231:   15        |
|      4:    39.658 -  49.573:  179   |   9:    89.231 -  99.146:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3696 r_free = 0.4425             target_work(ml) = 5.976         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3693 r_free = 0.4419             target_work(ml) = 5.975         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3693   r_free= 0.4419   ksol= 0.30   Bsol= 20.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.23,2.65,-0.01,0.00,-0.00,-0.00); trace/3= 0.47                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 5.974953                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3685   r_free= 0.4403   ksol= 0.32   Bsol= 50.17   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,2.15,0.45,0.00,0.00,0.00); trace/3= 0.59                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 5.974081                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.855983             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.013  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.963818              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.043  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3685      final r-factor (work) = 0.3182          |
| start r-factor (free) = 0.4403      final r-factor (free) = 0.3907          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.7966 = 13.86 * 0.50 * 6.1514 + 1.00 * 0.1800                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.1385 = 13.86 * 0.50 * 5.9226 + 1.00 * 0.1067                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3182      final r-factor (work) = 0.2965          |
| start r-factor (free) = 0.3907      final r-factor (free) = 0.3804          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.6587 = 1.96 * 1.00 * 5.9226 + 1.00 * 0.0278                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.8304 = 1.96 * 1.00 * 6.0100 + 1.00 * 0.0278                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.504)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    133.43  22.45    None  None   None       |
|    all(noH): 2823   0      0.00    133.43  22.45    None  None   None       |
|    Sol.    : 438    0      0.00    116.16  42.20    None  None   None       |
|    Mac.    : 2385   0      0.00    133.43  18.82    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 -  13.343: 1143   |   5:    66.713 -  80.055:   61        |
|      1:    13.343 -  26.685:  816   |   6:    80.055 -  93.398:   39        |
|      2:    26.685 -  40.028:  406   |   7:    93.398 - 106.740:   16        |
|      3:    40.028 -  53.370:  211   |   8:   106.740 - 120.083:    2        |
|      4:    53.370 -  66.713:  128   |   9:   120.083 - 133.425:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2965 r_free = 0.3804             target_work(ml) = 6.003         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2962 r_free = 0.3805             target_work(ml) = 6.002         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2962   r_free= 0.3805   ksol= 0.32   Bsol= 50.17   scale= 1.056   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,2.15,0.45,0.00,0.00,0.00); trace/3= 0.59                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.002173                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2966   r_free= 0.3800   ksol= 0.32   Bsol= 50.17   scale= 1.057   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.75,1.81,0.77,0.00,0.00,0.00); trace/3= 0.61                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.002992                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.059459              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.296  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.322232              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.245  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2966      final r-factor (work) = 0.2615          |
| start r-factor (free) = 0.3800      final r-factor (free) = 0.3423          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.3168 = 6.06 * 0.50 * 6.0105 + 1.00 * 0.1067                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.1229 = 6.06 * 0.50 * 5.9591 + 1.00 * 0.0684                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2615      final r-factor (work) = 0.2538          |
| start r-factor (free) = 0.3423      final r-factor (free) = 0.3156          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9474 = 0.32 * 1.00 * 5.9591 + 1.00 * 0.0272                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9132 = 0.32 * 1.00 * 5.8882 + 1.00 * 0.0158                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.504)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    125.57  19.81    None  None   None       |
|    all(noH): 2823   0      0.00    125.57  19.81    None  None   None       |
|    Sol.    : 438    0      2.89    110.09  39.80    None  None   None       |
|    Mac.    : 2385   0      0.00    125.57  16.14    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.557: 1276   |   5:    62.783 -  75.340:   54        |
|      1:    12.557 -  25.113:  803   |   6:    75.340 -  87.896:   25        |
|      2:    25.113 -  37.670:  364   |   7:    87.896 - 100.453:   13        |
|      3:    37.670 -  50.227:  196   |   8:   100.453 - 113.010:    2        |
|      4:    50.227 -  62.783:   89   |   9:   113.010 - 125.566:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2538 r_free = 0.3156             target_work(ml) = 5.852         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2536 r_free = 0.3155             target_work(ml) = 5.851         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2536   r_free= 0.3155   ksol= 0.32   Bsol= 50.17   scale= 1.062   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.75,1.81,0.77,0.00,0.00,0.00); trace/3= 0.61                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.851050                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2527   r_free= 0.3152   ksol= 0.30   Bsol= 40.02   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,0.38,-0.75,0.00,-0.00,-0.00); trace/3= -0.82                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.850459                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.258380              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.339  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.464321              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.884   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2527      final r-factor (work) = 0.2083          |
| start r-factor (free) = 0.3152      final r-factor (free) = 0.2586          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6630 = 3.26 * 0.50 * 5.8892 + 1.00 * 0.0683                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4614 = 3.26 * 0.50 * 5.7674 + 1.00 * 0.0653                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2083      final r-factor (work) = 0.1916          |
| start r-factor (free) = 0.2586      final r-factor (free) = 0.2465          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6902 = 0.46 * 1.00 * 5.7674 + 1.00 * 0.0123                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6279 = 0.46 * 1.00 * 5.6352 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.504)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.78  19.11    None  None   None       |
|    all(noH): 2823   0      0.00    107.78  19.11    None  None   None       |
|    Sol.    : 438    0      5.27    104.21  43.53    None  None   None       |
|    Mac.    : 2385   0      0.00    107.78  14.63    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.778: 1154   |   5:    53.889 -  64.667:   96        |
|      1:    10.778 -  21.556:  921   |   6:    64.667 -  75.444:   50        |
|      2:    21.556 -  32.333:  288   |   7:    75.444 -  86.222:   16        |
|      3:    32.333 -  43.111:  154   |   8:    86.222 -  97.000:   11        |
|      4:    43.111 -  53.889:  128   |   9:    97.000 - 107.778:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1916 r_free = 0.2465             target_work(ml) = 5.612         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1914 r_free = 0.2464             target_work(ml) = 5.611         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1914   r_free= 0.2464   ksol= 0.30   Bsol= 40.02   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,0.38,-0.75,0.00,-0.00,-0.00); trace/3= -0.82                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.611488                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1911   r_free= 0.2459   ksol= 0.30   Bsol= 40.02   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.01,-0.60,-1.60,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.612157                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.840939              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.587  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.162225              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.835  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1911      final r-factor (work) = 0.1560          |
| start r-factor (free) = 0.2459      final r-factor (free) = 0.2100          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0755 = 2.84 * 0.50 * 5.6391 + 1.00 * 0.0653                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9148 = 2.84 * 0.50 * 5.5269 + 1.00 * 0.0640                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1560      final r-factor (work) = 0.1496          |
| start r-factor (free) = 0.2100      final r-factor (free) = 0.1977          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9080 = 0.16 * 1.00 * 5.5269 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8875 = 0.16 * 1.00 * 5.4162 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.504)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.64    101.96  18.29    None  None   None       |
|    all(noH): 2823   0      1.64    101.96  18.29    None  None   None       |
|    Sol.    : 438    0      3.65    101.96  42.53    None  None   None       |
|    Mac.    : 2385   0      1.64    100.55  13.83    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:     1.645 -  11.676: 1326   |   5:    51.801 -  61.832:   97        |
|      1:    11.676 -  21.707:  873   |   6:    61.832 -  71.863:   38        |
|      2:    21.707 -  31.739:  193   |   7:    71.863 -  81.894:   21        |
|      3:    31.739 -  41.770:  132   |   8:    81.894 -  91.926:   10        |
|      4:    41.770 -  51.801:  127   |   9:    91.926 - 101.957:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1496 r_free = 0.1977             target_work(ml) = 5.387         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1494 r_free = 0.1977             target_work(ml) = 5.386         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1494   r_free= 0.1977   ksol= 0.30   Bsol= 40.02   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.01,-0.60,-1.60,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.385924                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9952 -  4.6574 0.99   1429  159 0.1066 0.1472      5.4668      5.6429|
|  2:  4.6574 -  3.7152 0.99   1368  152 0.1052 0.1364       5.611      5.8522|
|  3:  3.7152 -  3.2510 0.99   1356  149 0.1403 0.1916      5.7112       6.033|
|  4:  3.2510 -  2.9563 0.98   1326  147 0.1698 0.1948      5.7013      5.8187|
|  5:  2.9563 -  2.7458 0.99   1331  151 0.1810 0.2107      5.5842      5.7163|
|  6:  2.7458 -  2.5847 0.99   1317  146 0.1724 0.2650       5.475      5.6489|
|  7:  2.5847 -  2.4559 0.98   1316  148 0.1646 0.2040      5.4029      5.5653|
|  8:  2.4559 -  2.3494 0.98   1323  135 0.1681 0.2168      5.3478      5.5276|
|  9:  2.3494 -  2.2593 0.98   1299  147 0.1654 0.2304      5.2716      5.4701|
| 10:  2.2593 -  2.1816 0.99   1316  144 0.1583 0.2035       5.241      5.3886|
| 11:  2.1816 -  2.1135 0.98   1303  151 0.1557 0.2387      5.1517      5.4616|
| 12:  2.1135 -  2.0533 0.97   1267  145 0.1576 0.2085      5.1006      5.3274|
| 13:  2.0533 -  1.9993 0.86   1141  122 0.1519 0.2343      5.0196      5.3035|
| 14:  1.9993 -  1.9507 0.41    538   63 0.1571 0.1983      4.9918      5.0641|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9952 -  4.6574  1429   159  0.93  10.31   0.98     0.95       8660.73|
|  2:  4.6574 -  3.7152  1368   152  0.94  10.34   1.04     1.03      12660.73|
|  3:  3.7152 -  3.2510  1356   149  0.90  15.26   1.05     1.03      16100.78|
|  4:  3.2510 -  2.9563  1326   147  0.88  18.56   1.03     1.02      16179.21|
|  5:  2.9563 -  2.7458  1331   151  0.86  20.77   1.03     1.00      13160.94|
|  6:  2.7458 -  2.5847  1317   146  0.85  21.36   1.00     0.94      11338.67|
|  7:  2.5847 -  2.4559  1316   148  0.86  20.56   1.01     0.95       9805.90|
|  8:  2.4559 -  2.3494  1323   135  0.86  20.85   1.03     0.99       9133.71|
|  9:  2.3494 -  2.2593  1299   147  0.86  20.95   1.02     0.98       7811.82|
| 10:  2.2593 -  2.1816  1316   144  0.86  20.87   1.03     0.98       7474.84|
| 11:  2.1816 -  2.1135  1303   151  0.86  20.50   1.03     0.99       6528.23|
| 12:  2.1135 -  2.0533  1267   145  0.87  20.22   1.03     1.02       5871.98|
| 13:  2.0533 -  1.9993  1141   122  0.85  21.26   1.03     1.02       5298.56|
| 14:  1.9993 -  1.9507   538    63  0.85  21.79   1.01     0.93       4725.90|
|alpha:            min =        0.93 max =            1.03 mean =         0.99|
|beta:             min =     4725.90 max =        16179.21 mean =      9922.85|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           90.00 mean =        18.58|
|phase err.(test): min =        0.00 max =           89.85 mean =        18.25|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1497   r_free= 0.1973   ksol= 0.31   Bsol= 39.96   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.41,-1.27,-1.90,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.388182                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1497   r_free= 0.1973   ksol= 0.31   Bsol= 39.96   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.41,-1.27,-1.90,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.388182                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9952 -  4.6574 0.99   1429  159 0.1091 0.1452      5.4836      5.6392|
|  2:  4.6574 -  3.7152 0.99   1368  152 0.1069 0.1378      5.6208       5.864|
|  3:  3.7152 -  3.2510 0.99   1356  149 0.1415 0.1896      5.7161      6.0277|
|  4:  3.2510 -  2.9563 0.98   1326  147 0.1700 0.1944       5.705      5.8168|
|  5:  2.9563 -  2.7458 0.99   1331  151 0.1813 0.2113      5.5856      5.7215|
|  6:  2.7458 -  2.5847 0.99   1317  146 0.1722 0.2628      5.4738      5.6439|
|  7:  2.5847 -  2.4559 0.98   1316  148 0.1642 0.2054       5.401       5.565|
|  8:  2.4559 -  2.3494 0.98   1323  135 0.1674 0.2166      5.3457       5.528|
|  9:  2.3494 -  2.2593 0.98   1299  147 0.1651 0.2294      5.2696      5.4637|
| 10:  2.2593 -  2.1816 0.99   1316  144 0.1581 0.2045        5.24       5.391|
| 11:  2.1816 -  2.1135 0.98   1303  151 0.1555 0.2400      5.1506       5.463|
| 12:  2.1135 -  2.0533 0.97   1267  145 0.1577 0.2085      5.1019      5.3292|
| 13:  2.0533 -  1.9993 0.86   1141  122 0.1516 0.2336      5.0195      5.3012|
| 14:  1.9993 -  1.9507 0.41    538   63 0.1575 0.1984      4.9914      5.0619|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9952 -  4.6574  1429   159  0.93  10.40   0.97     0.95       8708.77|
|  2:  4.6574 -  3.7152  1368   152  0.94  10.45   1.03     1.02      12762.21|
|  3:  3.7152 -  3.2510  1356   149  0.90  15.30   1.04     1.02      16196.91|
|  4:  3.2510 -  2.9563  1326   147  0.88  18.59   1.01     1.01      16242.81|
|  5:  2.9563 -  2.7458  1331   151  0.86  20.75   1.01     0.98      13140.89|
|  6:  2.7458 -  2.5847  1317   146  0.85  21.35   0.98     0.93      11357.68|
|  7:  2.5847 -  2.4559  1316   148  0.86  20.50   0.99     0.93       9759.19|
|  8:  2.4559 -  2.3494  1323   135  0.86  20.81   1.01     0.97       9103.17|
|  9:  2.3494 -  2.2593  1299   147  0.86  20.88   1.00     0.95       7783.01|
| 10:  2.2593 -  2.1816  1316   144  0.86  20.83   1.00     0.95       7459.08|
| 11:  2.1816 -  2.1135  1303   151  0.86  20.48   1.01     0.96       6520.51|
| 12:  2.1135 -  2.0533  1267   145  0.87  20.24   1.00     0.99       5891.89|
| 13:  2.0533 -  1.9993  1141   122  0.85  21.27   1.00     0.99       5301.64|
| 14:  1.9993 -  1.9507   538    63  0.85  21.77   0.98     0.90       4707.32|
|alpha:            min =        0.90 max =            1.02 mean =         0.97|
|beta:             min =     4707.32 max =        16242.81 mean =      9938.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.98 mean =        18.58|
|phase err.(test): min =        0.00 max =           89.61 mean =        18.24|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.504)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.59    101.90  18.23    None  None   None       |
|    all(noH): 2823   0      1.59    101.90  18.23    None  None   None       |
|    Sol.    : 438    0      3.59    101.90  42.47    None  None   None       |
|    Mac.    : 2385   0      1.59    100.50  13.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.586 -  11.617: 1326   |   5:    51.742 -  61.773:   97        |
|      1:    11.617 -  21.649:  873   |   6:    61.773 -  71.804:   38        |
|      2:    21.649 -  31.680:  193   |   7:    71.804 -  81.836:   21        |
|      3:    31.680 -  41.711:  132   |   8:    81.836 -  91.867:   10        |
|      4:    41.711 -  51.742:  127   |   9:    91.867 - 101.898:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 341         
Filter by distance & map next to the model:
   mapped sites are within: 0.607 - 5.503
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 340 from: 341
   mapped sites are within: 0.711 - 5.503

peak=    8.765 closest distance to " O   HOH Z 138 " =    1.617
peak=    8.193 closest distance to " CB  SER A 216 " =    1.199
peak=    6.471 closest distance to " O   HOH Z  46 " =    1.632
peak=    6.121 closest distance to " O   HOH Z 400 " =    1.114
peak=    6.078 closest distance to " O   HOH Z 159 " =    1.145
peak=    5.977 closest distance to " O   HOH Z  53 " =    1.334
peak=    5.928 closest distance to " O   HOH Z 135 " =    1.358
peak=    5.874 closest distance to " CG  GLN A  77 " =    1.078
peak=    5.867 closest distance to " O   HOH Z  52 " =    2.039
peak=    5.657 closest distance to " O   ASN A 285 " =    1.008
peak=    5.514 closest distance to " O   HOH Z 278 " =    1.622
peak=    5.463 closest distance to " CB  GLN A  73 " =    1.140
peak=    5.384 closest distance to " O   HOH Z 404 " =    1.534
peak=    5.380 closest distance to " NH2 ARG A  36 " =    1.113
peak=    5.336 closest distance to " O   HOH Z 117 " =    1.672
peak=    5.279 closest distance to " O   HOH Z 199 " =    1.394
peak=    5.220 closest distance to " O   HOH Z 102 " =    1.643
peak=    5.217 closest distance to " O   HOH Z 210 " =    1.629
peak=    5.205 closest distance to " O   HOH Z 369 " =    1.458
peak=    5.071 closest distance to " O   HOH Z 389 " =    2.089
peak=    5.067 closest distance to " O   HOH Z 424 " =    1.329
peak=    5.037 closest distance to " O   HOH Z 116 " =    1.347
peak=    5.028 closest distance to " O   HOH Z 401 " =    2.176
peak=    5.014 closest distance to " O   HOH Z  45 " =    1.462
peak=    4.967 closest distance to " CB  SER A  62 " =    1.066
peak=    4.953 closest distance to " NH1 ARG A  36 " =    1.233
peak=    4.893 closest distance to " O   HOH Z 236 " =    1.909
peak=    4.882 closest distance to " O   HOH Z 422 " =    1.143
peak=    4.871 closest distance to " O   HOH Z 272 " =    1.587
peak=    4.831 closest distance to " O   HOH Z 411 " =    3.543
peak=    4.806 closest distance to " CB  ARG A 275 " =    1.002
peak=    4.800 closest distance to " CB  ASN A 285 " =    1.109
peak=    4.769 closest distance to " CD  ARG A  36 " =    1.179
peak=    4.755 closest distance to " NZ  LYS A  76 " =    0.961
peak=    4.755 closest distance to " O   HOH Z 249 " =    1.474
peak=    4.652 closest distance to " O   HOH Z 110 " =    1.202
peak=    4.648 closest distance to " O   HOH Z 130 " =    1.243
peak=    4.635 closest distance to " OD1 ASN A  60 " =    1.062
peak=    4.632 closest distance to " CG  ARG A  66 " =    1.317
peak=    4.599 closest distance to " O   HOH Z  54 " =    1.434
peak=    4.566 closest distance to " O   HOH Z  44 " =    2.003
peak=    4.532 closest distance to " O   HOH Z 247 " =    1.587
peak=    4.517 closest distance to " O   HOH Z  80 " =    2.384
peak=    4.488 closest distance to " OE1 GLN A  77 " =    1.149
peak=    4.483 closest distance to " O   HOH Z 124 " =    1.549
peak=    4.470 closest distance to " O   HOH Z 193 " =    1.866
peak=    4.440 closest distance to " CG AARG A 275 " =    1.318
peak=    4.420 closest distance to " O   HOH Z 427 " =    1.258
peak=    4.401 closest distance to " O   HOH Z  97 " =    1.558
peak=    4.385 closest distance to " O   HOH Z 163 " =    1.769
peak=    4.315 closest distance to " CB  SER A  63 " =    1.164
peak=    4.264 closest distance to " O   HOH Z 437 " =    2.566
peak=    4.220 closest distance to " CA  ILE A 120 " =    1.206
peak=    4.210 closest distance to " O   ARG A 275 " =    0.809
peak=    4.210 closest distance to " CA  TYR A  30 " =    1.092
peak=    4.207 closest distance to " CD  ARG A 269 " =    0.937
peak=    4.169 closest distance to " O   HOH Z 214 " =    1.434
peak=    4.168 closest distance to " O   HOH Z 188 " =    1.302
peak=    4.168 closest distance to " O   HOH Z 154 " =    1.974
peak=    4.163 closest distance to " NH1AARG A 275 " =    1.383
peak=    4.143 closest distance to " O   HOH Z 402 " =    1.564
peak=    4.142 closest distance to " O   HOH Z  49 " =    1.645
peak=    4.103 closest distance to " CA  ARG A  66 " =    1.056
peak=    4.101 closest distance to " CB  PRO A 213 " =    1.321
peak=    4.097 closest distance to " O   HOH Z 126 " =    1.636
peak=    4.087 closest distance to " O   HOH Z 146 " =    1.533
peak=    4.086 closest distance to " OE1 GLN A  11 " =    1.999
peak=    4.085 closest distance to " O   HOH Z 209 " =    2.116
peak=    4.069 closest distance to " ND2 ASN A  45 " =    1.251
peak=    4.059 closest distance to " CB  TRP A 179 " =    1.710
peak=    4.032 closest distance to " O   HOH Z 261 " =    2.178
peak=    4.000 closest distance to " CD2 TRP A 179 " =    1.305
peak=    3.999 closest distance to " CB  SER A 141 " =    0.943
peak=    3.998 closest distance to " CB  ASP A 286 " =    1.070
peak=    3.993 closest distance to " O   HOH Z 128 " =    1.528
peak=    3.986 closest distance to " O   HOH Z 414 " =    2.317
peak=    3.985 closest distance to " NH2 ARG A  56 " =    1.487
peak=    3.983 closest distance to " O   HOH Z 406 " =    1.546
peak=    3.981 closest distance to " O   VAL A  72 " =    1.346
peak=    3.979 closest distance to " O   HOH Z  43 " =    2.000
peak=    3.974 closest distance to " N   VAL A  72 " =    1.010
peak=    3.972 closest distance to " O   HOH Z 416 " =    1.432
peak=    3.961 closest distance to " O   HOH Z 303 " =    1.900
peak=    3.956 closest distance to " NH2 ARG A  56 " =    2.126
peak=    3.946 closest distance to " O   HOH Z  68 " =    1.859
peak=    3.938 closest distance to " O   HOH Z 255 " =    1.187
peak=    3.936 closest distance to " O   HOH Z 132 " =    1.734
peak=    3.930 closest distance to " CB  ASN A 187 " =    1.478
peak=    3.923 closest distance to " NH2 ARG A 156 " =    1.104
peak=    3.923 closest distance to " O   HOH Z  88 " =    3.316
peak=    3.904 closest distance to " CG2 THR A 251 " =    1.289
peak=    3.899 closest distance to " CB AVAL A  41 " =    1.034
peak=    3.896 closest distance to " O   HOH Z 433 " =    1.801
peak=    3.886 closest distance to " O   HOH Z 279 " =    1.105
peak=    3.885 closest distance to " O   HOH Z  84 " =    1.113
peak=    3.868 closest distance to " CA  SER A  62 " =    0.936
peak=    3.844 closest distance to " O   HOH Z   9 " =    2.366
peak=    3.839 closest distance to " N   ASN A 252 " =    1.127
peak=    3.824 closest distance to " CG2 VAL A 197 " =    1.213
peak=    3.820 closest distance to " O   HOH Z  30 " =    1.586
peak=    3.817 closest distance to " O   HOH Z 316 " =    2.494
peak=    3.813 closest distance to " O   HOH Z 425 " =    1.625
peak=    3.800 closest distance to " O   HOH Z 132 " =    2.696
peak=    3.799 closest distance to " O   HOH Z 173 " =    1.618
peak=    3.772 closest distance to " O   HOH Z 203 " =    1.764
peak=    3.771 closest distance to " CA  ALA A  21 " =    1.259
peak=    3.759 closest distance to " O   HOH Z 368 " =    1.150
peak=    3.752 closest distance to " O   LYS A 289 " =    1.147
peak=    3.750 closest distance to " CB  GLN A 194 " =    1.053
peak=    3.746 closest distance to " O   HOH Z 200 " =    1.778
peak=    3.736 closest distance to " N   ASP A 286 " =    0.971
peak=    3.714 closest distance to " OE1 GLU A   2 " =    1.666
peak=    3.709 closest distance to " CE  LYS A 119 " =    1.090
peak=    3.708 closest distance to " O   PRO A 198 " =    1.646
peak=    3.699 closest distance to " CD  PRO A  54 " =    0.889
peak=    3.694 closest distance to " ND1 HIS A  81 " =    1.423
peak=    3.691 closest distance to " CB  VAL A 265 " =    1.379
peak=    3.686 closest distance to " N   TYR A  15 " =    0.844
peak=    3.685 closest distance to " O   HOH Z 341 " =    1.356
peak=    3.684 closest distance to " O   HOH Z 133 " =    1.424
peak=    3.683 closest distance to " CG  MET A 185 " =    1.257
peak=    3.675 closest distance to " O   HOH Z 111 " =    1.901
peak=    3.672 closest distance to " O   SER A 164 " =    1.188
peak=    3.671 closest distance to " NZ  LYS A 117 " =    3.238
peak=    3.667 closest distance to " O   HOH Z  63 " =    2.225
peak=    3.663 closest distance to " O   HOH Z 357 " =    1.202
peak=    3.663 closest distance to " NH1 ARG A  36 " =    1.091
peak=    3.658 closest distance to " O   SER A  87 " =    2.194
peak=    3.645 closest distance to " OG ASER A 164 " =    0.809
peak=    3.640 closest distance to " CB  GLN A  58 " =    1.212
peak=    3.639 closest distance to " O   GLN A  11 " =    1.002
peak=    3.638 closest distance to " O   HOH Z  48 " =    1.778
peak=    3.634 closest distance to " O   GLY A  57 " =    1.161
peak=    3.629 closest distance to " O   HOH Z 196 " =    1.551
peak=    3.628 closest distance to " CG  PRO A 198 " =    1.418
peak=    3.626 closest distance to " O   HOH Z 127 " =    1.165
peak=    3.619 closest distance to " CB  GLU A 277 " =    0.828
peak=    3.618 closest distance to " O   HOH Z 349 " =    1.428
peak=    3.615 closest distance to " O   HOH Z 411 " =    1.264
peak=    3.615 closest distance to " O   HOH Z 154 " =    2.073
peak=    3.611 closest distance to " O   HOH Z 109 " =    1.672
peak=    3.607 closest distance to " O   HOH Z 297 " =    1.148
peak=    3.605 closest distance to " O   HOH Z  87 " =    1.796
peak=    3.605 closest distance to " O   HOH Z 234 " =    3.716
peak=    3.605 closest distance to " CZ  PHE A 218 " =    1.315
peak=    3.604 closest distance to " CD  LYS A 166 " =    1.563
peak=    3.603 closest distance to " CG  PRO A  90 " =    1.279
peak=    3.599 closest distance to " O   HOH Z 394 " =    1.625
peak=    3.599 closest distance to " CB  GLN A 183 " =    1.186
peak=    3.590 closest distance to " O   HOH Z 250 " =    2.227
peak=    3.585 closest distance to " O   HOH Z 339 " =    1.343
peak=    3.582 closest distance to " O   HOH Z 408 " =    2.339
peak=    3.579 closest distance to " O   HOH Z 147 " =    1.742
peak=    3.575 closest distance to " O   HOH Z 380 " =    2.133
peak=    3.573 closest distance to " CG  PRO A 243 " =    1.308
peak=    3.573 closest distance to " CZ3 TRP A 274 " =    4.743
peak=    3.573 closest distance to " O   HOH Z 178 " =    0.986
peak=    3.559 closest distance to " CB ASER A 164 " =    0.909
peak=    3.555 closest distance to " CG  LYS A 166 " =    1.742
peak=    3.554 closest distance to " CD2 LEU A  25 " =    1.393
peak=    3.552 closest distance to " OE1 GLU A  44 " =    1.132
peak=    3.550 closest distance to " O   HOH Z 185 " =    1.232
peak=    3.538 closest distance to " O   HOH Z 305 " =    1.945
peak=    3.536 closest distance to " O   HOH Z 151 " =    1.801
peak=    3.532 closest distance to " CD ALYS A 290 " =    0.988
peak=    3.529 closest distance to " CB  SER A  26 " =    0.945
peak=    3.529 closest distance to " CG1 ILE A  33 " =    1.423
peak=    3.523 closest distance to " CB  GLN A  88 " =    1.121
peak=    3.518 closest distance to " O   HOH Z 128 " =    1.625
peak=    3.516 closest distance to " O   HOH Z 358 " =    1.271
peak=    3.513 closest distance to " O   ASN A 285 " =    2.179
peak=    3.510 closest distance to " CD1 TRP A 274 " =    1.030
peak=    3.508 closest distance to " CB  ALA A 248 " =    1.420
peak=    3.506 closest distance to " CB  THR A  31 " =    1.753
peak=    3.504 closest distance to " OG  SER A 245 " =    1.372
peak=    3.504 closest distance to " O   HOH Z  66 " =    2.166
peak=    3.503 closest distance to " CA  GLY A 302 " =    2.158
peak=    3.494 closest distance to " O   HOH Z 431 " =    1.597
peak=    3.494 closest distance to " O   HOH Z 227 " =    1.664
peak=    3.486 closest distance to " CG1 VAL A 153 " =    1.219
peak=    3.485 closest distance to " CB  TRP A 179 " =    1.339
peak=    3.483 closest distance to " O   HOH Z 395 " =    1.624
peak=    3.483 closest distance to " OD1 ASN A  45 " =    1.285
peak=    3.479 closest distance to " O   HOH Z 298 " =    1.924
peak=    3.477 closest distance to " CA  SER A  63 " =    1.201
peak=    3.475 closest distance to " CB  ASN A 127 " =    0.770
peak=    3.473 closest distance to " O   HOH Z  59 " =    1.900
peak=    3.471 closest distance to " CE BMET A  47 " =    1.305
peak=    3.470 closest distance to " CA  GLY A 196 " =    0.808
peak=    3.468 closest distance to " O   HOH Z 371 " =    3.010
peak=    3.467 closest distance to " O   HOH Z  24 " =    1.471
peak=    3.465 closest distance to " ND2 ASN A 301 " =    1.018
peak=    3.461 closest distance to " CG2 VAL A  78 " =    0.933
peak=    3.461 closest distance to " CA  LEU A  83 " =    1.300
peak=    3.446 closest distance to " O   HOH Z  63 " =    1.976
peak=    3.445 closest distance to " NE2 GLN A  11 " =    1.085
peak=    3.445 closest distance to " O   HOH Z 365 " =    1.897
peak=    3.439 closest distance to " CD  GLN A  73 " =    1.040
peak=    3.434 closest distance to " O   HOH Z 134 " =    2.217
peak=    3.433 closest distance to " O   HOH Z  78 " =    1.608
peak=    3.426 closest distance to " O   HOH Z 274 " =    1.683
peak=    3.424 closest distance to " CB  PHE A 225 " =    1.285
peak=    3.420 closest distance to " CA  VAL A  41 " =    0.963
peak=    3.419 closest distance to " O   HOH Z  39 " =    2.176
peak=    3.419 closest distance to " CB  GLU A 152 " =    1.053
peak=    3.418 closest distance to " OG BSER A 210 " =    1.200
peak=    3.409 closest distance to " O   HOH Z 205 " =    1.456
peak=    3.408 closest distance to " O   HOH Z 369 " =    3.297
peak=    3.407 closest distance to " O   HOH Z 423 " =    1.777
peak=    3.405 closest distance to " CD  GLN A 240 " =    1.513
peak=    3.404 closest distance to " O   HOH Z  33 " =    1.931
peak=    3.396 closest distance to " O   HOH Z  40 " =    1.931
peak=    3.395 closest distance to " O   HOH Z  85 " =    1.725
peak=    3.395 closest distance to " CE1 TYR A  30 " =    0.946
peak=    3.391 closest distance to " O   HOH Z 324 " =    1.619
peak=    3.383 closest distance to " CB  SER A 245 " =    1.750
peak=    3.380 closest distance to " O   HOH Z 368 " =    3.100
peak=    3.379 closest distance to " O   HOH Z 225 " =    2.086
peak=    3.377 closest distance to " O   HOH Z 423 " =    3.152
peak=    3.376 closest distance to " O   HOH Z 124 " =    3.029
peak=    3.375 closest distance to " CB  VAL A 202 " =    1.583
peak=    3.375 closest distance to " O   HOH Z 132 " =    2.004
peak=    3.374 closest distance to " O   GLY A  91 " =    1.461
peak=    3.372 closest distance to " O   HOH Z 227 " =    1.974
peak=    3.372 closest distance to " O   HOH Z  67 " =    1.567
peak=    3.370 closest distance to " O   HOH Z  92 " =    1.143
peak=    3.368 closest distance to " CA  ARG A  36 " =    1.148
peak=    3.367 closest distance to " CZ2 TRP A 179 " =    1.851
peak=    3.363 closest distance to " O   HOH Z 261 " =    1.611
peak=    3.361 closest distance to " O   HOH Z  22 " =    2.308
peak=    3.360 closest distance to " O   HOH Z  56 " =    2.023
peak=    3.354 closest distance to " OD1 ASN A 301 " =    1.061
peak=    3.353 closest distance to " CB  VAL A  78 " =    1.247
peak=    3.350 closest distance to " CG1 ILE A 120 " =    1.226
peak=    3.349 closest distance to " O   HOH Z   6 " =    1.242
peak=    3.347 closest distance to " O   HOH Z 200 " =    4.016
peak=    3.344 closest distance to " CA  TRP A  85 " =    1.086
peak=    3.341 closest distance to " CA  ILE A 263 " =    1.270
peak=    3.340 closest distance to " O   HOH Z  38 " =    1.558
peak=    3.338 closest distance to " O   HOH Z   1 " =    3.248
peak=    3.335 closest distance to " O   HOH Z 301 " =    1.669
peak=    3.330 closest distance to " CB  PRO A 198 " =    1.287
peak=    3.330 closest distance to " N   ASN A  39 " =    1.150
peak=    3.325 closest distance to " CA  GLU A 152 " =    0.992
peak=    3.322 closest distance to " O   HOH Z 418 " =    2.846
peak=    3.318 closest distance to " CG2 ILE A  20 " =    1.219
peak=    3.316 closest distance to " CB  PHE A  16 " =    1.216
peak=    3.310 closest distance to " CG2 VAL A 268 " =    1.241
peak=    3.308 closest distance to " CB  PRO A  54 " =    0.769
peak=    3.308 closest distance to " CD2 TYR A  68 " =    0.985
peak=    3.307 closest distance to " NH2AARG A 145 " =    2.085
peak=    3.307 closest distance to " C   ILE A 106 " =    1.717
peak=    3.304 closest distance to " CA  GLN A  58 " =    0.790
peak=    3.304 closest distance to " CB  GLU A 128 " =    1.250
peak=    3.302 closest distance to " CB  PHE A  59 " =    0.918
peak=    3.300 closest distance to " O   SER A  26 " =    1.341
peak=    3.295 closest distance to " O   HOH Z   7 " =    1.729
peak=    3.294 closest distance to " O   HOH Z 433 " =    2.033
peak=    3.286 closest distance to " CA  ARG A 156 " =    1.055
peak=    3.282 closest distance to " O   HOH Z 139 " =    4.432
peak=    3.281 closest distance to " O   HOH Z  95 " =    1.897
peak=    3.279 closest distance to " CA  GLY A 133 " =    3.701
peak=    3.278 closest distance to " O   HOH Z 234 " =    3.855
peak=    3.277 closest distance to " NZ  LYS A 117 " =    3.525
peak=    3.271 closest distance to " CA  ALA A 100 " =    1.304
peak=    3.270 closest distance to " N   VAL A 121 " =    0.711
peak=    3.268 closest distance to " CA  ARG A 195 " =    1.065
peak=    3.266 closest distance to " O   HOH Z 112 " =    1.653
peak=    3.260 closest distance to " CG2 THR A 220 " =    0.809
peak=    3.258 closest distance to " O   HOH Z 291 " =    1.290
peak=    3.258 closest distance to " N   GLY A  75 " =    1.310
peak=    3.257 closest distance to " O   HOH Z 221 " =    1.139
peak=    3.255 closest distance to " OE1 GLN A  73 " =    1.701
peak=    3.254 closest distance to " CB  GLU A   2 " =    1.071
peak=    3.251 closest distance to " O   HOH Z 112 " =    1.959
peak=    3.245 closest distance to " O   HOH Z 428 " =    1.298
peak=    3.242 closest distance to " CD  PRO A 213 " =    1.398
peak=    3.240 closest distance to " CD2 HIS A  81 " =    1.472
peak=    3.235 closest distance to " O   HOH Z 258 " =    1.680
peak=    3.234 closest distance to " O   HOH Z 156 " =    3.153
peak=    3.231 closest distance to " N   ARG A 156 " =    1.577
peak=    3.230 closest distance to " O   HOH Z  71 " =    1.726
peak=    3.229 closest distance to " O   HOH Z 303 " =    1.678
peak=    3.225 closest distance to " O   SER A 273 " =    1.446
peak=    3.225 closest distance to " O   HOH Z 296 " =    1.668
peak=    3.224 closest distance to " O   HOH Z 427 " =    3.803
peak=    3.222 closest distance to " CB  ASN A 148 " =    2.060
peak=    3.221 closest distance to " CA  CYS A 260 " =    0.996
peak=    3.219 closest distance to " O   HOH Z 156 " =    2.297
peak=    3.217 closest distance to " CB  ALA A 114 " =    1.380
peak=    3.215 closest distance to " O   HOH Z  89 " =    1.908
peak=    3.213 closest distance to " CA  SER A  12 " =    1.305
peak=    3.213 closest distance to " CD  LYS A 289 " =    1.036
peak=    3.210 closest distance to " O   HOH Z 141 " =    1.400
peak=    3.209 closest distance to " O   HOH Z 383 " =    1.978
peak=    3.207 closest distance to " O   HOH Z  15 " =    1.128
peak=    3.197 closest distance to " O   HOH Z  49 " =    1.551
peak=    3.197 closest distance to " CB  LEU A  83 " =    0.797
peak=    3.192 closest distance to " O   HOH Z 129 " =    3.127
peak=    3.189 closest distance to " O   HOH Z 136 " =    1.211
peak=    3.186 closest distance to " O   HOH Z 332 " =    1.158
peak=    3.185 closest distance to " O   HOH Z 189 " =    1.820
peak=    3.184 closest distance to " O   HOH Z 250 " =    1.918
peak=    3.184 closest distance to " O   HOH Z 138 " =    1.353
peak=    3.180 closest distance to " CD2 LEU A 297 " =    1.093
peak=    3.179 closest distance to " CB  TRP A 123 " =    1.378
peak=    3.175 closest distance to " O   HOH Z  35 " =    1.767
peak=    3.173 closest distance to " CG2 VAL A 126 " =    1.219
peak=    3.171 closest distance to " O   HOH Z 299 " =    1.497
peak=    3.166 closest distance to " O   HOH Z 350 " =    1.266
peak=    3.164 closest distance to " NE BARG A 145 " =    0.803
peak=    3.163 closest distance to " N   LYS A 166 " =    0.915
peak=    3.158 closest distance to " CB  ARG A 139 " =    0.897
peak=    3.157 closest distance to " O   THR A 251 " =    1.291
peak=    3.156 closest distance to " O   HOH Z 419 " =    2.272
peak=    3.144 closest distance to " CB  PRO A  90 " =    1.466
peak=    3.144 closest distance to " N   PHE A 130 " =    1.303
peak=    3.134 closest distance to " NH1AARG A 275 " =    2.302
peak=    3.129 closest distance to " O   HOH Z 142 " =    1.401
peak=    3.126 closest distance to " O   HOH Z 413 " =    5.503
peak=    3.125 closest distance to " CB  ALA A  34 " =    1.111
peak=    3.119 closest distance to " CG  MET A 113 " =    1.438
peak=    3.118 closest distance to " CB  ALA A  71 " =    0.992
peak=    3.111 closest distance to " O   HOH Z 130 " =    2.548
peak=    3.110 closest distance to " O   ILE A 234 " =    1.544
peak=    3.102 closest distance to " OD2 ASP A  50 " =    1.011
peak=    3.101 closest distance to " CB  ASP A 191 " =    1.233
peak=    3.101 closest distance to " CA  THR A 246 " =    1.114
peak=    3.097 closest distance to " CA  LEU A 282 " =    1.109
peak=    3.096 closest distance to " OG  SER A  62 " =    2.840
peak=    3.092 closest distance to " O   HOH Z 425 " =    3.522
peak=    3.088 closest distance to " O   HOH Z 259 " =    1.738
peak=    3.086 closest distance to " O   HOH Z 147 " =    1.219
peak=    3.085 closest distance to " CA  SER A  62 " =    0.862
peak=    3.065 closest distance to " O   HOH Z  26 " =    1.176
peak=    3.062 closest distance to " CA  ASN A  74 " =    0.881
peak=    3.057 closest distance to " OG1 THR A 294 " =    4.030
peak=    3.039 closest distance to " CZ2 TRP A 150 " =    1.171
peak=    3.026 closest distance to " CB  GLN A 223 " =    1.493
peak=    3.025 closest distance to " O   HOH Z 120 " =    2.050

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.357 - 5.338
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 211
   mapped sites are within: 0.726 - 5.338

peak=   -5.129 closest distance to " O   HOH Z  52 " =    0.794
peak=   -4.750 closest distance to " CZ  ARG A  36 " =    1.180
peak=   -4.685 closest distance to " O   HOH Z 159 " =    0.980
peak=   -4.600 closest distance to " N   VAL A  72 " =    0.953
peak=   -4.532 closest distance to " CD2 LEU A 237 " =    2.376
peak=   -4.474 closest distance to " CG  ASP A 286 " =    0.938
peak=   -4.397 closest distance to " O   HOH Z 120 " =    0.959
peak=   -4.369 closest distance to " O   GLN A  11 " =    0.888
peak=   -4.349 closest distance to " CD1 TRP A 179 " =    1.019
peak=   -4.234 closest distance to " O   HOH Z 221 " =    1.233
peak=   -4.230 closest distance to " O   PRO A 198 " =    1.290
peak=   -4.219 closest distance to " OG  SER A  63 " =    1.092
peak=   -4.189 closest distance to " N   ARG A 275 " =    1.098
peak=   -4.165 closest distance to " O   VAL A 174 " =    1.895
peak=   -4.142 closest distance to " O   HOH Z 117 " =    0.726
peak=   -4.132 closest distance to " O   HOH Z 147 " =    0.870
peak=   -4.118 closest distance to " OG ASER A 216 " =    1.119
peak=   -4.114 closest distance to " O   HOH Z  52 " =    1.979
peak=   -4.094 closest distance to " O   HOH Z  56 " =    0.934
peak=   -4.077 closest distance to " O   TRP A  92 " =    2.012
peak=   -4.040 closest distance to " O  BHOH Z 338 " =    1.481
peak=   -4.037 closest distance to " O   HOH Z 198 " =    0.950
peak=   -4.033 closest distance to " CG BARG A 275 " =    1.315
peak=   -4.007 closest distance to " CD  GLN A 223 " =    0.972
peak=   -4.000 closest distance to " O   HOH Z 266 " =    4.230
peak=   -3.997 closest distance to " O   HOH Z 137 " =    1.363
peak=   -3.995 closest distance to " N   GLY A 133 " =    1.906
peak=   -3.981 closest distance to " O   THR A  52 " =    2.223
peak=   -3.968 closest distance to " OD1 ASN A 285 " =    0.891
peak=   -3.958 closest distance to " C   SER A 271 " =    1.302
peak=   -3.957 closest distance to " CB  GLN A  73 " =    0.894
peak=   -3.936 closest distance to " CB  SER A  26 " =    1.186
peak=   -3.927 closest distance to " CD1 PHE A  59 " =    1.792
peak=   -3.886 closest distance to " O   HOH Z 424 " =    0.984
peak=   -3.865 closest distance to " O   HOH Z  13 " =    1.668
peak=   -3.860 closest distance to " CE  MET A  93 " =    1.217
peak=   -3.850 closest distance to " O   HOH Z 400 " =    0.892
peak=   -3.850 closest distance to " O   GLN A  58 " =    0.850
peak=   -3.849 closest distance to " C   ASN A 285 " =    2.383
peak=   -3.849 closest distance to " SG  CYS A 254 " =    3.096
peak=   -3.846 closest distance to " O   HOH Z 380 " =    4.275
peak=   -3.841 closest distance to " OD1 ASN A 301 " =    0.819
peak=   -3.814 closest distance to " CD  LYS A 289 " =    2.347
peak=   -3.785 closest distance to " O   HOH Z 150 " =    1.968
peak=   -3.784 closest distance to " CA  SER A 164 " =    1.724
peak=   -3.775 closest distance to " O   VAL A 197 " =    1.035
peak=   -3.773 closest distance to " O   HOH Z 120 " =    1.007
peak=   -3.761 closest distance to " C   THR A 279 " =    1.158
peak=   -3.753 closest distance to " N   SER A 134 " =    1.105
peak=   -3.742 closest distance to " O   HOH Z 196 " =    1.765
peak=   -3.719 closest distance to " O   HOH Z 130 " =    2.097
peak=   -3.718 closest distance to " SD  MET A 105 " =    2.311
peak=   -3.714 closest distance to " NE  ARG A 156 " =    1.854
peak=   -3.710 closest distance to " O   HOH Z 423 " =    2.631
peak=   -3.703 closest distance to " CG2 THR A 182 " =    2.260
peak=   -3.691 closest distance to " O   HOH Z 281 " =    2.596
peak=   -3.689 closest distance to " O   HOH Z 422 " =    0.735
peak=   -3.684 closest distance to " O   HOH Z  84 " =    0.779
peak=   -3.682 closest distance to " O   HOH Z 391 " =    1.258
peak=   -3.672 closest distance to " O   LEU A 300 " =    2.384
peak=   -3.669 closest distance to " O   HOH Z 233 " =    2.225
peak=   -3.662 closest distance to " N   PHE A  59 " =    1.173
peak=   -3.661 closest distance to " O   ASN A 285 " =    1.056
peak=   -3.660 closest distance to " O   HOH Z 422 " =    0.982
peak=   -3.640 closest distance to " CG2 ILE A  20 " =    2.870
peak=   -3.620 closest distance to " OD1 ASP A 191 " =    2.023
peak=   -3.611 closest distance to " O   HOH Z  24 " =    1.084
peak=   -3.594 closest distance to " O   HOH Z 418 " =    1.440
peak=   -3.593 closest distance to " C   GLY A  91 " =    1.343
peak=   -3.593 closest distance to " O   HOH Z 193 " =    1.208
peak=   -3.583 closest distance to " CG  GLN A  58 " =    1.421
peak=   -3.575 closest distance to " N   GLY A  17 " =    1.298
peak=   -3.573 closest distance to " SD  MET A 188 " =    1.098
peak=   -3.572 closest distance to " O   HOH Z  37 " =    1.572
peak=   -3.563 closest distance to " O   LYS A 289 " =    0.824
peak=   -3.560 closest distance to " CA  ALA A 114 " =    1.016
peak=   -3.555 closest distance to " CB  LEU A 167 " =    1.993
peak=   -3.553 closest distance to " C   VAL A 265 " =    1.080
peak=   -3.549 closest distance to " CG2 THR A 279 " =    1.447
peak=   -3.544 closest distance to " O   HOH Z 145 " =    2.417
peak=   -3.526 closest distance to " O   HOH Z 176 " =    1.118
peak=   -3.516 closest distance to " CA  SER A 288 " =    1.225
peak=   -3.504 closest distance to " O   ALA A   1 " =    2.178
peak=   -3.500 closest distance to " O   HOH Z  39 " =    0.751
peak=   -3.496 closest distance to " O   HOH Z 197 " =    1.941
peak=   -3.494 closest distance to " CD  GLN A  77 " =    1.054
peak=   -3.492 closest distance to " NE1 TRP A 177 " =    2.134
peak=   -3.491 closest distance to " OXT GLY A 302 " =    2.591
peak=   -3.491 closest distance to " O   HOH Z  11 " =    1.323
peak=   -3.491 closest distance to " O   HOH Z 165 " =    1.853
peak=   -3.486 closest distance to " CG1AVAL A  41 " =    2.594
peak=   -3.485 closest distance to " CG  PRO A 163 " =    1.219
peak=   -3.481 closest distance to " O   HOH Z 393 " =    0.959
peak=   -3.479 closest distance to " O   HOH Z 400 " =    1.094
peak=   -3.475 closest distance to " OD2 ASP A 171 " =    1.505
peak=   -3.470 closest distance to " N   ARG A 275 " =    1.260
peak=   -3.459 closest distance to " OG  SER A   3 " =    1.861
peak=   -3.453 closest distance to " O   HOH Z 135 " =    1.642
peak=   -3.451 closest distance to " O   HOH Z 427 " =    0.935
peak=   -3.441 closest distance to " O   MET A  40 " =    2.514
peak=   -3.430 closest distance to " O   HOH Z 126 " =    2.165
peak=   -3.427 closest distance to " CD2 TYR A  30 " =    2.683
peak=   -3.406 closest distance to " CD1 TRP A  85 " =    0.877
peak=   -3.402 closest distance to " O   HOH Z 118 " =    4.159
peak=   -3.393 closest distance to " NH2 ARG A 156 " =    1.053
peak=   -3.388 closest distance to " O   SER A  26 " =    1.475
peak=   -3.382 closest distance to " O   HOH Z 109 " =    2.893
peak=   -3.381 closest distance to " CB  ALA A  43 " =    2.604
peak=   -3.377 closest distance to " O   HOH Z 120 " =    1.580
peak=   -3.377 closest distance to " ND2 ASN A  39 " =    1.386
peak=   -3.364 closest distance to " O   HOH Z 222 " =    1.142
peak=   -3.361 closest distance to " C   HIS A 108 " =    1.035
peak=   -3.355 closest distance to " N   GLY A  75 " =    1.147
peak=   -3.340 closest distance to " OG  SER A 273 " =    1.979
peak=   -3.337 closest distance to " O   HOH Z 428 " =    1.259
peak=   -3.332 closest distance to " O   HOH Z  88 " =    4.240
peak=   -3.330 closest distance to " O   THR A  31 " =    1.306
peak=   -3.329 closest distance to " OXT GLY A 302 " =    3.289
peak=   -3.319 closest distance to " O   HOH Z  46 " =    1.380
peak=   -3.316 closest distance to " N   LYS A 290 " =    0.795
peak=   -3.314 closest distance to " O   HOH Z  60 " =    0.809
peak=   -3.313 closest distance to " O   HOH Z 423 " =    2.841
peak=   -3.309 closest distance to " CE  MET A 105 " =    1.983
peak=   -3.308 closest distance to " CG  PRO A 243 " =    1.612
peak=   -3.305 closest distance to " NE2 GLN A  88 " =    2.152
peak=   -3.302 closest distance to " CD2 LEU A 143 " =    2.383
peak=   -3.300 closest distance to " N   VAL A 125 " =    1.851
peak=   -3.293 closest distance to " O   HOH Z 384 " =    2.035
peak=   -3.289 closest distance to " O   HOH Z  71 " =    1.255
peak=   -3.285 closest distance to " OG  SER A 206 " =    1.443
peak=   -3.285 closest distance to " O   HOH Z 424 " =    1.962
peak=   -3.272 closest distance to " O   HOH Z 320 " =    1.739
peak=   -3.272 closest distance to " O   HOH Z 395 " =    4.967
peak=   -3.264 closest distance to " C   PHE A  59 " =    2.461
peak=   -3.262 closest distance to " O   HOH Z 405 " =    1.515
peak=   -3.259 closest distance to " OD2 ASP A 162 " =    1.374
peak=   -3.258 closest distance to " OD2 ASP A 298 " =    1.005
peak=   -3.257 closest distance to " O   ARG A 275 " =    0.965
peak=   -3.253 closest distance to " NH1 ARG A 195 " =    2.541
peak=   -3.251 closest distance to " CG  TYR A 169 " =    2.084
peak=   -3.250 closest distance to " OD2 ASP A  27 " =    0.979
peak=   -3.249 closest distance to " CG  ASP A 231 " =    0.784
peak=   -3.248 closest distance to " CG  ASN A 252 " =    1.473
peak=   -3.232 closest distance to " O   HOH Z  91 " =    2.244
peak=   -3.226 closest distance to " CB  ALA A 244 " =    1.904
peak=   -3.225 closest distance to " O   HOH Z 102 " =    0.815
peak=   -3.225 closest distance to " O   PHE A 218 " =    1.386
peak=   -3.225 closest distance to " O   SER A 146 " =    0.893
peak=   -3.220 closest distance to " CB BSER A 164 " =    1.052
peak=   -3.217 closest distance to " O   LEU A 222 " =    1.355
peak=   -3.214 closest distance to " CD1 ILE A 109 " =    2.813
peak=   -3.210 closest distance to " O   HOH Z 109 " =    5.338
peak=   -3.209 closest distance to " O   HOH Z 100 " =    0.742
peak=   -3.207 closest distance to " CD1 ILE A 263 " =    1.959
peak=   -3.204 closest distance to " O   HOH Z  55 " =    1.580
peak=   -3.201 closest distance to " O   HOH Z 151 " =    1.678
peak=   -3.198 closest distance to " O   HOH Z  30 " =    0.965
peak=   -3.198 closest distance to " O   HOH Z  42 " =    0.899
peak=   -3.194 closest distance to " ND2 ASN A  69 " =    1.685
peak=   -3.190 closest distance to " CA  GLN A  58 " =    1.011
peak=   -3.189 closest distance to " CD1 ILE A 109 " =    2.181
peak=   -3.187 closest distance to " CD  GLN A  73 " =    0.978
peak=   -3.186 closest distance to " CD  PRO A 213 " =    2.222
peak=   -3.185 closest distance to " O   HOH Z 188 " =    2.340
peak=   -3.183 closest distance to " O   HOH Z 156 " =    2.184
peak=   -3.176 closest distance to " CB  SER A 210 " =    1.020
peak=   -3.168 closest distance to " CB  ALA A 161 " =    2.396
peak=   -3.167 closest distance to " O   HOH Z 121 " =    3.543
peak=   -3.156 closest distance to " O   HOH Z 351 " =    1.542
peak=   -3.153 closest distance to " O   HOH Z 363 " =    2.471
peak=   -3.150 closest distance to " CB  ASP A 132 " =    2.333
peak=   -3.149 closest distance to " O   HOH Z 235 " =    1.012
peak=   -3.147 closest distance to " O   HOH Z  62 " =    1.400
peak=   -3.143 closest distance to " OE1 GLN A 183 " =    0.851
peak=   -3.136 closest distance to " CD1 ILE A 151 " =    2.172
peak=   -3.135 closest distance to " O   HOH Z 250 " =    1.399
peak=   -3.133 closest distance to " O   HOH Z 212 " =    2.586
peak=   -3.130 closest distance to " OD1 ASN A 148 " =    1.495
peak=   -3.129 closest distance to " SD  MET A  93 " =    1.817
peak=   -3.120 closest distance to " O   HOH Z 234 " =    3.933
peak=   -3.119 closest distance to " CZ  PHE A 225 " =    1.863
peak=   -3.118 closest distance to " O   HOH Z  44 " =    2.447
peak=   -3.117 closest distance to " O   HOH Z 231 " =    0.780
peak=   -3.115 closest distance to " O   HOH Z 231 " =    1.007
peak=   -3.108 closest distance to " CD  GLU A   2 " =    1.577
peak=   -3.107 closest distance to " O   SER A  95 " =    1.736
peak=   -3.106 closest distance to " OG  SER A  97 " =    2.088
peak=   -3.105 closest distance to " O   HOH Z  35 " =    1.968
peak=   -3.103 closest distance to " O   HOH Z  65 " =    1.125
peak=   -3.101 closest distance to " CD2 TRP A 179 " =    1.106
peak=   -3.097 closest distance to " C   LEU A   5 " =    1.340
peak=   -3.097 closest distance to " OD1 ASN A 176 " =    1.549
peak=   -3.094 closest distance to " CG2 VAL A 189 " =    2.141
peak=   -3.093 closest distance to " O   GLY A 241 " =    2.124
peak=   -3.091 closest distance to " O   HOH Z 283 " =    1.189
peak=   -3.083 closest distance to " CG2 VAL A 232 " =    2.086
peak=   -3.083 closest distance to " O   HOH Z 166 " =    1.337
peak=   -3.082 closest distance to " CG AARG A 102 " =    1.931
peak=   -3.071 closest distance to " N   ALA A  43 " =    2.320
peak=   -3.055 closest distance to " C   SER A 206 " =    1.457
peak=   -3.045 closest distance to " O   HOH Z 424 " =    3.490
peak=   -3.040 closest distance to " C   GLN A 144 " =    0.792
peak=   -3.037 closest distance to " CE  MET A 105 " =    2.110

================= 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    :  0.5057 0.5047   6.305681e+00   6.301482e+00
   1_bss:  0.4997 0.4962   6.303392e+00   6.295429e+00
   1_xyz:  0.4117 0.4364   6.198047e+00   6.232571e+00
   1_adp:  0.3696 0.4425   5.975521e+00   6.058438e+00
   1_occ:  0.3693 0.4419   5.974953e+00   6.058577e+00
   2_bss:  0.3685 0.4403   5.974081e+00   6.058080e+00
   2_xyz:  0.3182 0.3907   6.034055e+00   6.165485e+00
   2_adp:  0.2965 0.3804   6.002826e+00   6.154640e+00
   2_occ:  0.2962 0.3805   6.002173e+00   6.154308e+00
   3_bss:  0.2966 0.3800   6.002992e+00   6.153237e+00
   3_xyz:  0.2615 0.3423   5.892326e+00   6.071234e+00
   3_adp:  0.2538 0.3156   5.851591e+00   6.010112e+00
   3_occ:  0.2536 0.3155   5.851050e+00   6.009958e+00
   4_bss:  0.2527 0.3152   5.850459e+00   6.008153e+00
   4_xyz:  0.2083 0.2586   5.673415e+00   5.847992e+00
   4_adp:  0.1916 0.2465   5.611817e+00   5.800874e+00
   4_occ:  0.1914 0.2464   5.611488e+00   5.801147e+00
   5_bss:  0.1911 0.2459   5.612157e+00   5.800791e+00
   5_xyz:  0.1560 0.2100   5.433302e+00   5.643176e+00
   5_adp:  0.1496 0.1977   5.386545e+00   5.585739e+00
   5_occ:  0.1494 0.1977   5.385924e+00   5.585570e+00
   5_bss:  0.1497 0.1973   5.388182e+00   5.585377e+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:  0.300  20.000  -1.234   2.654  -0.012   0.000  -0.000  -0.000
   1_xyz:  0.300  20.000  -1.234   2.654  -0.012   0.000  -0.000  -0.000
   1_adp:  0.300  20.000  -1.234   2.654  -0.012   0.000  -0.000  -0.000
   1_occ:  0.300  20.000  -1.234   2.654  -0.012   0.000  -0.000  -0.000
   2_bss:  0.318  50.167  -0.831   2.148   0.449   0.000   0.000   0.000
   2_xyz:  0.318  50.167  -0.831   2.148   0.449   0.000   0.000   0.000
   2_adp:  0.318  50.167  -0.831   2.148   0.449   0.000   0.000   0.000
   2_occ:  0.318  50.167  -0.831   2.148   0.449   0.000   0.000   0.000
   3_bss:  0.318  50.167  -0.746   1.806   0.775   0.000   0.000   0.000
   3_xyz:  0.318  50.167  -0.746   1.806   0.775   0.000   0.000   0.000
   3_adp:  0.318  50.167  -0.746   1.806   0.775   0.000   0.000   0.000
   3_occ:  0.318  50.167  -0.746   1.806   0.775   0.000   0.000   0.000
   4_bss:  0.304  40.017  -2.094   0.382  -0.745   0.000  -0.000  -0.000
   4_xyz:  0.304  40.017  -2.094   0.382  -0.745   0.000  -0.000  -0.000
   4_adp:  0.304  40.017  -2.094   0.382  -0.745   0.000  -0.000  -0.000
   4_occ:  0.304  40.017  -2.094   0.382  -0.745   0.000  -0.000  -0.000
   5_bss:  0.304  40.017  -3.015  -0.600  -1.600  -0.000  -0.000  -0.000
   5_xyz:  0.304  40.017  -3.015  -0.600  -1.600  -0.000  -0.000  -0.000
   5_adp:  0.304  40.017  -3.015  -0.600  -1.600  -0.000  -0.000  -0.000
   5_occ:  0.304  40.017  -3.015  -0.600  -1.600  -0.000  -0.000  -0.000
   5_bss:  0.309  39.958  -3.406  -1.272  -1.903  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  65.814 0.3183  0.4393    83974.065
   1_bss:  64.818 0.3302  0.4685    81385.212
   1_xyz:  52.196 0.4922  0.6831    58542.231
   1_adp:  53.540 0.4745  0.6789    60269.179
   1_occ:  53.620 0.4734  0.6754    60212.919
   2_bss:  53.498 0.4747  0.6827    59661.170
   2_xyz:  44.942 0.5809  0.8313    44283.106
   2_adp:  43.476 0.5992  0.8366    42611.832
   2_occ:  43.445 0.5996  0.8363    42539.441
   3_bss:  43.447 0.5996  0.8368    42527.875
   3_xyz:  37.083 0.6759  0.9291    32448.063
   3_adp:  32.760 0.7274  0.9736    27191.636
   3_occ:  32.714 0.7279  0.9745    27167.455
   4_bss:  32.617 0.7289  0.9259    26995.580
   4_xyz:  26.170 0.7990  0.9853    17789.455
   4_adp:  24.453 0.8174  0.9894    15999.424
   4_occ:  24.453 0.8174  0.9896    16017.745
   5_bss:  24.433 0.8177  0.9571    16012.618
   5_xyz:  20.047 0.8610  0.9860    11053.626
   5_adp:  18.557 0.8756  0.9891     9921.135
   5_occ:  18.549 0.8757  0.9891     9921.474
   5_bss:  18.551 0.8757  0.9711     9936.740
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.106   2.5836e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.106   2.5836e-01
   1_xyz:   1.807  0.014  0.104 16.898  0.007  4.103   1.8014e-01
   1_adp:   1.807  0.014  0.104 16.898  0.007  4.103   1.8014e-01
   1_occ:   1.807  0.014  0.104 16.898  0.007  4.103   1.8014e-01
   2_bss:   1.807  0.014  0.104 16.898  0.007  4.103   1.8014e-01
   2_xyz:   1.397  0.009  0.088 15.543  0.006  4.107   1.0672e-01
   2_adp:   1.397  0.009  0.088 15.543  0.006  4.107   1.0672e-01
   2_occ:   1.397  0.009  0.088 15.543  0.006  4.107   1.0672e-01
   3_bss:   1.397  0.009  0.088 15.543  0.006  4.107   1.0672e-01
   3_xyz:   1.032  0.007  0.070 15.215  0.004  4.117   6.8374e-02
   3_adp:   1.032  0.007  0.070 15.215  0.004  4.117   6.8374e-02
   3_occ:   1.032  0.007  0.070 15.215  0.004  4.117   6.8374e-02
   4_bss:   1.032  0.007  0.070 15.215  0.004  4.117   6.8374e-02
   4_xyz:   1.087  0.006  0.073 14.604  0.005  4.112   6.5320e-02
   4_adp:   1.087  0.006  0.073 14.604  0.005  4.112   6.5320e-02
   4_occ:   1.087  0.006  0.073 14.604  0.005  4.112   6.5320e-02
   5_bss:   1.087  0.006  0.073 14.604  0.005  4.112   6.5320e-02
   5_xyz:   1.018  0.007  0.067 14.828  0.004  4.110   6.4026e-02
   5_adp:   1.018  0.007  0.067 14.828  0.004  4.110   6.4026e-02
   5_occ:   1.018  0.007  0.067 14.828  0.004  4.110   6.4026e-02
   5_bss:   1.018  0.007  0.067 14.828  0.004  4.110   6.4026e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  0.955   2.4630e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  0.955   2.4630e-01
   1_xyz:  12.078  0.100  0.458 83.865  0.049  1.967   1.1284e-01
   1_adp:  12.078  0.100  0.458 83.865  0.049  1.967   1.1284e-01
   1_occ:  12.078  0.100  0.458 83.865  0.049  1.967   1.1284e-01
   2_bss:  12.078  0.100  0.458 83.865  0.049  1.967   1.1284e-01
   2_xyz:   9.652  0.072  0.301 84.237  0.055  2.159   9.0205e-02
   2_adp:   9.652  0.072  0.301 84.237  0.055  2.159   9.0205e-02
   2_occ:   9.652  0.072  0.301 84.237  0.055  2.159   9.0205e-02
   3_bss:   9.652  0.072  0.301 84.237  0.055  2.159   9.0205e-02
   3_xyz:   7.739  0.069  0.306 85.150  0.037  2.262   6.6724e-02
   3_adp:   7.739  0.069  0.306 85.150  0.037  2.262   6.6724e-02
   3_occ:   7.739  0.069  0.306 85.150  0.037  2.262   6.6724e-02
   4_bss:   7.739  0.069  0.306 85.150  0.037  2.262   6.6724e-02
   4_xyz:   7.738  0.045  0.197 78.536  0.052  2.267   5.6877e-02
   4_adp:   7.738  0.045  0.197 78.536  0.052  2.267   5.6877e-02
   4_occ:   7.738  0.045  0.197 78.536  0.052  2.267   5.6877e-02
   5_bss:   7.738  0.045  0.197 78.536  0.052  2.267   5.6877e-02
   5_xyz:   7.825  0.047  0.219 78.602  0.042  2.347   1.0684e-01
   5_adp:   7.825  0.047  0.219 78.602  0.042  2.347   1.0684e-01
   5_occ:   7.825  0.047  0.219 78.602  0.042  2.347   1.0684e-01
   5_bss:   7.825  0.047  0.219 78.602  0.042  2.347   1.0684e-01
------------------------------------------------------------------------
           |-----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:  99.15   0.00  21.80  91.73   0.00  18.62  99.15   0.00  39.09
   1_occ:  99.15   0.00  21.80  91.73   0.00  18.62  99.15   0.00  39.09
   2_bss:  99.15   0.00  21.80  91.73   0.00  18.62  99.15   0.00  39.09
   2_xyz:  99.15   0.00  21.80  91.73   0.00  18.62  99.15   0.00  39.09
   2_adp: 133.43   0.00  22.45 133.43   0.00  18.82 116.16   0.00  42.20
   2_occ: 133.43   0.00  22.45 133.43   0.00  18.82 116.16   0.00  42.20
   3_bss: 133.43   0.00  22.45 133.43   0.00  18.82 116.16   0.00  42.20
   3_xyz: 133.43   0.00  22.45 133.43   0.00  18.82 116.16   0.00  42.20
   3_adp: 125.57   0.00  19.81 125.57   0.00  16.14 110.09   2.89  39.80
   3_occ: 125.57   0.00  19.81 125.57   0.00  16.14 110.09   2.89  39.80
   4_bss: 125.57   0.00  19.81 125.57   0.00  16.14 110.09   2.89  39.80
   4_xyz: 125.57   0.00  19.81 125.57   0.00  16.14 110.09   2.89  39.80
   4_adp: 107.78   0.00  19.11 107.78   0.00  14.63 104.21   5.27  43.53
   4_occ: 107.78   0.00  19.11 107.78   0.00  14.63 104.21   5.27  43.53
   5_bss: 107.78   0.00  19.11 107.78   0.00  14.63 104.21   5.27  43.53
   5_xyz: 107.78   0.00  19.11 107.78   0.00  14.63 104.21   5.27  43.53
   5_adp: 101.96   1.64  18.29 100.55   1.64  13.83 101.96   3.65  42.53
   5_occ: 101.96   1.64  18.29 100.55   1.64  13.83 101.96   3.65  42.53
   5_bss: 101.90   1.59  18.23 100.50   1.59  13.77 101.90   3.59  42.47
------------------------------------------------------------------------
 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:    4.075    0.028    0.425
   1_adp:    4.075    0.028    0.425
   1_occ:    4.075    0.028    0.425
   2_bss:    4.075    0.028    0.425
   2_xyz:    2.907    0.053    0.613
   2_adp:    2.907    0.053    0.613
   2_occ:    2.907    0.053    0.613
   3_bss:    2.907    0.053    0.613
   3_xyz:    3.127    0.092    0.732
   3_adp:    3.127    0.092    0.732
   3_occ:    3.127    0.092    0.732
   4_bss:    3.127    0.092    0.732
   4_xyz:    2.911    0.090    0.843
   4_adp:    2.911    0.090    0.843
   4_occ:    2.911    0.090    0.843
   5_bss:    2.911    0.090    0.843
   5_xyz:    2.900    0.075    0.929
   5_adp:    2.900    0.075    0.929
   5_occ:    2.900    0.075    0.929
   5_bss:    2.900    0.075    0.929
------------------------------------------------------------------------

CPU time actual refinement: 348.64


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_111/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_111/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_111/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_111/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_111/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 348.48 
  Macro-tasks:
    bulk solvent and scale       = 43.77  
    individual site refinement   = 152.73 
    weights calculation          = 31.99  
    collect and process          = 6.55   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 235.16 
  Micro-tasks:
    mask                            = 3.04   
    f_calc                          = 109.20 
    alpha_beta                      = 8.56   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 118.88 
    fmodel                         = 7.38   
    r_factors                      = 0.24   
    phase_errors                   = 10.06  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 258.84 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.915 micro seconds
Total CPU time: 6.03 minutes
from_scatterers_fft:    610 calls, 108.71 s
gradients_fft:          555 calls, 105.33 s

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

# Date 2008-01-16 Time 04:02:34 PST -0800 (1200484954.17 s)
Start R-work = 0.5057, R-free = 0.5047 (no bulk solvent and anisotropic scale)
Final R-work = 0.1733, R-free = 0.2185 (no bulk solvent and anisotropic scale)

Start R-work = 0.4997, R-free = 0.4962
Final R-work = 0.1497, R-free = 0.1973