# Date 2008-01-16 Time 03:52:38 PST -0800 (1200484358.80 s)
#phil __OFF__

Command line arguments: "../86.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1226
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 86

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.4938, 47.3993, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.30, 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, 47.3993, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8784 1.95098
Completeness in resolution range: 0.912389
Completeness with d_max=infinity: 0.909678

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8784
                             d_min =   1.9510

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 47.3993, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8784 1.95098
Completeness in resolution range: 0.912389
Completeness with d_max=infinity: 0.909678

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8788 -  4.1752 [2247/2275]  2016   231  10.3%
  bin  2:  4.1752 -  3.3262 [2168/2191]  1955   213   9.8%
  bin  3:  3.3262 -  2.9093 [2142/2167]  1931   211   9.9%
  bin  4:  2.9093 -  2.6449 [2115/2131]  1901   214  10.1%
  bin  5:  2.6449 -  2.4562 [2089/2133]  1872   217  10.4%
  bin  6:  2.4562 -  2.3120 [2110/2138]  1907   203   9.6%
  bin  7:  2.3120 -  2.1966 [2072/2108]  1868   204   9.8%
  bin  8:  2.1966 -  2.1012 [2077/2119]  1874   203   9.8%
  bin  9:  2.1012 -  2.0205 [1972/2091]  1777   195   9.9%
  bin 10:  2.0205 -  1.9510 [ 597/2117]   529    68  11.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_86/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.07 -     1.84: 14
        1.84 -     2.60: 77
        2.60 -     3.37: 4173
        3.37 -     4.13: 9392
        4.13 -     4.90: 14731
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.072 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.133 3.040 -x+1,y-1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.248 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.349 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  57 " - " O   HOH Z 104 "  1.383 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28382 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_86/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_86/model_refine_001.geo

CPU time processing inputs: 9.58


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.49375 47.3993 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4515   r_free= 0.4527   ksol= 0.00   Bsol= 0.00   scale= 0.903    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.256127                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8788 -  4.6571 0.99   1463  161 0.3439 0.3648      6.5102      6.5387|
|  2:  4.6571 -  3.7154 0.99   1419  155 0.3779 0.3773      6.7307      6.7632|
|  3:  3.7154 -  3.2513 0.99   1370  159 0.4279 0.4248      6.6255      6.6504|
|  4:  3.2513 -  2.9566 0.99   1380  144 0.4463 0.4511       6.462       6.474|
|  5:  2.9566 -  2.7461 0.98   1359  152 0.4762 0.4657      6.3276      6.3669|
|  6:  2.7461 -  2.5851 0.99   1356  155 0.4786 0.5118      6.2445      6.1651|
|  7:  2.5851 -  2.4562 0.98   1328  160 0.4867 0.4081      6.1913      6.1167|
|  8:  2.4562 -  2.3497 0.99   1353  142 0.5153 0.5265      6.1591      6.1515|
|  9:  2.3497 -  2.2596 0.99   1356  147 0.5133 0.4859      6.1056      6.1527|
| 10:  2.2596 -  2.1819 0.98   1347  147 0.5130 0.5278      6.0725      6.0811|
| 11:  2.1819 -  2.1139 0.97   1315  152 0.5226 0.5193      5.9975      6.0195|
| 12:  2.1139 -  2.0536 0.99   1323  149 0.5087 0.5141      5.9362      5.9253|
| 13:  2.0536 -  1.9997 0.75   1030  107 0.5020 0.5284      5.8625      5.8201|
| 14:  1.9997 -  1.9510 0.17    231   29 0.4980 0.5230      5.9141      5.7531|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8788 -  4.6571  1463   161  0.72  32.35   0.84     0.73      63804.33|
|  2:  4.6571 -  3.7154  1419   155  0.72  33.33   0.93     0.82      96105.49|
|  3:  3.7154 -  3.2513  1370   159  0.62  42.42   0.91     0.79     102411.35|
|  4:  3.2513 -  2.9566  1380   144  0.52  50.04   0.92     0.71      91668.77|
|  5:  2.9566 -  2.7461  1359   152  0.46  55.00   0.90     0.64      73476.33|
|  6:  2.7461 -  2.5851  1356   155  0.44  56.77   0.90     0.62      64096.89|
|  7:  2.5851 -  2.4562  1328   160  0.45  55.64   0.91     0.62      56314.46|
|  8:  2.4562 -  2.3497  1353   142  0.43  57.34   0.93     0.63      51103.80|
|  9:  2.3497 -  2.2596  1356   147  0.44  56.73   0.91     0.65      47470.46|
| 10:  2.2596 -  2.1819  1347   147  0.43  57.98   0.92     0.61      43108.30|
| 11:  2.1819 -  2.1139  1315   152  0.36  62.82   0.91     0.57      44579.19|
| 12:  2.1139 -  2.0536  1323   149  0.29  68.08   0.96     0.48      43929.52|
| 13:  2.0536 -  1.9997  1030   107  0.26  70.40   0.94     0.44      40323.58|
| 14:  1.9997 -  1.9510   231    29  0.33  64.75   1.00     0.43      30116.84|
|alpha:            min =        0.43 max =            0.82 mean =         0.64|
|beta:             min =    30116.84 max =       102411.35 mean =     63238.35|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           89.99 mean =        53.33|
|phase err.(test): min =        0.00 max =           89.81 mean =        53.52|
|-----------------------------------------------------------------------------|

============================== 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 = 8.970005              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.964   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.964494              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.377   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.072 -  1.455:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.455 -  1.837:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.837 -  2.220:       17 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.220 -  2.603:       60 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.603 -  2.986:     1806 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.986 -  3.369:     2367 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.369 -  3.751:     3894 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.751 -  4.134:     5498 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.134 -  4.517:     6539 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.517 -  4.900:     8192 |
|-----------------------------------------------------------------------------|
|-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 |        0.227 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.072 |       1.125 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    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 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4515   r_free= 0.4527   ksol= 0.00   Bsol= 0.00   scale= 0.903    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.256127                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4442   r_free= 0.4416   ksol= 0.31   Bsol= 35.99   scale= 0.947   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.11,-0.69,3.10,-0.00,0.00,0.00); trace/3= 0.77                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.248551                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.558128              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.607   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.097081              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.983   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4442      final r-factor (work) = 0.3181          |
| start r-factor (free) = 0.4416      final r-factor (free) = 0.3462          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.8423 = 7.56 * 0.50 * 6.2491 + 1.00 * 0.2266                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.1896 = 7.56 * 0.50 * 6.1048 + 1.00 * 0.1193                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3181      final r-factor (work) = 0.2842          |
| start r-factor (free) = 0.3462      final r-factor (free) = 0.3548          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7035 = 1.10 * 1.00 * 6.1048 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5372 = 1.10 * 1.00 * 5.9423 + 1.00 * 0.0180                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.96   19.02    None  None   None       |
|    all(noH): 2823   0      0.00    99.96   19.02    None  None   None       |
|    Sol.    : 438    0      1.91    99.96   41.28    None  None   None       |
|    Mac.    : 2385   0      0.00    94.04   14.93    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 -   9.996:  949   |   5:    49.978 -  59.974:  112        |
|      1:     9.996 -  19.991:  934   |   6:    59.974 -  69.969:   39        |
|      2:    19.991 -  29.987:  415   |   7:    69.969 -  79.965:   28        |
|      3:    29.987 -  39.983:  203   |   8:    79.965 -  89.961:    8        |
|      4:    39.983 -  49.978:  130   |   9:    89.961 -  99.956:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2842 r_free = 0.3548             target_work(ml) = 5.951         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2839 r_free = 0.3551             target_work(ml) = 5.951         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2839   r_free= 0.3551   ksol= 0.31   Bsol= 35.99   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.11,-0.69,3.10,-0.00,0.00,0.00); trace/3= 0.77                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.951240                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2818   r_free= 0.3523   ksol= 0.33   Bsol= 57.42   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.63,-0.79,1.02,-0.00,0.00,0.00); trace/3= -0.47                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.945581                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.053952              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.207   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.335647              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.979  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2818      final r-factor (work) = 0.2021          |
| start r-factor (free) = 0.3523      final r-factor (free) = 0.2575          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.0765 = 7.05 * 0.50 * 5.9421 + 1.00 * 0.1190                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.6577 = 7.05 * 0.50 * 5.8340 + 1.00 * 0.0813                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2021      final r-factor (work) = 0.1878          |
| start r-factor (free) = 0.2575      final r-factor (free) = 0.2432          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9762 = 0.34 * 1.00 * 5.8340 + 1.00 * 0.0180                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9280 = 0.34 * 1.00 * 5.6160 + 1.00 * 0.0430                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.37   19.07    None  None   None       |
|    all(noH): 2823   0      0.00    99.37   19.07    None  None   None       |
|    Sol.    : 438    0      5.56    99.37   41.80    None  None   None       |
|    Mac.    : 2385   0      0.00    92.98   14.90    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 -   9.937:  884   |   5:    49.687 -  59.624:  103        |
|      1:     9.937 -  19.875: 1078   |   6:    59.624 -  69.562:   39        |
|      2:    19.875 -  29.812:  347   |   7:    69.562 -  79.499:   27        |
|      3:    29.812 -  39.750:  199   |   8:    79.499 -  89.437:    7        |
|      4:    39.750 -  49.687:  134   |   9:    89.437 -  99.374:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1878 r_free = 0.2432             target_work(ml) = 5.587         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1875 r_free = 0.2430             target_work(ml) = 5.586         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1875   r_free= 0.2430   ksol= 0.33   Bsol= 57.42   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.63,-0.79,1.02,-0.00,0.00,0.00); trace/3= -0.47                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.586004                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1867   r_free= 0.2414   ksol= 0.33   Bsol= 60.54   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.12,-1.75,-0.39,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.584747                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.441032              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.892  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.658460              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.685   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1867      final r-factor (work) = 0.1545          |
| start r-factor (free) = 0.2414      final r-factor (free) = 0.2025          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7480 = 3.44 * 0.50 * 5.6183 + 1.00 * 0.0817                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5406 = 3.44 * 0.50 * 5.5093 + 1.00 * 0.0618                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1545      final r-factor (work) = 0.1385          |
| start r-factor (free) = 0.2025      final r-factor (free) = 0.1879          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6475 = 0.66 * 1.00 * 5.5093 + 1.00 * 0.0199                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5473 = 0.66 * 1.00 * 5.3710 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.78    96.48   18.73    None  None   None       |
|    all(noH): 2823   0      0.78    96.48   18.73    None  None   None       |
|    Sol.    : 438    0      6.12    96.48   44.11    None  None   None       |
|    Mac.    : 2385   0      0.78    93.74   14.07    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:     0.782 -  10.352:  966   |   5:    48.632 -  58.202:  113        |
|      1:    10.352 -  19.922: 1144   |   6:    58.202 -  67.772:   71        |
|      2:    19.922 -  29.492:  239   |   7:    67.772 -  77.343:   29        |
|      3:    29.492 -  39.062:  118   |   8:    77.343 -  86.913:   12        |
|      4:    39.062 -  48.632:  126   |   9:    86.913 -  96.483:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1385 r_free = 0.1879             target_work(ml) = 5.331         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1384 r_free = 0.1880             target_work(ml) = 5.331         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1384   r_free= 0.1880   ksol= 0.33   Bsol= 60.54   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.12,-1.75,-0.39,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.330778                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1383   r_free= 0.1884   ksol= 0.33   Bsol= 60.78   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.84,-2.43,-1.14,-0.00,-0.00,-0.00); trace/3= -2.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.330308                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.727795              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.784  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.532003              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.345  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1383      final r-factor (work) = 0.1215          |
| start r-factor (free) = 0.1884      final r-factor (free) = 0.1700          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0823 = 3.73 * 0.50 * 5.3761 + 1.00 * 0.0618                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9132 = 3.73 * 0.50 * 5.2795 + 1.00 * 0.0728                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1215      final r-factor (work) = 0.1183          |
| start r-factor (free) = 0.1700      final r-factor (free) = 0.1653          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8193 = 0.53 * 1.00 * 5.2795 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7852 = 0.53 * 1.00 * 5.2170 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.47    93.65   18.34    None  None   None       |
|    all(noH): 2823   0      1.47    93.65   18.34    None  None   None       |
|    Sol.    : 438    0      6.11    93.65   43.11    None  None   None       |
|    Mac.    : 2385   0      1.47    90.38   13.79    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:     1.469 -  10.687: 1020   |   5:    47.559 -  56.777:  100        |
|      1:    10.687 -  19.905: 1122   |   6:    56.777 -  65.995:   63        |
|      2:    19.905 -  29.123:  225   |   7:    65.995 -  75.214:   30        |
|      3:    29.123 -  38.341:  117   |   8:    75.214 -  84.432:   18        |
|      4:    38.341 -  47.559:  121   |   9:    84.432 -  93.650:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1183 r_free = 0.1653             target_work(ml) = 5.203         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1182 r_free = 0.1653             target_work(ml) = 5.203         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1182   r_free= 0.1653   ksol= 0.33   Bsol= 60.78   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.84,-2.43,-1.14,-0.00,-0.00,-0.00); trace/3= -2.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.203055                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1182   r_free= 0.1653   ksol= 0.33   Bsol= 60.78   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.84,-2.43,-1.14,-0.00,-0.00,-0.00); trace/3= -2.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.203098                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.690881              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.424  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.307047              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.898  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1182      final r-factor (work) = 0.1126          |
| start r-factor (free) = 0.1653      final r-factor (free) = 0.1615          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7002 = 3.69 * 0.50 * 5.2169 + 1.00 * 0.0728                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6453 = 3.69 * 0.50 * 5.1840 + 1.00 * 0.0785                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1118          |
| start r-factor (free) = 0.1615      final r-factor (free) = 0.1595          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6015 = 0.31 * 1.00 * 5.1840 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5958 = 0.31 * 1.00 * 5.1692 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.72   17.77    None  None   None       |
|    all(noH): 2823   0      0.00    89.72   17.77    None  None   None       |
|    Sol.    : 438    0      0.00    89.37   40.92    None  None   None       |
|    Mac.    : 2385   0      1.86    89.72   13.52    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 -   8.972:  639   |   5:    44.860 -  53.832:  106        |
|      1:     8.972 -  17.944: 1405   |   6:    53.832 -  62.804:   57        |
|      2:    17.944 -  26.916:  308   |   7:    62.804 -  71.777:   34        |
|      3:    26.916 -  35.888:  123   |   8:    71.777 -  80.749:   14        |
|      4:    35.888 -  44.860:  130   |   9:    80.749 -  89.721:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1118 r_free = 0.1595             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1117 r_free = 0.1595             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1595   ksol= 0.33   Bsol= 60.78   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.84,-2.43,-1.14,-0.00,-0.00,-0.00); trace/3= -2.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.162834                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8788 -  4.6571 0.99   1463  161 0.0987 0.1368      5.4055      5.6012|
|  2:  4.6571 -  3.7154 0.99   1419  155 0.0816 0.1071      5.4129      5.6166|
|  3:  3.7154 -  3.2513 0.99   1370  159 0.1064 0.1472      5.4598      5.7957|
|  4:  3.2513 -  2.9566 0.99   1380  144 0.1246 0.1635      5.4362      5.6222|
|  5:  2.9566 -  2.7461 0.98   1359  152 0.1289 0.1613      5.3268      5.5106|
|  6:  2.7461 -  2.5851 0.99   1356  155 0.1244 0.2117       5.216      5.5325|
|  7:  2.5851 -  2.4562 0.98   1328  160 0.1260 0.1724       5.175      5.3771|
|  8:  2.4562 -  2.3497 0.99   1353  142 0.1186 0.1709      5.0992      5.2763|
|  9:  2.3497 -  2.2596 0.99   1356  147 0.1149 0.1794      5.0159      5.3175|
| 10:  2.2596 -  2.1819 0.98   1347  147 0.1159 0.1874       4.966      5.2174|
| 11:  2.1819 -  2.1139 0.97   1315  152 0.1159 0.1751       4.908      5.2512|
| 12:  2.1139 -  2.0536 0.99   1323  149 0.1135 0.1642      4.8695      5.1052|
| 13:  2.0536 -  1.9997 0.75   1030  107 0.1078 0.1887       4.752      4.9822|
| 14:  1.9997 -  1.9510 0.17    231   29 0.0992 0.1495      4.6945      4.8174|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8788 -  4.6571  1463   161  0.94   9.77   0.97     0.95       7931.06|
|  2:  4.6571 -  3.7154  1419   155  0.95   8.22   1.01     1.00       9226.92|
|  3:  3.7154 -  3.2513  1370   159  0.93  11.47   1.02     1.02      10235.70|
|  4:  3.2513 -  2.9566  1380   144  0.91  14.39   1.01     1.01      10255.05|
|  5:  2.9566 -  2.7461  1359   152  0.90  16.52   1.00     0.98       8846.67|
|  6:  2.7461 -  2.5851  1356   155  0.89  16.88   0.98     0.95       7251.37|
|  7:  2.5851 -  2.4562  1328   160  0.90  16.46   0.99     0.97       6629.43|
|  8:  2.4562 -  2.3497  1353   142  0.90  16.45   1.00     0.96       5836.96|
|  9:  2.3497 -  2.2596  1356   147  0.90  16.18   0.99     0.95       5018.68|
| 10:  2.2596 -  2.1819  1347   147  0.90  16.28   1.00     0.97       4629.46|
| 11:  2.1819 -  2.1139  1315   152  0.89  16.91   0.99     0.96       4282.45|
| 12:  2.1139 -  2.0536  1323   149  0.90  16.47   1.01     1.01       4024.19|
| 13:  2.0536 -  1.9997  1030   107  0.90  16.39   0.98     0.96       3225.18|
| 14:  1.9997 -  1.9510   231    29  0.92  12.99   0.98     0.94       2606.52|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2606.52 max =        10255.05 mean =      6769.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.68|
|phase err.(test): min =        0.00 max =           89.94 mean =        14.25|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1591   ksol= 0.32   Bsol= 54.35   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.85,-2.43,-1.14,-0.00,-0.00,-0.00); trace/3= -2.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.161972                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1591   ksol= 0.32   Bsol= 54.35   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.85,-2.43,-1.14,-0.00,-0.00,-0.00); trace/3= -2.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.161972                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8788 -  4.6571 0.99   1463  161 0.0986 0.1301       5.397      5.5684|
|  2:  4.6571 -  3.7154 0.99   1419  155 0.0819 0.1065        5.41      5.6142|
|  3:  3.7154 -  3.2513 0.99   1370  159 0.1067 0.1470      5.4589      5.7927|
|  4:  3.2513 -  2.9566 0.99   1380  144 0.1247 0.1648      5.4349      5.6269|
|  5:  2.9566 -  2.7461 0.98   1359  152 0.1286 0.1616       5.328      5.5093|
|  6:  2.7461 -  2.5851 0.99   1356  155 0.1243 0.2112      5.2159      5.5301|
|  7:  2.5851 -  2.4562 0.98   1328  160 0.1261 0.1733       5.176      5.3795|
|  8:  2.4562 -  2.3497 0.99   1353  142 0.1185 0.1712      5.0989      5.2767|
|  9:  2.3497 -  2.2596 0.99   1356  147 0.1148 0.1792      5.0159      5.3166|
| 10:  2.2596 -  2.1819 0.98   1347  147 0.1160 0.1878      4.9665       5.219|
| 11:  2.1819 -  2.1139 0.97   1315  152 0.1158 0.1750      4.9084      5.2507|
| 12:  2.1139 -  2.0536 0.99   1323  149 0.1134 0.1644      4.8695       5.105|
| 13:  2.0536 -  1.9997 0.75   1030  107 0.1077 0.1890      4.7525      4.9839|
| 14:  1.9997 -  1.9510 0.17    231   29 0.0994 0.1490      4.6958      4.8166|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8788 -  4.6571  1463   161  0.94   9.61   0.97     0.95       7674.91|
|  2:  4.6571 -  3.7154  1419   155  0.95   8.09   1.02     1.00       9000.56|
|  3:  3.7154 -  3.2513  1370   159  0.93  11.41   1.02     1.02      10139.52|
|  4:  3.2513 -  2.9566  1380   144  0.91  14.38   1.01     1.00      10208.98|
|  5:  2.9566 -  2.7461  1359   152  0.90  16.54   1.00     0.98       8866.61|
|  6:  2.7461 -  2.5851  1356   155  0.89  16.86   0.98     0.95       7245.64|
|  7:  2.5851 -  2.4562  1328   160  0.90  16.48   0.99     0.96       6652.16|
|  8:  2.4562 -  2.3497  1353   142  0.90  16.45   1.00     0.96       5838.82|
|  9:  2.3497 -  2.2596  1356   147  0.90  16.20   0.99     0.95       5027.58|
| 10:  2.2596 -  2.1819  1347   147  0.90  16.29   1.00     0.97       4636.25|
| 11:  2.1819 -  2.1139  1315   152  0.89  16.92   0.99     0.96       4288.61|
| 12:  2.1139 -  2.0536  1323   149  0.90  16.48   1.01     1.01       4027.13|
| 13:  2.0536 -  1.9997  1030   107  0.90  16.40   0.98     0.96       3229.65|
| 14:  1.9997 -  1.9510   231    29  0.92  13.01   0.98     0.94       2616.99|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2616.99 max =        10208.98 mean =      6724.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.65|
|phase err.(test): min =        0.00 max =           89.72 mean =        14.23|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.72   17.77    None  None   None       |
|    all(noH): 2823   0      0.00    89.72   17.77    None  None   None       |
|    Sol.    : 438    0      0.00    89.37   40.93    None  None   None       |
|    Mac.    : 2385   0      1.86    89.72   13.52    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   8.975:  639   |   5:    44.863 -  53.835:  106        |
|      1:     8.975 -  17.947: 1405   |   6:    53.835 -  62.807:   57        |
|      2:    17.947 -  26.919:  308   |   7:    62.807 -  71.780:   34        |
|      3:    26.919 -  35.891:  123   |   8:    71.780 -  80.752:   14        |
|      4:    35.891 -  44.863:  130   |   9:    80.752 -  89.724:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 307         
Filter by distance & map next to the model:
   mapped sites are within: 0.557 - 4.822
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 303 from: 307
   mapped sites are within: 0.701 - 4.822

peak=    5.490 closest distance to " CB  ARG A 275 " =    0.985
peak=    5.402 closest distance to " O   HOH Z 113 " =    2.086
peak=    5.233 closest distance to " O   HOH Z 188 " =    1.547
peak=    5.101 closest distance to " O   HOH Z  43 " =    2.196
peak=    5.063 closest distance to " O   HOH Z 417 " =    1.751
peak=    4.909 closest distance to " O   HOH Z 403 " =    1.734
peak=    4.856 closest distance to " CG  PRO A  54 " =    1.284
peak=    4.826 closest distance to " O   HOH Z  49 " =    1.159
peak=    4.659 closest distance to " O   HOH Z 369 " =    2.491
peak=    4.629 closest distance to " CB  ARG A 190 " =    1.680
peak=    4.605 closest distance to " CB  SER A  63 " =    1.102
peak=    4.594 closest distance to " NE2 GLN A  11 " =    1.167
peak=    4.564 closest distance to " O   HOH Z 232 " =    2.320
peak=    4.558 closest distance to " CD2 TRP A 179 " =    1.274
peak=    4.547 closest distance to " O   HOH Z 126 " =    1.777
peak=    4.543 closest distance to " O   HOH Z 406 " =    1.576
peak=    4.536 closest distance to " O   HOH Z  40 " =    1.949
peak=    4.527 closest distance to " CB  GLN A 223 " =    1.499
peak=    4.468 closest distance to " O   HOH Z  63 " =    1.857
peak=    4.424 closest distance to " CB  PRO A  54 " =    0.995
peak=    4.395 closest distance to " CZ  PHE A 218 " =    1.178
peak=    4.386 closest distance to " O   HOH Z 248 " =    1.526
peak=    4.341 closest distance to " CB  GLN A 183 " =    1.259
peak=    4.327 closest distance to " O   HOH Z 193 " =    1.668
peak=    4.324 closest distance to " CA  TYR A  30 " =    0.932
peak=    4.290 closest distance to " CB  GLU A 152 " =    1.146
peak=    4.277 closest distance to " CD  ARG A 269 " =    0.997
peak=    4.273 closest distance to " O   HOH Z 186 " =    1.199
peak=    4.269 closest distance to " O   HOH Z 287 " =    1.865
peak=    4.260 closest distance to " O   HOH Z 380 " =    2.070
peak=    4.238 closest distance to " O   HOH Z 234 " =    3.567
peak=    4.230 closest distance to " O   HOH Z 132 " =    1.128
peak=    4.218 closest distance to " CB  ARG A  79 " =    1.464
peak=    4.194 closest distance to " O   HOH Z  59 " =    2.164
peak=    4.186 closest distance to " O   HOH Z 188 " =    2.654
peak=    4.161 closest distance to " O   HOH Z 365 " =    2.539
peak=    4.150 closest distance to " O   HOH Z 368 " =    2.065
peak=    4.144 closest distance to " CA  ARG A  36 " =    1.059
peak=    4.115 closest distance to " O   HOH Z 298 " =    1.749
peak=    4.090 closest distance to " CB  ASN A 148 " =    1.477
peak=    4.085 closest distance to " O   SER A  87 " =    2.170
peak=    4.083 closest distance to " O   HOH Z 142 " =    1.504
peak=    4.052 closest distance to " O   HOH Z 250 " =    1.406
peak=    4.045 closest distance to " ND2 ASN A 187 " =    1.630
peak=    4.037 closest distance to " O   HOH Z 203 " =    1.403
peak=    4.028 closest distance to " O   HOH Z 132 " =    2.253
peak=    4.026 closest distance to " O   HOH Z 128 " =    2.413
peak=    4.020 closest distance to " O   HOH Z 327 " =    1.648
peak=    3.996 closest distance to " O   HOH Z 346 " =    1.630
peak=    3.995 closest distance to " O   HOH Z  97 " =    1.786
peak=    3.964 closest distance to " CB  SER A  26 " =    1.883
peak=    3.960 closest distance to " C   PRO A 198 " =    1.508
peak=    3.959 closest distance to " O  BHOH Z  74 " =    1.256
peak=    3.959 closest distance to " CG  ARG A  66 " =    2.516
peak=    3.955 closest distance to " O   HOH Z 427 " =    2.926
peak=    3.922 closest distance to " O   ALA A 165 " =    1.417
peak=    3.922 closest distance to " CB  PRO A 213 " =    1.239
peak=    3.898 closest distance to " O   HOH Z 251 " =    1.679
peak=    3.874 closest distance to " CB  GLU A 277 " =    3.580
peak=    3.861 closest distance to " O   HOH Z  62 " =    2.334
peak=    3.857 closest distance to " CG  PRO A 243 " =    1.067
peak=    3.849 closest distance to " CB  THR A  31 " =    1.798
peak=    3.836 closest distance to " NH2BARG A 145 " =    2.086
peak=    3.833 closest distance to " CZ3 TRP A 266 " =    1.031
peak=    3.801 closest distance to " O   HOH Z 209 " =    2.252
peak=    3.797 closest distance to " O   HOH Z 368 " =    3.675
peak=    3.790 closest distance to " ND2 ASN A 249 " =    0.922
peak=    3.787 closest distance to " O   HOH Z 214 " =    2.270
peak=    3.786 closest distance to " O   HOH Z 313 " =    2.079
peak=    3.784 closest distance to " CB  TRP A 266 " =    1.068
peak=    3.771 closest distance to " CA  ALA A  51 " =    0.920
peak=    3.770 closest distance to " O   HOH Z  85 " =    1.458
peak=    3.757 closest distance to " NH1AARG A 145 " =    1.386
peak=    3.752 closest distance to " CA  ALA A  84 " =    1.211
peak=    3.750 closest distance to " O   ASN A  74 " =    1.415
peak=    3.749 closest distance to " CD  LYS A  76 " =    1.756
peak=    3.747 closest distance to " O   HOH Z  21 " =    1.885
peak=    3.743 closest distance to " CD  LYS A 166 " =    1.357
peak=    3.736 closest distance to " CA  ARG A 195 " =    1.292
peak=    3.733 closest distance to " CB  PHE A 204 " =    0.769
peak=    3.731 closest distance to " O   HOH Z 421 " =    1.759
peak=    3.724 closest distance to " O   HOH Z   1 " =    2.176
peak=    3.721 closest distance to " CD  PRO A  54 " =    0.980
peak=    3.720 closest distance to " CG  GLN A  11 " =    1.761
peak=    3.713 closest distance to " NZ  LYS A 117 " =    3.059
peak=    3.707 closest distance to " OG BSER A 164 " =    2.155
peak=    3.703 closest distance to " O   HOH Z 291 " =    1.441
peak=    3.702 closest distance to " CB  TRP A 179 " =    1.279
peak=    3.693 closest distance to " O   HOH Z 423 " =    1.988
peak=    3.691 closest distance to " CG  PRO A  90 " =    1.283
peak=    3.688 closest distance to " CG2AVAL A 121 " =    2.253
peak=    3.686 closest distance to " N   ASN A  39 " =    1.351
peak=    3.677 closest distance to " O  BHOH Z 338 " =    2.168
peak=    3.668 closest distance to " CB  VAL A 202 " =    1.524
peak=    3.665 closest distance to " O   HOH Z 412 " =    3.818
peak=    3.663 closest distance to " O   HOH Z 353 " =    2.761
peak=    3.659 closest distance to " CZ  PHE A  38 " =    1.113
peak=    3.654 closest distance to " CE  LYS A 119 " =    1.156
peak=    3.654 closest distance to " CB  SER A  99 " =    1.446
peak=    3.650 closest distance to " O   HOH Z 227 " =    1.576
peak=    3.646 closest distance to " CE  LYS A  76 " =    0.883
peak=    3.646 closest distance to " O   HOH Z 303 " =    2.194
peak=    3.637 closest distance to " CB  VAL A 265 " =    1.218
peak=    3.635 closest distance to " O   HOH Z 359 " =    1.700
peak=    3.635 closest distance to " O   HOH Z  15 " =    2.169
peak=    3.634 closest distance to " O   HOH Z  44 " =    2.214
peak=    3.628 closest distance to " CB  SER A   3 " =    1.290
peak=    3.627 closest distance to " CG  GLN A  58 " =    0.957
peak=    3.625 closest distance to " O   HOH Z 158 " =    3.052
peak=    3.622 closest distance to " O   HOH Z 361 " =    2.486
peak=    3.621 closest distance to " O   HOH Z 422 " =    2.621
peak=    3.616 closest distance to " N   CYS A 260 " =    0.924
peak=    3.613 closest distance to " O   HOH Z 425 " =    1.864
peak=    3.602 closest distance to " O   HOH Z  88 " =    2.627
peak=    3.601 closest distance to " CB  GLN A  88 " =    1.135
peak=    3.598 closest distance to " O   HOH Z 417 " =    3.668
peak=    3.578 closest distance to " O   HOH Z 345 " =    1.674
peak=    3.572 closest distance to " CB  SER A  62 " =    0.945
peak=    3.572 closest distance to " O   HOH Z 285 " =    2.255
peak=    3.567 closest distance to " O   HOH Z 375 " =    2.194
peak=    3.565 closest distance to " O   HOH Z 261 " =    2.357
peak=    3.564 closest distance to " O   HOH Z 126 " =    1.549
peak=    3.556 closest distance to " O   HOH Z 299 " =    4.214
peak=    3.546 closest distance to " O   HOH Z 325 " =    2.347
peak=    3.541 closest distance to " O   HOH Z  78 " =    1.648
peak=    3.536 closest distance to " CG  MET A 185 " =    1.174
peak=    3.532 closest distance to " CG2 ILE A 120 " =    1.314
peak=    3.532 closest distance to " O   HOH Z  94 " =    2.260
peak=    3.530 closest distance to " N   PHE A 130 " =    1.321
peak=    3.524 closest distance to " CA  ASP A 162 " =    1.056
peak=    3.519 closest distance to " O   HOH Z  54 " =    1.657
peak=    3.516 closest distance to " O   HOH Z 128 " =    1.689
peak=    3.513 closest distance to " O   THR A 182 " =    1.476
peak=    3.512 closest distance to " CB  ASN A 110 " =    1.039
peak=    3.503 closest distance to " O   HOH Z 109 " =    2.484
peak=    3.499 closest distance to " O   HOH Z  80 " =    2.052
peak=    3.498 closest distance to " O   HOH Z 173 " =    2.037
peak=    3.486 closest distance to " O   HOH Z  61 " =    1.691
peak=    3.476 closest distance to " O   HOH Z 366 " =    2.422
peak=    3.475 closest distance to " CB  PRO A  90 " =    1.144
peak=    3.468 closest distance to " CB  ALA A 114 " =    1.061
peak=    3.467 closest distance to " O   HOH Z 389 " =    1.784
peak=    3.463 closest distance to " CA  ASN A 176 " =    1.524
peak=    3.460 closest distance to " O   HOH Z 185 " =    1.815
peak=    3.458 closest distance to " CG2 VAL A 257 " =    0.759
peak=    3.456 closest distance to " O   HOH Z 265 " =    2.044
peak=    3.455 closest distance to " O   THR A 220 " =    1.131
peak=    3.446 closest distance to " O   HOH Z 402 " =    1.352
peak=    3.430 closest distance to " CG1 ILE A  33 " =    1.184
peak=    3.429 closest distance to " CD2 LEU A 297 " =    0.882
peak=    3.426 closest distance to " O   HOH Z 350 " =    1.979
peak=    3.426 closest distance to " CA  ALA A 295 " =    1.006
peak=    3.420 closest distance to " OE1 GLN A  11 " =    2.048
peak=    3.406 closest distance to " O   HOH Z  97 " =    1.963
peak=    3.406 closest distance to " CD1 ILE A 199 " =    1.194
peak=    3.405 closest distance to " O   HOH Z  85 " =    1.518
peak=    3.402 closest distance to " CA  ALA A 129 " =    1.565
peak=    3.399 closest distance to " O   HOH Z 180 " =    2.218
peak=    3.399 closest distance to " CD  ARG A 159 " =    0.773
peak=    3.397 closest distance to " CG2 VAL A 197 " =    1.102
peak=    3.395 closest distance to " O   HOH Z 147 " =    1.893
peak=    3.395 closest distance to " O   HOH Z 148 " =    3.361
peak=    3.389 closest distance to " CD  ARG A  66 " =    2.654
peak=    3.389 closest distance to " O   HOH Z 273 " =    2.995
peak=    3.389 closest distance to " OG1 THR A 294 " =    1.589
peak=    3.388 closest distance to " O   HOH Z 337 " =    3.497
peak=    3.386 closest distance to " CG  GLU A  37 " =    0.937
peak=    3.386 closest distance to " CA  ALA A 100 " =    1.011
peak=    3.386 closest distance to " O   HOH Z 394 " =    3.715
peak=    3.373 closest distance to " CA  SER A  32 " =    1.628
peak=    3.369 closest distance to " CB  ALA A   9 " =    1.655
peak=    3.368 closest distance to " CB  ASN A 142 " =    1.136
peak=    3.367 closest distance to " O   HOH Z 298 " =    2.292
peak=    3.362 closest distance to " CG  LEU A 167 " =    1.223
peak=    3.353 closest distance to " CB  THR A  52 " =    0.741
peak=    3.352 closest distance to " OE1 GLU A   2 " =    2.168
peak=    3.349 closest distance to " CA  ALA A 291 " =    0.768
peak=    3.347 closest distance to " O   HOH Z 371 " =    3.000
peak=    3.346 closest distance to " O   HOH Z 336 " =    1.937
peak=    3.341 closest distance to " O   TYR A 116 " =    1.440
peak=    3.337 closest distance to " O   HOH Z  85 " =    2.114
peak=    3.336 closest distance to " CB  GLU A 128 " =    1.025
peak=    3.336 closest distance to " CA  ASN A 217 " =    1.212
peak=    3.336 closest distance to " O   HOH Z 305 " =    3.558
peak=    3.334 closest distance to " CD1 LEU A  96 " =    0.796
peak=    3.331 closest distance to " O   ASP A 124 " =    1.471
peak=    3.330 closest distance to " O   HOH Z 357 " =    2.013
peak=    3.326 closest distance to " CG  PRO A 198 " =    1.352
peak=    3.324 closest distance to " CB  ALA A   1 " =    4.822
peak=    3.323 closest distance to " CG2 ILE A  20 " =    1.277
peak=    3.320 closest distance to " CB  LEU A  83 " =    0.742
peak=    3.316 closest distance to " O   HOH Z 128 " =    1.926
peak=    3.315 closest distance to " CA  ASN A 127 " =    1.137
peak=    3.312 closest distance to " OH  TYR A 116 " =    1.067
peak=    3.311 closest distance to " O   HOH Z 282 " =    1.896
peak=    3.308 closest distance to " OE1 GLN A  73 " =    2.427
peak=    3.304 closest distance to " O   HOH Z 272 " =    1.818
peak=    3.303 closest distance to " O   HOH Z 334 " =    1.321
peak=    3.300 closest distance to " OG ASER A 258 " =    3.069
peak=    3.297 closest distance to " CB  GLN A  89 " =    1.405
peak=    3.295 closest distance to " O   HOH Z 193 " =    1.654
peak=    3.290 closest distance to " CB  ARG A 139 " =    1.192
peak=    3.287 closest distance to " CB  ASN A 285 " =    0.965
peak=    3.287 closest distance to " CB  GLU A  46 " =    1.043
peak=    3.284 closest distance to " O   HOH Z 285 " =    1.905
peak=    3.283 closest distance to " N   ARG A 156 " =    1.378
peak=    3.281 closest distance to " CB  ASN A  39 " =    0.757
peak=    3.276 closest distance to " O   HOH Z 250 " =    1.508
peak=    3.270 closest distance to " CG1 ILE A  20 " =    1.342
peak=    3.270 closest distance to " CA  SER A  87 " =    1.007
peak=    3.269 closest distance to " CA  ILE A 106 " =    0.862
peak=    3.265 closest distance to " O   ASN A 284 " =    1.688
peak=    3.265 closest distance to " O   HOH Z 132 " =    2.411
peak=    3.265 closest distance to " NH1BARG A 145 " =    1.098
peak=    3.265 closest distance to " O   HOH Z 162 " =    2.121
peak=    3.264 closest distance to " CA  ASP A 140 " =    1.344
peak=    3.260 closest distance to " NE2 GLN A  77 " =    3.195
peak=    3.257 closest distance to " CE1 TYR A 186 " =    1.247
peak=    3.253 closest distance to " O   HOH Z 258 " =    2.081
peak=    3.248 closest distance to " CB  ASP A 140 " =    1.107
peak=    3.247 closest distance to " CG BARG A 102 " =    1.771
peak=    3.242 closest distance to " O   HOH Z 394 " =    1.593
peak=    3.238 closest distance to " O   HOH Z  19 " =    1.466
peak=    3.236 closest distance to " CG1BVAL A  72 " =    1.769
peak=    3.233 closest distance to " CA  ASN A 215 " =    1.014
peak=    3.231 closest distance to " OG  SER A 135 " =    1.335
peak=    3.228 closest distance to " O   HOH Z 342 " =    0.983
peak=    3.224 closest distance to " O   HOH Z 213 " =    1.689
peak=    3.224 closest distance to " O   HOH Z 345 " =    2.955
peak=    3.223 closest distance to " O   HOH Z 426 " =    1.410
peak=    3.222 closest distance to " O   HOH Z 146 " =    2.308
peak=    3.221 closest distance to " O   HOH Z  80 " =    1.672
peak=    3.219 closest distance to " OG  SER A  22 " =    2.615
peak=    3.219 closest distance to " O   HOH Z 130 " =    2.275
peak=    3.218 closest distance to " CA  ALA A 248 " =    1.198
peak=    3.217 closest distance to " CE BLYS A 290 " =    0.933
peak=    3.216 closest distance to " N   GLU A   2 " =    1.682
peak=    3.212 closest distance to " O   HOH Z 329 " =    4.171
peak=    3.203 closest distance to " O   HOH Z 194 " =    1.984
peak=    3.203 closest distance to " O   HOH Z  89 " =    1.977
peak=    3.202 closest distance to " O   HOH Z 280 " =    2.993
peak=    3.202 closest distance to " OG  SER A  28 " =    1.449
peak=    3.199 closest distance to " O   HOH Z 279 " =    2.170
peak=    3.199 closest distance to " O   HOH Z 245 " =    1.389
peak=    3.191 closest distance to " CA  TYR A 116 " =    1.416
peak=    3.186 closest distance to " CA  ALA A 158 " =    1.387
peak=    3.185 closest distance to " CB  ASP A 124 " =    0.701
peak=    3.184 closest distance to " O   HOH Z 246 " =    1.308
peak=    3.184 closest distance to " O   HOH Z 162 " =    1.558
peak=    3.181 closest distance to " O   HOH Z   1 " =    2.081
peak=    3.179 closest distance to " CD  LYS A 119 " =    1.771
peak=    3.179 closest distance to " CA  VAL A 125 " =    1.158
peak=    3.178 closest distance to " O   HOH Z 298 " =    4.175
peak=    3.177 closest distance to " O   HOH Z 419 " =    1.675
peak=    3.173 closest distance to " O   HOH Z 343 " =    2.003
peak=    3.171 closest distance to " O   HOH Z 124 " =    1.162
peak=    3.171 closest distance to " CB  LYS A 289 " =    1.173
peak=    3.169 closest distance to " O   GLY A 147 " =    1.512
peak=    3.169 closest distance to " O   HOH Z 263 " =    1.887
peak=    3.166 closest distance to " O   HOH Z  68 " =    1.851
peak=    3.165 closest distance to " O   HOH Z 416 " =    2.789
peak=    3.163 closest distance to " CB  ARG A 156 " =    1.015
peak=    3.160 closest distance to " O   HOH Z 327 " =    2.275
peak=    3.159 closest distance to " N   TYR A 116 " =    1.584
peak=    3.159 closest distance to " OE1 GLN A 223 " =    2.348
peak=    3.154 closest distance to " O   HOH Z 358 " =    3.616
peak=    3.154 closest distance to " CG  LYS A 119 " =    0.956
peak=    3.150 closest distance to " OD2 ASP A 298 " =    3.868
peak=    3.150 closest distance to " OG  SER A  62 " =    2.738
peak=    3.146 closest distance to " N   HIS A 108 " =    1.805
peak=    3.145 closest distance to " CG2 ILE A 239 " =    0.714
peak=    3.142 closest distance to " O   ALA A   1 " =    1.671
peak=    3.140 closest distance to " O   HOH Z  10 " =    1.761
peak=    3.140 closest distance to " N   ASP A 162 " =    1.119
peak=    3.140 closest distance to " CB  TYR A 169 " =    0.911
peak=    3.137 closest distance to " CE1 HIS A  81 " =    1.688
peak=    3.135 closest distance to " O   HOH Z  63 " =    2.298
peak=    3.123 closest distance to " O   HOH Z 193 " =    1.890
peak=    3.118 closest distance to " CA  ALA A 154 " =    1.010
peak=    3.118 closest distance to " CG2 THR A 221 " =    1.164
peak=    3.117 closest distance to " N   GLU A  44 " =    2.202
peak=    3.117 closest distance to " O   HOH Z 294 " =    1.458
peak=    3.116 closest distance to " CG2 THR A  18 " =    1.606
peak=    3.102 closest distance to " OG1 THR A 221 " =    1.317
peak=    3.091 closest distance to " O   HOH Z 392 " =    2.513
peak=    3.087 closest distance to " CD  ARG A  79 " =    1.957
peak=    3.086 closest distance to " CB  ALA A 248 " =    1.449
peak=    3.085 closest distance to " CD1AILE A 234 " =    0.819
peak=    3.085 closest distance to " CZ  ARG A  14 " =    1.320
peak=    3.081 closest distance to " CB  ALA A  71 " =    1.402
peak=    3.075 closest distance to " CA  ALA A 233 " =    1.165
peak=    3.071 closest distance to " NH2BARG A 190 " =    1.697
peak=    3.067 closest distance to " O   HOH Z 134 " =    1.148
peak=    3.066 closest distance to " O   HOH Z  47 " =    1.610
peak=    3.064 closest distance to " CA  ARG A 159 " =    1.293
peak=    3.063 closest distance to " O   HOH Z 108 " =    2.876
peak=    3.063 closest distance to " O   HOH Z 371 " =    1.519
peak=    3.056 closest distance to " CA  SER A 146 " =    2.016
peak=    3.040 closest distance to " O   HOH Z  89 " =    1.897
peak=    3.034 closest distance to " O   SER A 164 " =    1.305
peak=    3.034 closest distance to " O   HOH Z 130 " =    2.405
peak=    3.024 closest distance to " O   HOH Z 421 " =    3.111
peak=    3.012 closest distance to " NH1AARG A 275 " =    1.146

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.619 - 6.000
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 210 from: 212
   mapped sites are within: 0.701 - 6.000

peak=   -4.858 closest distance to " CD  ARG A  14 " =    3.378
peak=   -4.560 closest distance to " CG  GLN A  58 " =    1.006
peak=   -4.463 closest distance to " C   HIS A 108 " =    1.181
peak=   -4.393 closest distance to " O   HOH Z 266 " =    5.345
peak=   -4.314 closest distance to " O   HOH Z 377 " =    2.164
peak=   -4.281 closest distance to " CA  VAL A  67 " =    2.986
peak=   -4.247 closest distance to " CB  PRO A 243 " =    2.731
peak=   -4.217 closest distance to " O   HOH Z 193 " =    1.192
peak=   -4.204 closest distance to " CG1 VAL A 250 " =    2.705
peak=   -4.165 closest distance to " O   PRO A 198 " =    1.331
peak=   -4.164 closest distance to " O   GLY A 241 " =    2.346
peak=   -4.160 closest distance to " CD1 LEU A 101 " =    2.429
peak=   -4.105 closest distance to " O   HOH Z 198 " =    1.405
peak=   -4.104 closest distance to " O   HOH Z  65 " =    0.833
peak=   -4.094 closest distance to " CG2 ILE A  49 " =    2.730
peak=   -4.092 closest distance to " O   VAL A  67 " =    2.729
peak=   -4.091 closest distance to " CD2 TYR A 293 " =    1.915
peak=   -4.054 closest distance to " O   HOH Z 348 " =    2.231
peak=   -3.975 closest distance to " OG BSER A 134 " =    1.562
peak=   -3.946 closest distance to " CD  ARG A 156 " =    2.148
peak=   -3.942 closest distance to " CH2 TRP A 179 " =    1.249
peak=   -3.936 closest distance to " OE1 GLN A 223 " =    2.245
peak=   -3.899 closest distance to " NE2 GLN A  88 " =    1.059
peak=   -3.881 closest distance to " O   VAL A 174 " =    2.270
peak=   -3.879 closest distance to " CG1 VAL A 112 " =    2.656
peak=   -3.870 closest distance to " CD2 TYR A 247 " =    2.437
peak=   -3.864 closest distance to " O   HOH Z 165 " =    1.949
peak=   -3.861 closest distance to " OXT GLY A 302 " =    3.046
peak=   -3.827 closest distance to " O   HOH Z 290 " =    1.016
peak=   -3.783 closest distance to " O   HOH Z 211 " =    1.378
peak=   -3.746 closest distance to " OG  SER A  97 " =    2.232
peak=   -3.745 closest distance to " O   HOH Z 394 " =    1.579
peak=   -3.739 closest distance to " O   PHE A 218 " =    1.521
peak=   -3.738 closest distance to " O   ALA A  34 " =    2.345
peak=   -3.725 closest distance to " O   HOH Z 174 " =    2.467
peak=   -3.693 closest distance to " O   HOH Z 351 " =    1.524
peak=   -3.685 closest distance to " CB  ALA A 161 " =    2.493
peak=   -3.684 closest distance to " CB  ASN A  39 " =    2.369
peak=   -3.670 closest distance to " O   HOH Z 374 " =    1.915
peak=   -3.660 closest distance to " OD1 ASP A 171 " =    1.538
peak=   -3.656 closest distance to " CD  GLN A 223 " =    1.212
peak=   -3.656 closest distance to " CA  ASP A 298 " =    1.072
peak=   -3.649 closest distance to " CE  MET A 105 " =    2.486
peak=   -3.646 closest distance to " O   HOH Z 113 " =    1.627
peak=   -3.626 closest distance to " CE2 TYR A  30 " =    2.702
peak=   -3.626 closest distance to " O   HOH Z  15 " =    1.479
peak=   -3.609 closest distance to " O   HOH Z   6 " =    2.087
peak=   -3.608 closest distance to " O   HOH Z 196 " =    1.879
peak=   -3.607 closest distance to " CD1 ILE A 106 " =    2.241
peak=   -3.598 closest distance to " CE BMET A  47 " =    1.498
peak=   -3.594 closest distance to " O   TRP A  92 " =    2.026
peak=   -3.593 closest distance to " O   HOH Z 264 " =    1.669
peak=   -3.586 closest distance to " O   HOH Z  13 " =    1.826
peak=   -3.583 closest distance to " CB  ALA A 184 " =    2.344
peak=   -3.573 closest distance to " O   HOH Z 191 " =    5.969
peak=   -3.570 closest distance to " CB  ALA A 248 " =    2.231
peak=   -3.566 closest distance to " O   HOH Z 395 " =    5.064
peak=   -3.562 closest distance to " CB  ALA A  43 " =    2.484
peak=   -3.562 closest distance to " OH  TYR A 172 " =    1.802
peak=   -3.551 closest distance to " NH2 ARG A  66 " =    1.021
peak=   -3.549 closest distance to " O   SER A 210 " =    2.005
peak=   -3.543 closest distance to " CD  PRO A 243 " =    2.007
peak=   -3.542 closest distance to " CG1 VAL A  78 " =    2.708
peak=   -3.540 closest distance to " O   HOH Z 421 " =    3.912
peak=   -3.539 closest distance to " CG1 VAL A 112 " =    2.655
peak=   -3.524 closest distance to " CZ3 TRP A 274 " =    2.387
peak=   -3.523 closest distance to " CZ  TYR A 169 " =    1.732
peak=   -3.512 closest distance to " CG1AVAL A  41 " =    2.606
peak=   -3.507 closest distance to " CG  TRP A 266 " =    2.017
peak=   -3.498 closest distance to " O   HOH Z   6 " =    1.662
peak=   -3.494 closest distance to " CB  TRP A  85 " =    2.573
peak=   -3.486 closest distance to " ND2 ASN A  69 " =    1.904
peak=   -3.474 closest distance to " NE2 GLN A  11 " =    1.643
peak=   -3.467 closest distance to " N   ALA A  43 " =    2.564
peak=   -3.464 closest distance to " CB  ALA A 291 " =    2.356
peak=   -3.463 closest distance to " O   HOH Z  60 " =    1.457
peak=   -3.461 closest distance to " N   ALA A 226 " =    1.928
peak=   -3.460 closest distance to " O   SER A   3 " =    0.995
peak=   -3.459 closest distance to " O   PRO A 163 " =    2.069
peak=   -3.456 closest distance to " CG  ARG A  66 " =    2.485
peak=   -3.452 closest distance to " CA  GLY A 241 " =    3.188
peak=   -3.449 closest distance to " O   HOH Z 422 " =    1.391
peak=   -3.447 closest distance to " O   HOH Z 216 " =    1.357
peak=   -3.446 closest distance to " O   ILE A  49 " =    1.714
peak=   -3.445 closest distance to " ND2 ASN A  45 " =    1.264
peak=   -3.445 closest distance to " OE1 GLN A 183 " =    1.388
peak=   -3.433 closest distance to " O   ALA A  10 " =    1.786
peak=   -3.432 closest distance to " O   SER A  95 " =    1.642
peak=   -3.428 closest distance to " CG  ARG A 219 " =    2.369
peak=   -3.415 closest distance to " O   HOH Z 281 " =    2.687
peak=   -3.410 closest distance to " O   HOH Z 274 " =    1.134
peak=   -3.406 closest distance to " CG1 VAL A  67 " =    3.012
peak=   -3.390 closest distance to " O   HOH Z  38 " =    1.815
peak=   -3.387 closest distance to " O   HOH Z 431 " =    4.065
peak=   -3.385 closest distance to " O   HOH Z 109 " =    2.577
peak=   -3.384 closest distance to " OD2 ASP A 171 " =    2.391
peak=   -3.378 closest distance to " CG  LEU A  83 " =    2.117
peak=   -3.378 closest distance to " CE3 TRP A 150 " =    2.238
peak=   -3.371 closest distance to " CD2 PHE A  61 " =    2.246
peak=   -3.368 closest distance to " CE2 PHE A  61 " =    2.711
peak=   -3.368 closest distance to " O   HOH Z 210 " =    1.015
peak=   -3.365 closest distance to " O   HOH Z 116 " =    1.652
peak=   -3.362 closest distance to " O   ILE A 106 " =    1.837
peak=   -3.361 closest distance to " CG1 VAL A 265 " =    2.611
peak=   -3.359 closest distance to " CD  GLN A  88 " =    0.875
peak=   -3.356 closest distance to " CG  PHE A 283 " =    2.550
peak=   -3.355 closest distance to " O   HOH Z 114 " =    3.378
peak=   -3.354 closest distance to " O   GLN A  94 " =    2.264
peak=   -3.347 closest distance to " O   HOH Z 185 " =    2.284
peak=   -3.343 closest distance to " CG  ARG A 269 " =    2.169
peak=   -3.340 closest distance to " CG  ASP A 132 " =    2.324
peak=   -3.338 closest distance to " CD  GLN A 223 " =    1.027
peak=   -3.338 closest distance to " ND2 ASN A 249 " =    2.317
peak=   -3.336 closest distance to " ND2 ASN A 187 " =    1.607
peak=   -3.328 closest distance to " CD2 PHE A 192 " =    2.072
peak=   -3.327 closest distance to " NE2 GLN A  88 " =    1.753
peak=   -3.319 closest distance to " O   VAL A 189 " =    1.909
peak=   -3.319 closest distance to " O   GLU A 152 " =    1.484
peak=   -3.316 closest distance to " O   HOH Z 218 " =    4.017
peak=   -3.311 closest distance to " O   HOH Z  71 " =    2.561
peak=   -3.302 closest distance to " O   HOH Z  88 " =    1.989
peak=   -3.302 closest distance to " CG  PRO A 243 " =    1.778
peak=   -3.300 closest distance to " NH2 ARG A  66 " =    6.000
peak=   -3.298 closest distance to " O   PRO A 198 " =    1.651
peak=   -3.297 closest distance to " O   HOH Z 285 " =    1.427
peak=   -3.297 closest distance to " O   ALA A 227 " =    1.301
peak=   -3.296 closest distance to " CD2 LEU A 282 " =    2.148
peak=   -3.296 closest distance to " O   HOH Z 110 " =    1.370
peak=   -3.289 closest distance to " O   HOH Z 313 " =    2.007
peak=   -3.289 closest distance to " O   HOH Z 102 " =    1.770
peak=   -3.286 closest distance to " CG  MET A 105 " =    1.005
peak=   -3.285 closest distance to " CB  HIS A  86 " =    1.222
peak=   -3.285 closest distance to " CD2 LEU A 237 " =    2.112
peak=   -3.281 closest distance to " O   HOH Z 198 " =    1.755
peak=   -3.277 closest distance to " CA  GLY A 203 " =    2.421
peak=   -3.277 closest distance to " CG2 VAL A 189 " =    2.167
peak=   -3.273 closest distance to " CD2 HIS A 207 " =    2.273
peak=   -3.273 closest distance to " CH2 TRP A 150 " =    1.117
peak=   -3.272 closest distance to " O   HOH Z 174 " =    3.703
peak=   -3.271 closest distance to " O   HOH Z 252 " =    3.980
peak=   -3.261 closest distance to " CZ  PHE A  38 " =    1.986
peak=   -3.259 closest distance to " CD1 ILE A 151 " =    2.390
peak=   -3.258 closest distance to " CG  GLU A  53 " =    1.590
peak=   -3.256 closest distance to " O   HOH Z  63 " =    1.492
peak=   -3.251 closest distance to " CD1 PHE A  59 " =    2.008
peak=   -3.246 closest distance to " O   HOH Z 108 " =    1.961
peak=   -3.241 closest distance to " N   SER A 276 " =    1.346
peak=   -3.239 closest distance to " CD  GLN A 223 " =    1.781
peak=   -3.238 closest distance to " O   HOH Z 183 " =    1.566
peak=   -3.238 closest distance to " O   HOH Z 244 " =    1.430
peak=   -3.235 closest distance to " SG ACYS A 201 " =    2.301
peak=   -3.231 closest distance to " O   HOH Z  89 " =    2.602
peak=   -3.227 closest distance to " O   HOH Z 262 " =    2.575
peak=   -3.225 closest distance to " CB  ALA A 291 " =    2.213
peak=   -3.224 closest distance to " CG1BVAL A  41 " =    2.861
peak=   -3.224 closest distance to " CZ  ARG A 259 " =    0.961
peak=   -3.221 closest distance to " O   GLY A  17 " =    2.159
peak=   -3.219 closest distance to " OE2 GLU A 152 " =    1.312
peak=   -3.219 closest distance to " O   HOH Z 265 " =    2.502
peak=   -3.218 closest distance to " ND2 ASN A  39 " =    1.120
peak=   -3.218 closest distance to " O   HOH Z 393 " =    1.322
peak=   -3.217 closest distance to " CB  ALA A  10 " =    2.327
peak=   -3.216 closest distance to " O   ASP A 298 " =    1.782
peak=   -3.213 closest distance to " O   HOH Z  10 " =    1.569
peak=   -3.213 closest distance to " O   SER A 146 " =    1.195
peak=   -3.212 closest distance to " O   HOH Z 111 " =    3.838
peak=   -3.199 closest distance to " CG2BVAL A  41 " =    1.260
peak=   -3.192 closest distance to " CB  ALA A 114 " =    2.431
peak=   -3.190 closest distance to " OG BSER A  99 " =    0.991
peak=   -3.188 closest distance to " O   ASN A 187 " =    1.547
peak=   -3.182 closest distance to " O   ALA A   1 " =    1.833
peak=   -3.180 closest distance to " O   GLY A 196 " =    1.018
peak=   -3.179 closest distance to " CD2 LEU A 237 " =    2.455
peak=   -3.175 closest distance to " O   HOH Z  53 " =    1.763
peak=   -3.173 closest distance to " O   HOH Z 139 " =    3.289
peak=   -3.171 closest distance to " O   HOH Z 394 " =    1.191
peak=   -3.168 closest distance to " O   HOH Z 234 " =    4.000
peak=   -3.168 closest distance to " CD  GLN A  11 " =    0.946
peak=   -3.167 closest distance to " OE1 GLN A 223 " =    2.134
peak=   -3.163 closest distance to " OD1 ASN A 301 " =    1.881
peak=   -3.162 closest distance to " CG  GLN A  58 " =    1.541
peak=   -3.148 closest distance to " ND2BASN A 224 " =    1.777
peak=   -3.147 closest distance to " CB  ASP A 286 " =    1.839
peak=   -3.138 closest distance to " OXT GLY A 302 " =    3.429
peak=   -3.137 closest distance to " CD  LYS A 289 " =    2.332
peak=   -3.134 closest distance to " ND2 ASN A  60 " =    1.265
peak=   -3.130 closest distance to " O   HOH Z 367 " =    2.329
peak=   -3.130 closest distance to " N   ALA A 248 " =    1.640
peak=   -3.129 closest distance to " ND2 ASN A  45 " =    1.914
peak=   -3.128 closest distance to " CG2BVAL A  41 " =    2.210
peak=   -3.125 closest distance to " CZ  PHE A  38 " =    2.334
peak=   -3.125 closest distance to " OD1 ASN A 148 " =    1.461
peak=   -3.122 closest distance to " O   HOH Z  64 " =    2.384
peak=   -3.119 closest distance to " CA  GLY A 133 " =    2.017
peak=   -3.117 closest distance to " NE2 GLN A 278 " =    1.705
peak=   -3.115 closest distance to " C   ASN A 285 " =    2.126
peak=   -3.103 closest distance to " CA  GLY A  57 " =    2.179
peak=   -3.099 closest distance to " O   HOH Z 297 " =    2.697
peak=   -3.094 closest distance to " OD1 ASP A 191 " =    1.459
peak=   -3.093 closest distance to " O   HOH Z 101 " =    1.603
peak=   -3.087 closest distance to " O   HOH Z 171 " =    2.573
peak=   -3.086 closest distance to " CB  PHE A  16 " =    2.383
peak=   -3.083 closest distance to " O   PRO A  54 " =    1.609
peak=   -3.082 closest distance to " CD1 ILE A 109 " =    2.632
peak=   -3.081 closest distance to " O   SER A 276 " =    1.684
peak=   -3.079 closest distance to " O   HOH Z  56 " =    0.701
peak=   -3.076 closest distance to " O   HOH Z 252 " =    3.532
peak=   -3.061 closest distance to " NE2 GLN A 223 " =    1.182
peak=   -3.043 closest distance to " O   HOH Z 197 " =    2.107
peak=   -3.023 closest distance to " O   HOH Z  58 " =    1.168

================= 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    :  0.4515 0.4527   6.256127e+00   6.254217e+00
   1_bss:  0.4442 0.4416   6.248551e+00   6.245448e+00
   1_xyz:  0.3181 0.3462   6.005124e+00   6.079796e+00
   1_adp:  0.2842 0.3548   5.951159e+00   6.094793e+00
   1_occ:  0.2839 0.3551   5.951240e+00   6.095974e+00
   2_bss:  0.2818 0.3523   5.945581e+00   6.091913e+00
   2_xyz:  0.2021 0.2575   5.649533e+00   5.839810e+00
   2_adp:  0.1878 0.2432   5.586832e+00   5.786398e+00
   2_occ:  0.1875 0.2430   5.586004e+00   5.785524e+00
   3_bss:  0.1867 0.2414   5.584747e+00   5.783292e+00
   3_xyz:  0.1545 0.2025   5.420707e+00   5.631228e+00
   3_adp:  0.1385 0.1879   5.330912e+00   5.557114e+00
   3_occ:  0.1384 0.1880   5.330778e+00   5.557158e+00
   4_bss:  0.1383 0.1884   5.330308e+00   5.556273e+00
   4_xyz:  0.1215 0.1700   5.228037e+00   5.467202e+00
   4_adp:  0.1183 0.1653   5.203221e+00   5.441045e+00
   4_occ:  0.1182 0.1653   5.203055e+00   5.440908e+00
   5_bss:  0.1182 0.1653   5.203098e+00   5.440900e+00
   5_xyz:  0.1126 0.1615   5.170976e+00   5.417204e+00
   5_adp:  0.1118 0.1595   5.163216e+00   5.405230e+00
   5_occ:  0.1117 0.1595   5.162834e+00   5.405052e+00
   5_bss:  0.1118 0.1591   5.161972e+00   5.402279e+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:  0.310  35.993  -0.115  -0.687   3.101  -0.000   0.000   0.000
   1_xyz:  0.310  35.993  -0.115  -0.687   3.101  -0.000   0.000   0.000
   1_adp:  0.310  35.993  -0.115  -0.687   3.101  -0.000   0.000   0.000
   1_occ:  0.310  35.993  -0.115  -0.687   3.101  -0.000   0.000   0.000
   2_bss:  0.328  57.421  -1.627  -0.789   1.019  -0.000   0.000   0.000
   2_xyz:  0.328  57.421  -1.627  -0.789   1.019  -0.000   0.000   0.000
   2_adp:  0.328  57.421  -1.627  -0.789   1.019  -0.000   0.000   0.000
   2_occ:  0.328  57.421  -1.627  -0.789   1.019  -0.000   0.000   0.000
   3_bss:  0.332  60.536  -3.116  -1.749  -0.386  -0.000  -0.000  -0.000
   3_xyz:  0.332  60.536  -3.116  -1.749  -0.386  -0.000  -0.000  -0.000
   3_adp:  0.332  60.536  -3.116  -1.749  -0.386  -0.000  -0.000  -0.000
   3_occ:  0.332  60.536  -3.116  -1.749  -0.386  -0.000  -0.000  -0.000
   4_bss:  0.328  60.783  -3.844  -2.427  -1.140  -0.000  -0.000  -0.000
   4_xyz:  0.328  60.783  -3.844  -2.427  -1.140  -0.000  -0.000  -0.000
   4_adp:  0.328  60.783  -3.844  -2.427  -1.140  -0.000  -0.000  -0.000
   4_occ:  0.328  60.783  -3.844  -2.427  -1.140  -0.000  -0.000  -0.000
   5_bss:  0.330  60.783  -3.844  -2.427  -1.140  -0.000  -0.000  -0.000
   5_xyz:  0.330  60.783  -3.844  -2.427  -1.140  -0.000  -0.000  -0.000
   5_adp:  0.330  60.783  -3.844  -2.427  -1.140  -0.000  -0.000  -0.000
   5_occ:  0.330  60.783  -3.844  -2.427  -1.140  -0.000  -0.000  -0.000
   5_bss:  0.321  54.349  -3.847  -2.430  -1.143  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.345 0.4790  0.6434    63236.498
   1_bss:  52.237 0.4917  0.6856    60500.163
   1_xyz:  37.023 0.6785  0.9033    33630.630
   1_adp:  38.353 0.6620  0.8849    35402.886
   1_occ:  38.417 0.6612  0.8837    35525.440
   2_bss:  38.076 0.6650  0.8515    34864.957
   2_xyz:  26.303 0.7964  0.9835    17401.896
   2_adp:  24.181 0.8195  1.0180    15453.949
   2_occ:  24.162 0.8197  1.0182    15418.796
   3_bss:  24.059 0.8206  0.9729    15291.374
   3_xyz:  19.619 0.8649  0.9950    10550.186
   3_adp:  17.856 0.8815  0.9966     9114.555
   3_occ:  17.854 0.8816  0.9966     9114.491
   4_bss:  17.808 0.8819  0.9719     9085.138
   4_xyz:  15.931 0.8984  0.9795     7516.022
   4_adp:  15.380 0.9033  0.9771     7188.330
   4_occ:  15.377 0.9033  0.9770     7184.557
   5_bss:  15.376 0.9033  0.9770     7185.016
   5_xyz:  14.866 0.9077  0.9789     6879.166
   5_adp:  14.639 0.9098  0.9750     6776.172
   5_occ:  14.634 0.9098  0.9749     6769.485
   5_bss:  14.611 0.9100  0.9748     6724.217
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   2.2659e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   2.2659e-01
   1_xyz:   1.526  0.011  0.089 15.172  0.006  4.107   1.1926e-01
   1_adp:   1.526  0.011  0.089 15.172  0.006  4.107   1.1926e-01
   1_occ:   1.526  0.011  0.089 15.172  0.006  4.107   1.1926e-01
   2_bss:   1.526  0.011  0.089 15.172  0.006  4.107   1.1926e-01
   2_xyz:   1.244  0.009  0.085 14.746  0.005  4.131   8.1312e-02
   2_adp:   1.244  0.009  0.085 14.746  0.005  4.131   8.1312e-02
   2_occ:   1.244  0.009  0.085 14.746  0.005  4.131   8.1312e-02
   3_bss:   1.244  0.009  0.085 14.746  0.005  4.131   8.1312e-02
   3_xyz:   1.032  0.008  0.073 14.607  0.004  4.120   6.1789e-02
   3_adp:   1.032  0.008  0.073 14.607  0.004  4.120   6.1789e-02
   3_occ:   1.032  0.008  0.073 14.607  0.004  4.120   6.1789e-02
   4_bss:   1.032  0.008  0.073 14.607  0.004  4.120   6.1789e-02
   4_xyz:   1.145  0.009  0.081 14.832  0.005  4.111   7.2776e-02
   4_adp:   1.145  0.009  0.081 14.832  0.005  4.111   7.2776e-02
   4_occ:   1.145  0.009  0.081 14.832  0.005  4.111   7.2776e-02
   5_bss:   1.145  0.009  0.081 14.832  0.005  4.111   7.2776e-02
   5_xyz:   1.170  0.010  0.086 14.847  0.005  4.112   7.8473e-02
   5_adp:   1.170  0.010  0.086 14.847  0.005  4.112   7.8473e-02
   5_occ:   1.170  0.010  0.086 14.847  0.005  4.112   7.8473e-02
   5_bss:   1.170  0.010  0.086 14.847  0.005  4.112   7.8473e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.072   2.4545e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.072   2.4545e-01
   1_xyz:  10.127  0.072  0.309 82.736  0.031  2.039   1.0115e-01
   1_adp:  10.127  0.072  0.309 82.736  0.031  2.039   1.0115e-01
   1_occ:  10.127  0.072  0.309 82.736  0.031  2.039   1.0115e-01
   2_bss:  10.127  0.072  0.309 82.736  0.031  2.039   1.0115e-01
   2_xyz:   7.416  0.061  0.295 80.138  0.037  2.142   7.8660e-02
   2_adp:   7.416  0.061  0.295 80.138  0.037  2.142   7.8660e-02
   2_occ:   7.416  0.061  0.295 80.138  0.037  2.142   7.8660e-02
   3_bss:   7.416  0.061  0.295 80.138  0.037  2.142   7.8660e-02
   3_xyz:   7.499  0.048  0.228 82.830  0.042  2.241   6.6313e-02
   3_adp:   7.499  0.048  0.228 82.830  0.042  2.241   6.6313e-02
   3_occ:   7.499  0.048  0.228 82.830  0.042  2.241   6.6313e-02
   4_bss:   7.499  0.048  0.228 82.830  0.042  2.241   6.6313e-02
   4_xyz:   8.048  0.054  0.268 83.451  0.042  2.274   5.4791e-02
   4_adp:   8.048  0.054  0.268 83.451  0.042  2.274   5.4791e-02
   4_occ:   8.048  0.054  0.268 83.451  0.042  2.274   5.4791e-02
   5_bss:   8.048  0.054  0.268 83.451  0.042  2.274   5.4791e-02
   5_xyz:   7.981  0.059  0.316 83.453  0.040  2.311   6.4791e-02
   5_adp:   7.981  0.059  0.316 83.453  0.040  2.311   6.4791e-02
   5_occ:   7.981  0.059  0.316 83.453  0.040  2.311   6.4791e-02
   5_bss:   7.981  0.059  0.316 83.453  0.040  2.311   6.4791e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  99.96   0.00  19.02  94.04   0.00  14.93  99.96   1.91  41.28
   1_occ:  99.96   0.00  19.02  94.04   0.00  14.93  99.96   1.91  41.28
   2_bss:  99.96   0.00  19.02  94.04   0.00  14.93  99.96   1.91  41.28
   2_xyz:  99.96   0.00  19.02  94.04   0.00  14.93  99.96   1.91  41.28
   2_adp:  99.37   0.00  19.07  92.98   0.00  14.90  99.37   5.56  41.80
   2_occ:  99.37   0.00  19.07  92.98   0.00  14.90  99.37   5.56  41.80
   3_bss:  99.37   0.00  19.07  92.98   0.00  14.90  99.37   5.56  41.80
   3_xyz:  99.37   0.00  19.07  92.98   0.00  14.90  99.37   5.56  41.80
   3_adp:  96.48   0.78  18.73  93.74   0.78  14.07  96.48   6.12  44.11
   3_occ:  96.48   0.78  18.73  93.74   0.78  14.07  96.48   6.12  44.11
   4_bss:  96.48   0.78  18.73  93.74   0.78  14.07  96.48   6.12  44.11
   4_xyz:  96.48   0.78  18.73  93.74   0.78  14.07  96.48   6.12  44.11
   4_adp:  93.65   1.47  18.34  90.38   1.47  13.79  93.65   6.11  43.11
   4_occ:  93.65   1.47  18.34  90.38   1.47  13.79  93.65   6.11  43.11
   5_bss:  93.65   1.47  18.34  90.38   1.47  13.79  93.65   6.11  43.11
   5_xyz:  93.65   1.47  18.34  90.38   1.47  13.79  93.65   6.11  43.11
   5_adp:  89.72   0.00  17.77  89.72   1.86  13.52  89.37   0.00  40.92
   5_occ:  89.72   0.00  17.77  89.72   1.86  13.52  89.37   0.00  40.92
   5_bss:  89.72   0.00  17.77  89.72   1.86  13.52  89.37   0.00  40.93
------------------------------------------------------------------------
 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:    2.739    0.019    0.383
   1_adp:    2.739    0.019    0.383
   1_occ:    2.739    0.019    0.383
   2_bss:    2.739    0.019    0.383
   2_xyz:    2.690    0.031    0.556
   2_adp:    2.690    0.031    0.556
   2_occ:    2.690    0.031    0.556
   3_bss:    2.690    0.031    0.556
   3_xyz:    2.655    0.068    0.633
   3_adp:    2.655    0.068    0.633
   3_occ:    2.655    0.068    0.633
   4_bss:    2.655    0.068    0.633
   4_xyz:    2.618    0.068    0.675
   4_adp:    2.618    0.068    0.675
   4_occ:    2.618    0.068    0.675
   5_bss:    2.618    0.068    0.675
   5_xyz:    2.615    0.054    0.691
   5_adp:    2.615    0.054    0.691
   5_occ:    2.615    0.054    0.691
   5_bss:    2.615    0.054    0.691
------------------------------------------------------------------------

CPU time actual refinement: 341.37


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_86/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_86/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_86/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_86/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_86/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 341.22 
  Macro-tasks:
    bulk solvent and scale       = 37.70  
    individual site refinement   = 139.51 
    weights calculation          = 30.48  
    collect and process          = 6.49   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 214.29 
  Micro-tasks:
    mask                            = 2.55   
    f_calc                          = 110.77 
    alpha_beta                      = 8.16   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 118.15 
    fmodel                         = 6.37   
    r_factors                      = 0.18   
    phase_errors                   = 10.40  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 258.00 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.870 micro seconds
Total CPU time: 5.92 minutes
from_scatterers_fft:    643 calls, 110.53 s
gradients_fft:          588 calls, 105.01 s

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

# Date 2008-01-16 Time 03:58:32 PST -0800 (1200484712.94 s)
Start R-work = 0.4515, R-free = 0.4527 (no bulk solvent and anisotropic scale)
Final R-work = 0.1405, R-free = 0.1815 (no bulk solvent and anisotropic scale)

Start R-work = 0.4442, R-free = 0.4416
Final R-work = 0.1118, R-free = 0.1591