# Date 2008-01-16 Time 06:29:39 PST -0800 (1200493779.11 s)
#phil __OFF__

Command line arguments: "../1166.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4031
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1166

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 47.3993, 84.2302, 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: 3.23, per 1000 atoms: 1.14


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 47.3993, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1017 1.95146
Completeness in resolution range: 0.913453
Completeness with d_max=infinity: 0.910777

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1017
                             d_min =   1.9515

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 47.3993, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1017 1.95146
Completeness in resolution range: 0.913453
Completeness with d_max=infinity: 0.910777

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1022 -  4.1774 [2262/2291]  2039   223   9.9%
  bin  2:  4.1774 -  3.3274 [2148/2171]  1933   215  10.0%
  bin  3:  3.3274 -  2.9102 [2134/2159]  1913   221  10.4%
  bin  4:  2.9102 -  2.6457 [2118/2134]  1909   209   9.9%
  bin  5:  2.6457 -  2.4569 [2086/2130]  1886   200   9.6%
  bin  6:  2.4569 -  2.3126 [2087/2115]  1870   217  10.4%
  bin  7:  2.3126 -  2.1972 [2095/2131]  1885   210  10.0%
  bin  8:  2.1972 -  2.1018 [2061/2103]  1858   203   9.8%
  bin  9:  2.1018 -  2.0211 [1998/2120]  1797   201  10.1%
  bin 10:  2.0211 -  1.9515 [ 600/2091]   540    60  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1166/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: 0.13 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:
        1.54 -     2.21: 28
        2.21 -     2.89: 1299
        2.89 -     3.56: 4469
        3.56 -     4.23: 9232
        4.23 -     4.90: 13308
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.542 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.558 3.040 -x+1/2,-y+1,z+1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.750 3.120 -x+1/2,-y+1,z-1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 324 " - " O   HOH Z 396 "  1.829 3.040 -x,y-1/2,-z+1/2
  ... (remaining 28331 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_1166/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1166/model_refine_001.geo

CPU time processing inputs: 9.04


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 47.3993 84.23025 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 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4504   r_free= 0.4518   ksol= 0.00   Bsol= 0.00   scale= 0.904    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.256635                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1022 -  4.6601 0.99   1464  166 0.3488 0.3517      6.5066      6.5152|
|  2:  4.6601 -  3.7170 0.99   1402  153 0.3732 0.3572      6.7448      6.7457|
|  3:  3.7170 -  3.2525 0.99   1382  149 0.4145 0.4104      6.6151      6.6524|
|  4:  3.2525 -  2.9576 0.99   1364  157 0.4403 0.4266      6.4615      6.4654|
|  5:  2.9576 -  2.7470 0.98   1363  149 0.4659 0.4470      6.3166      6.3177|
|  6:  2.7470 -  2.5858 0.99   1356  155 0.4845 0.5079      6.2503      6.1891|
|  7:  2.5858 -  2.4569 0.98   1349  139 0.4948 0.4599      6.2154       6.174|
|  8:  2.4569 -  2.3504 0.99   1345  155 0.4970 0.5116      6.1259      6.1803|
|  9:  2.3504 -  2.2602 0.99   1350  154 0.5156 0.5027      6.1403      6.1114|
| 10:  2.2602 -  2.1825 0.98   1326  150 0.5182 0.5459      6.0589      6.1172|
| 11:  2.1825 -  2.1144 0.97   1333  140 0.5107 0.6148      6.0298      5.9979|
| 12:  2.1144 -  2.0541 0.99   1328  151 0.5136 0.5363      5.9326      5.9622|
| 13:  2.0541 -  2.0002 0.74   1013  119 0.5314 0.4883      5.8597      5.8298|
| 14:  2.0002 -  1.9515 0.19    255   22 0.5804 0.4852      5.8145      5.8823|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1022 -  4.6601  1464   166  0.74  30.88   0.84     0.76      57641.97|
|  2:  4.6601 -  3.7170  1402   153  0.74  32.02   0.93     0.83      87461.13|
|  3:  3.7170 -  3.2525  1382   149  0.64  40.88   0.92     0.80      97345.21|
|  4:  3.2525 -  2.9576  1364   157  0.53  49.38   0.92     0.74      92164.33|
|  5:  2.9576 -  2.7470  1363   149  0.46  55.17   0.89     0.65      74741.03|
|  6:  2.7470 -  2.5858  1356   155  0.44  56.89   0.91     0.62      64544.77|
|  7:  2.5858 -  2.4569  1349   139  0.44  56.97   0.91     0.59      56472.33|
|  8:  2.4569 -  2.3504  1345   155  0.40  59.82   0.90     0.59      55012.84|
|  9:  2.3504 -  2.2602  1350   154  0.35  64.00   0.95     0.52      53830.77|
| 10:  2.2602 -  2.1825  1326   150  0.26  70.69   0.93     0.39      55506.55|
| 11:  2.1825 -  2.1144  1333   140  0.17  77.73   0.94     0.25      54483.57|
| 12:  2.1144 -  2.0541  1328   151  0.13  80.06   0.92     0.23      51092.22|
| 13:  2.0541 -  2.0002  1013   119  0.18  76.94   0.92     0.30      42239.31|
| 14:  2.0002 -  1.9515   255    22  0.27  70.11   0.87     0.42      31994.47|
|alpha:            min =        0.23 max =            0.83 mean =         0.56|
|beta:             min =    31994.47 max =        97345.21 mean =     64918.72|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           90.00 mean =        57.26|
|phase err.(test): min =        0.00 max =           89.71 mean =        57.17|
|-----------------------------------------------------------------------------|

============================== 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 = 14.953327             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.945   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.670035              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.923   (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 |  1.542 -  1.878:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.878 -  2.213:       21 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.213 -  2.549:       30 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.549 -  2.885:     1269 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.885 -  3.221:     1918 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.221 -  3.557:     2551 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.557 -  3.893:     4643 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.893 -  4.228:     4589 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.228 -  4.564:     6069 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.564 -  4.900:     7239 |
|-----------------------------------------------------------------------------|
|-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 |        0.185 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.542 |       0.513 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.935)------------------------------------------|
|    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 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4504   r_free= 0.4518   ksol= 0.00   Bsol= 0.00   scale= 0.904    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.256635                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4427   r_free= 0.4449   ksol= 0.30   Bsol= 50.00   scale= 0.946   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.50,-0.39,2.05,-0.00,0.00,0.00); trace/3= 0.72                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.253574                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.586342             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.145   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.191254              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.560   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4427      final r-factor (work) = 0.3071          |
| start r-factor (free) = 0.4449      final r-factor (free) = 0.3477          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.3843 = 11.59 * 0.50 * 6.2486 + 1.00 * 0.1851                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.5020 = 11.59 * 0.50 * 6.1048 + 1.00 * 0.1360                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3071      final r-factor (work) = 0.2805          |
| start r-factor (free) = 0.3477      final r-factor (free) = 0.3536          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2790 = 1.19 * 1.00 * 6.1048 + 1.00 * 0.0066                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1025 = 1.19 * 1.00 * 5.9359 + 1.00 * 0.0313                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.935)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.70  18.15    None  None   None       |
|    all(noH): 2823   0      0.00    114.70  18.15    None  None   None       |
|    Sol.    : 438    0      1.90    69.54   39.90    None  None   None       |
|    Mac.    : 2385   0      0.00    114.70  14.16    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 -  11.470: 1090   |   5:    57.350 -  68.820:   34        |
|      1:    11.470 -  22.940:  976   |   6:    68.820 -  80.290:    1        |
|      2:    22.940 -  34.410:  370   |   7:    80.290 -  91.760:    0        |
|      3:    34.410 -  45.880:  205   |   8:    91.760 - 103.230:    0        |
|      4:    45.880 -  57.350:  146   |   9:   103.230 - 114.700:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2805 r_free = 0.3536             target_work(ml) = 5.942         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2802 r_free = 0.3534             target_work(ml) = 5.940         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2802   r_free= 0.3534   ksol= 0.30   Bsol= 50.00   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.50,-0.39,2.05,-0.00,0.00,0.00); trace/3= 0.72                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.939988                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2783   r_free= 0.3514   ksol= 0.33   Bsol= 61.01   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.21,-1.30,-0.18,-0.00,-0.00,-0.00); trace/3= -0.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.938309                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.681009              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.928   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.666932              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.559   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2783      final r-factor (work) = 0.1942          |
| start r-factor (free) = 0.3514      final r-factor (free) = 0.2536          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.8792 = 9.68 * 0.50 * 5.9381 + 1.00 * 0.1360                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.2464 = 9.68 * 0.50 * 5.8183 + 1.00 * 0.0827                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1942      final r-factor (work) = 0.1681          |
| start r-factor (free) = 0.2536      final r-factor (free) = 0.2236          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9107 = 0.67 * 1.00 * 5.8183 + 1.00 * 0.0302                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7237 = 0.67 * 1.00 * 5.5660 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.935)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.99   18.60    None  None   None       |
|    all(noH): 2823   0      0.00    94.99   18.60    None  None   None       |
|    Sol.    : 438    0      5.71    90.35   44.72    None  None   None       |
|    Mac.    : 2385   0      0.00    94.99   13.80    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 -   9.499:  853   |   5:    47.493 -  56.991:  107        |
|      1:     9.499 -  18.997: 1194   |   6:    56.991 -  66.490:   73        |
|      2:    18.997 -  28.496:  292   |   7:    66.490 -  75.988:   40        |
|      3:    28.496 -  37.994:  123   |   8:    75.988 -  85.487:   20        |
|      4:    37.994 -  47.493:  114   |   9:    85.487 -  94.985:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1681 r_free = 0.2236             target_work(ml) = 5.501         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1680 r_free = 0.2234             target_work(ml) = 5.501         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1680   r_free= 0.2234   ksol= 0.33   Bsol= 61.01   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.21,-1.30,-0.18,-0.00,-0.00,-0.00); trace/3= -0.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.500651                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1678   r_free= 0.2225   ksol= 0.33   Bsol= 61.41   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-2.10,-1.72,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.499344                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.055317              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.232  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.238550              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.271  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1678      final r-factor (work) = 0.1388          |
| start r-factor (free) = 0.2225      final r-factor (free) = 0.1865          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5936 = 3.06 * 0.50 * 5.5712 + 1.00 * 0.0827                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3563 = 3.06 * 0.50 * 5.4319 + 1.00 * 0.0582                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1388      final r-factor (work) = 0.1325          |
| start r-factor (free) = 0.1865      final r-factor (free) = 0.1781          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3072 = 0.24 * 1.00 * 5.4319 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2770 = 0.24 * 1.00 * 5.3159 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.935)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.42    93.79   17.94    None  None   None       |
|    all(noH): 2823   0      2.42    93.79   17.94    None  None   None       |
|    Sol.    : 438    0      5.67    86.46   42.57    None  None   None       |
|    Mac.    : 2385   0      2.42    93.79   13.41    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.417 -  11.554: 1290   |   5:    48.103 -  57.240:   94        |
|      1:    11.554 -  20.691:  892   |   6:    57.240 -  66.377:   60        |
|      2:    20.691 -  29.829:  214   |   7:    66.377 -  75.514:   31        |
|      3:    29.829 -  38.966:  114   |   8:    75.514 -  84.652:   16        |
|      4:    38.966 -  48.103:  107   |   9:    84.652 -  93.789:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1325 r_free = 0.1781             target_work(ml) = 5.291         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1324 r_free = 0.1777             target_work(ml) = 5.290         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1324   r_free= 0.1777   ksol= 0.33   Bsol= 61.41   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-2.10,-1.72,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.290025                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1326   r_free= 0.1782   ksol= 0.33   Bsol= 57.18   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-2.44,-2.30,-0.00,-0.00,-0.00); trace/3= -2.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.292056                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.128468              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 127.713  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.658329              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.357  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1326      final r-factor (work) = 0.1187          |
| start r-factor (free) = 0.1782      final r-factor (free) = 0.1648          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3770 = 3.13 * 0.50 * 5.3181 + 1.00 * 0.0582                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2780 = 3.13 * 0.50 * 5.2475 + 1.00 * 0.0696                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1187      final r-factor (work) = 0.1157          |
| start r-factor (free) = 0.1648      final r-factor (free) = 0.1639          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4634 = 0.66 * 1.00 * 5.2475 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4263 = 0.66 * 1.00 * 5.1898 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.935)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.87    99.50   17.94    None  None   None       |
|    all(noH): 2823   0      1.87    99.50   17.94    None  None   None       |
|    Sol.    : 438    0      5.65    86.04   42.85    None  None   None       |
|    Mac.    : 2385   0      1.87    99.50   13.37    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:     1.875 -  11.638: 1325   |   5:    50.690 -  60.453:  101        |
|      1:    11.638 -  21.401:  888   |   6:    60.453 -  70.216:   50        |
|      2:    21.401 -  31.164:  198   |   7:    70.216 -  79.979:   29        |
|      3:    31.164 -  40.927:  122   |   8:    79.979 -  89.742:    8        |
|      4:    40.927 -  50.690:   97   |   9:    89.742 -  99.505:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1157 r_free = 0.1639             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1156 r_free = 0.1638             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1156   r_free= 0.1638   ksol= 0.33   Bsol= 57.18   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-2.44,-2.30,-0.00,-0.00,-0.00); trace/3= -2.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.186670                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1156   r_free= 0.1637   ksol= 0.32   Bsol= 52.59   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-2.36,-2.30,-0.00,-0.00,-0.00); trace/3= -2.34                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.186681                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.141030              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.910  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.225146              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.921  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1156      final r-factor (work) = 0.1116          |
| start r-factor (free) = 0.1637      final r-factor (free) = 0.1620          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2201 = 3.14 * 0.50 * 5.1897 + 1.00 * 0.0696                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1971 = 3.14 * 0.50 * 5.1736 + 1.00 * 0.0719                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1116      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1620      final r-factor (free) = 0.1608          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1744 = 0.23 * 1.00 * 5.1736 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1719 = 0.23 * 1.00 * 5.1693 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.935)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.20    96.72   17.25    None  None   None       |
|    all(noH): 2823   0      2.20    96.72   17.25    None  None   None       |
|    Sol.    : 438    0      5.89    81.35   39.98    None  None   None       |
|    Mac.    : 2385   0      2.20    96.72   13.07    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:     2.201 -  11.652: 1359   |   5:    49.459 -  58.910:   85        |
|      1:    11.652 -  21.104:  869   |   6:    58.910 -  68.362:   33        |
|      2:    21.104 -  30.556:  190   |   7:    68.362 -  77.813:   21        |
|      3:    30.556 -  40.007:  140   |   8:    77.813 -  87.265:    5        |
|      4:    40.007 -  49.459:  116   |   9:    87.265 -  96.717:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1120 r_free = 0.1608             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1119 r_free = 0.1605             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1605   ksol= 0.32   Bsol= 52.59   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-2.36,-2.30,-0.00,-0.00,-0.00); trace/3= -2.34                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.165196                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1022 -  4.6601 0.99   1464  166 0.0954 0.1315       5.363      5.5661|
|  2:  4.6601 -  3.7170 0.99   1402  153 0.0827 0.1043      5.4116      5.6188|
|  3:  3.7170 -  3.2525 0.99   1382  149 0.1051 0.1714      5.4524      5.9125|
|  4:  3.2525 -  2.9576 0.99   1364  157 0.1294 0.1585      5.4785      5.6185|
|  5:  2.9576 -  2.7470 0.98   1363  149 0.1332 0.1824      5.3383      5.5406|
|  6:  2.7470 -  2.5858 0.99   1356  155 0.1248 0.1882      5.2199      5.4255|
|  7:  2.5858 -  2.4569 0.98   1349  139 0.1230 0.1705      5.1623      5.4015|
|  8:  2.4569 -  2.3504 0.99   1345  155 0.1181 0.1621      5.0612      5.2509|
|  9:  2.3504 -  2.2602 0.99   1350  154 0.1160 0.1985      5.0326      5.3432|
| 10:  2.2602 -  2.1825 0.98   1326  150 0.1139 0.1726      4.9771      5.2819|
| 11:  2.1825 -  2.1144 0.97   1333  140 0.1133 0.1850      4.9381      5.2218|
| 12:  2.1144 -  2.0541 0.99   1328  151 0.1163 0.1783      4.8818      5.1395|
| 13:  2.0541 -  2.0002 0.74   1013  119 0.1158 0.1722      4.7773      4.9928|
| 14:  2.0002 -  1.9515 0.19    255   22 0.1178 0.1600      4.6747      4.9409|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1022 -  4.6601  1464   166  0.94   8.86   0.97     0.95       6968.79|
|  2:  4.6601 -  3.7170  1402   153  0.95   7.77   1.01     0.99       8771.47|
|  3:  3.7170 -  3.2525  1382   149  0.93  11.60   1.02     1.02      10230.68|
|  4:  3.2525 -  2.9576  1364   157  0.91  15.17   1.00     0.97      11094.63|
|  5:  2.9576 -  2.7470  1363   149  0.89  16.72   0.99     0.97       8759.48|
|  6:  2.7470 -  2.5858  1356   155  0.90  16.39   0.98     0.95       7298.14|
|  7:  2.5858 -  2.4569  1349   139  0.90  15.88   0.99     0.96       6324.23|
|  8:  2.4569 -  2.3504  1345   155  0.90  15.91   0.99     0.96       5467.17|
|  9:  2.3504 -  2.2602  1350   154  0.89  16.90   1.00     0.96       5155.16|
| 10:  2.2602 -  2.1825  1326   150  0.90  16.00   0.98     0.95       4714.84|
| 11:  2.1825 -  2.1144  1333   140  0.90  16.56   0.99     0.95       4502.87|
| 12:  2.1144 -  2.0541  1328   151  0.90  16.91   0.99     0.99       4167.44|
| 13:  2.0541 -  2.0002  1013   119  0.90  16.75   0.98     0.97       3340.20|
| 14:  2.0002 -  1.9515   255    22  0.89  16.34   0.97     0.95       2605.26|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2605.26 max =        11094.63 mean =      6709.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.64|
|phase err.(test): min =        0.00 max =           87.60 mean =        14.00|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1605   ksol= 0.32   Bsol= 52.51   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-2.18,-2.14,-0.00,-0.00,-0.00); trace/3= -2.16                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.165272                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1605   ksol= 0.32   Bsol= 52.51   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-2.18,-2.14,-0.00,-0.00,-0.00); trace/3= -2.16                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.165272                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1022 -  4.6601 0.99   1464  166 0.0954 0.1316      5.3635      5.5669|
|  2:  4.6601 -  3.7170 0.99   1402  153 0.0827 0.1043      5.4119      5.6188|
|  3:  3.7170 -  3.2525 0.99   1382  149 0.1051 0.1714      5.4523      5.9126|
|  4:  3.2525 -  2.9576 0.99   1364  157 0.1294 0.1585      5.4785      5.6185|
|  5:  2.9576 -  2.7470 0.98   1363  149 0.1331 0.1824      5.3382      5.5404|
|  6:  2.7470 -  2.5858 0.99   1356  155 0.1248 0.1883        5.22      5.4256|
|  7:  2.5858 -  2.4569 0.98   1349  139 0.1230 0.1705      5.1625      5.4017|
|  8:  2.4569 -  2.3504 0.99   1345  155 0.1181 0.1621      5.0613      5.2511|
|  9:  2.3504 -  2.2602 0.99   1350  154 0.1160 0.1985      5.0328      5.3431|
| 10:  2.2602 -  2.1825 0.98   1326  150 0.1139 0.1725      4.9772      5.2817|
| 11:  2.1825 -  2.1144 0.97   1333  140 0.1133 0.1849      4.9381      5.2219|
| 12:  2.1144 -  2.0541 0.99   1328  151 0.1163 0.1782      4.8815      5.1389|
| 13:  2.0541 -  2.0002 0.74   1013  119 0.1158 0.1722      4.7771      4.9926|
| 14:  2.0002 -  1.9515 0.19    255   22 0.1178 0.1601      4.6746      4.9414|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1022 -  4.6601  1464   166  0.94   8.86   0.98     0.95       6976.07|
|  2:  4.6601 -  3.7170  1402   153  0.95   7.77   1.01     0.99       8776.67|
|  3:  3.7170 -  3.2525  1382   149  0.93  11.60   1.02     1.02      10232.31|
|  4:  3.2525 -  2.9576  1364   157  0.91  15.17   1.00     0.97      11092.99|
|  5:  2.9576 -  2.7470  1363   149  0.89  16.72   0.99     0.97       8759.30|
|  6:  2.7470 -  2.5858  1356   155  0.90  16.39   0.98     0.96       7299.22|
|  7:  2.5858 -  2.4569  1349   139  0.90  15.88   0.99     0.96       6326.46|
|  8:  2.4569 -  2.3504  1345   155  0.90  15.91   0.99     0.96       5468.35|
|  9:  2.3504 -  2.2602  1350   154  0.89  16.91   1.00     0.96       5155.12|
| 10:  2.2602 -  2.1825  1326   150  0.90  16.01   0.99     0.95       4715.17|
| 11:  2.1825 -  2.1144  1333   140  0.90  16.56   0.99     0.96       4502.23|
| 12:  2.1144 -  2.0541  1328   151  0.90  16.91   1.00     0.99       4165.09|
| 13:  2.0541 -  2.0002  1013   119  0.90  16.74   0.99     0.97       3338.98|
| 14:  2.0002 -  1.9515   255    22  0.89  16.33   0.98     0.95       2604.98|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2604.98 max =        11092.99 mean =      6710.54|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.64|
|phase err.(test): min =        0.00 max =           87.60 mean =        14.00|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.935)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.12    96.64   17.17    None  None   None       |
|    all(noH): 2823   0      2.12    96.64   17.17    None  None   None       |
|    Sol.    : 438    0      5.81    81.27   39.90    None  None   None       |
|    Mac.    : 2385   0      2.12    96.64   12.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.121 -  11.573: 1359   |   5:    49.379 -  58.831:   85        |
|      1:    11.573 -  21.024:  869   |   6:    58.831 -  68.282:   33        |
|      2:    21.024 -  30.476:  190   |   7:    68.282 -  77.734:   21        |
|      3:    30.476 -  39.928:  140   |   8:    77.734 -  87.185:    5        |
|      4:    39.928 -  49.379:  116   |   9:    87.185 -  96.637:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 327         
Filter by distance & map next to the model:
   mapped sites are within: 0.530 - 5.881
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 321 from: 327
   mapped sites are within: 0.712 - 5.881

peak=    5.747 closest distance to " CB  GLN A 223 " =    1.492
peak=    5.627 closest distance to " O   HOH Z 111 " =    2.110
peak=    5.586 closest distance to " CB  SER A  63 " =    1.295
peak=    5.337 closest distance to " CG  PRO A  54 " =    1.206
peak=    4.825 closest distance to " CB  PRO A  54 " =    0.837
peak=    4.792 closest distance to " O   HOH Z 126 " =    1.649
peak=    4.736 closest distance to " O   HOH Z 193 " =    2.032
peak=    4.721 closest distance to " O   HOH Z  15 " =    2.069
peak=    4.703 closest distance to " CB  GLU A 152 " =    1.155
peak=    4.666 closest distance to " O   HOH Z 232 " =    2.250
peak=    4.659 closest distance to " CB  ARG A 275 " =    0.882
peak=    4.625 closest distance to " CB  LEU A 228 " =    1.104
peak=    4.625 closest distance to " CG  PRO A 213 " =    1.181
peak=    4.603 closest distance to " OD2 ASP A 286 " =    2.921
peak=    4.603 closest distance to " C   PRO A 198 " =    1.541
peak=    4.512 closest distance to " CB  GLU A 128 " =    1.164
peak=    4.446 closest distance to " CB  GLN A 183 " =    1.228
peak=    4.444 closest distance to " CB  SER A   3 " =    1.361
peak=    4.444 closest distance to " O   HOH Z  68 " =    1.898
peak=    4.441 closest distance to " O   HOH Z 368 " =    2.005
peak=    4.364 closest distance to " CA  THR A 221 " =    0.949
peak=    4.359 closest distance to " O   HOH Z 108 " =    1.761
peak=    4.339 closest distance to " O   HOH Z 236 " =    1.855
peak=    4.324 closest distance to " CB  VAL A 202 " =    1.633
peak=    4.309 closest distance to " CG  PRO A  90 " =    1.061
peak=    4.304 closest distance to " O   HOH Z 132 " =    1.119
peak=    4.299 closest distance to " O   HOH Z 234 " =    3.808
peak=    4.297 closest distance to " CB  ASN A 148 " =    1.244
peak=    4.292 closest distance to " O   HOH Z  20 " =    2.121
peak=    4.291 closest distance to " CA  ALA A  21 " =    1.241
peak=    4.290 closest distance to " O   HOH Z 207 " =    1.938
peak=    4.280 closest distance to " OD1 ASN A  69 " =    2.515
peak=    4.243 closest distance to " O   HOH Z 180 " =    2.162
peak=    4.227 closest distance to " O   HOH Z 426 " =    1.492
peak=    4.220 closest distance to " CB  GLU A 277 " =    3.660
peak=    4.198 closest distance to " O   HOH Z 298 " =    1.763
peak=    4.176 closest distance to " ND2 ASN A 187 " =    1.671
peak=    4.171 closest distance to " NH2BARG A 145 " =    2.098
peak=    4.152 closest distance to " NH2 ARG A 156 " =    1.221
peak=    4.126 closest distance to " O   HOH Z 134 " =    1.541
peak=    4.117 closest distance to " O   HOH Z  80 " =    1.736
peak=    4.104 closest distance to " CB  TYR A 169 " =    0.778
peak=    4.098 closest distance to " CB  ASN A 148 " =    1.744
peak=    4.090 closest distance to " O   HOH Z 425 " =    1.499
peak=    4.069 closest distance to " CA  TYR A  30 " =    0.962
peak=    4.059 closest distance to " O   HOH Z 135 " =    1.824
peak=    4.050 closest distance to " CG  PRO A 198 " =    1.352
peak=    4.038 closest distance to " CB  ARG A  79 " =    1.333
peak=    4.022 closest distance to " O   HOH Z 313 " =    1.911
peak=    4.021 closest distance to " CA  ALA A  51 " =    0.929
peak=    4.009 closest distance to " O   HOH Z  21 " =    1.678
peak=    3.999 closest distance to " O   HOH Z  61 " =    1.650
peak=    3.997 closest distance to " O   HOH Z 371 " =    3.488
peak=    3.995 closest distance to " O   HOH Z 132 " =    2.158
peak=    3.995 closest distance to " CG  PRO A 243 " =    1.101
peak=    3.994 closest distance to " NE2 GLN A  11 " =    1.091
peak=    3.992 closest distance to " O   HOH Z 403 " =    1.715
peak=    3.964 closest distance to " O   HOH Z  49 " =    2.250
peak=    3.960 closest distance to " O   SER A  87 " =    2.209
peak=    3.958 closest distance to " CB  TRP A 179 " =    1.411
peak=    3.948 closest distance to " O   HOH Z 389 " =    1.961
peak=    3.931 closest distance to " O   HOH Z 369 " =    2.023
peak=    3.924 closest distance to " CG  PRO A 280 " =    0.712
peak=    3.920 closest distance to " O   HOH Z  78 " =    2.170
peak=    3.913 closest distance to " O   HOH Z 272 " =    1.971
peak=    3.910 closest distance to " O   HOH Z 316 " =    3.053
peak=    3.906 closest distance to " O   HOH Z 303 " =    2.157
peak=    3.899 closest distance to " CD BLYS A 290 " =    1.095
peak=    3.890 closest distance to " O   HOH Z 209 " =    2.381
peak=    3.889 closest distance to " O   HOH Z 132 " =    2.460
peak=    3.884 closest distance to " CD1 LEU A 300 " =    1.221
peak=    3.884 closest distance to " CA  MET A  40 " =    1.074
peak=    3.883 closest distance to " O   HOH Z  54 " =    1.766
peak=    3.879 closest distance to " NH1AARG A 145 " =    1.052
peak=    3.878 closest distance to " O   HOH Z 344 " =    3.003
peak=    3.866 closest distance to " CG2 THR A 221 " =    0.955
peak=    3.837 closest distance to " O   HOH Z 261 " =    2.053
peak=    3.834 closest distance to " O   HOH Z 214 " =    0.998
peak=    3.833 closest distance to " O   HOH Z 352 " =    1.909
peak=    3.822 closest distance to " OD1 ASN A 217 " =    1.770
peak=    3.820 closest distance to " O   HOH Z 193 " =    2.207
peak=    3.815 closest distance to " CB  ARG A 190 " =    1.664
peak=    3.812 closest distance to " N   ASN A  39 " =    1.288
peak=    3.806 closest distance to " O   HOH Z 427 " =    2.917
peak=    3.805 closest distance to " O   HOH Z 189 " =    2.289
peak=    3.803 closest distance to " O   HOH Z 411 " =    3.627
peak=    3.800 closest distance to " CG1 ILE A  33 " =    1.244
peak=    3.797 closest distance to " O   HOH Z 247 " =    1.338
peak=    3.779 closest distance to " CD  LYS A 166 " =    1.336
peak=    3.773 closest distance to " O   HOH Z 284 " =    3.008
peak=    3.729 closest distance to " O   HOH Z  88 " =    3.626
peak=    3.728 closest distance to " O   HOH Z 423 " =    1.940
peak=    3.722 closest distance to " O   HOH Z 197 " =    2.412
peak=    3.719 closest distance to " CB  MET A  47 " =    0.942
peak=    3.713 closest distance to " O   HOH Z 144 " =    1.553
peak=    3.709 closest distance to " O   HOH Z  48 " =    1.480
peak=    3.702 closest distance to " O   HOH Z 374 " =    2.711
peak=    3.689 closest distance to " O   HOH Z  40 " =    1.587
peak=    3.688 closest distance to " CA  ASP A 124 " =    0.740
peak=    3.687 closest distance to " O   HOH Z  93 " =    2.516
peak=    3.683 closest distance to " O   HOH Z  97 " =    1.934
peak=    3.668 closest distance to " O   HOH Z   6 " =    2.189
peak=    3.667 closest distance to " O   HOH Z 128 " =    2.226
peak=    3.664 closest distance to " O   MET A 105 " =    1.840
peak=    3.664 closest distance to " NH2AARG A 190 " =    1.527
peak=    3.663 closest distance to " O   HOH Z 126 " =    1.744
peak=    3.654 closest distance to " NZ  LYS A 117 " =    3.322
peak=    3.648 closest distance to " CB  TRP A 266 " =    0.927
peak=    3.645 closest distance to " CB  GLU A 152 " =    1.538
peak=    3.636 closest distance to " CB  LEU A 143 " =    1.109
peak=    3.636 closest distance to " O   HOH Z 279 " =    2.314
peak=    3.634 closest distance to " O   HOH Z 265 " =    2.241
peak=    3.631 closest distance to " O   HOH Z 166 " =    1.609
peak=    3.621 closest distance to " O   HOH Z 227 " =    1.698
peak=    3.620 closest distance to " CA  ASP A 191 " =    0.789
peak=    3.619 closest distance to " CA  GLU A 152 " =    0.939
peak=    3.614 closest distance to " O   HOH Z 326 " =    1.481
peak=    3.609 closest distance to " O   HOH Z 281 " =    4.102
peak=    3.601 closest distance to " CD  ARG A 159 " =    0.829
peak=    3.585 closest distance to " O   HOH Z  98 " =    2.167
peak=    3.583 closest distance to " NH2BARG A 102 " =    0.933
peak=    3.582 closest distance to " CB  PHE A  16 " =    1.047
peak=    3.580 closest distance to " CD2 LEU A 255 " =    1.295
peak=    3.569 closest distance to " O   ALA A 165 " =    1.375
peak=    3.558 closest distance to " O   HOH Z 183 " =    1.611
peak=    3.558 closest distance to " CA  THR A 264 " =    0.891
peak=    3.548 closest distance to " O   HOH Z  53 " =    2.485
peak=    3.547 closest distance to " OG BSER A 164 " =    2.590
peak=    3.544 closest distance to " O   HOH Z 260 " =    1.173
peak=    3.539 closest distance to " O   HOH Z 133 " =    1.732
peak=    3.537 closest distance to " O   HOH Z  10 " =    1.836
peak=    3.532 closest distance to " O   HOH Z  30 " =    1.604
peak=    3.524 closest distance to " O   HOH Z 368 " =    2.600
peak=    3.520 closest distance to " O   HOH Z 345 " =    1.736
peak=    3.519 closest distance to " ND1 HIS A  81 " =    1.593
peak=    3.514 closest distance to " CB  TYR A 116 " =    1.082
peak=    3.513 closest distance to " CB  VAL A 265 " =    1.215
peak=    3.511 closest distance to " O   HOH Z 174 " =    2.481
peak=    3.506 closest distance to " O   HOH Z 387 " =    2.533
peak=    3.506 closest distance to " O   HOH Z 118 " =    1.720
peak=    3.504 closest distance to " CB  TYR A  30 " =    1.400
peak=    3.492 closest distance to " O   HOH Z 147 " =    1.749
peak=    3.488 closest distance to " O   HOH Z  44 " =    1.878
peak=    3.488 closest distance to " O   HOH Z 116 " =    1.869
peak=    3.481 closest distance to " CA  ARG A  36 " =    1.238
peak=    3.473 closest distance to " O   HOH Z 214 " =    2.261
peak=    3.472 closest distance to " CA  GLN A 223 " =    0.978
peak=    3.471 closest distance to " O   TRP A 274 " =    1.846
peak=    3.468 closest distance to " ND1 HIS A  86 " =    1.709
peak=    3.465 closest distance to " O   HOH Z 261 " =    2.041
peak=    3.462 closest distance to " O   HOH Z   1 " =    2.143
peak=    3.458 closest distance to " O   HOH Z 437 " =    1.498
peak=    3.453 closest distance to " CZ  PHE A 192 " =    0.940
peak=    3.449 closest distance to " O   HOH Z 172 " =    4.027
peak=    3.445 closest distance to " CB  SER A 216 " =    0.799
peak=    3.445 closest distance to " CG BARG A 102 " =    1.934
peak=    3.445 closest distance to " O   HOH Z 345 " =    3.379
peak=    3.444 closest distance to " O   HOH Z 243 " =    1.847
peak=    3.439 closest distance to " O   HOH Z 124 " =    1.419
peak=    3.436 closest distance to " O   HOH Z 337 " =    3.755
peak=    3.433 closest distance to " CB  MET A  40 " =    0.869
peak=    3.431 closest distance to " O   HOH Z 334 " =    1.457
peak=    3.423 closest distance to " O   HOH Z 171 " =    3.842
peak=    3.421 closest distance to " CB  ALA A 248 " =    0.949
peak=    3.418 closest distance to " CG2 THR A 220 " =    1.053
peak=    3.416 closest distance to " CA  ASN A 215 " =    1.208
peak=    3.411 closest distance to " CG  GLU A 277 " =    2.290
peak=    3.404 closest distance to " O   HOH Z 411 " =    1.715
peak=    3.403 closest distance to " O   HOH Z 295 " =    1.463
peak=    3.401 closest distance to " O   HOH Z 383 " =    2.057
peak=    3.400 closest distance to " O   HOH Z 327 " =    1.982
peak=    3.400 closest distance to " O   HOH Z 108 " =    1.755
peak=    3.397 closest distance to " O   HOH Z 163 " =    1.612
peak=    3.396 closest distance to " CA  ALA A 160 " =    0.859
peak=    3.393 closest distance to " CG2 ILE A 120 " =    1.196
peak=    3.389 closest distance to " CG  MET A 185 " =    1.036
peak=    3.388 closest distance to " CD  ARG A  66 " =    2.497
peak=    3.385 closest distance to " N   ARG A 156 " =    1.418
peak=    3.380 closest distance to " CG1 VAL A 202 " =    2.010
peak=    3.378 closest distance to " CG2 VAL A 197 " =    1.159
peak=    3.377 closest distance to " O   HOH Z 112 " =    1.543
peak=    3.372 closest distance to " N   ASN A 127 " =    1.255
peak=    3.372 closest distance to " O   HOH Z 217 " =    1.307
peak=    3.371 closest distance to " CB  ARG A 139 " =    0.940
peak=    3.368 closest distance to " CD1 ILE A 106 " =    0.982
peak=    3.367 closest distance to " O   HOH Z 128 " =    2.400
peak=    3.363 closest distance to " O   HOH Z 189 " =    1.582
peak=    3.362 closest distance to " O   THR A 251 " =    1.220
peak=    3.357 closest distance to " CD2 HIS A  81 " =    1.100
peak=    3.355 closest distance to " O   HOH Z  63 " =    1.818
peak=    3.354 closest distance to " O   HOH Z 173 " =    1.984
peak=    3.351 closest distance to " O   ALA A   1 " =    1.513
peak=    3.350 closest distance to " O   HOH Z 329 " =    3.543
peak=    3.346 closest distance to " O   HOH Z  85 " =    2.231
peak=    3.341 closest distance to " CA  LYS A 117 " =    1.242
peak=    3.339 closest distance to " CB  SER A 212 " =    1.124
peak=    3.339 closest distance to " CB  ARG A 259 " =    1.868
peak=    3.337 closest distance to " CD  LYS A 119 " =    1.422
peak=    3.337 closest distance to " O   THR A  31 " =    1.550
peak=    3.337 closest distance to " CZ  PHE A 208 " =    1.132
peak=    3.336 closest distance to " O   HOH Z 139 " =    3.112
peak=    3.335 closest distance to " CB  ILE A 199 " =    1.009
peak=    3.328 closest distance to " OE1 GLN A  11 " =    1.938
peak=    3.328 closest distance to " O   HOH Z 425 " =    2.122
peak=    3.326 closest distance to " CG1BVAL A  72 " =    1.630
peak=    3.323 closest distance to " O   HOH Z 394 " =    1.663
peak=    3.319 closest distance to " CG2 VAL A 112 " =    1.451
peak=    3.316 closest distance to " CG  LEU A 167 " =    1.156
peak=    3.315 closest distance to " OG  SER A  22 " =    2.874
peak=    3.314 closest distance to " O   HOH Z  11 " =    1.182
peak=    3.313 closest distance to " CG AARG A 275 " =    1.070
peak=    3.310 closest distance to " CB  ASN A 187 " =    1.100
peak=    3.305 closest distance to " CB  TRP A 150 " =    1.505
peak=    3.304 closest distance to " CD  ARG A 269 " =    0.888
peak=    3.304 closest distance to " CG2BVAL A  41 " =    0.801
peak=    3.302 closest distance to " O   HOH Z 427 " =    3.090
peak=    3.300 closest distance to " CB  SER A 141 " =    0.980
peak=    3.295 closest distance to " O   HOH Z  47 " =    1.329
peak=    3.294 closest distance to " CB  HIS A 108 " =    0.945
peak=    3.288 closest distance to " CA  GLY A 267 " =    0.974
peak=    3.288 closest distance to " CA  ASP A 140 " =    1.196
peak=    3.286 closest distance to " CZ  PHE A 218 " =    1.011
peak=    3.285 closest distance to " NZ  LYS A 166 " =    3.010
peak=    3.283 closest distance to " CB  GLU A  46 " =    1.003
peak=    3.282 closest distance to " CG  GLN A  88 " =    1.062
peak=    3.281 closest distance to " O   HOH Z 207 " =    1.872
peak=    3.278 closest distance to " CB  ALA A 291 " =    1.429
peak=    3.277 closest distance to " O   HOH Z 353 " =    2.679
peak=    3.276 closest distance to " CA  ASN A  74 " =    1.157
peak=    3.273 closest distance to " O   HOH Z 276 " =    1.280
peak=    3.272 closest distance to " CA  ALA A 295 " =    1.083
peak=    3.272 closest distance to " O   HOH Z 305 " =    3.628
peak=    3.269 closest distance to " O   HOH Z 343 " =    2.288
peak=    3.268 closest distance to " OE1 GLN A  58 " =    5.881
peak=    3.265 closest distance to " CB  ALA A 100 " =    1.247
peak=    3.264 closest distance to " O   HOH Z 282 " =    1.413
peak=    3.263 closest distance to " O   HOH Z 355 " =    1.595
peak=    3.259 closest distance to " CA  LEU A 282 " =    1.042
peak=    3.256 closest distance to " CD1 TRP A 266 " =    1.149
peak=    3.255 closest distance to " O   HOH Z 409 " =    3.126
peak=    3.255 closest distance to " CA  TYR A 116 " =    1.478
peak=    3.251 closest distance to " O   HOH Z 114 " =    1.630
peak=    3.251 closest distance to " CE1 HIS A 115 " =    0.931
peak=    3.250 closest distance to " O   HOH Z  43 " =    1.976
peak=    3.249 closest distance to " O   HOH Z 214 " =    1.829
peak=    3.248 closest distance to " O   HOH Z 157 " =    1.586
peak=    3.246 closest distance to " CG2 VAL A  78 " =    0.974
peak=    3.241 closest distance to " CA  SER A  87 " =    0.886
peak=    3.240 closest distance to " O   HOH Z 438 " =    2.193
peak=    3.238 closest distance to " O   HOH Z 346 " =    1.565
peak=    3.236 closest distance to " O   HOH Z 273 " =    2.592
peak=    3.235 closest distance to " O   GLY A  57 " =    2.490
peak=    3.234 closest distance to " CE  LYS A  76 " =    0.864
peak=    3.234 closest distance to " CB  ASN A 285 " =    0.889
peak=    3.234 closest distance to " O   HOH Z 245 " =    1.326
peak=    3.231 closest distance to " CG  GLN A  58 " =    2.536
peak=    3.231 closest distance to " C   SER A  32 " =    0.983
peak=    3.231 closest distance to " CA  ALA A 154 " =    0.973
peak=    3.229 closest distance to " NE AARG A 275 " =    1.492
peak=    3.228 closest distance to " CA  GLU A  46 " =    0.716
peak=    3.227 closest distance to " O   HOH Z 193 " =    1.559
peak=    3.225 closest distance to " CA  ARG A 195 " =    1.282
peak=    3.225 closest distance to " O   HOH Z 109 " =    2.794
peak=    3.224 closest distance to " CB  ASN A  39 " =    0.832
peak=    3.223 closest distance to " O   HOH Z 192 " =    2.011
peak=    3.222 closest distance to " O   HOH Z  63 " =    2.246
peak=    3.211 closest distance to " C   ALA A 299 " =    0.962
peak=    3.211 closest distance to " O   HOH Z  22 " =    2.483
peak=    3.210 closest distance to " O   HOH Z 388 " =    1.862
peak=    3.208 closest distance to " O   HOH Z 182 " =    1.323
peak=    3.206 closest distance to " O   THR A 220 " =    1.501
peak=    3.203 closest distance to " CG  MET A  93 " =    1.002
peak=    3.203 closest distance to " CA  TYR A 186 " =    1.340
peak=    3.196 closest distance to " O   HOH Z 266 " =    2.767
peak=    3.194 closest distance to " CA  ALA A 158 " =    1.072
peak=    3.190 closest distance to " CG BARG A 275 " =    1.503
peak=    3.190 closest distance to " O   HOH Z 422 " =    2.720
peak=    3.190 closest distance to " O   HOH Z 286 " =    2.129
peak=    3.190 closest distance to " O   HOH Z  59 " =    2.612
peak=    3.188 closest distance to " O   ALA A 158 " =    1.231
peak=    3.184 closest distance to " O   HOH Z  87 " =    2.504
peak=    3.182 closest distance to " O   HOH Z 175 " =    3.651
peak=    3.181 closest distance to " O   HOH Z 291 " =    1.564
peak=    3.174 closest distance to " NH1 ARG A  56 " =    1.189
peak=    3.171 closest distance to " O   HOH Z 158 " =    2.984
peak=    3.166 closest distance to " CA  ILE A  33 " =    1.656
peak=    3.164 closest distance to " CB  PRO A 198 " =    1.061
peak=    3.164 closest distance to " C   LYS A 290 " =    1.331
peak=    3.164 closest distance to " O   HOH Z 156 " =    3.097
peak=    3.158 closest distance to " OG ASER A  99 " =    2.147
peak=    3.158 closest distance to " CG1 ILE A 151 " =    0.859
peak=    3.156 closest distance to " NZ  LYS A  76 " =    1.187
peak=    3.155 closest distance to " CA  ASP A 162 " =    1.183
peak=    3.153 closest distance to " CB  MET A 105 " =    1.234
peak=    3.151 closest distance to " O   HOH Z 188 " =    2.150
peak=    3.151 closest distance to " O   HOH Z 156 " =    2.642
peak=    3.151 closest distance to " OG  SER A  97 " =    3.576
peak=    3.148 closest distance to " O   HOH Z 185 " =    1.858
peak=    3.146 closest distance to " CG2 VAL A 174 " =    1.386
peak=    3.145 closest distance to " O   HOH Z 368 " =    3.660
peak=    3.142 closest distance to " CD2 TRP A 179 " =    1.286
peak=    3.140 closest distance to " CG1 VAL A 153 " =    1.013
peak=    3.139 closest distance to " OG1 THR A 294 " =    1.650
peak=    3.132 closest distance to " OD1 ASP A 238 " =    0.929
peak=    3.129 closest distance to " O   GLY A 229 " =    1.955
peak=    3.127 closest distance to " CG2 VAL A 112 " =    0.743
peak=    3.124 closest distance to " O   HOH Z 211 " =    2.356
peak=    3.120 closest distance to " NH1 ARG A 138 " =    1.158
peak=    3.120 closest distance to " O   HOH Z 419 " =    2.979
peak=    3.104 closest distance to " NH1BARG A 145 " =    1.047
peak=    3.097 closest distance to " CG  MET A 113 " =    1.495
peak=    3.087 closest distance to " CB  SER A  62 " =    1.278
peak=    3.081 closest distance to " O   HOH Z 128 " =    1.677
peak=    3.079 closest distance to " CA  ALA A 248 " =    1.188
peak=    3.068 closest distance to " O   HOH Z 171 " =    2.376
peak=    3.054 closest distance to " O   HOH Z 285 " =    1.935
peak=    3.050 closest distance to " CD  ARG A 219 " =    0.978
peak=    3.041 closest distance to " CD2 HIS A  81 " =    1.093
peak=    3.040 closest distance to " O   HOH Z 166 " =    3.050
peak=    3.031 closest distance to " O   HOH Z 197 " =    2.163
peak=    3.017 closest distance to " O   HOH Z  85 " =    1.999

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.738 - 5.515
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 210
   mapped sites are within: 0.738 - 5.515

peak=   -4.561 closest distance to " O   HOH Z 266 " =    4.271
peak=   -4.413 closest distance to " O   HOH Z 290 " =    1.043
peak=   -4.203 closest distance to " CG  LEU A 101 " =    2.600
peak=   -4.177 closest distance to " N   ALA A  43 " =    2.421
peak=   -4.147 closest distance to " CB  PRO A 243 " =    2.618
peak=   -4.128 closest distance to " CD1 LEU A 228 " =    2.406
peak=   -4.116 closest distance to " O   HOH Z  10 " =    1.575
peak=   -4.103 closest distance to " CD  ARG A 156 " =    1.986
peak=   -4.062 closest distance to " O   HOH Z 377 " =    1.794
peak=   -4.049 closest distance to " O   HOH Z  52 " =    1.432
peak=   -4.034 closest distance to " CD2 LEU A 300 " =    2.970
peak=   -3.967 closest distance to " O   ILE A 109 " =    2.701
peak=   -3.936 closest distance to " O   HOH Z 283 " =    1.797
peak=   -3.909 closest distance to " O   VAL A  67 " =    2.772
peak=   -3.909 closest distance to " OG  SER A  97 " =    2.199
peak=   -3.898 closest distance to " CD  ARG A 139 " =    1.651
peak=   -3.880 closest distance to " CH2 TRP A 179 " =    1.178
peak=   -3.861 closest distance to " CD2 LEU A 237 " =    2.616
peak=   -3.859 closest distance to " O   HOH Z 388 " =    1.969
peak=   -3.856 closest distance to " O   HOH Z  92 " =    1.511
peak=   -3.854 closest distance to " O   PRO A 163 " =    2.069
peak=   -3.848 closest distance to " O   HOH Z  13 " =    1.352
peak=   -3.841 closest distance to " C   ALA A 158 " =    1.241
peak=   -3.828 closest distance to " O   HOH Z 372 " =    2.604
peak=   -3.821 closest distance to " O   HOH Z 353 " =    2.203
peak=   -3.821 closest distance to " CD  LYS A 289 " =    2.439
peak=   -3.820 closest distance to " OXT GLY A 302 " =    2.929
peak=   -3.819 closest distance to " O   HOH Z  17 " =    1.514
peak=   -3.818 closest distance to " CG1 VAL A 112 " =    2.604
peak=   -3.815 closest distance to " C   ASN A 187 " =    1.821
peak=   -3.805 closest distance to " O   HOH Z 231 " =    2.076
peak=   -3.793 closest distance to " O   HOH Z  43 " =    1.551
peak=   -3.780 closest distance to " O   HOH Z 292 " =    4.547
peak=   -3.778 closest distance to " O   HOH Z  98 " =    1.829
peak=   -3.766 closest distance to " O   HOH Z  19 " =    2.097
peak=   -3.763 closest distance to " O   HOH Z  93 " =    1.436
peak=   -3.760 closest distance to " O   HOH Z  11 " =    1.826
peak=   -3.752 closest distance to " NH2 ARG A  66 " =    1.941
peak=   -3.744 closest distance to " O   HOH Z  38 " =    1.278
peak=   -3.740 closest distance to " CD2 PHE A  59 " =    2.528
peak=   -3.736 closest distance to " CG  GLU A  53 " =    1.526
peak=   -3.722 closest distance to " O   PRO A 198 " =    1.359
peak=   -3.698 closest distance to " N   SER A 276 " =    1.420
peak=   -3.698 closest distance to " OE1 GLN A 223 " =    1.996
peak=   -3.697 closest distance to " C   ASN A 285 " =    2.456
peak=   -3.694 closest distance to " O   GLY A 196 " =    1.158
peak=   -3.682 closest distance to " CB  ALA A 291 " =    2.368
peak=   -3.678 closest distance to " CZ  TYR A 169 " =    1.804
peak=   -3.675 closest distance to " OG  SER A  62 " =    1.503
peak=   -3.667 closest distance to " N   GLN A  58 " =    1.695
peak=   -3.665 closest distance to " OG ASER A 134 " =    1.370
peak=   -3.663 closest distance to " OD1 ASN A 148 " =    1.668
peak=   -3.658 closest distance to " O   HOH Z 377 " =    1.069
peak=   -3.658 closest distance to " CG  GLN A  58 " =    1.288
peak=   -3.646 closest distance to " CE  MET A  93 " =    1.268
peak=   -3.645 closest distance to " CA  VAL A 232 " =    2.485
peak=   -3.639 closest distance to " CA  SER A 146 " =    2.209
peak=   -3.638 closest distance to " OG  SER A  87 " =    1.552
peak=   -3.634 closest distance to " O   HOH Z 407 " =    3.473
peak=   -3.624 closest distance to " O   HOH Z  15 " =    1.664
peak=   -3.617 closest distance to " O   HOH Z 435 " =    2.628
peak=   -3.610 closest distance to " CG  ASP A 231 " =    0.803
peak=   -3.604 closest distance to " O   SER A 210 " =    1.957
peak=   -3.592 closest distance to " OG BSER A 134 " =    1.720
peak=   -3.591 closest distance to " CD  GLN A  88 " =    0.738
peak=   -3.590 closest distance to " CD1 PHE A  59 " =    1.831
peak=   -3.586 closest distance to " CD1 LEU A 101 " =    2.638
peak=   -3.586 closest distance to " CD  GLN A  88 " =    2.055
peak=   -3.577 closest distance to " O   HOH Z 275 " =    1.540
peak=   -3.563 closest distance to " CB  SER A 258 " =    2.031
peak=   -3.563 closest distance to " CG2 THR A   4 " =    1.959
peak=   -3.551 closest distance to " O   HOH Z  97 " =    2.075
peak=   -3.545 closest distance to " C   HIS A 108 " =    1.101
peak=   -3.543 closest distance to " CD  ARG A  14 " =    3.185
peak=   -3.538 closest distance to " O   HOH Z  76 " =    1.923
peak=   -3.538 closest distance to " CB  TYR A  15 " =    2.230
peak=   -3.519 closest distance to " ND2 ASN A  45 " =    0.988
peak=   -3.514 closest distance to " NE2 GLN A  58 " =    1.002
peak=   -3.513 closest distance to " O   HOH Z 241 " =    1.178
peak=   -3.489 closest distance to " CB  LEU A 167 " =    2.129
peak=   -3.489 closest distance to " O   VAL A 174 " =    2.089
peak=   -3.479 closest distance to " N   THR A 157 " =    1.753
peak=   -3.475 closest distance to " O   VAL A 153 " =    2.456
peak=   -3.460 closest distance to " N   ALA A 226 " =    2.114
peak=   -3.455 closest distance to " CA  ASP A 298 " =    1.081
peak=   -3.443 closest distance to " SG ACYS A 201 " =    2.188
peak=   -3.442 closest distance to " O   HOH Z 166 " =    1.786
peak=   -3.441 closest distance to " CG  MET A 105 " =    0.979
peak=   -3.437 closest distance to " O   ASN A 301 " =    1.518
peak=   -3.433 closest distance to " CD2 TYR A 293 " =    2.112
peak=   -3.428 closest distance to " OD1 ASP A 191 " =    1.700
peak=   -3.427 closest distance to " OE2 GLU A   2 " =    1.562
peak=   -3.426 closest distance to " C   GLN A 240 " =    2.326
peak=   -3.425 closest distance to " O   HOH Z 176 " =    0.850
peak=   -3.421 closest distance to " NH2 ARG A  79 " =    1.871
peak=   -3.417 closest distance to " O   HOH Z  98 " =    1.388
peak=   -3.416 closest distance to " N   GLN A 122 " =    1.649
peak=   -3.408 closest distance to " CD  ARG A 195 " =    5.232
peak=   -3.408 closest distance to " O   HOH Z 266 " =    4.705
peak=   -3.405 closest distance to " O   HOH Z  60 " =    2.037
peak=   -3.392 closest distance to " NH2 ARG A 159 " =    2.408
peak=   -3.388 closest distance to " O   GLY A 118 " =    2.239
peak=   -3.384 closest distance to " O   HOH Z 385 " =    2.075
peak=   -3.382 closest distance to " O   HOH Z 185 " =    2.347
peak=   -3.378 closest distance to " CE2 TYR A  30 " =    2.766
peak=   -3.378 closest distance to " O   HOH Z  88 " =    2.248
peak=   -3.372 closest distance to " O   HOH Z 313 " =    1.005
peak=   -3.368 closest distance to " O   HOH Z 396 " =    1.535
peak=   -3.363 closest distance to " CB  ILE A 239 " =    2.154
peak=   -3.362 closest distance to " CB  TRP A  85 " =    2.544
peak=   -3.360 closest distance to " O   HOH Z 234 " =    4.302
peak=   -3.342 closest distance to " CG  ARG A  66 " =    2.334
peak=   -3.340 closest distance to " ND2 ASN A 249 " =    2.051
peak=   -3.337 closest distance to " CZ  PHE A  59 " =    1.728
peak=   -3.332 closest distance to " CG  LEU A  83 " =    2.004
peak=   -3.330 closest distance to " CG  PHE A 283 " =    2.829
peak=   -3.329 closest distance to " OD2 ASP A  65 " =    1.723
peak=   -3.328 closest distance to " CE3 TRP A  70 " =    1.795
peak=   -3.328 closest distance to " O   HOH Z 385 " =    3.824
peak=   -3.323 closest distance to " O   LEU A 167 " =    1.536
peak=   -3.319 closest distance to " OD2 ASP A 171 " =    2.267
peak=   -3.318 closest distance to " O   HOH Z 151 " =    1.333
peak=   -3.315 closest distance to " SG  CYS A 254 " =    3.127
peak=   -3.313 closest distance to " CB  ALA A 291 " =    2.263
peak=   -3.304 closest distance to " ND2 ASN A 187 " =    1.504
peak=   -3.298 closest distance to " CB  ASN A  39 " =    2.145
peak=   -3.295 closest distance to " O   HOH Z  71 " =    1.140
peak=   -3.290 closest distance to " CD1 PHE A  16 " =    2.660
peak=   -3.289 closest distance to " CA  VAL A 197 " =    1.033
peak=   -3.289 closest distance to " CE  LYS A  76 " =    2.830
peak=   -3.289 closest distance to " O   HOH Z 166 " =    1.471
peak=   -3.287 closest distance to " O   HOH Z 141 " =    1.528
peak=   -3.287 closest distance to " CA  SER A 245 " =    2.432
peak=   -3.284 closest distance to " OG  SER A 245 " =    0.949
peak=   -3.283 closest distance to " O   HOH Z 213 " =    1.358
peak=   -3.283 closest distance to " CE3 TRP A 150 " =    1.922
peak=   -3.277 closest distance to " O   VAL A 125 " =    2.132
peak=   -3.277 closest distance to " CB  ASP A 132 " =    2.313
peak=   -3.276 closest distance to " N   PHE A  59 " =    2.181
peak=   -3.272 closest distance to " CB  PRO A 163 " =    2.650
peak=   -3.272 closest distance to " CB  ALA A  43 " =    2.419
peak=   -3.272 closest distance to " NH1 ARG A 195 " =    2.588
peak=   -3.269 closest distance to " NH2 ARG A  66 " =    5.151
peak=   -3.269 closest distance to " OD2 ASP A 171 " =    1.726
peak=   -3.269 closest distance to " CB  CYS A 254 " =    2.355
peak=   -3.269 closest distance to " O   VAL A  67 " =    2.758
peak=   -3.267 closest distance to " O   HOH Z 148 " =    1.807
peak=   -3.266 closest distance to " CE  MET A 105 " =    1.894
peak=   -3.266 closest distance to " O   HOH Z 118 " =    2.815
peak=   -3.263 closest distance to " CG  ASP A  50 " =    2.520
peak=   -3.250 closest distance to " CA  GLY A 241 " =    2.283
peak=   -3.245 closest distance to " O   HOH Z 165 " =    2.076
peak=   -3.242 closest distance to " ND2 ASN A  60 " =    1.585
peak=   -3.238 closest distance to " CG2 THR A 221 " =    2.287
peak=   -3.237 closest distance to " OG1 THR A 178 " =    1.178
peak=   -3.227 closest distance to " CG  PRO A 163 " =    2.371
peak=   -3.226 closest distance to " O   GLY A 211 " =    1.520
peak=   -3.225 closest distance to " CD  ARG A 159 " =    1.241
peak=   -3.224 closest distance to " CG  ARG A 269 " =    2.423
peak=   -3.223 closest distance to " O   HOH Z 236 " =    1.265
peak=   -3.218 closest distance to " OG BSER A 134 " =    1.298
peak=   -3.215 closest distance to " CG  TRP A 266 " =    1.704
peak=   -3.213 closest distance to " O   HOH Z  37 " =    1.998
peak=   -3.212 closest distance to " O   HOH Z 371 " =    2.242
peak=   -3.210 closest distance to " NE  ARG A 259 " =    1.248
peak=   -3.207 closest distance to " NH1 ARG A 195 " =    2.294
peak=   -3.204 closest distance to " O   HOH Z 412 " =    5.515
peak=   -3.197 closest distance to " O   ASP A 191 " =    1.416
peak=   -3.197 closest distance to " CD  GLN A  88 " =    1.100
peak=   -3.196 closest distance to " O   PRO A 198 " =    1.313
peak=   -3.192 closest distance to " O   HOH Z 323 " =    1.385
peak=   -3.190 closest distance to " O   HOH Z 252 " =    4.165
peak=   -3.187 closest distance to " O   HOH Z 127 " =    2.164
peak=   -3.185 closest distance to " CG  GLN A 278 " =    2.291
peak=   -3.171 closest distance to " CZ  ARG A 259 " =    0.887
peak=   -3.170 closest distance to " O   HOH Z  90 " =    3.391
peak=   -3.169 closest distance to " O   HOH Z 163 " =    4.764
peak=   -3.165 closest distance to " CG2 VAL A 189 " =    2.150
peak=   -3.163 closest distance to " O   HOH Z  92 " =    1.425
peak=   -3.160 closest distance to " CA  GLY A 241 " =    2.980
peak=   -3.160 closest distance to " CB  PHE A 208 " =    2.192
peak=   -3.157 closest distance to " ND2 ASN A 215 " =    2.209
peak=   -3.151 closest distance to " CD2 LEU A 167 " =    1.740
peak=   -3.148 closest distance to " O   HOH Z 409 " =    4.578
peak=   -3.142 closest distance to " O   HOH Z 390 " =    2.247
peak=   -3.140 closest distance to " N   GLY A  23 " =    2.105
peak=   -3.135 closest distance to " CB  ASP A 286 " =    2.238
peak=   -3.132 closest distance to " O   HOH Z 231 " =    1.227
peak=   -3.129 closest distance to " C   LEU A 143 " =    1.352
peak=   -3.127 closest distance to " O   HOH Z 108 " =    2.533
peak=   -3.122 closest distance to " O   HOH Z 389 " =    1.801
peak=   -3.118 closest distance to " O   HOH Z 417 " =    2.588
peak=   -3.115 closest distance to " N   THR A 264 " =    1.365
peak=   -3.107 closest distance to " CD2 LEU A 143 " =    2.650
peak=   -3.100 closest distance to " OG1 THR A 246 " =    1.500
peak=   -3.095 closest distance to " O   HOH Z  90 " =    1.696
peak=   -3.090 closest distance to " CB  ASP A 132 " =    2.236
peak=   -3.087 closest distance to " CE  MET A 105 " =    2.051
peak=   -3.085 closest distance to " O   PHE A 218 " =    1.498
peak=   -3.074 closest distance to " O   HOH Z 222 " =    1.309
peak=   -3.073 closest distance to " CA  GLY A 133 " =    1.937
peak=   -3.070 closest distance to " CE BMET A  47 " =    2.330
peak=   -3.057 closest distance to " N   VAL A 189 " =    1.693
peak=   -3.057 closest distance to " O   HOH Z 264 " =    1.781
peak=   -3.051 closest distance to " CE1 TYR A 169 " =    2.447
peak=   -3.047 closest distance to " O   HOH Z   1 " =    3.594
peak=   -3.038 closest distance to " CG  PHE A 283 " =    2.678
peak=   -3.026 closest distance to " ND2 ASN A  60 " =    1.601
peak=   -3.024 closest distance to " ND2 ASN A  45 " =    1.214

================= 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    :  0.4504 0.4518   6.256635e+00   6.257564e+00
   1_bss:  0.4427 0.4449   6.253574e+00   6.248628e+00
   1_xyz:  0.3071 0.3477   5.988442e+00   6.078959e+00
   1_adp:  0.2805 0.3536   5.941568e+00   6.092862e+00
   1_occ:  0.2802 0.3534   5.939988e+00   6.091853e+00
   2_bss:  0.2783 0.3514   5.938309e+00   6.087987e+00
   2_xyz:  0.1942 0.2536   5.624211e+00   5.835635e+00
   2_adp:  0.1681 0.2236   5.501234e+00   5.723497e+00
   2_occ:  0.1680 0.2234   5.500651e+00   5.722835e+00
   3_bss:  0.1678 0.2225   5.499344e+00   5.720148e+00
   3_xyz:  0.1388 0.1865   5.332774e+00   5.560549e+00
   3_adp:  0.1325 0.1781   5.290914e+00   5.514774e+00
   3_occ:  0.1324 0.1777   5.290025e+00   5.513810e+00
   4_bss:  0.1326 0.1782   5.292056e+00   5.515764e+00
   4_xyz:  0.1187 0.1648   5.199983e+00   5.435558e+00
   4_adp:  0.1157 0.1639   5.186752e+00   5.429877e+00
   4_occ:  0.1156 0.1638   5.186670e+00   5.430159e+00
   5_bss:  0.1156 0.1637   5.186681e+00   5.430089e+00
   5_xyz:  0.1116 0.1620   5.167635e+00   5.418452e+00
   5_adp:  0.1120 0.1608   5.165404e+00   5.412327e+00
   5_occ:  0.1119 0.1605   5.165196e+00   5.412467e+00
   5_bss:  0.1119 0.1605   5.165272e+00   5.412489e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  50.000   0.497  -0.391   2.047  -0.000   0.000   0.000
   1_xyz:  0.300  50.000   0.497  -0.391   2.047  -0.000   0.000   0.000
   1_adp:  0.300  50.000   0.497  -0.391   2.047  -0.000   0.000   0.000
   1_occ:  0.300  50.000   0.497  -0.391   2.047  -0.000   0.000   0.000
   2_bss:  0.331  61.009  -1.209  -1.301  -0.184  -0.000  -0.000  -0.000
   2_xyz:  0.331  61.009  -1.209  -1.301  -0.184  -0.000  -0.000  -0.000
   2_adp:  0.331  61.009  -1.209  -1.301  -0.184  -0.000  -0.000  -0.000
   2_occ:  0.331  61.009  -1.209  -1.301  -0.184  -0.000  -0.000  -0.000
   3_bss:  0.330  61.410  -2.014  -2.102  -1.720  -0.000  -0.000  -0.000
   3_xyz:  0.330  61.410  -2.014  -2.102  -1.720  -0.000  -0.000  -0.000
   3_adp:  0.330  61.410  -2.014  -2.102  -1.720  -0.000  -0.000  -0.000
   3_occ:  0.330  61.410  -2.014  -2.102  -1.720  -0.000  -0.000  -0.000
   4_bss:  0.325  57.182  -2.455  -2.445  -2.302  -0.000  -0.000  -0.000
   4_xyz:  0.325  57.182  -2.455  -2.445  -2.302  -0.000  -0.000  -0.000
   4_adp:  0.325  57.182  -2.455  -2.445  -2.302  -0.000  -0.000  -0.000
   4_occ:  0.325  57.182  -2.455  -2.445  -2.302  -0.000  -0.000  -0.000
   5_bss:  0.318  52.589  -2.354  -2.361  -2.303  -0.000  -0.000  -0.000
   5_xyz:  0.318  52.589  -2.354  -2.361  -2.303  -0.000  -0.000  -0.000
   5_adp:  0.318  52.589  -2.354  -2.361  -2.303  -0.000  -0.000  -0.000
   5_occ:  0.318  52.589  -2.354  -2.361  -2.303  -0.000  -0.000  -0.000
   5_bss:  0.318  52.509  -2.156  -2.182  -2.139  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.251 0.4267  0.5649    64916.421
   1_bss:  56.423 0.4350  0.5923    61905.649
   1_xyz:  37.258 0.6747  0.9045    33314.446
   1_adp:  38.450 0.6597  0.8960    34877.788
   1_occ:  38.382 0.6604  0.8957    34707.494
   2_bss:  38.198 0.6624  0.8503    34418.197
   2_xyz:  26.192 0.7969  0.9790    17101.673
   2_adp:  22.360 0.8376  1.0003    13324.796
   2_occ:  22.342 0.8378  1.0004    13298.078
   3_bss:  22.238 0.8388  0.9641    13194.292
   3_xyz:  18.031 0.8794  0.9823     9127.211
   3_adp:  16.814 0.8912  0.9832     8350.933
   3_occ:  16.789 0.8915  0.9832     8335.942
   4_bss:  16.834 0.8911  0.9669     8394.176
   4_xyz:  15.171 0.9051  0.9744     7039.159
   4_adp:  14.994 0.9068  0.9711     6967.470
   4_occ:  14.991 0.9068  0.9709     6966.579
   5_bss:  14.991 0.9068  0.9728     6963.863
   5_xyz:  14.743 0.9090  0.9719     6764.565
   5_adp:  14.581 0.9105  0.9673     6711.079
   5_occ:  14.576 0.9105  0.9672     6709.455
   5_bss:  14.579 0.9105  0.9706     6710.524
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.8513e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.8513e-01
   1_xyz:   1.550  0.013  0.097 16.013  0.006  4.118   1.3600e-01
   1_adp:   1.550  0.013  0.097 16.013  0.006  4.118   1.3600e-01
   1_occ:   1.550  0.013  0.097 16.013  0.006  4.118   1.3600e-01
   2_bss:   1.550  0.013  0.097 16.013  0.006  4.118   1.3600e-01
   2_xyz:   1.220  0.009  0.086 14.839  0.005  4.115   8.2682e-02
   2_adp:   1.220  0.009  0.086 14.839  0.005  4.115   8.2682e-02
   2_occ:   1.220  0.009  0.086 14.839  0.005  4.115   8.2682e-02
   3_bss:   1.220  0.009  0.086 14.839  0.005  4.115   8.2682e-02
   3_xyz:   0.999  0.007  0.068 14.377  0.004  4.124   5.8218e-02
   3_adp:   0.999  0.007  0.068 14.377  0.004  4.124   5.8218e-02
   3_occ:   0.999  0.007  0.068 14.377  0.004  4.124   5.8218e-02
   4_bss:   0.999  0.007  0.068 14.377  0.004  4.124   5.8218e-02
   4_xyz:   1.102  0.009  0.079 14.666  0.004  4.113   6.9605e-02
   4_adp:   1.102  0.009  0.079 14.666  0.004  4.113   6.9605e-02
   4_occ:   1.102  0.009  0.079 14.666  0.004  4.113   6.9605e-02
   5_bss:   1.102  0.009  0.079 14.666  0.004  4.113   6.9605e-02
   5_xyz:   1.129  0.009  0.079 14.651  0.004  4.114   7.1949e-02
   5_adp:   1.129  0.009  0.079 14.651  0.004  4.114   7.1949e-02
   5_occ:   1.129  0.009  0.079 14.651  0.004  4.114   7.1949e-02
   5_bss:   1.129  0.009  0.079 14.651  0.004  4.114   7.1949e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.542   2.4185e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.542   2.4185e-01
   1_xyz:  10.009  0.099  0.366 88.922  0.027  2.047   1.1779e-01
   1_adp:  10.009  0.099  0.366 88.922  0.027  2.047   1.1779e-01
   1_occ:  10.009  0.099  0.366 88.922  0.027  2.047   1.1779e-01
   2_bss:  10.009  0.099  0.366 88.922  0.027  2.047   1.1779e-01
   2_xyz:   8.216  0.053  0.328 85.190  0.042  2.204   7.9086e-02
   2_adp:   8.216  0.053  0.328 85.190  0.042  2.204   7.9086e-02
   2_occ:   8.216  0.053  0.328 85.190  0.042  2.204   7.9086e-02
   3_bss:   8.216  0.053  0.328 85.190  0.042  2.204   7.9086e-02
   3_xyz:   8.216  0.048  0.242 81.522  0.040  2.287   4.3208e-02
   3_adp:   8.216  0.048  0.242 81.522  0.040  2.287   4.3208e-02
   3_occ:   8.216  0.048  0.242 81.522  0.040  2.287   4.3208e-02
   4_bss:   8.216  0.048  0.242 81.522  0.040  2.287   4.3208e-02
   4_xyz:   7.617  0.042  0.247 83.603  0.033  2.290   7.4507e-02
   4_adp:   7.617  0.042  0.247 83.603  0.033  2.290   7.4507e-02
   4_occ:   7.617  0.042  0.247 83.603  0.033  2.290   7.4507e-02
   5_bss:   7.617  0.042  0.247 83.603  0.033  2.290   7.4507e-02
   5_xyz:   8.024  0.045  0.248 81.865  0.036  2.266   5.4717e-02
   5_adp:   8.024  0.045  0.248 81.865  0.036  2.266   5.4717e-02
   5_occ:   8.024  0.045  0.248 81.865  0.036  2.266   5.4717e-02
   5_bss:   8.024  0.045  0.248 81.865  0.036  2.266   5.4717e-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: 114.70   0.00  18.15 114.70   0.00  14.16  69.54   1.90  39.90
   1_occ: 114.70   0.00  18.15 114.70   0.00  14.16  69.54   1.90  39.90
   2_bss: 114.70   0.00  18.15 114.70   0.00  14.16  69.54   1.90  39.90
   2_xyz: 114.70   0.00  18.15 114.70   0.00  14.16  69.54   1.90  39.90
   2_adp:  94.99   0.00  18.60  94.99   0.00  13.80  90.35   5.71  44.72
   2_occ:  94.99   0.00  18.60  94.99   0.00  13.80  90.35   5.71  44.72
   3_bss:  94.99   0.00  18.60  94.99   0.00  13.80  90.35   5.71  44.72
   3_xyz:  94.99   0.00  18.60  94.99   0.00  13.80  90.35   5.71  44.72
   3_adp:  93.79   2.42  17.94  93.79   2.42  13.41  86.46   5.67  42.57
   3_occ:  93.79   2.42  17.94  93.79   2.42  13.41  86.46   5.67  42.57
   4_bss:  93.79   2.42  17.94  93.79   2.42  13.41  86.46   5.67  42.57
   4_xyz:  93.79   2.42  17.94  93.79   2.42  13.41  86.46   5.67  42.57
   4_adp:  99.50   1.87  17.94  99.50   1.87  13.37  86.04   5.65  42.85
   4_occ:  99.50   1.87  17.94  99.50   1.87  13.37  86.04   5.65  42.85
   5_bss:  99.50   1.87  17.94  99.50   1.87  13.37  86.04   5.65  42.85
   5_xyz:  99.50   1.87  17.94  99.50   1.87  13.37  86.04   5.65  42.85
   5_adp:  96.72   2.20  17.25  96.72   2.20  13.07  81.35   5.89  39.98
   5_occ:  96.72   2.20  17.25  96.72   2.20  13.07  81.35   5.89  39.98
   5_bss:  96.64   2.12  17.17  96.64   2.12  12.99  81.27   5.81  39.90
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.823    0.017    0.421
   1_adp:    1.823    0.017    0.421
   1_occ:    1.823    0.017    0.421
   2_bss:    1.823    0.017    0.421
   2_xyz:    1.349    0.053    0.607
   2_adp:    1.349    0.053    0.607
   2_occ:    1.349    0.053    0.607
   3_bss:    1.349    0.053    0.607
   3_xyz:    1.396    0.077    0.663
   3_adp:    1.396    0.077    0.663
   3_occ:    1.396    0.077    0.663
   4_bss:    1.396    0.077    0.663
   4_xyz:    1.450    0.040    0.699
   4_adp:    1.450    0.040    0.699
   4_occ:    1.450    0.040    0.699
   5_bss:    1.450    0.040    0.699
   5_xyz:    1.608    0.097    0.710
   5_adp:    1.608    0.097    0.710
   5_occ:    1.608    0.097    0.710
   5_bss:    1.608    0.097    0.710
------------------------------------------------------------------------

CPU time actual refinement: 349.33


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1166/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_1166/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1166/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1166/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1166/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 349.17 
  Macro-tasks:
    bulk solvent and scale       = 38.68  
    individual site refinement   = 143.51 
    weights calculation          = 30.39  
    collect and process          = 6.57   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 219.28 
  Micro-tasks:
    mask                            = 1.89   
    f_calc                          = 115.48 
    alpha_beta                      = 8.21   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 122.06 
    fmodel                         = 6.72   
    r_factors                      = 0.18   
    phase_errors                   = 10.73  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 266.68 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 5.017 micro seconds
Total CPU time: 6.05 minutes
from_scatterers_fft:    628 calls, 115.13 s
gradients_fft:          573 calls, 109.18 s

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

# Date 2008-01-16 Time 06:35:40 PST -0800 (1200494140.89 s)
Start R-work = 0.4504, R-free = 0.4518 (no bulk solvent and anisotropic scale)
Final R-work = 0.1367, R-free = 0.1812 (no bulk solvent and anisotropic scale)

Start R-work = 0.4427, R-free = 0.4449
Final R-work = 0.1119, R-free = 0.1605