# Date 2008-01-16 Time 06:19:41 PST -0800 (1200493181.91 s)
#phil __OFF__

Command line arguments: "../1102.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 12588
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1102

-------------------------------------------------------------------------------
  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, 45.9914, 85.0941, 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: 3.27, per 1000 atoms: 1.16


================================== 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, 45.9914, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1461 1.96157
Completeness in resolution range: 0.944412
Completeness with d_max=infinity: 0.941688

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1461
                             d_min =   1.9616

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, 45.9914, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1461 1.96157
Completeness in resolution range: 0.944412
Completeness with d_max=infinity: 0.941688

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1465 -  4.1989 [2173/2200]  1959   214   9.8%
  bin  2:  4.1989 -  3.3446 [2092/2112]  1880   212  10.1%
  bin  3:  3.3446 -  2.9253 [2062/2081]  1856   206  10.0%
  bin  4:  2.9253 -  2.6594 [2035/2065]  1832   203  10.0%
  bin  5:  2.6594 -  2.4696 [2046/2065]  1845   201   9.8%
  bin  6:  2.4696 -  2.3246 [2026/2051]  1811   215  10.6%
  bin  7:  2.3246 -  2.2085 [2030/2058]  1831   199   9.8%
  bin  8:  2.2085 -  2.1127 [1985/2021]  1791   194   9.8%
  bin  9:  2.1127 -  2.0315 [1987/2040]  1796   191   9.6%
  bin 10:  2.0315 -  1.9616 [1153/2049]  1029   124  10.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1102/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.54 -     2.21: 19
        2.21 -     2.88: 1310
        2.88 -     3.55: 4518
        3.55 -     4.23: 9312
        4.23 -     4.90: 13403
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.536 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.819 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.821 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  ... (remaining 28557 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_1102/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1102/model_refine_001.geo

CPU time processing inputs: 9.60


============================ 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 45.9914 85.09415 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: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4736   r_free= 0.4718   ksol= 0.00   Bsol= 0.00   scale= 0.893    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.278369                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1465 -  4.6840 0.99   1414  161 0.3784 0.3850      6.5519      6.5824|
|  2:  4.6840 -  3.7362 0.99   1357  146 0.4089 0.4009      6.8144      6.7856|
|  3:  3.7362 -  3.2693 0.99   1324  144 0.4424 0.4164      6.6661      6.7186|
|  4:  3.2693 -  2.9729 0.99   1345  158 0.4645 0.4903      6.5357      6.5001|
|  5:  2.9729 -  2.7612 0.99   1310  144 0.4975 0.5084      6.3645      6.3818|
|  6:  2.7612 -  2.5992 0.99   1313  145 0.5079 0.4893      6.2819      6.2472|
|  7:  2.5992 -  2.4696 0.99   1309  138 0.5140 0.4979      6.2468      6.2062|
|  8:  2.4696 -  2.3625 0.98   1281  152 0.5225 0.4836      6.1686      6.1598|
|  9:  2.3625 -  2.2719 0.98   1305  145 0.5107 0.5271      6.1326      6.1379|
| 10:  2.2719 -  2.1937 1.00   1289  151 0.5208 0.5346      6.0807      6.1078|
| 11:  2.1937 -  2.1253 0.98   1299  132 0.5245 0.5304      6.0436      6.0679|
| 12:  2.1253 -  2.0647 0.98   1275  151 0.5250 0.5705      5.9582      5.9899|
| 13:  2.0647 -  2.0105 0.93   1214  127 0.5348 0.5100      5.8777      5.8154|
| 14:  2.0105 -  1.9616 0.45    595   65 0.5325 0.4861       5.834      5.8143|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1465 -  4.6840  1414   161  0.69  34.69   0.82     0.75      73277.92|
|  2:  4.6840 -  3.7362  1357   146  0.69  35.77   0.91     0.81     109578.62|
|  3:  3.7362 -  3.2693  1324   144  0.57  45.99   0.92     0.76     120535.37|
|  4:  3.2693 -  2.9729  1345   158  0.46  55.17   0.91     0.65     114830.17|
|  5:  2.9729 -  2.7612  1310   144  0.36  63.19   0.87     0.51      91413.78|
|  6:  2.7612 -  2.5992  1313   145  0.34  64.39   0.89     0.49      78808.38|
|  7:  2.5992 -  2.4696  1309   138  0.36  63.23   0.90     0.50      66138.92|
|  8:  2.4696 -  2.3625  1281   152  0.37  62.33   0.89     0.54      59320.50|
|  9:  2.3625 -  2.2719  1305   145  0.36  63.26   0.93     0.51      54012.43|
| 10:  2.2719 -  2.1937  1289   151  0.31  67.12   0.92     0.46      52533.22|
| 11:  2.1937 -  2.1253  1299   132  0.26  70.51   0.96     0.40      51655.34|
| 12:  2.1253 -  2.0647  1275   151  0.25  71.47   0.93     0.40      47140.36|
| 13:  2.0647 -  2.0105  1214   127  0.26  70.30   0.93     0.43      39289.33|
| 14:  2.0105 -  1.9616   595    65  0.33  65.49   0.94     0.51      31453.05|
|alpha:            min =        0.40 max =            0.81 mean =         0.56|
|beta:             min =    31453.05 max =       120535.37 mean =     72828.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           89.98 mean =        58.92|
|phase err.(test): min =        0.00 max =           90.00 mean =        59.22|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.681390             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.893   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.170854              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.676   (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 |  1.536 -  1.872:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.872 -  2.209:       15 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.209 -  2.545:       48 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.545 -  2.882:     1262 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.882 -  3.218:     1946 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.218 -  3.554:     2572 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.554 -  3.891:     4709 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.891 -  4.227:     4603 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.227 -  4.564:     6127 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.564 -  4.900:     7276 |
|-----------------------------------------------------------------------------|
|-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 |        0.177 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.536 |       0.411 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.713)------------------------------------------|
|    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: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4736   r_free= 0.4718   ksol= 0.00   Bsol= 0.00   scale= 0.893    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.278369                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4661   r_free= 0.4656   ksol= 0.30   Bsol= 20.00   scale= 0.929   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.20,1.42,-0.22,0.00,-0.00,-0.00); trace/3= 0.47                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.274920                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.592470              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.930   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.440532              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.320   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4661      final r-factor (work) = 0.3702          |
| start r-factor (free) = 0.4656      final r-factor (free) = 0.4059          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.1191 = 8.59 * 0.50 * 6.2711 + 1.00 * 0.1770                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.6774 = 8.59 * 0.50 * 6.1817 + 1.00 * 0.1195                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3702      final r-factor (work) = 0.3347          |
| start r-factor (free) = 0.4059      final r-factor (free) = 0.4139          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.9112 = 1.44 * 1.00 * 6.1817 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7977 = 1.44 * 1.00 * 6.0821 + 1.00 * 0.0362                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.713)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.42  19.57    None  None   None       |
|    all(noH): 2823   0      0.00    114.42  19.57    None  None   None       |
|    Sol.    : 438    0      0.00    114.42  37.61    None  None   None       |
|    Mac.    : 2385   0      0.00    91.24   16.26    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 -  11.442: 1008   |   5:    57.210 -  68.653:   51        |
|      1:    11.442 -  22.884:  918   |   6:    68.653 -  80.095:   27        |
|      2:    22.884 -  34.326:  456   |   7:    80.095 -  91.537:    9        |
|      3:    34.326 -  45.768:  234   |   8:    91.537 - 102.979:    2        |
|      4:    45.768 -  57.210:  117   |   9:   102.979 - 114.421:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3347 r_free = 0.4139             target_work(ml) = 6.085         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3341 r_free = 0.4138             target_work(ml) = 6.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3341   r_free= 0.4138   ksol= 0.30   Bsol= 20.00   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.20,1.42,-0.22,0.00,-0.00,-0.00); trace/3= 0.47                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.084122                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3339   r_free= 0.4120   ksol= 0.35   Bsol= 57.98   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.15,0.09,-0.11,0.00,-0.00,-0.00); trace/3= -0.05                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.085106                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.602078              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.034   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.041570              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.231   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3339      final r-factor (work) = 0.2721          |
| start r-factor (free) = 0.4120      final r-factor (free) = 0.3474          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.1565 = 5.60 * 0.50 * 6.0824 + 1.00 * 0.1195                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.9265 = 5.60 * 0.50 * 6.0111 + 1.00 * 0.0892                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2721      final r-factor (work) = 0.2558          |
| start r-factor (free) = 0.3474      final r-factor (free) = 0.3355          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2830 = 1.04 * 1.00 * 6.0111 + 1.00 * 0.0220                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1590 = 1.04 * 1.00 * 5.8960 + 1.00 * 0.0180                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.713)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    117.92  19.44    None  None   None       |
|    all(noH): 2823   0      0.00    117.92  19.44    None  None   None       |
|    Sol.    : 438    0      0.00    117.92  41.31    None  None   None       |
|    Mac.    : 2385   0      0.00    100.10  15.42    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 -  11.792: 1135   |   5:    58.962 -  70.754:   60        |
|      1:    11.792 -  23.585:  901   |   6:    70.754 -  82.547:   29        |
|      2:    23.585 -  35.377:  371   |   7:    82.547 -  94.339:    9        |
|      3:    35.377 -  47.170:  192   |   8:    94.339 - 106.132:    3        |
|      4:    47.170 -  58.962:  121   |   9:   106.132 - 117.924:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2558 r_free = 0.3355             target_work(ml) = 5.882         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2558 r_free = 0.3349             target_work(ml) = 5.881         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2558   r_free= 0.3349   ksol= 0.35   Bsol= 57.98   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.15,0.09,-0.11,0.00,-0.00,-0.00); trace/3= -0.05                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.880990                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2564   r_free= 0.3344   ksol= 0.35   Bsol= 64.50   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.10,-0.31,0.21,-0.00,0.00,0.00); trace/3= -0.07                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.881177                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.758049              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.134   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.304601              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.299  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2564      final r-factor (work) = 0.1953          |
| start r-factor (free) = 0.3344      final r-factor (free) = 0.2624          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.9636 = 7.76 * 0.50 * 5.8969 + 1.00 * 0.0892                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.4808 = 7.76 * 0.50 * 5.7764 + 1.00 * 0.0741                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1953      final r-factor (work) = 0.1734          |
| start r-factor (free) = 0.2624      final r-factor (free) = 0.2271          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7774 = 0.30 * 1.00 * 5.7764 + 1.00 * 0.0179                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7134 = 0.30 * 1.00 * 5.5937 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.713)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.69    108.06  17.69    None  None   None       |
|    all(noH): 2823   0      1.69    108.06  17.69    None  None   None       |
|    Sol.    : 438    0      4.46    108.06  41.76    None  None   None       |
|    Mac.    : 2385   0      1.69    94.39   13.27    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:     1.692 -  12.328: 1448   |   5:    54.875 -  65.511:   68        |
|      1:    12.328 -  22.965:  773   |   6:    65.511 -  76.148:   28        |
|      2:    22.965 -  33.601:  195   |   7:    76.148 -  86.784:    8        |
|      3:    33.601 -  44.238:  165   |   8:    86.784 -  97.421:    4        |
|      4:    44.238 -  54.875:  133   |   9:    97.421 - 108.057:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1734 r_free = 0.2271             target_work(ml) = 5.524         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1730 r_free = 0.2260             target_work(ml) = 5.521         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1730   r_free= 0.2260   ksol= 0.35   Bsol= 64.50   scale= 1.043   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.10,-0.31,0.21,-0.00,0.00,0.00); trace/3= -0.07                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.521231                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1725   r_free= 0.2246   ksol= 0.33   Bsol= 54.19   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.14,-1.84,-0.85,-0.00,-0.00,-0.00); trace/3= -1.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.517801                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.214109              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.941  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.572240              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.203  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1725      final r-factor (work) = 0.1403          |
| start r-factor (free) = 0.2246      final r-factor (free) = 0.1892          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0730 = 3.21 * 0.50 * 5.5997 + 1.00 * 0.0741                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7890 = 3.21 * 0.50 * 5.4325 + 1.00 * 0.0588                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1403      final r-factor (work) = 0.1312          |
| start r-factor (free) = 0.1892      final r-factor (free) = 0.1807          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1182 = 0.57 * 1.00 * 5.4325 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0453 = 0.57 * 1.00 * 5.3038 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.713)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.59  17.61    None  None   None       |
|    all(noH): 2823   0      0.00    101.59  17.61    None  None   None       |
|    Sol.    : 438    0      3.08    99.51   43.76    None  None   None       |
|    Mac.    : 2385   0      0.00    101.59  12.80    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 -  10.159: 1135   |   5:    50.796 -  60.955:   98        |
|      1:    10.159 -  20.318: 1037   |   6:    60.955 -  71.114:   57        |
|      2:    20.318 -  30.477:  221   |   7:    71.114 -  81.273:   23        |
|      3:    30.477 -  40.637:  123   |   8:    81.273 -  91.432:   10        |
|      4:    40.637 -  50.796:  115   |   9:    91.432 - 101.591:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1312 r_free = 0.1807             target_work(ml) = 5.277         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1311 r_free = 0.1802             target_work(ml) = 5.276         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1311   r_free= 0.1802   ksol= 0.33   Bsol= 54.19   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.14,-1.84,-0.85,-0.00,-0.00,-0.00); trace/3= -1.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.276067                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1311   r_free= 0.1798   ksol= 0.32   Bsol= 54.19   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.52,-2.28,-1.23,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.275155                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.874827              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.758  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.283824              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.214  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1311      final r-factor (work) = 0.1220          |
| start r-factor (free) = 0.1798      final r-factor (free) = 0.1702          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0317 = 1.87 * 0.50 * 5.3049 + 1.00 * 0.0588                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9705 = 1.87 * 0.50 * 5.2463 + 1.00 * 0.0526                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1220      final r-factor (work) = 0.1201          |
| start r-factor (free) = 0.1702      final r-factor (free) = 0.1665          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4993 = 0.28 * 1.00 * 5.2463 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4880 = 0.28 * 1.00 * 5.2106 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.713)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.52    102.01  17.13    None  None   None       |
|    all(noH): 2823   0      0.52    102.01  17.13    None  None   None       |
|    Sol.    : 438    0      3.79    97.54   41.76    None  None   None       |
|    Mac.    : 2385   0      0.52    102.01  12.61    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:     0.516 -  10.665: 1261   |   5:    51.264 -  61.414:   90        |
|      1:    10.665 -  20.815:  954   |   6:    61.414 -  71.564:   38        |
|      2:    20.815 -  30.965:  210   |   7:    71.564 -  81.714:   19        |
|      3:    30.965 -  41.115:  126   |   8:    81.714 -  91.863:    8        |
|      4:    41.115 -  51.264:  113   |   9:    91.863 - 102.013:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1201 r_free = 0.1665             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1199 r_free = 0.1662             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1199   r_free= 0.1662   ksol= 0.32   Bsol= 54.19   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.52,-2.28,-1.23,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.199507                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1465 -  4.6840 0.99   1414  161 0.0993 0.1324      5.3811      5.5959|
|  2:  4.6840 -  3.7362 0.99   1357  146 0.0886 0.1159      5.4792      5.6892|
|  3:  3.7362 -  3.2693 0.99   1324  144 0.1170 0.1618       5.539      5.8808|
|  4:  3.2693 -  2.9729 0.99   1345  158 0.1362 0.1723      5.5377      5.6571|
|  5:  2.9729 -  2.7612 0.99   1310  144 0.1418 0.1895      5.3588       5.614|
|  6:  2.7612 -  2.5992 0.99   1313  145 0.1290 0.1698       5.228      5.4362|
|  7:  2.5992 -  2.4696 0.99   1309  138 0.1362 0.1786      5.2031      5.3838|
|  8:  2.4696 -  2.3625 0.98   1281  152 0.1278 0.1858      5.1201      5.4015|
|  9:  2.3625 -  2.2719 0.98   1305  145 0.1238 0.1886      5.0887      5.3738|
| 10:  2.2719 -  2.1937 1.00   1289  151 0.1199 0.1802      4.9934      5.2595|
| 11:  2.1937 -  2.1253 0.98   1299  132 0.1217 0.1948      5.0126      5.3658|
| 12:  2.1253 -  2.0647 0.98   1275  151 0.1206 0.1800      4.9224      5.1395|
| 13:  2.0647 -  2.0105 0.93   1214  127 0.1276 0.1935      4.8709      5.1411|
| 14:  2.0105 -  1.9616 0.45    595   65 0.1130 0.1572      4.7216      4.9287|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1465 -  4.6840  1414   161  0.94   9.31   0.98     0.95       7334.75|
|  2:  4.6840 -  3.7362  1357   146  0.95   8.32   1.02     1.01       9660.72|
|  3:  3.7362 -  3.2693  1324   144  0.93  12.21   1.04     1.03      11529.39|
|  4:  3.2693 -  2.9729  1345   158  0.90  15.85   1.01     0.98      12059.77|
|  5:  2.9729 -  2.7612  1310   144  0.91  15.35   1.00     0.99       8081.31|
|  6:  2.7612 -  2.5992  1313   145  0.90  15.90   0.99     0.97       6963.71|
|  7:  2.5992 -  2.4696  1309   138  0.90  15.68   1.00     0.98       6378.29|
|  8:  2.4696 -  2.3625  1281   152  0.90  16.70   0.99     0.97       5825.28|
|  9:  2.3625 -  2.2719  1305   145  0.90  16.65   1.01     0.97       5595.59|
| 10:  2.2719 -  2.1937  1289   151  0.90  16.24   1.00     0.97       4723.97|
| 11:  2.1937 -  2.1253  1299   132  0.89  17.54   1.01     0.96       5002.22|
| 12:  2.1253 -  2.0647  1275   151  0.90  16.69   1.00     0.99       4403.89|
| 13:  2.0647 -  2.0105  1214   127  0.89  17.48   1.01     1.01       3889.86|
| 14:  2.0105 -  1.9616   595    65  0.90  15.79   0.99     0.96       2901.92|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2901.92 max =        12059.77 mean =      6946.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.88 mean =        14.87|
|phase err.(test): min =        0.00 max =           89.22 mean =        14.51|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1199   r_free= 0.1662   ksol= 0.32   Bsol= 49.28   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.54,-2.34,-1.27,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.199532                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1199   r_free= 0.1662   ksol= 0.32   Bsol= 49.28   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.54,-2.34,-1.27,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.199532                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1465 -  4.6840 0.99   1414  161 0.0992 0.1322        5.38       5.594|
|  2:  4.6840 -  3.7362 0.99   1357  146 0.0883 0.1156      5.4763      5.6866|
|  3:  3.7362 -  3.2693 0.99   1324  144 0.1168 0.1614      5.5374      5.8781|
|  4:  3.2693 -  2.9729 0.99   1345  158 0.1362 0.1721      5.5371      5.6565|
|  5:  2.9729 -  2.7612 0.99   1310  144 0.1419 0.1897      5.3591      5.6145|
|  6:  2.7612 -  2.5992 0.99   1313  145 0.1291 0.1702       5.229      5.4376|
|  7:  2.5992 -  2.4696 0.99   1309  138 0.1363 0.1788      5.2043       5.385|
|  8:  2.4696 -  2.3625 0.98   1281  152 0.1279 0.1863      5.1212      5.4034|
|  9:  2.3625 -  2.2719 0.98   1305  145 0.1239 0.1887      5.0896       5.374|
| 10:  2.2719 -  2.1937 1.00   1289  151 0.1200 0.1805      4.9942      5.2606|
| 11:  2.1937 -  2.1253 0.98   1299  132 0.1217 0.1950      5.0132       5.366|
| 12:  2.1253 -  2.0647 0.98   1275  151 0.1207 0.1801      4.9228      5.1399|
| 13:  2.0647 -  2.0105 0.93   1214  127 0.1276 0.1935      4.8713      5.1417|
| 14:  2.0105 -  1.9616 0.45    595   65 0.1130 0.1570      4.7217      4.9285|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1465 -  4.6840  1414   161  0.94   9.29   0.98     0.95       7314.58|
|  2:  4.6840 -  3.7362  1357   146  0.95   8.29   1.02     1.01       9621.44|
|  3:  3.7362 -  3.2693  1324   144  0.93  12.18   1.04     1.03      11471.19|
|  4:  3.2693 -  2.9729  1345   158  0.90  15.82   1.01     0.98      12025.26|
|  5:  2.9729 -  2.7612  1310   144  0.91  15.36   1.00     0.99       8082.11|
|  6:  2.7612 -  2.5992  1313   145  0.90  15.91   0.99     0.97       6977.96|
|  7:  2.5992 -  2.4696  1309   138  0.90  15.70   1.00     0.98       6397.07|
|  8:  2.4696 -  2.3625  1281   152  0.90  16.72   0.98     0.96       5841.52|
|  9:  2.3625 -  2.2719  1305   145  0.90  16.67   1.01     0.97       5607.95|
| 10:  2.2719 -  2.1937  1289   151  0.90  16.26   1.00     0.97       4733.38|
| 11:  2.1937 -  2.1253  1299   132  0.89  17.56   1.00     0.95       5012.49|
| 12:  2.1253 -  2.0647  1275   151  0.90  16.70   1.00     0.99       4409.18|
| 13:  2.0647 -  2.0105  1214   127  0.89  17.48   1.01     1.00       3892.80|
| 14:  2.0105 -  1.9616   595    65  0.90  15.79   0.98     0.96       2902.60|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2902.60 max =        12025.26 mean =      6941.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.82 mean =        14.87|
|phase err.(test): min =        0.00 max =           89.35 mean =        14.51|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.713)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.50    102.00  17.12    None  None   None       |
|    all(noH): 2823   0      0.50    102.00  17.12    None  None   None       |
|    Sol.    : 438    0      3.78    97.52   41.74    None  None   None       |
|    Mac.    : 2385   0      0.50    102.00  12.59    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:     0.499 -  10.649: 1261   |   5:    51.248 -  61.398:   90        |
|      1:    10.649 -  20.799:  954   |   6:    61.398 -  71.547:   38        |
|      2:    20.799 -  30.949:  210   |   7:    71.547 -  81.697:   19        |
|      3:    30.949 -  41.098:  126   |   8:    81.697 -  91.847:    8        |
|      4:    41.098 -  51.248:  113   |   9:    91.847 - 101.997:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 340         
Filter by distance & map next to the model:
   mapped sites are within: 0.538 - 5.869
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 337 from: 340
   mapped sites are within: 0.745 - 5.869

peak=    6.013 closest distance to " NE2 GLN A  11 " =    1.363
peak=    5.674 closest distance to " O   HOH Z   7 " =    1.700
peak=    5.624 closest distance to " O   HOH Z 214 " =    1.626
peak=    5.412 closest distance to " CG  PRO A  54 " =    1.382
peak=    5.244 closest distance to " O   HOH Z 126 " =    2.034
peak=    5.044 closest distance to " O   HOH Z  65 " =    1.055
peak=    5.029 closest distance to " O   HOH Z 144 " =    1.752
peak=    5.023 closest distance to " O   HOH Z 427 " =    1.256
peak=    4.974 closest distance to " CB  GLN A 223 " =    1.501
peak=    4.824 closest distance to " CB  PRO A  54 " =    0.989
peak=    4.814 closest distance to " CB  SER A  63 " =    1.345
peak=    4.814 closest distance to " O   HOH Z 111 " =    2.016
peak=    4.809 closest distance to " CB  ASN A 148 " =    1.285
peak=    4.693 closest distance to " CG  PRO A 198 " =    1.351
peak=    4.677 closest distance to " O   HOH Z 425 " =    1.614
peak=    4.656 closest distance to " O   HOH Z 222 " =    1.033
peak=    4.635 closest distance to " O   HOH Z 427 " =    2.229
peak=    4.628 closest distance to " CB  SER A   3 " =    1.471
peak=    4.623 closest distance to " CG  PRO A  90 " =    1.149
peak=    4.617 closest distance to " O   HOH Z 403 " =    1.419
peak=    4.605 closest distance to " O   HOH Z  63 " =    1.670
peak=    4.569 closest distance to " O   HOH Z  49 " =    1.381
peak=    4.565 closest distance to " O   HOH Z 369 " =    2.015
peak=    4.555 closest distance to " CB  GLU A 128 " =    1.008
peak=    4.519 closest distance to " O   HOH Z 287 " =    2.185
peak=    4.494 closest distance to " O   HOH Z 423 " =    1.951
peak=    4.458 closest distance to " O   HOH Z 232 " =    2.183
peak=    4.446 closest distance to " O   HOH Z 298 " =    2.009
peak=    4.445 closest distance to " CB  ARG A 275 " =    0.966
peak=    4.413 closest distance to " O   HOH Z 134 " =    1.516
peak=    4.403 closest distance to " O   HOH Z 417 " =    1.352
peak=    4.396 closest distance to " NH2BARG A 102 " =    1.051
peak=    4.370 closest distance to " O   HOH Z 183 " =    1.576
peak=    4.363 closest distance to " O   HOH Z  78 " =    1.581
peak=    4.339 closest distance to " CB  SER A 216 " =    0.953
peak=    4.292 closest distance to " O   HOH Z 193 " =    1.733
peak=    4.281 closest distance to " CA  TYR A  30 " =    1.055
peak=    4.261 closest distance to " CB  GLN A 183 " =    1.153
peak=    4.253 closest distance to " CG2 VAL A 257 " =    1.002
peak=    4.239 closest distance to " O   HOH Z   9 " =    2.184
peak=    4.233 closest distance to " O   HOH Z  97 " =    1.336
peak=    4.226 closest distance to " O   SER A  87 " =    2.154
peak=    4.194 closest distance to " CG  LEU A 167 " =    1.267
peak=    4.187 closest distance to " O   HOH Z 380 " =    1.831
peak=    4.157 closest distance to " O   HOH Z 193 " =    1.916
peak=    4.156 closest distance to " O   HOH Z 272 " =    1.882
peak=    4.149 closest distance to " O   HOH Z 186 " =    1.205
peak=    4.144 closest distance to " O   HOH Z  61 " =    1.627
peak=    4.118 closest distance to " O   HOH Z 234 " =    3.807
peak=    4.108 closest distance to " O   HOH Z   1 " =    1.846
peak=    4.103 closest distance to " CB  GLU A 152 " =    1.361
peak=    4.083 closest distance to " ND2 ASN A 187 " =    1.522
peak=    4.069 closest distance to " O   HOH Z  78 " =    1.981
peak=    4.066 closest distance to " OD1BASN A 224 " =    2.275
peak=    4.062 closest distance to " O   HOH Z 282 " =    1.689
peak=    4.048 closest distance to " O   HOH Z 316 " =    3.089
peak=    4.038 closest distance to " ND1 HIS A  86 " =    1.836
peak=    4.002 closest distance to " O   HOH Z 130 " =    0.878
peak=    4.001 closest distance to " CD BLYS A 290 " =    1.082
peak=    3.987 closest distance to " O   HOH Z 126 " =    1.490
peak=    3.977 closest distance to " O   HOH Z 258 " =    2.192
peak=    3.961 closest distance to " O   HOH Z 368 " =    1.950
peak=    3.954 closest distance to " O   HOH Z   2 " =    2.037
peak=    3.942 closest distance to " O   HOH Z 394 " =    1.609
peak=    3.932 closest distance to " CD  ARG A 159 " =    0.850
peak=    3.919 closest distance to " O   HOH Z 261 " =    1.975
peak=    3.916 closest distance to " O   HOH Z 302 " =    1.556
peak=    3.905 closest distance to " NZ  LYS A 117 " =    1.248
peak=    3.888 closest distance to " O   HOH Z 419 " =    2.317
peak=    3.888 closest distance to " O   HOH Z 139 " =    1.342
peak=    3.879 closest distance to " O   HOH Z 217 " =    2.642
peak=    3.877 closest distance to " O   HOH Z 263 " =    2.356
peak=    3.870 closest distance to " O   HOH Z 389 " =    1.984
peak=    3.862 closest distance to " O   HOH Z 133 " =    2.411
peak=    3.860 closest distance to " CB  ASN A 148 " =    1.922
peak=    3.857 closest distance to " CB  TYR A 169 " =    0.843
peak=    3.852 closest distance to " CB  ASN A 187 " =    0.971
peak=    3.847 closest distance to " CB  VAL A 202 " =    1.635
peak=    3.841 closest distance to " NH1AARG A 145 " =    1.115
peak=    3.839 closest distance to " CG  GLN A  55 " =    1.873
peak=    3.832 closest distance to " O   HOH Z  68 " =    1.773
peak=    3.830 closest distance to " N   GLN A 278 " =    0.950
peak=    3.827 closest distance to " O   HOH Z 411 " =    3.386
peak=    3.826 closest distance to " O   HOH Z  10 " =    1.877
peak=    3.820 closest distance to " O   HOH Z 171 " =    2.604
peak=    3.815 closest distance to " CG1 ILE A  33 " =    1.237
peak=    3.809 closest distance to " O   HOH Z 313 " =    1.854
peak=    3.797 closest distance to " O   HOH Z 409 " =    2.067
peak=    3.791 closest distance to " CB  ASP A 124 " =    0.901
peak=    3.790 closest distance to " O   HOH Z  17 " =    2.254
peak=    3.786 closest distance to " CB  MET A  47 " =    1.103
peak=    3.784 closest distance to " O   HOH Z 155 " =    1.755
peak=    3.772 closest distance to " CG  GLN A  11 " =    2.125
peak=    3.757 closest distance to " CG  GLN A 278 " =    3.772
peak=    3.751 closest distance to " CB  VAL A 265 " =    1.319
peak=    3.750 closest distance to " CB  LEU A 228 " =    1.075
peak=    3.742 closest distance to " CZ  PHE A 192 " =    0.919
peak=    3.738 closest distance to " O   HOH Z 108 " =    1.979
peak=    3.735 closest distance to " ND2 ASN A  60 " =    3.000
peak=    3.730 closest distance to " O   HOH Z 437 " =    2.027
peak=    3.717 closest distance to " O   HOH Z 182 " =    1.307
peak=    3.711 closest distance to " NZ BLYS A 290 " =    1.010
peak=    3.705 closest distance to " CB  TRP A 266 " =    1.053
peak=    3.695 closest distance to " O   HOH Z 145 " =    1.632
peak=    3.689 closest distance to " CA  THR A 264 " =    0.790
peak=    3.686 closest distance to " O   HOH Z 135 " =    1.724
peak=    3.678 closest distance to " O   HOH Z  88 " =    3.095
peak=    3.670 closest distance to " CB  GLU A 236 " =    1.309
peak=    3.664 closest distance to " NE AARG A 275 " =    1.550
peak=    3.664 closest distance to " CA  GLU A 152 " =    1.203
peak=    3.658 closest distance to " CA  ILE A 234 " =    1.038
peak=    3.648 closest distance to " O   HOH Z 371 " =    1.978
peak=    3.642 closest distance to " O   HOH Z 132 " =    2.107
peak=    3.636 closest distance to " O   HOH Z  21 " =    1.733
peak=    3.634 closest distance to " CA  ALA A 299 " =    0.907
peak=    3.634 closest distance to " OD1 ASN A  69 " =    2.510
peak=    3.633 closest distance to " O   PRO A 198 " =    1.535
peak=    3.632 closest distance to " CA  SER A  87 " =    0.946
peak=    3.626 closest distance to " O   HOH Z 152 " =    2.326
peak=    3.618 closest distance to " CB  SER A 276 " =    1.133
peak=    3.615 closest distance to " O   HOH Z 247 " =    1.277
peak=    3.610 closest distance to " CG  GLN A  88 " =    1.053
peak=    3.607 closest distance to " OG BSER A 258 " =    0.815
peak=    3.602 closest distance to " O   HOH Z 175 " =    3.652
peak=    3.600 closest distance to " CG  ARG A 159 " =    0.798
peak=    3.589 closest distance to " CB  LEU A 300 " =    0.991
peak=    3.579 closest distance to " O   HOH Z 115 " =    1.808
peak=    3.578 closest distance to " CG2 THR A 221 " =    1.226
peak=    3.577 closest distance to " O   HOH Z  61 " =    1.706
peak=    3.576 closest distance to " O   HOH Z  59 " =    2.070
peak=    3.576 closest distance to " CG  TRP A 179 " =    2.278
peak=    3.575 closest distance to " CA  ASN A 127 " =    0.907
peak=    3.574 closest distance to " OD2 ASP A 286 " =    2.778
peak=    3.567 closest distance to " CA  ASN A 215 " =    1.279
peak=    3.563 closest distance to " CD  LYS A 166 " =    1.443
peak=    3.563 closest distance to " O   HOH Z 345 " =    1.720
peak=    3.562 closest distance to " CD1 LEU A 300 " =    1.258
peak=    3.561 closest distance to " O   HOH Z  48 " =    1.524
peak=    3.558 closest distance to " O   HOH Z 120 " =    0.932
peak=    3.557 closest distance to " O   HOH Z 195 " =    1.455
peak=    3.554 closest distance to " CD  GLN A 240 " =    1.683
peak=    3.551 closest distance to " O   HOH Z 288 " =    1.858
peak=    3.550 closest distance to " O   HOH Z 352 " =    1.689
peak=    3.550 closest distance to " O   HOH Z 392 " =    1.313
peak=    3.548 closest distance to " O   HOH Z 207 " =    2.172
peak=    3.547 closest distance to " O   HOH Z 260 " =    1.293
peak=    3.547 closest distance to " O   HOH Z 344 " =    3.221
peak=    3.545 closest distance to " O   HOH Z  44 " =    3.004
peak=    3.543 closest distance to " N   PHE A 130 " =    1.220
peak=    3.540 closest distance to " O   HOH Z  59 " =    1.485
peak=    3.539 closest distance to " CA  GLY A 267 " =    1.274
peak=    3.538 closest distance to " CB  TYR A 116 " =    1.004
peak=    3.535 closest distance to " O   HOH Z  40 " =    2.180
peak=    3.533 closest distance to " O   HOH Z 358 " =    1.310
peak=    3.527 closest distance to " O   HOH Z 147 " =    1.364
peak=    3.526 closest distance to " O   HOH Z 236 " =    1.571
peak=    3.517 closest distance to " N   TYR A  15 " =    0.976
peak=    3.513 closest distance to " CB  TRP A 179 " =    1.518
peak=    3.508 closest distance to " CD BARG A 102 " =    1.227
peak=    3.507 closest distance to " O   HOH Z 207 " =    1.848
peak=    3.503 closest distance to " O   HOH Z 180 " =    2.056
peak=    3.501 closest distance to " OD1 ASN A 217 " =    1.556
peak=    3.501 closest distance to " CA  TYR A 186 " =    1.573
peak=    3.489 closest distance to " CB  THR A 157 " =    1.071
peak=    3.487 closest distance to " OG BSER A  99 " =    2.349
peak=    3.486 closest distance to " CG  PRO A 243 " =    1.107
peak=    3.485 closest distance to " O   HOH Z 184 " =    1.855
peak=    3.479 closest distance to " NE2 GLN A  58 " =    3.460
peak=    3.477 closest distance to " CE3 TRP A 274 " =    2.149
peak=    3.470 closest distance to " CA  ALA A 160 " =    0.914
peak=    3.464 closest distance to " O   HOH Z 119 " =    1.525
peak=    3.458 closest distance to " O   HOH Z  44 " =    1.808
peak=    3.458 closest distance to " CG  GLU A   2 " =    1.197
peak=    3.453 closest distance to " CB  LYS A 117 " =    1.227
peak=    3.450 closest distance to " O   HOH Z 410 " =    1.716
peak=    3.450 closest distance to " O   HOH Z  42 " =    1.536
peak=    3.442 closest distance to " CB  ALA A  21 " =    1.683
peak=    3.442 closest distance to " NE1 TRP A 274 " =    0.973
peak=    3.439 closest distance to " CA  TYR A  30 " =    1.088
peak=    3.439 closest distance to " O   HOH Z 378 " =    1.130
peak=    3.436 closest distance to " O   HOH Z 112 " =    0.912
peak=    3.435 closest distance to " O   HOH Z  88 " =    2.697
peak=    3.431 closest distance to " O   HOH Z 116 " =    2.925
peak=    3.428 closest distance to " N   ALA A   1 " =    2.240
peak=    3.422 closest distance to " CB  LEU A 237 " =    0.782
peak=    3.418 closest distance to " OG  SER A  62 " =    2.959
peak=    3.417 closest distance to " O   HOH Z 193 " =    2.133
peak=    3.414 closest distance to " C   GLU A 277 " =    1.357
peak=    3.414 closest distance to " N   ARG A 156 " =    1.302
peak=    3.407 closest distance to " CA  ALA A  21 " =    1.191
peak=    3.407 closest distance to " O   HOH Z 380 " =    3.272
peak=    3.403 closest distance to " NE  ARG A  66 " =    3.388
peak=    3.402 closest distance to " O   HOH Z 106 " =    2.531
peak=    3.400 closest distance to " O   HOH Z 345 " =    3.491
peak=    3.399 closest distance to " CD  LYS A 119 " =    1.180
peak=    3.399 closest distance to " CA  ASP A 191 " =    0.767
peak=    3.396 closest distance to " O   HOH Z 334 " =    2.801
peak=    3.393 closest distance to " O   HOH Z 414 " =    1.299
peak=    3.391 closest distance to " O   ALA A 233 " =    1.816
peak=    3.386 closest distance to " O   HOH Z 166 " =    1.294
peak=    3.384 closest distance to " O   HOH Z 422 " =    2.829
peak=    3.384 closest distance to " N   GLY A 196 " =    1.084
peak=    3.380 closest distance to " O   HOH Z 151 " =    1.657
peak=    3.377 closest distance to " O   HOH Z 225 " =    1.390
peak=    3.376 closest distance to " CB  ALA A  43 " =    0.936
peak=    3.369 closest distance to " O   HOH Z 211 " =    1.120
peak=    3.369 closest distance to " O   HOH Z 303 " =    1.695
peak=    3.368 closest distance to " N   ASN A 127 " =    1.477
peak=    3.367 closest distance to " OH  TYR A 186 " =    1.063
peak=    3.364 closest distance to " O   HOH Z 368 " =    3.781
peak=    3.363 closest distance to " CH2 TRP A 150 " =    1.021
peak=    3.359 closest distance to " CB  ARG A 139 " =    1.046
peak=    3.359 closest distance to " CB  ALA A  34 " =    1.260
peak=    3.357 closest distance to " O   PRO A 198 " =    1.300
peak=    3.357 closest distance to " CE  LYS A  76 " =    0.896
peak=    3.350 closest distance to " CA  THR A 221 " =    0.920
peak=    3.350 closest distance to " O   HOH Z 139 " =    2.178
peak=    3.349 closest distance to " CA  ALA A 158 " =    1.121
peak=    3.346 closest distance to " CA  GLY A 196 " =    0.916
peak=    3.345 closest distance to " O   HOH Z 271 " =    2.322
peak=    3.340 closest distance to " O   HOH Z  50 " =    1.694
peak=    3.339 closest distance to " O   HOH Z 227 " =    1.742
peak=    3.334 closest distance to " O   HOH Z 148 " =    1.622
peak=    3.331 closest distance to " O   HOH Z 217 " =    1.677
peak=    3.330 closest distance to " O   HOH Z 250 " =    1.389
peak=    3.327 closest distance to " O   HOH Z 373 " =    1.498
peak=    3.323 closest distance to " O   HOH Z 130 " =    0.827
peak=    3.322 closest distance to " O   HOH Z 371 " =    2.729
peak=    3.321 closest distance to " CA  ARG A 102 " =    1.203
peak=    3.320 closest distance to " CA  LEU A 282 " =    1.198
peak=    3.317 closest distance to " O   HOH Z 295 " =    1.551
peak=    3.316 closest distance to " O   HOH Z 222 " =    2.482
peak=    3.315 closest distance to " O   HOH Z 405 " =    1.597
peak=    3.309 closest distance to " O   HOH Z  57 " =    1.051
peak=    3.308 closest distance to " O   HOH Z 175 " =    2.155
peak=    3.305 closest distance to " O   HOH Z 132 " =    1.101
peak=    3.304 closest distance to " CD1 ILE A  33 " =    1.610
peak=    3.304 closest distance to " O   HOH Z 130 " =    2.008
peak=    3.301 closest distance to " OE2 GLU A  53 " =    2.083
peak=    3.299 closest distance to " O   HOH Z 209 " =    2.450
peak=    3.297 closest distance to " CA  ALA A 154 " =    0.963
peak=    3.296 closest distance to " CG1 VAL A 153 " =    0.913
peak=    3.290 closest distance to " CE BMET A  47 " =    1.446
peak=    3.286 closest distance to " NH2 ARG A 219 " =    1.713
peak=    3.279 closest distance to " SD  MET A  93 " =    1.324
peak=    3.278 closest distance to " O   HOH Z 393 " =    1.332
peak=    3.276 closest distance to " O   GLN A 278 " =    1.317
peak=    3.273 closest distance to " NH1 ARG A  56 " =    1.169
peak=    3.266 closest distance to " O   HOH Z 128 " =    2.168
peak=    3.265 closest distance to " O   HOH Z  37 " =    1.247
peak=    3.265 closest distance to " O   HOH Z   1 " =    1.525
peak=    3.264 closest distance to " O   HOH Z  68 " =    2.067
peak=    3.263 closest distance to " O   HOH Z 244 " =    1.624
peak=    3.261 closest distance to " O   HOH Z 225 " =    1.923
peak=    3.260 closest distance to " O   TYR A 116 " =    1.385
peak=    3.259 closest distance to " O   HOH Z 390 " =    1.243
peak=    3.258 closest distance to " O   MET A 105 " =    1.738
peak=    3.257 closest distance to " CA  LYS A  48 " =    1.451
peak=    3.256 closest distance to " CA  ARG A 195 " =    1.453
peak=    3.256 closest distance to " O   HOH Z  51 " =    1.849
peak=    3.254 closest distance to " O   HOH Z 359 " =    1.396
peak=    3.252 closest distance to " CB  ALA A 184 " =    1.110
peak=    3.251 closest distance to " O   HOH Z 362 " =    1.949
peak=    3.250 closest distance to " NH2 ARG A 159 " =    1.620
peak=    3.249 closest distance to " O   HOH Z 418 " =    1.764
peak=    3.245 closest distance to " O   HOH Z 329 " =    3.459
peak=    3.244 closest distance to " O   THR A 220 " =    1.520
peak=    3.244 closest distance to " O   HOH Z 158 " =    2.642
peak=    3.241 closest distance to " O   HOH Z 145 " =    3.632
peak=    3.238 closest distance to " N   ALA A   1 " =    2.902
peak=    3.237 closest distance to " O   GLY A 302 " =    1.554
peak=    3.232 closest distance to " N   SER A  97 " =    0.822
peak=    3.231 closest distance to " O   HOH Z 128 " =    2.050
peak=    3.229 closest distance to " NH2BARG A 190 " =    1.575
peak=    3.228 closest distance to " O   HOH Z 213 " =    2.006
peak=    3.226 closest distance to " O   HOH Z 222 " =    2.275
peak=    3.225 closest distance to " O   HOH Z 148 " =    3.440
peak=    3.223 closest distance to " O   HOH Z 209 " =    2.305
peak=    3.223 closest distance to " CB  ASN A 170 " =    1.420
peak=    3.223 closest distance to " O   HOH Z 245 " =    1.321
peak=    3.222 closest distance to " CA  MET A 105 " =    0.908
peak=    3.222 closest distance to " O   HOH Z 112 " =    2.555
peak=    3.222 closest distance to " NZ  LYS A  76 " =    1.460
peak=    3.220 closest distance to " CZ  PHE A  38 " =    1.374
peak=    3.218 closest distance to " CE  MET A  93 " =    1.352
peak=    3.217 closest distance to " CB  GLU A 152 " =    1.383
peak=    3.217 closest distance to " O   HOH Z 133 " =    1.610
peak=    3.213 closest distance to " O   HOH Z 154 " =    1.987
peak=    3.213 closest distance to " O   ASN A 209 " =    1.539
peak=    3.213 closest distance to " CB  ARG A 102 " =    0.770
peak=    3.210 closest distance to " CD  ARG A  66 " =    2.298
peak=    3.209 closest distance to " O   HOH Z 108 " =    1.623
peak=    3.208 closest distance to " CA  ASP A  50 " =    0.985
peak=    3.196 closest distance to " O   HOH Z  20 " =    1.825
peak=    3.195 closest distance to " CA  ALA A  51 " =    1.132
peak=    3.190 closest distance to " CE1 TYR A 186 " =    1.426
peak=    3.183 closest distance to " CG  GLN A 144 " =    1.018
peak=    3.177 closest distance to " O   ARG A  56 " =    1.839
peak=    3.171 closest distance to " NH1 ARG A  14 " =    1.039
peak=    3.171 closest distance to " O   HOH Z 122 " =    1.548
peak=    3.154 closest distance to " CA  LEU A 101 " =    1.498
peak=    3.154 closest distance to " O   HOH Z   6 " =    1.880
peak=    3.147 closest distance to " CB  ARG A 190 " =    1.775
peak=    3.146 closest distance to " O   HOH Z 116 " =    1.682
peak=    3.144 closest distance to " O   HOH Z 368 " =    4.341
peak=    3.140 closest distance to " CA  ASP A 124 " =    0.745
peak=    3.140 closest distance to " CE AMET A  47 " =    1.365
peak=    3.138 closest distance to " CE3 TRP A 274 " =    1.187
peak=    3.133 closest distance to " CA  ALA A 233 " =    1.377
peak=    3.131 closest distance to " O   HOH Z 374 " =    2.882
peak=    3.131 closest distance to " O   HOH Z 220 " =    1.313
peak=    3.124 closest distance to " CB  MET A  40 " =    0.912
peak=    3.122 closest distance to " CG  LEU A 101 " =    1.183
peak=    3.120 closest distance to " O   HOH Z 282 " =    2.051
peak=    3.116 closest distance to " OE1 GLN A 194 " =    1.377
peak=    3.113 closest distance to " O   HOH Z 365 " =    5.869
peak=    3.110 closest distance to " CB  ALA A 114 " =    1.284
peak=    3.108 closest distance to " O   HOH Z 170 " =    1.184
peak=    3.097 closest distance to " NH2AARG A 190 " =    1.323
peak=    3.097 closest distance to " O   HOH Z 284 " =    1.462
peak=    3.096 closest distance to " O   HOH Z   1 " =    1.498
peak=    3.094 closest distance to " O   HOH Z 215 " =    1.429
peak=    3.093 closest distance to " ND1 HIS A  81 " =    1.586
peak=    3.092 closest distance to " O   HOH Z  30 " =    1.681
peak=    3.090 closest distance to " O   GLN A 240 " =    1.772
peak=    3.087 closest distance to " O   HOH Z  51 " =    1.800
peak=    3.085 closest distance to " O   HOH Z 327 " =    1.975
peak=    3.084 closest distance to " O   HOH Z 425 " =    1.954
peak=    3.084 closest distance to " O   HOH Z 140 " =    2.100
peak=    3.084 closest distance to " O   HOH Z 128 " =    2.087
peak=    3.076 closest distance to " CZ  PHE A 218 " =    1.032
peak=    3.075 closest distance to " CA  SER A  32 " =    1.610
peak=    3.065 closest distance to " CG2 VAL A 232 " =    0.925
peak=    3.064 closest distance to " CG2AVAL A 121 " =    2.514
peak=    3.053 closest distance to " CB  ASN A  39 " =    0.926
peak=    3.040 closest distance to " O   HOH Z 181 " =    2.264
peak=    3.029 closest distance to " O   HOH Z 273 " =    2.880

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 196         
Filter by distance & map next to the model:
   mapped sites are within: 0.481 - 5.641
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 196
   mapped sites are within: 0.737 - 5.641

peak=   -4.703 closest distance to " OE1 GLN A  88 " =    0.953
peak=   -4.627 closest distance to " O   HOH Z  65 " =    0.962
peak=   -4.593 closest distance to " CG  MET A 105 " =    0.960
peak=   -4.587 closest distance to " O   PRO A 198 " =    1.291
peak=   -4.566 closest distance to " CD  ARG A  14 " =    3.200
peak=   -4.477 closest distance to " O   HOH Z 290 " =    1.082
peak=   -4.385 closest distance to " CG  GLN A  88 " =    0.879
peak=   -4.347 closest distance to " CB  PRO A 243 " =    2.535
peak=   -4.236 closest distance to " C   ALA A 158 " =    1.402
peak=   -4.221 closest distance to " O   HOH Z 166 " =    1.107
peak=   -4.109 closest distance to " CA  GLY A  98 " =    1.889
peak=   -4.088 closest distance to " O   HOH Z 198 " =    2.319
peak=   -4.036 closest distance to " O   HOH Z 377 " =    1.449
peak=   -4.013 closest distance to " O   HOH Z  52 " =    1.225
peak=   -4.003 closest distance to " CA  ASP A  27 " =    2.404
peak=   -3.995 closest distance to " O   HOH Z 407 " =    3.449
peak=   -3.962 closest distance to " C   ASN A 285 " =    2.384
peak=   -3.944 closest distance to " OG BSER A 134 " =    1.329
peak=   -3.894 closest distance to " O   HOH Z  28 " =    1.606
peak=   -3.887 closest distance to " CB  ALA A 291 " =    2.177
peak=   -3.867 closest distance to " O   HOH Z 438 " =    0.851
peak=   -3.867 closest distance to " O   HOH Z 231 " =    1.762
peak=   -3.848 closest distance to " O   HOH Z 185 " =    2.261
peak=   -3.832 closest distance to " O   HOH Z 231 " =    0.757
peak=   -3.779 closest distance to " O   HOH Z 117 " =    0.737
peak=   -3.764 closest distance to " O   HOH Z  76 " =    1.111
peak=   -3.758 closest distance to " O   ALA A   1 " =    1.065
peak=   -3.746 closest distance to " CD1 LEU A 101 " =    2.433
peak=   -3.743 closest distance to " O   HOH Z  97 " =    1.446
peak=   -3.743 closest distance to " O   HOH Z  60 " =    1.681
peak=   -3.739 closest distance to " CB  TYR A  15 " =    2.158
peak=   -3.723 closest distance to " O   HOH Z 266 " =    4.524
peak=   -3.718 closest distance to " O   HOH Z 388 " =    1.835
peak=   -3.704 closest distance to " O   HOH Z 211 " =    1.541
peak=   -3.694 closest distance to " O   HOH Z  43 " =    1.509
peak=   -3.689 closest distance to " CD  ARG A 156 " =    1.903
peak=   -3.682 closest distance to " N   GLN A  58 " =    1.660
peak=   -3.682 closest distance to " N   THR A 157 " =    1.478
peak=   -3.672 closest distance to " CD2 LEU A 237 " =    2.778
peak=   -3.665 closest distance to " O   HOH Z 298 " =    1.050
peak=   -3.654 closest distance to " OG  SER A  87 " =    1.273
peak=   -3.650 closest distance to " CA  GLY A 203 " =    2.161
peak=   -3.648 closest distance to " OG1 THR A 279 " =    1.470
peak=   -3.644 closest distance to " O   HOH Z  20 " =    2.459
peak=   -3.639 closest distance to " O   HOH Z 102 " =    1.779
peak=   -3.636 closest distance to " OD1 ASP A 191 " =    1.911
peak=   -3.629 closest distance to " CB  ALA A 248 " =    1.980
peak=   -3.626 closest distance to " OE1 GLN A 223 " =    2.326
peak=   -3.625 closest distance to " O   HOH Z 351 " =    1.456
peak=   -3.622 closest distance to " CG  ASP A 231 " =    0.752
peak=   -3.619 closest distance to " CE  LYS A  76 " =    2.909
peak=   -3.609 closest distance to " CD2 TYR A 293 " =    1.916
peak=   -3.608 closest distance to " ND2 ASN A  45 " =    1.033
peak=   -3.602 closest distance to " O   HOH Z  13 " =    1.436
peak=   -3.599 closest distance to " O   HOH Z 409 " =    5.641
peak=   -3.597 closest distance to " N   ALA A  43 " =    2.377
peak=   -3.594 closest distance to " CA  GLY A 241 " =    2.165
peak=   -3.591 closest distance to " O   HOH Z 384 " =    3.117
peak=   -3.588 closest distance to " O   VAL A 189 " =    2.336
peak=   -3.564 closest distance to " O   PRO A 243 " =    2.329
peak=   -3.537 closest distance to " O   HOH Z 111 " =    2.205
peak=   -3.515 closest distance to " O   HOH Z 168 " =    1.777
peak=   -3.503 closest distance to " CG2AVAL A  41 " =    2.852
peak=   -3.498 closest distance to " O   HOH Z 247 " =    1.593
peak=   -3.498 closest distance to " O   HOH Z  71 " =    0.986
peak=   -3.486 closest distance to " O   HOH Z 124 " =    1.200
peak=   -3.483 closest distance to " CB  CYS A 201 " =    2.355
peak=   -3.475 closest distance to " CZ  PHE A  59 " =    1.480
peak=   -3.473 closest distance to " CD  LYS A 289 " =    2.405
peak=   -3.472 closest distance to " O   HOH Z  90 " =    2.817
peak=   -3.466 closest distance to " CE2 TYR A  30 " =    2.613
peak=   -3.461 closest distance to " CB  PHE A 192 " =    1.683
peak=   -3.452 closest distance to " O   HOH Z  51 " =    1.040
peak=   -3.451 closest distance to " O   HOH Z 372 " =    2.436
peak=   -3.445 closest distance to " OG  SER A  97 " =    2.184
peak=   -3.444 closest distance to " CZ3 TRP A 123 " =    1.645
peak=   -3.439 closest distance to " OG  SER A   3 " =    1.529
peak=   -3.435 closest distance to " CB  CYS A 254 " =    2.042
peak=   -3.434 closest distance to " O   HOH Z  39 " =    1.425
peak=   -3.432 closest distance to " OD1 ASN A 301 " =    1.940
peak=   -3.428 closest distance to " CB  PRO A  90 " =    1.451
peak=   -3.428 closest distance to " CD  GLN A 223 " =    1.327
peak=   -3.427 closest distance to " C   GLY A  13 " =    1.045
peak=   -3.423 closest distance to " O   HOH Z 209 " =    2.659
peak=   -3.423 closest distance to " O   PRO A 163 " =    1.932
peak=   -3.417 closest distance to " C   LEU A 143 " =    1.352
peak=   -3.415 closest distance to " O   HOH Z  24 " =    1.306
peak=   -3.411 closest distance to " CA  GLY A 133 " =    1.985
peak=   -3.410 closest distance to " NH2 ARG A  79 " =    1.819
peak=   -3.405 closest distance to " OD2 ASP A 171 " =    1.832
peak=   -3.397 closest distance to " OE1 GLN A 278 " =    1.189
peak=   -3.385 closest distance to " O   HOH Z 317 " =    2.285
peak=   -3.384 closest distance to " OG BSER A 134 " =    1.682
peak=   -3.384 closest distance to " O   SER A 135 " =    1.443
peak=   -3.382 closest distance to " CG  PRO A 163 " =    2.322
peak=   -3.379 closest distance to " CB  ASP A 132 " =    2.251
peak=   -3.379 closest distance to " OG  SER A  26 " =    0.874
peak=   -3.377 closest distance to " O   HOH Z 313 " =    1.893
peak=   -3.370 closest distance to " O   SER A  62 " =    2.280
peak=   -3.364 closest distance to " O   SER A  22 " =    2.776
peak=   -3.363 closest distance to " O   GLN A 194 " =    1.340
peak=   -3.361 closest distance to " N   GLN A 122 " =    1.500
peak=   -3.361 closest distance to " O   HOH Z 198 " =    1.574
peak=   -3.359 closest distance to " CB  PRO A  54 " =    2.405
peak=   -3.344 closest distance to " CE1 TYR A 169 " =    2.504
peak=   -3.336 closest distance to " NH2AARG A 275 " =    5.606
peak=   -3.336 closest distance to " OE1 GLU A 277 " =    2.248
peak=   -3.335 closest distance to " O   HOH Z 389 " =    1.930
peak=   -3.325 closest distance to " O   ALA A 180 " =    1.284
peak=   -3.324 closest distance to " O   VAL A 197 " =    1.756
peak=   -3.323 closest distance to " CG  GLU A 152 " =    2.189
peak=   -3.320 closest distance to " CG1 VAL A  78 " =    2.431
peak=   -3.320 closest distance to " CD  GLN A  58 " =    1.102
peak=   -3.318 closest distance to " CB  ASP A  50 " =    2.414
peak=   -3.318 closest distance to " N   ALA A   1 " =    3.137
peak=   -3.317 closest distance to " OXT GLY A 302 " =    3.068
peak=   -3.312 closest distance to " O   HOH Z 152 " =    4.850
peak=   -3.310 closest distance to " NH1 ARG A 195 " =    2.159
peak=   -3.305 closest distance to " O   HOH Z  88 " =    1.994
peak=   -3.300 closest distance to " O   HOH Z 318 " =    1.484
peak=   -3.297 closest distance to " O   HOH Z 432 " =    3.691
peak=   -3.295 closest distance to " O   HOH Z  49 " =    1.961
peak=   -3.292 closest distance to " OG  SER A 245 " =    1.084
peak=   -3.290 closest distance to " O   HOH Z 137 " =    1.278
peak=   -3.289 closest distance to " O   HOH Z 222 " =    1.167
peak=   -3.288 closest distance to " O   HOH Z 140 " =    4.782
peak=   -3.287 closest distance to " CE  LYS A 166 " =    1.118
peak=   -3.279 closest distance to " O   HOH Z 213 " =    1.150
peak=   -3.278 closest distance to " ND2 ASN A 249 " =    2.367
peak=   -3.277 closest distance to " NH2 ARG A 219 " =    1.829
peak=   -3.273 closest distance to " O   HOH Z 148 " =    2.318
peak=   -3.272 closest distance to " CB  ALA A   7 " =    1.957
peak=   -3.267 closest distance to " OD1 ASN A 148 " =    1.653
peak=   -3.265 closest distance to " OG ASER A 134 " =    1.147
peak=   -3.265 closest distance to " O   VAL A  67 " =    2.709
peak=   -3.260 closest distance to " CB  ALA A 248 " =    2.528
peak=   -3.256 closest distance to " CB  ALA A 227 " =    2.319
peak=   -3.253 closest distance to " CE  MET A  93 " =    1.138
peak=   -3.250 closest distance to " O   ILE A  49 " =    1.627
peak=   -3.247 closest distance to " CA  ASN A 127 " =    1.275
peak=   -3.246 closest distance to " O   HOH Z 298 " =    2.561
peak=   -3.237 closest distance to " O   HOH Z 275 " =    1.546
peak=   -3.219 closest distance to " O   HOH Z  22 " =    2.486
peak=   -3.219 closest distance to " O   HOH Z 417 " =    2.079
peak=   -3.217 closest distance to " CD1 TRP A 179 " =    0.977
peak=   -3.215 closest distance to " O   HOH Z 234 " =    4.245
peak=   -3.213 closest distance to " N   HIS A 115 " =    2.033
peak=   -3.212 closest distance to " CD  PRO A 198 " =    1.439
peak=   -3.210 closest distance to " CZ BARG A 275 " =    1.661
peak=   -3.204 closest distance to " ND2 ASN A  60 " =    4.309
peak=   -3.201 closest distance to " O   HOH Z 385 " =    1.621
peak=   -3.199 closest distance to " CZ2 TRP A 179 " =    2.262
peak=   -3.198 closest distance to " CB  PHE A 283 " =    2.608
peak=   -3.197 closest distance to " O   HOH Z 390 " =    2.402
peak=   -3.197 closest distance to " N   ASP A 171 " =    2.398
peak=   -3.196 closest distance to " O   VAL A 153 " =    2.436
peak=   -3.194 closest distance to " CB  SER A 271 " =    1.092
peak=   -3.192 closest distance to " O   HOH Z 403 " =    1.575
peak=   -3.188 closest distance to " CD  LYS A 166 " =    2.307
peak=   -3.182 closest distance to " OG1 THR A   4 " =    1.885
peak=   -3.179 closest distance to " O   ALA A   7 " =    1.233
peak=   -3.170 closest distance to " O   VAL A  67 " =    2.647
peak=   -3.170 closest distance to " N   ALA A   1 " =    1.436
peak=   -3.169 closest distance to " CE2 TYR A 116 " =    3.014
peak=   -3.159 closest distance to " CG1 VAL A 250 " =    2.572
peak=   -3.157 closest distance to " O   SER A  95 " =    1.105
peak=   -3.155 closest distance to " OE1 GLU A  44 " =    1.492
peak=   -3.153 closest distance to " O   HOH Z 303 " =    1.379
peak=   -3.152 closest distance to " O   HOH Z 130 " =    0.872
peak=   -3.151 closest distance to " O   HOH Z 300 " =    2.026
peak=   -3.149 closest distance to " O   PRO A 243 " =    2.160
peak=   -3.142 closest distance to " CZ  TYR A 169 " =    1.867
peak=   -3.141 closest distance to " CD1 LEU A 228 " =    2.246
peak=   -3.137 closest distance to " CD1 LEU A 255 " =    2.986
peak=   -3.127 closest distance to " O   HOH Z 411 " =    1.034
peak=   -3.124 closest distance to " CG  LEU A  83 " =    2.026
peak=   -3.116 closest distance to " CB  ALA A  43 " =    2.283
peak=   -3.116 closest distance to " O   HOH Z   2 " =    1.468
peak=   -3.109 closest distance to " O   HOH Z 275 " =    1.766
peak=   -3.109 closest distance to " O   HOH Z 414 " =    1.662
peak=   -3.103 closest distance to " O   HOH Z 111 " =    0.921
peak=   -3.103 closest distance to " O   HOH Z 108 " =    2.507
peak=   -3.095 closest distance to " CZ2 TRP A  92 " =    2.657
peak=   -3.090 closest distance to " CG BLYS A 290 " =    0.893
peak=   -3.078 closest distance to " O   ASP A 162 " =    2.306
peak=   -3.077 closest distance to " CD1 ILE A 239 " =    2.275
peak=   -3.077 closest distance to " O   HOH Z 255 " =    2.231
peak=   -3.073 closest distance to " C   ILE A 234 " =    1.242
peak=   -3.052 closest distance to " N   ARG A 159 " =    2.017
peak=   -3.043 closest distance to " CA  HIS A  86 " =    2.088
peak=   -3.025 closest distance to " OG1 THR A 246 " =    1.543
peak=   -3.021 closest distance to " O   HOH Z 193 " =    1.925
peak=   -3.018 closest distance to " CB  ALA A 100 " =    2.342

================= 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    :  0.4736 0.4718   6.278369e+00   6.277027e+00
   1_bss:  0.4661 0.4656   6.274920e+00   6.268543e+00
   1_xyz:  0.3702 0.4059   6.134199e+00   6.184894e+00
   1_adp:  0.3347 0.4139   6.085307e+00   6.194290e+00
   1_occ:  0.3341 0.4138   6.084122e+00   6.193763e+00
   2_bss:  0.3339 0.4120   6.085106e+00   6.192703e+00
   2_xyz:  0.2721 0.3474   5.919813e+00   6.074983e+00
   2_adp:  0.2558 0.3355   5.881549e+00   6.053437e+00
   2_occ:  0.2558 0.3349   5.880990e+00   6.052865e+00
   3_bss:  0.2564 0.3344   5.881177e+00   6.052652e+00
   3_xyz:  0.1953 0.2624   5.641204e+00   5.851911e+00
   3_adp:  0.1734 0.2271   5.523992e+00   5.738501e+00
   3_occ:  0.1730 0.2260   5.521231e+00   5.735013e+00
   4_bss:  0.1725 0.2246   5.517801e+00   5.730190e+00
   4_xyz:  0.1403 0.1892   5.331827e+00   5.563711e+00
   4_adp:  0.1312 0.1807   5.276947e+00   5.515615e+00
   4_occ:  0.1311 0.1802   5.276067e+00   5.514639e+00
   5_bss:  0.1311 0.1798   5.275155e+00   5.513445e+00
   5_xyz:  0.1220 0.1702   5.215656e+00   5.459795e+00
   5_adp:  0.1201 0.1665   5.200283e+00   5.444050e+00
   5_occ:  0.1199 0.1662   5.199507e+00   5.443527e+00
   5_bss:  0.1199 0.1662   5.199532e+00   5.443498e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000   0.198   1.420  -0.219   0.000  -0.000  -0.000
   1_xyz:  0.300  20.000   0.198   1.420  -0.219   0.000  -0.000  -0.000
   1_adp:  0.300  20.000   0.198   1.420  -0.219   0.000  -0.000  -0.000
   1_occ:  0.300  20.000   0.198   1.420  -0.219   0.000  -0.000  -0.000
   2_bss:  0.347  57.980  -0.146   0.089  -0.107   0.000  -0.000  -0.000
   2_xyz:  0.347  57.980  -0.146   0.089  -0.107   0.000  -0.000  -0.000
   2_adp:  0.347  57.980  -0.146   0.089  -0.107   0.000  -0.000  -0.000
   2_occ:  0.347  57.980  -0.146   0.089  -0.107   0.000  -0.000  -0.000
   3_bss:  0.349  64.498  -0.100  -0.311   0.208  -0.000   0.000   0.000
   3_xyz:  0.349  64.498  -0.100  -0.311   0.208  -0.000   0.000   0.000
   3_adp:  0.349  64.498  -0.100  -0.311   0.208  -0.000   0.000   0.000
   3_occ:  0.349  64.498  -0.100  -0.311   0.208  -0.000   0.000   0.000
   4_bss:  0.329  54.190  -1.142  -1.841  -0.845  -0.000  -0.000  -0.000
   4_xyz:  0.329  54.190  -1.142  -1.841  -0.845  -0.000  -0.000  -0.000
   4_adp:  0.329  54.190  -1.142  -1.841  -0.845  -0.000  -0.000  -0.000
   4_occ:  0.329  54.190  -1.142  -1.841  -0.845  -0.000  -0.000  -0.000
   5_bss:  0.322  54.190  -1.517  -2.283  -1.228  -0.000  -0.000  -0.000
   5_xyz:  0.322  54.190  -1.517  -2.283  -1.228  -0.000  -0.000  -0.000
   5_adp:  0.322  54.190  -1.517  -2.283  -1.228  -0.000  -0.000  -0.000
   5_occ:  0.322  54.190  -1.517  -2.283  -1.228  -0.000  -0.000  -0.000
   5_bss:  0.317  49.281  -1.544  -2.338  -1.269  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.949 0.4070  0.5579    72832.988
   1_bss:  58.137 0.4160  0.5828    70113.826
   1_xyz:  45.758 0.5726  0.7793    48581.230
   1_adp:  46.645 0.5609  0.7673    49599.884
   1_occ:  46.646 0.5608  0.7660    49501.223
   2_bss:  46.449 0.5632  0.7577    49191.012
   2_xyz:  37.199 0.6742  0.8882    32739.436
   2_adp:  35.232 0.6976  0.8979    30557.203
   2_occ:  35.219 0.6977  0.8973    30491.001
   3_bss:  35.139 0.6985  0.8974    30334.326
   3_xyz:  26.590 0.7937  0.9905    17903.338
   3_adp:  22.334 0.8391  1.0128    13609.147
   3_occ:  22.223 0.8401  1.0131    13461.608
   4_bss:  22.051 0.8415  0.9707    13213.056
   4_xyz:  17.842 0.8813  0.9918     9022.859
   4_adp:  16.583 0.8932  0.9914     8217.446
   4_occ:  16.556 0.8934  0.9914     8191.598
   5_bss:  16.529 0.8936  0.9773     8166.133
   5_xyz:  15.321 0.9040  0.9832     7201.094
   5_adp:  14.857 0.9082  0.9833     6969.282
   5_occ:  14.835 0.9084  0.9832     6947.236
   5_bss:  14.836 0.9083  0.9810     6942.253
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.7704e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.7704e-01
   1_xyz:   1.504  0.011  0.100 15.725  0.006  4.107   1.1951e-01
   1_adp:   1.504  0.011  0.100 15.725  0.006  4.107   1.1951e-01
   1_occ:   1.504  0.011  0.100 15.725  0.006  4.107   1.1951e-01
   2_bss:   1.504  0.011  0.100 15.725  0.006  4.107   1.1951e-01
   2_xyz:   1.227  0.010  0.081 14.790  0.005  4.107   8.9210e-02
   2_adp:   1.227  0.010  0.081 14.790  0.005  4.107   8.9210e-02
   2_occ:   1.227  0.010  0.081 14.790  0.005  4.107   8.9210e-02
   3_bss:   1.227  0.010  0.081 14.790  0.005  4.107   8.9210e-02
   3_xyz:   1.149  0.008  0.077 14.862  0.004  4.107   7.4086e-02
   3_adp:   1.149  0.008  0.077 14.862  0.004  4.107   7.4086e-02
   3_occ:   1.149  0.008  0.077 14.862  0.004  4.107   7.4086e-02
   4_bss:   1.149  0.008  0.077 14.862  0.004  4.107   7.4086e-02
   4_xyz:   0.992  0.006  0.073 14.556  0.004  4.115   5.8779e-02
   4_adp:   0.992  0.006  0.073 14.556  0.004  4.115   5.8779e-02
   4_occ:   0.992  0.006  0.073 14.556  0.004  4.115   5.8779e-02
   5_bss:   0.992  0.006  0.073 14.556  0.004  4.115   5.8779e-02
   5_xyz:   0.918  0.006  0.067 14.611  0.003  4.109   5.2608e-02
   5_adp:   0.918  0.006  0.067 14.611  0.003  4.109   5.2608e-02
   5_occ:   0.918  0.006  0.067 14.611  0.003  4.109   5.2608e-02
   5_bss:   0.918  0.006  0.067 14.611  0.003  4.109   5.2608e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.536   2.3967e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.536   2.3967e-01
   1_xyz:  10.407  0.089  0.530 88.663  0.033  1.986   9.0218e-02
   1_adp:  10.407  0.089  0.530 88.663  0.033  1.986   9.0218e-02
   1_occ:  10.407  0.089  0.530 88.663  0.033  1.986   9.0218e-02
   2_bss:  10.407  0.089  0.530 88.663  0.033  1.986   9.0218e-02
   2_xyz:  10.087  0.058  0.234 84.577  0.037  2.189   1.7930e-01
   2_adp:  10.087  0.058  0.234 84.577  0.037  2.189   1.7930e-01
   2_occ:  10.087  0.058  0.234 84.577  0.037  2.189   1.7930e-01
   3_bss:  10.087  0.058  0.234 84.577  0.037  2.189   1.7930e-01
   3_xyz:   8.632  0.037  0.347 83.131  0.023  2.193   6.7345e-02
   3_adp:   8.632  0.037  0.347 83.131  0.023  2.193   6.7345e-02
   3_occ:   8.632  0.037  0.347 83.131  0.023  2.193   6.7345e-02
   4_bss:   8.632  0.037  0.347 83.131  0.023  2.193   6.7345e-02
   4_xyz:   8.476  0.042  0.224 83.972  0.029  2.278   4.6829e-02
   4_adp:   8.476  0.042  0.224 83.972  0.029  2.278   4.6829e-02
   4_occ:   8.476  0.042  0.224 83.972  0.029  2.278   4.6829e-02
   5_bss:   8.476  0.042  0.224 83.972  0.029  2.278   4.6829e-02
   5_xyz:   7.821  0.037  0.212 84.587  0.035  2.333   3.6819e-02
   5_adp:   7.821  0.037  0.212 84.587  0.035  2.333   3.6819e-02
   5_occ:   7.821  0.037  0.212 84.587  0.035  2.333   3.6819e-02
   5_bss:   7.821  0.037  0.212 84.587  0.035  2.333   3.6819e-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: 114.42   0.00  19.57  91.24   0.00  16.26 114.42   0.00  37.61
   1_occ: 114.42   0.00  19.57  91.24   0.00  16.26 114.42   0.00  37.61
   2_bss: 114.42   0.00  19.57  91.24   0.00  16.26 114.42   0.00  37.61
   2_xyz: 114.42   0.00  19.57  91.24   0.00  16.26 114.42   0.00  37.61
   2_adp: 117.92   0.00  19.44 100.10   0.00  15.42 117.92   0.00  41.31
   2_occ: 117.92   0.00  19.44 100.10   0.00  15.42 117.92   0.00  41.31
   3_bss: 117.92   0.00  19.44 100.10   0.00  15.42 117.92   0.00  41.31
   3_xyz: 117.92   0.00  19.44 100.10   0.00  15.42 117.92   0.00  41.31
   3_adp: 108.06   1.69  17.69  94.39   1.69  13.27 108.06   4.46  41.76
   3_occ: 108.06   1.69  17.69  94.39   1.69  13.27 108.06   4.46  41.76
   4_bss: 108.06   1.69  17.69  94.39   1.69  13.27 108.06   4.46  41.76
   4_xyz: 108.06   1.69  17.69  94.39   1.69  13.27 108.06   4.46  41.76
   4_adp: 101.59   0.00  17.61 101.59   0.00  12.80  99.51   3.08  43.76
   4_occ: 101.59   0.00  17.61 101.59   0.00  12.80  99.51   3.08  43.76
   5_bss: 101.59   0.00  17.61 101.59   0.00  12.80  99.51   3.08  43.76
   5_xyz: 101.59   0.00  17.61 101.59   0.00  12.80  99.51   3.08  43.76
   5_adp: 102.01   0.52  17.13 102.01   0.52  12.61  97.54   3.79  41.76
   5_occ: 102.01   0.52  17.13 102.01   0.52  12.61  97.54   3.79  41.76
   5_bss: 102.00   0.50  17.12 102.00   0.50  12.59  97.52   3.78  41.74
------------------------------------------------------------------------
 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:    1.795    0.019    0.310
   1_adp:    1.795    0.019    0.310
   1_occ:    1.795    0.019    0.310
   2_bss:    1.795    0.019    0.310
   2_xyz:    1.423    0.022    0.485
   2_adp:    1.423    0.022    0.485
   2_occ:    1.423    0.022    0.485
   3_bss:    1.423    0.022    0.485
   3_xyz:    1.632    0.058    0.678
   3_adp:    1.632    0.058    0.678
   3_occ:    1.632    0.058    0.678
   4_bss:    1.632    0.058    0.678
   4_xyz:    1.656    0.054    0.746
   4_adp:    1.656    0.054    0.746
   4_occ:    1.656    0.054    0.746
   5_bss:    1.656    0.054    0.746
   5_xyz:    1.725    0.060    0.773
   5_adp:    1.725    0.060    0.773
   5_occ:    1.725    0.060    0.773
   5_bss:    1.725    0.060    0.773
------------------------------------------------------------------------

CPU time actual refinement: 356.57


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1102/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_1102/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1102/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1102/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1102/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 356.42 
  Macro-tasks:
    bulk solvent and scale       = 44.57  
    individual site refinement   = 143.71 
    weights calculation          = 29.94  
    collect and process          = 6.42   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 224.75 
  Micro-tasks:
    mask                            = 2.57   
    f_calc                          = 116.55 
    alpha_beta                      = 8.49   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 123.03 
    fmodel                         = 7.24   
    r_factors                      = 0.21   
    phase_errors                   = 10.11  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 269.63 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.100 micro seconds
Total CPU time: 6.17 minutes
from_scatterers_fft:    636 calls, 116.18 s
gradients_fft:          581 calls, 110.41 s

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

# Date 2008-01-16 Time 06:25:50 PST -0800 (1200493550.72 s)
Start R-work = 0.4736, R-free = 0.4718 (no bulk solvent and anisotropic scale)
Final R-work = 0.1414, R-free = 0.1857 (no bulk solvent and anisotropic scale)

Start R-work = 0.4661, R-free = 0.4656
Final R-work = 0.1199, R-free = 0.1662