# Date 2008-01-16 Time 02:38:56 PST -0800 (1200479936.31 s)
#phil __OFF__

Command line arguments: "../918.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 6084
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 918

-------------------------------------------------------------------------------
  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.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 47.1647, 86.39, 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: 3.26, per 1000 atoms: 1.15


================================== 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: (70.9525, 47.1647, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1028 2.00102
Completeness in resolution range: 0.972786
Completeness with d_max=infinity: 0.969704

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1028
                             d_min =   2.0010

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: (70.9525, 47.1647, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1028 2.00102
Completeness in resolution range: 0.972786
Completeness with d_max=infinity: 0.969704

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1032 -  4.2814 [2104/2128]  1894   210  10.0%
  bin  2:  4.2814 -  3.4112 [2038/2057]  1834   204  10.0%
  bin  3:  3.4112 -  2.9837 [2007/2026]  1803   204  10.2%
  bin  4:  2.9837 -  2.7127 [1988/2018]  1794   194   9.8%
  bin  5:  2.7127 -  2.5192 [1979/1998]  1781   198  10.0%
  bin  6:  2.5192 -  2.3712 [1944/1969]  1750   194  10.0%
  bin  7:  2.3712 -  2.2529 [1967/1995]  1766   201  10.2%
  bin  8:  2.2529 -  2.1551 [1945/1981]  1754   191   9.8%
  bin  9:  2.1551 -  2.0724 [1939/1981]  1747   192   9.9%
  bin 10:  2.0724 -  2.0010 [1678/1984]  1507   171  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_918/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:
        1.81 -     2.42: 7
        2.42 -     3.04: 2185
        3.04 -     3.66: 4604
        3.66 -     4.28: 8985
        4.28 -     4.90: 12260
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.921 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " NH2BARG A 275 " - " O   HOH Z 335 "  2.406 3.120
  ... (remaining 28036 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 =====================

Setting all isotropic ADP = 10.000: selected atoms: all (2823)
Shaking sites (RMS = 0.500): selected atoms: all (2823)

==================== 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/trial/run_918/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_918/model_refine_001.geo

CPU time processing inputs: 9.17


============================ 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 = 70.9525 47.16465 86.39 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
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4198   r_free= 0.4031   ksol= 0.00   Bsol= 0.00   scale= 0.825    |
|                                                                             |
| 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:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.207495                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1032 -  4.7751 0.99   1376  153 0.3566 0.3328      6.5106      6.3966|
|  2:  4.7751 -  3.8102 0.99   1322  146 0.3073 0.3189      6.5973       6.649|
|  3:  3.8102 -  3.3345 0.99   1297  145 0.3552 0.3419      6.5265      6.5243|
|  4:  3.3345 -  3.0323 0.99   1278  144 0.3975 0.3378      6.4326      6.3119|
|  5:  3.0323 -  2.8164 0.99   1283  141 0.4324 0.4117      6.2865      6.3231|
|  6:  2.8164 -  2.6513 0.99   1280  139 0.4420 0.4800      6.2212      6.1961|
|  7:  2.6513 -  2.5192 0.99   1270  142 0.4719 0.4606      6.1982      6.1727|
|  8:  2.5192 -  2.4100 0.98   1261  145 0.4707 0.4117      6.1423      6.0763|
|  9:  2.4100 -  2.3175 0.98   1257  137 0.4659 0.4791      6.0791      6.0865|
| 10:  2.3175 -  2.2378 0.99   1241  141 0.4761 0.4695      6.0814      6.0783|
| 11:  2.2378 -  2.1681 0.98   1265  135 0.4777 0.4185      6.0118      5.9525|
| 12:  2.1681 -  2.1063 0.97   1235  139 0.4833 0.4705      5.9667      6.0084|
| 13:  2.1063 -  2.0509 1.00   1248  144 0.5008 0.5042       5.885      5.8847|
| 14:  2.0509 -  2.0010 0.79   1017  108 0.4810 0.4428      5.8205      5.6887|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1032 -  4.7751  1376   153  0.75  29.69   0.81     0.77      53458.41|
|  2:  4.7751 -  3.8102  1322   146  0.80  26.55   0.92     0.83      65431.18|
|  3:  3.8102 -  3.3345  1297   145  0.74  31.95   0.87     0.81      67539.87|
|  4:  3.3345 -  3.0323  1278   144  0.68  37.16   0.84     0.74      61352.42|
|  5:  3.0323 -  2.8164  1283   141  0.59  45.01   0.78     0.66      56274.23|
|  6:  2.8164 -  2.6513  1280   139  0.56  47.38   0.77     0.61      52130.90|
|  7:  2.6513 -  2.5192  1270   142  0.54  49.21   0.75     0.59      48657.03|
|  8:  2.5192 -  2.4100  1261   145  0.53  50.02   0.77     0.60      44316.51|
|  9:  2.4100 -  2.3175  1257   137  0.54  49.09   0.75     0.59      39206.17|
| 10:  2.3175 -  2.2378  1241   141  0.54  49.18   0.78     0.60      35722.94|
| 11:  2.2378 -  2.1681  1265   135  0.52  50.84   0.77     0.58      33439.45|
| 12:  2.1681 -  2.1063  1235   139  0.49  52.74   0.79     0.57      33225.20|
| 13:  2.1063 -  2.0509  1248   144  0.48  53.90   0.75     0.56      28993.45|
| 14:  2.0509 -  2.0010  1017   108  0.55  48.66   0.74     0.59      21716.70|
|alpha:            min =        0.56 max =            0.83 mean =         0.65|
|beta:             min =    21716.70 max =        67539.87 mean =     46391.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.60|
|phase err.(work): min =        0.00 max =           89.99 mean =        44.12|
|phase err.(test): min =        0.00 max =           89.97 mean =        44.11|
|-----------------------------------------------------------------------------|

============================== 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 = 7.079830              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 73.339   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.547449              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.450   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      161 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      675 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1495 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2602 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3889 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4994 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6592 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7624 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.118 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.618 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.108)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    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:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 12.108)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4275   r_free= 0.4088   ksol= 0.00   Bsol= 0.00   scale= 0.794    |
|                                                                             |
| 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:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.214018                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4115   r_free= 0.3896   ksol= 0.30   Bsol= 20.00   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.11,8.55,8.13,0.00,0.00,0.00); trace/3= 8.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.203357                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.710252              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.287   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.550262              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.467   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4115      final r-factor (work) = 0.2970          |
| start r-factor (free) = 0.3896      final r-factor (free) = 0.3221          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 75.0083 = 6.71 * 0.50 * 6.2265 + 1.00 * 54.1177                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.3189 = 6.71 * 0.50 * 6.0225 + 1.00 * 0.1127                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2970      final r-factor (work) = 0.2285          |
| start r-factor (free) = 0.3221      final r-factor (free) = 0.2611          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3287 = 0.55 * 1.00 * 6.0225 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2148 = 0.55 * 1.00 * 5.8223 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.108)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    55.56   9.87     None  None   None       |
|    all(noH): 2823   0      0.00    55.56   9.87     None  None   None       |
|    Sol.    : 438    0      0.00    55.56   26.64    None  None   None       |
|    Mac.    : 2385   0      0.00    50.37   6.80     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 -   5.556: 1285   |   5:    27.781 -  33.337:  118        |
|      1:     5.556 -  11.112:  772   |   6:    33.337 -  38.893:   61        |
|      2:    11.112 -  16.668:  269   |   7:    38.893 -  44.449:   63        |
|      3:    16.668 -  22.224:  108   |   8:    44.449 -  50.005:   18        |
|      4:    22.224 -  27.781:  122   |   9:    50.005 -  55.561:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2285 r_free = 0.2611             target_work(ml) = 5.728         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2279 r_free = 0.2612             target_work(ml) = 5.726         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2279   r_free= 0.2612   ksol= 0.30   Bsol= 20.00   scale= 1.078   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.11,8.55,8.13,0.00,0.00,0.00); trace/3= 8.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.726353                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2228   r_free= 0.2540   ksol= 0.33   Bsol= 50.00   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.60,4.86,5.08,0.00,0.00,0.00); trace/3= 4.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.724890                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.737820              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.825   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.288908              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.601  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2228      final r-factor (work) = 0.1510          |
| start r-factor (free) = 0.2540      final r-factor (free) = 0.1886          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0180 = 3.74 * 0.50 * 5.8352 + 1.00 * 0.1124                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4326 = 3.74 * 0.50 * 5.5451 + 1.00 * 0.0693                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1510      final r-factor (work) = 0.1376          |
| start r-factor (free) = 0.1886      final r-factor (free) = 0.1786          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6307 = 0.29 * 1.00 * 5.5451 + 1.00 * 0.0287                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6408 = 0.29 * 1.00 * 5.3318 + 1.00 * 0.1004                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.108)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.37   10.40    None  None   None       |
|    all(noH): 2823   0      0.00    75.37   10.40    None  None   None       |
|    Sol.    : 438    0      0.57    54.41   29.97    None  None   None       |
|    Mac.    : 2385   0      0.00    75.37   6.81     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 -   7.537: 1704   |   5:    37.686 -  45.224:  112        |
|      1:     7.537 -  15.075:  535   |   6:    45.224 -  52.761:   39        |
|      2:    15.075 -  22.612:  175   |   7:    52.761 -  60.298:    6        |
|      3:    22.612 -  30.149:  118   |   8:    60.298 -  67.835:    0        |
|      4:    30.149 -  37.686:  133   |   9:    67.835 -  75.373:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1376 r_free = 0.1786             target_work(ml) = 5.302         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1375 r_free = 0.1787             target_work(ml) = 5.301         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1375   r_free= 0.1787   ksol= 0.33   Bsol= 50.00   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.60,4.86,5.08,0.00,0.00,0.00); trace/3= 4.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.301307                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1373   r_free= 0.1783   ksol= 0.33   Bsol= 50.00   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.58,3.89,4.58,0.00,0.00,0.00); trace/3= 4.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.302136                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.371451              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.641  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.004884              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.508   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1373      final r-factor (work) = 0.1213          |
| start r-factor (free) = 0.1783      final r-factor (free) = 0.1625          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3964 = 2.37 * 0.50 * 5.3360 + 1.00 * 0.0693                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2876 = 2.37 * 0.50 * 5.2466 + 1.00 * 0.0666                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1213      final r-factor (work) = 0.1165          |
| start r-factor (free) = 0.1625      final r-factor (free) = 0.1600          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.5329 = 2.00 * 1.00 * 5.2466 + 1.00 * 0.0142                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.3995 = 2.00 * 1.00 * 5.1800 + 1.00 * 0.0143                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.108)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.52   11.37    None  None   None       |
|    all(noH): 2823   0      0.00    75.52   11.37    None  None   None       |
|    Sol.    : 438    0      0.12    73.66   34.59    None  None   None       |
|    Mac.    : 2385   0      0.00    75.52   7.11     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 -   7.552: 1676   |   5:    37.760 -  45.311:   71        |
|      1:     7.552 -  15.104:  550   |   6:    45.311 -  52.863:   90        |
|      2:    15.104 -  22.656:  161   |   7:    52.863 -  60.415:   50        |
|      3:    22.656 -  30.208:  102   |   8:    60.415 -  67.967:   16        |
|      4:    30.208 -  37.760:   98   |   9:    67.967 -  75.519:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1165 r_free = 0.1600             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1164 r_free = 0.1600             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1600   ksol= 0.33   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.58,3.89,4.58,0.00,0.00,0.00); trace/3= 4.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.175030                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1600   ksol= 0.33   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.58,3.89,4.58,0.00,0.00,0.00); trace/3= 4.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.175030                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.082145              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.053  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.193977              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.392  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1164      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1600      final r-factor (free) = 0.1592          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0492 = 3.08 * 0.50 * 5.1799 + 1.00 * 0.0666                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0196 = 3.08 * 0.50 * 5.1539 + 1.00 * 0.0771                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1107      final r-factor (work) = 0.1119          |
| start r-factor (free) = 0.1592      final r-factor (free) = 0.1569          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0141 = 0.19 * 1.00 * 5.1539 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0107 = 0.19 * 1.00 * 5.1549 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 34     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.108)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.75   11.01    None  None   None       |
|    all(noH): 2823   0      0.00    74.75   11.01    None  None   None       |
|    Sol.    : 438    0      0.91    69.80   33.13    None  None   None       |
|    Mac.    : 2385   0      0.00    74.75   6.95     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 -   7.476: 1716   |   5:    37.377 -  44.853:   64        |
|      1:     7.476 -  14.951:  523   |   6:    44.853 -  52.328:   85        |
|      2:    14.951 -  22.426:  161   |   7:    52.328 -  59.804:   42        |
|      3:    22.426 -  29.902:  104   |   8:    59.804 -  67.279:   15        |
|      4:    29.902 -  37.377:  106   |   9:    67.279 -  74.754:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1119 r_free = 0.1569             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1119 r_free = 0.1570             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1570   ksol= 0.33   Bsol= 50.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.58,3.89,4.58,0.00,0.00,0.00); trace/3= 4.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.145006                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1122   r_free= 0.1569   ksol= 0.32   Bsol= 49.44   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.48,3.73,4.57,0.00,0.00,0.00); trace/3= 3.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.144753                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.516501              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 158.522  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.691462              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.577  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1122      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1569      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9859 = 1.52 * 0.50 * 5.1544 + 1.00 * 0.0776                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9706 = 1.52 * 0.50 * 5.1584 + 1.00 * 0.0593                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1154      final r-factor (work) = 0.1139          |
| start r-factor (free) = 0.1575      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5776 = 0.69 * 1.00 * 5.1584 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5798 = 0.69 * 1.00 * 5.1553 + 1.00 * 0.0151                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.108)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.30   11.09    None  None   None       |
|    all(noH): 2823   0      0.00    76.30   11.09    None  None   None       |
|    Sol.    : 438    0      0.72    70.73   33.40    None  None   None       |
|    Mac.    : 2385   0      0.00    76.30   6.99     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.630: 1718   |   5:    38.150 -  45.780:   79        |
|      1:     7.630 -  15.260:  514   |   6:    45.780 -  53.410:   74        |
|      2:    15.260 -  22.890:  159   |   7:    53.410 -  61.040:   39        |
|      3:    22.890 -  30.520:  112   |   8:    61.040 -  68.671:   13        |
|      4:    30.520 -  38.150:  109   |   9:    68.671 -  76.301:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1139 r_free = 0.1588             target_work(ml) = 5.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1139 r_free = 0.1588             target_work(ml) = 5.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1588   ksol= 0.32   Bsol= 49.44   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.48,3.73,4.57,0.00,0.00,0.00); trace/3= 3.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.161931                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1032 -  4.7751 0.99   1376  153 0.1017 0.1302      5.3934      5.5124|
|  2:  4.7751 -  3.8102 0.99   1322  146 0.0889 0.1093      5.4551      5.6273|
|  3:  3.8102 -  3.3345 0.99   1297  145 0.1059 0.1521      5.4804      5.8605|
|  4:  3.3345 -  3.0323 0.99   1278  144 0.1214 0.1497      5.4646      5.5882|
|  5:  3.0323 -  2.8164 0.99   1283  141 0.1340 0.1773      5.3444      5.5648|
|  6:  2.8164 -  2.6513 0.99   1280  139 0.1223 0.1844      5.2284      5.4533|
|  7:  2.6513 -  2.5192 0.99   1270  142 0.1297 0.1657      5.1922        5.41|
|  8:  2.5192 -  2.4100 0.98   1261  145 0.1212 0.1778      5.1072       5.391|
|  9:  2.4100 -  2.3175 0.98   1257  137 0.1199 0.1815      5.0706      5.3152|
| 10:  2.3175 -  2.2378 0.99   1241  141 0.1141 0.1682      4.9864      5.2367|
| 11:  2.2378 -  2.1681 0.98   1265  135 0.1169 0.1781      4.9598      5.2614|
| 12:  2.1681 -  2.1063 0.97   1235  139 0.1129 0.1749      4.8883      5.2306|
| 13:  2.1063 -  2.0509 1.00   1248  144 0.1168 0.1708      4.8261      5.0773|
| 14:  2.0509 -  2.0010 0.79   1017  108 0.1116 0.1917      4.7203      4.9857|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1032 -  4.7751  1376   153  0.94   9.01   0.97     0.95       7021.78|
|  2:  4.7751 -  3.8102  1322   146  0.95   7.92   1.01     0.99       8925.61|
|  3:  3.8102 -  3.3345  1297   145  0.94  11.11   1.02     1.01      10411.76|
|  4:  3.3345 -  3.0323  1278   144  0.92  13.38   1.00     0.98      10293.59|
|  5:  3.0323 -  2.8164  1283   141  0.90  15.99   0.99     0.96       8477.01|
|  6:  2.8164 -  2.6513  1280   139  0.90  15.85   0.98     0.96       7330.56|
|  7:  2.6513 -  2.5192  1270   142  0.90  16.06   0.98     0.95       6455.53|
|  8:  2.5192 -  2.4100  1261   145  0.91  15.52   0.99     0.96       5669.61|
|  9:  2.4100 -  2.3175  1257   137  0.91  15.87   1.00     0.97       5413.04|
| 10:  2.3175 -  2.2378  1241   141  0.90  15.48   1.00     0.95       4468.90|
| 11:  2.2378 -  2.1681  1265   135  0.90  16.53   0.99     0.95       4498.66|
| 12:  2.1681 -  2.1063  1235   139  0.92  14.72   1.00     0.98       3902.46|
| 13:  2.1063 -  2.0509  1248   144  0.90  16.48   1.00     0.98       3621.67|
| 14:  2.0509 -  2.0010  1017   108  0.91  15.51   0.97     0.93       2818.75|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2818.75 max =        10411.76 mean =      6464.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.78 mean =        14.17|
|phase err.(test): min =        0.00 max =           88.77 mean =        13.70|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1588   ksol= 0.32   Bsol= 53.37   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.45,-0.21,0.66,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.161929                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1588   ksol= 0.32   Bsol= 53.37   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.45,-0.21,0.66,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.161929                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1032 -  4.7751 0.99   1376  153 0.1017 0.1302      5.3934      5.5124|
|  2:  4.7751 -  3.8102 0.99   1322  146 0.0889 0.1093      5.4551      5.6273|
|  3:  3.8102 -  3.3345 0.99   1297  145 0.1059 0.1521      5.4804      5.8605|
|  4:  3.3345 -  3.0323 0.99   1278  144 0.1214 0.1497      5.4646      5.5881|
|  5:  3.0323 -  2.8164 0.99   1283  141 0.1340 0.1774      5.3444      5.5648|
|  6:  2.8164 -  2.6513 0.99   1280  139 0.1223 0.1843      5.2284      5.4531|
|  7:  2.6513 -  2.5192 0.99   1270  142 0.1297 0.1657      5.1921      5.4099|
|  8:  2.5192 -  2.4100 0.98   1261  145 0.1212 0.1779      5.1071       5.391|
|  9:  2.4100 -  2.3175 0.98   1257  137 0.1199 0.1815      5.0706      5.3152|
| 10:  2.3175 -  2.2378 0.99   1241  141 0.1141 0.1682      4.9864      5.2368|
| 11:  2.2378 -  2.1681 0.98   1265  135 0.1169 0.1782      4.9599      5.2617|
| 12:  2.1681 -  2.1063 0.97   1235  139 0.1129 0.1749      4.8884      5.2307|
| 13:  2.1063 -  2.0509 1.00   1248  144 0.1168 0.1709      4.8261      5.0774|
| 14:  2.0509 -  2.0010 0.79   1017  108 0.1116 0.1916      4.7201      4.9854|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1032 -  4.7751  1376   153  0.94   9.01   0.97     0.95       7022.20|
|  2:  4.7751 -  3.8102  1322   146  0.95   7.92   1.01     0.99       8925.72|
|  3:  3.8102 -  3.3345  1297   145  0.94  11.11   1.02     1.01      10411.84|
|  4:  3.3345 -  3.0323  1278   144  0.92  13.38   1.00     0.98      10293.41|
|  5:  3.0323 -  2.8164  1283   141  0.90  15.99   0.99     0.96       8475.19|
|  6:  2.8164 -  2.6513  1280   139  0.90  15.85   0.98     0.96       7329.59|
|  7:  2.6513 -  2.5192  1270   142  0.90  16.06   0.98     0.95       6454.09|
|  8:  2.5192 -  2.4100  1261   145  0.91  15.51   0.99     0.96       5668.91|
|  9:  2.4100 -  2.3175  1257   137  0.91  15.87   1.00     0.97       5413.01|
| 10:  2.3175 -  2.2378  1241   141  0.90  15.48   1.00     0.95       4469.21|
| 11:  2.2378 -  2.1681  1265   135  0.90  16.53   0.99     0.95       4500.26|
| 12:  2.1681 -  2.1063  1235   139  0.92  14.73   1.00     0.98       3903.29|
| 13:  2.1063 -  2.0509  1248   144  0.90  16.48   1.00     0.98       3621.72|
| 14:  2.0509 -  2.0010  1017   108  0.91  15.50   0.97     0.93       2817.56|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2817.56 max =        10411.84 mean =      6464.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.78 mean =        14.17|
|phase err.(test): min =        0.00 max =           88.77 mean =        13.70|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.108)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.93    80.23   15.02    None  None   None       |
|    all(noH): 2823   0      3.93    80.23   15.02    None  None   None       |
|    Sol.    : 438    0      4.65    74.66   37.33    None  None   None       |
|    Mac.    : 2385   0      3.93    80.23   10.92    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:     3.931 -  11.561: 1718   |   5:    42.082 -  49.712:   79        |
|      1:    11.561 -  19.191:  514   |   6:    49.712 -  57.342:   74        |
|      2:    19.191 -  26.822:  159   |   7:    57.342 -  64.972:   39        |
|      3:    26.822 -  34.452:  112   |   8:    64.972 -  72.602:   13        |
|      4:    34.452 -  42.082:  109   |   9:    72.602 -  80.232:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 316         
Filter by distance & map next to the model:
   mapped sites are within: 0.331 - 4.760
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 306 from: 316
   mapped sites are within: 0.724 - 4.760

peak=   10.070 closest distance to " CG2 VAL A 230 " =    1.309
peak=    7.020 closest distance to " CG2 VAL A 296 " =    1.112
peak=    6.223 closest distance to " CG  LEU A   5 " =    1.231
peak=    6.172 closest distance to " NH2 ARG A  56 " =    2.280
peak=    5.849 closest distance to " CB  GLN A 223 " =    1.432
peak=    5.696 closest distance to " CG  LEU A 228 " =    1.189
peak=    5.463 closest distance to " CD2 LEU A   5 " =    1.154
peak=    5.265 closest distance to " CB  VAL A 230 " =    1.207
peak=    4.978 closest distance to " CB  VAL A 296 " =    1.099
peak=    4.902 closest distance to " CB  SER A  63 " =    1.321
peak=    4.798 closest distance to " CB  GLN A 183 " =    1.267
peak=    4.795 closest distance to " CG  PRO A 213 " =    1.240
peak=    4.763 closest distance to " CG  PRO A 198 " =    1.229
peak=    4.729 closest distance to " NE2 GLN A  11 " =    1.114
peak=    4.661 closest distance to " CB  ARG A 275 " =    0.872
peak=    4.622 closest distance to " O   HOH Z 232 " =    2.382
peak=    4.587 closest distance to " O   HOH Z 126 " =    1.912
peak=    4.491 closest distance to " CZ  PHE A 218 " =    1.059
peak=    4.447 closest distance to " O   HOH Z 298 " =    1.816
peak=    4.445 closest distance to " CG  PRO A 243 " =    1.123
peak=    4.420 closest distance to " C   PRO A 198 " =    1.531
peak=    4.360 closest distance to " CB  GLU A 128 " =    1.051
peak=    4.301 closest distance to " O   HOH Z 427 " =    3.036
peak=    4.294 closest distance to " CB  ASN A 148 " =    1.375
peak=    4.291 closest distance to " O   HOH Z 369 " =    2.126
peak=    4.264 closest distance to " O   HOH Z 316 " =    3.138
peak=    4.262 closest distance to " OD1 ASN A  69 " =    2.624
peak=    4.255 closest distance to " O   HOH Z  44 " =    2.236
peak=    4.254 closest distance to " O   HOH Z 368 " =    2.201
peak=    4.206 closest distance to " O   HOH Z  54 " =    2.384
peak=    4.180 closest distance to " CA  TYR A  30 " =    0.936
peak=    4.175 closest distance to " O   HOH Z 142 " =    1.570
peak=    4.173 closest distance to " O   HOH Z 272 " =    1.911
peak=    4.171 closest distance to " O   HOH Z  78 " =    1.716
peak=    4.148 closest distance to " CB  TRP A 266 " =    0.957
peak=    4.126 closest distance to " O   HOH Z  43 " =    1.960
peak=    4.122 closest distance to " O   HOH Z 236 " =    2.010
peak=    4.060 closest distance to " CB  GLU A 152 " =    1.173
peak=    4.047 closest distance to " CB  ARG A  79 " =    1.435
peak=    4.045 closest distance to " CD2 LEU A 228 " =    1.149
peak=    4.038 closest distance to " CB  SER A   3 " =    1.284
peak=    4.037 closest distance to " CZ  PHE A 192 " =    0.993
peak=    4.034 closest distance to " O   HOH Z 158 " =    3.145
peak=    4.033 closest distance to " CB  ARG A 190 " =    1.608
peak=    4.029 closest distance to " O   HOH Z 261 " =    2.079
peak=    4.026 closest distance to " O   HOH Z  68 " =    2.159
peak=    4.026 closest distance to " O   HOH Z  15 " =    2.147
peak=    4.017 closest distance to " O   SER A  87 " =    2.311
peak=    4.017 closest distance to " ND2 ASN A 187 " =    1.456
peak=    4.016 closest distance to " O   HOH Z 423 " =    1.725
peak=    4.013 closest distance to " O   HOH Z 303 " =    2.064
peak=    4.008 closest distance to " NH2 ARG A 156 " =    1.136
peak=    4.008 closest distance to " CB  GLU A 277 " =    3.639
peak=    3.989 closest distance to " CB  ASN A 187 " =    1.335
peak=    3.973 closest distance to " CB  VAL A 265 " =    1.283
peak=    3.951 closest distance to " O   HOH Z 346 " =    1.646
peak=    3.950 closest distance to " O   HOH Z 189 " =    2.738
peak=    3.949 closest distance to " O   HOH Z 203 " =    1.783
peak=    3.942 closest distance to " CB  ASN A  39 " =    0.898
peak=    3.924 closest distance to " CB  PRO A  54 " =    0.779
peak=    3.911 closest distance to " O   HOH Z  61 " =    1.634
peak=    3.901 closest distance to " CA  THR A 264 " =    0.757
peak=    3.888 closest distance to " O   HOH Z 403 " =    1.655
peak=    3.882 closest distance to " CA  ALA A  51 " =    0.949
peak=    3.853 closest distance to " O   HOH Z 234 " =    3.689
peak=    3.847 closest distance to " CG  MET A 185 " =    1.217
peak=    3.845 closest distance to " N   ASN A  39 " =    1.208
peak=    3.842 closest distance to " CB  ASP A 140 " =    0.882
peak=    3.838 closest distance to " CB BVAL A  41 " =    1.035
peak=    3.838 closest distance to " NH1AARG A 145 " =    1.151
peak=    3.836 closest distance to " CD  ARG A 269 " =    0.968
peak=    3.822 closest distance to " CG1 VAL A 153 " =    0.974
peak=    3.820 closest distance to " CB  ALA A 291 " =    1.375
peak=    3.802 closest distance to " O   HOH Z  63 " =    2.025
peak=    3.800 closest distance to " O   HOH Z 280 " =    2.961
peak=    3.799 closest distance to " CA  ASN A 215 " =    1.242
peak=    3.798 closest distance to " CB  LEU A 143 " =    1.170
peak=    3.797 closest distance to " CD  ARG A  66 " =    2.602
peak=    3.790 closest distance to " CG1BVAL A  72 " =    1.694
peak=    3.779 closest distance to " CD  LYS A 166 " =    1.304
peak=    3.776 closest distance to " O   HOH Z 248 " =    1.718
peak=    3.775 closest distance to " ND2 ASN A 249 " =    1.883
peak=    3.774 closest distance to " CB  VAL A 202 " =    1.570
peak=    3.773 closest distance to " CD BLYS A 290 " =    1.000
peak=    3.769 closest distance to " CG2 VAL A 257 " =    0.913
peak=    3.765 closest distance to " CD1 LEU A 300 " =    1.158
peak=    3.752 closest distance to " CB  LEU A 228 " =    1.239
peak=    3.752 closest distance to " CB  SER A 216 " =    0.830
peak=    3.747 closest distance to " O   HOH Z 402 " =    1.503
peak=    3.733 closest distance to " O   HOH Z 411 " =    3.702
peak=    3.729 closest distance to " O   TRP A 274 " =    1.883
peak=    3.722 closest distance to " CG1 VAL A 296 " =    1.224
peak=    3.721 closest distance to " O   MET A 105 " =    1.830
peak=    3.708 closest distance to " CD  ARG A 159 " =    0.755
peak=    3.707 closest distance to " O   HOH Z 214 " =    2.093
peak=    3.685 closest distance to " CB  ASN A 142 " =    1.104
peak=    3.683 closest distance to " CB  TRP A 179 " =    1.427
peak=    3.675 closest distance to " O   HOH Z 245 " =    1.377
peak=    3.660 closest distance to " CA  ARG A 195 " =    1.212
peak=    3.651 closest distance to " O   HOH Z  21 " =    1.719
peak=    3.648 closest distance to " O   HOH Z  19 " =    2.359
peak=    3.644 closest distance to " O   HOH Z 147 " =    1.747
peak=    3.643 closest distance to " O   HOH Z  88 " =    3.227
peak=    3.640 closest distance to " OD2 ASP A 286 " =    2.831
peak=    3.638 closest distance to " O   HOH Z 180 " =    2.149
peak=    3.635 closest distance to " O   HOH Z 197 " =    3.018
peak=    3.634 closest distance to " O   HOH Z 285 " =    3.018
peak=    3.633 closest distance to " O   HOH Z  80 " =    1.699
peak=    3.631 closest distance to " O   HOH Z  97 " =    2.077
peak=    3.628 closest distance to " CA  TYR A  30 " =    1.069
peak=    3.627 closest distance to " CA  ALA A 295 " =    1.082
peak=    3.624 closest distance to " CG2 THR A 221 " =    1.161
peak=    3.620 closest distance to " CB  ALA A 248 " =    1.394
peak=    3.617 closest distance to " CG1 ILE A  49 " =    1.487
peak=    3.613 closest distance to " O   HOH Z 193 " =    1.886
peak=    3.612 closest distance to " O   HOH Z 425 " =    1.351
peak=    3.611 closest distance to " O   HOH Z 344 " =    3.071
peak=    3.607 closest distance to " CA  SER A  87 " =    1.034
peak=    3.605 closest distance to " O   HOH Z 437 " =    1.877
peak=    3.602 closest distance to " CA  ALA A  21 " =    1.162
peak=    3.598 closest distance to " O   ASP A 124 " =    1.070
peak=    3.595 closest distance to " CA  ARG A  36 " =    1.110
peak=    3.584 closest distance to " O   HOH Z 263 " =    1.668
peak=    3.580 closest distance to " CB  ALA A   9 " =    1.603
peak=    3.574 closest distance to " CG1 ILE A  33 " =    1.310
peak=    3.572 closest distance to " O   HOH Z 172 " =    3.639
peak=    3.571 closest distance to " N   VAL A 126 " =    1.407
peak=    3.569 closest distance to " O   HOH Z 128 " =    2.155
peak=    3.565 closest distance to " CB  THR A 157 " =    1.177
peak=    3.559 closest distance to " CB  ARG A 139 " =    0.847
peak=    3.558 closest distance to " O   HOH Z 193 " =    1.662
peak=    3.556 closest distance to " O   HOH Z  40 " =    1.717
peak=    3.552 closest distance to " CA  ALA A 158 " =    1.200
peak=    3.540 closest distance to " O   HOH Z 273 " =    2.736
peak=    3.535 closest distance to " CB  MET A  40 " =    0.807
peak=    3.534 closest distance to " O   HOH Z  48 " =    1.704
peak=    3.525 closest distance to " CB  GLU A  46 " =    0.974
peak=    3.519 closest distance to " CA  THR A 221 " =    0.907
peak=    3.516 closest distance to " N   PHE A 130 " =    1.241
peak=    3.510 closest distance to " O   HOH Z 291 " =    1.619
peak=    3.509 closest distance to " O   HOH Z 247 " =    1.318
peak=    3.507 closest distance to " CB  ARG A  79 " =    0.901
peak=    3.504 closest distance to " O   HOH Z 133 " =    1.669
peak=    3.500 closest distance to " O   HOH Z 227 " =    1.666
peak=    3.492 closest distance to " CD  ARG A  66 " =    2.490
peak=    3.491 closest distance to " CE1 TYR A 186 " =    1.326
peak=    3.491 closest distance to " O   HOH Z 193 " =    2.040
peak=    3.487 closest distance to " ND1 HIS A  81 " =    1.691
peak=    3.481 closest distance to " O   HOH Z 128 " =    2.150
peak=    3.479 closest distance to " CA  LYS A 117 " =    1.256
peak=    3.479 closest distance to " O   HOH Z  59 " =    2.143
peak=    3.470 closest distance to " O   HOH Z 145 " =    2.098
peak=    3.467 closest distance to " O   HOH Z 383 " =    1.955
peak=    3.457 closest distance to " O   HOH Z 290 " =    1.090
peak=    3.455 closest distance to " CE  LYS A  76 " =    0.856
peak=    3.449 closest distance to " CB  SER A 212 " =    1.207
peak=    3.448 closest distance to " CB  THR A  31 " =    1.670
peak=    3.448 closest distance to " O   HOH Z 371 " =    3.141
peak=    3.445 closest distance to " CB  SER A 273 " =    0.867
peak=    3.436 closest distance to " CG  LEU A 167 " =    1.155
peak=    3.433 closest distance to " NE2 GLN A  77 " =    3.384
peak=    3.429 closest distance to " CA  VAL A  41 " =    0.810
peak=    3.428 closest distance to " CB  MET A  47 " =    1.071
peak=    3.418 closest distance to " O   HOH Z  97 " =    2.526
peak=    3.418 closest distance to " CG1 ILE A 151 " =    1.043
peak=    3.416 closest distance to " O   HOH Z 327 " =    2.379
peak=    3.415 closest distance to " O   HOH Z 422 " =    2.673
peak=    3.415 closest distance to " O   HOH Z 126 " =    1.633
peak=    3.408 closest distance to " CB  HIS A 108 " =    0.772
peak=    3.405 closest distance to " O   HOH Z 135 " =    1.888
peak=    3.404 closest distance to " CB  ALA A  34 " =    0.827
peak=    3.401 closest distance to " O   HOH Z 313 " =    1.750
peak=    3.399 closest distance to " CB  TRP A 150 " =    1.420
peak=    3.399 closest distance to " O   HOH Z 133 " =    2.390
peak=    3.398 closest distance to " CA  ASP A 140 " =    1.236
peak=    3.398 closest distance to " CB  ALA A 242 " =    0.822
peak=    3.396 closest distance to " CG2 THR A 220 " =    0.900
peak=    3.395 closest distance to " O   HOH Z 305 " =    3.629
peak=    3.391 closest distance to " O   HOH Z 134 " =    1.408
peak=    3.388 closest distance to " O   HOH Z 368 " =    3.542
peak=    3.382 closest distance to " O   HOH Z 426 " =    1.568
peak=    3.382 closest distance to " CB  ALA A 104 " =    0.755
peak=    3.373 closest distance to " CZ  PHE A  38 " =    1.162
peak=    3.373 closest distance to " CA  LEU A 282 " =    1.026
peak=    3.365 closest distance to " CD2 LEU A   5 " =    0.724
peak=    3.364 closest distance to " OG BSER A 164 " =    2.229
peak=    3.361 closest distance to " O   HOH Z 102 " =    1.289
peak=    3.361 closest distance to " CG  GLN A  88 " =    1.067
peak=    3.357 closest distance to " CB  ALA A 248 " =    1.099
peak=    3.357 closest distance to " N   SER A 135 " =    1.421
peak=    3.353 closest distance to " CD1 LEU A   5 " =    1.361
peak=    3.348 closest distance to " O   HOH Z 250 " =    1.353
peak=    3.347 closest distance to " OG  SER A  22 " =    2.789
peak=    3.345 closest distance to " O   HOH Z 353 " =    2.696
peak=    3.344 closest distance to " CB  THR A  82 " =    1.401
peak=    3.341 closest distance to " NZ  LYS A 117 " =    3.263
peak=    3.341 closest distance to " CG  MET A 185 " =    1.093
peak=    3.340 closest distance to " O   HOH Z 295 " =    1.500
peak=    3.340 closest distance to " O   HOH Z 417 " =    2.093
peak=    3.336 closest distance to " CB  PRO A 198 " =    1.021
peak=    3.328 closest distance to " C   TYR A 214 " =    1.511
peak=    3.325 closest distance to " CB  ALA A 114 " =    1.212
peak=    3.323 closest distance to " O   HOH Z 250 " =    1.320
peak=    3.322 closest distance to " O   HOH Z 132 " =    2.712
peak=    3.322 closest distance to " O   HOH Z 329 " =    3.904
peak=    3.320 closest distance to " NE2 HIS A 207 " =    1.333
peak=    3.317 closest distance to " CD1 ILE A  33 " =    1.612
peak=    3.317 closest distance to " N   ARG A 190 " =    1.078
peak=    3.312 closest distance to " CB  LYS A 117 " =    1.192
peak=    3.311 closest distance to " CD2 TRP A 179 " =    1.397
peak=    3.310 closest distance to " CB  ILE A 120 " =    1.281
peak=    3.308 closest distance to " O   HOH Z 417 " =    3.184
peak=    3.308 closest distance to " O   HOH Z 345 " =    3.406
peak=    3.304 closest distance to " O   HOH Z 350 " =    1.624
peak=    3.304 closest distance to " O   ALA A 158 " =    1.411
peak=    3.304 closest distance to " O   HOH Z  20 " =    1.596
peak=    3.303 closest distance to " O   ALA A 165 " =    1.497
peak=    3.303 closest distance to " CA  ALA A 154 " =    0.966
peak=    3.301 closest distance to " CA  ASP A 191 " =    0.727
peak=    3.294 closest distance to " CB  ALA A 161 " =    0.870
peak=    3.293 closest distance to " O   HOH Z 403 " =    1.397
peak=    3.287 closest distance to " O   HOH Z 171 " =    3.831
peak=    3.282 closest distance to " OG1 THR A 294 " =    2.364
peak=    3.282 closest distance to " O   HOH Z 216 " =    2.789
peak=    3.280 closest distance to " CA  ALA A 291 " =    0.903
peak=    3.280 closest distance to " CA  MET A  40 " =    1.105
peak=    3.279 closest distance to " CA  ALA A 233 " =    1.447
peak=    3.276 closest distance to " O   HOH Z 407 " =    2.379
peak=    3.272 closest distance to " N   GLN A 278 " =    1.085
peak=    3.266 closest distance to " O   HOH Z  66 " =    2.248
peak=    3.259 closest distance to " CE1 HIS A 108 " =    1.171
peak=    3.258 closest distance to " O   HOH Z 112 " =    1.628
peak=    3.258 closest distance to " CA  MET A 105 " =    0.975
peak=    3.253 closest distance to " CA  ASN A 127 " =    1.059
peak=    3.251 closest distance to " CB  GLN A  89 " =    1.162
peak=    3.248 closest distance to " OG BSER A 134 " =    2.912
peak=    3.248 closest distance to " N   ARG A 156 " =    1.398
peak=    3.246 closest distance to " O   HOH Z 421 " =    1.747
peak=    3.240 closest distance to " CB  GLN A  88 " =    1.234
peak=    3.238 closest distance to " CA  LYS A 181 " =    1.048
peak=    3.236 closest distance to " O   HOH Z 365 " =    3.000
peak=    3.235 closest distance to " O   HOH Z 420 " =    1.851
peak=    3.231 closest distance to " O   HOH Z  10 " =    1.755
peak=    3.228 closest distance to " OH  TYR A 214 " =    1.214
peak=    3.224 closest distance to " O   HOH Z 187 " =    2.347
peak=    3.222 closest distance to " NZ  LYS A  76 " =    1.556
peak=    3.219 closest distance to " CB  VAL A 268 " =    0.830
peak=    3.219 closest distance to " OG1 THR A 294 " =    1.746
peak=    3.219 closest distance to " CA  ALA A 248 " =    1.220
peak=    3.217 closest distance to " N   ASN A 127 " =    1.207
peak=    3.217 closest distance to " CA  LYS A 290 " =    1.226
peak=    3.217 closest distance to " CG AARG A 275 " =    1.227
peak=    3.216 closest distance to " CG BARG A 275 " =    1.384
peak=    3.213 closest distance to " O   HOH Z 148 " =    3.271
peak=    3.213 closest distance to " O   HOH Z 435 " =    1.982
peak=    3.212 closest distance to " N   GLY A  98 " =    1.067
peak=    3.211 closest distance to " ND1 HIS A  86 " =    1.705
peak=    3.202 closest distance to " CB  ALA A 137 " =    1.072
peak=    3.202 closest distance to " O   GLN A 278 " =    1.534
peak=    3.200 closest distance to " CG2 VAL A 197 " =    1.045
peak=    3.196 closest distance to " CA  ILE A 106 " =    0.778
peak=    3.196 closest distance to " CB  LEU A 255 " =    0.789
peak=    3.195 closest distance to " CA  GLY A 211 " =    1.332
peak=    3.193 closest distance to " CA  ASP A 191 " =    1.011
peak=    3.193 closest distance to " O   HOH Z 251 " =    1.493
peak=    3.192 closest distance to " CB  ASN A 215 " =    1.158
peak=    3.186 closest distance to " CB  ASN A 110 " =    1.175
peak=    3.175 closest distance to " CD1 ILE A 106 " =    0.977
peak=    3.175 closest distance to " CA  ASN A 176 " =    1.102
peak=    3.174 closest distance to " O   HOH Z 141 " =    1.591
peak=    3.171 closest distance to " O   HOH Z 313 " =    1.752
peak=    3.166 closest distance to " CG2 ILE A 120 " =    1.159
peak=    3.164 closest distance to " CB  GLN A 278 " =    0.896
peak=    3.161 closest distance to " C   ALA A 299 " =    0.977
peak=    3.156 closest distance to " CB  ALA A   1 " =    4.760
peak=    3.150 closest distance to " CA  ASP A 162 " =    1.066
peak=    3.138 closest distance to " CD1 LEU A 228 " =    1.945
peak=    3.138 closest distance to " O   HOH Z 294 " =    1.602
peak=    3.137 closest distance to " CD  LYS A 119 " =    1.545
peak=    3.134 closest distance to " CG2 VAL A 202 " =    1.131
peak=    3.134 closest distance to " ND2 ASN A 110 " =    1.652
peak=    3.123 closest distance to " CB  GLN A 205 " =    1.038
peak=    3.119 closest distance to " CB  PRO A 243 " =    1.510
peak=    3.117 closest distance to " O   HOH Z 293 " =    1.833
peak=    3.116 closest distance to " CG BARG A 102 " =    1.815
peak=    3.113 closest distance to " CG  GLN A  77 " =    2.170
peak=    3.112 closest distance to " O   HOH Z  49 " =    2.569
peak=    3.108 closest distance to " CB  GLN A 103 " =    1.012
peak=    3.098 closest distance to " O   HOH Z 163 " =    1.496
peak=    3.098 closest distance to " NE  ARG A  79 " =    1.224
peak=    3.092 closest distance to " O   HOH Z 327 " =    1.871
peak=    3.083 closest distance to " CD1 LEU A 261 " =    1.235
peak=    3.083 closest distance to " CG  ARG A 159 " =    1.010
peak=    3.079 closest distance to " CB  LYS A 193 " =    1.054
peak=    3.077 closest distance to " O   HOH Z 384 " =    3.095
peak=    3.076 closest distance to " N   ASP A 162 " =    1.342
peak=    3.072 closest distance to " O   HOH Z 406 " =    1.517
peak=    3.071 closest distance to " O   HOH Z 261 " =    1.414
peak=    3.068 closest distance to " O   HOH Z 201 " =    3.137
peak=    3.057 closest distance to " OG  SER A 206 " =    1.187
peak=    3.049 closest distance to " N   TYR A  15 " =    0.790
peak=    3.047 closest distance to " O   HOH Z 302 " =    1.976
peak=    3.041 closest distance to " CB  ILE A  20 " =    1.353
peak=    3.038 closest distance to " C   ASN A  39 " =    1.066
peak=    3.030 closest distance to " O   ALA A 292 " =    1.662
peak=    3.017 closest distance to " CB  TYR A 116 " =    0.831

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.670 - 5.524
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 198
   mapped sites are within: 0.790 - 5.524

peak=   -5.389 closest distance to " CG2 VAL A 230 " =    0.800
peak=   -4.615 closest distance to " CD  ARG A 156 " =    2.041
peak=   -4.332 closest distance to " SG  CYS A 254 " =    3.337
peak=   -4.311 closest distance to " O   HOH Z 266 " =    5.098
peak=   -4.192 closest distance to " CB  PRO A 243 " =    2.670
peak=   -4.178 closest distance to " CD  GLN A  58 " =    1.052
peak=   -4.080 closest distance to " O   ILE A 109 " =    2.575
peak=   -4.051 closest distance to " O   HOH Z 351 " =    1.520
peak=   -4.013 closest distance to " O   HOH Z 196 " =    2.149
peak=   -4.009 closest distance to " C   HIS A 108 " =    1.146
peak=   -4.000 closest distance to " CG  ASP A 231 " =    0.790
peak=   -3.983 closest distance to " O   HOH Z 290 " =    1.198
peak=   -3.949 closest distance to " CG2BVAL A  41 " =    2.633
peak=   -3.937 closest distance to " CE2 TYR A  30 " =    2.766
peak=   -3.934 closest distance to " CG  GLN A 223 " =    2.069
peak=   -3.919 closest distance to " O   HOH Z  11 " =    1.890
peak=   -3.908 closest distance to " O   HOH Z 114 " =    3.133
peak=   -3.873 closest distance to " CG1 VAL A 296 " =    1.311
peak=   -3.863 closest distance to " CZ3 TRP A 179 " =    1.194
peak=   -3.828 closest distance to " CD2 LEU A 300 " =    2.783
peak=   -3.828 closest distance to " O   HOH Z 166 " =    1.960
peak=   -3.806 closest distance to " CG2 VAL A 296 " =    1.402
peak=   -3.795 closest distance to " O   HOH Z  52 " =    1.607
peak=   -3.781 closest distance to " O   HOH Z 231 " =    2.053
peak=   -3.748 closest distance to " N   ALA A 226 " =    2.140
peak=   -3.746 closest distance to " NH2AARG A 275 " =    5.265
peak=   -3.741 closest distance to " OG BSER A 134 " =    1.165
peak=   -3.725 closest distance to " CA  ASP A 298 " =    1.038
peak=   -3.724 closest distance to " CG1 VAL A 112 " =    2.968
peak=   -3.709 closest distance to " O   PRO A 163 " =    2.162
peak=   -3.705 closest distance to " C   ALA A 158 " =    1.303
peak=   -3.700 closest distance to " CG1 VAL A 112 " =    2.642
peak=   -3.693 closest distance to " O   HOH Z 394 " =    1.534
peak=   -3.683 closest distance to " CG2 ILE A 263 " =    2.430
peak=   -3.680 closest distance to " CG1 VAL A 250 " =    2.744
peak=   -3.674 closest distance to " OXT GLY A 302 " =    2.920
peak=   -3.672 closest distance to " CB  PHE A 192 " =    1.958
peak=   -3.671 closest distance to " O   HOH Z 185 " =    2.397
peak=   -3.653 closest distance to " O   VAL A  67 " =    2.679
peak=   -3.637 closest distance to " OG  SER A  97 " =    2.299
peak=   -3.616 closest distance to " ND2 ASN A  45 " =    1.059
peak=   -3.612 closest distance to " O   GLY A 203 " =    2.343
peak=   -3.598 closest distance to " CA  GLY A 241 " =    3.058
peak=   -3.592 closest distance to " O   HOH Z 435 " =    2.819
peak=   -3.591 closest distance to " CD1 LEU A 228 " =    2.346
peak=   -3.589 closest distance to " CE  MET A 105 " =    2.175
peak=   -3.581 closest distance to " O   HOH Z 211 " =    1.622
peak=   -3.570 closest distance to " O   HOH Z  73 " =    2.178
peak=   -3.569 closest distance to " O   HOH Z 389 " =    1.943
peak=   -3.552 closest distance to " OD1 ASN A 148 " =    1.448
peak=   -3.552 closest distance to " CB  ALA A  43 " =    2.542
peak=   -3.549 closest distance to " O   HOH Z  19 " =    2.331
peak=   -3.549 closest distance to " O   HOH Z 103 " =    1.911
peak=   -3.546 closest distance to " O   HOH Z 426 " =    1.675
peak=   -3.539 closest distance to " CE3 TRP A 150 " =    2.061
peak=   -3.534 closest distance to " O   HOH Z 222 " =    1.503
peak=   -3.530 closest distance to " NE2 GLN A  88 " =    2.021
peak=   -3.523 closest distance to " ND2 ASN A  45 " =    1.703
peak=   -3.509 closest distance to " O   VAL A 189 " =    2.593
peak=   -3.507 closest distance to " CG  LEU A 101 " =    2.474
peak=   -3.501 closest distance to " N   THR A 157 " =    1.499
peak=   -3.489 closest distance to " O   HOH Z  10 " =    1.531
peak=   -3.489 closest distance to " CG  HIS A  86 " =    1.037
peak=   -3.487 closest distance to " O   PRO A 198 " =    1.231
peak=   -3.476 closest distance to " CB  ALA A 248 " =    2.089
peak=   -3.473 closest distance to " CB  ALA A 248 " =    2.434
peak=   -3.473 closest distance to " CB  PRO A 163 " =    2.583
peak=   -3.464 closest distance to " CB  ASP A 132 " =    2.308
peak=   -3.461 closest distance to " CG  TRP A 266 " =    1.846
peak=   -3.459 closest distance to " CG  MET A 105 " =    0.939
peak=   -3.456 closest distance to " CD  ARG A 139 " =    1.631
peak=   -3.449 closest distance to " O   HOH Z 241 " =    1.227
peak=   -3.447 closest distance to " O   HOH Z 350 " =    1.716
peak=   -3.446 closest distance to " N   ALA A  43 " =    2.420
peak=   -3.444 closest distance to " CD  LYS A 289 " =    2.545
peak=   -3.444 closest distance to " CG  ARG A 269 " =    2.498
peak=   -3.443 closest distance to " C   MET A 188 " =    1.396
peak=   -3.439 closest distance to " CE2 PHE A 218 " =    2.595
peak=   -3.433 closest distance to " O   HOH Z  13 " =    1.459
peak=   -3.431 closest distance to " O   HOH Z 353 " =    2.107
peak=   -3.429 closest distance to " CD1 LEU A 101 " =    2.670
peak=   -3.422 closest distance to " NH2 ARG A  79 " =    2.000
peak=   -3.422 closest distance to " CB  ALA A 291 " =    2.233
peak=   -3.421 closest distance to " CD2 LEU A 167 " =    1.736
peak=   -3.419 closest distance to " ND2 ASN A 187 " =    1.652
peak=   -3.412 closest distance to " CG  GLU A 277 " =    1.142
peak=   -3.408 closest distance to " NE2 GLN A 103 " =    1.812
peak=   -3.404 closest distance to " O   HOH Z 377 " =    2.135
peak=   -3.400 closest distance to " OG BSER A 134 " =    1.834
peak=   -3.398 closest distance to " O   HOH Z 275 " =    1.523
peak=   -3.397 closest distance to " O   GLY A  17 " =    1.342
peak=   -3.396 closest distance to " O   SER A 271 " =    2.212
peak=   -3.389 closest distance to " O   HOH Z 102 " =    1.660
peak=   -3.385 closest distance to " O   HOH Z 407 " =    3.128
peak=   -3.384 closest distance to " O   HOH Z  38 " =    1.543
peak=   -3.381 closest distance to " C   LEU A 222 " =    0.889
peak=   -3.379 closest distance to " O   HOH Z  43 " =    1.754
peak=   -3.374 closest distance to " CD2 TYR A 293 " =    2.085
peak=   -3.373 closest distance to " CZ  TYR A 169 " =    1.708
peak=   -3.368 closest distance to " N   GLN A  58 " =    1.710
peak=   -3.362 closest distance to " O   HOH Z  60 " =    2.188
peak=   -3.360 closest distance to " NH2 ARG A  79 " =    1.548
peak=   -3.360 closest distance to " C   LEU A 143 " =    1.072
peak=   -3.358 closest distance to " O   HOH Z 165 " =    1.859
peak=   -3.354 closest distance to " CB  ASN A  69 " =    1.159
peak=   -3.353 closest distance to " CB  ASN A  39 " =    2.246
peak=   -3.351 closest distance to " C   ASN A 285 " =    2.451
peak=   -3.351 closest distance to " CD2 PHE A  61 " =    2.449
peak=   -3.350 closest distance to " OD1 ASN A 187 " =    1.611
peak=   -3.348 closest distance to " O   HOH Z  44 " =    2.184
peak=   -3.348 closest distance to " O   LEU A 167 " =    1.479
peak=   -3.342 closest distance to " O   HOH Z  63 " =    1.181
peak=   -3.342 closest distance to " OG  SER A  87 " =    1.505
peak=   -3.333 closest distance to " CA  GLY A 203 " =    2.448
peak=   -3.331 closest distance to " O   HOH Z  17 " =    1.582
peak=   -3.330 closest distance to " NH2 ARG A  66 " =    1.885
peak=   -3.329 closest distance to " CG  ASP A  50 " =    2.402
peak=   -3.327 closest distance to " CB  ALA A 291 " =    2.251
peak=   -3.323 closest distance to " OG  SER A  62 " =    1.794
peak=   -3.321 closest distance to " O   HOH Z 191 " =    5.524
peak=   -3.320 closest distance to " OG  SER A 206 " =    1.730
peak=   -3.315 closest distance to " N   VAL A 230 " =    1.103
peak=   -3.315 closest distance to " OE1 GLN A  88 " =    1.057
peak=   -3.309 closest distance to " O   HOH Z 388 " =    2.105
peak=   -3.308 closest distance to " O   HOH Z 234 " =    4.257
peak=   -3.302 closest distance to " N   SER A 212 " =    1.694
peak=   -3.299 closest distance to " C   ASN A 187 " =    1.880
peak=   -3.299 closest distance to " O   GLY A 211 " =    1.362
peak=   -3.296 closest distance to " O   GLY A 196 " =    1.161
peak=   -3.294 closest distance to " O   HOH Z 113 " =    2.374
peak=   -3.286 closest distance to " CG1 VAL A 197 " =    2.272
peak=   -3.283 closest distance to " CD1 LEU A  25 " =    2.453
peak=   -3.282 closest distance to " CD1 PHE A  59 " =    1.928
peak=   -3.280 closest distance to " NH1 ARG A 195 " =    2.580
peak=   -3.268 closest distance to " NE2 GLN A 194 " =    1.832
peak=   -3.268 closest distance to " O   HOH Z 292 " =    4.607
peak=   -3.266 closest distance to " CB  VAL A 230 " =    1.058
peak=   -3.264 closest distance to " CD1 ILE A 239 " =    2.114
peak=   -3.264 closest distance to " CE BMET A  47 " =    1.880
peak=   -3.256 closest distance to " CG  GLU A  53 " =    1.474
peak=   -3.252 closest distance to " NZ  LYS A 119 " =    3.526
peak=   -3.252 closest distance to " NE2 GLN A  88 " =    1.011
peak=   -3.242 closest distance to " CG2 VAL A 112 " =    2.538
peak=   -3.234 closest distance to " CG  ARG A 269 " =    3.031
peak=   -3.228 closest distance to " O   GLY A  80 " =    2.564
peak=   -3.227 closest distance to " CA  GLY A 241 " =    2.299
peak=   -3.225 closest distance to " O   HOH Z 311 " =    3.737
peak=   -3.223 closest distance to " N   SER A 276 " =    1.327
peak=   -3.222 closest distance to " O   SER A  95 " =    1.701
peak=   -3.221 closest distance to " NE2 GLN A 278 " =    1.993
peak=   -3.211 closest distance to " CA  GLY A 133 " =    2.303
peak=   -3.210 closest distance to " O   HOH Z 369 " =    2.255
peak=   -3.210 closest distance to " O   HOH Z 423 " =    2.076
peak=   -3.209 closest distance to " CG2 VAL A 189 " =    2.050
peak=   -3.209 closest distance to " ND2 ASN A  60 " =    1.389
peak=   -3.199 closest distance to " O   HOH Z 298 " =    2.784
peak=   -3.198 closest distance to " CD  ARG A 195 " =    5.122
peak=   -3.198 closest distance to " O   ARG A  24 " =    2.109
peak=   -3.198 closest distance to " CG1 VAL A 296 " =    1.300
peak=   -3.196 closest distance to " O   ALA A  10 " =    1.739
peak=   -3.195 closest distance to " O   HOH Z  90 " =    1.653
peak=   -3.192 closest distance to " O   HOH Z 174 " =    2.454
peak=   -3.189 closest distance to " ND2 ASN A  60 " =    1.785
peak=   -3.186 closest distance to " O   MET A  40 " =    2.734
peak=   -3.185 closest distance to " OG ASER A 134 " =    1.512
peak=   -3.185 closest distance to " O   HOH Z 310 " =    1.892
peak=   -3.180 closest distance to " C   ASP A 231 " =    2.596
peak=   -3.178 closest distance to " O   HOH Z 243 " =    2.022
peak=   -3.177 closest distance to " CB  ASP A 132 " =    2.329
peak=   -3.172 closest distance to " OD2 ASP A 171 " =    1.820
peak=   -3.170 closest distance to " O   HOH Z 377 " =    1.648
peak=   -3.166 closest distance to " CB  TYR A  15 " =    2.227
peak=   -3.165 closest distance to " O   HOH Z  47 " =    1.602
peak=   -3.155 closest distance to " CA  ASN A 127 " =    1.120
peak=   -3.147 closest distance to " NH1 ARG A  36 " =    2.034
peak=   -3.145 closest distance to " CG2 THR A 178 " =    2.248
peak=   -3.141 closest distance to " CD  PRO A 243 " =    2.104
peak=   -3.136 closest distance to " CD  PRO A 213 " =    2.150
peak=   -3.135 closest distance to " N   SER A   3 " =    1.979
peak=   -3.125 closest distance to " N   ASN A  60 " =    1.299
peak=   -3.114 closest distance to " O   HOH Z 252 " =    4.031
peak=   -3.110 closest distance to " CB  ASP A 171 " =    2.325
peak=   -3.107 closest distance to " O   HOH Z 166 " =    1.632
peak=   -3.100 closest distance to " O   HOH Z 123 " =    2.387
peak=   -3.090 closest distance to " N   VAL A 296 " =    2.641
peak=   -3.089 closest distance to " O   HOH Z 111 " =    2.412
peak=   -3.083 closest distance to " O   ASP A 270 " =    1.655
peak=   -3.082 closest distance to " CD2 TYR A 247 " =    2.263
peak=   -3.081 closest distance to " CD2 LEU A 237 " =    2.860
peak=   -3.066 closest distance to " O   HOH Z 313 " =    1.133
peak=   -3.064 closest distance to " CB  LEU A  83 " =    2.358
peak=   -3.060 closest distance to " O   HOH Z 139 " =    3.016
peak=   -3.056 closest distance to " O   HOH Z 175 " =    4.315
peak=   -3.051 closest distance to " O   HOH Z   6 " =    1.711
peak=   -3.025 closest distance to " O   HOH Z 313 " =    1.775
peak=   -3.024 closest distance to " O   HOH Z 193 " =    1.842

================= 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    :  0.4198 0.4031   6.207495e+00   6.179776e+00
   1_bss:  0.4115 0.3896   6.203357e+00   6.164789e+00
   1_xyz:  0.2970 0.3221   5.961238e+00   6.022571e+00
   1_adp:  0.2285 0.2611   5.727965e+00   5.849222e+00
   1_occ:  0.2279 0.2612   5.726353e+00   5.850329e+00
   2_bss:  0.2228 0.2540   5.724890e+00   5.844334e+00
   2_xyz:  0.1510 0.1886   5.377883e+00   5.567994e+00
   2_adp:  0.1376 0.1786   5.301586e+00   5.508009e+00
   2_occ:  0.1375 0.1787   5.301307e+00   5.508113e+00
   3_bss:  0.1373 0.1783   5.302136e+00   5.508182e+00
   3_xyz:  0.1213 0.1625   5.199002e+00   5.425835e+00
   3_adp:  0.1165 0.1600   5.174920e+00   5.413976e+00
   3_occ:  0.1164 0.1600   5.175030e+00   5.414348e+00
   4_bss:  0.1164 0.1600   5.175030e+00   5.414348e+00
   4_xyz:  0.1107 0.1592   5.148143e+00   5.404672e+00
   4_adp:  0.1119 0.1569   5.144845e+00   5.389180e+00
   4_occ:  0.1119 0.1570   5.145006e+00   5.389682e+00
   5_bss:  0.1122 0.1569   5.144753e+00   5.388044e+00
   5_xyz:  0.1154 0.1575   5.162277e+00   5.394641e+00
   5_adp:  0.1139 0.1588   5.162001e+00   5.403563e+00
   5_occ:  0.1139 0.1588   5.161931e+00   5.403524e+00
   5_bss:  0.1139 0.1588   5.161929e+00   5.403526e+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   8.107   8.553   8.131   0.000   0.000   0.000
   1_xyz:  0.300  20.000   8.107   8.553   8.131   0.000   0.000   0.000
   1_adp:  0.300  20.000   8.107   8.553   8.131   0.000   0.000   0.000
   1_occ:  0.300  20.000   8.107   8.553   8.131   0.000   0.000   0.000
   2_bss:  0.333  50.001   4.601   4.858   5.082   0.000   0.000   0.000
   2_xyz:  0.333  50.001   4.601   4.858   5.082   0.000   0.000   0.000
   2_adp:  0.333  50.001   4.601   4.858   5.082   0.000   0.000   0.000
   2_occ:  0.333  50.001   4.601   4.858   5.082   0.000   0.000   0.000
   3_bss:  0.330  50.001   3.578   3.888   4.580   0.000   0.000   0.000
   3_xyz:  0.330  50.001   3.578   3.888   4.580   0.000   0.000   0.000
   3_adp:  0.330  50.001   3.578   3.888   4.580   0.000   0.000   0.000
   3_occ:  0.330  50.001   3.578   3.888   4.580   0.000   0.000   0.000
   4_bss:  0.330  50.001   3.578   3.888   4.580   0.000   0.000   0.000
   4_xyz:  0.330  50.001   3.578   3.888   4.580   0.000   0.000   0.000
   4_adp:  0.330  50.001   3.578   3.888   4.580   0.000   0.000   0.000
   4_occ:  0.330  50.001   3.578   3.888   4.580   0.000   0.000   0.000
   5_bss:  0.325  49.436   3.478   3.730   4.573   0.000   0.000   0.000
   5_xyz:  0.325  49.436   3.478   3.730   4.573   0.000   0.000   0.000
   5_adp:  0.325  49.436   3.478   3.730   4.573   0.000   0.000   0.000
   5_occ:  0.325  49.436   3.478   3.730   4.573   0.000   0.000   0.000
   5_bss:  0.325  53.367  -0.452  -0.210   0.663   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  44.115 0.5952  0.6523    46394.754
   1_bss:  43.678 0.5987  0.8412    44032.099
   1_xyz:  34.541 0.7059  0.9638    28468.639
   1_adp:  25.716 0.8051  1.0518    17431.486
   1_occ:  25.732 0.8048  1.0511    17440.150
   2_bss:  25.503 0.8072  0.9318    17172.108
   2_xyz:  17.864 0.8817  0.9882     9128.015
   2_adp:  16.391 0.8953  0.9981     8103.262
   2_occ:  16.395 0.8953  0.9979     8108.110
   3_bss:  16.401 0.8953  0.9676     8128.973
   3_xyz:  14.590 0.9105  0.9733     6826.632
   3_adp:  14.356 0.9125  0.9722     6629.267
   3_occ:  14.358 0.9125  0.9721     6634.795
   4_bss:  14.358 0.9125  0.9721     6634.795
   4_xyz:  14.160 0.9141  0.9730     6514.707
   4_adp:  13.812 0.9169  0.9744     6334.160
   4_occ:  13.821 0.9168  0.9743     6341.037
   5_bss:  13.813 0.9168  0.9705     6300.562
   5_xyz:  13.899 0.9163  0.9692     6353.706
   5_adp:  14.120 0.9145  0.9663     6465.048
   5_occ:  14.119 0.9145  0.9662     6465.094
   5_bss:  14.120 0.9145  0.9663     6464.899
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4118e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4118e+01
   1_xyz:   1.473  0.011  0.099 17.884  0.006  4.125   1.1274e-01
   1_adp:   1.473  0.011  0.099 17.884  0.006  4.125   1.1274e-01
   1_occ:   1.473  0.011  0.099 17.884  0.006  4.125   1.1274e-01
   2_bss:   1.473  0.011  0.099 17.884  0.006  4.125   1.1274e-01
   2_xyz:   1.058  0.008  0.079 16.458  0.004  4.130   6.9341e-02
   2_adp:   1.058  0.008  0.079 16.458  0.004  4.130   6.9341e-02
   2_occ:   1.058  0.008  0.079 16.458  0.004  4.130   6.9341e-02
   3_bss:   1.058  0.008  0.079 16.458  0.004  4.130   6.9341e-02
   3_xyz:   1.040  0.008  0.084 16.043  0.004  4.138   6.6643e-02
   3_adp:   1.040  0.008  0.084 16.043  0.004  4.138   6.6643e-02
   3_occ:   1.040  0.008  0.084 16.043  0.004  4.138   6.6643e-02
   4_bss:   1.040  0.008  0.084 16.043  0.004  4.138   6.6643e-02
   4_xyz:   1.118  0.010  0.093 15.993  0.004  4.142   7.7073e-02
   4_adp:   1.118  0.010  0.093 15.993  0.004  4.142   7.7073e-02
   4_occ:   1.118  0.010  0.093 15.993  0.004  4.142   7.7073e-02
   5_bss:   1.118  0.010  0.093 15.993  0.004  4.142   7.7073e-02
   5_xyz:   0.964  0.007  0.079 15.641  0.003  4.124   5.9292e-02
   5_adp:   0.964  0.007  0.079 15.641  0.003  4.124   5.9292e-02
   5_occ:   0.964  0.007  0.079 15.641  0.003  4.124   5.9292e-02
   5_bss:   0.964  0.007  0.079 15.641  0.003  4.124   5.9292e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0173e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0173e+00
   1_xyz:  12.152  0.131  0.403 88.023  0.039  2.284   8.5052e-02
   1_adp:  12.152  0.131  0.403 88.023  0.039  2.284   8.5052e-02
   1_occ:  12.152  0.131  0.403 88.023  0.039  2.284   8.5052e-02
   2_bss:  12.152  0.131  0.403 88.023  0.039  2.284   8.5052e-02
   2_xyz:   8.385  0.069  0.383 82.924  0.039  2.366   5.0757e-02
   2_adp:   8.385  0.069  0.383 82.924  0.039  2.366   5.0757e-02
   2_occ:   8.385  0.069  0.383 82.924  0.039  2.366   5.0757e-02
   3_bss:   8.385  0.069  0.383 82.924  0.039  2.366   5.0757e-02
   3_xyz:   6.954  0.045  0.583 83.698  0.041  2.372   4.2185e-02
   3_adp:   6.954  0.045  0.583 83.698  0.041  2.372   4.2185e-02
   3_occ:   6.954  0.045  0.583 83.698  0.041  2.372   4.2185e-02
   4_bss:   6.954  0.045  0.583 83.698  0.041  2.372   4.2185e-02
   4_xyz:   7.517  0.049  0.677 82.621  0.041  2.294   5.5923e-02
   4_adp:   7.517  0.049  0.677 82.621  0.041  2.294   5.5923e-02
   4_occ:   7.517  0.049  0.677 82.621  0.041  2.294   5.5923e-02
   5_bss:   7.517  0.049  0.677 82.621  0.041  2.294   5.5923e-02
   5_xyz:   7.390  0.044  0.502 82.794  0.038  2.391   3.7701e-02
   5_adp:   7.390  0.044  0.502 82.794  0.038  2.391   3.7701e-02
   5_occ:   7.390  0.044  0.502 82.794  0.038  2.391   3.7701e-02
   5_bss:   7.390  0.044  0.502 82.794  0.038  2.391   3.7701e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  55.56   0.00   9.87  50.37   0.00   6.80  55.56   0.00  26.64
   1_occ:  55.56   0.00   9.87  50.37   0.00   6.80  55.56   0.00  26.64
   2_bss:  55.56   0.00   9.87  50.37   0.00   6.80  55.56   0.00  26.64
   2_xyz:  55.56   0.00   9.87  50.37   0.00   6.80  55.56   0.00  26.64
   2_adp:  75.37   0.00  10.40  75.37   0.00   6.81  54.41   0.57  29.97
   2_occ:  75.37   0.00  10.40  75.37   0.00   6.81  54.41   0.57  29.97
   3_bss:  75.37   0.00  10.40  75.37   0.00   6.81  54.41   0.57  29.97
   3_xyz:  75.37   0.00  10.40  75.37   0.00   6.81  54.41   0.57  29.97
   3_adp:  75.52   0.00  11.37  75.52   0.00   7.11  73.66   0.12  34.59
   3_occ:  75.52   0.00  11.37  75.52   0.00   7.11  73.66   0.12  34.59
   4_bss:  75.52   0.00  11.37  75.52   0.00   7.11  73.66   0.12  34.59
   4_xyz:  75.52   0.00  11.37  75.52   0.00   7.11  73.66   0.12  34.59
   4_adp:  74.75   0.00  11.01  74.75   0.00   6.95  69.80   0.91  33.13
   4_occ:  74.75   0.00  11.01  74.75   0.00   6.95  69.80   0.91  33.13
   5_bss:  74.75   0.00  11.01  74.75   0.00   6.95  69.80   0.91  33.13
   5_xyz:  74.75   0.00  11.01  74.75   0.00   6.95  69.80   0.91  33.13
   5_adp:  76.30   0.00  11.09  76.30   0.00   6.99  70.73   0.72  33.40
   5_occ:  76.30   0.00  11.09  76.30   0.00   6.99  70.73   0.72  33.40
   5_bss:  80.23   3.93  15.02  80.23   3.93  10.92  74.66   4.65  37.33
------------------------------------------------------------------------
 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:    1.173    0.012    0.401
   1_adp:    1.173    0.012    0.401
   1_occ:    1.173    0.012    0.401
   2_bss:    1.173    0.012    0.401
   2_xyz:    1.425    0.007    0.492
   2_adp:    1.425    0.007    0.492
   2_occ:    1.425    0.007    0.492
   3_bss:    1.425    0.007    0.492
   3_xyz:    1.404    0.044    0.515
   3_adp:    1.404    0.044    0.515
   3_occ:    1.404    0.044    0.515
   4_bss:    1.404    0.044    0.515
   4_xyz:    1.392    0.032    0.529
   4_adp:    1.392    0.032    0.529
   4_occ:    1.392    0.032    0.529
   5_bss:    1.392    0.032    0.529
   5_xyz:    1.441    0.055    0.533
   5_adp:    1.441    0.055    0.533
   5_occ:    1.441    0.055    0.533
   5_bss:    1.441    0.055    0.533
------------------------------------------------------------------------

CPU time actual refinement: 322.15


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_918/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/trial/run_918/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_918/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_918/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_918/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 322.00 
  Macro-tasks:
    bulk solvent and scale       = 41.08  
    individual site refinement   = 135.41 
    weights calculation          = 31.73  
    collect and process          = 6.46   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 214.79 
  Micro-tasks:
    mask                            = 1.69   
    f_calc                          = 96.56  
    alpha_beta                      = 8.11   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 109.37 
    fmodel                         = 7.21   
    r_factors                      = 0.29   
    phase_errors                   = 10.94  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 235.55 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.450 micro seconds
Total CPU time: 5.59 minutes
from_scatterers_fft:    659 calls, 96.07 s
gradients_fft:          604 calls, 94.83 s

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

# Date 2008-01-16 Time 02:44:30 PST -0800 (1200480270.48 s)
Start R-work = 0.4198, R-free = 0.4031 (no bulk solvent and anisotropic scale)
Final R-work = 0.1306, R-free = 0.1742 (no bulk solvent and anisotropic scale)

Start R-work = 0.4115, R-free = 0.3896
Final R-work = 0.1139, R-free = 0.1588