# Date 2008-01-16 Time 02:15:35 PST -0800 (1200478535.60 s)
#phil __OFF__

Command line arguments: "../755.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 32703
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 755

-------------------------------------------------------------------------------
  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: (70.6012, 46.2261, 87.2539, 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: 3.31, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.2261, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0892 1.97302
Completeness in resolution range: 0.946649
Completeness with d_max=infinity: 0.943821

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0892
                             d_min =   1.9730

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: (70.6012, 46.2261, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0892 1.97302
Completeness in resolution range: 0.946649
Completeness with d_max=infinity: 0.943821

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0896 -  4.2226 [2172/2197]  1952   220  10.1%
  bin  2:  4.2226 -  3.3638 [2089/2109]  1884   205   9.8%
  bin  3:  3.3638 -  2.9422 [2073/2092]  1865   208  10.0%
  bin  4:  2.9422 -  2.6748 [2030/2060]  1825   205  10.1%
  bin  5:  2.6748 -  2.4840 [2026/2045]  1829   197   9.7%
  bin  6:  2.4840 -  2.3381 [2018/2043]  1811   207  10.3%
  bin  7:  2.3381 -  2.2214 [2011/2039]  1808   203  10.1%
  bin  8:  2.2214 -  2.1250 [1998/2034]  1800   198   9.9%
  bin  9:  2.1250 -  2.0434 [1988/2030]  1792   196   9.9%
  bin 10:  2.0434 -  1.9730 [1184/2044]  1064   120  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_755/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: 30
        2.42 -     3.04: 2180
        3.04 -     3.66: 4705
        3.66 -     4.28: 9045
        4.28 -     4.90: 12328
  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
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z  70 " - " O   HOH Z 302 "  2.127 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  2.148 3.040 x,y+1,z
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.176 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28283 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_755/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_755/model_refine_001.geo

CPU time processing inputs: 9.41


============================ 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 = 70.60125 46.22605 87.2539 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: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4678   r_free= 0.4557   ksol= 0.00   Bsol= 0.00   scale= 0.801    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.269029                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0896 -  4.7101 0.99   1410  156 0.3934 0.3729      6.5895      6.5581|
|  2:  4.7101 -  3.7575 0.99   1361  153 0.3746 0.3541        6.75      6.7038|
|  3:  3.7575 -  3.2881 0.99   1328  142 0.4035 0.3592      6.6206      6.5815|
|  4:  3.2881 -  2.9901 0.99   1327  152 0.4537 0.4357      6.5172       6.476|
|  5:  2.9901 -  2.7772 0.99   1317  148 0.4975 0.4742      6.3521      6.3542|
|  6:  2.7772 -  2.6143 0.99   1315  144 0.4973 0.5243      6.2638      6.2136|
|  7:  2.6143 -  2.4840 0.99   1297  140 0.5183 0.5020      6.2389      6.1905|
|  8:  2.4840 -  2.3763 0.98   1287  146 0.5186 0.4683      6.1732      6.1825|
|  9:  2.3763 -  2.2851 0.98   1289  147 0.5088 0.5257      6.1084      6.1594|
| 10:  2.2851 -  2.2065 1.00   1289  145 0.5273 0.5071      6.1042      6.0599|
| 11:  2.2065 -  2.1377 0.98   1308  138 0.5148 0.5109      6.0325      6.0315|
| 12:  2.1377 -  2.0768 0.98   1259  142 0.5235 0.5605      5.9568      6.0194|
| 13:  2.0768 -  2.0222 0.99   1285  139 0.5284 0.4953      5.8737      5.7909|
| 14:  2.0222 -  1.9730 0.42    558   67 0.5409 0.5538      5.8877      5.8138|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0896 -  4.7101  1410   156  0.71  33.13   0.80     0.76      67230.70|
|  2:  4.7101 -  3.7575  1361   153  0.75  31.00   0.88     0.82      87409.64|
|  3:  3.7575 -  3.2881  1328   142  0.66  38.81   0.87     0.77      93308.55|
|  4:  3.2881 -  2.9901  1327   152  0.58  45.52   0.80     0.67      85369.04|
|  5:  2.9901 -  2.7772  1317   148  0.48  53.86   0.75     0.57      74174.65|
|  6:  2.7772 -  2.6143  1315   144  0.44  56.84   0.73     0.50      66227.13|
|  7:  2.6143 -  2.4840  1297   140  0.39  60.97   0.74     0.45      63952.32|
|  8:  2.4840 -  2.3763  1287   146  0.36  63.07   0.73     0.42      58895.58|
|  9:  2.3763 -  2.2851  1289   147  0.37  61.91   0.74     0.44      53083.62|
| 10:  2.2851 -  2.2065  1289   145  0.39  60.95   0.75     0.46      45922.17|
| 11:  2.2065 -  2.1377  1308   138  0.38  61.61   0.77     0.47      44543.41|
| 12:  2.1377 -  2.0768  1259   142  0.34  64.52   0.75     0.43      42291.87|
| 13:  2.0768 -  2.0222  1285   139  0.32  66.19   0.72     0.41      37548.29|
| 14:  2.0222 -  1.9730   558    67  0.38  61.70   0.73     0.41      29459.98|
|alpha:            min =        0.41 max =            0.82 mean =         0.55|
|beta:             min =    29459.98 max =        93308.55 mean =     62296.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           90.00 mean =        53.68|
|phase err.(test): min =        0.00 max =           89.98 mean =        53.98|
|-----------------------------------------------------------------------------|

============================== 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 = 11.533223             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.143   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.034207              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.921   (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:       28 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      172 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      685 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1506 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2615 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3959 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5066 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6549 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7700 |
|-----------------------------------------------------------------------------|
|-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 |       53.787 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.819 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.880)------------------------------------------|
|    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 = 11.880)------------------------------------------|
|    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: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4747   r_free= 0.4561   ksol= 0.00   Bsol= 0.00   scale= 0.770    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.272164                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4601   r_free= 0.4375   ksol= 0.30   Bsol= 20.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.64,9.21,8.78,0.00,0.00,0.00); trace/3= 8.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.264715                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.593124              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.677   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.936098              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.033   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4601      final r-factor (work) = 0.3672          |
| start r-factor (free) = 0.4375      final r-factor (free) = 0.3844          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 83.8406 = 9.59 * 0.50 * 6.2656 + 1.00 * 53.7871                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.6794 = 9.59 * 0.50 * 6.1601 + 1.00 * 0.1322                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3672      final r-factor (work) = 0.3154          |
| start r-factor (free) = 0.3844      final r-factor (free) = 0.3659          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7809 = 0.94 * 1.00 * 6.1601 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6800 = 0.94 * 1.00 * 6.0514 + 1.00 * 0.0153                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.880)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.42   13.01    None  None   None       |
|    all(noH): 2823   0      0.00    83.42   13.01    None  None   None       |
|    Sol.    : 438    0      0.00    83.42   28.22    None  None   None       |
|    Mac.    : 2385   0      0.00    68.57   10.21    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.342: 1286   |   5:    41.710 -  50.052:   61        |
|      1:     8.342 -  16.684:  771   |   6:    50.052 -  58.394:   26        |
|      2:    16.684 -  25.026:  372   |   7:    58.394 -  66.736:   16        |
|      3:    25.026 -  33.368:  173   |   8:    66.736 -  75.078:    4        |
|      4:    33.368 -  41.710:  113   |   9:    75.078 -  83.420:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3154 r_free = 0.3659             target_work(ml) = 6.026         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3148 r_free = 0.3663             target_work(ml) = 6.026         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3148   r_free= 0.3663   ksol= 0.30   Bsol= 20.00   scale= 1.101   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.64,9.21,8.78,0.00,0.00,0.00); trace/3= 8.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.025647                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3113   r_free= 0.3615   ksol= 0.34   Bsol= 48.43   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.47,5.05,5.25,0.00,0.00,0.00); trace/3= 4.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.026897                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.927395              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.041   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.409429              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.719  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3113      final r-factor (work) = 0.2241          |
| start r-factor (free) = 0.3615      final r-factor (free) = 0.2765          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.0600 = 5.93 * 0.50 * 6.0492 + 1.00 * 0.1322                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.5166 = 5.93 * 0.50 * 5.8842 + 1.00 * 0.0778                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2241      final r-factor (work) = 0.2010          |
| start r-factor (free) = 0.2765      final r-factor (free) = 0.2554          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4244 = 0.41 * 1.00 * 5.8842 + 1.00 * 0.0152                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3382 = 0.41 * 1.00 * 5.6829 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.880)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.77   12.73    None  None   None       |
|    all(noH): 2823   0      0.00    86.77   12.73    None  None   None       |
|    Sol.    : 438    0      0.00    86.77   33.14    None  None   None       |
|    Mac.    : 2385   0      0.00    70.73   8.99     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 -   8.677: 1485   |   5:    43.387 -  52.064:   68        |
|      1:     8.677 -  17.355:  704   |   6:    52.064 -  60.741:   28        |
|      2:    17.355 -  26.032:  220   |   7:    60.741 -  69.418:   11        |
|      3:    26.032 -  34.709:  157   |   8:    69.418 -  78.096:    3        |
|      4:    34.709 -  43.387:  146   |   9:    78.096 -  86.773:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2010 r_free = 0.2554             target_work(ml) = 5.649         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2009 r_free = 0.2548             target_work(ml) = 5.648         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2009   r_free= 0.2548   ksol= 0.34   Bsol= 48.43   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.47,5.05,5.25,0.00,0.00,0.00); trace/3= 4.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.648232                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1999   r_free= 0.2527   ksol= 0.33   Bsol= 48.43   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.33,2.81,3.88,0.00,0.00,0.00); trace/3= 3.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.647886                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.542187              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.603  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.520533              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.290  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1999      final r-factor (work) = 0.1469          |
| start r-factor (free) = 0.2527      final r-factor (free) = 0.1947          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1531 = 3.54 * 0.50 * 5.6887 + 1.00 * 0.0778                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8381 = 3.54 * 0.50 * 5.5173 + 1.00 * 0.0665                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1469      final r-factor (work) = 0.1344          |
| start r-factor (free) = 0.1947      final r-factor (free) = 0.1855          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 19.4353 = 3.52 * 1.00 * 5.5173 + 1.00 * 0.0115                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.7914 = 3.52 * 1.00 * 5.3333 + 1.00 * 0.0154                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.880)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.58   13.66    None  None   None       |
|    all(noH): 2823   0      0.00    92.58   13.66    None  None   None       |
|    Sol.    : 438    0      1.34    92.58   39.78    None  None   None       |
|    Mac.    : 2385   0      0.00    86.76   8.86     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.258: 1648   |   5:    46.292 -  55.551:   97        |
|      1:     9.258 -  18.517:  585   |   6:    55.551 -  64.809:   66        |
|      2:    18.517 -  27.775:  181   |   7:    64.809 -  74.067:   33        |
|      3:    27.775 -  37.034:  104   |   8:    74.067 -  83.326:   12        |
|      4:    37.034 -  46.292:   95   |   9:    83.326 -  92.584:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1344 r_free = 0.1855             target_work(ml) = 5.309         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1343 r_free = 0.1855             target_work(ml) = 5.308         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1343   r_free= 0.1855   ksol= 0.33   Bsol= 48.43   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.33,2.81,3.88,0.00,0.00,0.00); trace/3= 3.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.308350                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1343   r_free= 0.1852   ksol= 0.33   Bsol= 56.87   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.14,2.20,3.67,0.00,0.00,0.00); trace/3= 2.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.307065                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.451964              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.169  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.561187              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.239  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1343      final r-factor (work) = 0.1217          |
| start r-factor (free) = 0.1852      final r-factor (free) = 0.1735          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6057 = 2.45 * 0.50 * 5.3339 + 1.00 * 0.0665                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5211 = 2.45 * 0.50 * 5.2694 + 1.00 * 0.0609                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1217      final r-factor (work) = 0.1193          |
| start r-factor (free) = 0.1735      final r-factor (free) = 0.1685          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9724 = 0.56 * 1.00 * 5.2694 + 1.00 * 0.0153                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9450 = 0.56 * 1.00 * 5.2240 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.880)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.41   13.23    None  None   None       |
|    all(noH): 2823   0      0.00    91.41   13.23    None  None   None       |
|    Sol.    : 438    0      1.78    91.41   38.73    None  None   None       |
|    Mac.    : 2385   0      0.00    88.42   8.54     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.141: 1709   |   5:    45.706 -  54.848:   94        |
|      1:     9.141 -  18.283:  556   |   6:    54.848 -  63.989:   62        |
|      2:    18.283 -  27.424:  162   |   7:    63.989 -  73.130:   29        |
|      3:    27.424 -  36.565:  100   |   8:    73.130 -  82.272:   16        |
|      4:    36.565 -  45.706:   93   |   9:    82.272 -  91.413:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1193 r_free = 0.1685             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1191 r_free = 0.1683             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1191   r_free= 0.1683   ksol= 0.33   Bsol= 56.87   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.14,2.20,3.67,0.00,0.00,0.00); trace/3= 2.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.207009                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1191   r_free= 0.1683   ksol= 0.33   Bsol= 56.87   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.20,2.11,3.75,0.00,0.00,0.00); trace/3= 2.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.206893                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.956486              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.068  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.237917              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.930  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1191      final r-factor (work) = 0.1164          |
| start r-factor (free) = 0.1683      final r-factor (free) = 0.1628          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1712 = 1.96 * 0.50 * 5.2238 + 1.00 * 0.0610                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1414 = 1.96 * 0.50 * 5.1978 + 1.00 * 0.0567                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1164      final r-factor (work) = 0.1167          |
| start r-factor (free) = 0.1628      final r-factor (free) = 0.1611          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2499 = 0.24 * 1.00 * 5.1978 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2453 = 0.24 * 1.00 * 5.1878 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.880)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.88   12.48    None  None   None       |
|    all(noH): 2823   0      0.00    86.88   12.48    None  None   None       |
|    Sol.    : 438    0      2.24    84.28   35.49    None  None   None       |
|    Mac.    : 2385   0      0.00    86.88   8.26     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.688: 1680   |   5:    43.440 -  52.127:   74        |
|      1:     8.688 -  17.376:  591   |   6:    52.127 -  60.815:   54        |
|      2:    17.376 -  26.064:  158   |   7:    60.815 -  69.503:   22        |
|      3:    26.064 -  34.752:  118   |   8:    69.503 -  78.191:   13        |
|      4:    34.752 -  43.440:  110   |   9:    78.191 -  86.879:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1167 r_free = 0.1611             target_work(ml) = 5.182         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1165 r_free = 0.1609             target_work(ml) = 5.182         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1165   r_free= 0.1609   ksol= 0.33   Bsol= 56.87   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.20,2.11,3.75,0.00,0.00,0.00); trace/3= 2.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.181573                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0896 -  4.7101 0.99   1410  156 0.0987 0.1284      5.3787      5.5623|
|  2:  4.7101 -  3.7575 0.99   1361  153 0.0885 0.1168      5.4604      5.6475|
|  3:  3.7575 -  3.2881 0.99   1328  142 0.1100 0.1506      5.5042       5.854|
|  4:  3.2881 -  2.9901 0.99   1327  152 0.1257 0.1779      5.4753      5.6405|
|  5:  2.9901 -  2.7772 0.99   1317  148 0.1380 0.1737      5.3569       5.571|
|  6:  2.7772 -  2.6143 0.99   1315  144 0.1263 0.1960      5.2235      5.5179|
|  7:  2.6143 -  2.4840 0.99   1297  140 0.1345 0.1648      5.2169      5.3471|
|  8:  2.4840 -  2.3763 0.98   1287  146 0.1235 0.1684      5.1126      5.3402|
|  9:  2.3763 -  2.2851 0.98   1289  147 0.1271 0.1910      5.0929      5.3587|
| 10:  2.2851 -  2.2065 1.00   1289  145 0.1194 0.1709      4.9911      5.2243|
| 11:  2.2065 -  2.1377 0.98   1308  138 0.1189 0.1839       4.986      5.3112|
| 12:  2.1377 -  2.0768 0.98   1259  142 0.1199 0.1737      4.8978      5.2145|
| 13:  2.0768 -  2.0222 0.99   1285  139 0.1194 0.1635      4.8066      5.0149|
| 14:  2.0222 -  1.9730 0.42    558   67 0.1083 0.1478      4.7082       4.816|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0896 -  4.7101  1410   156  0.94   9.30   0.98     0.95       7226.21|
|  2:  4.7101 -  3.7575  1361   153  0.95   8.05   1.01     1.00       9312.95|
|  3:  3.7575 -  3.2881  1328   142  0.93  11.64   1.02     1.02      10896.59|
|  4:  3.2881 -  2.9901  1327   152  0.92  14.21   1.01     0.99      10733.31|
|  5:  2.9901 -  2.7772  1317   148  0.90  16.22   1.00     0.98       8701.44|
|  6:  2.7772 -  2.6143  1315   144  0.90  16.48   0.98     0.95       7144.14|
|  7:  2.6143 -  2.4840  1297   140  0.90  16.01   0.99     0.96       6523.33|
|  8:  2.4840 -  2.3763  1287   146  0.90  15.96   0.99     0.97       5736.97|
|  9:  2.3763 -  2.2851  1289   147  0.90  16.37   1.00     0.96       5589.82|
| 10:  2.2851 -  2.2065  1289   145  0.89  16.77   1.01     0.97       4726.18|
| 11:  2.2065 -  2.1377  1308   138  0.90  16.63   1.00     0.95       4667.75|
| 12:  2.1377 -  2.0768  1259   142  0.90  16.13   1.01     1.01       4068.20|
| 13:  2.0768 -  2.0222  1285   139  0.90  16.72   1.00     0.98       3415.97|
| 14:  2.0222 -  1.9730   558    67  0.92  13.99   0.99     0.97       2701.47|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2701.47 max =        10896.59 mean =      6732.72|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.56|
|phase err.(test): min =        0.00 max =           88.03 mean =        13.92|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1165   r_free= 0.1609   ksol= 0.32   Bsol= 50.75   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,-0.62,1.10,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.181589                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1165   r_free= 0.1609   ksol= 0.32   Bsol= 50.75   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,-0.62,1.10,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.181589                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0896 -  4.7101 0.99   1410  156 0.0982 0.1280      5.3756       5.559|
|  2:  4.7101 -  3.7575 0.99   1361  153 0.0879 0.1159      5.4547      5.6395|
|  3:  3.7575 -  3.2881 0.99   1328  142 0.1094 0.1502      5.5007      5.8514|
|  4:  3.2881 -  2.9901 0.99   1327  152 0.1257 0.1782      5.4759      5.6422|
|  5:  2.9901 -  2.7772 0.99   1317  148 0.1384 0.1745      5.3592      5.5751|
|  6:  2.7772 -  2.6143 0.99   1315  144 0.1266 0.1964       5.226      5.5195|
|  7:  2.6143 -  2.4840 0.99   1297  140 0.1348 0.1651      5.2191      5.3488|
|  8:  2.4840 -  2.3763 0.98   1287  146 0.1238 0.1688      5.1143      5.3419|
|  9:  2.3763 -  2.2851 0.98   1289  147 0.1272 0.1906      5.0942      5.3577|
| 10:  2.2851 -  2.2065 1.00   1289  145 0.1196 0.1716      4.9923      5.2273|
| 11:  2.2065 -  2.1377 0.98   1308  138 0.1189 0.1839       4.987      5.3118|
| 12:  2.1377 -  2.0768 0.98   1259  142 0.1199 0.1742      4.8982      5.2157|
| 13:  2.0768 -  2.0222 0.99   1285  139 0.1195 0.1631      4.8069      5.0144|
| 14:  2.0222 -  1.9730 0.42    558   67 0.1082 0.1477      4.7079      4.8158|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0896 -  4.7101  1410   156  0.94   9.25   0.98     0.95       7177.71|
|  2:  4.7101 -  3.7575  1361   153  0.95   7.98   1.01     1.00       9228.14|
|  3:  3.7575 -  3.2881  1328   142  0.93  11.56   1.02     1.02      10807.66|
|  4:  3.2881 -  2.9901  1327   152  0.92  14.21   1.01     0.99      10732.97|
|  5:  2.9901 -  2.7772  1317   148  0.90  16.27   1.00     0.98       8741.72|
|  6:  2.7772 -  2.6143  1315   144  0.89  16.53   0.98     0.95       7186.45|
|  7:  2.6143 -  2.4840  1297   140  0.90  16.05   0.99     0.96       6557.64|
|  8:  2.4840 -  2.3763  1287   146  0.90  15.99   0.99     0.97       5758.31|
|  9:  2.3763 -  2.2851  1289   147  0.90  16.39   1.00     0.96       5604.32|
| 10:  2.2851 -  2.2065  1289   145  0.89  16.80   1.01     0.97       4739.73|
| 11:  2.2065 -  2.1377  1308   138  0.90  16.66   0.99     0.95       4684.61|
| 12:  2.1377 -  2.0768  1259   142  0.90  16.16   1.01     1.01       4076.98|
| 13:  2.0768 -  2.0222  1285   139  0.90  16.72   1.00     0.98       3418.53|
| 14:  2.0222 -  1.9730   558    67  0.92  13.97   0.99     0.97       2699.36|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2699.36 max =        10807.66 mean =      6729.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.75 mean =        14.57|
|phase err.(test): min =        0.00 max =           87.91 mean =        13.92|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.880)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.68    89.56   15.17    None  None   None       |
|    all(noH): 2823   0      2.68    89.56   15.17    None  None   None       |
|    Sol.    : 438    0      4.92    86.96   38.17    None  None   None       |
|    Mac.    : 2385   0      2.68    89.56   10.94    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.682 -  11.370: 1680   |   5:    46.122 -  54.810:   74        |
|      1:    11.370 -  20.058:  591   |   6:    54.810 -  63.497:   54        |
|      2:    20.058 -  28.746:  158   |   7:    63.497 -  72.185:   22        |
|      3:    28.746 -  37.434:  118   |   8:    72.185 -  80.873:   13        |
|      4:    37.434 -  46.122:  110   |   9:    80.873 -  89.561:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 321         
Filter by distance & map next to the model:
   mapped sites are within: 0.330 - 4.743
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 319 from: 321
   mapped sites are within: 0.708 - 4.743

peak=   10.948 closest distance to " CB  VAL A 230 " =    1.469
peak=    9.160 closest distance to " CG2 VAL A 296 " =    1.443
peak=    6.723 closest distance to " CD2 LEU A   5 " =    1.299
peak=    6.557 closest distance to " O   HOH Z 130 " =    1.247
peak=    6.002 closest distance to " NE2 GLN A  11 " =    1.222
peak=    5.679 closest distance to " CG  PRO A  54 " =    1.417
peak=    5.643 closest distance to " NH2 ARG A  56 " =    2.048
peak=    5.521 closest distance to " CG  LEU A   5 " =    1.205
peak=    5.442 closest distance to " O   HOH Z   9 " =    1.970
peak=    5.382 closest distance to " O   HOH Z 142 " =    2.092
peak=    5.358 closest distance to " O   HOH Z 232 " =    2.286
peak=    5.328 closest distance to " CG  LEU A 228 " =    1.232
peak=    5.196 closest distance to " CD1AILE A 234 " =    1.069
peak=    5.171 closest distance to " CB  PRO A  54 " =    1.052
peak=    4.943 closest distance to " O   HOH Z 427 " =    2.440
peak=    4.910 closest distance to " CB  GLN A 223 " =    1.461
peak=    4.891 closest distance to " CG  PRO A 198 " =    1.317
peak=    4.682 closest distance to " O   HOH Z 425 " =    1.543
peak=    4.668 closest distance to " CB  GLN A 183 " =    1.217
peak=    4.655 closest distance to " ND2 ASN A 187 " =    1.627
peak=    4.525 closest distance to " O   HOH Z 209 " =    2.337
peak=    4.521 closest distance to " CB  SER A  63 " =    1.272
peak=    4.453 closest distance to " CB  SER A   3 " =    1.417
peak=    4.405 closest distance to " CB  ASN A 148 " =    1.332
peak=    4.399 closest distance to " O   HOH Z 126 " =    2.037
peak=    4.388 closest distance to " O   HOH Z 287 " =    2.056
peak=    4.369 closest distance to " O   HOH Z   7 " =    1.341
peak=    4.349 closest distance to " O   HOH Z 298 " =    1.787
peak=    4.343 closest distance to " O   PRO A 198 " =    1.591
peak=    4.333 closest distance to " O   HOH Z 369 " =    2.043
peak=    4.277 closest distance to " O   HOH Z  78 " =    1.678
peak=    4.253 closest distance to " CG  LEU A 167 " =    1.248
peak=    4.251 closest distance to " CA  SER A  87 " =    0.928
peak=    4.231 closest distance to " CB  ASN A  39 " =    0.936
peak=    4.226 closest distance to " CB  VAL A 265 " =    1.381
peak=    4.225 closest distance to " CB  ARG A 275 " =    0.924
peak=    4.222 closest distance to " CB  ASN A 142 " =    1.013
peak=    4.217 closest distance to " CG  PRO A 243 " =    1.182
peak=    4.216 closest distance to " O   HOH Z   2 " =    1.670
peak=    4.215 closest distance to " CB  VAL A 230 " =    1.178
peak=    4.213 closest distance to " O   HOH Z  55 " =    2.171
peak=    4.208 closest distance to " CG  PRO A 213 " =    1.247
peak=    4.196 closest distance to " O   HOH Z 303 " =    2.233
peak=    4.159 closest distance to " NH2AARG A 190 " =    1.764
peak=    4.155 closest distance to " CB  TRP A 266 " =    1.013
peak=    4.147 closest distance to " CB  SER A 216 " =    0.836
peak=    4.141 closest distance to " CD2 LEU A 228 " =    1.195
peak=    4.125 closest distance to " CB  ASP A 124 " =    0.790
peak=    4.095 closest distance to " O   HOH Z 346 " =    1.584
peak=    4.060 closest distance to " O   HOH Z 423 " =    1.559
peak=    4.045 closest distance to " CB BVAL A  41 " =    1.264
peak=    4.031 closest distance to " O   HOH Z  63 " =    1.316
peak=    4.029 closest distance to " O   HOH Z  65 " =    1.072
peak=    4.015 closest distance to " O   HOH Z 234 " =    3.738
peak=    4.011 closest distance to " O   SER A  87 " =    2.206
peak=    4.003 closest distance to " CB  ARG A  79 " =    1.421
peak=    3.979 closest distance to " O   HOH Z 316 " =    3.073
peak=    3.953 closest distance to " O   HOH Z 214 " =    2.167
peak=    3.951 closest distance to " O   HOH Z 362 " =    2.507
peak=    3.940 closest distance to " O   HOH Z 380 " =    1.805
peak=    3.934 closest distance to " O   HOH Z 272 " =    1.802
peak=    3.923 closest distance to " N   PHE A 130 " =    1.260
peak=    3.916 closest distance to " O   HOH Z 389 " =    1.818
peak=    3.913 closest distance to " CG2 VAL A 257 " =    0.908
peak=    3.901 closest distance to " CB  GLU A 128 " =    1.009
peak=    3.900 closest distance to " O   HOH Z 422 " =    2.619
peak=    3.897 closest distance to " O   HOH Z 222 " =    2.358
peak=    3.894 closest distance to " CZ  PHE A 218 " =    1.096
peak=    3.876 closest distance to " O   HOH Z  30 " =    1.681
peak=    3.871 closest distance to " CB  VAL A 202 " =    1.612
peak=    3.861 closest distance to " CA  VAL A 296 " =    1.069
peak=    3.816 closest distance to " CD  ARG A  66 " =    2.474
peak=    3.810 closest distance to " O   HOH Z 126 " =    1.513
peak=    3.807 closest distance to " O   HOH Z   1 " =    1.869
peak=    3.806 closest distance to " CB  GLU A 277 " =    3.562
peak=    3.794 closest distance to " CB  ASN A 187 " =    1.039
peak=    3.792 closest distance to " CB  ARG A 190 " =    1.653
peak=    3.771 closest distance to " CB  TRP A 179 " =    1.456
peak=    3.771 closest distance to " NH1AARG A 145 " =    1.178
peak=    3.770 closest distance to " CB  GLU A 152 " =    1.163
peak=    3.767 closest distance to " CD  ARG A 159 " =    0.743
peak=    3.764 closest distance to " O   HOH Z 193 " =    1.709
peak=    3.755 closest distance to " O   HOH Z 368 " =    2.027
peak=    3.740 closest distance to " O   HOH Z  88 " =    3.118
peak=    3.736 closest distance to " CB  SER A 210 " =    0.819
peak=    3.736 closest distance to " CA  TYR A  30 " =    0.982
peak=    3.732 closest distance to " CG  ARG A 138 " =    1.178
peak=    3.729 closest distance to " CG2 THR A 221 " =    1.011
peak=    3.728 closest distance to " CA  ASN A 215 " =    1.140
peak=    3.721 closest distance to " ND1 HIS A  86 " =    1.745
peak=    3.711 closest distance to " O   HOH Z  61 " =    1.618
peak=    3.710 closest distance to " O   HOH Z  68 " =    2.066
peak=    3.698 closest distance to " OD1 ASN A  69 " =    2.473
peak=    3.697 closest distance to " O   HOH Z  78 " =    2.133
peak=    3.696 closest distance to " CA  THR A 264 " =    0.779
peak=    3.693 closest distance to " O   HOH Z 261 " =    2.151
peak=    3.687 closest distance to " CB  LEU A 143 " =    1.153
peak=    3.680 closest distance to " O   HOH Z 128 " =    1.817
peak=    3.678 closest distance to " CD  ARG A 269 " =    0.976
peak=    3.677 closest distance to " CB  LYS A 117 " =    1.232
peak=    3.675 closest distance to " CG BARG A 102 " =    1.905
peak=    3.674 closest distance to " O   HOH Z 411 " =    3.609
peak=    3.651 closest distance to " O   HOH Z 203 " =    1.768
peak=    3.650 closest distance to " O   PRO A 198 " =    1.315
peak=    3.640 closest distance to " O   HOH Z  22 " =    2.017
peak=    3.638 closest distance to " O   HOH Z  40 " =    1.975
peak=    3.637 closest distance to " CB  ALA A 104 " =    0.708
peak=    3.637 closest distance to " CB  GLN A  88 " =    1.276
peak=    3.625 closest distance to " CB  THR A 157 " =    1.189
peak=    3.620 closest distance to " O   HOH Z 437 " =    2.014
peak=    3.617 closest distance to " O   HOH Z 273 " =    2.833
peak=    3.614 closest distance to " O   HOH Z 193 " =    1.901
peak=    3.614 closest distance to " CB  ASN A 110 " =    1.060
peak=    3.607 closest distance to " O   HOH Z 419 " =    2.018
peak=    3.604 closest distance to " CA  ALA A  51 " =    1.037
peak=    3.603 closest distance to " O   HOH Z  97 " =    2.056
peak=    3.597 closest distance to " O   HOH Z 368 " =    3.507
peak=    3.591 closest distance to " CB  SER A 212 " =    1.298
peak=    3.585 closest distance to " CE  LYS A  76 " =    0.886
peak=    3.583 closest distance to " OE2 GLU A   2 " =    1.947
peak=    3.576 closest distance to " O   HOH Z  61 " =    1.606
peak=    3.575 closest distance to " O   HOH Z 403 " =    1.560
peak=    3.574 closest distance to " O   HOH Z 392 " =    1.287
peak=    3.574 closest distance to " O   HOH Z  21 " =    1.755
peak=    3.567 closest distance to " CA  ALA A 154 " =    1.012
peak=    3.563 closest distance to " O   HOH Z  10 " =    1.770
peak=    3.562 closest distance to " CH2 TRP A 266 " =    1.159
peak=    3.561 closest distance to " O   HOH Z 248 " =    1.628
peak=    3.549 closest distance to " CD  LYS A 166 " =    1.328
peak=    3.547 closest distance to " CD1 LEU A 300 " =    1.151
peak=    3.539 closest distance to " OG BSER A 164 " =    2.269
peak=    3.535 closest distance to " O   HOH Z 424 " =    2.574
peak=    3.534 closest distance to " CG1BVAL A  72 " =    1.531
peak=    3.529 closest distance to " CG  GLN A  88 " =    1.088
peak=    3.526 closest distance to " O   HOH Z 193 " =    1.890
peak=    3.521 closest distance to " OG  SER A  97 " =    2.965
peak=    3.516 closest distance to " CA  LYS A 117 " =    1.175
peak=    3.514 closest distance to " CD1 ILE A  33 " =    1.772
peak=    3.512 closest distance to " O   HOH Z 158 " =    3.129
peak=    3.510 closest distance to " CB  LEU A 228 " =    1.254
peak=    3.510 closest distance to " O   HOH Z 343 " =    3.292
peak=    3.505 closest distance to " NZ  LYS A  48 " =    1.243
peak=    3.503 closest distance to " O   HOH Z  59 " =    1.757
peak=    3.499 closest distance to " O   HOH Z 366 " =    2.999
peak=    3.496 closest distance to " CB  SER A  26 " =    1.705
peak=    3.495 closest distance to " NE2 HIS A 207 " =    1.167
peak=    3.495 closest distance to " O   HOH Z 184 " =    1.353
peak=    3.491 closest distance to " O   HOH Z 146 " =    1.563
peak=    3.485 closest distance to " CB  VAL A 250 " =    1.110
peak=    3.478 closest distance to " CA  ALA A 291 " =    0.902
peak=    3.473 closest distance to " O   HOH Z  90 " =    2.104
peak=    3.472 closest distance to " CE3 TRP A  85 " =    1.198
peak=    3.470 closest distance to " CA  ALA A 299 " =    0.987
peak=    3.461 closest distance to " O   HOH Z 263 " =    1.658
peak=    3.459 closest distance to " CA  ILE A 106 " =    0.783
peak=    3.458 closest distance to " CB  SER A  62 " =    1.107
peak=    3.457 closest distance to " O   HOH Z   1 " =    1.757
peak=    3.450 closest distance to " CA  PHE A 283 " =    1.197
peak=    3.450 closest distance to " CE3 TRP A 150 " =    0.988
peak=    3.449 closest distance to " O   HOH Z 153 " =    3.713
peak=    3.443 closest distance to " OG  SER A  62 " =    2.772
peak=    3.441 closest distance to " N   SER A 135 " =    1.256
peak=    3.439 closest distance to " O   HOH Z 128 " =    2.111
peak=    3.437 closest distance to " CA  ASN A 127 " =    1.063
peak=    3.437 closest distance to " CG2 ILE A  20 " =    1.588
peak=    3.432 closest distance to " CB  MET A  40 " =    0.823
peak=    3.421 closest distance to " O   HOH Z   3 " =    1.980
peak=    3.420 closest distance to " CG1 ILE A  33 " =    1.360
peak=    3.413 closest distance to " O   HOH Z 145 " =    1.765
peak=    3.411 closest distance to " CA  TYR A 116 " =    1.468
peak=    3.408 closest distance to " OG BSER A 212 " =    2.817
peak=    3.408 closest distance to " CG1 VAL A 153 " =    0.899
peak=    3.407 closest distance to " CG  GLN A  89 " =    1.432
peak=    3.405 closest distance to " O   HOH Z 359 " =    1.314
peak=    3.396 closest distance to " O   HOH Z 260 " =    1.498
peak=    3.394 closest distance to " CB  HIS A 108 " =    0.814
peak=    3.393 closest distance to " CA  ALA A 158 " =    1.211
peak=    3.391 closest distance to " O   TYR A 116 " =    1.265
peak=    3.387 closest distance to " O   HOH Z 258 " =    2.150
peak=    3.387 closest distance to " CD  ARG A  24 " =    1.085
peak=    3.384 closest distance to " CD2 TRP A 179 " =    1.275
peak=    3.381 closest distance to " O   HOH Z  44 " =    1.723
peak=    3.378 closest distance to " OG BSER A 134 " =    2.960
peak=    3.375 closest distance to " CD  ARG A 138 " =    0.831
peak=    3.375 closest distance to " N   GLN A 278 " =    1.166
peak=    3.374 closest distance to " O   HOH Z 250 " =    1.396
peak=    3.369 closest distance to " CA  LYS A 290 " =    1.255
peak=    3.361 closest distance to " N   SER A 271 " =    0.996
peak=    3.359 closest distance to " O   PHE A 192 " =    1.345
peak=    3.358 closest distance to " NH2BARG A 190 " =    1.487
peak=    3.356 closest distance to " CA  ILE A 234 " =    0.966
peak=    3.356 closest distance to " CB  GLU A  46 " =    0.932
peak=    3.353 closest distance to " OG  SER A  62 " =    2.997
peak=    3.352 closest distance to " O   HOH Z 180 " =    2.064
peak=    3.351 closest distance to " O   HOH Z 133 " =    2.534
peak=    3.350 closest distance to " CD2 TYR A 186 " =    1.094
peak=    3.349 closest distance to " CD1 LEU A   5 " =    1.461
peak=    3.348 closest distance to " O   HOH Z 195 " =    1.319
peak=    3.346 closest distance to " CA  ASP A 162 " =    0.871
peak=    3.343 closest distance to " O   HOH Z 148 " =    3.471
peak=    3.334 closest distance to " O   HOH Z 116 " =    2.977
peak=    3.334 closest distance to " CG  GLN A 278 " =    1.312
peak=    3.332 closest distance to " N   ARG A 156 " =    1.306
peak=    3.329 closest distance to " O   HOH Z 371 " =    2.749
peak=    3.328 closest distance to " CA  ARG A  36 " =    1.064
peak=    3.328 closest distance to " N   CYS A 260 " =    0.732
peak=    3.327 closest distance to " O   CYS A 168 " =    1.181
peak=    3.325 closest distance to " CG  LYS A 119 " =    1.138
peak=    3.321 closest distance to " CA  ALA A  21 " =    1.204
peak=    3.320 closest distance to " CB  ALA A   1 " =    4.743
peak=    3.319 closest distance to " CD  LYS A  76 " =    1.803
peak=    3.318 closest distance to " CB  TRP A 150 " =    1.307
peak=    3.318 closest distance to " O   HOH Z 109 " =    2.446
peak=    3.316 closest distance to " O   HOH Z 213 " =    1.996
peak=    3.315 closest distance to " CA  THR A 221 " =    0.974
peak=    3.311 closest distance to " O   HOH Z 189 " =    2.923
peak=    3.306 closest distance to " CB  ARG A 138 " =    0.841
peak=    3.301 closest distance to " CB  ASP A 140 " =    0.901
peak=    3.297 closest distance to " O   HOH Z 325 " =    2.227
peak=    3.295 closest distance to " O   HOH Z 425 " =    1.925
peak=    3.293 closest distance to " O   HOH Z 406 " =    1.545
peak=    3.287 closest distance to " CG2 ILE A 239 " =    0.715
peak=    3.283 closest distance to " CE1 TYR A 186 " =    1.332
peak=    3.280 closest distance to " CG  MET A 113 " =    1.159
peak=    3.271 closest distance to " CG1 ILE A 151 " =    1.212
peak=    3.271 closest distance to " CB  SER A 276 " =    1.162
peak=    3.269 closest distance to " O   HOH Z 357 " =    2.019
peak=    3.268 closest distance to " O   HOH Z 329 " =    3.938
peak=    3.268 closest distance to " O   HOH Z 332 " =    1.507
peak=    3.267 closest distance to " O   HOH Z 133 " =    1.625
peak=    3.264 closest distance to " O   HOH Z  59 " =    2.082
peak=    3.257 closest distance to " CB  ALA A   9 " =    1.553
peak=    3.257 closest distance to " ND2 ASN A 249 " =    0.859
peak=    3.256 closest distance to " O   HOH Z 305 " =    3.543
peak=    3.255 closest distance to " CB  ALA A 114 " =    1.218
peak=    3.254 closest distance to " O   HOH Z 225 " =    1.568
peak=    3.250 closest distance to " N   ALA A 233 " =    0.791
peak=    3.244 closest distance to " CZ  PHE A  38 " =    1.189
peak=    3.239 closest distance to " O   LEU A 228 " =    2.038
peak=    3.236 closest distance to " CA  ARG A 195 " =    1.179
peak=    3.233 closest distance to " CA  GLY A 267 " =    0.982
peak=    3.231 closest distance to " CA  LEU A 282 " =    1.134
peak=    3.231 closest distance to " O   HOH Z 359 " =    4.149
peak=    3.230 closest distance to " O   HOH Z 294 " =    1.490
peak=    3.226 closest distance to " CA  ALA A 160 " =    0.977
peak=    3.222 closest distance to " CD1 LEU A 281 " =    1.041
peak=    3.221 closest distance to " NZ  LYS A 117 " =    2.959
peak=    3.221 closest distance to " OE2 GLU A  53 " =    1.924
peak=    3.221 closest distance to " O   HOH Z  85 " =    2.078
peak=    3.215 closest distance to " CG2 ILE A 120 " =    1.355
peak=    3.215 closest distance to " O   HOH Z  43 " =    1.869
peak=    3.212 closest distance to " CD  GLN A 240 " =    1.598
peak=    3.212 closest distance to " O   HOH Z 285 " =    2.408
peak=    3.211 closest distance to " CZ3 TRP A  92 " =    1.311
peak=    3.209 closest distance to " CZ  PHE A 192 " =    0.915
peak=    3.209 closest distance to " CB  LEU A  83 " =    0.734
peak=    3.207 closest distance to " O   HOH Z 147 " =    1.693
peak=    3.206 closest distance to " CG  MET A 185 " =    1.194
peak=    3.201 closest distance to " CB  GLN A  89 " =    1.212
peak=    3.199 closest distance to " CA  ARG A 102 " =    1.131
peak=    3.197 closest distance to " CB  TYR A 247 " =    0.976
peak=    3.196 closest distance to " O   HOH Z 175 " =    2.100
peak=    3.195 closest distance to " CB  ALA A  34 " =    1.120
peak=    3.192 closest distance to " O   HOH Z 409 " =    2.639
peak=    3.190 closest distance to " CA  ASN A 217 " =    1.275
peak=    3.190 closest distance to " O   HOH Z 132 " =    2.480
peak=    3.190 closest distance to " ND2 ASN A 110 " =    1.657
peak=    3.189 closest distance to " CB  ASN A 215 " =    1.177
peak=    3.188 closest distance to " N   ALA A 256 " =    1.055
peak=    3.188 closest distance to " NZ  LYS A  76 " =    1.565
peak=    3.187 closest distance to " O   HOH Z 145 " =    1.719
peak=    3.184 closest distance to " O   ASN A 209 " =    1.396
peak=    3.182 closest distance to " O   HOH Z 222 " =    1.427
peak=    3.181 closest distance to " N   ASN A 127 " =    1.340
peak=    3.178 closest distance to " O   HOH Z 371 " =    1.689
peak=    3.178 closest distance to " O   HOH Z 340 " =    2.093
peak=    3.177 closest distance to " N   SER A 146 " =    1.725
peak=    3.176 closest distance to " CA  VAL A  41 " =    0.764
peak=    3.174 closest distance to " NE2 GLN A 278 " =    3.582
peak=    3.171 closest distance to " CZ3 TRP A 123 " =    1.524
peak=    3.170 closest distance to " CA  ARG A 156 " =    0.990
peak=    3.166 closest distance to " O   HOH Z  44 " =    2.684
peak=    3.166 closest distance to " CG1 ILE A  49 " =    1.481
peak=    3.160 closest distance to " O   HOH Z 290 " =    1.124
peak=    3.159 closest distance to " CB  GLU A 175 " =    1.067
peak=    3.154 closest distance to " CG2 ILE A 151 " =    0.751
peak=    3.154 closest distance to " CB  TYR A 116 " =    0.962
peak=    3.152 closest distance to " O   HOH Z 344 " =    2.886
peak=    3.152 closest distance to " O   HOH Z 154 " =    1.886
peak=    3.150 closest distance to " O   PRO A  90 " =    1.691
peak=    3.147 closest distance to " CA  MET A 105 " =    0.893
peak=    3.146 closest distance to " O   HOH Z 394 " =    3.823
peak=    3.143 closest distance to " O   HOH Z 417 " =    1.160
peak=    3.142 closest distance to " O   HOH Z 291 " =    1.583
peak=    3.141 closest distance to " O   HOH Z 251 " =    1.638
peak=    3.140 closest distance to " CB  ALA A 114 " =    1.348
peak=    3.140 closest distance to " NH1BARG A 145 " =    1.263
peak=    3.137 closest distance to " NH2BARG A 145 " =    1.966
peak=    3.128 closest distance to " CB  ALA A 137 " =    1.085
peak=    3.125 closest distance to " CB  ALA A 291 " =    1.303
peak=    3.121 closest distance to " CB  ALA A 180 " =    1.287
peak=    3.118 closest distance to " O   HOH Z 389 " =    3.268
peak=    3.117 closest distance to " CB  ASN A 224 " =    0.989
peak=    3.111 closest distance to " O   HOH Z 148 " =    2.177
peak=    3.094 closest distance to " O   HOH Z 301 " =    1.666
peak=    3.087 closest distance to " O   HOH Z 390 " =    2.619
peak=    3.078 closest distance to " O   HOH Z 172 " =    2.928
peak=    3.076 closest distance to " CG  ARG A 159 " =    0.910
peak=    3.076 closest distance to " O   ALA A 292 " =    1.739
peak=    3.070 closest distance to " CA  ALA A 233 " =    1.000
peak=    3.062 closest distance to " O  BHOH Z 338 " =    2.461
peak=    3.058 closest distance to " N   ASP A 162 " =    1.153
peak=    3.052 closest distance to " CB  VAL A 268 " =    0.839
peak=    3.035 closest distance to " O   HOH Z 156 " =    3.449
peak=    3.030 closest distance to " O   HOH Z 173 " =    1.627
peak=    3.030 closest distance to " O   HOH Z 173 " =    2.060
peak=    3.025 closest distance to " O   HOH Z 113 " =    2.110
peak=    3.012 closest distance to " CB  PHE A 204 " =    0.805
peak=    3.011 closest distance to " O   HOH Z 124 " =    2.191

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.686 - 5.361
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 202
   mapped sites are within: 0.702 - 5.361

peak=   -5.634 closest distance to " CG2 VAL A 230 " =    0.702
peak=   -4.458 closest distance to " CB  PRO A 243 " =    2.675
peak=   -4.358 closest distance to " CD  ARG A  14 " =    3.169
peak=   -4.303 closest distance to " CD  ARG A 156 " =    2.029
peak=   -4.259 closest distance to " O   HOH Z 290 " =    1.123
peak=   -4.171 closest distance to " O   HOH Z 231 " =    0.928
peak=   -4.157 closest distance to " OG BSER A 134 " =    1.358
peak=   -4.079 closest distance to " CD1 LEU A 255 " =    2.884
peak=   -4.041 closest distance to " CG2 VAL A 202 " =    2.726
peak=   -4.030 closest distance to " O   HOH Z 231 " =    1.723
peak=   -4.022 closest distance to " CB  ALA A  43 " =    2.527
peak=   -3.989 closest distance to " O   HOH Z 266 " =    5.232
peak=   -3.987 closest distance to " N   THR A 157 " =    1.463
peak=   -3.987 closest distance to " O   HOH Z 185 " =    2.271
peak=   -3.978 closest distance to " O   VAL A  67 " =    2.492
peak=   -3.961 closest distance to " O   HOH Z 351 " =    1.539
peak=   -3.930 closest distance to " O   HOH Z 211 " =    1.294
peak=   -3.900 closest distance to " N   ALA A  43 " =    2.637
peak=   -3.877 closest distance to " O   PRO A 198 " =    1.190
peak=   -3.859 closest distance to " NH2 ARG A  79 " =    1.991
peak=   -3.845 closest distance to " CD2 LEU A   5 " =    0.948
peak=   -3.841 closest distance to " CA  GLY A  98 " =    1.874
peak=   -3.838 closest distance to " O   HOH Z 176 " =    0.713
peak=   -3.838 closest distance to " O   HOH Z 394 " =    1.455
peak=   -3.835 closest distance to " O   HOH Z 359 " =    3.276
peak=   -3.834 closest distance to " O   HOH Z 389 " =    2.052
peak=   -3.828 closest distance to " ND2 ASN A 249 " =    2.416
peak=   -3.812 closest distance to " CB  ALA A 161 " =    2.533
peak=   -3.807 closest distance to " CG2 VAL A 296 " =    1.704
peak=   -3.807 closest distance to " C   HIS A 108 " =    1.234
peak=   -3.795 closest distance to " CD  GLN A  58 " =    0.964
peak=   -3.793 closest distance to " O   PRO A 163 " =    1.978
peak=   -3.747 closest distance to " CA  GLY A 241 " =    2.312
peak=   -3.744 closest distance to " O   HOH Z  52 " =    1.431
peak=   -3.742 closest distance to " ND2 ASN A 187 " =    1.533
peak=   -3.734 closest distance to " O   HOH Z 191 " =    5.361
peak=   -3.727 closest distance to " O   HOH Z  51 " =    0.819
peak=   -3.715 closest distance to " O   HOH Z 359 " =    1.592
peak=   -3.710 closest distance to " CG  LEU A   5 " =    0.926
peak=   -3.703 closest distance to " CE2 TYR A  30 " =    2.702
peak=   -3.680 closest distance to " O   HOH Z  65 " =    1.151
peak=   -3.667 closest distance to " CG2 VAL A 296 " =    0.979
peak=   -3.662 closest distance to " CZ2 TRP A 274 " =    0.931
peak=   -3.643 closest distance to " CD  GLN A 223 " =    2.248
peak=   -3.632 closest distance to " O   HOH Z  43 " =    1.803
peak=   -3.626 closest distance to " O   HOH Z 429 " =    2.013
peak=   -3.605 closest distance to " CD2 LEU A 237 " =    2.870
peak=   -3.598 closest distance to " O   GLY A 203 " =    2.491
peak=   -3.593 closest distance to " N   ALA A 226 " =    2.081
peak=   -3.585 closest distance to " CE2 PHE A 218 " =    2.476
peak=   -3.577 closest distance to " O   HOH Z 131 " =    4.089
peak=   -3.566 closest distance to " O   HOH Z 100 " =    1.124
peak=   -3.557 closest distance to " ND2 ASN A  45 " =    1.222
peak=   -3.535 closest distance to " O   HOH Z 140 " =    1.421
peak=   -3.530 closest distance to " CG1 VAL A 112 " =    3.007
peak=   -3.523 closest distance to " CA  GLY A 203 " =    2.409
peak=   -3.523 closest distance to " CG1 VAL A 112 " =    2.627
peak=   -3.505 closest distance to " CB  PHE A 192 " =    1.772
peak=   -3.504 closest distance to " O   ARG A 145 " =    1.498
peak=   -3.502 closest distance to " O   HOH Z  11 " =    1.890
peak=   -3.500 closest distance to " C   MET A 188 " =    1.448
peak=   -3.500 closest distance to " CB  PRO A 163 " =    2.424
peak=   -3.487 closest distance to " C   GLU A 236 " =    0.867
peak=   -3.486 closest distance to " CD  PRO A 213 " =    2.060
peak=   -3.468 closest distance to " O   SER A  22 " =    2.423
peak=   -3.467 closest distance to " O   HOH Z  39 " =    1.043
peak=   -3.467 closest distance to " O   HOH Z 114 " =    2.979
peak=   -3.461 closest distance to " ND2 ASN A  45 " =    1.965
peak=   -3.461 closest distance to " CZ3 TRP A 179 " =    1.254
peak=   -3.458 closest distance to " ND2 ASN A  69 " =    1.331
peak=   -3.450 closest distance to " O   HOH Z 350 " =    2.041
peak=   -3.450 closest distance to " OG  SER A  87 " =    1.378
peak=   -3.449 closest distance to " CD2 TYR A 293 " =    1.891
peak=   -3.434 closest distance to " CD1 ILE A 199 " =    2.517
peak=   -3.428 closest distance to " C   LEU A 222 " =    0.762
peak=   -3.424 closest distance to " CB  ALA A 244 " =    2.105
peak=   -3.424 closest distance to " O   ILE A  49 " =    1.716
peak=   -3.424 closest distance to " OG  SER A  63 " =    1.126
peak=   -3.422 closest distance to " CD1 TYR A 169 " =    2.599
peak=   -3.422 closest distance to " O   VAL A  67 " =    2.861
peak=   -3.420 closest distance to " O   HOH Z  52 " =    0.723
peak=   -3.407 closest distance to " O   HOH Z 198 " =    2.240
peak=   -3.402 closest distance to " OE1 GLN A  88 " =    1.189
peak=   -3.385 closest distance to " O   HOH Z 103 " =    1.923
peak=   -3.385 closest distance to " O   HOH Z 166 " =    1.988
peak=   -3.380 closest distance to " O   SER A 135 " =    1.433
peak=   -3.379 closest distance to " O   HOH Z 389 " =    1.435
peak=   -3.378 closest distance to " CB  ASP A 132 " =    2.365
peak=   -3.377 closest distance to " CG  TRP A 266 " =    1.853
peak=   -3.374 closest distance to " OG  SER A  97 " =    2.238
peak=   -3.367 closest distance to " N   GLN A  58 " =    1.909
peak=   -3.366 closest distance to " CE BMET A  47 " =    1.388
peak=   -3.361 closest distance to " CB  ALA A 114 " =    2.391
peak=   -3.361 closest distance to " CB  GLN A  55 " =    1.337
peak=   -3.357 closest distance to " CB  TYR A  15 " =    2.161
peak=   -3.355 closest distance to " SG BCYS A 201 " =    2.281
peak=   -3.355 closest distance to " O   HOH Z 111 " =    1.793
peak=   -3.354 closest distance to " CA  GLY A 133 " =    1.949
peak=   -3.350 closest distance to " O   HOH Z 134 " =    3.837
peak=   -3.349 closest distance to " CB  ALA A 248 " =    2.406
peak=   -3.347 closest distance to " O   VAL A 189 " =    2.528
peak=   -3.347 closest distance to " O   HOH Z 281 " =    2.633
peak=   -3.345 closest distance to " OH  TYR A 172 " =    1.816
peak=   -3.339 closest distance to " CB  CYS A 201 " =    2.489
peak=   -3.337 closest distance to " O   HOH Z 407 " =    3.202
peak=   -3.337 closest distance to " OXT GLY A 302 " =    3.144
peak=   -3.336 closest distance to " O   HOH Z 134 " =    3.272
peak=   -3.334 closest distance to " O   ALA A  10 " =    1.792
peak=   -3.334 closest distance to " CE  LYS A  76 " =    2.704
peak=   -3.331 closest distance to " OG  SER A  62 " =    4.488
peak=   -3.329 closest distance to " CA  ASP A  27 " =    2.410
peak=   -3.325 closest distance to " CA  ASP A 298 " =    1.085
peak=   -3.317 closest distance to " O   PRO A 243 " =    2.504
peak=   -3.317 closest distance to " CD1 LEU A 101 " =    2.266
peak=   -3.316 closest distance to " CG  MET A 105 " =    0.947
peak=   -3.316 closest distance to " N   ASP A 270 " =    1.464
peak=   -3.314 closest distance to " CB  TRP A  85 " =    2.625
peak=   -3.314 closest distance to " O   HOH Z   2 " =    1.924
peak=   -3.313 closest distance to " O   GLY A  80 " =    2.490
peak=   -3.304 closest distance to " CD1 LEU A 228 " =    2.308
peak=   -3.293 closest distance to " NH2AARG A 275 " =    5.249
peak=   -3.291 closest distance to " CD  LYS A 289 " =    2.393
peak=   -3.290 closest distance to " O   PRO A 198 " =    1.318
peak=   -3.289 closest distance to " CB  CYS A 254 " =    2.131
peak=   -3.289 closest distance to " O   HOH Z 353 " =    1.712
peak=   -3.285 closest distance to " CG  GLN A  88 " =    0.724
peak=   -3.284 closest distance to " C   ALA A 158 " =    1.494
peak=   -3.282 closest distance to " CG2 THR A  42 " =    1.828
peak=   -3.278 closest distance to " O   HOH Z 427 " =    1.657
peak=   -3.272 closest distance to " O   HOH Z  44 " =    2.297
peak=   -3.272 closest distance to " N   MET A 105 " =    2.713
peak=   -3.270 closest distance to " CD2 HIS A 207 " =    2.381
peak=   -3.257 closest distance to " CD  GLU A 277 " =    1.084
peak=   -3.254 closest distance to " C   LYS A  76 " =    1.334
peak=   -3.254 closest distance to " O   HOH Z 133 " =    1.478
peak=   -3.253 closest distance to " O   HOH Z  63 " =    1.970
peak=   -3.252 closest distance to " CD  PRO A 243 " =    2.027
peak=   -3.251 closest distance to " CE  MET A 105 " =    2.464
peak=   -3.251 closest distance to " ND2BASN A 224 " =    1.603
peak=   -3.250 closest distance to " CG1 VAL A 197 " =    2.353
peak=   -3.250 closest distance to " CG2 ILE A 263 " =    2.358
peak=   -3.234 closest distance to " O   GLY A 211 " =    1.235
peak=   -3.231 closest distance to " O   HOH Z  73 " =    2.302
peak=   -3.230 closest distance to " O   HOH Z  24 " =    1.140
peak=   -3.226 closest distance to " O   HOH Z 241 " =    1.317
peak=   -3.225 closest distance to " O   GLY A 229 " =    1.833
peak=   -3.222 closest distance to " CZ  ARG A 259 " =    0.911
peak=   -3.221 closest distance to " OD1 ASN A 148 " =    1.410
peak=   -3.221 closest distance to " O   GLY A  17 " =    1.241
peak=   -3.221 closest distance to " CG1 VAL A 230 " =    1.979
peak=   -3.217 closest distance to " C   ASN A 285 " =    2.275
peak=   -3.215 closest distance to " O   HOH Z  60 " =    2.361
peak=   -3.215 closest distance to " O   HOH Z 243 " =    1.815
peak=   -3.211 closest distance to " O   HOH Z 108 " =    1.510
peak=   -3.211 closest distance to " NE2 GLN A 278 " =    2.145
peak=   -3.211 closest distance to " CB  PRO A  54 " =    2.500
peak=   -3.210 closest distance to " N   ALA A 248 " =    1.497
peak=   -3.207 closest distance to " CG2 THR A  52 " =    3.021
peak=   -3.205 closest distance to " CG  ASP A 231 " =    0.724
peak=   -3.201 closest distance to " CB  PRO A 213 " =    2.191
peak=   -3.192 closest distance to " OG BSER A 134 " =    1.876
peak=   -3.190 closest distance to " O   HOH Z 412 " =    4.194
peak=   -3.190 closest distance to " CG1 VAL A 250 " =    2.767
peak=   -3.189 closest distance to " CB  ALA A 291 " =    2.200
peak=   -3.188 closest distance to " NE2 GLN A 278 " =    1.951
peak=   -3.184 closest distance to " CE2 TRP A  70 " =    2.189
peak=   -3.183 closest distance to " O   HOH Z 292 " =    1.676
peak=   -3.177 closest distance to " O   LYS A 289 " =    2.995
peak=   -3.176 closest distance to " O   PHE A 218 " =    1.561
peak=   -3.176 closest distance to " O   HOH Z 247 " =    0.884
peak=   -3.169 closest distance to " CG  LEU A 167 " =    0.916
peak=   -3.165 closest distance to " CD1 PHE A  61 " =    2.774
peak=   -3.165 closest distance to " O   HOH Z 139 " =    0.955
peak=   -3.164 closest distance to " O   HOH Z 166 " =    1.428
peak=   -3.164 closest distance to " O   ALA A 161 " =    1.705
peak=   -3.161 closest distance to " O   HOH Z 384 " =    2.412
peak=   -3.156 closest distance to " O   HOH Z 377 " =    1.889
peak=   -3.149 closest distance to " OE2 GLU A 152 " =    1.153
peak=   -3.148 closest distance to " O   HOH Z 426 " =    1.703
peak=   -3.147 closest distance to " OG1 THR A 178 " =    1.290
peak=   -3.146 closest distance to " O   HOH Z 357 " =    2.060
peak=   -3.145 closest distance to " CB  PHE A 130 " =    1.230
peak=   -3.144 closest distance to " O   SER A 271 " =    2.219
peak=   -3.141 closest distance to " O   GLU A 152 " =    1.417
peak=   -3.141 closest distance to " OD1 ASN A 187 " =    1.573
peak=   -3.137 closest distance to " O   GLN A 240 " =    2.451
peak=   -3.127 closest distance to " O   SER A 210 " =    1.869
peak=   -3.126 closest distance to " O   HOH Z  63 " =    1.770
peak=   -3.126 closest distance to " OE1 GLU A 277 " =    2.268
peak=   -3.124 closest distance to " O   HOH Z 371 " =    2.268
peak=   -3.121 closest distance to " CZ  TYR A 169 " =    1.636
peak=   -3.120 closest distance to " O   HOH Z 189 " =    2.078
peak=   -3.120 closest distance to " O   HOH Z 313 " =    1.539
peak=   -3.107 closest distance to " OH  TYR A 247 " =    1.872
peak=   -3.099 closest distance to " O   HOH Z 111 " =    4.340
peak=   -3.093 closest distance to " O   ASP A  27 " =    1.828
peak=   -3.093 closest distance to " O   HOH Z 385 " =    2.100
peak=   -3.091 closest distance to " CG  PRO A 163 " =    2.579
peak=   -3.079 closest distance to " OD1 ASN A 301 " =    1.949
peak=   -3.067 closest distance to " CD  ARG A 139 " =    1.706
peak=   -3.052 closest distance to " O   ALA A 292 " =    2.019

================= 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    :  0.4678 0.4557   6.269029e+00   6.246971e+00
   1_bss:  0.4601 0.4375   6.264715e+00   6.236236e+00
   1_xyz:  0.3672 0.3844   6.128780e+00   6.154362e+00
   1_adp:  0.3154 0.3659   6.026446e+00   6.121099e+00
   1_occ:  0.3148 0.3663   6.025647e+00   6.121913e+00
   2_bss:  0.3113 0.3615   6.026897e+00   6.119892e+00
   2_xyz:  0.2241 0.2765   5.737694e+00   5.889808e+00
   2_adp:  0.2010 0.2554   5.649041e+00   5.823973e+00
   2_occ:  0.2009 0.2548   5.648232e+00   5.823343e+00
   3_bss:  0.1999 0.2527   5.647886e+00   5.820990e+00
   3_xyz:  0.1469 0.1947   5.374818e+00   5.590635e+00
   3_adp:  0.1344 0.1855   5.308525e+00   5.540255e+00
   3_occ:  0.1343 0.1855   5.308350e+00   5.540163e+00
   4_bss:  0.1343 0.1852   5.307065e+00   5.538481e+00
   4_xyz:  0.1217 0.1735   5.230393e+00   5.475301e+00
   4_adp:  0.1193 0.1685   5.207542e+00   5.446129e+00
   4_occ:  0.1191 0.1683   5.207009e+00   5.445425e+00
   5_bss:  0.1191 0.1683   5.206893e+00   5.445231e+00
   5_xyz:  0.1164 0.1628   5.184709e+00   5.422942e+00
   5_adp:  0.1167 0.1611   5.182244e+00   5.415116e+00
   5_occ:  0.1165 0.1609   5.181573e+00   5.414054e+00
   5_bss:  0.1165 0.1609   5.181589e+00   5.414034e+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   6.642   9.214   8.777   0.000   0.000   0.000
   1_xyz:  0.300  20.000   6.642   9.214   8.777   0.000   0.000   0.000
   1_adp:  0.300  20.000   6.642   9.214   8.777   0.000   0.000   0.000
   1_occ:  0.300  20.000   6.642   9.214   8.777   0.000   0.000   0.000
   2_bss:  0.343  48.429   3.470   5.050   5.245   0.000   0.000   0.000
   2_xyz:  0.343  48.429   3.470   5.050   5.245   0.000   0.000   0.000
   2_adp:  0.343  48.429   3.470   5.050   5.245   0.000   0.000   0.000
   2_occ:  0.343  48.429   3.470   5.050   5.245   0.000   0.000   0.000
   3_bss:  0.326  48.429   2.326   2.807   3.876   0.000   0.000   0.000
   3_xyz:  0.326  48.429   2.326   2.807   3.876   0.000   0.000   0.000
   3_adp:  0.326  48.429   2.326   2.807   3.876   0.000   0.000   0.000
   3_occ:  0.326  48.429   2.326   2.807   3.876   0.000   0.000   0.000
   4_bss:  0.325  56.874   2.143   2.198   3.668   0.000   0.000   0.000
   4_xyz:  0.325  56.874   2.143   2.198   3.668   0.000   0.000   0.000
   4_adp:  0.325  56.874   2.143   2.198   3.668   0.000   0.000   0.000
   4_occ:  0.325  56.874   2.143   2.198   3.668   0.000   0.000   0.000
   5_bss:  0.327  56.874   2.200   2.105   3.749   0.000   0.000   0.000
   5_xyz:  0.327  56.874   2.200   2.105   3.749   0.000   0.000   0.000
   5_adp:  0.327  56.874   2.200   2.105   3.749   0.000   0.000   0.000
   5_occ:  0.327  56.874   2.200   2.105   3.749   0.000   0.000   0.000
   5_bss:  0.320  50.750  -0.482  -0.622   1.104  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.713 0.4740  0.5500    62292.938
   1_bss:  53.363 0.4770  0.7022    59952.864
   1_xyz:  43.970 0.5932  0.8470    43124.058
   1_adp:  39.768 0.6448  0.9589    37824.377
   1_occ:  39.836 0.6439  0.9563    37885.894
   2_bss:  39.530 0.6476  0.8474    37526.411
   2_xyz:  27.910 0.7797  0.9798    19636.854
   2_adp:  25.145 0.8099  0.9974    16650.661
   2_occ:  25.114 0.8102  0.9974    16604.809
   3_bss:  25.002 0.8113  0.9433    16504.530
   3_xyz:  18.682 0.8737  0.9867     9724.392
   3_adp:  17.468 0.8851  0.9845     8795.592
   3_occ:  17.467 0.8851  0.9843     8788.831
   4_bss:  17.427 0.8855  0.9726     8749.622
   4_xyz:  15.942 0.8985  0.9786     7559.411
   4_adp:  15.262 0.9047  0.9752     7163.353
   4_occ:  15.250 0.9048  0.9751     7144.302
   5_bss:  15.248 0.9048  0.9757     7143.599
   5_xyz:  14.750 0.9090  0.9778     6815.877
   5_adp:  14.515 0.9112  0.9761     6749.524
   5_occ:  14.500 0.9113  0.9761     6732.391
   5_bss:  14.506 0.9112  0.9758     6729.548
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3787e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3787e+01
   1_xyz:   1.629  0.013  0.105 18.201  0.006  4.109   1.3216e-01
   1_adp:   1.629  0.013  0.105 18.201  0.006  4.109   1.3216e-01
   1_occ:   1.629  0.013  0.105 18.201  0.006  4.109   1.3216e-01
   2_bss:   1.629  0.013  0.105 18.201  0.006  4.109   1.3216e-01
   2_xyz:   1.108  0.008  0.082 16.247  0.005  4.111   7.7755e-02
   2_adp:   1.108  0.008  0.082 16.247  0.005  4.111   7.7755e-02
   2_occ:   1.108  0.008  0.082 16.247  0.005  4.111   7.7755e-02
   3_bss:   1.108  0.008  0.082 16.247  0.005  4.111   7.7755e-02
   3_xyz:   1.042  0.007  0.079 15.938  0.004  4.122   6.6487e-02
   3_adp:   1.042  0.007  0.079 15.938  0.004  4.122   6.6487e-02
   3_occ:   1.042  0.007  0.079 15.938  0.004  4.122   6.6487e-02
   4_bss:   1.042  0.007  0.079 15.938  0.004  4.122   6.6487e-02
   4_xyz:   0.984  0.007  0.076 15.613  0.003  4.127   6.0922e-02
   4_adp:   0.984  0.007  0.076 15.613  0.003  4.127   6.0922e-02
   4_occ:   0.984  0.007  0.076 15.613  0.003  4.127   6.0922e-02
   5_bss:   0.984  0.007  0.076 15.613  0.003  4.127   6.0922e-02
   5_xyz:   0.947  0.006  0.075 15.349  0.003  4.116   5.6683e-02
   5_adp:   0.947  0.006  0.075 15.349  0.003  4.116   5.6683e-02
   5_occ:   0.947  0.006  0.075 15.349  0.003  4.116   5.6683e-02
   5_bss:   0.947  0.006  0.075 15.349  0.003  4.116   5.6683e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9730e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9730e+00
   1_xyz:  12.929  0.178  0.406 86.417  0.032  2.201   9.4947e-02
   1_adp:  12.929  0.178  0.406 86.417  0.032  2.201   9.4947e-02
   1_occ:  12.929  0.178  0.406 86.417  0.032  2.201   9.4947e-02
   2_bss:  12.929  0.178  0.406 86.417  0.032  2.201   9.4947e-02
   2_xyz:   6.343  0.074  0.298 88.824  0.034  2.298   6.1640e-02
   2_adp:   6.343  0.074  0.298 88.824  0.034  2.298   6.1640e-02
   2_occ:   6.343  0.074  0.298 88.824  0.034  2.298   6.1640e-02
   3_bss:   6.343  0.074  0.298 88.824  0.034  2.298   6.1640e-02
   3_xyz:   8.370  0.060  0.377 82.091  0.026  2.289   6.7542e-02
   3_adp:   8.370  0.060  0.377 82.091  0.026  2.289   6.7542e-02
   3_occ:   8.370  0.060  0.377 82.091  0.026  2.289   6.7542e-02
   4_bss:   8.370  0.060  0.377 82.091  0.026  2.289   6.7542e-02
   4_xyz:   7.240  0.052  0.376 83.036  0.038  2.331   4.0638e-02
   4_adp:   7.240  0.052  0.376 83.036  0.038  2.331   4.0638e-02
   4_occ:   7.240  0.052  0.376 83.036  0.038  2.331   4.0638e-02
   5_bss:   7.240  0.052  0.376 83.036  0.038  2.331   4.0638e-02
   5_xyz:   7.152  0.045  0.363 83.981  0.039  2.346   3.6588e-02
   5_adp:   7.152  0.045  0.363 83.981  0.039  2.346   3.6588e-02
   5_occ:   7.152  0.045  0.363 83.981  0.039  2.346   3.6588e-02
   5_bss:   7.152  0.045  0.363 83.981  0.039  2.346   3.6588e-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:  83.42   0.00  13.01  68.57   0.00  10.21  83.42   0.00  28.22
   1_occ:  83.42   0.00  13.01  68.57   0.00  10.21  83.42   0.00  28.22
   2_bss:  83.42   0.00  13.01  68.57   0.00  10.21  83.42   0.00  28.22
   2_xyz:  83.42   0.00  13.01  68.57   0.00  10.21  83.42   0.00  28.22
   2_adp:  86.77   0.00  12.73  70.73   0.00   8.99  86.77   0.00  33.14
   2_occ:  86.77   0.00  12.73  70.73   0.00   8.99  86.77   0.00  33.14
   3_bss:  86.77   0.00  12.73  70.73   0.00   8.99  86.77   0.00  33.14
   3_xyz:  86.77   0.00  12.73  70.73   0.00   8.99  86.77   0.00  33.14
   3_adp:  92.58   0.00  13.66  86.76   0.00   8.86  92.58   1.34  39.78
   3_occ:  92.58   0.00  13.66  86.76   0.00   8.86  92.58   1.34  39.78
   4_bss:  92.58   0.00  13.66  86.76   0.00   8.86  92.58   1.34  39.78
   4_xyz:  92.58   0.00  13.66  86.76   0.00   8.86  92.58   1.34  39.78
   4_adp:  91.41   0.00  13.23  88.42   0.00   8.54  91.41   1.78  38.73
   4_occ:  91.41   0.00  13.23  88.42   0.00   8.54  91.41   1.78  38.73
   5_bss:  91.41   0.00  13.23  88.42   0.00   8.54  91.41   1.78  38.73
   5_xyz:  91.41   0.00  13.23  88.42   0.00   8.54  91.41   1.78  38.73
   5_adp:  86.88   0.00  12.48  86.88   0.00   8.26  84.28   2.24  35.49
   5_occ:  86.88   0.00  12.48  86.88   0.00   8.26  84.28   2.24  35.49
   5_bss:  89.56   2.68  15.17  89.56   2.68  10.94  86.96   4.92  38.17
------------------------------------------------------------------------
 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:    1.238    0.015    0.406
   1_adp:    1.238    0.015    0.406
   1_occ:    1.238    0.015    0.406
   2_bss:    1.238    0.015    0.406
   2_xyz:    1.451    0.052    0.564
   2_adp:    1.451    0.052    0.564
   2_occ:    1.451    0.052    0.564
   3_bss:    1.451    0.052    0.564
   3_xyz:    1.598    0.036    0.636
   3_adp:    1.598    0.036    0.636
   3_occ:    1.598    0.036    0.636
   4_bss:    1.598    0.036    0.636
   4_xyz:    1.717    0.055    0.661
   4_adp:    1.717    0.055    0.661
   4_occ:    1.717    0.055    0.661
   5_bss:    1.717    0.055    0.661
   5_xyz:    1.725    0.031    0.672
   5_adp:    1.725    0.031    0.672
   5_occ:    1.725    0.031    0.672
   5_bss:    1.725    0.031    0.672
------------------------------------------------------------------------

CPU time actual refinement: 342.64


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_755/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_755/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_755/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_755/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_755/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 342.48 
  Macro-tasks:
    bulk solvent and scale       = 42.00  
    individual site refinement   = 140.14 
    weights calculation          = 33.03  
    collect and process          = 6.68   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 221.96 
  Micro-tasks:
    mask                            = 1.77   
    f_calc                          = 105.08 
    alpha_beta                      = 8.50   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 116.10 
    fmodel                         = 7.46   
    r_factors                      = 0.20   
    phase_errors                   = 10.72  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 251.26 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.771 micro seconds
Total CPU time: 5.94 minutes
from_scatterers_fft:    673 calls, 104.70 s
gradients_fft:          618 calls, 102.10 s

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

# Date 2008-01-16 Time 02:21:31 PST -0800 (1200478891.76 s)
Start R-work = 0.4678, R-free = 0.4557 (no bulk solvent and anisotropic scale)
Final R-work = 0.1338, R-free = 0.1780 (no bulk solvent and anisotropic scale)

Start R-work = 0.4601, R-free = 0.4375
Final R-work = 0.1165, R-free = 0.1609