# Date 2008-01-16 Time 02:31:33 PST -0800 (1200479493.17 s)
#phil __OFF__

Command line arguments: "../863.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1378
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 863

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 45.9914, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 45.9914, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1028 1.96347
Completeness in resolution range: 0.943503
Completeness with d_max=infinity: 0.940784

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1028
                             d_min =   1.9635

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 45.9914, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1028 1.96347
Completeness in resolution range: 0.943503
Completeness with d_max=infinity: 0.940784

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1033 -  4.2026 [2185/2212]  1965   220  10.1%
  bin  2:  4.2026 -  3.3477 [2096/2116]  1889   207   9.9%
  bin  3:  3.3477 -  2.9280 [2072/2091]  1863   209  10.1%
  bin  4:  2.9280 -  2.6619 [2047/2077]  1840   207  10.1%
  bin  5:  2.6619 -  2.4720 [2036/2055]  1841   195   9.6%
  bin  6:  2.4720 -  2.3268 [2024/2049]  1813   211  10.4%
  bin  7:  2.3268 -  2.2107 [2017/2045]  1818   199   9.9%
  bin  8:  2.2107 -  2.1147 [1999/2035]  1797   202  10.1%
  bin  9:  2.1147 -  2.0335 [2010/2052]  1816   194   9.7%
  bin 10:  2.0335 -  1.9635 [1103/2030]   988   115  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_863/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: 32
        2.42 -     3.04: 2216
        3.04 -     3.66: 4730
        3.66 -     4.28: 9096
        4.28 -     4.90: 12334
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.830 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  2.019 3.120 x,y-1,z
  ... (remaining 28403 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_863/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_863/model_refine_001.geo

CPU time processing inputs: 9.11


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 45.9914 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4789   r_free= 0.4720   ksol= 0.00   Bsol= 0.00   scale= 0.794    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.284191                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1033 -  4.6880 0.99   1415  158 0.4106 0.4000      6.6041      6.6297|
|  2:  4.6880 -  3.7396 0.99   1356  152 0.3966 0.3642      6.8083      6.7403|
|  3:  3.7396 -  3.2724 0.99   1345  143 0.4211 0.3996      6.6586      6.6421|
|  4:  3.2724 -  2.9757 0.99   1333  155 0.4730 0.4570      6.5328      6.5061|
|  5:  2.9757 -  2.7638 0.99   1321  149 0.5135 0.5164      6.3693       6.381|
|  6:  2.7638 -  2.6017 0.99   1307  143 0.5078 0.5179       6.281       6.211|
|  7:  2.6017 -  2.4720 0.99   1321  138 0.5226 0.4830      6.2509      6.1833|
|  8:  2.4720 -  2.3648 0.98   1291  147 0.5221 0.4732      6.1714      6.1952|
|  9:  2.3648 -  2.2741 0.98   1282  152 0.5183 0.5274      6.1179      6.1517|
| 10:  2.2741 -  2.1959 1.00   1313  142 0.5204 0.5228      6.0987      6.0774|
| 11:  2.1959 -  2.1274 0.98   1299  137 0.5011 0.5054      6.0372      6.0296|
| 12:  2.1274 -  2.0667 0.98   1283  146 0.5283 0.5923      5.9519      6.0183|
| 13:  2.0667 -  2.0125 0.98   1271  139 0.5368 0.5422      5.8778      5.8038|
| 14:  2.0125 -  1.9635 0.38    493   58 0.5675 0.4959      5.8856       5.836|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1033 -  4.6880  1415   158  0.66  37.63   0.79     0.72      83758.84|
|  2:  4.6880 -  3.7396  1356   152  0.72  33.93   0.87     0.79     104247.59|
|  3:  3.7396 -  3.2724  1345   143  0.62  42.41   0.86     0.75     109070.58|
|  4:  3.2724 -  2.9757  1333   155  0.52  50.00   0.79     0.63      98529.84|
|  5:  2.9757 -  2.7638  1321   149  0.41  59.17   0.74     0.51      84356.70|
|  6:  2.7638 -  2.6017  1307   143  0.38  61.15   0.72     0.44      74096.74|
|  7:  2.6017 -  2.4720  1321   138  0.34  64.44   0.75     0.40      67641.41|
|  8:  2.4720 -  2.3648  1291   147  0.32  65.81   0.72     0.39      61539.25|
|  9:  2.3648 -  2.2741  1282   152  0.33  64.96   0.73     0.39      55243.45|
| 10:  2.2741 -  2.1959  1313   142  0.34  64.25   0.74     0.41      49508.81|
| 11:  2.1959 -  2.1274  1299   137  0.31  66.88   0.79     0.38      49493.48|
| 12:  2.1274 -  2.0667  1283   146  0.26  71.05   0.76     0.33      46467.66|
| 13:  2.0667 -  2.0125  1271   139  0.24  72.34   0.71     0.31      40950.14|
| 14:  2.0125 -  1.9635   493    58  0.33  65.67   0.71     0.37      30109.52|
|alpha:            min =        0.31 max =            0.79 mean =         0.50|
|beta:             min =    30109.52 max =       109070.58 mean =     70427.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           90.00 mean =        57.92|
|phase err.(test): min =        0.00 max =           89.98 mean =        58.16|
|-----------------------------------------------------------------------------|

============================== 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 = 16.208800             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.400   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.373178              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.376   (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:       35 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      165 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      694 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1524 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2670 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3922 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5117 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6573 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7743 |
|-----------------------------------------------------------------------------|
|-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 |       53.554 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       1.991 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      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 = 11.775)------------------------------------------|
|    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: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4839   r_free= 0.4746   ksol= 0.00   Bsol= 0.00   scale= 0.765    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.285968                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4700   r_free= 0.4586   ksol= 0.35   Bsol= 4.81   scale= 0.997    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.75,10.24,7.61,0.00,0.00,0.00); trace/3= 8.53                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.276704                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.671439             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.620   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.331286              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.111   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4700      final r-factor (work) = 0.3915          |
| start r-factor (free) = 0.4586      final r-factor (free) = 0.4180          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 96.4851 = 13.67 * 0.50 * 6.2804 + 1.00 * 53.5542                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.5322 = 13.67 * 0.50 * 6.2014 + 1.00 * 0.1411                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3915      final r-factor (work) = 0.3472          |
| start r-factor (free) = 0.4180      final r-factor (free) = 0.4073          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2703 = 1.33 * 1.00 * 6.2014 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1728 = 1.33 * 1.00 * 6.1260 + 1.00 * 0.0174                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.83   13.73    None  None   None       |
|    all(noH): 2823   0      0.00    77.83   13.73    None  None   None       |
|    Sol.    : 438    0      0.00    77.83   24.68    None  None   None       |
|    Mac.    : 2385   0      0.00    71.34   11.72    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.783: 1078   |   5:    38.914 -  46.697:   75        |
|      1:     7.783 -  15.566:  781   |   6:    46.697 -  54.480:   31        |
|      2:    15.566 -  23.348:  461   |   7:    54.480 -  62.262:   15        |
|      3:    23.348 -  31.131:  242   |   8:    62.262 -  70.045:    5        |
|      4:    31.131 -  38.914:  133   |   9:    70.045 -  77.828:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3472 r_free = 0.4073             target_work(ml) = 6.112         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3472 r_free = 0.4070             target_work(ml) = 6.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3472   r_free= 0.4070   ksol= 0.35   Bsol= 4.81   scale= 1.111    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.75,10.24,7.61,0.00,0.00,0.00); trace/3= 8.53                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.111829                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3438   r_free= 0.4014   ksol= 0.35   Bsol= 41.08   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.31,5.84,4.46,0.00,0.00,0.00); trace/3= 4.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.111151                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.079337              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.076  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.664327              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.797  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3438      final r-factor (work) = 0.2770          |
| start r-factor (free) = 0.4014      final r-factor (free) = 0.3375          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.8709 = 8.08 * 0.50 * 6.1217 + 1.00 * 0.1411                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.4103 = 8.08 * 0.50 * 6.0217 + 1.00 * 0.0845                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2770      final r-factor (work) = 0.2585          |
| start r-factor (free) = 0.3375      final r-factor (free) = 0.3265          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0177 = 0.66 * 1.00 * 6.0217 + 1.00 * 0.0173                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9367 = 0.66 * 1.00 * 5.9003 + 1.00 * 0.0169                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.19   13.87    None  None   None       |
|    all(noH): 2823   0      0.00    80.19   13.87    None  None   None       |
|    Sol.    : 438    0      0.00    80.19   28.36    None  None   None       |
|    Mac.    : 2385   0      0.00    71.71   11.21    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 -   8.019: 1122   |   5:    40.093 -  48.111:   65        |
|      1:     8.019 -  16.037:  776   |   6:    48.111 -  56.130:   27        |
|      2:    16.037 -  24.056:  426   |   7:    56.130 -  64.148:   15        |
|      3:    24.056 -  32.074:  257   |   8:    64.148 -  72.167:    3        |
|      4:    32.074 -  40.093:  131   |   9:    72.167 -  80.185:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2585 r_free = 0.3265             target_work(ml) = 5.882         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2583 r_free = 0.3266             target_work(ml) = 5.882         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2583   r_free= 0.3266   ksol= 0.35   Bsol= 41.08   scale= 1.065   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.31,5.84,4.46,0.00,0.00,0.00); trace/3= 4.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.881823                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2570   r_free= 0.3232   ksol= 0.34   Bsol= 41.08   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.79,3.08,3.37,0.00,0.00,0.00); trace/3= 3.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.880192                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.491380              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.769  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.403584              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 102.822  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2570      final r-factor (work) = 0.1983          |
| start r-factor (free) = 0.3232      final r-factor (free) = 0.2624          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.2827 = 5.49 * 0.50 * 5.8995 + 1.00 * 0.0845                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.9241 = 5.49 * 0.50 * 5.7719 + 1.00 * 0.0763                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1983      final r-factor (work) = 0.1762          |
| start r-factor (free) = 0.2624      final r-factor (free) = 0.2326          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3455 = 0.40 * 1.00 * 5.7719 + 1.00 * 0.0161                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2700 = 0.40 * 1.00 * 5.5990 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.15   13.59    None  None   None       |
|    all(noH): 2823   0      0.00    83.15   13.59    None  None   None       |
|    Sol.    : 438    0      2.48    83.15   34.18    None  None   None       |
|    Mac.    : 2385   0      0.00    77.14   9.81     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.315: 1345   |   5:    41.575 -  49.891:  100        |
|      1:     8.315 -  16.630:  777   |   6:    49.891 -  58.206:   49        |
|      2:    16.630 -  24.945:  238   |   7:    58.206 -  66.521:    9        |
|      3:    24.945 -  33.260:  160   |   8:    66.521 -  74.836:    3        |
|      4:    33.260 -  41.575:  140   |   9:    74.836 -  83.151:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1762 r_free = 0.2326             target_work(ml) = 5.536         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1760 r_free = 0.2323             target_work(ml) = 5.535         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1760   r_free= 0.2323   ksol= 0.34   Bsol= 41.08   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.79,3.08,3.37,0.00,0.00,0.00); trace/3= 3.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.535037                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1757   r_free= 0.2316   ksol= 0.32   Bsol= 45.60   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.62,1.51,2.57,0.00,0.00,0.00); trace/3= 1.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.534413                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.427258              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.315  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.366284              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.786  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1757      final r-factor (work) = 0.1450          |
| start r-factor (free) = 0.2316      final r-factor (free) = 0.1952          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8783 = 2.43 * 0.50 * 5.6047 + 1.00 * 0.0763                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6714 = 2.43 * 0.50 * 5.4502 + 1.00 * 0.0569                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1450      final r-factor (work) = 0.1354          |
| start r-factor (free) = 0.1952      final r-factor (free) = 0.1878          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4566 = 1.37 * 1.00 * 5.4502 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3100 = 1.37 * 1.00 * 5.3404 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.74   14.35    None  None   None       |
|    all(noH): 2823   0      0.00    92.74   14.35    None  None   None       |
|    Sol.    : 438    0      2.61    89.23   40.35    None  None   None       |
|    Mac.    : 2385   0      0.00    92.74   9.57     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 -   9.274: 1576   |   5:    46.368 -  55.641:   93        |
|      1:     9.274 -  18.547:  649   |   6:    55.641 -  64.915:   66        |
|      2:    18.547 -  27.821:  169   |   7:    64.915 -  74.188:   32        |
|      3:    27.821 -  37.094:  120   |   8:    74.188 -  83.462:   10        |
|      4:    37.094 -  46.368:  103   |   9:    83.462 -  92.735:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1354 r_free = 0.1878             target_work(ml) = 5.319         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1354 r_free = 0.1876             target_work(ml) = 5.319         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1354   r_free= 0.1876   ksol= 0.32   Bsol= 45.60   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.62,1.51,2.57,0.00,0.00,0.00); trace/3= 1.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.318952                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1357   r_free= 0.1872   ksol= 0.32   Bsol= 51.56   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.55,1.18,2.52,0.00,0.00,0.00); trace/3= 1.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.317734                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.585711              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.071  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.046750              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.766  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1357      final r-factor (work) = 0.1203          |
| start r-factor (free) = 0.1872      final r-factor (free) = 0.1728          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6318 = 3.59 * 0.50 * 5.3406 + 1.00 * 0.0569                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5204 = 3.59 * 0.50 * 5.2706 + 1.00 * 0.0710                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1203      final r-factor (work) = 0.1173          |
| start r-factor (free) = 0.1728      final r-factor (free) = 0.1696          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5305 = 1.05 * 1.00 * 5.2706 + 1.00 * 0.0135                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4713 = 1.05 * 1.00 * 5.2144 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.05   14.02    None  None   None       |
|    all(noH): 2823   0      0.00    97.05   14.02    None  None   None       |
|    Sol.    : 438    0      2.41    94.52   39.77    None  None   None       |
|    Mac.    : 2385   0      0.00    97.05   9.29     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 -   9.705: 1681   |   5:    48.523 -  58.227:   88        |
|      1:     9.705 -  19.409:  591   |   6:    58.227 -  67.932:   55        |
|      2:    19.409 -  29.114:  164   |   7:    67.932 -  77.636:   28        |
|      3:    29.114 -  38.818:  114   |   8:    77.636 -  87.341:    5        |
|      4:    38.818 -  48.523:   92   |   9:    87.341 -  97.045:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1173 r_free = 0.1696             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1172 r_free = 0.1695             target_work(ml) = 5.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1172   r_free= 0.1695   ksol= 0.32   Bsol= 51.56   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.55,1.18,2.52,0.00,0.00,0.00); trace/3= 1.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.204476                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1033 -  4.6880 0.99   1415  158 0.0961 0.1321      5.3688      5.5933|
|  2:  4.6880 -  3.7396 0.99   1356  152 0.0852 0.1154      5.4487      5.6665|
|  3:  3.7396 -  3.2724 0.99   1345  143 0.1095 0.1553      5.5121      5.8647|
|  4:  3.2724 -  2.9757 0.99   1333  155 0.1308 0.1834      5.5114      5.6831|
|  5:  2.9757 -  2.7638 0.99   1321  149 0.1401 0.1825      5.3744      5.6154|
|  6:  2.7638 -  2.6017 0.99   1307  143 0.1275 0.1996      5.2492      5.5204|
|  7:  2.6017 -  2.4720 0.99   1321  138 0.1324 0.1755      5.2224      5.3913|
|  8:  2.4720 -  2.3648 0.98   1291  147 0.1254 0.1857      5.1374      5.4236|
|  9:  2.3648 -  2.2741 0.98   1282  152 0.1295 0.2020      5.1192      5.3983|
| 10:  2.2741 -  2.1959 1.00   1313  142 0.1199 0.1807      5.0261      5.2476|
| 11:  2.1959 -  2.1274 0.98   1299  137 0.1192 0.2067      5.0232      5.4109|
| 12:  2.1274 -  2.0667 0.98   1283  146 0.1212 0.1782      4.9455      5.2011|
| 13:  2.0667 -  2.0125 0.98   1271  139 0.1203 0.1838      4.8464      5.0787|
| 14:  2.0125 -  1.9635 0.38    493   58 0.1049 0.1492      4.7174      4.9027|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1033 -  4.6880  1415   158  0.93   9.67   0.98     0.95       7581.86|
|  2:  4.6880 -  3.7396  1356   152  0.95   8.41   1.02     1.01       9795.09|
|  3:  3.7396 -  3.2724  1345   143  0.93  12.20   1.04     1.03      11539.30|
|  4:  3.2724 -  2.9757  1333   155  0.90  15.44   1.02     0.99      11897.35|
|  5:  2.9757 -  2.7638  1321   149  0.89  17.22   1.00     0.98       9359.72|
|  6:  2.7638 -  2.6017  1307   143  0.89  17.41   0.98     0.96       7888.86|
|  7:  2.6017 -  2.4720  1321   138  0.90  16.61   1.00     0.96       7031.62|
|  8:  2.4720 -  2.3648  1291   147  0.89  17.39   0.98     0.96       6332.24|
|  9:  2.3648 -  2.2741  1282   152  0.89  17.63   1.00     0.95       6110.49|
| 10:  2.2741 -  2.1959  1313   142  0.89  17.73   1.00     0.96       5334.84|
| 11:  2.1959 -  2.1274  1299   137  0.89  17.94   0.99     0.94       5250.11|
| 12:  2.1274 -  2.0667  1283   146  0.89  17.89   1.01     1.00       4776.21|
| 13:  2.0667 -  2.0125  1271   139  0.88  18.38   0.99     0.97       3948.61|
| 14:  2.0125 -  1.9635   493    58  0.91  15.65   0.98     0.96       3022.45|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     3022.45 max =        11897.35 mean =      7363.78|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.91 mean =        15.61|
|phase err.(test): min =        0.00 max =           89.97 mean =        14.96|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1172   r_free= 0.1694   ksol= 0.32   Bsol= 50.69   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.19,-0.63,0.82,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.204529                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1172   r_free= 0.1694   ksol= 0.32   Bsol= 50.69   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.19,-0.63,0.82,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.204529                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1033 -  4.6880 0.99   1415  158 0.0960 0.1322      5.3692      5.5939|
|  2:  4.6880 -  3.7396 0.99   1356  152 0.0851 0.1151      5.4478      5.6643|
|  3:  3.7396 -  3.2724 0.99   1345  143 0.1093 0.1553      5.5111      5.8639|
|  4:  3.2724 -  2.9757 0.99   1333  155 0.1308 0.1835      5.5114      5.6834|
|  5:  2.9757 -  2.7638 0.99   1321  149 0.1402 0.1826      5.3745      5.6155|
|  6:  2.7638 -  2.6017 0.99   1307  143 0.1276 0.1996      5.2495      5.5202|
|  7:  2.6017 -  2.4720 0.99   1321  138 0.1324 0.1756      5.2228      5.3917|
|  8:  2.4720 -  2.3648 0.98   1291  147 0.1254 0.1858      5.1378      5.4242|
|  9:  2.3648 -  2.2741 0.98   1282  152 0.1296 0.2017      5.1195      5.3975|
| 10:  2.2741 -  2.1959 1.00   1313  142 0.1199 0.1809      5.0266      5.2494|
| 11:  2.1959 -  2.1274 0.98   1299  137 0.1192 0.2068      5.0236      5.4111|
| 12:  2.1274 -  2.0667 0.98   1283  146 0.1211 0.1782      4.9456      5.2016|
| 13:  2.0667 -  2.0125 0.98   1271  139 0.1204 0.1837      4.8464       5.078|
| 14:  2.0125 -  1.9635 0.38    493   58 0.1047 0.1491      4.7168      4.9028|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1033 -  4.6880  1415   158  0.93   9.68   0.98     0.95       7593.93|
|  2:  4.6880 -  3.7396  1356   152  0.95   8.40   1.02     1.01       9784.16|
|  3:  3.7396 -  3.2724  1345   143  0.93  12.18   1.04     1.03      11508.94|
|  4:  3.2724 -  2.9757  1333   155  0.90  15.43   1.02     1.00      11887.55|
|  5:  2.9757 -  2.7638  1321   149  0.89  17.22   1.01     0.98       9357.51|
|  6:  2.7638 -  2.6017  1307   143  0.89  17.42   0.99     0.96       7893.57|
|  7:  2.6017 -  2.4720  1321   138  0.90  16.62   1.00     0.97       7037.69|
|  8:  2.4720 -  2.3648  1291   147  0.89  17.41   0.99     0.96       6336.82|
|  9:  2.3648 -  2.2741  1282   152  0.89  17.64   1.01     0.96       6113.14|
| 10:  2.2741 -  2.1959  1313   142  0.89  17.74   1.00     0.96       5342.08|
| 11:  2.1959 -  2.1274  1299   137  0.88  17.96   1.00     0.94       5258.92|
| 12:  2.1274 -  2.0667  1283   146  0.89  17.91   1.02     1.01       4781.13|
| 13:  2.0667 -  2.0125  1271   139  0.88  18.39   1.00     0.98       3949.04|
| 14:  2.0125 -  1.9635   493    58  0.91  15.64   0.99     0.97       3018.93|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     3018.93 max =        11887.55 mean =      7363.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.91 mean =        15.61|
|phase err.(test): min =        0.00 max =           89.90 mean =        14.97|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.90    98.94   15.92    None  None   None       |
|    all(noH): 2823   0      1.90    98.94   15.92    None  None   None       |
|    Sol.    : 438    0      4.30    96.42   41.66    None  None   None       |
|    Mac.    : 2385   0      1.90    98.94   11.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.895 -  11.600: 1681   |   5:    50.418 -  60.122:   88        |
|      1:    11.600 -  21.304:  591   |   6:    60.122 -  69.827:   55        |
|      2:    21.304 -  31.009:  164   |   7:    69.827 -  79.531:   28        |
|      3:    31.009 -  40.713:  114   |   8:    79.531 -  89.236:    5        |
|      4:    40.713 -  50.418:   92   |   9:    89.236 -  98.940:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 337         
Filter by distance & map next to the model:
   mapped sites are within: 0.323 - 5.738
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 336 from: 337
   mapped sites are within: 0.713 - 5.738

peak=    9.962 closest distance to " CB  VAL A 230 " =    1.452
peak=    8.192 closest distance to " O   HOH Z 130 " =    1.650
peak=    7.031 closest distance to " CG2 VAL A 296 " =    1.152
peak=    6.780 closest distance to " CD2 LEU A   5 " =    1.272
peak=    6.231 closest distance to " CG  ARG A 138 " =    1.066
peak=    6.198 closest distance to " NE2 GLN A  11 " =    1.171
peak=    6.193 closest distance to " O   HOH Z  65 " =    1.429
peak=    5.294 closest distance to " O   HOH Z   9 " =    1.693
peak=    5.269 closest distance to " CG  PRO A  54 " =    1.334
peak=    5.252 closest distance to " O   HOH Z 222 " =    1.352
peak=    5.244 closest distance to " NH2 ARG A  56 " =    2.087
peak=    5.160 closest distance to " O   HOH Z 142 " =    1.996
peak=    5.134 closest distance to " CG  LEU A 228 " =    1.186
peak=    5.051 closest distance to " CG  LEU A   5 " =    1.181
peak=    5.025 closest distance to " O   HOH Z 427 " =    2.351
peak=    4.991 closest distance to " O   HOH Z 232 " =    2.242
peak=    4.979 closest distance to " CB  GLN A 183 " =    1.253
peak=    4.899 closest distance to " O   HOH Z 427 " =    1.157
peak=    4.888 closest distance to " O   HOH Z 424 " =    1.181
peak=    4.851 closest distance to " CD1AILE A 234 " =    1.004
peak=    4.841 closest distance to " O   HOH Z 425 " =    1.726
peak=    4.836 closest distance to " CB  VAL A 230 " =    1.191
peak=    4.835 closest distance to " O   HOH Z   7 " =    1.564
peak=    4.822 closest distance to " O   HOH Z 126 " =    2.102
peak=    4.775 closest distance to " CB  VAL A 296 " =    1.150
peak=    4.753 closest distance to " O   HOH Z  63 " =    1.636
peak=    4.751 closest distance to " CB  PRO A  54 " =    1.026
peak=    4.751 closest distance to " O   HOH Z 139 " =    1.452
peak=    4.579 closest distance to " O   HOH Z 287 " =    1.835
peak=    4.561 closest distance to " O   HOH Z 369 " =    2.049
peak=    4.542 closest distance to " O   HOH Z 417 " =    1.486
peak=    4.541 closest distance to " O   HOH Z 410 " =    1.440
peak=    4.490 closest distance to " CB  GLN A 223 " =    1.516
peak=    4.452 closest distance to " O   PRO A 198 " =    1.288
peak=    4.441 closest distance to " CB  SER A  63 " =    1.282
peak=    4.438 closest distance to " CG  LEU A 167 " =    1.223
peak=    4.438 closest distance to " O   HOH Z 298 " =    1.909
peak=    4.399 closest distance to " CB  SER A   3 " =    1.498
peak=    4.385 closest distance to " O   HOH Z   2 " =    1.865
peak=    4.381 closest distance to " O   HOH Z 193 " =    1.780
peak=    4.348 closest distance to " O   HOH Z 361 " =    1.466
peak=    4.320 closest distance to " CD2 LEU A 228 " =    1.186
peak=    4.312 closest distance to " O   HOH Z 414 " =    1.315
peak=    4.274 closest distance to " O   SER A  87 " =    2.407
peak=    4.258 closest distance to " O   HOH Z 392 " =    1.358
peak=    4.245 closest distance to " O   HOH Z  78 " =    1.574
peak=    4.230 closest distance to " CB  ASN A 148 " =    1.434
peak=    4.205 closest distance to " O   HOH Z 127 " =    1.069
peak=    4.161 closest distance to " CD2 TRP A 179 " =    2.204
peak=    4.143 closest distance to " O   HOH Z 225 " =    1.500
peak=    4.142 closest distance to " O   HOH Z 316 " =    3.012
peak=    4.136 closest distance to " O   HOH Z 380 " =    1.853
peak=    4.115 closest distance to " NH1 ARG A 138 " =    0.984
peak=    4.112 closest distance to " CB  ASP A 124 " =    0.828
peak=    4.106 closest distance to " O   HOH Z  59 " =    1.691
peak=    4.102 closest distance to " CB  VAL A 202 " =    1.649
peak=    4.095 closest distance to " O   HOH Z 375 " =    0.916
peak=    4.089 closest distance to " O   HOH Z  61 " =    1.571
peak=    4.087 closest distance to " CB  ARG A 275 " =    0.967
peak=    4.085 closest distance to " CG  PRO A 213 " =    1.234
peak=    4.079 closest distance to " O   HOH Z 209 " =    2.392
peak=    4.060 closest distance to " CG  PRO A 198 " =    1.223
peak=    4.045 closest distance to " O   HOH Z 124 " =    1.273
peak=    4.039 closest distance to " CB  SER A 216 " =    0.987
peak=    4.035 closest distance to " O   HOH Z 371 " =    2.682
peak=    4.022 closest distance to " CD  GLN A 240 " =    1.569
peak=    3.981 closest distance to " O   HOH Z 133 " =    1.545
peak=    3.975 closest distance to " O   HOH Z 214 " =    2.078
peak=    3.970 closest distance to " CG  GLN A  88 " =    1.227
peak=    3.955 closest distance to " CB  TRP A 266 " =    1.079
peak=    3.917 closest distance to " O   HOH Z 193 " =    1.680
peak=    3.903 closest distance to " O   HOH Z 217 " =    2.912
peak=    3.902 closest distance to " O   HOH Z  24 " =    1.936
peak=    3.890 closest distance to " O   HOH Z 418 " =    0.967
peak=    3.887 closest distance to " OG BSER A  99 " =    2.125
peak=    3.877 closest distance to " O   HOH Z 411 " =    3.318
peak=    3.869 closest distance to " O   HOH Z 419 " =    1.988
peak=    3.855 closest distance to " O   HOH Z 236 " =    1.678
peak=    3.853 closest distance to " NH1AARG A 145 " =    1.051
peak=    3.837 closest distance to " O   HOH Z 195 " =    1.484
peak=    3.835 closest distance to " O   HOH Z 222 " =    1.909
peak=    3.833 closest distance to " O   ASN A 209 " =    1.582
peak=    3.828 closest distance to " CA  ASN A 127 " =    1.082
peak=    3.824 closest distance to " O   HOH Z  59 " =    2.022
peak=    3.818 closest distance to " OG  SER A  62 " =    3.123
peak=    3.808 closest distance to " O   HOH Z 423 " =    1.583
peak=    3.795 closest distance to " CE3 TRP A 274 " =    2.408
peak=    3.787 closest distance to " O   HOH Z 352 " =    1.556
peak=    3.786 closest distance to " CB  ASN A  39 " =    0.980
peak=    3.781 closest distance to " CB  LEU A 237 " =    0.878
peak=    3.779 closest distance to " CG  LYS A  76 " =    1.686
peak=    3.773 closest distance to " O   HOH Z 234 " =    3.805
peak=    3.772 closest distance to " OD2 ASP A 286 " =    2.697
peak=    3.770 closest distance to " CB  GLU A 128 " =    1.117
peak=    3.768 closest distance to " O   HOH Z 158 " =    2.833
peak=    3.767 closest distance to " O   HOH Z 184 " =    1.438
peak=    3.764 closest distance to " CA  GLY A 267 " =    1.116
peak=    3.758 closest distance to " CG2 THR A 221 " =    1.176
peak=    3.757 closest distance to " O   HOH Z   1 " =    1.891
peak=    3.746 closest distance to " CB  LEU A 228 " =    1.311
peak=    3.742 closest distance to " CB  GLU A 277 " =    3.592
peak=    3.735 closest distance to " O   HOH Z 425 " =    1.990
peak=    3.720 closest distance to " O   HOH Z 122 " =    2.125
peak=    3.718 closest distance to " CG1 ILE A 151 " =    1.111
peak=    3.706 closest distance to " O   MET A 105 " =    1.663
peak=    3.699 closest distance to " CG  GLN A  11 " =    2.207
peak=    3.686 closest distance to " O   HOH Z 359 " =    1.255
peak=    3.686 closest distance to " O   HOH Z 193 " =    1.888
peak=    3.685 closest distance to " CB AVAL A  41 " =    1.232
peak=    3.675 closest distance to " CD  ARG A  66 " =    2.479
peak=    3.673 closest distance to " O   HOH Z  55 " =    1.870
peak=    3.673 closest distance to " O   HOH Z  88 " =    3.468
peak=    3.659 closest distance to " O   HOH Z  58 " =    1.823
peak=    3.654 closest distance to " O   HOH Z 133 " =    2.605
peak=    3.647 closest distance to " OG  SER A  62 " =    2.846
peak=    3.645 closest distance to " CA  ALA A  51 " =    1.079
peak=    3.635 closest distance to " CD  ARG A 159 " =    0.723
peak=    3.629 closest distance to " O   HOH Z 422 " =    2.661
peak=    3.619 closest distance to " CA  SER A  87 " =    0.963
peak=    3.618 closest distance to " CA  ASN A 215 " =    1.266
peak=    3.615 closest distance to " O   HOH Z 207 " =    2.303
peak=    3.613 closest distance to " CB  MET A  40 " =    0.898
peak=    3.612 closest distance to " O   HOH Z 132 " =    1.080
peak=    3.610 closest distance to " O   HOH Z 438 " =    2.215
peak=    3.593 closest distance to " O   HOH Z 403 " =    1.537
peak=    3.592 closest distance to " O   HOH Z 368 " =    2.046
peak=    3.592 closest distance to " CD BLYS A 290 " =    1.083
peak=    3.586 closest distance to " CB  VAL A 265 " =    1.322
peak=    3.585 closest distance to " O   HOH Z 305 " =    3.430
peak=    3.583 closest distance to " N   PHE A 130 " =    1.283
peak=    3.582 closest distance to " O   HOH Z 405 " =    1.496
peak=    3.582 closest distance to " CB  TRP A 179 " =    1.489
peak=    3.577 closest distance to " CG2 ILE A 234 " =    0.902
peak=    3.573 closest distance to " N   GLN A 278 " =    1.278
peak=    3.569 closest distance to " O   HOH Z 133 " =    2.480
peak=    3.565 closest distance to " O   HOH Z 181 " =    2.293
peak=    3.564 closest distance to " CB  GLU A 152 " =    1.437
peak=    3.558 closest distance to " CA  ILE A 234 " =    1.008
peak=    3.555 closest distance to " CE1 TYR A 186 " =    1.343
peak=    3.549 closest distance to " N   SER A 271 " =    0.972
peak=    3.543 closest distance to " NE AARG A 275 " =    1.413
peak=    3.541 closest distance to " CB  GLN A  88 " =    1.373
peak=    3.529 closest distance to " O   HOH Z 156 " =    3.131
peak=    3.529 closest distance to " O   HOH Z  68 " =    2.062
peak=    3.516 closest distance to " CA  LYS A 117 " =    1.160
peak=    3.515 closest distance to " CB  ILE A 234 " =    1.069
peak=    3.513 closest distance to " O   HOH Z 289 " =    1.675
peak=    3.510 closest distance to " CG BARG A 102 " =    1.978
peak=    3.508 closest distance to " CB  GLN A  89 " =    1.222
peak=    3.504 closest distance to " O   HOH Z 389 " =    1.751
peak=    3.503 closest distance to " O   HOH Z 126 " =    1.493
peak=    3.503 closest distance to " O   HOH Z 258 " =    2.116
peak=    3.492 closest distance to " CB  SER A 276 " =    1.114
peak=    3.491 closest distance to " O   HOH Z 167 " =    1.837
peak=    3.490 closest distance to " N   ALA A 256 " =    1.064
peak=    3.484 closest distance to " CE  MET A  93 " =    1.428
peak=    3.479 closest distance to " CA  PHE A 283 " =    1.348
peak=    3.474 closest distance to " CA  LEU A 101 " =    1.488
peak=    3.474 closest distance to " CB  THR A 157 " =    1.119
peak=    3.474 closest distance to " O   HOH Z 327 " =    1.568
peak=    3.473 closest distance to " CD1 ILE A  33 " =    1.767
peak=    3.465 closest distance to " O   HOH Z 175 " =    2.095
peak=    3.459 closest distance to " CD  LYS A 166 " =    1.439
peak=    3.458 closest distance to " O   HOH Z  32 " =    2.230
peak=    3.457 closest distance to " NZ BLYS A 290 " =    1.008
peak=    3.454 closest distance to " CD  ARG A 138 " =    1.205
peak=    3.454 closest distance to " O   HOH Z 424 " =    2.549
peak=    3.452 closest distance to " O   HOH Z 384 " =    1.278
peak=    3.450 closest distance to " O   HOH Z 290 " =    0.921
peak=    3.448 closest distance to " CA  ALA A 299 " =    0.944
peak=    3.446 closest distance to " CA  TYR A  30 " =    0.986
peak=    3.441 closest distance to " ND1 HIS A  81 " =    1.679
peak=    3.436 closest distance to " O   HOH Z  10 " =    1.732
peak=    3.433 closest distance to " O   HOH Z  40 " =    2.016
peak=    3.427 closest distance to " O   HOH Z  44 " =    2.562
peak=    3.426 closest distance to " CB  ARG A 190 " =    1.727
peak=    3.426 closest distance to " CG1BVAL A  72 " =    0.741
peak=    3.424 closest distance to " O   HOH Z 213 " =    2.056
peak=    3.424 closest distance to " O   HOH Z 323 " =    1.630
peak=    3.423 closest distance to " CB  SER A 212 " =    1.293
peak=    3.422 closest distance to " CD1 LEU A 300 " =    1.237
peak=    3.420 closest distance to " O   PRO A 198 " =    1.522
peak=    3.418 closest distance to " CB  ALA A 114 " =    1.507
peak=    3.418 closest distance to " NE2 GLN A  58 " =    3.688
peak=    3.413 closest distance to " CG  GLN A  89 " =    1.483
peak=    3.411 closest distance to " O   HOH Z 385 " =    3.639
peak=    3.410 closest distance to " CG1 ILE A  33 " =    1.285
peak=    3.409 closest distance to " O   GLY A 302 " =    2.198
peak=    3.409 closest distance to " CG  ARG A 159 " =    1.034
peak=    3.406 closest distance to " O   HOH Z 313 " =    1.504
peak=    3.406 closest distance to " OE2 GLU A   2 " =    1.809
peak=    3.406 closest distance to " O   HOH Z 334 " =    1.488
peak=    3.403 closest distance to " O   HOH Z 209 " =    2.447
peak=    3.402 closest distance to " O   HOH Z 345 " =    3.306
peak=    3.401 closest distance to " O   HOH Z 154 " =    1.938
peak=    3.397 closest distance to " O   HOH Z 368 " =    3.708
peak=    3.396 closest distance to " O   HOH Z 233 " =    1.567
peak=    3.396 closest distance to " CB  ASN A 142 " =    0.913
peak=    3.395 closest distance to " O   HOH Z 128 " =    1.852
peak=    3.392 closest distance to " O   HOH Z 189 " =    2.685
peak=    3.388 closest distance to " N   ASN A 127 " =    1.372
peak=    3.387 closest distance to " O   HOH Z   6 " =    2.036
peak=    3.385 closest distance to " CA  ALA A 160 " =    0.944
peak=    3.383 closest distance to " O   HOH Z  20 " =    1.550
peak=    3.377 closest distance to " CG  PRO A 243 " =    1.139
peak=    3.377 closest distance to " NH2BARG A 145 " =    2.166
peak=    3.371 closest distance to " O   HOH Z 119 " =    1.487
peak=    3.371 closest distance to " CB  ASN A 187 " =    1.088
peak=    3.369 closest distance to " O   HOH Z  55 " =    1.640
peak=    3.360 closest distance to " OE2 GLU A  53 " =    1.917
peak=    3.359 closest distance to " ND2 ASN A 187 " =    1.685
peak=    3.358 closest distance to " O   HOH Z 373 " =    1.459
peak=    3.353 closest distance to " N   GLU A   2 " =    1.410
peak=    3.351 closest distance to " O   HOH Z 108 " =    2.520
peak=    3.349 closest distance to " O   HOH Z 356 " =    1.430
peak=    3.347 closest distance to " O   HOH Z 144 " =    2.577
peak=    3.344 closest distance to " CE BMET A  47 " =    1.060
peak=    3.344 closest distance to " CE3 TRP A 150 " =    1.057
peak=    3.342 closest distance to " O   HOH Z  97 " =    1.887
peak=    3.341 closest distance to " CB  HIS A 108 " =    0.826
peak=    3.338 closest distance to " CA  TYR A 116 " =    1.425
peak=    3.337 closest distance to " O   HOH Z 272 " =    1.817
peak=    3.332 closest distance to " ND2 ASN A 110 " =    1.825
peak=    3.331 closest distance to " O   HOH Z 132 " =    2.300
peak=    3.329 closest distance to " O   HOH Z 145 " =    2.114
peak=    3.328 closest distance to " O   HOH Z 268 " =    0.993
peak=    3.327 closest distance to " O   HOH Z  44 " =    1.926
peak=    3.325 closest distance to " CH2 TRP A 266 " =    1.109
peak=    3.325 closest distance to " N   TYR A  15 " =    1.024
peak=    3.322 closest distance to " CB  ALA A   1 " =    4.665
peak=    3.317 closest distance to " NE AARG A 145 " =    1.241
peak=    3.310 closest distance to " NH2BARG A 190 " =    1.491
peak=    3.309 closest distance to " OG BSER A 212 " =    2.700
peak=    3.309 closest distance to " CB  ASN A 110 " =    1.075
peak=    3.305 closest distance to " CH2 TRP A 150 " =    0.918
peak=    3.302 closest distance to " NE1 TRP A 274 " =    0.957
peak=    3.300 closest distance to " O   HOH Z 329 " =    3.137
peak=    3.298 closest distance to " CB  LEU A 143 " =    1.033
peak=    3.296 closest distance to " CG1 ILE A 120 " =    1.442
peak=    3.295 closest distance to " CB  ASP A 140 " =    1.026
peak=    3.295 closest distance to " OD1 ASN A 217 " =    1.723
peak=    3.295 closest distance to " CA  ASN A  74 " =    1.209
peak=    3.294 closest distance to " CB  ARG A 139 " =    1.071
peak=    3.293 closest distance to " NH2AARG A 190 " =    1.722
peak=    3.288 closest distance to " CB  GLU A 236 " =    1.104
peak=    3.288 closest distance to " O   HOH Z 222 " =    2.157
peak=    3.285 closest distance to " O   HOH Z 217 " =    1.562
peak=    3.277 closest distance to " CB  TYR A 169 " =    0.713
peak=    3.273 closest distance to " CG1 ILE A 263 " =    1.235
peak=    3.272 closest distance to " O   HOH Z 302 " =    1.507
peak=    3.265 closest distance to " O   HOH Z 371 " =    1.832
peak=    3.264 closest distance to " O   HOH Z 329 " =    3.904
peak=    3.263 closest distance to " O   HOH Z 189 " =    3.137
peak=    3.260 closest distance to " O   HOH Z 153 " =    3.667
peak=    3.260 closest distance to " O   HOH Z 146 " =    1.653
peak=    3.252 closest distance to " CB  LEU A 300 " =    0.874
peak=    3.251 closest distance to " N   ALA A   1 " =    1.177
peak=    3.250 closest distance to " CA  ALA A 158 " =    1.125
peak=    3.249 closest distance to " O   HOH Z 115 " =    1.386
peak=    3.246 closest distance to " NZ  LYS A 117 " =    1.264
peak=    3.241 closest distance to " O   HOH Z 183 " =    1.322
peak=    3.234 closest distance to " CA  ALA A 291 " =    0.971
peak=    3.233 closest distance to " CD  PRO A 243 " =    1.550
peak=    3.232 closest distance to " O   HOH Z 345 " =    1.806
peak=    3.223 closest distance to " N   ARG A 156 " =    1.238
peak=    3.219 closest distance to " CB  PHE A 225 " =    1.508
peak=    3.215 closest distance to " O   HOH Z  76 " =    1.108
peak=    3.213 closest distance to " O   HOH Z 412 " =    5.176
peak=    3.210 closest distance to " ND2BASN A 224 " =    0.845
peak=    3.206 closest distance to " CA  ALA A 248 " =    1.237
peak=    3.206 closest distance to " O   HOH Z  22 " =    2.096
peak=    3.206 closest distance to " N   CYS A 260 " =    0.852
peak=    3.204 closest distance to " CA  THR A 221 " =    0.945
peak=    3.202 closest distance to " O   HOH Z 109 " =    2.182
peak=    3.202 closest distance to " NE  ARG A  56 " =    3.506
peak=    3.201 closest distance to " O   HOH Z 128 " =    2.097
peak=    3.201 closest distance to " O   HOH Z 148 " =    2.378
peak=    3.196 closest distance to " OG1 THR A 221 " =    1.504
peak=    3.195 closest distance to " O   HOH Z 362 " =    2.157
peak=    3.193 closest distance to " CB  SER A 210 " =    0.942
peak=    3.193 closest distance to " CA  MET A  47 " =    1.155
peak=    3.187 closest distance to " CG  GLN A 278 " =    3.809
peak=    3.186 closest distance to " O   HOH Z  51 " =    1.311
peak=    3.186 closest distance to " O   HOH Z 130 " =    2.724
peak=    3.184 closest distance to " CD1 LEU A 167 " =    1.222
peak=    3.182 closest distance to " CA  ARG A 195 " =    1.308
peak=    3.179 closest distance to " CA  ALA A 114 " =    1.935
peak=    3.175 closest distance to " CA  ARG A 156 " =    1.077
peak=    3.174 closest distance to " O   HOH Z  61 " =    1.607
peak=    3.173 closest distance to " CB  THR A  82 " =    1.173
peak=    3.166 closest distance to " O   HOH Z 244 " =    1.642
peak=    3.165 closest distance to " N   ILE A  33 " =    1.088
peak=    3.164 closest distance to " O   HOH Z 145 " =    1.821
peak=    3.161 closest distance to " CG1BVAL A  72 " =    0.842
peak=    3.160 closest distance to " N   SER A 135 " =    1.268
peak=    3.160 closest distance to " ND2 ASN A 249 " =    0.772
peak=    3.159 closest distance to " CE3 TRP A  85 " =    1.281
peak=    3.157 closest distance to " O   HOH Z 303 " =    2.821
peak=    3.153 closest distance to " CG BARG A 190 " =    1.223
peak=    3.149 closest distance to " O   HOH Z   9 " =    1.645
peak=    3.148 closest distance to " O   HOH Z 367 " =    2.389
peak=    3.147 closest distance to " O   HOH Z 273 " =    2.710
peak=    3.146 closest distance to " O   HOH Z 392 " =    2.089
peak=    3.145 closest distance to " O   HOH Z 409 " =    2.384
peak=    3.144 closest distance to " CZ3 TRP A  92 " =    1.202
peak=    3.133 closest distance to " CG2 ILE A  20 " =    1.738
peak=    3.123 closest distance to " CB  GLU A 152 " =    1.428
peak=    3.118 closest distance to " O   HOH Z 272 " =    2.255
peak=    3.117 closest distance to " O   HOH Z 180 " =    2.097
peak=    3.117 closest distance to " CB  LYS A 290 " =    1.276
peak=    3.113 closest distance to " CZ  PHE A 192 " =    0.927
peak=    3.112 closest distance to " OG BSER A 164 " =    2.212
peak=    3.111 closest distance to " O   HOH Z 263 " =    1.586
peak=    3.111 closest distance to " NE2 GLN A  58 " =    5.738
peak=    3.110 closest distance to " O   ALA A 158 " =    1.364
peak=    3.110 closest distance to " O   HOH Z 357 " =    2.145
peak=    3.110 closest distance to " CA  LEU A 282 " =    0.992
peak=    3.105 closest distance to " CA  ILE A 106 " =    0.743
peak=    3.104 closest distance to " O   HOH Z  39 " =    1.194
peak=    3.103 closest distance to " O   ALA A 233 " =    1.808
peak=    3.091 closest distance to " CA  ALA A 233 " =    1.109
peak=    3.090 closest distance to " O   HOH Z 334 " =    3.034
peak=    3.089 closest distance to " CG2 ILE A 151 " =    0.814
peak=    3.086 closest distance to " O   HOH Z 325 " =    3.640
peak=    3.082 closest distance to " O   HOH Z 171 " =    2.858
peak=    3.080 closest distance to " CA  THR A 264 " =    0.795
peak=    3.079 closest distance to " O   HOH Z   1 " =    1.738
peak=    3.079 closest distance to " CD  ARG A 195 " =    0.762
peak=    3.075 closest distance to " O   HOH Z 285 " =    2.745
peak=    3.074 closest distance to " OG  SER A  22 " =    2.947
peak=    3.070 closest distance to " O   THR A 294 " =    1.087
peak=    3.067 closest distance to " O   HOH Z 271 " =    1.942
peak=    3.051 closest distance to " CB  LYS A 117 " =    1.212
peak=    3.043 closest distance to " CB  LEU A 143 " =    0.989
peak=    3.024 closest distance to " O   HOH Z 418 " =    1.429
peak=    3.021 closest distance to " O   HOH Z  88 " =    3.398

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 213         
Filter by distance & map next to the model:
   mapped sites are within: 0.611 - 5.971
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 213
   mapped sites are within: 0.774 - 5.971

peak=   -4.690 closest distance to " OG BSER A 134 " =    1.575
peak=   -4.655 closest distance to " CG2 VAL A 230 " =    0.774
peak=   -4.404 closest distance to " CD  ARG A  14 " =    3.036
peak=   -4.222 closest distance to " N   THR A 157 " =    1.546
peak=   -4.150 closest distance to " O   HOH Z 266 " =    4.826
peak=   -4.090 closest distance to " CD  ARG A 156 " =    1.988
peak=   -4.085 closest distance to " O   HOH Z 131 " =    3.955
peak=   -4.061 closest distance to " CG2 VAL A 296 " =    1.219
peak=   -4.053 closest distance to " OG  SER A  87 " =    1.359
peak=   -4.032 closest distance to " CE2 PHE A 218 " =    2.494
peak=   -4.013 closest distance to " CB  PRO A 243 " =    2.589
peak=   -4.006 closest distance to " O   PRO A 198 " =    1.228
peak=   -3.973 closest distance to " CB  ALA A  43 " =    2.381
peak=   -3.955 closest distance to " O   HOH Z  43 " =    1.791
peak=   -3.936 closest distance to " OE1 GLU A 277 " =    2.307
peak=   -3.930 closest distance to " CD  LYS A 289 " =    2.381
peak=   -3.879 closest distance to " O   HOH Z 198 " =    2.442
peak=   -3.865 closest distance to " CG  ARG A 138 " =    1.014
peak=   -3.864 closest distance to " O   HOH Z  52 " =    1.420
peak=   -3.854 closest distance to " O   SER A  22 " =    2.576
peak=   -3.843 closest distance to " CE2 TYR A  30 " =    2.529
peak=   -3.841 closest distance to " O   HOH Z 231 " =    1.790
peak=   -3.797 closest distance to " CD1 LEU A 101 " =    2.251
peak=   -3.793 closest distance to " CD2 LEU A   5 " =    0.943
peak=   -3.785 closest distance to " NH2 ARG A  79 " =    1.999
peak=   -3.776 closest distance to " O   HOH Z 185 " =    2.082
peak=   -3.773 closest distance to " O   HOH Z 377 " =    1.772
peak=   -3.770 closest distance to " CD1 LEU A 255 " =    2.964
peak=   -3.754 closest distance to " O   HOH Z 409 " =    5.971
peak=   -3.748 closest distance to " O   PRO A 243 " =    2.408
peak=   -3.733 closest distance to " N   ALA A  43 " =    2.601
peak=   -3.726 closest distance to " O   SER A 135 " =    1.550
peak=   -3.721 closest distance to " CG  GLN A 223 " =    2.394
peak=   -3.708 closest distance to " CB  ASN A  39 " =    2.117
peak=   -3.702 closest distance to " CB  ASP A 132 " =    2.380
peak=   -3.702 closest distance to " O   HOH Z 350 " =    1.776
peak=   -3.695 closest distance to " CB  ALA A 227 " =    2.365
peak=   -3.683 closest distance to " CA  GLY A  98 " =    1.816
peak=   -3.675 closest distance to " O   PRO A 163 " =    1.931
peak=   -3.672 closest distance to " O   HOH Z 352 " =    2.075
peak=   -3.666 closest distance to " CA  GLY A 133 " =    2.013
peak=   -3.659 closest distance to " O   HOH Z 389 " =    2.004
peak=   -3.658 closest distance to " CB  ASP A  27 " =    2.399
peak=   -3.654 closest distance to " CB  PRO A  54 " =    2.403
peak=   -3.641 closest distance to " CB  ALA A   9 " =    2.413
peak=   -3.638 closest distance to " O   HOH Z  11 " =    1.881
peak=   -3.629 closest distance to " CZ2 TRP A 274 " =    0.893
peak=   -3.626 closest distance to " OG ASER A 134 " =    1.165
peak=   -3.624 closest distance to " O   HOH Z 407 " =    3.183
peak=   -3.623 closest distance to " O   HOH Z 103 " =    1.484
peak=   -3.620 closest distance to " O   HOH Z 359 " =    1.624
peak=   -3.609 closest distance to " O   HOH Z 211 " =    1.387
peak=   -3.594 closest distance to " O   HOH Z 166 " =    1.464
peak=   -3.578 closest distance to " O   ALA A  84 " =    1.743
peak=   -3.576 closest distance to " CB  ALA A 248 " =    2.019
peak=   -3.571 closest distance to " O   HOH Z 348 " =    1.855
peak=   -3.570 closest distance to " O   GLY A  80 " =    2.437
peak=   -3.567 closest distance to " O   HOH Z 352 " =    1.685
peak=   -3.563 closest distance to " CE2 TYR A 116 " =    3.077
peak=   -3.563 closest distance to " O   GLY A 203 " =    2.527
peak=   -3.562 closest distance to " O   SER A 141 " =    1.825
peak=   -3.553 closest distance to " O   MET A  40 " =    2.835
peak=   -3.540 closest distance to " O   HOH Z 216 " =    1.855
peak=   -3.534 closest distance to " CG1 VAL A 296 " =    1.449
peak=   -3.524 closest distance to " O   ILE A  49 " =    1.666
peak=   -3.518 closest distance to " O   HOH Z 191 " =    5.412
peak=   -3.517 closest distance to " O   HOH Z 290 " =    1.279
peak=   -3.506 closest distance to " CG  MET A 105 " =    0.969
peak=   -3.503 closest distance to " N   PRO A 163 " =    1.504
peak=   -3.501 closest distance to " O   TYR A  30 " =    2.657
peak=   -3.497 closest distance to " CG  PRO A 163 " =    2.538
peak=   -3.495 closest distance to " CB  VAL A 230 " =    1.012
peak=   -3.492 closest distance to " OG  SER A  26 " =    1.064
peak=   -3.490 closest distance to " CD2 TYR A 293 " =    1.867
peak=   -3.484 closest distance to " O   HOH Z 389 " =    1.443
peak=   -3.482 closest distance to " C   HIS A 108 " =    1.214
peak=   -3.478 closest distance to " O   ARG A 145 " =    1.516
peak=   -3.477 closest distance to " OG  SER A 245 " =    1.298
peak=   -3.474 closest distance to " OG  SER A  62 " =    4.401
peak=   -3.465 closest distance to " C   ARG A 269 " =    1.374
peak=   -3.457 closest distance to " CB  TYR A  15 " =    2.064
peak=   -3.452 closest distance to " CG2 THR A 178 " =    2.144
peak=   -3.448 closest distance to " O   HOH Z  51 " =    0.865
peak=   -3.447 closest distance to " CB  PHE A 130 " =    1.284
peak=   -3.444 closest distance to " O   ALA A   1 " =    1.262
peak=   -3.443 closest distance to " CA  GLY A 241 " =    2.164
peak=   -3.441 closest distance to " NH2AARG A 275 " =    5.527
peak=   -3.433 closest distance to " O   HOH Z  60 " =    2.048
peak=   -3.415 closest distance to " O   HOH Z 111 " =    2.092
peak=   -3.414 closest distance to " O   HOH Z 286 " =    1.810
peak=   -3.409 closest distance to " CG2 ILE A  20 " =    2.975
peak=   -3.403 closest distance to " O   HOH Z  90 " =    2.943
peak=   -3.402 closest distance to " OG  SER A  97 " =    2.216
peak=   -3.398 closest distance to " N   SER A 276 " =    1.278
peak=   -3.397 closest distance to " O   HOH Z  60 " =    2.256
peak=   -3.394 closest distance to " CE  LYS A  76 " =    2.779
peak=   -3.393 closest distance to " O   HOH Z 368 " =    2.412
peak=   -3.372 closest distance to " O   HOH Z 351 " =    1.598
peak=   -3.368 closest distance to " CB  TRP A  85 " =    2.612
peak=   -3.366 closest distance to " O   HOH Z 427 " =    1.719
peak=   -3.365 closest distance to " O   HOH Z 426 " =    1.649
peak=   -3.358 closest distance to " O   HOH Z 298 " =    1.032
peak=   -3.346 closest distance to " CG2 VAL A 202 " =    2.708
peak=   -3.343 closest distance to " O   VAL A  67 " =    2.374
peak=   -3.337 closest distance to " O   HOH Z 111 " =    1.042
peak=   -3.335 closest distance to " NH2 ARG A 219 " =    1.826
peak=   -3.333 closest distance to " C   ASN A 285 " =    2.171
peak=   -3.330 closest distance to " O   HOH Z 207 " =    1.858
peak=   -3.320 closest distance to " O   HOH Z 377 " =    1.038
peak=   -3.318 closest distance to " O   HOH Z 359 " =    3.397
peak=   -3.318 closest distance to " O   HOH Z 292 " =    1.670
peak=   -3.315 closest distance to " O   HOH Z 415 " =    1.176
peak=   -3.315 closest distance to " CG1 VAL A 197 " =    2.327
peak=   -3.314 closest distance to " O   HOH Z 365 " =    1.575
peak=   -3.302 closest distance to " ND2 ASN A 249 " =    2.547
peak=   -3.300 closest distance to " N   ARG A 138 " =    1.478
peak=   -3.293 closest distance to " CG  TRP A 266 " =    1.733
peak=   -3.289 closest distance to " N   THR A 235 " =    1.211
peak=   -3.283 closest distance to " N   VAL A  72 " =    1.632
peak=   -3.280 closest distance to " C   LYS A  76 " =    1.249
peak=   -3.280 closest distance to " ND2 ASN A 285 " =    2.029
peak=   -3.278 closest distance to " O   GLY A 211 " =    1.206
peak=   -3.275 closest distance to " CD2 HIS A 207 " =    2.493
peak=   -3.269 closest distance to " CG  ASN A 301 " =    1.907
peak=   -3.269 closest distance to " CB  PRO A 163 " =    2.314
peak=   -3.266 closest distance to " C   LEU A 143 " =    1.395
peak=   -3.266 closest distance to " O   HOH Z 435 " =    2.271
peak=   -3.265 closest distance to " C   ALA A 158 " =    1.319
peak=   -3.265 closest distance to " CA  GLY A 203 " =    2.248
peak=   -3.264 closest distance to " O   HOH Z  64 " =    2.314
peak=   -3.262 closest distance to " O   ASP A 191 " =    1.914
peak=   -3.262 closest distance to " CB  ALA A 131 " =    1.853
peak=   -3.259 closest distance to " O   HOH Z 368 " =    1.409
peak=   -3.259 closest distance to " O   HOH Z  39 " =    1.197
peak=   -3.251 closest distance to " N   HIS A 115 " =    2.224
peak=   -3.250 closest distance to " O   HOH Z 298 " =    2.700
peak=   -3.248 closest distance to " C   ASN A 187 " =    1.846
peak=   -3.244 closest distance to " CH2 TRP A 123 " =    2.262
peak=   -3.240 closest distance to " OE1 GLN A  88 " =    1.142
peak=   -3.236 closest distance to " O   VAL A 197 " =    1.656
peak=   -3.235 closest distance to " O   HOH Z 385 " =    1.872
peak=   -3.230 closest distance to " O   HOH Z 420 " =    3.274
peak=   -3.229 closest distance to " O   ASP A 270 " =    1.539
peak=   -3.226 closest distance to " CD1 PHE A  59 " =    2.012
peak=   -3.225 closest distance to " O   HOH Z 238 " =    0.945
peak=   -3.225 closest distance to " O   HOH Z 166 " =    1.715
peak=   -3.225 closest distance to " CE  MET A 105 " =    2.336
peak=   -3.224 closest distance to " CB  LYS A 289 " =    3.082
peak=   -3.218 closest distance to " O   HOH Z 198 " =    1.835
peak=   -3.217 closest distance to " O   HOH Z 189 " =    2.748
peak=   -3.216 closest distance to " O   HOH Z 140 " =    1.354
peak=   -3.214 closest distance to " O   HOH Z 353 " =    1.435
peak=   -3.214 closest distance to " CA  ASN A 127 " =    1.116
peak=   -3.214 closest distance to " CB  ALA A 248 " =    2.388
peak=   -3.212 closest distance to " OG  SER A 206 " =    1.803
peak=   -3.211 closest distance to " CD  ARG A 138 " =    1.629
peak=   -3.209 closest distance to " OG  SER A  87 " =    1.605
peak=   -3.208 closest distance to " OD2 ASP A 171 " =    1.713
peak=   -3.205 closest distance to " O   HOH Z  76 " =    1.396
peak=   -3.204 closest distance to " CB  ALA A 114 " =    2.338
peak=   -3.204 closest distance to " ND2BASN A 224 " =    1.577
peak=   -3.202 closest distance to " O   HOH Z 394 " =    1.524
peak=   -3.202 closest distance to " CG1 VAL A 250 " =    2.666
peak=   -3.196 closest distance to " O   HOH Z 125 " =    3.148
peak=   -3.195 closest distance to " NH1BARG A 145 " =    3.986
peak=   -3.186 closest distance to " CD2 PHE A  61 " =    2.039
peak=   -3.186 closest distance to " O   VAL A 189 " =    2.524
peak=   -3.186 closest distance to " O   HOH Z 100 " =    1.227
peak=   -3.185 closest distance to " O   HOH Z 388 " =    2.215
peak=   -3.185 closest distance to " N   GLN A  58 " =    1.950
peak=   -3.183 closest distance to " O   HOH Z  67 " =    3.029
peak=   -3.182 closest distance to " CD2 LEU A 237 " =    2.580
peak=   -3.179 closest distance to " CG2 ILE A 151 " =    2.485
peak=   -3.178 closest distance to " O   HOH Z  53 " =    1.784
peak=   -3.174 closest distance to " CZ2 TRP A  92 " =    2.822
peak=   -3.172 closest distance to " O   HOH Z 155 " =    1.225
peak=   -3.171 closest distance to " O   HOH Z 426 " =    2.160
peak=   -3.168 closest distance to " N   PHE A  59 " =    2.066
peak=   -3.163 closest distance to " OG BSER A 134 " =    1.847
peak=   -3.161 closest distance to " O   HOH Z 275 " =    1.595
peak=   -3.160 closest distance to " CZ  PHE A  59 " =    1.599
peak=   -3.159 closest distance to " O   HOH Z 313 " =    1.432
peak=   -3.156 closest distance to " ND2 ASN A 209 " =    1.965
peak=   -3.155 closest distance to " N   ALA A 295 " =    1.616
peak=   -3.153 closest distance to " O   HOH Z 193 " =    2.024
peak=   -3.152 closest distance to " CB  PRO A  90 " =    1.580
peak=   -3.145 closest distance to " N   ALA A   1 " =    1.403
peak=   -3.145 closest distance to " O   HOH Z 200 " =    3.557
peak=   -3.143 closest distance to " O   HOH Z 208 " =    2.030
peak=   -3.139 closest distance to " O   HOH Z 108 " =    1.978
peak=   -3.126 closest distance to " O   HOH Z 414 " =    1.952
peak=   -3.117 closest distance to " CE2 TRP A  70 " =    2.409
peak=   -3.116 closest distance to " O   HOH Z 337 " =    1.641
peak=   -3.115 closest distance to " O   HOH Z 111 " =    4.695
peak=   -3.114 closest distance to " O   GLN A  11 " =    1.875
peak=   -3.112 closest distance to " OH  TYR A 172 " =    1.761
peak=   -3.110 closest distance to " CB  ALA A 291 " =    2.017
peak=   -3.105 closest distance to " N   ALA A 248 " =    1.564
peak=   -3.101 closest distance to " CG  LEU A 281 " =    1.744
peak=   -3.100 closest distance to " O   SER A 271 " =    2.054
peak=   -3.099 closest distance to " CD1 ILE A 199 " =    2.569
peak=   -3.096 closest distance to " CB  PHE A 192 " =    1.610
peak=   -3.089 closest distance to " CD  GLN A  58 " =    1.036
peak=   -3.085 closest distance to " CD  LYS A 166 " =    2.367
peak=   -3.084 closest distance to " O   GLN A 240 " =    2.450
peak=   -3.072 closest distance to " O   HOH Z 174 " =    2.927
peak=   -3.062 closest distance to " O   PHE A 218 " =    1.450
peak=   -3.046 closest distance to " OG ASER A 216 " =    1.221
peak=   -3.013 closest distance to " CB  ASP A 132 " =    2.379
peak=   -3.011 closest distance to " CE1 PHE A  59 " =    2.154
peak=   -3.008 closest distance to " O   HOH Z  56 " =    1.768

================= 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    :  0.4789 0.4720   6.284191e+00   6.269126e+00
   1_bss:  0.4700 0.4586   6.276704e+00   6.259832e+00
   1_xyz:  0.3915 0.4180   6.176434e+00   6.209117e+00
   1_adp:  0.3472 0.4073   6.112290e+00   6.197665e+00
   1_occ:  0.3472 0.4070   6.111829e+00   6.197865e+00
   2_bss:  0.3438 0.4014   6.111151e+00   6.195751e+00
   2_xyz:  0.2770 0.3375   5.927774e+00   6.060923e+00
   2_adp:  0.2585 0.3265   5.881826e+00   6.030737e+00
   2_occ:  0.2583 0.3266   5.881823e+00   6.031140e+00
   3_bss:  0.2570 0.3232   5.880192e+00   6.027660e+00
   3_xyz:  0.1983 0.2624   5.651739e+00   5.845387e+00
   3_adp:  0.1762 0.2326   5.535825e+00   5.741533e+00
   3_occ:  0.1760 0.2323   5.535037e+00   5.740589e+00
   4_bss:  0.1757 0.2316   5.534413e+00   5.738688e+00
   4_xyz:  0.1450 0.1952   5.370021e+00   5.595184e+00
   4_adp:  0.1354 0.1878   5.319221e+00   5.551132e+00
   4_occ:  0.1354 0.1876   5.318952e+00   5.550706e+00
   5_bss:  0.1357 0.1872   5.317734e+00   5.548844e+00
   5_xyz:  0.1203 0.1728   5.223085e+00   5.472918e+00
   5_adp:  0.1173 0.1696   5.205033e+00   5.456871e+00
   5_occ:  0.1172 0.1695   5.204476e+00   5.456147e+00
   5_bss:  0.1172 0.1694   5.204529e+00   5.456133e+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:  0.355   4.812   7.751  10.242   7.606   0.000   0.000   0.000
   1_xyz:  0.355   4.812   7.751  10.242   7.606   0.000   0.000   0.000
   1_adp:  0.355   4.812   7.751  10.242   7.606   0.000   0.000   0.000
   1_occ:  0.355   4.812   7.751  10.242   7.606   0.000   0.000   0.000
   2_bss:  0.354  41.078   4.308   5.843   4.461   0.000   0.000   0.000
   2_xyz:  0.354  41.078   4.308   5.843   4.461   0.000   0.000   0.000
   2_adp:  0.354  41.078   4.308   5.843   4.461   0.000   0.000   0.000
   2_occ:  0.354  41.078   4.308   5.843   4.461   0.000   0.000   0.000
   3_bss:  0.335  41.078   2.789   3.084   3.367   0.000   0.000   0.000
   3_xyz:  0.335  41.078   2.789   3.084   3.367   0.000   0.000   0.000
   3_adp:  0.335  41.078   2.789   3.084   3.367   0.000   0.000   0.000
   3_occ:  0.335  41.078   2.789   3.084   3.367   0.000   0.000   0.000
   4_bss:  0.319  45.596   1.621   1.511   2.565   0.000   0.000   0.000
   4_xyz:  0.319  45.596   1.621   1.511   2.565   0.000   0.000   0.000
   4_adp:  0.319  45.596   1.621   1.511   2.565   0.000   0.000   0.000
   4_occ:  0.319  45.596   1.621   1.511   2.565   0.000   0.000   0.000
   5_bss:  0.322  51.559   1.546   1.180   2.522   0.000   0.000   0.000
   5_xyz:  0.322  51.559   1.546   1.180   2.522   0.000   0.000   0.000
   5_adp:  0.322  51.559   1.546   1.180   2.522   0.000   0.000   0.000
   5_occ:  0.322  51.559   1.546   1.180   2.522   0.000   0.000   0.000
   5_bss:  0.318  50.687  -0.189  -0.630   0.819  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.944 0.4200  0.4962    70424.919
   1_bss:  57.394 0.4260  0.6409    68155.827
   1_xyz:  49.815 0.5213  0.7686    53654.245
   1_adp:  47.370 0.5521  0.8661    50780.514
   1_occ:  47.424 0.5515  0.8645    50873.785
   2_bss:  46.919 0.5576  0.7736    50109.693
   2_xyz:  36.773 0.6795  0.9195    32330.017
   2_adp:  34.422 0.7076  0.9611    29557.215
   2_occ:  34.457 0.7071  0.9603    29605.360
   3_bss:  34.156 0.7104  0.9044    29181.738
   3_xyz:  26.294 0.7966  0.9839    17716.489
   3_adp:  22.466 0.8370  1.0051    13663.181
   3_occ:  22.448 0.8372  1.0050    13631.897
   4_bss:  22.363 0.8380  0.9636    13544.920
   4_xyz:  18.796 0.8728  0.9788     9882.460
   4_adp:  17.752 0.8827  0.9745     9092.081
   4_occ:  17.745 0.8828  0.9742     9076.207
   5_bss:  17.699 0.8830  0.9692     9016.274
   5_xyz:  16.003 0.8979  0.9778     7616.231
   5_adp:  15.559 0.9021  0.9732     7381.424
   5_occ:  15.544 0.9022  0.9731     7364.104
   5_bss:  15.549 0.9021  0.9782     7363.822
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3554e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3554e+01
   1_xyz:   1.678  0.013  0.106 18.347  0.007  4.107   1.4107e-01
   1_adp:   1.678  0.013  0.106 18.347  0.007  4.107   1.4107e-01
   1_occ:   1.678  0.013  0.106 18.347  0.007  4.107   1.4107e-01
   2_bss:   1.678  0.013  0.106 18.347  0.007  4.107   1.4107e-01
   2_xyz:   1.158  0.008  0.084 16.353  0.005  4.106   8.4525e-02
   2_adp:   1.158  0.008  0.084 16.353  0.005  4.106   8.4525e-02
   2_occ:   1.158  0.008  0.084 16.353  0.005  4.106   8.4525e-02
   3_bss:   1.158  0.008  0.084 16.353  0.005  4.106   8.4525e-02
   3_xyz:   1.135  0.008  0.082 15.921  0.004  4.118   7.6324e-02
   3_adp:   1.135  0.008  0.082 15.921  0.004  4.118   7.6324e-02
   3_occ:   1.135  0.008  0.082 15.921  0.004  4.118   7.6324e-02
   4_bss:   1.135  0.008  0.082 15.921  0.004  4.118   7.6324e-02
   4_xyz:   0.931  0.006  0.072 15.655  0.003  4.109   5.6918e-02
   4_adp:   0.931  0.006  0.072 15.655  0.003  4.109   5.6918e-02
   4_occ:   0.931  0.006  0.072 15.655  0.003  4.109   5.6918e-02
   5_bss:   0.931  0.006  0.072 15.655  0.003  4.109   5.6918e-02
   5_xyz:   1.089  0.008  0.085 15.843  0.004  4.114   7.1035e-02
   5_adp:   1.089  0.008  0.085 15.843  0.004  4.114   7.1035e-02
   5_occ:   1.089  0.008  0.085 15.843  0.004  4.114   7.1035e-02
   5_bss:   1.089  0.008  0.085 15.843  0.004  4.114   7.1035e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9415e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9415e+00
   1_xyz:  13.156  0.185  0.422 88.083  0.038  2.182   9.9785e-02
   1_adp:  13.156  0.185  0.422 88.083  0.038  2.182   9.9785e-02
   1_occ:  13.156  0.185  0.422 88.083  0.038  2.182   9.9785e-02
   2_bss:  13.156  0.185  0.422 88.083  0.038  2.182   9.9785e-02
   2_xyz:   7.156  0.080  0.321 78.397  0.050  2.174   6.5826e-02
   2_adp:   7.156  0.080  0.321 78.397  0.050  2.174   6.5826e-02
   2_occ:   7.156  0.080  0.321 78.397  0.050  2.174   6.5826e-02
   3_bss:   7.156  0.080  0.321 78.397  0.050  2.174   6.5826e-02
   3_xyz:   7.415  0.072  0.387 80.138  0.024  2.185   5.7956e-02
   3_adp:   7.415  0.072  0.387 80.138  0.024  2.185   5.7956e-02
   3_occ:   7.415  0.072  0.387 80.138  0.024  2.185   5.7956e-02
   4_bss:   7.415  0.072  0.387 80.138  0.024  2.185   5.7956e-02
   4_xyz:   7.295  0.047  0.355 81.992  0.035  2.338   4.5209e-02
   4_adp:   7.295  0.047  0.355 81.992  0.035  2.338   4.5209e-02
   4_occ:   7.295  0.047  0.355 81.992  0.035  2.338   4.5209e-02
   5_bss:   7.295  0.047  0.355 81.992  0.035  2.338   4.5209e-02
   5_xyz:   9.526  0.060  0.529 82.701  0.039  2.287   5.2969e-02
   5_adp:   9.526  0.060  0.529 82.701  0.039  2.287   5.2969e-02
   5_occ:   9.526  0.060  0.529 82.701  0.039  2.287   5.2969e-02
   5_bss:   9.526  0.060  0.529 82.701  0.039  2.287   5.2969e-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:  77.83   0.00  13.73  71.34   0.00  11.72  77.83   0.00  24.68
   1_occ:  77.83   0.00  13.73  71.34   0.00  11.72  77.83   0.00  24.68
   2_bss:  77.83   0.00  13.73  71.34   0.00  11.72  77.83   0.00  24.68
   2_xyz:  77.83   0.00  13.73  71.34   0.00  11.72  77.83   0.00  24.68
   2_adp:  80.19   0.00  13.87  71.71   0.00  11.21  80.19   0.00  28.36
   2_occ:  80.19   0.00  13.87  71.71   0.00  11.21  80.19   0.00  28.36
   3_bss:  80.19   0.00  13.87  71.71   0.00  11.21  80.19   0.00  28.36
   3_xyz:  80.19   0.00  13.87  71.71   0.00  11.21  80.19   0.00  28.36
   3_adp:  83.15   0.00  13.59  77.14   0.00   9.81  83.15   2.48  34.18
   3_occ:  83.15   0.00  13.59  77.14   0.00   9.81  83.15   2.48  34.18
   4_bss:  83.15   0.00  13.59  77.14   0.00   9.81  83.15   2.48  34.18
   4_xyz:  83.15   0.00  13.59  77.14   0.00   9.81  83.15   2.48  34.18
   4_adp:  92.74   0.00  14.35  92.74   0.00   9.57  89.23   2.61  40.35
   4_occ:  92.74   0.00  14.35  92.74   0.00   9.57  89.23   2.61  40.35
   5_bss:  92.74   0.00  14.35  92.74   0.00   9.57  89.23   2.61  40.35
   5_xyz:  92.74   0.00  14.35  92.74   0.00   9.57  89.23   2.61  40.35
   5_adp:  97.05   0.00  14.02  97.05   0.00   9.29  94.52   2.41  39.77
   5_occ:  97.05   0.00  14.02  97.05   0.00   9.29  94.52   2.41  39.77
   5_bss:  98.94   1.90  15.92  98.94   1.90  11.19  96.42   4.30  41.66
------------------------------------------------------------------------
 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:    1.235    0.010    0.411
   1_adp:    1.235    0.010    0.411
   1_occ:    1.235    0.010    0.411
   2_bss:    1.235    0.010    0.411
   2_xyz:    1.441    0.028    0.573
   2_adp:    1.441    0.028    0.573
   2_occ:    1.441    0.028    0.573
   3_bss:    1.441    0.028    0.573
   3_xyz:    1.718    0.037    0.668
   3_adp:    1.718    0.037    0.668
   3_occ:    1.718    0.037    0.668
   4_bss:    1.718    0.037    0.668
   4_xyz:    1.955    0.054    0.735
   4_adp:    1.955    0.054    0.735
   4_occ:    1.955    0.054    0.735
   5_bss:    1.955    0.054    0.735
   5_xyz:    2.017    0.030    0.762
   5_adp:    2.017    0.030    0.762
   5_occ:    2.017    0.030    0.762
   5_bss:    2.017    0.030    0.762
------------------------------------------------------------------------

CPU time actual refinement: 353.03


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_863/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_863/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_863/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_863/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_863/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 352.87 
  Macro-tasks:
    bulk solvent and scale       = 41.74  
    individual site refinement   = 147.69 
    weights calculation          = 32.69  
    collect and process          = 6.55   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 228.80 
  Micro-tasks:
    mask                            = 2.45   
    f_calc                          = 111.84 
    alpha_beta                      = 8.10   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 121.59 
    fmodel                         = 7.19   
    r_factors                      = 0.17   
    phase_errors                   = 10.51  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 263.29 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.948 micro seconds
Total CPU time: 6.11 minutes
from_scatterers_fft:    649 calls, 111.59 s
gradients_fft:          594 calls, 108.11 s

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

# Date 2008-01-16 Time 02:37:38 PST -0800 (1200479858.91 s)
Start R-work = 0.4789, R-free = 0.4720 (no bulk solvent and anisotropic scale)
Final R-work = 0.1336, R-free = 0.1837 (no bulk solvent and anisotropic scale)

Start R-work = 0.4700, R-free = 0.4586
Final R-work = 0.1172, R-free = 0.1694