# Date 2008-01-16 Time 02:23:12 PST -0800 (1200478992.97 s)
#phil __OFF__

Command line arguments: "../815.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21007
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 815

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.6339, 84.6622, 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: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.6339, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9645 1.96144
Completeness in resolution range: 0.931302
Completeness with d_max=infinity: 0.928521

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9645
                             d_min =   1.9614

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.6339, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9645 1.96144
Completeness in resolution range: 0.931302
Completeness with d_max=infinity: 0.928521

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9649 -  4.1976 [2212/2241]  1993   219   9.9%
  bin  2:  4.1976 -  3.3440 [2113/2136]  1902   211  10.0%
  bin  3:  3.3440 -  2.9249 [2092/2117]  1879   213  10.2%
  bin  4:  2.9249 -  2.6591 [2075/2091]  1872   203   9.8%
  bin  5:  2.6591 -  2.4694 [2061/2105]  1852   209  10.1%
  bin  6:  2.4694 -  2.3244 [2051/2079]  1850   201   9.8%
  bin  7:  2.3244 -  2.2084 [2025/2061]  1821   204  10.1%
  bin  8:  2.2084 -  2.1125 [2027/2069]  1824   203  10.0%
  bin  9:  2.1125 -  2.0314 [2028/2074]  1826   202  10.0%
  bin 10:  2.0314 -  1.9614 [ 905/2061]   811    94  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_815/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:
        1.67 -     2.32: 23
        2.32 -     2.96: 1733
        2.96 -     3.61: 4521
        3.61 -     4.25: 9189
        4.25 -     4.90: 12858
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.670 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.779 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.800 3.040 -x+1/2,-y+1,z+1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.802 3.040 -x+1/2,-y+1,z-1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28319 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_815/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_815/model_refine_001.geo

CPU time processing inputs: 9.62


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 47.63395 84.6622 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 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4812   r_free= 0.4808   ksol= 0.00   Bsol= 0.00   scale= 0.792    |
|                                                                             |
| 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:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.284417                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9649 -  4.6821 0.99   1433  161 0.3938 0.3917      6.5981      6.5964|
|  2:  4.6821 -  3.7353 0.99   1374  147 0.4004 0.4259      6.7928      6.8043|
|  3:  3.7353 -  3.2688 0.99   1357  156 0.4474 0.3977      6.6728      6.6878|
|  4:  3.2688 -  2.9725 0.99   1341  146 0.4561 0.4645      6.5022      6.5014|
|  5:  2.9725 -  2.7608 0.98   1335  149 0.5086 0.5297      6.3736      6.3674|
|  6:  2.7608 -  2.5990 0.99   1335  147 0.5028 0.5185      6.2705      6.2027|
|  7:  2.5990 -  2.4694 0.98   1323  149 0.5132 0.4350      6.2607      6.1557|
|  8:  2.4694 -  2.3623 0.99   1305  142 0.5326 0.5345       6.153      6.1951|
|  9:  2.3623 -  2.2717 0.99   1332  153 0.5509 0.5450      6.1433      6.1498|
| 10:  2.2717 -  2.1936 0.98   1304  143 0.5142 0.5560       6.092       6.141|
| 11:  2.1936 -  2.1252 0.97   1294  139 0.5253 0.5101      6.0323       5.994|
| 12:  2.1252 -  2.0646 0.99   1310  154 0.5420 0.5737      5.9487      5.9814|
| 13:  2.0646 -  2.0104 0.92   1225  135 0.5477 0.5495      5.8772      5.8317|
| 14:  2.0104 -  1.9614 0.27    362   38 0.5708 0.5788      5.8397      5.7788|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9649 -  4.6821  1433   161  0.70  34.61   0.80     0.72      71832.23|
|  2:  4.6821 -  3.7353  1374   147  0.69  35.73   0.88     0.76     105710.27|
|  3:  3.7353 -  3.2688  1357   156  0.58  45.21   0.83     0.70     116030.43|
|  4:  3.2688 -  2.9725  1341   146  0.49  52.64   0.81     0.59     104390.10|
|  5:  2.9725 -  2.7608  1335   149  0.40  59.96   0.73     0.49      86471.03|
|  6:  2.7608 -  2.5990  1335   147  0.40  59.62   0.74     0.48      70219.99|
|  7:  2.5990 -  2.4694  1323   149  0.42  58.32   0.74     0.47      60243.81|
|  8:  2.4694 -  2.3623  1305   142  0.39  60.88   0.70     0.46      56317.13|
|  9:  2.3623 -  2.2717  1332   153  0.30  67.22   0.72     0.37      56711.80|
| 10:  2.2717 -  2.1936  1304   143  0.24  71.94   0.76     0.29      56959.70|
| 11:  2.1936 -  2.1252  1294   139  0.18  76.43   0.76     0.24      54245.52|
| 12:  2.1252 -  2.0646  1310   154  0.16  78.19   0.74     0.21      49891.34|
| 13:  2.0646 -  2.0104  1225   135  0.17  77.73   0.72     0.22      42359.19|
| 14:  2.0104 -  1.9614   362    38  0.19  75.75   0.69     0.24      35833.61|
|alpha:            min =        0.21 max =            0.76 mean =         0.46|
|beta:             min =    35833.61 max =       116030.43 mean =     71368.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           90.00 mean =        59.80|
|phase err.(test): min =        0.00 max =           89.89 mean =        60.03|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.927143             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.517   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.380942              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.112   (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 |  1.120 -  1.498:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.498 -  1.876:       16 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.876 -  2.254:      149 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.254 -  2.632:      610 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.632 -  3.010:     1415 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.010 -  3.388:     2553 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.388 -  3.766:     3963 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.766 -  4.144:     5093 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.144 -  4.522:     6680 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.522 -  4.900:     7893 |
|-----------------------------------------------------------------------------|
|-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 |       53.658 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.120 |       1.983 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.891)------------------------------------------|
|    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 = 11.891)------------------------------------------|
|    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 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4869   r_free= 0.4859   ksol= 0.00   Bsol= 0.00   scale= 0.762    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.285734                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4735   r_free= 0.4687   ksol= 0.30   Bsol= 20.00   scale= 0.978   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.34,9.90,8.17,0.00,0.00,0.00); trace/3= 8.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.282993                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.376568             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.622   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.166276              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.962   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4735      final r-factor (work) = 0.4035          |
| start r-factor (free) = 0.4687      final r-factor (free) = 0.4260          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 92.5332 = 12.38 * 0.50 * 6.2820 + 1.00 * 53.6584                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.5172 = 12.38 * 0.50 * 6.2008 + 1.00 * 0.1449                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4035      final r-factor (work) = 0.3606          |
| start r-factor (free) = 0.4260      final r-factor (free) = 0.4109          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2462 = 1.17 * 1.00 * 6.2008 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1676 = 1.17 * 1.00 * 6.1321 + 1.00 * 0.0159                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.891)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.63   13.65    None  None   None       |
|    all(noH): 2823   0      0.00    95.63   13.65    None  None   None       |
|    Sol.    : 438    0      0.00    95.63   27.11    None  None   None       |
|    Mac.    : 2385   0      0.00    79.02   11.17    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 -   9.563: 1327   |   5:    47.817 -  57.380:   40        |
|      1:     9.563 -  19.127:  825   |   6:    57.380 -  66.944:   13        |
|      2:    19.127 -  28.690:  367   |   7:    66.944 -  76.507:   10        |
|      3:    28.690 -  38.253:  144   |   8:    76.507 -  86.070:    4        |
|      4:    38.253 -  47.817:   92   |   9:    86.070 -  95.634:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3606 r_free = 0.4109             target_work(ml) = 6.115         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3602 r_free = 0.4116             target_work(ml) = 6.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3602   r_free= 0.4116   ksol= 0.30   Bsol= 20.00   scale= 1.091   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.34,9.90,8.17,0.00,0.00,0.00); trace/3= 8.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.115019                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3583   r_free= 0.4067   ksol= 0.33   Bsol= 41.99   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.26,6.44,5.50,0.00,0.00,0.00); trace/3= 5.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.116055                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.967936              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.413   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.590329              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.091  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3583      final r-factor (work) = 0.2705          |
| start r-factor (free) = 0.4067      final r-factor (free) = 0.3330          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.5612 = 7.97 * 0.50 * 6.1287 + 1.00 * 0.1449                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.0072 = 7.97 * 0.50 * 6.0031 + 1.00 * 0.0912                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2705      final r-factor (work) = 0.2480          |
| start r-factor (free) = 0.3330      final r-factor (free) = 0.3114          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5598 = 0.59 * 1.00 * 6.0031 + 1.00 * 0.0160                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4713 = 0.59 * 1.00 * 5.8592 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.891)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.61   14.09    None  None   None       |
|    all(noH): 2823   0      0.00    87.61   14.09    None  None   None       |
|    Sol.    : 438    0      1.38    87.61   33.41    None  None   None       |
|    Mac.    : 2385   0      0.00    71.64   10.54    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.761: 1308   |   5:    43.805 -  52.566:   86        |
|      1:     8.761 -  17.522:  793   |   6:    52.566 -  61.327:   31        |
|      2:    17.522 -  26.283:  285   |   7:    61.327 -  70.088:   17        |
|      3:    26.283 -  35.044:  170   |   8:    70.088 -  78.849:    7        |
|      4:    35.044 -  43.805:  124   |   9:    78.849 -  87.610:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2480 r_free = 0.3114             target_work(ml) = 5.829         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2477 r_free = 0.3112             target_work(ml) = 5.828         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2477   r_free= 0.3112   ksol= 0.33   Bsol= 41.99   scale= 1.069   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.26,6.44,5.50,0.00,0.00,0.00); trace/3= 5.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.828286                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2443   r_free= 0.3083   ksol= 0.31   Bsol= 49.63   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.55,3.15,2.60,0.00,0.00,0.00); trace/3= 2.43                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.827001                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.061735              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.208   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.382233              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 109.652  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2443      final r-factor (work) = 0.1749          |
| start r-factor (free) = 0.3083      final r-factor (free) = 0.2253          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.9415 = 5.06 * 0.50 * 5.8677 + 1.00 * 0.0912                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.5098 = 5.06 * 0.50 * 5.7026 + 1.00 * 0.0774                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1749      final r-factor (work) = 0.1581          |
| start r-factor (free) = 0.2253      final r-factor (free) = 0.2088          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1918 = 0.38 * 1.00 * 5.7026 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1049 = 0.38 * 1.00 * 5.4792 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.891)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.59   14.20    None  None   None       |
|    all(noH): 2823   0      0.00    82.59   14.20    None  None   None       |
|    Sol.    : 438    0      2.70    82.59   37.40    None  None   None       |
|    Mac.    : 2385   0      0.00    79.62   9.94     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.259: 1326   |   5:    41.294 -  49.553:  101        |
|      1:     8.259 -  16.518:  816   |   6:    49.553 -  57.812:   77        |
|      2:    16.518 -  24.777:  220   |   7:    57.812 -  66.071:   32        |
|      3:    24.777 -  33.036:  104   |   8:    66.071 -  74.330:    9        |
|      4:    33.036 -  41.294:  129   |   9:    74.330 -  82.589:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1581 r_free = 0.2088             target_work(ml) = 5.440         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1578 r_free = 0.2087             target_work(ml) = 5.439         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1578   r_free= 0.2087   ksol= 0.31   Bsol= 49.63   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.55,3.15,2.60,0.00,0.00,0.00); trace/3= 2.43                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.439302                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1575   r_free= 0.2085   ksol= 0.32   Bsol= 49.63   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.82,1.97,1.62,0.00,0.00,0.00); trace/3= 1.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.441611                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.683578              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.396   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.476336              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.375  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1575      final r-factor (work) = 0.1301          |
| start r-factor (free) = 0.2085      final r-factor (free) = 0.1742          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1797 = 3.68 * 0.50 * 5.4850 + 1.00 * 0.0775                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9513 = 3.68 * 0.50 * 5.3655 + 1.00 * 0.0692                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1301      final r-factor (work) = 0.1244          |
| start r-factor (free) = 0.1742      final r-factor (free) = 0.1688          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5662 = 0.48 * 1.00 * 5.3655 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5110 = 0.48 * 1.00 * 5.2480 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.891)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.55   14.27    None  None   None       |
|    all(noH): 2823   0      0.00    90.55   14.27    None  None   None       |
|    Sol.    : 438    0      2.82    83.78   38.78    None  None   None       |
|    Mac.    : 2385   0      0.00    90.55   9.77     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 -   9.055: 1499   |   5:    45.276 -  54.331:   96        |
|      1:     9.055 -  18.110:  736   |   6:    54.331 -  63.386:   69        |
|      2:    18.110 -  27.166:  173   |   7:    63.386 -  72.442:   22        |
|      3:    27.166 -  36.221:  109   |   8:    72.442 -  81.497:   11        |
|      4:    36.221 -  45.276:  102   |   9:    81.497 -  90.552:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1244 r_free = 0.1688             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1242 r_free = 0.1689             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1242   r_free= 0.1689   ksol= 0.32   Bsol= 49.63   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.82,1.97,1.62,0.00,0.00,0.00); trace/3= 1.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.234464                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1247   r_free= 0.1695   ksol= 0.32   Bsol= 48.02   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.74,1.58,1.42,0.00,0.00,0.00); trace/3= 1.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.237703                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.680272              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.354  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.391197              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.997  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1247      final r-factor (work) = 0.1220          |
| start r-factor (free) = 0.1695      final r-factor (free) = 0.1669          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4793 = 1.68 * 0.50 * 5.2493 + 1.00 * 0.0692                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4490 = 1.68 * 0.50 * 5.2313 + 1.00 * 0.0540                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1220      final r-factor (work) = 0.1212          |
| start r-factor (free) = 0.1669      final r-factor (free) = 0.1660          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0576 = 0.39 * 1.00 * 5.2313 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0528 = 0.39 * 1.00 * 5.2194 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.891)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.58   14.09    None  None   None       |
|    all(noH): 2823   0      0.00    91.58   14.09    None  None   None       |
|    Sol.    : 438    0      1.95    83.69   38.30    None  None   None       |
|    Mac.    : 2385   0      0.00    91.58   9.64     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 -   9.158: 1566   |   5:    45.792 -  54.950:   97        |
|      1:     9.158 -  18.317:  683   |   6:    54.950 -  64.108:   62        |
|      2:    18.317 -  27.475:  170   |   7:    64.108 -  73.266:   20        |
|      3:    27.475 -  36.633:  112   |   8:    73.266 -  82.425:    8        |
|      4:    36.633 -  45.792:  100   |   9:    82.425 -  91.583:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1212 r_free = 0.1660             target_work(ml) = 5.217         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1211 r_free = 0.1661             target_work(ml) = 5.217         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1211   r_free= 0.1661   ksol= 0.32   Bsol= 48.02   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.74,1.58,1.42,0.00,0.00,0.00); trace/3= 1.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.217087                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9649 -  4.6821 0.99   1433  161 0.1007 0.1217      5.3913      5.5152|
|  2:  4.6821 -  3.7353 0.99   1374  147 0.0908 0.1182      5.4663      5.6956|
|  3:  3.7353 -  3.2688 0.99   1357  156 0.1119 0.1669      5.5237      5.9095|
|  4:  3.2688 -  2.9725 0.99   1341  146 0.1364 0.1587      5.5251      5.6663|
|  5:  2.9725 -  2.7608 0.98   1335  149 0.1457 0.1806      5.4045      5.5415|
|  6:  2.7608 -  2.5990 0.99   1335  147 0.1356 0.2138      5.3006       5.584|
|  7:  2.5990 -  2.4694 0.98   1323  149 0.1359 0.1772      5.2407      5.4352|
|  8:  2.4694 -  2.3623 0.99   1305  142 0.1291 0.1722      5.1402      5.3329|
|  9:  2.3623 -  2.2717 0.99   1332  153 0.1249 0.1923      5.0848      5.3493|
| 10:  2.2717 -  2.1936 0.98   1304  143 0.1223 0.1859      5.0404      5.3518|
| 11:  2.1936 -  2.1252 0.97   1294  139 0.1258 0.1832      4.9865      5.2476|
| 12:  2.1252 -  2.0646 0.99   1310  154 0.1241 0.1876      4.9313      5.1652|
| 13:  2.0646 -  2.0104 0.92   1225  135 0.1262 0.1859      4.8444      5.0424|
| 14:  2.0104 -  1.9614 0.27    362   38 0.1149 0.1959      4.7262      5.0758|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9649 -  4.6821  1433   161  0.94   8.97   0.97     0.95       7128.62|
|  2:  4.6821 -  3.7353  1374   147  0.95   8.33   1.01     0.99       9302.71|
|  3:  3.7353 -  3.2688  1357   156  0.92  12.56   1.02     1.02      11765.66|
|  4:  3.2688 -  2.9725  1341   146  0.91  15.20   1.00     0.97      11604.42|
|  5:  2.9725 -  2.7608  1335   149  0.88  17.97   0.99     0.96       9801.91|
|  6:  2.7608 -  2.5990  1335   147  0.89  17.59   0.99     0.96       8493.86|
|  7:  2.5990 -  2.4694  1323   149  0.89  16.93   0.98     0.96       7190.27|
|  8:  2.4694 -  2.3623  1305   142  0.89  17.24   0.99     0.95       6249.61|
|  9:  2.3623 -  2.2717  1332   153  0.89  17.46   1.00     0.96       5687.64|
| 10:  2.2717 -  2.1936  1304   143  0.90  16.49   1.00     0.96       5217.16|
| 11:  2.1936 -  2.1252  1294   139  0.89  17.58   0.99     0.95       4737.36|
| 12:  2.1252 -  2.0646  1310   154  0.90  16.36   0.99     0.98       4353.24|
| 13:  2.0646 -  2.0104  1225   135  0.89  17.82   0.99     0.98       3752.43|
| 14:  2.0104 -  1.9614   362    38  0.89  17.36   0.98     0.95       3034.37|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     3034.37 max =        11765.66 mean =      7290.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        15.38|
|phase err.(test): min =        0.00 max =           89.94 mean =        14.79|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1211   r_free= 0.1661   ksol= 0.32   Bsol= 49.89   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,0.29,0.18,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.217121                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1211   r_free= 0.1661   ksol= 0.32   Bsol= 49.89   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,0.29,0.18,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.217121                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9649 -  4.6821 0.99   1433  161 0.1007 0.1218      5.3916       5.516|
|  2:  4.6821 -  3.7353 0.99   1374  147 0.0909 0.1184       5.467      5.6964|
|  3:  3.7353 -  3.2688 0.99   1357  156 0.1119 0.1669      5.5241      5.9099|
|  4:  3.2688 -  2.9725 0.99   1341  146 0.1364 0.1587      5.5251      5.6662|
|  5:  2.9725 -  2.7608 0.98   1335  149 0.1457 0.1805      5.4042      5.5412|
|  6:  2.7608 -  2.5990 0.99   1335  147 0.1356 0.2137      5.3003      5.5837|
|  7:  2.5990 -  2.4694 0.98   1323  149 0.1359 0.1773      5.2406      5.4353|
|  8:  2.4694 -  2.3623 0.99   1305  142 0.1291 0.1721      5.1402      5.3326|
|  9:  2.3623 -  2.2717 0.99   1332  153 0.1248 0.1924      5.0846      5.3497|
| 10:  2.2717 -  2.1936 0.98   1304  143 0.1223 0.1858      5.0404      5.3517|
| 11:  2.1936 -  2.1252 0.97   1294  139 0.1258 0.1832      4.9863      5.2474|
| 12:  2.1252 -  2.0646 0.99   1310  154 0.1240 0.1877      4.9313      5.1655|
| 13:  2.0646 -  2.0104 0.92   1225  135 0.1262 0.1858      4.8443      5.0419|
| 14:  2.0104 -  1.9614 0.27    362   38 0.1149 0.1958       4.726      5.0756|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9649 -  4.6821  1433   161  0.94   8.98   0.97     0.95       7136.64|
|  2:  4.6821 -  3.7353  1374   147  0.95   8.34   1.01     0.99       9314.73|
|  3:  3.7353 -  3.2688  1357   156  0.92  12.57   1.02     1.02      11781.23|
|  4:  3.2688 -  2.9725  1341   146  0.91  15.20   1.00     0.97      11605.03|
|  5:  2.9725 -  2.7608  1335   149  0.88  17.96   0.99     0.96       9797.44|
|  6:  2.7608 -  2.5990  1335   147  0.89  17.58   0.99     0.96       8488.55|
|  7:  2.5990 -  2.4694  1323   149  0.89  16.92   0.99     0.96       7188.70|
|  8:  2.4694 -  2.3623  1305   142  0.89  17.24   1.00     0.95       6249.31|
|  9:  2.3623 -  2.2717  1332   153  0.89  17.46   1.00     0.96       5688.68|
| 10:  2.2717 -  2.1936  1304   143  0.90  16.50   1.00     0.96       5217.19|
| 11:  2.1936 -  2.1252  1294   139  0.89  17.57   0.99     0.95       4735.92|
| 12:  2.1252 -  2.0646  1310   154  0.90  16.36   0.99     0.98       4353.33|
| 13:  2.0646 -  2.0104  1225   135  0.89  17.82   0.99     0.98       3750.38|
| 14:  2.0104 -  1.9614   362    38  0.89  17.34   0.98     0.95       3030.97|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     3030.97 max =        11781.23 mean =      7291.87|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.38|
|phase err.(test): min =        0.00 max =           89.98 mean =        14.79|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.891)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.27    92.85   15.36    None  None   None       |
|    all(noH): 2823   0      1.27    92.85   15.36    None  None   None       |
|    Sol.    : 438    0      3.22    84.96   39.57    None  None   None       |
|    Mac.    : 2385   0      1.27    92.85   10.91    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:     1.272 -  10.430: 1566   |   5:    47.063 -  56.222:   97        |
|      1:    10.430 -  19.589:  683   |   6:    56.222 -  65.380:   62        |
|      2:    19.589 -  28.747:  170   |   7:    65.380 -  74.538:   20        |
|      3:    28.747 -  37.905:  112   |   8:    74.538 -  83.697:    8        |
|      4:    37.905 -  47.063:  100   |   9:    83.697 -  92.855:    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)= 353         
Filter by distance & map next to the model:
   mapped sites are within: 0.619 - 5.971
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 348 from: 353
   mapped sites are within: 0.726 - 5.971

peak=    9.704 closest distance to " CG2 VAL A 230 " =    1.394
peak=    8.540 closest distance to " CG2 VAL A 296 " =    1.247
peak=    7.729 closest distance to " O   HOH Z 120 " =    1.205
peak=    6.297 closest distance to " CG  LEU A   5 " =    1.331
peak=    6.164 closest distance to " O   HOH Z 279 " =    1.231
peak=    5.909 closest distance to " NH2 ARG A  56 " =    2.284
peak=    5.426 closest distance to " CB  GLN A 223 " =    1.375
peak=    5.410 closest distance to " O   HOH Z 278 " =    1.143
peak=    5.407 closest distance to " O   HOH Z 247 " =    1.541
peak=    5.393 closest distance to " O   HOH Z 124 " =    1.644
peak=    5.352 closest distance to " CG  PRO A  54 " =    1.288
peak=    5.280 closest distance to " CD2 LEU A   5 " =    1.204
peak=    5.278 closest distance to " O   HOH Z  48 " =    2.042
peak=    5.116 closest distance to " CG  PRO A 198 " =    1.285
peak=    5.108 closest distance to " CD1AILE A 234 " =    1.056
peak=    4.931 closest distance to " CG  PRO A 280 " =    0.827
peak=    4.910 closest distance to " CB  PRO A  54 " =    0.880
peak=    4.899 closest distance to " O   HOH Z 132 " =    1.178
peak=    4.894 closest distance to " O   HOH Z  11 " =    1.347
peak=    4.733 closest distance to " CB  SER A  63 " =    1.261
peak=    4.682 closest distance to " CG  PRO A 213 " =    1.289
peak=    4.669 closest distance to " CB  VAL A 230 " =    1.288
peak=    4.609 closest distance to " O   HOH Z  80 " =    1.820
peak=    4.558 closest distance to " CG  LEU A 228 " =    1.292
peak=    4.521 closest distance to " C   PRO A 198 " =    1.534
peak=    4.486 closest distance to " O   HOH Z 126 " =    1.680
peak=    4.455 closest distance to " O   HOH Z 210 " =    1.105
peak=    4.415 closest distance to " O   HOH Z 411 " =    3.527
peak=    4.414 closest distance to " CB  ARG A 275 " =    0.898
peak=    4.401 closest distance to " O   HOH Z 316 " =    2.770
peak=    4.400 closest distance to " CB  SER A   3 " =    1.329
peak=    4.390 closest distance to " O   HOH Z  97 " =    1.906
peak=    4.381 closest distance to " O   HOH Z  37 " =    1.038
peak=    4.355 closest distance to " CA  ALA A  21 " =    1.287
peak=    4.339 closest distance to " O   HOH Z 389 " =    1.914
peak=    4.306 closest distance to " O   HOH Z 426 " =    1.469
peak=    4.296 closest distance to " CD2 LEU A 228 " =    1.228
peak=    4.291 closest distance to " CA  TYR A  30 " =    1.015
peak=    4.289 closest distance to " O   HOH Z 272 " =    1.929
peak=    4.280 closest distance to " CB  TYR A 169 " =    0.904
peak=    4.280 closest distance to " O   HOH Z  43 " =    1.487
peak=    4.267 closest distance to " O   HOH Z   9 " =    2.247
peak=    4.245 closest distance to " CB  GLN A 183 " =    1.318
peak=    4.229 closest distance to " O   HOH Z 371 " =    3.224
peak=    4.221 closest distance to " O   HOH Z 423 " =    1.823
peak=    4.204 closest distance to " O   HOH Z 130 " =    2.767
peak=    4.201 closest distance to " O   SER A  87 " =    2.324
peak=    4.200 closest distance to " O   HOH Z 193 " =    1.771
peak=    4.199 closest distance to " O   HOH Z 234 " =    3.838
peak=    4.199 closest distance to " CB  VAL A 296 " =    0.972
peak=    4.197 closest distance to " O   HOH Z 394 " =    1.652
peak=    4.150 closest distance to " CB  GLU A 152 " =    1.099
peak=    4.144 closest distance to " O   HOH Z 232 " =    2.284
peak=    4.143 closest distance to " CA  VAL A  41 " =    0.805
peak=    4.136 closest distance to " NE2 GLN A  11 " =    1.088
peak=    4.132 closest distance to " O   HOH Z 403 " =    1.750
peak=    4.119 closest distance to " O   HOH Z 134 " =    1.735
peak=    4.110 closest distance to " CG2 THR A 221 " =    0.983
peak=    4.093 closest distance to " CD  ARG A 269 " =    1.007
peak=    4.092 closest distance to " CG  PRO A 198 " =    1.767
peak=    4.087 closest distance to " O   HOH Z 369 " =    2.242
peak=    4.075 closest distance to " CB  GLU A 128 " =    1.113
peak=    4.068 closest distance to " O   HOH Z 263 " =    1.446
peak=    4.037 closest distance to " N   ASN A  39 " =    1.232
peak=    4.032 closest distance to " CB  TRP A 179 " =    1.306
peak=    4.007 closest distance to " O   HOH Z  48 " =    2.121
peak=    4.000 closest distance to " CG1BVAL A  72 " =    1.640
peak=    3.999 closest distance to " CA  ASP A 191 " =    0.852
peak=    3.988 closest distance to " CD  ARG A 159 " =    0.803
peak=    3.986 closest distance to " OD2 ASP A 286 " =    2.820
peak=    3.966 closest distance to " O   HOH Z  40 " =    1.702
peak=    3.955 closest distance to " O   HOH Z  78 " =    1.742
peak=    3.949 closest distance to " O   HOH Z 128 " =    1.913
peak=    3.944 closest distance to " O   HOH Z  61 " =    1.543
peak=    3.933 closest distance to " O   HOH Z 163 " =    1.559
peak=    3.932 closest distance to " O   HOH Z 227 " =    1.790
peak=    3.928 closest distance to " O   HOH Z 133 " =    2.039
peak=    3.925 closest distance to " O   HOH Z 189 " =    2.729
peak=    3.922 closest distance to " O   HOH Z 221 " =    1.262
peak=    3.916 closest distance to " CB  VAL A 265 " =    1.165
peak=    3.911 closest distance to " O   HOH Z 155 " =    1.635
peak=    3.890 closest distance to " CB  ASN A 148 " =    1.224
peak=    3.889 closest distance to " O   HOH Z 280 " =    3.048
peak=    3.889 closest distance to " CB  PRO A 198 " =    1.064
peak=    3.888 closest distance to " O   HOH Z 433 " =    1.546
peak=    3.878 closest distance to " O   HOH Z 368 " =    2.268
peak=    3.871 closest distance to " NH2 ARG A 156 " =    1.184
peak=    3.868 closest distance to " O   HOH Z  63 " =    1.661
peak=    3.860 closest distance to " CB  SER A 141 " =    1.115
peak=    3.852 closest distance to " O   HOH Z 402 " =    1.477
peak=    3.850 closest distance to " OE1 GLN A  11 " =    1.850
peak=    3.849 closest distance to " O   HOH Z 344 " =    2.830
peak=    3.825 closest distance to " CG1 VAL A 153 " =    1.058
peak=    3.822 closest distance to " CB  LEU A 228 " =    1.370
peak=    3.816 closest distance to " O   HOH Z 136 " =    1.394
peak=    3.813 closest distance to " O   HOH Z 108 " =    1.279
peak=    3.805 closest distance to " CG1 ILE A  33 " =    1.327
peak=    3.804 closest distance to " O   HOH Z 346 " =    1.479
peak=    3.800 closest distance to " O   HOH Z  88 " =    3.084
peak=    3.800 closest distance to " OE1 GLU A   2 " =    2.122
peak=    3.800 closest distance to " CA  ASP A 140 " =    1.249
peak=    3.795 closest distance to " O   HOH Z  20 " =    1.866
peak=    3.794 closest distance to " CA  ALA A 295 " =    1.078
peak=    3.791 closest distance to " O   HOH Z  97 " =    2.654
peak=    3.773 closest distance to " O   HOH Z 395 " =    1.436
peak=    3.773 closest distance to " O   HOH Z 427 " =    2.981
peak=    3.772 closest distance to " OD1 ASN A  69 " =    2.489
peak=    3.770 closest distance to " O   HOH Z 133 " =    1.663
peak=    3.761 closest distance to " CE  LYS A 119 " =    1.068
peak=    3.759 closest distance to " O   HOH Z 102 " =    1.272
peak=    3.734 closest distance to " O   HOH Z 112 " =    1.527
peak=    3.733 closest distance to " O   TRP A 274 " =    1.818
peak=    3.727 closest distance to " O   HOH Z 236 " =    1.791
peak=    3.721 closest distance to " O   HOH Z  67 " =    1.860
peak=    3.721 closest distance to " O   HOH Z  44 " =    1.825
peak=    3.703 closest distance to " OE1 GLN A  58 " =    5.971
peak=    3.702 closest distance to " CB  ALA A 256 " =    1.020
peak=    3.702 closest distance to " NZ  LYS A 166 " =    2.977
peak=    3.698 closest distance to " O   HOH Z 193 " =    2.218
peak=    3.698 closest distance to " O   HOH Z 108 " =    2.306
peak=    3.694 closest distance to " O   HOH Z 142 " =    1.544
peak=    3.692 closest distance to " O   HOH Z 298 " =    1.946
peak=    3.691 closest distance to " NZ  LYS A 117 " =    3.167
peak=    3.689 closest distance to " CD2 HIS A  81 " =    1.225
peak=    3.674 closest distance to " CA  ALA A 160 " =    0.850
peak=    3.674 closest distance to " CA  ARG A  36 " =    1.111
peak=    3.667 closest distance to " CD2 LEU A 255 " =    1.156
peak=    3.664 closest distance to " O   HOH Z 260 " =    1.295
peak=    3.662 closest distance to " O   HOH Z 406 " =    1.717
peak=    3.660 closest distance to " CG  PRO A 243 " =    1.175
peak=    3.652 closest distance to " O   HOH Z 345 " =    3.106
peak=    3.651 closest distance to " O   HOH Z  85 " =    1.384
peak=    3.650 closest distance to " O   HOH Z  69 " =    1.119
peak=    3.648 closest distance to " C   SER A  32 " =    1.107
peak=    3.645 closest distance to " O   HOH Z  44 " =    2.375
peak=    3.644 closest distance to " O   HOH Z  30 " =    1.255
peak=    3.642 closest distance to " O   HOH Z 295 " =    1.554
peak=    3.640 closest distance to " CB  GLU A 277 " =    3.640
peak=    3.640 closest distance to " CA  LYS A 117 " =    1.259
peak=    3.629 closest distance to " CD1 LEU A 300 " =    1.108
peak=    3.623 closest distance to " O   HOH Z   4 " =    1.733
peak=    3.612 closest distance to " O   MET A 105 " =    1.864
peak=    3.607 closest distance to " CB  VAL A 202 " =    1.547
peak=    3.604 closest distance to " O   HOH Z 303 " =    2.172
peak=    3.602 closest distance to " CB  ILE A 199 " =    1.057
peak=    3.599 closest distance to " CD  LYS A 119 " =    1.449
peak=    3.598 closest distance to " CG AARG A 275 " =    1.045
peak=    3.598 closest distance to " O   HOH Z 132 " =    2.871
peak=    3.594 closest distance to " O   HOH Z  21 " =    1.897
peak=    3.584 closest distance to " O   GLY A  91 " =    1.305
peak=    3.582 closest distance to " O   HOH Z 131 " =    2.461
peak=    3.581 closest distance to " O   HOH Z 373 " =    1.600
peak=    3.581 closest distance to " NH1 ARG A  14 " =    1.082
peak=    3.576 closest distance to " CB  ASN A 187 " =    1.167
peak=    3.570 closest distance to " CB  LEU A 143 " =    1.144
peak=    3.569 closest distance to " O   HOH Z 276 " =    1.364
peak=    3.563 closest distance to " OG  SER A 276 " =    1.430
peak=    3.544 closest distance to " CA  GLY A  80 " =    1.117
peak=    3.543 closest distance to " CB  ALA A   9 " =    1.485
peak=    3.542 closest distance to " NH1 ARG A 269 " =    0.853
peak=    3.529 closest distance to " O   HOH Z 126 " =    1.671
peak=    3.527 closest distance to " CA  GLY A 211 " =    1.184
peak=    3.526 closest distance to " NE1 TRP A 274 " =    0.881
peak=    3.526 closest distance to " O   HOH Z 214 " =    2.272
peak=    3.525 closest distance to " CA  THR A 246 " =    1.122
peak=    3.522 closest distance to " O   HOH Z 203 " =    1.726
peak=    3.521 closest distance to " O   HOH Z 301 " =    1.884
peak=    3.521 closest distance to " CB  SER A 273 " =    0.860
peak=    3.516 closest distance to " CB  TRP A 266 " =    0.889
peak=    3.515 closest distance to " O   HOH Z 344 " =    1.832
peak=    3.508 closest distance to " O   HOH Z 374 " =    2.541
peak=    3.506 closest distance to " CB  ALA A 291 " =    1.309
peak=    3.502 closest distance to " CG2 VAL A 257 " =    0.807
peak=    3.495 closest distance to " NH2BARG A 102 " =    0.930
peak=    3.490 closest distance to " CB  GLN A  58 " =    0.779
peak=    3.488 closest distance to " O   HOH Z 291 " =    1.520
peak=    3.484 closest distance to " O   HOH Z 245 " =    1.351
peak=    3.483 closest distance to " N   LYS A 166 " =    0.932
peak=    3.482 closest distance to " O   HOH Z 280 " =    2.371
peak=    3.481 closest distance to " O   HOH Z   9 " =    2.278
peak=    3.479 closest distance to " O   GLN A 278 " =    1.302
peak=    3.479 closest distance to " CA  THR A 264 " =    0.790
peak=    3.478 closest distance to " O   HOH Z  54 " =    1.508
peak=    3.476 closest distance to " CA  ARG A 195 " =    1.170
peak=    3.474 closest distance to " CA  ASN A 176 " =    1.038
peak=    3.468 closest distance to " CB  ARG A 139 " =    0.874
peak=    3.465 closest distance to " O   HOH Z 383 " =    2.024
peak=    3.462 closest distance to " O   HOH Z 366 " =    2.966
peak=    3.456 closest distance to " CB  ARG A  79 " =    1.358
peak=    3.455 closest distance to " CD1 LEU A 222 " =    0.819
peak=    3.453 closest distance to " CD  LYS A 166 " =    1.401
peak=    3.446 closest distance to " N   SER A 164 " =    0.994
peak=    3.446 closest distance to " O   ASP A 124 " =    1.276
peak=    3.446 closest distance to " O   THR A  31 " =    1.480
peak=    3.444 closest distance to " O   HOH Z  54 " =    2.436
peak=    3.438 closest distance to " O   ALA A 158 " =    1.267
peak=    3.436 closest distance to " CB  ARG A 190 " =    1.723
peak=    3.435 closest distance to " O   HOH Z 185 " =    1.678
peak=    3.433 closest distance to " O   HOH Z  48 " =    1.939
peak=    3.425 closest distance to " CA  GLN A 194 " =    0.981
peak=    3.421 closest distance to " CZ  PHE A 192 " =    1.061
peak=    3.419 closest distance to " O   GLY A  23 " =    2.449
peak=    3.416 closest distance to " CB  SER A  28 " =    0.989
peak=    3.412 closest distance to " O   HOH Z 217 " =    1.406
peak=    3.409 closest distance to " O   HOH Z 145 " =    2.385
peak=    3.408 closest distance to " O   HOH Z 149 " =    2.135
peak=    3.405 closest distance to " CD1 TRP A 266 " =    1.192
peak=    3.400 closest distance to " O   HOH Z 130 " =    1.179
peak=    3.394 closest distance to " OG1 THR A 294 " =    2.235
peak=    3.393 closest distance to " O   HOH Z 261 " =    1.786
peak=    3.390 closest distance to " CB  ALA A 137 " =    1.175
peak=    3.388 closest distance to " O   HOH Z 151 " =    1.951
peak=    3.381 closest distance to " O   HOH Z 114 " =    1.236
peak=    3.381 closest distance to " CD BLYS A 290 " =    1.034
peak=    3.380 closest distance to " CG2 ILE A 106 " =    0.881
peak=    3.379 closest distance to " O   HOH Z 420 " =    2.188
peak=    3.377 closest distance to " CA  ALA A  51 " =    0.985
peak=    3.374 closest distance to " CB AVAL A  41 " =    1.178
peak=    3.373 closest distance to " O   HOH Z 327 " =    2.667
peak=    3.371 closest distance to " O   HOH Z 227 " =    1.656
peak=    3.366 closest distance to " CG2 THR A 220 " =    0.880
peak=    3.365 closest distance to " CA  GLU A 152 " =    0.886
peak=    3.365 closest distance to " OD1 ASP A 238 " =    0.867
peak=    3.363 closest distance to " O   HOH Z 128 " =    2.013
peak=    3.361 closest distance to " CA  THR A 221 " =    0.880
peak=    3.359 closest distance to " CB  ALA A 100 " =    1.336
peak=    3.356 closest distance to " C   ALA A 299 " =    0.955
peak=    3.355 closest distance to " O   HOH Z 128 " =    1.622
peak=    3.352 closest distance to " CA  PHE A  59 " =    1.042
peak=    3.347 closest distance to " O   HOH Z 273 " =    2.753
peak=    3.347 closest distance to " ND2 ASN A 187 " =    1.621
peak=    3.343 closest distance to " O   HOH Z 197 " =    1.940
peak=    3.343 closest distance to " CB  SER A 216 " =    0.726
peak=    3.342 closest distance to " NH2BARG A 145 " =    2.179
peak=    3.341 closest distance to " NZ  LYS A  76 " =    1.299
peak=    3.339 closest distance to " O   HOH Z 280 " =    1.577
peak=    3.337 closest distance to " CA  VAL A 126 " =    0.951
peak=    3.334 closest distance to " O   HOH Z 180 " =    2.145
peak=    3.334 closest distance to " O   HOH Z 313 " =    1.869
peak=    3.331 closest distance to " O   HOH Z  66 " =    2.206
peak=    3.331 closest distance to " CG  ASP A 231 " =    1.124
peak=    3.330 closest distance to " N   TYR A 247 " =    1.119
peak=    3.324 closest distance to " O   HOH Z 326 " =    1.440
peak=    3.323 closest distance to " O   HOH Z 211 " =    2.493
peak=    3.320 closest distance to " CG  ARG A  66 " =    0.959
peak=    3.314 closest distance to " CD  ARG A 195 " =    3.419
peak=    3.314 closest distance to " OD1 ASN A 217 " =    1.760
peak=    3.314 closest distance to " CG  ASN A 252 " =    1.087
peak=    3.314 closest distance to " O   HOH Z 419 " =    1.684
peak=    3.314 closest distance to " CA  LEU A 282 " =    1.161
peak=    3.313 closest distance to " CB  GLN A  88 " =    1.168
peak=    3.313 closest distance to " CA  LEU A 101 " =    1.437
peak=    3.305 closest distance to " CG1 ILE A  49 " =    1.727
peak=    3.305 closest distance to " O   HOH Z 409 " =    3.535
peak=    3.302 closest distance to " N   ALA A 256 " =    0.851
peak=    3.298 closest distance to " O   ALA A   1 " =    1.482
peak=    3.297 closest distance to " OG BSER A 164 " =    2.231
peak=    3.293 closest distance to " O   HOH Z 403 " =    1.357
peak=    3.291 closest distance to " CG1 VAL A 296 " =    1.132
peak=    3.288 closest distance to " O   HOH Z 355 " =    1.775
peak=    3.287 closest distance to " O   HOH Z 261 " =    2.050
peak=    3.285 closest distance to " O   HOH Z 155 " =    2.739
peak=    3.284 closest distance to " CD2 LEU A 297 " =    0.841
peak=    3.283 closest distance to " O   HOH Z 214 " =    2.405
peak=    3.279 closest distance to " O   HOH Z 139 " =    5.151
peak=    3.276 closest distance to " CG BARG A 102 " =    1.891
peak=    3.272 closest distance to " O   HOH Z  90 " =    3.252
peak=    3.270 closest distance to " CA  ILE A 263 " =    0.996
peak=    3.269 closest distance to " O   HOH Z 423 " =    3.252
peak=    3.269 closest distance to " O   HOH Z 411 " =    1.847
peak=    3.264 closest distance to " OG  SER A  97 " =    2.565
peak=    3.262 closest distance to " NH1 ARG A 138 " =    1.090
peak=    3.254 closest distance to " O   HOH Z 387 " =    2.632
peak=    3.252 closest distance to " CG2 ILE A 120 " =    1.415
peak=    3.251 closest distance to " O   GLY A  57 " =    2.432
peak=    3.250 closest distance to " O   HOH Z 118 " =    1.360
peak=    3.249 closest distance to " CE1 TYR A 186 " =    1.272
peak=    3.249 closest distance to " N   ARG A 190 " =    1.068
peak=    3.243 closest distance to " OG  SER A  22 " =    2.823
peak=    3.242 closest distance to " CG2 VAL A 174 " =    1.222
peak=    3.241 closest distance to " O   HOH Z 196 " =    1.040
peak=    3.240 closest distance to " O   HOH Z 166 " =    1.549
peak=    3.234 closest distance to " CB  ARG A 259 " =    1.912
peak=    3.233 closest distance to " CG2 THR A  82 " =    0.883
peak=    3.232 closest distance to " CB  TYR A 247 " =    0.979
peak=    3.232 closest distance to " CE1 HIS A 108 " =    1.114
peak=    3.231 closest distance to " CA  SER A  87 " =    0.902
peak=    3.230 closest distance to " NH2AARG A 275 " =    3.852
peak=    3.230 closest distance to " O   HOH Z 422 " =    2.627
peak=    3.226 closest distance to " O   HOH Z  19 " =    1.781
peak=    3.225 closest distance to " O   HOH Z 425 " =    1.353
peak=    3.223 closest distance to " CG1BVAL A 121 " =    1.251
peak=    3.221 closest distance to " CB  ALA A 248 " =    1.294
peak=    3.219 closest distance to " O   HOH Z 329 " =    3.600
peak=    3.218 closest distance to " O   HOH Z 217 " =    2.388
peak=    3.216 closest distance to " CG  MET A 185 " =    1.219
peak=    3.212 closest distance to " O   HOH Z 175 " =    3.596
peak=    3.212 closest distance to " CG  GLN A  58 " =    2.525
peak=    3.211 closest distance to " CB  ASN A  39 " =    0.842
peak=    3.207 closest distance to " N   ARG A 156 " =    1.405
peak=    3.201 closest distance to " CB  ASP A 124 " =    0.795
peak=    3.200 closest distance to " O   HOH Z 116 " =    1.697
peak=    3.200 closest distance to " CD2 TYR A 186 " =    1.045
peak=    3.195 closest distance to " CB  ALA A  71 " =    1.241
peak=    3.192 closest distance to " O   ASN A 217 " =    1.278
peak=    3.192 closest distance to " O   HOH Z 173 " =    2.258
peak=    3.192 closest distance to " CB  SER A  62 " =    0.783
peak=    3.189 closest distance to " CA  TYR A 116 " =    1.466
peak=    3.184 closest distance to " CG2 VAL A 202 " =    1.199
peak=    3.178 closest distance to " CA  ASP A 162 " =    1.189
peak=    3.175 closest distance to " O   HOH Z 277 " =    2.451
peak=    3.174 closest distance to " CA  GLU A  46 " =    0.811
peak=    3.167 closest distance to " CA  MET A  40 " =    1.039
peak=    3.161 closest distance to " CB  TYR A  30 " =    1.461
peak=    3.160 closest distance to " O   HOH Z 368 " =    3.324
peak=    3.160 closest distance to " O   ALA A   1 " =    1.647
peak=    3.156 closest distance to " NH1AARG A 145 " =    0.943
peak=    3.150 closest distance to " O   HOH Z 194 " =    1.943
peak=    3.147 closest distance to " CB  THR A 157 " =    1.029
peak=    3.146 closest distance to " O   HOH Z 298 " =    5.064
peak=    3.145 closest distance to " O   HOH Z 248 " =    1.599
peak=    3.139 closest distance to " CG  MET A 188 " =    1.345
peak=    3.137 closest distance to " O   HOH Z 345 " =    1.821
peak=    3.131 closest distance to " CG1 ILE A 120 " =    1.036
peak=    3.124 closest distance to " O   HOH Z 156 " =    2.430
peak=    3.124 closest distance to " CG  LEU A 167 " =    1.119
peak=    3.124 closest distance to " O   HOH Z 109 " =    2.518
peak=    3.124 closest distance to " CD1 ILE A 199 " =    1.011
peak=    3.123 closest distance to " O   HOH Z 279 " =    2.191
peak=    3.122 closest distance to " O   HOH Z 404 " =    2.260
peak=    3.120 closest distance to " OG  SER A 206 " =    1.236
peak=    3.117 closest distance to " CB  GLU A 236 " =    1.234
peak=    3.117 closest distance to " CG2 VAL A 268 " =    0.961
peak=    3.115 closest distance to " O   HOH Z 367 " =    3.477
peak=    3.111 closest distance to " CG2 VAL A  67 " =    0.938
peak=    3.110 closest distance to " O   HOH Z  49 " =    1.811
peak=    3.108 closest distance to " CG  GLN A  55 " =    2.113
peak=    3.103 closest distance to " O   HOH Z 377 " =    1.207
peak=    3.092 closest distance to " NE2 GLN A  58 " =    4.219
peak=    3.083 closest distance to " OG1 THR A 294 " =    4.023
peak=    3.081 closest distance to " O   HOH Z  50 " =    1.877
peak=    3.073 closest distance to " CA  ALA A 158 " =    1.114
peak=    3.070 closest distance to " CB  ASN A 142 " =    1.102
peak=    3.065 closest distance to " CB  ALA A 248 " =    1.052
peak=    3.062 closest distance to " OD2 ASP A 298 " =    4.001
peak=    3.050 closest distance to " O   HOH Z 406 " =    3.031
peak=    3.046 closest distance to " O   HOH Z 214 " =    1.509
peak=    3.034 closest distance to " CG  MET A  93 " =    1.097

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 190         
Filter by distance & map next to the model:
   mapped sites are within: 0.753 - 5.517
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 189 from: 190
   mapped sites are within: 0.753 - 5.517

peak=   -5.283 closest distance to " CG2 VAL A 230 " =    0.865
peak=   -4.407 closest distance to " O   HOH Z 166 " =    1.749
peak=   -4.396 closest distance to " NH2 ARG A  66 " =    1.306
peak=   -4.319 closest distance to " OG ASER A 134 " =    1.175
peak=   -4.305 closest distance to " O   HOH Z  13 " =    1.391
peak=   -4.292 closest distance to " OG1 THR A   4 " =    1.856
peak=   -4.261 closest distance to " CG  ASP A 231 " =    0.831
peak=   -4.090 closest distance to " CD  ARG A 156 " =    2.040
peak=   -4.026 closest distance to " O   HOH Z 266 " =    4.482
peak=   -4.013 closest distance to " N   ALA A 226 " =    2.076
peak=   -4.013 closest distance to " O   HOH Z  71 " =    1.064
peak=   -4.011 closest distance to " O   HOH Z 290 " =    0.954
peak=   -4.007 closest distance to " CD2 LEU A 237 " =    2.617
peak=   -4.000 closest distance to " O   HOH Z  92 " =    1.290
peak=   -3.976 closest distance to " O   HOH Z 351 " =    1.383
peak=   -3.958 closest distance to " CA  SER A 164 " =    1.939
peak=   -3.951 closest distance to " O   HOH Z 407 " =    3.216
peak=   -3.930 closest distance to " O   HOH Z 266 " =    4.631
peak=   -3.929 closest distance to " N   SER A 276 " =    1.408
peak=   -3.926 closest distance to " CD1 PHE A  59 " =    1.943
peak=   -3.889 closest distance to " CE2 TYR A  30 " =    2.783
peak=   -3.867 closest distance to " OXT GLY A 302 " =    2.802
peak=   -3.816 closest distance to " OE2 GLU A   2 " =    1.610
peak=   -3.814 closest distance to " NH2AARG A 275 " =    5.099
peak=   -3.805 closest distance to " O   HOH Z 103 " =    1.967
peak=   -3.800 closest distance to " CH2 TRP A 179 " =    1.214
peak=   -3.788 closest distance to " ND2 ASN A  60 " =    1.423
peak=   -3.782 closest distance to " O   ILE A 109 " =    2.645
peak=   -3.782 closest distance to " CG  GLU A  53 " =    1.493
peak=   -3.769 closest distance to " O   HOH Z 165 " =    2.034
peak=   -3.747 closest distance to " O   HOH Z 151 " =    1.413
peak=   -3.745 closest distance to " CA  ASP A 298 " =    1.060
peak=   -3.738 closest distance to " CA  GLY A 203 " =    2.196
peak=   -3.736 closest distance to " O   HOH Z  52 " =    1.844
peak=   -3.728 closest distance to " CZ  TYR A 169 " =    1.865
peak=   -3.721 closest distance to " O   VAL A  67 " =    2.696
peak=   -3.718 closest distance to " CD  GLN A  88 " =    2.239
peak=   -3.717 closest distance to " O   HOH Z 377 " =    1.108
peak=   -3.712 closest distance to " O   HOH Z  17 " =    1.300
peak=   -3.709 closest distance to " CD2 LEU A 300 " =    2.770
peak=   -3.708 closest distance to " CD1 LEU A 101 " =    2.712
peak=   -3.707 closest distance to " O   HOH Z  10 " =    1.514
peak=   -3.700 closest distance to " CD  LYS A 289 " =    2.499
peak=   -3.687 closest distance to " C   THR A 279 " =    1.187
peak=   -3.672 closest distance to " CG2 VAL A 112 " =    2.554
peak=   -3.663 closest distance to " O   HOH Z 423 " =    2.346
peak=   -3.649 closest distance to " O   HOH Z 210 " =    0.792
peak=   -3.648 closest distance to " C   ASN A 285 " =    2.298
peak=   -3.646 closest distance to " O   HOH Z 221 " =    1.208
peak=   -3.637 closest distance to " O   HOH Z 231 " =    1.923
peak=   -3.637 closest distance to " CG  ASP A  50 " =    2.337
peak=   -3.636 closest distance to " C   ALA A 158 " =    1.180
peak=   -3.621 closest distance to " OD1 ASN A 249 " =    1.107
peak=   -3.605 closest distance to " CB  ALA A 291 " =    2.517
peak=   -3.601 closest distance to " O   SER A 271 " =    2.154
peak=   -3.600 closest distance to " C   HIS A 108 " =    1.159
peak=   -3.595 closest distance to " O   ASP A 191 " =    1.430
peak=   -3.590 closest distance to " O   HOH Z  11 " =    1.585
peak=   -3.581 closest distance to " OG  SER A  97 " =    2.270
peak=   -3.572 closest distance to " CA  ASN A 127 " =    0.962
peak=   -3.571 closest distance to " CG1 VAL A 296 " =    1.256
peak=   -3.570 closest distance to " C   ASN A 187 " =    1.922
peak=   -3.567 closest distance to " O   HOH Z 234 " =    4.340
peak=   -3.558 closest distance to " SG  CYS A 254 " =    3.095
peak=   -3.557 closest distance to " CA  ASP A  27 " =    2.452
peak=   -3.542 closest distance to " O   PRO A 198 " =    1.263
peak=   -3.534 closest distance to " N   GLN A  58 " =    1.776
peak=   -3.533 closest distance to " ND2 ASN A  45 " =    1.037
peak=   -3.530 closest distance to " OE1 GLN A 223 " =    2.457
peak=   -3.528 closest distance to " O   HOH Z 426 " =    1.820
peak=   -3.525 closest distance to " CD  ARG A 139 " =    1.557
peak=   -3.523 closest distance to " O   ASN A 187 " =    1.492
peak=   -3.519 closest distance to " O   ALA A 256 " =    1.392
peak=   -3.512 closest distance to " CB  ALA A 248 " =    1.931
peak=   -3.508 closest distance to " CB  TYR A  15 " =    2.209
peak=   -3.497 closest distance to " CD2 LEU A 167 " =    1.735
peak=   -3.495 closest distance to " CB  SER A 134 " =    1.821
peak=   -3.490 closest distance to " CG  MET A 105 " =    0.868
peak=   -3.482 closest distance to " O   HOH Z  38 " =    1.479
peak=   -3.478 closest distance to " CD2 TYR A 293 " =    2.190
peak=   -3.477 closest distance to " N   THR A 235 " =    1.253
peak=   -3.474 closest distance to " NE2 GLN A  88 " =    1.028
peak=   -3.473 closest distance to " N   ALA A  43 " =    2.528
peak=   -3.471 closest distance to " O   HOH Z  15 " =    1.640
peak=   -3.470 closest distance to " O   ALA A 161 " =    1.513
peak=   -3.469 closest distance to " O   HOH Z  43 " =    1.719
peak=   -3.467 closest distance to " O   HOH Z  37 " =    1.370
peak=   -3.461 closest distance to " O   HOH Z 360 " =    2.542
peak=   -3.448 closest distance to " O   HOH Z 222 " =    1.276
peak=   -3.431 closest distance to " OG  SER A  32 " =    1.099
peak=   -3.424 closest distance to " O   HOH Z 275 " =    1.508
peak=   -3.422 closest distance to " O   HOH Z 292 " =    4.377
peak=   -3.418 closest distance to " O   HOH Z 177 " =    1.662
peak=   -3.418 closest distance to " O   HOH Z 191 " =    5.517
peak=   -3.410 closest distance to " O   HOH Z 185 " =    2.176
peak=   -3.408 closest distance to " CE  MET A 105 " =    2.163
peak=   -3.408 closest distance to " CG  TRP A 266 " =    1.783
peak=   -3.408 closest distance to " CB  CYS A 254 " =    2.410
peak=   -3.408 closest distance to " OG  SER A  62 " =    1.500
peak=   -3.401 closest distance to " O   HOH Z 184 " =    1.370
peak=   -3.388 closest distance to " O   HOH Z 388 " =    1.990
peak=   -3.384 closest distance to " CB  ALA A  43 " =    2.629
peak=   -3.383 closest distance to " O   HOH Z  98 " =    1.938
peak=   -3.382 closest distance to " CD  ARG A 195 " =    4.970
peak=   -3.382 closest distance to " O   HOH Z 150 " =    1.354
peak=   -3.378 closest distance to " CA  VAL A 296 " =    0.953
peak=   -3.377 closest distance to " CG2 ILE A 263 " =    2.382
peak=   -3.375 closest distance to " CE3 TRP A 150 " =    2.309
peak=   -3.372 closest distance to " O   VAL A  67 " =    2.457
peak=   -3.371 closest distance to " CB  PHE A 208 " =    2.292
peak=   -3.365 closest distance to " O   HOH Z 350 " =    1.877
peak=   -3.362 closest distance to " CG  LYS A 193 " =    2.299
peak=   -3.357 closest distance to " CB  ASP A 162 " =    2.708
peak=   -3.340 closest distance to " CD1 LEU A 228 " =    2.411
peak=   -3.339 closest distance to " CD1 LEU A  25 " =    2.531
peak=   -3.338 closest distance to " O   HOH Z 208 " =    1.375
peak=   -3.326 closest distance to " CG  PRO A 243 " =    1.610
peak=   -3.322 closest distance to " O   HOH Z 396 " =    1.705
peak=   -3.322 closest distance to " O   HOH Z  97 " =    1.467
peak=   -3.320 closest distance to " CA  GLY A 133 " =    1.916
peak=   -3.315 closest distance to " CD2 PHE A  61 " =    1.669
peak=   -3.312 closest distance to " OD2 ASP A 171 " =    1.728
peak=   -3.307 closest distance to " OXT GLY A 302 " =    3.518
peak=   -3.303 closest distance to " CE  MET A 105 " =    2.025
peak=   -3.301 closest distance to " CG  GLU A 277 " =    1.172
peak=   -3.298 closest distance to " O   HOH Z 241 " =    1.351
peak=   -3.293 closest distance to " O   HOH Z  63 " =    0.753
peak=   -3.286 closest distance to " O   HOH Z 353 " =    2.343
peak=   -3.284 closest distance to " CA  VAL A 197 " =    1.030
peak=   -3.283 closest distance to " O   GLY A 211 " =    1.457
peak=   -3.278 closest distance to " O   LEU A 228 " =    2.431
peak=   -3.267 closest distance to " N   GLN A  55 " =    1.522
peak=   -3.261 closest distance to " O   HOH Z 136 " =    2.124
peak=   -3.260 closest distance to " OG BSER A 134 " =    1.236
peak=   -3.259 closest distance to " O   GLY A 118 " =    1.976
peak=   -3.246 closest distance to " O   HOH Z 166 " =    2.056
peak=   -3.245 closest distance to " O   HOH Z 198 " =    2.331
peak=   -3.244 closest distance to " O   HOH Z  60 " =    2.424
peak=   -3.240 closest distance to " CD  GLN A  88 " =    0.825
peak=   -3.239 closest distance to " O   HOH Z 189 " =    1.718
peak=   -3.232 closest distance to " N   THR A 157 " =    1.609
peak=   -3.232 closest distance to " OD1 ASP A 191 " =    1.616
peak=   -3.232 closest distance to " ND2BASN A 224 " =    1.799
peak=   -3.230 closest distance to " O   HOH Z  48 " =    1.533
peak=   -3.226 closest distance to " O   HOH Z 308 " =    1.735
peak=   -3.225 closest distance to " O   HOH Z 193 " =    1.826
peak=   -3.223 closest distance to " CE  MET A  93 " =    1.269
peak=   -3.222 closest distance to " OH  TYR A 172 " =    1.734
peak=   -3.219 closest distance to " O   HOH Z 283 " =    1.952
peak=   -3.218 closest distance to " O   TRP A  92 " =    1.865
peak=   -3.212 closest distance to " CD1 TRP A 179 " =    1.058
peak=   -3.206 closest distance to " N   ALA A 248 " =    1.850
peak=   -3.202 closest distance to " O   HOH Z 252 " =    4.184
peak=   -3.194 closest distance to " CG1 VAL A 112 " =    2.638
peak=   -3.182 closest distance to " O   ALA A 100 " =    2.356
peak=   -3.181 closest distance to " O   HOH Z 100 " =    0.877
peak=   -3.179 closest distance to " OD1 ASN A 148 " =    1.609
peak=   -3.178 closest distance to " NH2 ARG A  79 " =    1.866
peak=   -3.178 closest distance to " O   HOH Z 295 " =    1.365
peak=   -3.174 closest distance to " CZ3 TRP A  92 " =    1.118
peak=   -3.174 closest distance to " CD  PRO A 198 " =    1.170
peak=   -3.171 closest distance to " O   SER A 146 " =    0.930
peak=   -3.162 closest distance to " CG  GLN A  58 " =    1.277
peak=   -3.158 closest distance to " ND2 ASN A 215 " =    2.154
peak=   -3.156 closest distance to " OG1 THR A  82 " =    1.366
peak=   -3.146 closest distance to " O   HOH Z 341 " =    1.135
peak=   -3.145 closest distance to " O   HOH Z 313 " =    2.153
peak=   -3.139 closest distance to " CG  ARG A 269 " =    2.275
peak=   -3.138 closest distance to " O   HOH Z 231 " =    1.442
peak=   -3.134 closest distance to " CZ  ARG A  66 " =    1.220
peak=   -3.134 closest distance to " O   HOH Z 431 " =    2.278
peak=   -3.129 closest distance to " O   HOH Z 313 " =    1.219
peak=   -3.126 closest distance to " O   HOH Z 414 " =    1.448
peak=   -3.125 closest distance to " O   GLY A  80 " =    2.201
peak=   -3.125 closest distance to " CB  ALA A  51 " =    1.866
peak=   -3.120 closest distance to " O   HOH Z 297 " =    2.852
peak=   -3.120 closest distance to " O   HOH Z 171 " =    2.143
peak=   -3.115 closest distance to " CB  SER A 245 " =    2.375
peak=   -3.113 closest distance to " NH1 ARG A 195 " =    2.632
peak=   -3.113 closest distance to " O   HOH Z 418 " =    1.619
peak=   -3.111 closest distance to " C   GLU A  46 " =    1.137
peak=   -3.104 closest distance to " O   HOH Z 108 " =    2.166
peak=   -3.104 closest distance to " OE2 GLU A 277 " =    2.837
peak=   -3.102 closest distance to " O   HOH Z 120 " =    1.426
peak=   -3.100 closest distance to " O   VAL A 197 " =    1.383
peak=   -3.100 closest distance to " C   SER A 206 " =    1.603
peak=   -3.069 closest distance to " O   GLY A 203 " =    2.477
peak=   -3.066 closest distance to " O   HOH Z 366 " =    1.695
peak=   -3.004 closest distance to " O   HOH Z 193 " =    2.344

================= 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    :  0.4812 0.4808   6.284417e+00   6.274858e+00
   1_bss:  0.4735 0.4687   6.282993e+00   6.266467e+00
   1_xyz:  0.4035 0.4260   6.182477e+00   6.216161e+00
   1_adp:  0.3606 0.4109   6.115302e+00   6.195247e+00
   1_occ:  0.3602 0.4116   6.115019e+00   6.195547e+00
   2_bss:  0.3583 0.4067   6.116055e+00   6.193969e+00
   2_xyz:  0.2705 0.3330   5.900464e+00   6.046348e+00
   2_adp:  0.2480 0.3114   5.828829e+00   5.989364e+00
   2_occ:  0.2477 0.3112   5.828286e+00   5.989110e+00
   3_bss:  0.2443 0.3083   5.827001e+00   5.987005e+00
   3_xyz:  0.1749 0.2253   5.525001e+00   5.727987e+00
   3_adp:  0.1581 0.2088   5.440045e+00   5.654022e+00
   3_occ:  0.1578 0.2087   5.439302e+00   5.653756e+00
   4_bss:  0.1575 0.2085   5.441611e+00   5.654877e+00
   4_xyz:  0.1301 0.1742   5.267164e+00   5.490755e+00
   4_adp:  0.1244 0.1688   5.234472e+00   5.465511e+00
   4_occ:  0.1242 0.1689   5.234464e+00   5.466228e+00
   5_bss:  0.1247 0.1695   5.237703e+00   5.469149e+00
   5_xyz:  0.1220 0.1669   5.222828e+00   5.451577e+00
   5_adp:  0.1212 0.1660   5.217163e+00   5.446507e+00
   5_occ:  0.1211 0.1661   5.217087e+00   5.446779e+00
   5_bss:  0.1211 0.1661   5.217121e+00   5.446855e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000   6.343   9.903   8.170   0.000   0.000   0.000
   1_xyz:  0.300  20.000   6.343   9.903   8.170   0.000   0.000   0.000
   1_adp:  0.300  20.000   6.343   9.903   8.170   0.000   0.000   0.000
   1_occ:  0.300  20.000   6.343   9.903   8.170   0.000   0.000   0.000
   2_bss:  0.326  41.989   3.262   6.437   5.497   0.000   0.000   0.000
   2_xyz:  0.326  41.989   3.262   6.437   5.497   0.000   0.000   0.000
   2_adp:  0.326  41.989   3.262   6.437   5.497   0.000   0.000   0.000
   2_occ:  0.326  41.989   3.262   6.437   5.497   0.000   0.000   0.000
   3_bss:  0.309  49.629   1.546   3.153   2.597   0.000   0.000   0.000
   3_xyz:  0.309  49.629   1.546   3.153   2.597   0.000   0.000   0.000
   3_adp:  0.309  49.629   1.546   3.153   2.597   0.000   0.000   0.000
   3_occ:  0.309  49.629   1.546   3.153   2.597   0.000   0.000   0.000
   4_bss:  0.319  49.629   0.820   1.973   1.623   0.000   0.000   0.000
   4_xyz:  0.319  49.629   0.820   1.973   1.623   0.000   0.000   0.000
   4_adp:  0.319  49.629   0.820   1.973   1.623   0.000   0.000   0.000
   4_occ:  0.319  49.629   0.820   1.973   1.623   0.000   0.000   0.000
   5_bss:  0.319  48.015   0.739   1.578   1.418   0.000   0.000   0.000
   5_xyz:  0.319  48.015   0.739   1.578   1.418   0.000   0.000   0.000
   5_adp:  0.319  48.015   0.739   1.578   1.418   0.000   0.000   0.000
   5_occ:  0.319  48.015   0.739   1.578   1.418   0.000   0.000   0.000
   5_bss:  0.320  49.893  -0.476   0.291   0.185   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.818 0.3951  0.4612    71365.625
   1_bss:  59.739 0.3936  0.5709    68439.647
   1_xyz:  51.574 0.4974  0.7167    54300.616
   1_adp:  47.436 0.5502  0.8490    48802.602
   1_occ:  47.504 0.5494  0.8472    48954.741
   2_bss:  47.184 0.5533  0.7695    48477.289
   2_xyz:  35.288 0.6973  0.9574    30208.270
   2_adp:  32.155 0.7336  0.9965    25893.151
   2_occ:  32.159 0.7335  0.9961    25877.725
   3_bss:  31.980 0.7355  0.9099    25682.620
   3_xyz:  22.411 0.8371  0.9864    13257.912
   3_adp:  20.168 0.8599  0.9946    11301.837
   3_occ:  20.164 0.8599  0.9944    11297.182
   4_bss:  20.206 0.8597  0.9609    11363.689
   4_xyz:  16.439 0.8941  0.9808     7945.980
   4_adp:  15.824 0.8997  0.9815     7562.552
   4_occ:  15.834 0.8996  0.9812     7574.563
   5_bss:  15.883 0.8993  0.9729     7658.682
   5_xyz:  15.444 0.9033  0.9721     7322.537
   5_adp:  15.319 0.9045  0.9687     7283.615
   5_occ:  15.322 0.9045  0.9685     7290.065
   5_bss:  15.322 0.9045  0.9695     7291.790
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3658e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3658e+01
   1_xyz:   1.722  0.013  0.108 18.204  0.007  4.111   1.4486e-01
   1_adp:   1.722  0.013  0.108 18.204  0.007  4.111   1.4486e-01
   1_occ:   1.722  0.013  0.108 18.204  0.007  4.111   1.4486e-01
   2_bss:   1.722  0.013  0.108 18.204  0.007  4.111   1.4486e-01
   2_xyz:   1.239  0.009  0.082 16.272  0.005  4.114   9.1162e-02
   2_adp:   1.239  0.009  0.082 16.272  0.005  4.114   9.1162e-02
   2_occ:   1.239  0.009  0.082 16.272  0.005  4.114   9.1162e-02
   3_bss:   1.239  0.009  0.082 16.272  0.005  4.114   9.1162e-02
   3_xyz:   1.111  0.008  0.079 15.624  0.004  4.132   7.7372e-02
   3_adp:   1.111  0.008  0.079 15.624  0.004  4.132   7.7372e-02
   3_occ:   1.111  0.008  0.079 15.624  0.004  4.132   7.7372e-02
   4_bss:   1.111  0.008  0.079 15.624  0.004  4.132   7.7372e-02
   4_xyz:   1.086  0.008  0.083 15.605  0.004  4.126   6.9197e-02
   4_adp:   1.086  0.008  0.083 15.605  0.004  4.126   6.9197e-02
   4_occ:   1.086  0.008  0.083 15.605  0.004  4.126   6.9197e-02
   5_bss:   1.086  0.008  0.083 15.605  0.004  4.126   6.9197e-02
   5_xyz:   0.935  0.006  0.071 15.176  0.003  4.126   5.3994e-02
   5_adp:   0.935  0.006  0.071 15.176  0.003  4.126   5.3994e-02
   5_occ:   0.935  0.006  0.071 15.176  0.003  4.126   5.3994e-02
   5_bss:   0.935  0.006  0.071 15.176  0.003  4.126   5.3994e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.120   6.9549e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.120   6.9549e+00
   1_xyz:  15.220  0.171  0.502 87.608  0.056  2.207   1.0137e-01
   1_adp:  15.220  0.171  0.502 87.608  0.056  2.207   1.0137e-01
   1_occ:  15.220  0.171  0.502 87.608  0.056  2.207   1.0137e-01
   2_bss:  15.220  0.171  0.502 87.608  0.056  2.207   1.0137e-01
   2_xyz:   8.572  0.087  0.291 82.950  0.038  2.186   1.0739e-01
   2_adp:   8.572  0.087  0.291 82.950  0.038  2.186   1.0739e-01
   2_occ:   8.572  0.087  0.291 82.950  0.038  2.186   1.0739e-01
   3_bss:   8.572  0.087  0.291 82.950  0.038  2.186   1.0739e-01
   3_xyz:   9.106  0.055  0.340 87.964  0.041  2.327   1.4762e-01
   3_adp:   9.106  0.055  0.340 87.964  0.041  2.327   1.4762e-01
   3_occ:   9.106  0.055  0.340 87.964  0.041  2.327   1.4762e-01
   4_bss:   9.106  0.055  0.340 87.964  0.041  2.327   1.4762e-01
   4_xyz:   7.122  0.050  0.560 79.955  0.028  2.293   4.6300e-02
   4_adp:   7.122  0.050  0.560 79.955  0.028  2.293   4.6300e-02
   4_occ:   7.122  0.050  0.560 79.955  0.028  2.293   4.6300e-02
   5_bss:   7.122  0.050  0.560 79.955  0.028  2.293   4.6300e-02
   5_xyz:   6.714  0.038  0.403 83.244  0.033  2.377   3.5661e-02
   5_adp:   6.714  0.038  0.403 83.244  0.033  2.377   3.5661e-02
   5_occ:   6.714  0.038  0.403 83.244  0.033  2.377   3.5661e-02
   5_bss:   6.714  0.038  0.403 83.244  0.033  2.377   3.5661e-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:  95.63   0.00  13.65  79.02   0.00  11.17  95.63   0.00  27.11
   1_occ:  95.63   0.00  13.65  79.02   0.00  11.17  95.63   0.00  27.11
   2_bss:  95.63   0.00  13.65  79.02   0.00  11.17  95.63   0.00  27.11
   2_xyz:  95.63   0.00  13.65  79.02   0.00  11.17  95.63   0.00  27.11
   2_adp:  87.61   0.00  14.09  71.64   0.00  10.54  87.61   1.38  33.41
   2_occ:  87.61   0.00  14.09  71.64   0.00  10.54  87.61   1.38  33.41
   3_bss:  87.61   0.00  14.09  71.64   0.00  10.54  87.61   1.38  33.41
   3_xyz:  87.61   0.00  14.09  71.64   0.00  10.54  87.61   1.38  33.41
   3_adp:  82.59   0.00  14.20  79.62   0.00   9.94  82.59   2.70  37.40
   3_occ:  82.59   0.00  14.20  79.62   0.00   9.94  82.59   2.70  37.40
   4_bss:  82.59   0.00  14.20  79.62   0.00   9.94  82.59   2.70  37.40
   4_xyz:  82.59   0.00  14.20  79.62   0.00   9.94  82.59   2.70  37.40
   4_adp:  90.55   0.00  14.27  90.55   0.00   9.77  83.78   2.82  38.78
   4_occ:  90.55   0.00  14.27  90.55   0.00   9.77  83.78   2.82  38.78
   5_bss:  90.55   0.00  14.27  90.55   0.00   9.77  83.78   2.82  38.78
   5_xyz:  90.55   0.00  14.27  90.55   0.00   9.77  83.78   2.82  38.78
   5_adp:  91.58   0.00  14.09  91.58   0.00   9.64  83.69   1.95  38.30
   5_occ:  91.58   0.00  14.09  91.58   0.00   9.64  83.69   1.95  38.30
   5_bss:  92.85   1.27  15.36  92.85   1.27  10.91  84.96   3.22  39.57
------------------------------------------------------------------------
 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:    1.175    0.021    0.412
   1_adp:    1.175    0.021    0.412
   1_occ:    1.175    0.021    0.412
   2_bss:    1.175    0.021    0.412
   2_xyz:    1.887    0.025    0.599
   2_adp:    1.887    0.025    0.599
   2_occ:    1.887    0.025    0.599
   3_bss:    1.887    0.025    0.599
   3_xyz:    1.588    0.062    0.694
   3_adp:    1.588    0.062    0.694
   3_occ:    1.588    0.062    0.694
   4_bss:    1.588    0.062    0.694
   4_xyz:    1.640    0.042    0.752
   4_adp:    1.640    0.042    0.752
   4_occ:    1.640    0.042    0.752
   5_bss:    1.640    0.042    0.752
   5_xyz:    1.792    0.028    0.765
   5_adp:    1.792    0.028    0.765
   5_occ:    1.792    0.028    0.765
   5_bss:    1.792    0.028    0.765
------------------------------------------------------------------------

CPU time actual refinement: 339.23


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_815/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_815/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_815/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_815/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_815/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 339.08 
  Macro-tasks:
    bulk solvent and scale       = 42.32  
    individual site refinement   = 135.43 
    weights calculation          = 32.88  
    collect and process          = 6.48   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 217.22 
  Micro-tasks:
    mask                            = 2.57   
    f_calc                          = 106.35 
    alpha_beta                      = 7.94   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 114.35 
    fmodel                         = 7.17   
    r_factors                      = 0.25   
    phase_errors                   = 10.17  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 250.19 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.838 micro seconds
Total CPU time: 5.88 minutes
from_scatterers_fft:    628 calls, 106.07 s
gradients_fft:          572 calls, 101.77 s

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

# Date 2008-01-16 Time 02:29:04 PST -0800 (1200479344.65 s)
Start R-work = 0.4812, R-free = 0.4808 (no bulk solvent and anisotropic scale)
Final R-work = 0.1369, R-free = 0.1830 (no bulk solvent and anisotropic scale)

Start R-work = 0.4735, R-free = 0.4687
Final R-work = 0.1211, R-free = 0.1661