# Date 2008-01-16 Time 01:03:23 PST -0800 (1200474203.76 s)
#phil __OFF__

Command line arguments: "../256.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27234
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 256

-------------------------------------------------------------------------------
  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: (69.1963, 45.9914, 85.5261, 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: 3.35, per 1000 atoms: 1.19


================================== 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: (69.1963, 45.9914, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7893 1.96192
Completeness in resolution range: 0.974092
Completeness with d_max=infinity: 0.97105

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7893
                             d_min =   1.9619

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: (69.1963, 45.9914, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7893 1.96192
Completeness in resolution range: 0.974092
Completeness with d_max=infinity: 0.97105

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7897 -  4.1976 [2114/2138]  1901   213  10.1%
  bin  2:  4.1976 -  3.3445 [2030/2050]  1828   202  10.0%
  bin  3:  3.3445 -  2.9254 [2000/2019]  1802   198   9.9%
  bin  4:  2.9254 -  2.6596 [1982/2012]  1781   201  10.1%
  bin  5:  2.6596 -  2.4699 [1976/1995]  1778   198  10.0%
  bin  6:  2.4699 -  2.3249 [1969/1994]  1769   200  10.2%
  bin  7:  2.3249 -  2.2089 [1935/1963]  1746   189   9.8%
  bin  8:  2.2089 -  2.1130 [1956/1992]  1760   196  10.0%
  bin  9:  2.1130 -  2.0319 [1932/1974]  1739   193  10.0%
  bin 10:  2.0319 -  1.9619 [1695/1973]  1526   169  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_256/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: 0.15 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:
        1.39 -     2.09: 19
        2.09 -     2.79: 725
        2.79 -     3.49: 4626
        3.49 -     4.20: 9553
        4.20 -     4.90: 14062
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.385 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.593 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.734 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 112 " - " O   HOH Z 408 "  1.747 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.750 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28980 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_256/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_256/model_refine_001.geo

CPU time processing inputs: 9.32


============================ 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 = 69.19625 45.9914 85.5261 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 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4945   r_free= 0.4896   ksol= 0.00   Bsol= 0.00   scale= 0.795    |
|                                                                             |
| 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:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.293479                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7897 -  4.6816 0.99   1376  152 0.4157 0.4179       6.613      6.6565|
|  2:  4.6816 -  3.7357 0.99   1316  148 0.4315 0.3907      6.8291      6.7918|
|  3:  3.7357 -  3.2693 0.99   1293  144 0.4590 0.4518       6.715      6.7594|
|  4:  3.2693 -  2.9730 0.99   1285  142 0.4762 0.4405      6.5585      6.4811|
|  5:  2.9730 -  2.7614 0.99   1273  141 0.5211 0.5146      6.3932       6.423|
|  6:  2.7614 -  2.5995 0.99   1285  141 0.5257 0.5722      6.3054       6.218|
|  7:  2.5995 -  2.4699 0.99   1262  144 0.5217 0.4797      6.2586      6.2021|
|  8:  2.4699 -  2.3629 0.98   1267  136 0.5423 0.5221      6.2012      6.2191|
|  9:  2.3629 -  2.2722 0.98   1256  141 0.5269 0.5971      6.1304      6.1683|
| 10:  2.2722 -  2.1941 1.00   1255  144 0.5342 0.5419      6.1286      6.1368|
| 11:  2.1941 -  2.1257 0.97   1253  136 0.5280 0.5229      6.0458      6.0792|
| 12:  2.1257 -  2.0651 0.98   1246  138 0.5194 0.5331      5.9979      6.0345|
| 13:  2.0651 -  2.0109 0.99   1252  138 0.5547 0.5251      5.9062      5.8784|
| 14:  2.0109 -  1.9619 0.80   1011  114 0.5395 0.5047      5.8621      5.7762|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7897 -  4.6816  1376   152  0.62  41.41   0.79     0.67      96875.33|
|  2:  4.6816 -  3.7357  1316   148  0.66  38.87   0.87     0.75     125468.12|
|  3:  3.7357 -  3.2693  1293   144  0.56  46.84   0.85     0.70     128482.59|
|  4:  3.2693 -  2.9730  1285   142  0.48  53.71   0.80     0.58     111915.09|
|  5:  2.9730 -  2.7614  1273   141  0.36  62.73   0.74     0.44      91094.80|
|  6:  2.7614 -  2.5995  1285   141  0.31  66.49   0.72     0.36      80315.06|
|  7:  2.5995 -  2.4699  1262   144  0.23  73.02   0.74     0.27      76304.42|
|  8:  2.4699 -  2.3629  1267   136  0.20  75.44   0.74     0.24      70826.32|
|  9:  2.3629 -  2.2722  1256   141  0.20  75.30   0.72     0.24      65069.87|
| 10:  2.2722 -  2.1941  1255   144  0.24  72.08   0.76     0.29      55690.85|
| 11:  2.1941 -  2.1257  1253   136  0.23  73.14   0.77     0.29      53365.16|
| 12:  2.1257 -  2.0651  1246   138  0.22  73.45   0.80     0.28      48517.92|
| 13:  2.0651 -  2.0109  1252   138  0.22  73.70   0.73     0.28      42001.58|
| 14:  2.0109 -  1.9619  1011   114  0.29  68.17   0.73     0.33      31238.10|
|alpha:            min =        0.24 max =            0.75 mean =         0.41|
|beta:             min =    31238.10 max =       128482.59 mean =     78086.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.35|
|phase err.(work): min =        0.00 max =           90.00 mean =        63.54|
|phase err.(test): min =        0.00 max =           89.95 mean =        63.65|
|-----------------------------------------------------------------------------|

============================== 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 = 21.211993             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.252   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.161323              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 84.292   (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 |  1.082 -  1.464:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.464 -  1.846:       16 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.846 -  2.228:      134 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.228 -  2.609:      617 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.609 -  2.991:     1425 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.991 -  3.373:     2596 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.373 -  3.755:     4034 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.755 -  4.136:     5278 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.136 -  4.518:     6801 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.518 -  4.900:     8099 |
|-----------------------------------------------------------------------------|
|-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 |       52.772 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.086    4.900  1.082 |       2.612 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.359)------------------------------------------|
|    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 = 11.359)------------------------------------------|
|    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 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4989   r_free= 0.4910   ksol= 0.00   Bsol= 0.00   scale= 0.764    |
|                                                                             |
| 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:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.294332                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4855   r_free= 0.4786   ksol= 0.41   Bsol= 20.00   scale= 0.980   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.52,9.53,7.20,0.00,0.00,0.00); trace/3= 7.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.286416                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.276223             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.156   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.892893              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.177   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4855      final r-factor (work) = 0.4195          |
| start r-factor (free) = 0.4786      final r-factor (free) = 0.4428          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 103.9690 = 16.28 * 0.50 * 6.2910 + 1.00 * 52.7718                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 50.8559 = 16.28 * 0.50 * 6.2309 + 1.00 * 0.1481                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4195      final r-factor (work) = 0.3759          |
| start r-factor (free) = 0.4428      final r-factor (free) = 0.4298          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.8088 = 1.89 * 1.00 * 6.2309 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.6975 = 1.89 * 1.00 * 6.1676 + 1.00 * 0.0229                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.359)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.47   14.83    None  None   None       |
|    all(noH): 2823   0      0.00    91.47   14.83    None  None   None       |
|    Sol.    : 438    0      0.00    88.40   25.32    None  None   None       |
|    Mac.    : 2385   0      0.00    91.47   12.90    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 -   9.147: 1149   |   5:    45.733 -  54.880:   50        |
|      1:     9.147 -  18.293:  786   |   6:    54.880 -  64.027:   29        |
|      2:    18.293 -  27.440:  451   |   7:    64.027 -  73.173:    5        |
|      3:    27.440 -  36.587:  252   |   8:    73.173 -  82.320:    4        |
|      4:    36.587 -  45.733:   95   |   9:    82.320 -  91.467:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3759 r_free = 0.4298             target_work(ml) = 6.153         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3750 r_free = 0.4294             target_work(ml) = 6.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3750   r_free= 0.4294   ksol= 0.41   Bsol= 20.00   scale= 1.102   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.52,9.53,7.20,0.00,0.00,0.00); trace/3= 7.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.151923                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3736   r_free= 0.4255   ksol= 0.36   Bsol= 30.88   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.76,5.77,4.69,0.00,0.00,0.00); trace/3= 4.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.151798                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.474310             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.198  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.799148              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.502  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3736      final r-factor (work) = 0.2921          |
| start r-factor (free) = 0.4255      final r-factor (free) = 0.3513          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.7462 = 14.47 * 0.50 * 6.1624 + 1.00 * 0.1481                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.9809 = 14.47 * 0.50 * 6.0615 + 1.00 * 0.1131                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2921      final r-factor (work) = 0.2660          |
| start r-factor (free) = 0.3513      final r-factor (free) = 0.3343          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8693 = 0.80 * 1.00 * 6.0615 + 1.00 * 0.0252                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8306 = 0.80 * 1.00 * 5.9207 + 1.00 * 0.0991                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.359)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    180.62  14.66    None  None   None       |
|    all(noH): 2823   0      0.00    180.62  14.66    None  None   None       |
|    Sol.    : 438    0      0.00    85.73   29.94    None  None   None       |
|    Mac.    : 2385   0      0.00    180.62  11.85    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 -  18.062: 1962   |   5:    90.312 - 108.374:    2        |
|      1:    18.062 -  36.125:  678   |   6:   108.374 - 126.437:    0        |
|      2:    36.125 -  54.187:  146   |   7:   126.437 - 144.499:    0        |
|      3:    54.187 -  72.250:   31   |   8:   144.499 - 162.562:    0        |
|      4:    72.250 -  90.312:    3   |   9:   162.562 - 180.624:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2660 r_free = 0.3343             target_work(ml) = 5.896         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2654 r_free = 0.3346             target_work(ml) = 5.896         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2654   r_free= 0.3346   ksol= 0.36   Bsol= 30.88   scale= 1.080   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.76,5.77,4.69,0.00,0.00,0.00); trace/3= 4.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.895770                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2642   r_free= 0.3325   ksol= 0.33   Bsol= 30.88   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.28,3.17,3.36,0.00,0.00,0.00); trace/3= 2.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.892822                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.038318              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.835  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.425487              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.486   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2642      final r-factor (work) = 0.2039          |
| start r-factor (free) = 0.3325      final r-factor (free) = 0.2632          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.9822 = 6.04 * 0.50 * 5.9186 + 1.00 * 0.1131                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.5654 = 6.04 * 0.50 * 5.7915 + 1.00 * 0.0799                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2039      final r-factor (work) = 0.1763          |
| start r-factor (free) = 0.2632      final r-factor (free) = 0.2315          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6002 = 0.43 * 1.00 * 5.7915 + 1.00 * 0.1360                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3918 = 0.43 * 1.00 * 5.5957 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.359)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.43  13.76    None  None   None       |
|    all(noH): 2823   0      0.00    109.43  13.76    None  None   None       |
|    Sol.    : 438    0      2.13    78.42   35.55    None  None   None       |
|    Mac.    : 2385   0      0.00    109.43  9.76     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.943: 1747   |   5:    54.716 -  65.659:   36        |
|      1:    10.943 -  21.886:  542   |   6:    65.659 -  76.602:    8        |
|      2:    21.886 -  32.830:  204   |   7:    76.602 -  87.545:    2        |
|      3:    32.830 -  43.773:  159   |   8:    87.545 -  98.488:    1        |
|      4:    43.773 -  54.716:  122   |   9:    98.488 - 109.432:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1763 r_free = 0.2315             target_work(ml) = 5.530         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1759 r_free = 0.2311             target_work(ml) = 5.528         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1759   r_free= 0.2311   ksol= 0.33   Bsol= 30.88   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.28,3.17,3.36,0.00,0.00,0.00); trace/3= 2.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.528249                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1752   r_free= 0.2298   ksol= 0.32   Bsol= 30.88   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.40,1.78,2.63,0.00,0.00,0.00); trace/3= 1.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.524700                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.959653              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.946   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.618888              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.256  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1752      final r-factor (work) = 0.1405          |
| start r-factor (free) = 0.2298      final r-factor (free) = 0.1908          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3637 = 2.96 * 0.50 * 5.5978 + 1.00 * 0.0799                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1051 = 2.96 * 0.50 * 5.4359 + 1.00 * 0.0609                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1405      final r-factor (work) = 0.1318          |
| start r-factor (free) = 0.1908      final r-factor (free) = 0.1828          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3750 = 0.62 * 1.00 * 5.4359 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2955 = 0.62 * 1.00 * 5.3036 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.359)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.10   14.10    None  None   None       |
|    all(noH): 2823   0      0.00    98.10   14.10    None  None   None       |
|    Sol.    : 438    0      1.36    85.22   39.22    None  None   None       |
|    Mac.    : 2385   0      0.00    98.10   9.49     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 -   9.810: 1682   |   5:    49.050 -  58.860:   91        |
|      1:     9.810 -  19.620:  584   |   6:    58.860 -  68.670:   49        |
|      2:    19.620 -  29.430:  161   |   7:    68.670 -  78.480:   17        |
|      3:    29.430 -  39.240:  119   |   8:    78.480 -  88.291:    7        |
|      4:    39.240 -  49.050:  112   |   9:    88.291 -  98.101:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1318 r_free = 0.1828             target_work(ml) = 5.279         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1316 r_free = 0.1825             target_work(ml) = 5.278         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1316   r_free= 0.1825   ksol= 0.32   Bsol= 30.88   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.40,1.78,2.63,0.00,0.00,0.00); trace/3= 1.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.277544                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1319   r_free= 0.1819   ksol= 0.31   Bsol= 34.39   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.10,1.31,2.46,0.00,0.00,0.00); trace/3= 1.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.276840                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.453677              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.593  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.190144              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.787   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1319      final r-factor (work) = 0.1178          |
| start r-factor (free) = 0.1819      final r-factor (free) = 0.1688          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2207 = 3.45 * 0.50 * 5.3043 + 1.00 * 0.0609                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0990 = 3.45 * 0.50 * 5.2300 + 1.00 * 0.0677                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1178      final r-factor (work) = 0.1166          |
| start r-factor (free) = 0.1688      final r-factor (free) = 0.1664          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0086 = 0.19 * 1.00 * 5.2300 + 1.00 * 0.0142                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0245 = 0.19 * 1.00 * 5.1881 + 1.00 * 0.0380                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.359)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.95   14.06    None  None   None       |
|    all(noH): 2823   0      0.00    97.95   14.06    None  None   None       |
|    Sol.    : 438    0      2.03    85.20   38.96    None  None   None       |
|    Mac.    : 2385   0      0.00    97.95   9.49     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 -   9.795: 1706   |   5:    48.973 -  58.767:   90        |
|      1:     9.795 -  19.589:  569   |   6:    58.767 -  68.562:   49        |
|      2:    19.589 -  29.384:  151   |   7:    68.562 -  78.356:   18        |
|      3:    29.384 -  39.178:  120   |   8:    78.356 -  88.151:    7        |
|      4:    39.178 -  48.973:  112   |   9:    88.151 -  97.945:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1166 r_free = 0.1664             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1164 r_free = 0.1663             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1663   ksol= 0.31   Bsol= 34.39   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.10,1.31,2.46,0.00,0.00,0.00); trace/3= 1.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.176682                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7897 -  4.6816 0.99   1376  152 0.1016 0.1351      5.4206      5.5743|
|  2:  4.6816 -  3.7357 0.99   1316  148 0.0873 0.1201      5.4704      5.6831|
|  3:  3.7357 -  3.2693 0.99   1293  144 0.1104 0.1500      5.5285      5.8875|
|  4:  3.2693 -  2.9730 0.99   1285  142 0.1295 0.1867      5.5114      5.7018|
|  5:  2.9730 -  2.7614 0.99   1273  141 0.1329 0.1813      5.3722      5.5806|
|  6:  2.7614 -  2.5995 0.99   1285  141 0.1253 0.1908      5.2501      5.4775|
|  7:  2.5995 -  2.4699 0.99   1262  144 0.1333 0.1740      5.2095       5.416|
|  8:  2.4699 -  2.3629 0.98   1267  136 0.1266 0.1736       5.127      5.3929|
|  9:  2.3629 -  2.2722 0.98   1256  141 0.1220 0.1727      5.0663      5.2899|
| 10:  2.2722 -  2.1941 1.00   1255  144 0.1181 0.1848      5.0067      5.2732|
| 11:  2.1941 -  2.1257 0.97   1253  136 0.1175 0.1855      4.9742      5.2931|
| 12:  2.1257 -  2.0651 0.98   1246  138 0.1200 0.1769      4.9265      5.2352|
| 13:  2.0651 -  2.0109 0.99   1252  138 0.1139 0.1791      4.8032      5.0892|
| 14:  2.0109 -  1.9619 0.80   1011  114 0.0966 0.1703      4.6388      4.9492|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7897 -  4.6816  1376   152  0.93   9.98   0.99     0.96       8141.59|
|  2:  4.6816 -  3.7357  1316   148  0.95   8.66   1.04     1.02      10035.31|
|  3:  3.7357 -  3.2693  1293   144  0.93  12.26   1.06     1.04      11757.50|
|  4:  3.2693 -  2.9730  1285   142  0.91  14.69   1.02     1.01      11474.97|
|  5:  2.9730 -  2.7614  1273   141  0.90  16.56   1.01     0.98       9268.41|
|  6:  2.7614 -  2.5995  1285   141  0.89  16.67   0.99     0.96       7622.59|
|  7:  2.5995 -  2.4699  1262   144  0.89  17.05   1.01     0.98       6898.57|
|  8:  2.4699 -  2.3629  1267   136  0.90  15.83   1.01     1.00       5788.91|
|  9:  2.3629 -  2.2722  1256   141  0.90  16.02   1.01     0.99       5386.57|
| 10:  2.2722 -  2.1941  1255   144  0.90  16.29   1.01     0.98       4819.54|
| 11:  2.1941 -  2.1257  1253   136  0.89  17.04   1.02     0.98       4786.18|
| 12:  2.1257 -  2.0651  1246   138  0.90  16.50   1.03     1.03       4339.74|
| 13:  2.0651 -  2.0109  1252   138  0.90  16.11   1.03     1.01       3415.89|
| 14:  2.0109 -  1.9619  1011   114  0.92  13.63   1.01     0.99       2476.35|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2476.35 max =        11757.50 mean =      6976.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.77|
|phase err.(test): min =        0.00 max =           89.94 mean =        14.23|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1662   ksol= 0.32   Bsol= 39.20   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.52,-0.31,0.83,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.176473                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1662   ksol= 0.32   Bsol= 39.20   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.52,-0.31,0.83,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.176473                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7897 -  4.6816 0.99   1376  152 0.1017 0.1352      5.4218      5.5754|
|  2:  4.6816 -  3.7357 0.99   1316  148 0.0874 0.1204      5.4719      5.6853|
|  3:  3.7357 -  3.2693 0.99   1293  144 0.1106 0.1503      5.5299      5.8894|
|  4:  3.2693 -  2.9730 0.99   1285  142 0.1295 0.1868      5.5115       5.701|
|  5:  2.9730 -  2.7614 0.99   1273  141 0.1328 0.1812      5.3718      5.5798|
|  6:  2.7614 -  2.5995 0.99   1285  141 0.1252 0.1906      5.2495      5.4767|
|  7:  2.5995 -  2.4699 0.99   1262  144 0.1333 0.1739      5.2086      5.4156|
|  8:  2.4699 -  2.3629 0.98   1267  136 0.1265 0.1732      5.1259      5.3913|
|  9:  2.3629 -  2.2722 0.98   1256  141 0.1220 0.1727      5.0654      5.2898|
| 10:  2.2722 -  2.1941 1.00   1255  144 0.1181 0.1845      5.0058      5.2721|
| 11:  2.1941 -  2.1257 0.97   1253  136 0.1174 0.1851      4.9733      5.2918|
| 12:  2.1257 -  2.0651 0.98   1246  138 0.1200 0.1769       4.926      5.2353|
| 13:  2.0651 -  2.0109 0.99   1252  138 0.1138 0.1790      4.8026      5.0892|
| 14:  2.0109 -  1.9619 0.80   1011  114 0.0966 0.1702      4.6379      4.9483|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7897 -  4.6816  1376   152  0.93   9.99   0.99     0.96       8164.63|
|  2:  4.6816 -  3.7357  1316   148  0.95   8.68   1.04     1.02      10064.92|
|  3:  3.7357 -  3.2693  1293   144  0.93  12.29   1.06     1.04      11790.07|
|  4:  3.2693 -  2.9730  1285   142  0.91  14.70   1.02     1.01      11481.99|
|  5:  2.9730 -  2.7614  1273   141  0.90  16.56   1.02     0.98       9263.03|
|  6:  2.7614 -  2.5995  1285   141  0.89  16.65   0.99     0.96       7612.49|
|  7:  2.5995 -  2.4699  1262   144  0.89  17.04   1.01     0.98       6884.15|
|  8:  2.4699 -  2.3629  1267   136  0.90  15.81   1.01     1.00       5772.59|
|  9:  2.3629 -  2.2722  1256   141  0.90  16.00   1.01     0.99       5373.96|
| 10:  2.2722 -  2.1941  1255   144  0.90  16.27   1.01     0.98       4809.04|
| 11:  2.1941 -  2.1257  1253   136  0.89  17.02   1.02     0.98       4777.77|
| 12:  2.1257 -  2.0651  1246   138  0.90  16.49   1.03     1.03       4335.00|
| 13:  2.0651 -  2.0109  1252   138  0.90  16.11   1.03     1.01       3412.41|
| 14:  2.0109 -  1.9619  1011   114  0.92  13.61   1.01     0.99       2471.20|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2471.20 max =        11790.07 mean =      6976.64|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.76|
|phase err.(test): min =        0.00 max =           89.66 mean =        14.22|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.359)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.62    99.57   15.68    None  None   None       |
|    all(noH): 2823   0      1.62    99.57   15.68    None  None   None       |
|    Sol.    : 438    0      3.65    86.82   40.58    None  None   None       |
|    Mac.    : 2385   0      1.62    99.57   11.11    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.624 -  11.419: 1706   |   5:    50.597 -  60.391:   90        |
|      1:    11.419 -  21.213:  569   |   6:    60.391 -  70.186:   49        |
|      2:    21.213 -  31.008:  151   |   7:    70.186 -  79.980:   18        |
|      3:    31.008 -  40.802:  120   |   8:    79.980 -  89.775:    7        |
|      4:    40.802 -  50.597:  112   |   9:    89.775 -  99.569:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 320         
Filter by distance & map next to the model:
   mapped sites are within: 0.167 - 5.514
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 313 from: 320
   mapped sites are within: 0.744 - 5.514

peak=   10.939 closest distance to " CB  VAL A 296 " =    1.518
peak=    9.769 closest distance to " CB  VAL A 230 " =    1.370
peak=    7.506 closest distance to " O   HOH Z 130 " =    1.664
peak=    6.463 closest distance to " CD2 LEU A   5 " =    1.269
peak=    6.177 closest distance to " NE2 GLN A  11 " =    1.148
peak=    6.136 closest distance to " O   HOH Z 424 " =    1.388
peak=    6.026 closest distance to " O   HOH Z  65 " =    1.547
peak=    5.601 closest distance to " O   HOH Z 385 " =    0.982
peak=    5.502 closest distance to " O   HOH Z 142 " =    1.906
peak=    5.488 closest distance to " O   HOH Z  28 " =    1.449
peak=    5.455 closest distance to " O   HOH Z   9 " =    1.658
peak=    5.324 closest distance to " O   HOH Z 112 " =    1.505
peak=    5.287 closest distance to " CG  LEU A   5 " =    1.245
peak=    5.258 closest distance to " CG  PRO A  54 " =    1.272
peak=    5.257 closest distance to " O   HOH Z 124 " =    1.462
peak=    5.229 closest distance to " O   HOH Z 193 " =    1.699
peak=    5.211 closest distance to " O   HOH Z   7 " =    1.617
peak=    4.841 closest distance to " O   HOH Z 369 " =    2.262
peak=    4.786 closest distance to " O   HOH Z 427 " =    2.440
peak=    4.785 closest distance to " CB  VAL A 230 " =    1.187
peak=    4.742 closest distance to " O   HOH Z 423 " =    1.583
peak=    4.681 closest distance to " O   HOH Z 236 " =    1.451
peak=    4.654 closest distance to " CB  ARG A 275 " =    0.999
peak=    4.652 closest distance to " CG  LEU A 228 " =    1.185
peak=    4.612 closest distance to " O   HOH Z 126 " =    1.889
peak=    4.595 closest distance to " O   HOH Z  78 " =    1.581
peak=    4.574 closest distance to " CB  PRO A  54 " =    1.045
peak=    4.555 closest distance to " O   HOH Z 232 " =    2.387
peak=    4.528 closest distance to " NH2 ARG A  56 " =    1.835
peak=    4.478 closest distance to " O   HOH Z 272 " =    1.832
peak=    4.477 closest distance to " O   HOH Z  63 " =    1.530
peak=    4.393 closest distance to " O   HOH Z 123 " =    1.259
peak=    4.372 closest distance to " CB  SER A  63 " =    1.280
peak=    4.367 closest distance to " CB  SER A   3 " =    1.328
peak=    4.355 closest distance to " O   SER A  87 " =    2.354
peak=    4.351 closest distance to " CG  PRO A 213 " =    1.174
peak=    4.345 closest distance to " O   HOH Z 422 " =    2.353
peak=    4.316 closest distance to " CA  PHE A 283 " =    1.287
peak=    4.303 closest distance to " O   HOH Z  51 " =    1.947
peak=    4.290 closest distance to " CB  GLN A 223 " =    1.574
peak=    4.275 closest distance to " O   HOH Z 380 " =    1.837
peak=    4.240 closest distance to " O   HOH Z 222 " =    1.126
peak=    4.215 closest distance to " O   HOH Z 417 " =    1.349
peak=    4.206 closest distance to " CB  GLN A 183 " =    1.230
peak=    4.189 closest distance to " O   HOH Z 145 " =    1.860
peak=    4.187 closest distance to " O   HOH Z 130 " =    1.899
peak=    4.187 closest distance to " CD2 LEU A 228 " =    1.095
peak=    4.174 closest distance to " O   HOH Z 427 " =    0.907
peak=    4.118 closest distance to " O   HOH Z  30 " =    1.729
peak=    4.112 closest distance to " O   HOH Z 425 " =    1.468
peak=    4.111 closest distance to " OG  SER A  62 " =    2.966
peak=    4.084 closest distance to " O   HOH Z  59 " =    1.539
peak=    4.080 closest distance to " O   HOH Z 316 " =    2.914
peak=    4.079 closest distance to " O   HOH Z 410 " =    1.171
peak=    4.074 closest distance to " O   HOH Z 362 " =    2.068
peak=    4.073 closest distance to " O   HOH Z 144 " =    2.383
peak=    4.070 closest distance to " OD2 ASP A 286 " =    2.486
peak=    4.062 closest distance to " O   HOH Z 389 " =    1.334
peak=    4.051 closest distance to " CB  VAL A 202 " =    1.685
peak=    4.047 closest distance to " O   HOH Z 371 " =    1.902
peak=    4.047 closest distance to " NZ  LYS A 117 " =    3.225
peak=    4.046 closest distance to " O   HOH Z 414 " =    1.199
peak=    4.040 closest distance to " O   HOH Z 117 " =    1.892
peak=    4.030 closest distance to " O   HOH Z 384 " =    1.329
peak=    4.023 closest distance to " O   HOH Z 143 " =    1.346
peak=    3.997 closest distance to " O   HOH Z  48 " =    1.574
peak=    3.984 closest distance to " O   HOH Z  78 " =    1.900
peak=    3.983 closest distance to " CB BVAL A  41 " =    1.189
peak=    3.980 closest distance to " O   HOH Z 371 " =    2.951
peak=    3.978 closest distance to " O   HOH Z 298 " =    1.666
peak=    3.947 closest distance to " O   PRO A 198 " =    1.227
peak=    3.937 closest distance to " O   HOH Z 213 " =    1.568
peak=    3.936 closest distance to " NH2BARG A 145 " =    1.183
peak=    3.933 closest distance to " O   HOH Z 258 " =    2.214
peak=    3.933 closest distance to " O   HOH Z 419 " =    1.977
peak=    3.931 closest distance to " O   HOH Z 289 " =    1.622
peak=    3.920 closest distance to " O   HOH Z  11 " =    1.950
peak=    3.918 closest distance to " O   HOH Z  69 " =    2.240
peak=    3.907 closest distance to " CB  TRP A 179 " =    1.282
peak=    3.900 closest distance to " O   HOH Z 189 " =    2.538
peak=    3.885 closest distance to " CG2 THR A 221 " =    1.297
peak=    3.869 closest distance to " O   HOH Z 327 " =    1.544
peak=    3.860 closest distance to " O   HOH Z 227 " =    2.118
peak=    3.848 closest distance to " O   HOH Z 234 " =    3.350
peak=    3.846 closest distance to " CA  ASN A 127 " =    1.021
peak=    3.846 closest distance to " O   HOH Z 411 " =    3.621
peak=    3.845 closest distance to " O   HOH Z 303 " =    2.206
peak=    3.836 closest distance to " CB  VAL A 265 " =    1.416
peak=    3.819 closest distance to " O   HOH Z 287 " =    1.778
peak=    3.819 closest distance to " CB  GLU A 277 " =    3.390
peak=    3.816 closest distance to " O   HOH Z 358 " =    1.246
peak=    3.815 closest distance to " O   HOH Z 126 " =    1.557
peak=    3.804 closest distance to " O   HOH Z  39 " =    1.511
peak=    3.796 closest distance to " CB  ARG A  79 " =    1.341
peak=    3.784 closest distance to " O   HOH Z 278 " =    0.844
peak=    3.781 closest distance to " O   HOH Z 405 " =    1.513
peak=    3.772 closest distance to " O   HOH Z 166 " =    1.359
peak=    3.772 closest distance to " O   HOH Z 418 " =    0.809
peak=    3.771 closest distance to " OG BSER A 212 " =    2.728
peak=    3.765 closest distance to " OG BSER A 164 " =    2.166
peak=    3.744 closest distance to " N   PHE A 130 " =    1.225
peak=    3.742 closest distance to " O   HOH Z  47 " =    1.813
peak=    3.739 closest distance to " O   GLN A  58 " =    1.473
peak=    3.732 closest distance to " CB  ASN A 148 " =    1.259
peak=    3.717 closest distance to " O   HOH Z 425 " =    1.877
peak=    3.716 closest distance to " CB  ALA A 114 " =    1.572
peak=    3.715 closest distance to " O   HOH Z 222 " =    2.074
peak=    3.707 closest distance to " O   HOH Z  85 " =    1.445
peak=    3.702 closest distance to " O   HOH Z 366 " =    2.617
peak=    3.701 closest distance to " CB  LEU A 255 " =    0.808
peak=    3.695 closest distance to " O   HOH Z 263 " =    1.364
peak=    3.689 closest distance to " O   HOH Z 176 " =    1.575
peak=    3.679 closest distance to " NH1 ARG A 138 " =    1.091
peak=    3.675 closest distance to " CB  GLU A 152 " =    1.228
peak=    3.665 closest distance to " CG2 VAL A 257 " =    0.928
peak=    3.665 closest distance to " NH2BARG A 190 " =    1.498
peak=    3.663 closest distance to " O   HOH Z 352 " =    1.312
peak=    3.663 closest distance to " O   HOH Z 211 " =    0.990
peak=    3.659 closest distance to " CE  MET A  93 " =    1.623
peak=    3.650 closest distance to " CG  GLN A  11 " =    2.161
peak=    3.640 closest distance to " O   PRO A 198 " =    1.576
peak=    3.639 closest distance to " O   HOH Z 403 " =    1.695
peak=    3.634 closest distance to " O   HOH Z 203 " =    1.580
peak=    3.632 closest distance to " CG  PRO A 198 " =    1.302
peak=    3.595 closest distance to " O   HOH Z 128 " =    1.940
peak=    3.593 closest distance to " CG  LYS A  76 " =    1.480
peak=    3.582 closest distance to " O   HOH Z 344 " =    1.137
peak=    3.570 closest distance to " O   HOH Z 118 " =    1.838
peak=    3.566 closest distance to " O   HOH Z 276 " =    1.220
peak=    3.565 closest distance to " O   HOH Z 128 " =    1.986
peak=    3.560 closest distance to " O   HOH Z 244 " =    1.688
peak=    3.558 closest distance to " CG1BVAL A  72 " =    1.147
peak=    3.552 closest distance to " O   HOH Z 250 " =    1.464
peak=    3.552 closest distance to " CG1 VAL A 153 " =    0.859
peak=    3.550 closest distance to " CA  ALA A 299 " =    0.981
peak=    3.548 closest distance to " CB  TYR A 169 " =    0.904
peak=    3.548 closest distance to " O   HOH Z  69 " =    1.027
peak=    3.542 closest distance to " O   HOH Z  48 " =    1.589
peak=    3.535 closest distance to " O   HOH Z  58 " =    1.788
peak=    3.534 closest distance to " O   HOH Z  93 " =    2.109
peak=    3.532 closest distance to " CD  PRO A 243 " =    1.439
peak=    3.528 closest distance to " O   HOH Z   1 " =    1.529
peak=    3.521 closest distance to " O   HOH Z 392 " =    1.139
peak=    3.518 closest distance to " O   HOH Z  44 " =    1.716
peak=    3.514 closest distance to " O   HOH Z  89 " =    2.102
peak=    3.513 closest distance to " OG BSER A  99 " =    2.143
peak=    3.509 closest distance to " O   HOH Z 148 " =    1.502
peak=    3.506 closest distance to " CG1BVAL A 121 " =    2.257
peak=    3.505 closest distance to " O   HOH Z 152 " =    2.165
peak=    3.494 closest distance to " O   HOH Z  71 " =    0.990
peak=    3.492 closest distance to " O   HOH Z 108 " =    2.144
peak=    3.492 closest distance to " O   HOH Z 128 " =    2.128
peak=    3.488 closest distance to " NZ  LYS A 117 " =    1.088
peak=    3.487 closest distance to " O   HOH Z 272 " =    2.152
peak=    3.485 closest distance to " N   SER A 135 " =    1.355
peak=    3.484 closest distance to " O   HOH Z 193 " =    1.837
peak=    3.479 closest distance to " O   HOH Z 383 " =    2.285
peak=    3.476 closest distance to " O   HOH Z 193 " =    1.925
peak=    3.468 closest distance to " O   HOH Z 423 " =    1.773
peak=    3.457 closest distance to " O   HOH Z 435 " =    2.040
peak=    3.449 closest distance to " O   HOH Z 361 " =    1.460
peak=    3.445 closest distance to " CB  TRP A 266 " =    1.088
peak=    3.438 closest distance to " CB  GLU A 128 " =    0.965
peak=    3.437 closest distance to " O   HOH Z 145 " =    3.344
peak=    3.436 closest distance to " NH2BARG A 145 " =    1.692
peak=    3.434 closest distance to " O   HOH Z  90 " =    5.046
peak=    3.425 closest distance to " CG1 ILE A  33 " =    1.364
peak=    3.420 closest distance to " CB  PRO A  90 " =    1.216
peak=    3.418 closest distance to " NE2 GLN A 278 " =    3.612
peak=    3.416 closest distance to " O   HOH Z   6 " =    2.145
peak=    3.415 closest distance to " O   HOH Z 106 " =    2.457
peak=    3.409 closest distance to " O   HOH Z  50 " =    1.431
peak=    3.409 closest distance to " CG  GLN A  88 " =    1.157
peak=    3.408 closest distance to " O   HOH Z 426 " =    1.776
peak=    3.407 closest distance to " O   HOH Z 413 " =    1.424
peak=    3.405 closest distance to " CD1 ILE A  33 " =    1.731
peak=    3.401 closest distance to " O   HOH Z 132 " =    0.943
peak=    3.399 closest distance to " NE2 GLN A  58 " =    3.633
peak=    3.397 closest distance to " O   HOH Z 410 " =    2.950
peak=    3.396 closest distance to " CB  THR A  31 " =    1.698
peak=    3.393 closest distance to " O   HOH Z 326 " =    1.881
peak=    3.392 closest distance to " CA  ALA A 158 " =    1.224
peak=    3.392 closest distance to " O   HOH Z 302 " =    1.695
peak=    3.387 closest distance to " CA  ASN A 215 " =    0.957
peak=    3.386 closest distance to " NH1 ARG A  14 " =    1.067
peak=    3.386 closest distance to " CG  LEU A 167 " =    1.169
peak=    3.375 closest distance to " ND2 ASN A 187 " =    1.657
peak=    3.368 closest distance to " O   HOH Z 424 " =    2.127
peak=    3.368 closest distance to " O   HOH Z 284 " =    1.454
peak=    3.365 closest distance to " CG2 THR A 294 " =    1.716
peak=    3.364 closest distance to " O   HOH Z 209 " =    2.496
peak=    3.362 closest distance to " OE2 GLU A  53 " =    2.010
peak=    3.360 closest distance to " OG  SER A  62 " =    2.687
peak=    3.356 closest distance to " OE1 GLN A  58 " =    3.999
peak=    3.356 closest distance to " O   HOH Z 214 " =    2.168
peak=    3.354 closest distance to " CD1 LEU A   5 " =    1.716
peak=    3.353 closest distance to " O   HOH Z 345 " =    3.014
peak=    3.352 closest distance to " O   HOH Z  61 " =    1.534
peak=    3.350 closest distance to " OG BSER A 210 " =    1.447
peak=    3.350 closest distance to " O   HOH Z 322 " =    1.921
peak=    3.348 closest distance to " CD1 ILE A 263 " =    1.318
peak=    3.347 closest distance to " O   HOH Z  61 " =    1.584
peak=    3.338 closest distance to " O   HOH Z 406 " =    1.343
peak=    3.337 closest distance to " SD  MET A 185 " =    1.550
peak=    3.337 closest distance to " ND1 HIS A  81 " =    1.521
peak=    3.333 closest distance to " CG  PRO A 243 " =    1.126
peak=    3.328 closest distance to " O   HOH Z 194 " =    2.036
peak=    3.328 closest distance to " NE2 GLN A 223 " =    1.641
peak=    3.327 closest distance to " O   HOH Z  80 " =    2.282
peak=    3.325 closest distance to " CA  TYR A  30 " =    1.003
peak=    3.322 closest distance to " CB  ARG A 139 " =    1.126
peak=    3.321 closest distance to " O   HOH Z 313 " =    1.578
peak=    3.316 closest distance to " O   HOH Z  88 " =    2.940
peak=    3.316 closest distance to " O   HOH Z  80 " =    1.904
peak=    3.310 closest distance to " O   HOH Z  54 " =    1.449
peak=    3.306 closest distance to " N   TYR A  15 " =    1.106
peak=    3.305 closest distance to " CA  LYS A 117 " =    1.163
peak=    3.305 closest distance to " CB  ALA A  10 " =    1.208
peak=    3.298 closest distance to " CB  LEU A 300 " =    0.887
peak=    3.298 closest distance to " NZ  LYS A  76 " =    1.377
peak=    3.295 closest distance to " O   HOH Z 181 " =    2.212
peak=    3.289 closest distance to " O   HOH Z 251 " =    1.656
peak=    3.280 closest distance to " O   HOH Z 368 " =    3.665
peak=    3.279 closest distance to " O   HOH Z 119 " =    1.571
peak=    3.278 closest distance to " CA  ARG A 195 " =    1.367
peak=    3.273 closest distance to " CB  ASN A 215 " =    1.092
peak=    3.271 closest distance to " N   ALA A   1 " =    1.068
peak=    3.269 closest distance to " O   HOH Z 234 " =    2.101
peak=    3.269 closest distance to " CB  THR A 157 " =    1.145
peak=    3.266 closest distance to " O   HOH Z 313 " =    1.730
peak=    3.265 closest distance to " OH  TYR A 116 " =    1.197
peak=    3.262 closest distance to " O   ALA A   1 " =    1.368
peak=    3.260 closest distance to " O   HOH Z   4 " =    1.115
peak=    3.260 closest distance to " N   VAL A 126 " =    1.235
peak=    3.254 closest distance to " CB  GLN A  88 " =    1.392
peak=    3.247 closest distance to " OG ASER A 134 " =    1.500
peak=    3.245 closest distance to " CA  ILE A 234 " =    1.035
peak=    3.244 closest distance to " OG1 THR A 294 " =    2.318
peak=    3.243 closest distance to " O   HOH Z   9 " =    1.762
peak=    3.240 closest distance to " O   HOH Z 305 " =    3.259
peak=    3.239 closest distance to " CD1AILE A 234 " =    0.853
peak=    3.236 closest distance to " O   HOH Z 280 " =    2.574
peak=    3.236 closest distance to " O   HOH Z  64 " =    2.227
peak=    3.234 closest distance to " O   HOH Z  65 " =    1.526
peak=    3.232 closest distance to " CG1 ILE A 120 " =    1.372
peak=    3.229 closest distance to " CG  GLN A  77 " =    2.504
peak=    3.225 closest distance to " CE3 TRP A 150 " =    0.847
peak=    3.225 closest distance to " O   HOH Z 130 " =    1.557
peak=    3.225 closest distance to " O   HOH Z  68 " =    2.030
peak=    3.222 closest distance to " O   HOH Z  44 " =    2.818
peak=    3.221 closest distance to " N   ASN A 127 " =    1.335
peak=    3.218 closest distance to " CB  SER A 273 " =    0.744
peak=    3.218 closest distance to " OD1BASN A 224 " =    2.253
peak=    3.216 closest distance to " NE2 GLN A  73 " =    1.435
peak=    3.212 closest distance to " O   GLY A 147 " =    1.445
peak=    3.211 closest distance to " O   HOH Z 174 " =    2.436
peak=    3.208 closest distance to " N   ASP A 162 " =    1.144
peak=    3.206 closest distance to " CA  LEU A 282 " =    1.086
peak=    3.206 closest distance to " N   SER A 271 " =    1.049
peak=    3.205 closest distance to " CG  MET A 185 " =    1.108
peak=    3.203 closest distance to " CE BMET A  47 " =    0.923
peak=    3.201 closest distance to " O   HOH Z 213 " =    1.708
peak=    3.200 closest distance to " CD1 LEU A 228 " =    1.804
peak=    3.199 closest distance to " N   SER A  97 " =    0.803
peak=    3.199 closest distance to " O   HOH Z 345 " =    1.707
peak=    3.193 closest distance to " O   HOH Z   1 " =    1.667
peak=    3.187 closest distance to " O   HOH Z 412 " =    1.809
peak=    3.187 closest distance to " O  BHOH Z  74 " =    1.407
peak=    3.187 closest distance to " O  BHOH Z 338 " =    2.477
peak=    3.186 closest distance to " NH2BARG A 145 " =    2.442
peak=    3.186 closest distance to " O   HOH Z 344 " =    2.721
peak=    3.185 closest distance to " CG2 ILE A 234 " =    0.884
peak=    3.184 closest distance to " O   HOH Z 273 " =    2.865
peak=    3.182 closest distance to " O   HOH Z 139 " =    1.088
peak=    3.182 closest distance to " O   HOH Z 368 " =    1.975
peak=    3.173 closest distance to " CB  ASN A 187 " =    1.021
peak=    3.173 closest distance to " O   HOH Z 356 " =    1.235
peak=    3.168 closest distance to " CB  ALA A 248 " =    1.373
peak=    3.166 closest distance to " NH1AARG A 145 " =    1.129
peak=    3.165 closest distance to " CB  MET A  40 " =    0.925
peak=    3.162 closest distance to " O   HOH Z 154 " =    2.113
peak=    3.154 closest distance to " O   HOH Z  88 " =    2.607
peak=    3.149 closest distance to " C   GLU A 277 " =    1.262
peak=    3.148 closest distance to " CB  ASN A 148 " =    1.886
peak=    3.147 closest distance to " O   HOH Z   1 " =    4.210
peak=    3.146 closest distance to " O   HOH Z 365 " =    5.514
peak=    3.140 closest distance to " NE AARG A 275 " =    1.649
peak=    3.139 closest distance to " N   VAL A 257 " =    1.607
peak=    3.138 closest distance to " O   HOH Z 109 " =    2.434
peak=    3.135 closest distance to " O   HOH Z 173 " =    2.197
peak=    3.133 closest distance to " CB  ARG A 138 " =    0.946
peak=    3.132 closest distance to " CB  SER A 216 " =    0.792
peak=    3.127 closest distance to " N   ARG A 156 " =    1.283
peak=    3.127 closest distance to " O   HOH Z  11 " =    1.054
peak=    3.126 closest distance to " O   GLY A 302 " =    1.963
peak=    3.125 closest distance to " CA  SER A  87 " =    0.971
peak=    3.122 closest distance to " O   ASN A 209 " =    1.499
peak=    3.118 closest distance to " O   HOH Z 374 " =    2.332
peak=    3.115 closest distance to " O   HOH Z 329 " =    3.564
peak=    3.115 closest distance to " OG1 THR A 220 " =    1.773
peak=    3.112 closest distance to " CA  ALA A  51 " =    0.955
peak=    3.109 closest distance to " O   HOH Z 353 " =    2.343
peak=    3.107 closest distance to " CB  SER A  62 " =    1.221
peak=    3.105 closest distance to " CA  ILE A 263 " =    1.260
peak=    3.104 closest distance to " O   HOH Z 410 " =    1.323
peak=    3.103 closest distance to " CA  CYS A 168 " =    0.847
peak=    3.098 closest distance to " O   HOH Z  40 " =    2.016
peak=    3.095 closest distance to " O   HOH Z  59 " =    1.940
peak=    3.093 closest distance to " O   HOH Z 390 " =    2.362
peak=    3.076 closest distance to " CG  LEU A 281 " =    1.025
peak=    3.068 closest distance to " O   HOH Z 406 " =    1.041
peak=    3.063 closest distance to " O   HOH Z 323 " =    1.518
peak=    3.028 closest distance to " CG  GLN A 240 " =    3.436

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 196         
Filter by distance & map next to the model:
   mapped sites are within: 0.541 - 5.318
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 196
   mapped sites are within: 0.730 - 5.318

peak=   -4.882 closest distance to " CG2 VAL A 230 " =    0.731
peak=   -4.449 closest distance to " CD  ARG A  14 " =    2.959
peak=   -4.394 closest distance to " NH2 ARG A  79 " =    1.913
peak=   -4.327 closest distance to " OG BSER A 134 " =    1.393
peak=   -4.190 closest distance to " C   ASN A 285 " =    2.055
peak=   -4.150 closest distance to " O   HOH Z 290 " =    1.096
peak=   -4.129 closest distance to " CA  GLY A  98 " =    1.797
peak=   -4.125 closest distance to " C   HIS A 108 " =    1.209
peak=   -4.095 closest distance to " O   HOH Z 131 " =    3.970
peak=   -4.092 closest distance to " O   HOH Z  69 " =    1.945
peak=   -4.076 closest distance to " O   HOH Z  43 " =    1.990
peak=   -4.057 closest distance to " CD  ARG A 156 " =    1.929
peak=   -4.029 closest distance to " CB  TYR A  15 " =    2.108
peak=   -3.984 closest distance to " O   ALA A 292 " =    2.223
peak=   -3.972 closest distance to " O   HOH Z 412 " =    5.152
peak=   -3.957 closest distance to " O   PRO A 198 " =    1.225
peak=   -3.955 closest distance to " N   GLN A  58 " =    1.776
peak=   -3.954 closest distance to " CE2 PHE A 218 " =    2.442
peak=   -3.916 closest distance to " CB  PRO A 243 " =    2.616
peak=   -3.909 closest distance to " O   HOH Z 427 " =    1.659
peak=   -3.874 closest distance to " O   HOH Z  37 " =    1.560
peak=   -3.861 closest distance to " O   VAL A  67 " =    2.890
peak=   -3.860 closest distance to " O   HOH Z  11 " =    1.803
peak=   -3.857 closest distance to " CB  ALA A  43 " =    2.272
peak=   -3.831 closest distance to " O   HOH Z 385 " =    1.615
peak=   -3.822 closest distance to " OE1 GLU A 277 " =    2.221
peak=   -3.814 closest distance to " O   VAL A  67 " =    2.639
peak=   -3.812 closest distance to " O   HOH Z 351 " =    1.499
peak=   -3.810 closest distance to " O   HOH Z 231 " =    1.894
peak=   -3.786 closest distance to " OG ASER A 134 " =    1.314
peak=   -3.773 closest distance to " N   ALA A 248 " =    1.725
peak=   -3.752 closest distance to " O   HOH Z 385 " =    1.768
peak=   -3.735 closest distance to " CB  ALA A 248 " =    2.128
peak=   -3.735 closest distance to " O   HOH Z 125 " =    3.309
peak=   -3.722 closest distance to " O   SER A 135 " =    1.530
peak=   -3.722 closest distance to " CG  GLN A  58 " =    1.102
peak=   -3.722 closest distance to " O   HOH Z 407 " =    3.016
peak=   -3.714 closest distance to " O   HOH Z 426 " =    2.139
peak=   -3.707 closest distance to " CD1 ILE A 239 " =    2.561
peak=   -3.704 closest distance to " NH1 ARG A  56 " =    2.477
peak=   -3.690 closest distance to " CE  LYS A  76 " =    2.983
peak=   -3.690 closest distance to " CB  ALA A   7 " =    1.978
peak=   -3.681 closest distance to " N   VAL A  72 " =    1.601
peak=   -3.674 closest distance to " O   HOH Z 185 " =    1.928
peak=   -3.659 closest distance to " O   ALA A 161 " =    1.769
peak=   -3.657 closest distance to " CB  ALA A  64 " =    2.715
peak=   -3.649 closest distance to " ND2 ASN A 209 " =    1.996
peak=   -3.649 closest distance to " O   HOH Z 191 " =    5.318
peak=   -3.647 closest distance to " CA  GLY A 133 " =    1.934
peak=   -3.647 closest distance to " O   SER A  22 " =    2.355
peak=   -3.635 closest distance to " CZ  PHE A  59 " =    1.388
peak=   -3.629 closest distance to " O   HOH Z 313 " =    1.664
peak=   -3.623 closest distance to " O   HOH Z 266 " =    4.529
peak=   -3.618 closest distance to " N   MET A 188 " =    1.894
peak=   -3.613 closest distance to " CD2 LEU A 237 " =    2.623
peak=   -3.606 closest distance to " O   HOH Z 166 " =    1.787
peak=   -3.603 closest distance to " CD  LYS A 289 " =    2.424
peak=   -3.598 closest distance to " CD1 LEU A 101 " =    2.245
peak=   -3.594 closest distance to " OD2 ASP A 191 " =    1.351
peak=   -3.568 closest distance to " OD2 ASP A  27 " =    1.382
peak=   -3.566 closest distance to " O   HOH Z  56 " =    1.770
peak=   -3.565 closest distance to " O   HOH Z 130 " =    2.002
peak=   -3.556 closest distance to " O   PRO A 163 " =    2.059
peak=   -3.555 closest distance to " O   HOH Z  60 " =    2.164
peak=   -3.546 closest distance to " O   HOH Z 234 " =    3.885
peak=   -3.539 closest distance to " O   HOH Z  65 " =    0.870
peak=   -3.532 closest distance to " N   THR A 157 " =    1.473
peak=   -3.531 closest distance to " CD1 LEU A 255 " =    2.756
peak=   -3.530 closest distance to " OG ASER A 216 " =    1.138
peak=   -3.520 closest distance to " CB  ASN A  39 " =    2.142
peak=   -3.506 closest distance to " O   HOH Z 193 " =    1.665
peak=   -3.506 closest distance to " CG  LEU A   5 " =    0.874
peak=   -3.506 closest distance to " O   HOH Z 339 " =    1.789
peak=   -3.504 closest distance to " O   HOH Z 183 " =    1.615
peak=   -3.504 closest distance to " O   THR A 235 " =    1.595
peak=   -3.477 closest distance to " C   ARG A 269 " =    1.322
peak=   -3.469 closest distance to " O   ILE A 106 " =    2.161
peak=   -3.469 closest distance to " CG1 VAL A 197 " =    2.169
peak=   -3.459 closest distance to " O   ALA A  51 " =    1.268
peak=   -3.458 closest distance to " O   HOH Z 140 " =    1.296
peak=   -3.454 closest distance to " CG  PHE A 283 " =    2.483
peak=   -3.453 closest distance to " OG  SER A   3 " =    1.340
peak=   -3.450 closest distance to " O   HOH Z 423 " =    2.302
peak=   -3.449 closest distance to " O   HOH Z  52 " =    1.618
peak=   -3.446 closest distance to " O   PRO A 198 " =    1.410
peak=   -3.438 closest distance to " O   ARG A  24 " =    1.759
peak=   -3.437 closest distance to " O   HOH Z 102 " =    1.500
peak=   -3.423 closest distance to " C   ILE A 239 " =    2.193
peak=   -3.414 closest distance to " O   HOH Z 211 " =    1.427
peak=   -3.414 closest distance to " CE2 TYR A  30 " =    2.820
peak=   -3.412 closest distance to " O   HOH Z 368 " =    2.479
peak=   -3.397 closest distance to " O   GLN A 240 " =    1.829
peak=   -3.395 closest distance to " CD2 LEU A   5 " =    1.182
peak=   -3.392 closest distance to " O   HOH Z 137 " =    1.531
peak=   -3.387 closest distance to " OG  SER A  87 " =    1.282
peak=   -3.377 closest distance to " OG  SER A 206 " =    1.772
peak=   -3.375 closest distance to " O   HOH Z  71 " =    1.202
peak=   -3.368 closest distance to " CG  ARG A 219 " =    2.210
peak=   -3.361 closest distance to " CG  ASP A 286 " =    1.585
peak=   -3.356 closest distance to " ND2 ASN A  45 " =    1.330
peak=   -3.355 closest distance to " OG  SER A  97 " =    2.167
peak=   -3.355 closest distance to " CD1 PHE A  61 " =    2.850
peak=   -3.355 closest distance to " CH2 TRP A 123 " =    1.940
peak=   -3.346 closest distance to " CD  GLN A  88 " =    0.941
peak=   -3.346 closest distance to " CZ  TYR A 169 " =    1.977
peak=   -3.344 closest distance to " CG1 VAL A 268 " =    2.800
peak=   -3.343 closest distance to " O   HOH Z 148 " =    2.156
peak=   -3.342 closest distance to " O   SER A 146 " =    1.173
peak=   -3.335 closest distance to " O   HOH Z  90 " =    2.260
peak=   -3.334 closest distance to " CD2 LEU A 237 " =    2.456
peak=   -3.332 closest distance to " CG  LEU A 228 " =    0.900
peak=   -3.331 closest distance to " N   THR A  52 " =    1.760
peak=   -3.327 closest distance to " O   HOH Z 389 " =    1.945
peak=   -3.323 closest distance to " CG  GLU A 152 " =    1.988
peak=   -3.322 closest distance to " N   ASN A 127 " =    1.394
peak=   -3.319 closest distance to " CB  PHE A 192 " =    1.759
peak=   -3.319 closest distance to " N   HIS A 115 " =    1.987
peak=   -3.316 closest distance to " OE1 GLN A 183 " =    1.367
peak=   -3.312 closest distance to " CZ2 TRP A 274 " =    1.018
peak=   -3.311 closest distance to " N   VAL A 189 " =    1.574
peak=   -3.310 closest distance to " O   ASN A 187 " =    1.491
peak=   -3.308 closest distance to " O   HOH Z 165 " =    2.281
peak=   -3.308 closest distance to " CG1BVAL A  72 " =    2.062
peak=   -3.298 closest distance to " O   HOH Z 298 " =    1.256
peak=   -3.295 closest distance to " C   LEU A 222 " =    0.730
peak=   -3.295 closest distance to " C   ALA A 158 " =    1.297
peak=   -3.292 closest distance to " O   HOH Z  13 " =    1.653
peak=   -3.291 closest distance to " O   HOH Z  15 " =    1.486
peak=   -3.290 closest distance to " CG  MET A 105 " =    0.866
peak=   -3.288 closest distance to " OD2 ASP A 171 " =    2.171
peak=   -3.286 closest distance to " CG  GLU A   2 " =    2.065
peak=   -3.277 closest distance to " O   HOH Z 134 " =    2.739
peak=   -3.275 closest distance to " N   PHE A  59 " =    2.167
peak=   -3.274 closest distance to " O   HOH Z 134 " =    3.582
peak=   -3.273 closest distance to " CB  ASP A 132 " =    2.350
peak=   -3.272 closest distance to " C   GLN A 205 " =    1.982
peak=   -3.272 closest distance to " CA  ASP A  27 " =    2.407
peak=   -3.269 closest distance to " O   HOH Z  60 " =    1.727
peak=   -3.266 closest distance to " O   HOH Z 208 " =    1.911
peak=   -3.262 closest distance to " CG  ASN A 301 " =    1.917
peak=   -3.261 closest distance to " CE3 TRP A 274 " =    2.259
peak=   -3.251 closest distance to " O   HOH Z 174 " =    4.583
peak=   -3.250 closest distance to " O   HOH Z 388 " =    1.932
peak=   -3.248 closest distance to " OG  SER A  62 " =    0.831
peak=   -3.244 closest distance to " O   HOH Z 426 " =    1.630
peak=   -3.234 closest distance to " O   HOH Z 111 " =    4.509
peak=   -3.232 closest distance to " O   HOH Z  64 " =    1.135
peak=   -3.230 closest distance to " O   TRP A  70 " =    1.384
peak=   -3.227 closest distance to " CG  GLN A 223 " =    1.819
peak=   -3.227 closest distance to " O   ASP A 298 " =    2.060
peak=   -3.223 closest distance to " OD2 ASP A 270 " =    1.229
peak=   -3.217 closest distance to " C   LEU A 222 " =    1.600
peak=   -3.211 closest distance to " ND2 ASN A 173 " =    1.640
peak=   -3.209 closest distance to " CB  ALA A 161 " =    2.455
peak=   -3.207 closest distance to " CG  PRO A 163 " =    2.763
peak=   -3.206 closest distance to " C   ASP A 231 " =    2.353
peak=   -3.198 closest distance to " ND2 ASN A  45 " =    1.995
peak=   -3.196 closest distance to " CB  SER A 210 " =    1.240
peak=   -3.184 closest distance to " O   ALA A 292 " =    1.979
peak=   -3.181 closest distance to " O   HOH Z 166 " =    1.756
peak=   -3.177 closest distance to " CG2 THR A  52 " =    3.036
peak=   -3.176 closest distance to " NE  ARG A  36 " =    1.698
peak=   -3.170 closest distance to " O   HOH Z 435 " =    2.158
peak=   -3.164 closest distance to " OG BSER A 134 " =    1.792
peak=   -3.156 closest distance to " CE BMET A  47 " =    1.444
peak=   -3.156 closest distance to " NE2 GLN A  58 " =    2.204
peak=   -3.153 closest distance to " OG  SER A 245 " =    1.308
peak=   -3.151 closest distance to " O   HOH Z 359 " =    1.624
peak=   -3.147 closest distance to " O   GLY A  57 " =    1.326
peak=   -3.137 closest distance to " O   HOH Z  68 " =    1.780
peak=   -3.131 closest distance to " ND2 ASN A  60 " =    1.533
peak=   -3.130 closest distance to " O   HOH Z 243 " =    1.930
peak=   -3.129 closest distance to " N   SER A 276 " =    1.234
peak=   -3.128 closest distance to " NH1BARG A 145 " =    3.502
peak=   -3.128 closest distance to " ND2 ASN A 142 " =    2.014
peak=   -3.118 closest distance to " CG1 ILE A 263 " =    2.141
peak=   -3.113 closest distance to " O   HOH Z 213 " =    1.328
peak=   -3.108 closest distance to " CE  MET A 105 " =    2.382
peak=   -3.108 closest distance to " O   HOH Z 250 " =    1.357
peak=   -3.106 closest distance to " O   HOH Z 158 " =    1.980
peak=   -3.102 closest distance to " OD1 ASP A 200 " =    1.460
peak=   -3.099 closest distance to " O   HOH Z 100 " =    1.366
peak=   -3.094 closest distance to " CB  SER A 245 " =    1.710
peak=   -3.093 closest distance to " O   MET A  40 " =    2.884
peak=   -3.090 closest distance to " CD1 ILE A 151 " =    2.400
peak=   -3.081 closest distance to " CB  TYR A 172 " =    2.443
peak=   -3.078 closest distance to " O   HOH Z 147 " =    1.154
peak=   -3.069 closest distance to " N   GLN A  77 " =    1.653
peak=   -3.065 closest distance to " CB  ALA A 248 " =    2.291
peak=   -3.058 closest distance to " CD2 TRP A 150 " =    0.980
peak=   -3.049 closest distance to " CG  ARG A 219 " =    2.334
peak=   -3.040 closest distance to " OE2 GLU A 152 " =    1.088
peak=   -3.017 closest distance to " O   HOH Z 350 " =    1.902
peak=   -3.016 closest distance to " O   HOH Z 210 " =    1.899

================= 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    :  0.4945 0.4896   6.293479e+00   6.286156e+00
   1_bss:  0.4855 0.4786   6.286416e+00   6.275083e+00
   1_xyz:  0.4195 0.4428   6.209609e+00   6.235150e+00
   1_adp:  0.3759 0.4298   6.152727e+00   6.224968e+00
   1_occ:  0.3750 0.4294   6.151923e+00   6.225414e+00
   2_bss:  0.3736 0.4255   6.151798e+00   6.222941e+00
   2_xyz:  0.2921 0.3513   5.959212e+00   6.096126e+00
   2_adp:  0.2660 0.3343   5.895730e+00   6.050579e+00
   2_occ:  0.2654 0.3346   5.895770e+00   6.051700e+00
   3_bss:  0.2642 0.3325   5.892822e+00   6.047624e+00
   3_xyz:  0.2039 0.2632   5.662783e+00   5.854740e+00
   3_adp:  0.1763 0.2315   5.529784e+00   5.741194e+00
   3_occ:  0.1759 0.2311   5.528249e+00   5.739817e+00
   4_bss:  0.1752 0.2298   5.524700e+00   5.735015e+00
   4_xyz:  0.1405 0.1908   5.330691e+00   5.558155e+00
   4_adp:  0.1318 0.1828   5.278619e+00   5.514504e+00
   4_occ:  0.1316 0.1825   5.277544e+00   5.512800e+00
   5_bss:  0.1319 0.1819   5.276840e+00   5.511492e+00
   5_xyz:  0.1178 0.1688   5.191032e+00   5.444906e+00
   5_adp:  0.1166 0.1664   5.177613e+00   5.428745e+00
   5_occ:  0.1164 0.1663   5.176682e+00   5.427481e+00
   5_bss:  0.1164 0.1662   5.176473e+00   5.427332e+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:  0.411  20.000   6.521   9.535   7.199   0.000   0.000   0.000
   1_xyz:  0.411  20.000   6.521   9.535   7.199   0.000   0.000   0.000
   1_adp:  0.411  20.000   6.521   9.535   7.199   0.000   0.000   0.000
   1_occ:  0.411  20.000   6.521   9.535   7.199   0.000   0.000   0.000
   2_bss:  0.361  30.884   3.764   5.772   4.694   0.000   0.000   0.000
   2_xyz:  0.361  30.884   3.764   5.772   4.694   0.000   0.000   0.000
   2_adp:  0.361  30.884   3.764   5.772   4.694   0.000   0.000   0.000
   2_occ:  0.361  30.884   3.764   5.772   4.694   0.000   0.000   0.000
   3_bss:  0.333  30.884   2.278   3.170   3.358   0.000   0.000   0.000
   3_xyz:  0.333  30.884   2.278   3.170   3.358   0.000   0.000   0.000
   3_adp:  0.333  30.884   2.278   3.170   3.358   0.000   0.000   0.000
   3_occ:  0.333  30.884   2.278   3.170   3.358   0.000   0.000   0.000
   4_bss:  0.318  30.884   1.401   1.780   2.634   0.000   0.000   0.000
   4_xyz:  0.318  30.884   1.401   1.780   2.634   0.000   0.000   0.000
   4_adp:  0.318  30.884   1.401   1.780   2.634   0.000   0.000   0.000
   4_occ:  0.318  30.884   1.401   1.780   2.634   0.000   0.000   0.000
   5_bss:  0.313  34.386   1.101   1.313   2.458   0.000   0.000   0.000
   5_xyz:  0.313  34.386   1.101   1.313   2.458   0.000   0.000   0.000
   5_adp:  0.313  34.386   1.101   1.313   2.458   0.000   0.000   0.000
   5_occ:  0.313  34.386   1.101   1.313   2.458   0.000   0.000   0.000
   5_bss:  0.320  39.196  -0.523  -0.311   0.834   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  63.547 0.3476  0.4135    78086.987
   1_bss:  62.915 0.3544  0.5220    74860.022
   1_xyz:  53.768 0.4717  0.6909    60478.454
   1_adp:  50.465 0.5144  0.8077    57440.440
   1_occ:  50.507 0.5138  0.8051    57494.861
   2_bss:  50.149 0.5181  0.7298    56635.989
   2_xyz:  38.208 0.6635  0.9224    35414.815
   2_adp:  35.151 0.6997  0.9720    30986.932
   2_occ:  35.222 0.6989  0.9697    31064.004
   3_bss:  34.978 0.7013  0.9110    30579.255
   3_xyz:  26.460 0.7955  0.9920    17913.301
   3_adp:  22.390 0.8385  1.0107    13723.803
   3_occ:  22.340 0.8389  1.0111    13649.761
   4_bss:  22.211 0.8400  0.9747    13456.913
   4_xyz:  17.804 0.8820  0.9975     9126.287
   4_adp:  16.655 0.8927  0.9964     8402.532
   4_occ:  16.622 0.8930  0.9964     8365.629
   5_bss:  16.576 0.8934  0.9847     8325.179
   5_xyz:  15.134 0.9057  0.9915     7214.822
   5_adp:  14.738 0.9091  0.9940     7001.478
   5_occ:  14.715 0.9093  0.9940     6976.093
   5_bss:  14.709 0.9094  0.9942     6976.553
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.086   5.2772e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.086   5.2772e+01
   1_xyz:   1.728  0.014  0.107 18.240  0.007  4.105   1.4810e-01
   1_adp:   1.728  0.014  0.107 18.240  0.007  4.105   1.4810e-01
   1_occ:   1.728  0.014  0.107 18.240  0.007  4.105   1.4810e-01
   2_bss:   1.728  0.014  0.107 18.240  0.007  4.105   1.4810e-01
   2_xyz:   1.414  0.011  0.094 16.544  0.006  4.115   1.1311e-01
   2_adp:   1.414  0.011  0.094 16.544  0.006  4.115   1.1311e-01
   2_occ:   1.414  0.011  0.094 16.544  0.006  4.115   1.1311e-01
   3_bss:   1.414  0.011  0.094 16.544  0.006  4.115   1.1311e-01
   3_xyz:   1.135  0.008  0.082 16.313  0.004  4.110   7.9935e-02
   3_adp:   1.135  0.008  0.082 16.313  0.004  4.110   7.9935e-02
   3_occ:   1.135  0.008  0.082 16.313  0.004  4.110   7.9935e-02
   4_bss:   1.135  0.008  0.082 16.313  0.004  4.110   7.9935e-02
   4_xyz:   0.981  0.006  0.070 15.762  0.004  4.113   6.0920e-02
   4_adp:   0.981  0.006  0.070 15.762  0.004  4.113   6.0920e-02
   4_occ:   0.981  0.006  0.070 15.762  0.004  4.113   6.0920e-02
   5_bss:   0.981  0.006  0.070 15.762  0.004  4.113   6.0920e-02
   5_xyz:   1.064  0.007  0.077 15.805  0.004  4.106   6.7679e-02
   5_adp:   1.064  0.007  0.077 15.805  0.004  4.106   6.7679e-02
   5_occ:   1.064  0.007  0.077 15.805  0.004  4.106   6.7679e-02
   5_bss:   1.064  0.007  0.077 15.805  0.004  4.106   6.7679e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.082   6.8353e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.082   6.8353e+00
   1_xyz:  14.890  0.174  0.470 87.731  0.044  2.064   9.9590e-02
   1_adp:  14.890  0.174  0.470 87.731  0.044  2.064   9.9590e-02
   1_occ:  14.890  0.174  0.470 87.731  0.044  2.064   9.9590e-02
   2_bss:  14.890  0.174  0.470 87.731  0.044  2.064   9.9590e-02
   2_xyz:   8.982  0.113  0.365 85.304  0.054  2.066   7.5385e-02
   2_adp:   8.982  0.113  0.365 85.304  0.054  2.066   7.5385e-02
   2_occ:   8.982  0.113  0.365 85.304  0.054  2.066   7.5385e-02
   3_bss:   8.982  0.113  0.365 85.304  0.054  2.066   7.5385e-02
   3_xyz:   7.826  0.058  0.309 79.318  0.031  2.274   1.1885e-01
   3_adp:   7.826  0.058  0.309 79.318  0.031  2.274   1.1885e-01
   3_occ:   7.826  0.058  0.309 79.318  0.031  2.274   1.1885e-01
   4_bss:   7.826  0.058  0.309 79.318  0.031  2.274   1.1885e-01
   4_xyz:   7.918  0.038  0.234 83.558  0.024  2.339   4.5294e-02
   4_adp:   7.918  0.038  0.234 83.558  0.024  2.339   4.5294e-02
   4_occ:   7.918  0.038  0.234 83.558  0.024  2.339   4.5294e-02
   5_bss:   7.918  0.038  0.234 83.558  0.024  2.339   4.5294e-02
   5_xyz:   7.553  0.049  0.263 83.152  0.040  2.246   5.1204e-02
   5_adp:   7.553  0.049  0.263 83.152  0.040  2.246   5.1204e-02
   5_occ:   7.553  0.049  0.263 83.152  0.040  2.246   5.1204e-02
   5_bss:   7.553  0.049  0.263 83.152  0.040  2.246   5.1204e-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:  91.47   0.00  14.83  91.47   0.00  12.90  88.40   0.00  25.32
   1_occ:  91.47   0.00  14.83  91.47   0.00  12.90  88.40   0.00  25.32
   2_bss:  91.47   0.00  14.83  91.47   0.00  12.90  88.40   0.00  25.32
   2_xyz:  91.47   0.00  14.83  91.47   0.00  12.90  88.40   0.00  25.32
   2_adp: 180.62   0.00  14.66 180.62   0.00  11.85  85.73   0.00  29.94
   2_occ: 180.62   0.00  14.66 180.62   0.00  11.85  85.73   0.00  29.94
   3_bss: 180.62   0.00  14.66 180.62   0.00  11.85  85.73   0.00  29.94
   3_xyz: 180.62   0.00  14.66 180.62   0.00  11.85  85.73   0.00  29.94
   3_adp: 109.43   0.00  13.76 109.43   0.00   9.76  78.42   2.13  35.55
   3_occ: 109.43   0.00  13.76 109.43   0.00   9.76  78.42   2.13  35.55
   4_bss: 109.43   0.00  13.76 109.43   0.00   9.76  78.42   2.13  35.55
   4_xyz: 109.43   0.00  13.76 109.43   0.00   9.76  78.42   2.13  35.55
   4_adp:  98.10   0.00  14.10  98.10   0.00   9.49  85.22   1.36  39.22
   4_occ:  98.10   0.00  14.10  98.10   0.00   9.49  85.22   1.36  39.22
   5_bss:  98.10   0.00  14.10  98.10   0.00   9.49  85.22   1.36  39.22
   5_xyz:  98.10   0.00  14.10  98.10   0.00   9.49  85.22   1.36  39.22
   5_adp:  97.95   0.00  14.06  97.95   0.00   9.49  85.20   2.03  38.96
   5_occ:  97.95   0.00  14.06  97.95   0.00   9.49  85.20   2.03  38.96
   5_bss:  99.57   1.62  15.68  99.57   1.62  11.11  86.82   3.65  40.58
------------------------------------------------------------------------
 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:    1.253    0.010    0.414
   1_adp:    1.253    0.010    0.414
   1_occ:    1.253    0.010    0.414
   2_bss:    1.253    0.010    0.414
   2_xyz:    1.577    0.044    0.610
   2_adp:    1.577    0.044    0.610
   2_occ:    1.577    0.044    0.610
   3_bss:    1.577    0.044    0.610
   3_xyz:    1.712    0.048    0.746
   3_adp:    1.712    0.048    0.746
   3_occ:    1.712    0.048    0.746
   4_bss:    1.712    0.048    0.746
   4_xyz:    1.798    0.044    0.794
   4_adp:    1.798    0.044    0.794
   4_occ:    1.798    0.044    0.794
   5_bss:    1.798    0.044    0.794
   5_xyz:    1.824    0.048    0.824
   5_adp:    1.824    0.048    0.824
   5_occ:    1.824    0.048    0.824
   5_bss:    1.824    0.048    0.824
------------------------------------------------------------------------

CPU time actual refinement: 330.98


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_256/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_256/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_256/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_256/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_256/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 330.83 
  Macro-tasks:
    bulk solvent and scale       = 41.18  
    individual site refinement   = 131.62 
    weights calculation          = 32.02  
    collect and process          = 6.46   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 211.42 
  Micro-tasks:
    mask                            = 2.39   
    f_calc                          = 102.66 
    alpha_beta                      = 8.16   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 110.84 
    fmodel                         = 7.05   
    r_factors                      = 0.25   
    phase_errors                   = 10.26  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 243.04 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.746 micro seconds
Total CPU time: 5.74 minutes
from_scatterers_fft:    630 calls, 102.31 s
gradients_fft:          574 calls,  98.52 s

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

# Date 2008-01-16 Time 01:09:09 PST -0800 (1200474549.00 s)
Start R-work = 0.4945, R-free = 0.4896 (no bulk solvent and anisotropic scale)
Final R-work = 0.1332, R-free = 0.1799 (no bulk solvent and anisotropic scale)

Start R-work = 0.4855, R-free = 0.4786
Final R-work = 0.1164, R-free = 0.1662