# Date 2008-01-16 Time 02:15:01 PST -0800 (1200478501.26 s)
#phil __OFF__

Command line arguments: "../752.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 20794
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 752

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 46.2261, 85.9581, 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: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.2261, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0278 1.97275
Completeness in resolution range: 0.961376
Completeness with d_max=infinity: 0.95846

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0278
                             d_min =   1.9728

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.2261, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0278 1.97275
Completeness in resolution range: 0.961376
Completeness with d_max=infinity: 0.95846

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0283 -  4.2217 [2138/2163]  1925   213  10.0%
  bin  2:  4.2217 -  3.3632 [2049/2069]  1844   205  10.0%
  bin  3:  3.3632 -  2.9417 [2042/2061]  1837   205  10.0%
  bin  4:  2.9417 -  2.6744 [2008/2038]  1809   199   9.9%
  bin  5:  2.6744 -  2.4836 [2010/2029]  1813   197   9.8%
  bin  6:  2.4836 -  2.3378 [1983/2008]  1777   206  10.4%
  bin  7:  2.3378 -  2.2211 [1972/2000]  1774   198  10.0%
  bin  8:  2.2211 -  2.1247 [1971/2007]  1776   195   9.9%
  bin  9:  2.1247 -  2.0431 [1974/2016]  1779   195   9.9%
  bin 10:  2.0431 -  1.9728 [1442/1985]  1296   146  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_752/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: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 28
        2.42 -     3.04: 2207
        3.04 -     3.66: 4732
        3.66 -     4.28: 9126
        4.28 -     4.90: 12382
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z 204 " - " O   HOH Z 296 "  2.099 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.114 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  2.148 3.040 x,y+1,z
  ... (remaining 28470 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_752/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_752/model_refine_001.geo

CPU time processing inputs: 9.07


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.22605 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4566   r_free= 0.4422   ksol= 0.00   Bsol= 0.00   scale= 0.812    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.257593                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7089 0.99   1390  155 0.3881 0.3812      6.5606      6.5677|
|  2:  4.7089 -  3.7568 0.99   1340  150 0.3654 0.3463      6.7365       6.673|
|  3:  3.7568 -  3.2876 0.99   1314  141 0.3934 0.3616      6.6095      6.6423|
|  4:  3.2876 -  2.9896 0.99   1304  152 0.4373 0.4085      6.5103      6.4328|
|  5:  2.9896 -  2.7768 0.99   1295  144 0.4862 0.4727      6.3437      6.3644|
|  6:  2.7768 -  2.6139 0.99   1298  137 0.4811 0.5221      6.2645      6.1898|
|  7:  2.6139 -  2.4836 0.99   1287  140 0.4986 0.4503      6.2312      6.2172|
|  8:  2.4836 -  2.3760 0.98   1267  148 0.5113 0.4530      6.1742      6.1482|
|  9:  2.3760 -  2.2848 0.98   1257  145 0.4902 0.5047      6.1025      6.1289|
| 10:  2.2848 -  2.2062 1.00   1296  138 0.5051 0.5111      6.1024      6.0802|
| 11:  2.2062 -  2.1374 0.97   1266  138 0.5060 0.4725      6.0238      6.0325|
| 12:  2.1374 -  2.0765 0.98   1252  142 0.5024 0.5277      5.9801      6.0098|
| 13:  2.0765 -  2.0220 0.99   1279  140 0.5286 0.5188      5.8773      5.8277|
| 14:  2.0220 -  1.9728 0.62    785   89 0.5417 0.5005      5.8629      5.8034|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0283 -  4.7089  1390   155  0.69  34.83   0.80     0.74      72380.06|
|  2:  4.7089 -  3.7568  1340   150  0.75  31.11   0.89     0.82      88414.40|
|  3:  3.7568 -  3.2876  1314   141  0.67  38.30   0.87     0.79      91383.42|
|  4:  3.2876 -  2.9896  1304   152  0.60  43.96   0.82     0.69      82481.72|
|  5:  2.9896 -  2.7768  1295   144  0.48  53.24   0.76     0.58      72182.19|
|  6:  2.7768 -  2.6139  1298   137  0.46  55.08   0.74     0.52      64219.30|
|  7:  2.6139 -  2.4836  1287   140  0.43  57.61   0.76     0.49      60028.50|
|  8:  2.4836 -  2.3760  1267   148  0.42  58.25   0.74     0.49      54376.15|
|  9:  2.3760 -  2.2848  1257   145  0.44  56.56   0.74     0.50      48059.47|
| 10:  2.2848 -  2.2062  1296   138  0.43  57.25   0.78     0.51      42576.37|
| 11:  2.2062 -  2.1374  1266   138  0.41  59.05   0.77     0.50      42405.39|
| 12:  2.1374 -  2.0765  1252   142  0.36  62.94   0.79     0.45      42229.71|
| 13:  2.0765 -  2.0220  1279   140  0.30  67.63   0.73     0.38      38023.05|
| 14:  2.0220 -  1.9728   785    89  0.32  65.95   0.72     0.35      29499.61|
|alpha:            min =        0.35 max =            0.82 mean =         0.57|
|beta:             min =    29499.61 max =        91383.42 mean =     60331.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           90.00 mean =        52.37|
|phase err.(test): min =        0.00 max =           89.94 mean =        52.52|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.213673             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.757   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.993425              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.487   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       29 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      168 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      692 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1526 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2650 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3968 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5100 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6600 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7749 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.485 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.824 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.738)------------------------------------------|
|    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 = 11.738)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4638   r_free= 0.4484   ksol= 0.00   Bsol= 0.00   scale= 0.781    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.261574                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4476   r_free= 0.4303   ksol= 0.36   Bsol= 5.66   scale= 1.019    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.55,10.23,7.88,0.00,0.00,0.00); trace/3= 8.55                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.251197                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.592071              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.317   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.933586              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.024   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4476      final r-factor (work) = 0.3544          |
| start r-factor (free) = 0.4303      final r-factor (free) = 0.3799          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 83.5065 = 9.59 * 0.50 * 6.2597 + 1.00 * 53.4846                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.5863 = 9.59 * 0.50 * 6.1420 + 1.00 * 0.1289                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3544      final r-factor (work) = 0.3039          |
| start r-factor (free) = 0.3799      final r-factor (free) = 0.3496          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7488 = 0.93 * 1.00 * 6.1420 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6396 = 0.93 * 1.00 * 6.0254 + 1.00 * 0.0144                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.738)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.55   12.00    None  None   None       |
|    all(noH): 2823   0      0.00    75.55   12.00    None  None   None       |
|    Sol.    : 438    0      0.00    75.55   26.23    None  None   None       |
|    Mac.    : 2385   0      0.00    74.86   9.38     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.555: 1257   |   5:    37.773 -  45.328:   68        |
|      1:     7.555 -  15.109:  771   |   6:    45.328 -  52.882:   29        |
|      2:    15.109 -  22.664:  381   |   7:    52.882 -  60.437:   12        |
|      3:    22.664 -  30.218:  178   |   8:    60.437 -  67.991:    2        |
|      4:    30.218 -  37.773:  123   |   9:    67.991 -  75.546:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3039 r_free = 0.3496             target_work(ml) = 5.992         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3035 r_free = 0.3497             target_work(ml) = 5.991         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3035   r_free= 0.3497   ksol= 0.36   Bsol= 5.66   scale= 1.108    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.55,10.23,7.88,0.00,0.00,0.00); trace/3= 8.55                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.991494                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2985   r_free= 0.3430   ksol= 0.35   Bsol= 33.14   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.93,5.55,4.65,0.00,0.00,0.00); trace/3= 4.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.989273                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.432182              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.759   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.520240              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.513  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2985      final r-factor (work) = 0.2257          |
| start r-factor (free) = 0.3430      final r-factor (free) = 0.2792          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4682 = 3.43 * 0.50 * 6.0252 + 1.00 * 0.1284                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1148 = 3.43 * 0.50 * 5.8560 + 1.00 * 0.0653                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2257      final r-factor (work) = 0.2077          |
| start r-factor (free) = 0.2792      final r-factor (free) = 0.2643          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0608 = 0.52 * 1.00 * 5.8560 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9920 = 0.52 * 1.00 * 5.7089 + 1.00 * 0.0220                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.738)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.02   12.14    None  None   None       |
|    all(noH): 2823   0      0.00    79.02   12.14    None  None   None       |
|    Sol.    : 438    0      0.00    79.02   30.50    None  None   None       |
|    Mac.    : 2385   0      0.00    76.79   8.77     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.902: 1421   |   5:    39.509 -  47.411:   83        |
|      1:     7.902 -  15.804:  691   |   6:    47.411 -  55.312:   28        |
|      2:    15.804 -  23.705:  269   |   7:    55.312 -  63.214:   13        |
|      3:    23.705 -  31.607:  171   |   8:    63.214 -  71.116:    0        |
|      4:    31.607 -  39.509:  145   |   9:    71.116 -  79.018:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2077 r_free = 0.2643             target_work(ml) = 5.686         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2076 r_free = 0.2642             target_work(ml) = 5.686         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2076   r_free= 0.2642   ksol= 0.35   Bsol= 33.14   scale= 1.043   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.93,5.55,4.65,0.00,0.00,0.00); trace/3= 4.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.686084                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2068   r_free= 0.2618   ksol= 0.33   Bsol= 33.14   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.01,3.51,3.90,0.00,0.00,0.00); trace/3= 3.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.684057                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.095212              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.746   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.701408              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.084   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2068      final r-factor (work) = 0.1577          |
| start r-factor (free) = 0.2618      final r-factor (free) = 0.2070          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0471 = 2.10 * 0.50 * 5.7100 + 1.00 * 0.0653                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8836 = 2.10 * 0.50 * 5.5615 + 1.00 * 0.0573                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1577      final r-factor (work) = 0.1487          |
| start r-factor (free) = 0.2070      final r-factor (free) = 0.2012          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9152 = 0.70 * 1.00 * 5.5615 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5553 = 0.70 * 1.00 * 5.4072 + 1.00 * 0.7626                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 7      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.738)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.64   12.13    None  None   None       |
|    all(noH): 2823   0      0.00    86.64   12.13    None  None   None       |
|    Sol.    : 438    0      1.04    79.37   31.61    None  None   None       |
|    Mac.    : 2385   0      0.00    86.64   8.55     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.665: 1568   |   5:    43.322 -  51.987:   60        |
|      1:     8.665 -  17.329:  626   |   6:    51.987 -  60.651:   18        |
|      2:    17.329 -  25.994:  224   |   7:    60.651 -  69.316:    3        |
|      3:    25.994 -  34.658:  176   |   8:    69.316 -  77.980:    1        |
|      4:    34.658 -  43.322:  145   |   9:    77.980 -  86.645:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1487 r_free = 0.2012             target_work(ml) = 5.391         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1486 r_free = 0.2014             target_work(ml) = 5.391         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1486   r_free= 0.2014   ksol= 0.33   Bsol= 33.14   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.01,3.51,3.90,0.00,0.00,0.00); trace/3= 3.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.391485                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1489   r_free= 0.2008   ksol= 0.33   Bsol= 36.73   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.68,2.68,3.65,0.00,0.00,0.00); trace/3= 3.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.391049                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.953017              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.449   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 6.940281              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.747   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1489      final r-factor (work) = 0.1290          |
| start r-factor (free) = 0.2008      final r-factor (free) = 0.1814          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0442 = 2.95 * 0.50 * 5.4094 + 1.00 * 0.0572                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9306 = 2.95 * 0.50 * 5.3293 + 1.00 * 0.0618                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1290      final r-factor (work) = 0.1205          |
| start r-factor (free) = 0.1814      final r-factor (free) = 0.1710          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 37.0107 = 6.94 * 1.00 * 5.3293 + 1.00 * 0.0237                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 36.4414 = 6.94 * 1.00 * 5.2486 + 1.00 * 0.0143                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.738)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.93   12.71    None  None   None       |
|    all(noH): 2823   0      0.00    90.93   12.71    None  None   None       |
|    Sol.    : 438    0      1.05    84.30   36.71    None  None   None       |
|    Mac.    : 2385   0      0.00    90.93   8.31     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 -   9.093: 1731   |   5:    45.463 -  54.556:   93        |
|      1:     9.093 -  18.185:  534   |   6:    54.556 -  63.648:   56        |
|      2:    18.185 -  27.278:  157   |   7:    63.648 -  72.741:   22        |
|      3:    27.278 -  36.370:  122   |   8:    72.741 -  81.833:    5        |
|      4:    36.370 -  45.463:  101   |   9:    81.833 -  90.926:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1205 r_free = 0.1710             target_work(ml) = 5.214         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1205 r_free = 0.1709             target_work(ml) = 5.214         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1205   r_free= 0.1709   ksol= 0.33   Bsol= 36.73   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.68,2.68,3.65,0.00,0.00,0.00); trace/3= 3.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.213942                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1204   r_free= 0.1707   ksol= 0.31   Bsol= 36.73   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.68,2.54,3.68,0.00,0.00,0.00); trace/3= 2.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.212871                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.669650              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.082  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.211105              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.495  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1204      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1707      final r-factor (free) = 0.1638          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6911 = 3.67 * 0.50 * 5.2481 + 1.00 * 0.0618                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5840 = 3.67 * 0.50 * 5.1854 + 1.00 * 0.0697                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1121      final r-factor (work) = 0.1119          |
| start r-factor (free) = 0.1638      final r-factor (free) = 0.1587          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1098 = 0.21 * 1.00 * 5.1854 + 1.00 * 0.0151                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1014 = 0.21 * 1.00 * 5.1671 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.738)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.27   12.15    None  None   None       |
|    all(noH): 2823   0      0.00    90.27   12.15    None  None   None       |
|    Sol.    : 438    0      1.67    82.19   34.99    None  None   None       |
|    Mac.    : 2385   0      0.00    90.27   7.95     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.027: 1789   |   5:    45.136 -  54.163:   85        |
|      1:     9.027 -  18.054:  512   |   6:    54.163 -  63.190:   43        |
|      2:    18.054 -  27.082:  146   |   7:    63.190 -  72.218:   17        |
|      3:    27.082 -  36.109:  126   |   8:    72.218 -  81.245:    5        |
|      4:    36.109 -  45.136:   98   |   9:    81.245 -  90.272:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1119 r_free = 0.1587             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1118 r_free = 0.1584             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1584   ksol= 0.31   Bsol= 36.73   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.68,2.54,3.68,0.00,0.00,0.00); trace/3= 2.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.148108                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7089 0.99   1390  155 0.0967 0.1246      5.3641      5.5246|
|  2:  4.7089 -  3.7568 0.99   1340  150 0.0839 0.1198      5.4332      5.6694|
|  3:  3.7568 -  3.2876 0.99   1314  141 0.1063 0.1467      5.4856      5.8519|
|  4:  3.2876 -  2.9896 0.99   1304  152 0.1204 0.1686       5.458      5.6141|
|  5:  2.9896 -  2.7768 0.99   1295  144 0.1327 0.1723      5.3341      5.5574|
|  6:  2.7768 -  2.6139 0.99   1298  137 0.1170 0.1823      5.1882       5.448|
|  7:  2.6139 -  2.4836 0.99   1287  140 0.1290 0.1635      5.1786      5.3683|
|  8:  2.4836 -  2.3760 0.98   1267  148 0.1167 0.1702      5.0649      5.3407|
|  9:  2.3760 -  2.2848 0.98   1257  145 0.1202 0.1811       5.051      5.3113|
| 10:  2.2848 -  2.2062 1.00   1296  138 0.1144 0.1739      4.9665      5.2477|
| 11:  2.2062 -  2.1374 0.97   1266  138 0.1171 0.1789      4.9611      5.2834|
| 12:  2.1374 -  2.0765 0.98   1252  142 0.1120 0.1666      4.8837      5.1538|
| 13:  2.0765 -  2.0220 0.99   1279  140 0.1169 0.1772      4.7923      5.0745|
| 14:  2.0220 -  1.9728 0.62    785   89 0.1049 0.1531      4.6689      4.8537|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0283 -  4.7089  1390   155  0.94   9.17   0.98     0.96       7122.23|
|  2:  4.7089 -  3.7568  1340   150  0.95   8.14   1.02     1.01       9290.97|
|  3:  3.7568 -  3.2876  1314   141  0.93  11.71   1.03     1.02      10807.87|
|  4:  3.2876 -  2.9896  1304   152  0.92  14.02   1.02     0.99      10610.01|
|  5:  2.9896 -  2.7768  1295   144  0.90  16.13   1.00     0.97       8476.27|
|  6:  2.7768 -  2.6139  1298   137  0.90  15.84   0.99     0.96       6897.68|
|  7:  2.6139 -  2.4836  1287   140  0.91  15.62   1.00     0.96       6148.63|
|  8:  2.4836 -  2.3760  1267   148  0.91  15.30   0.99     0.98       5223.50|
|  9:  2.3760 -  2.2848  1257   145  0.91  15.68   1.01     0.99       5196.71|
| 10:  2.2848 -  2.2062  1296   138  0.90  15.80   1.01     0.97       4470.25|
| 11:  2.2062 -  2.1374  1266   138  0.90  16.57   1.00     0.96       4473.95|
| 12:  2.1374 -  2.0765  1252   142  0.91  15.08   1.02     1.02       3996.54|
| 13:  2.0765 -  2.0220  1279   140  0.90  16.59   1.02     1.00       3320.49|
| 14:  2.0220 -  1.9728   785    89  0.92  13.98   1.00     0.98       2545.43|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2545.43 max =        10807.87 mean =      6471.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.21|
|phase err.(test): min =        0.00 max =           88.49 mean =        13.56|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1586   ksol= 0.31   Bsol= 39.66   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.30,-0.48,0.78,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.149110                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1586   ksol= 0.31   Bsol= 39.66   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.30,-0.48,0.78,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.149110                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7089 0.99   1390  155 0.0960 0.1253      5.3683      5.5264|
|  2:  4.7089 -  3.7568 0.99   1340  150 0.0852 0.1195        5.44       5.663|
|  3:  3.7568 -  3.2876 0.99   1314  141 0.1065 0.1458      5.4857      5.8463|
|  4:  3.2876 -  2.9896 0.99   1304  152 0.1207 0.1699      5.4584      5.6186|
|  5:  2.9896 -  2.7768 0.99   1295  144 0.1333 0.1733       5.336      5.5541|
|  6:  2.7768 -  2.6139 0.99   1298  137 0.1173 0.1825      5.1882      5.4444|
|  7:  2.6139 -  2.4836 0.99   1287  140 0.1288 0.1635      5.1769      5.3673|
|  8:  2.4836 -  2.3760 0.98   1267  148 0.1168 0.1709      5.0645      5.3415|
|  9:  2.3760 -  2.2848 0.98   1257  145 0.1201 0.1811      5.0515      5.3127|
| 10:  2.2848 -  2.2062 1.00   1296  138 0.1143 0.1737      4.9672      5.2503|
| 11:  2.2062 -  2.1374 0.97   1266  138 0.1171 0.1787      4.9621      5.2847|
| 12:  2.1374 -  2.0765 0.98   1252  142 0.1119 0.1667      4.8843      5.1537|
| 13:  2.0765 -  2.0220 0.99   1279  140 0.1169 0.1772      4.7923      5.0755|
| 14:  2.0220 -  1.9728 0.62    785   89 0.1050 0.1531      4.6674      4.8506|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0283 -  4.7089  1390   155  0.94   9.21   0.98     0.95       7248.28|
|  2:  4.7089 -  3.7568  1340   150  0.95   8.18   1.02     1.01       9295.02|
|  3:  3.7568 -  3.2876  1314   141  0.93  11.62   1.03     1.02      10714.64|
|  4:  3.2876 -  2.9896  1304   152  0.91  14.08   1.01     0.99      10629.35|
|  5:  2.9896 -  2.7768  1295   144  0.90  16.13   1.00     0.97       8476.95|
|  6:  2.7768 -  2.6139  1298   137  0.90  15.79   0.98     0.96       6874.57|
|  7:  2.6139 -  2.4836  1287   140  0.91  15.60   1.00     0.96       6131.69|
|  8:  2.4836 -  2.3760  1267   148  0.91  15.31   0.99     0.98       5229.86|
|  9:  2.3760 -  2.2848  1257   145  0.91  15.72   1.01     0.99       5209.14|
| 10:  2.2848 -  2.2062  1296   138  0.90  15.82   1.00     0.97       4486.91|
| 11:  2.2062 -  2.1374  1266   138  0.90  16.60   1.00     0.96       4482.57|
| 12:  2.1374 -  2.0765  1252   142  0.91  15.11   1.02     1.01       4009.44|
| 13:  2.0765 -  2.0220  1279   140  0.90  16.59   1.01     1.00       3320.04|
| 14:  2.0220 -  1.9728   785    89  0.92  13.94   0.99     0.98       2531.08|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2531.08 max =        10714.64 mean =      6476.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.22|
|phase err.(test): min =        0.00 max =           88.90 mean =        13.61|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.738)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.93    93.20   15.08    None  None   None       |
|    all(noH): 2823   0      2.93    93.20   15.08    None  None   None       |
|    Sol.    : 438    0      4.60    85.12   37.92    None  None   None       |
|    Mac.    : 2385   0      2.93    93.20   10.88    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.929 -  11.957: 1789   |   5:    48.065 -  57.093:   85        |
|      1:    11.957 -  20.984:  512   |   6:    57.093 -  66.120:   43        |
|      2:    20.984 -  30.011:  146   |   7:    66.120 -  75.147:   17        |
|      3:    30.011 -  39.038:  126   |   8:    75.147 -  84.174:    5        |
|      4:    39.038 -  48.065:   98   |   9:    84.174 -  93.201:    2        |
|                               =>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: 0.373 - 4.668
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 315 from: 320
   mapped sites are within: 0.719 - 4.668

peak=   11.278 closest distance to " CB  VAL A 230 " =    1.447
peak=    9.328 closest distance to " CG2 VAL A 296 " =    1.386
peak=    6.766 closest distance to " O   HOH Z 130 " =    1.150
peak=    6.442 closest distance to " CD2 LEU A   5 " =    1.285
peak=    6.255 closest distance to " NE2 GLN A  11 " =    1.181
peak=    6.158 closest distance to " NH2 ARG A  56 " =    2.113
peak=    5.564 closest distance to " CG  LEU A   5 " =    1.207
peak=    5.550 closest distance to " CD1AILE A 234 " =    1.006
peak=    5.437 closest distance to " O   HOH Z 142 " =    1.972
peak=    5.386 closest distance to " CG  PRO A  54 " =    1.290
peak=    5.154 closest distance to " O   HOH Z   9 " =    1.405
peak=    5.067 closest distance to " O   HOH Z   7 " =    1.348
peak=    5.020 closest distance to " CB  SER A   3 " =    1.394
peak=    5.010 closest distance to " CG  LEU A 228 " =    1.191
peak=    4.901 closest distance to " O   HOH Z 425 " =    1.482
peak=    4.887 closest distance to " O   HOH Z 427 " =    2.571
peak=    4.789 closest distance to " O   HOH Z 126 " =    1.904
peak=    4.750 closest distance to " CB  GLN A 183 " =    1.214
peak=    4.733 closest distance to " CB  SER A  63 " =    1.206
peak=    4.696 closest distance to " CB  PRO A  54 " =    0.977
peak=    4.636 closest distance to " O   HOH Z 232 " =    2.350
peak=    4.596 closest distance to " O   HOH Z 298 " =    1.712
peak=    4.578 closest distance to " O   HOH Z 369 " =    1.966
peak=    4.515 closest distance to " CB  GLN A 223 " =    1.522
peak=    4.473 closest distance to " CD2 LEU A 228 " =    1.216
peak=    4.429 closest distance to " O   HOH Z 209 " =    2.277
peak=    4.376 closest distance to " O   HOH Z  68 " =    2.104
peak=    4.374 closest distance to " O   HOH Z  78 " =    1.639
peak=    4.358 closest distance to " O   SER A  87 " =    2.288
peak=    4.322 closest distance to " O   PRO A 198 " =    1.563
peak=    4.301 closest distance to " O   HOH Z  63 " =    1.384
peak=    4.273 closest distance to " O   HOH Z 272 " =    1.822
peak=    4.262 closest distance to " O   HOH Z 236 " =    2.000
peak=    4.261 closest distance to " NH1 ARG A 138 " =    1.117
peak=    4.226 closest distance to " O   HOH Z 124 " =    1.437
peak=    4.220 closest distance to " CB  GLU A 152 " =    1.210
peak=    4.214 closest distance to " CB  ASN A 148 " =    1.370
peak=    4.196 closest distance to " O   HOH Z 193 " =    1.820
peak=    4.181 closest distance to " CB  ARG A 275 " =    0.842
peak=    4.168 closest distance to " O   HOH Z 263 " =    1.701
peak=    4.157 closest distance to " O   HOH Z   2 " =    1.738
peak=    4.148 closest distance to " O   HOH Z 273 " =    2.657
peak=    4.147 closest distance to " ND2 ASN A 187 " =    1.604
peak=    4.137 closest distance to " O   HOH Z 193 " =    1.706
peak=    4.134 closest distance to " O   HOH Z 303 " =    2.323
peak=    4.131 closest distance to " CG  LEU A 167 " =    1.216
peak=    4.130 closest distance to " O   HOH Z  30 " =    1.669
peak=    4.122 closest distance to " O   HOH Z 316 " =    3.046
peak=    4.094 closest distance to " O   HOH Z  55 " =    2.206
peak=    4.088 closest distance to " CB  ASN A  39 " =    0.904
peak=    4.075 closest distance to " O   HOH Z 234 " =    3.594
peak=    4.073 closest distance to " CB  GLU A 128 " =    1.071
peak=    4.052 closest distance to " CB  VAL A 202 " =    1.591
peak=    4.042 closest distance to " N   PHE A 130 " =    1.268
peak=    4.024 closest distance to " OD1 ASN A  69 " =    2.623
peak=    4.005 closest distance to " O   HOH Z 346 " =    1.630
peak=    4.001 closest distance to " O   HOH Z 368 " =    1.896
peak=    3.973 closest distance to " CB  VAL A 230 " =    1.161
peak=    3.956 closest distance to " CB  VAL A 265 " =    1.361
peak=    3.953 closest distance to " OD2 ASP A 286 " =    2.782
peak=    3.944 closest distance to " O   HOH Z  61 " =    1.582
peak=    3.917 closest distance to " CB  VAL A 296 " =    1.137
peak=    3.916 closest distance to " NZ  LYS A 117 " =    3.243
peak=    3.905 closest distance to " O   HOH Z 371 " =    2.685
peak=    3.902 closest distance to " CG  PRO A 213 " =    1.172
peak=    3.894 closest distance to " O   HOH Z 144 " =    2.303
peak=    3.887 closest distance to " O   HOH Z 180 " =    2.059
peak=    3.882 closest distance to " CB  TRP A 266 " =    0.987
peak=    3.882 closest distance to " O   HOH Z 419 " =    1.950
peak=    3.880 closest distance to " O   HOH Z  40 " =    2.404
peak=    3.866 closest distance to " CG  PRO A 243 " =    1.204
peak=    3.861 closest distance to " CB BVAL A  41 " =    1.151
peak=    3.858 closest distance to " O   HOH Z 203 " =    1.782
peak=    3.853 closest distance to " O   HOH Z 380 " =    1.591
peak=    3.852 closest distance to " CB  GLU A 277 " =    3.510
peak=    3.849 closest distance to " O   HOH Z   9 " =    1.817
peak=    3.848 closest distance to " O   HOH Z 403 " =    1.651
peak=    3.821 closest distance to " CD1 ILE A  33 " =    1.668
peak=    3.821 closest distance to " CB  ARG A  79 " =    1.433
peak=    3.804 closest distance to " O   HOH Z 366 " =    2.903
peak=    3.787 closest distance to " CB  LEU A 143 " =    1.133
peak=    3.781 closest distance to " CG2 THR A 221 " =    1.147
peak=    3.763 closest distance to " O   HOH Z 411 " =    3.644
peak=    3.758 closest distance to " O   HOH Z 193 " =    1.847
peak=    3.755 closest distance to " O   HOH Z 195 " =    1.329
peak=    3.743 closest distance to " CG BARG A 102 " =    1.831
peak=    3.741 closest distance to " O   HOH Z 128 " =    1.939
peak=    3.740 closest distance to " O   HOH Z  61 " =    1.563
peak=    3.739 closest distance to " O   HOH Z  10 " =    1.728
peak=    3.738 closest distance to " O   HOH Z   1 " =    1.813
peak=    3.738 closest distance to " O   HOH Z   3 " =    1.974
peak=    3.722 closest distance to " O   HOH Z 435 " =    2.062
peak=    3.719 closest distance to " O   HOH Z 405 " =    1.352
peak=    3.708 closest distance to " NH1AARG A 145 " =    1.066
peak=    3.701 closest distance to " NH2AARG A 190 " =    1.840
peak=    3.694 closest distance to " CG1BVAL A  72 " =    1.472
peak=    3.682 closest distance to " CB  GLN A  88 " =    1.283
peak=    3.672 closest distance to " CB  TRP A 179 " =    1.389
peak=    3.667 closest distance to " O   HOH Z 126 " =    1.521
peak=    3.666 closest distance to " O   HOH Z 222 " =    2.347
peak=    3.662 closest distance to " O   HOH Z 423 " =    1.433
peak=    3.654 closest distance to " O   HOH Z 189 " =    2.689
peak=    3.652 closest distance to " CB  ASN A 187 " =    1.090
peak=    3.645 closest distance to " CA  THR A 264 " =    0.765
peak=    3.639 closest distance to " O   HOH Z   1 " =    1.762
peak=    3.636 closest distance to " CB  ARG A 139 " =    1.014
peak=    3.629 closest distance to " O   HOH Z 422 " =    2.593
peak=    3.628 closest distance to " O   HOH Z 145 " =    1.515
peak=    3.622 closest distance to " CA  PHE A 283 " =    1.213
peak=    3.621 closest distance to " O   PRO A 198 " =    1.334
peak=    3.620 closest distance to " CA  ALA A  51 " =    1.000
peak=    3.609 closest distance to " O   HOH Z  40 " =    2.055
peak=    3.606 closest distance to " CB  ASN A 142 " =    0.956
peak=    3.605 closest distance to " O   HOH Z 258 " =    2.214
peak=    3.601 closest distance to " O   HOH Z 389 " =    1.882
peak=    3.594 closest distance to " CD1 LEU A 300 " =    1.220
peak=    3.590 closest distance to " CB  TYR A 169 " =    0.722
peak=    3.585 closest distance to " O   HOH Z 303 " =    1.825
peak=    3.585 closest distance to " O   HOH Z 291 " =    1.658
peak=    3.579 closest distance to " NH2BARG A 145 " =    2.026
peak=    3.574 closest distance to " CG1 ILE A  33 " =    1.298
peak=    3.573 closest distance to " CB  SER A 216 " =    0.786
peak=    3.566 closest distance to " O   HOH Z 128 " =    2.112
peak=    3.563 closest distance to " OG  SER A  62 " =    3.055
peak=    3.552 closest distance to " O   HOH Z 437 " =    2.225
peak=    3.549 closest distance to " O   HOH Z 410 " =    1.426
peak=    3.548 closest distance to " CG1AVAL A 121 " =    0.745
peak=    3.543 closest distance to " OE2 GLU A  53 " =    1.997
peak=    3.541 closest distance to " CG  GLN A  88 " =    1.133
peak=    3.539 closest distance to " O   HOH Z 392 " =    1.222
peak=    3.534 closest distance to " CA  TYR A  30 " =    0.983
peak=    3.532 closest distance to " O   HOH Z 207 " =    1.793
peak=    3.529 closest distance to " O   HOH Z 344 " =    2.870
peak=    3.525 closest distance to " CE  MET A  93 " =    1.531
peak=    3.521 closest distance to " O   HOH Z 359 " =    1.305
peak=    3.519 closest distance to " CB  MET A  40 " =    0.847
peak=    3.518 closest distance to " O   HOH Z 272 " =    2.285
peak=    3.516 closest distance to " O   HOH Z 409 " =    2.725
peak=    3.503 closest distance to " OG  SER A  62 " =    2.920
peak=    3.502 closest distance to " CB  SER A 212 " =    1.263
peak=    3.501 closest distance to " O   HOH Z 214 " =    2.048
peak=    3.498 closest distance to " CA  SER A  87 " =    0.876
peak=    3.487 closest distance to " O   HOH Z 158 " =    3.148
peak=    3.483 closest distance to " CA  ALA A 158 " =    1.132
peak=    3.480 closest distance to " CG2 ILE A  20 " =    1.652
peak=    3.479 closest distance to " O   HOH Z 113 " =    2.020
peak=    3.477 closest distance to " O   HOH Z 250 " =    1.381
peak=    3.473 closest distance to " O   HOH Z 290 " =    0.987
peak=    3.472 closest distance to " CB  THR A 157 " =    1.095
peak=    3.469 closest distance to " O   HOH Z  97 " =    1.974
peak=    3.467 closest distance to " O   HOH Z 313 " =    1.541
peak=    3.466 closest distance to " O   HOH Z  88 " =    2.613
peak=    3.465 closest distance to " CA  ALA A  21 " =    1.213
peak=    3.464 closest distance to " O   HOH Z 353 " =    2.486
peak=    3.463 closest distance to " O   HOH Z 197 " =    3.246
peak=    3.463 closest distance to " N   ASN A 127 " =    1.405
peak=    3.462 closest distance to " ND1 HIS A  86 " =    1.808
peak=    3.451 closest distance to " CG  LYS A  76 " =    1.639
peak=    3.451 closest distance to " CB  LEU A 228 " =    1.275
peak=    3.449 closest distance to " CD BLYS A 290 " =    1.148
peak=    3.442 closest distance to " O   HOH Z 145 " =    3.526
peak=    3.431 closest distance to " O   HOH Z 329 " =    3.815
peak=    3.426 closest distance to " CA  GLY A 267 " =    0.945
peak=    3.425 closest distance to " CA  LYS A 117 " =    1.179
peak=    3.424 closest distance to " NH2 ARG A 156 " =    1.081
peak=    3.423 closest distance to " CA  ALA A 299 " =    0.893
peak=    3.416 closest distance to " O   HOH Z  59 " =    1.727
peak=    3.405 closest distance to " O   HOH Z 334 " =    1.538
peak=    3.405 closest distance to " CA  ILE A 234 " =    0.992
peak=    3.400 closest distance to " CD  LYS A 166 " =    1.374
peak=    3.396 closest distance to " OG BSER A 164 " =    2.276
peak=    3.396 closest distance to " CA  ASN A 215 " =    1.089
peak=    3.393 closest distance to " O   HOH Z 368 " =    3.581
peak=    3.391 closest distance to " O   HOH Z  88 " =    3.290
peak=    3.388 closest distance to " NH1BARG A 145 " =    1.162
peak=    3.388 closest distance to " CD1 LEU A   5 " =    1.456
peak=    3.385 closest distance to " O   HOH Z  93 " =    2.358
peak=    3.383 closest distance to " CG  ARG A 138 " =    1.127
peak=    3.382 closest distance to " O   HOH Z 133 " =    1.587
peak=    3.382 closest distance to " CD  PRO A 243 " =    1.427
peak=    3.380 closest distance to " O   HOH Z 175 " =    2.164
peak=    3.379 closest distance to " O   HOH Z  44 " =    1.591
peak=    3.378 closest distance to " NH2BARG A 190 " =    1.561
peak=    3.371 closest distance to " CE1 TYR A 186 " =    1.346
peak=    3.369 closest distance to " O   HOH Z 425 " =    1.778
peak=    3.365 closest distance to " CZ  PHE A 218 " =    1.076
peak=    3.364 closest distance to " CB  ALA A  34 " =    1.054
peak=    3.364 closest distance to " CG  PRO A 198 " =    1.270
peak=    3.360 closest distance to " O   HOH Z  58 " =    1.651
peak=    3.354 closest distance to " O   HOH Z  85 " =    2.012
peak=    3.354 closest distance to " CB  VAL A 250 " =    1.090
peak=    3.351 closest distance to " O   HOH Z 184 " =    1.481
peak=    3.350 closest distance to " CG2 VAL A 197 " =    1.119
peak=    3.350 closest distance to " O   HOH Z 343 " =    3.422
peak=    3.348 closest distance to " CA  ASN A  74 " =    1.202
peak=    3.347 closest distance to " O   HOH Z  47 " =    1.709
peak=    3.346 closest distance to " O   HOH Z 305 " =    3.458
peak=    3.345 closest distance to " CG1 VAL A 153 " =    0.940
peak=    3.344 closest distance to " CB  ALA A 248 " =    1.005
peak=    3.340 closest distance to " O   HOH Z 248 " =    1.709
peak=    3.339 closest distance to " O   HOH Z  43 " =    1.928
peak=    3.338 closest distance to " CB  SER A 276 " =    1.090
peak=    3.331 closest distance to " O   HOH Z 295 " =    1.659
peak=    3.330 closest distance to " O   HOH Z 427 " =    1.178
peak=    3.330 closest distance to " NE AARG A 275 " =    1.318
peak=    3.328 closest distance to " O   HOH Z 145 " =    1.747
peak=    3.323 closest distance to " O   HOH Z   6 " =    2.058
peak=    3.321 closest distance to " O   ASN A 209 " =    1.308
peak=    3.320 closest distance to " O   HOH Z 173 " =    2.038
peak=    3.315 closest distance to " OE1 GLN A  11 " =    2.076
peak=    3.313 closest distance to " C   GLU A 277 " =    1.274
peak=    3.312 closest distance to " CG2 VAL A 257 " =    0.898
peak=    3.309 closest distance to " NE2 GLN A  58 " =    3.559
peak=    3.301 closest distance to " O   HOH Z  89 " =    2.003
peak=    3.301 closest distance to " O   HOH Z  80 " =    1.653
peak=    3.300 closest distance to " O   HOH Z 406 " =    1.654
peak=    3.299 closest distance to " O   HOH Z 255 " =    1.743
peak=    3.298 closest distance to " O   HOH Z  59 " =    1.911
peak=    3.296 closest distance to " O   HOH Z 108 " =    2.472
peak=    3.292 closest distance to " CG  GLN A  89 " =    1.402
peak=    3.289 closest distance to " O   HOH Z 352 " =    1.409
peak=    3.285 closest distance to " O   HOH Z  85 " =    1.312
peak=    3.283 closest distance to " CB  SER A  62 " =    1.241
peak=    3.282 closest distance to " O   HOH Z  65 " =    0.791
peak=    3.280 closest distance to " CD  ARG A 269 " =    1.033
peak=    3.279 closest distance to " O   HOH Z 371 " =    1.674
peak=    3.278 closest distance to " CG1 ILE A 151 " =    1.205
peak=    3.277 closest distance to " CB  ARG A 190 " =    1.664
peak=    3.277 closest distance to " CA  LEU A 282 " =    1.171
peak=    3.277 closest distance to " CB  SER A  26 " =    1.506
peak=    3.274 closest distance to " CE BLYS A 290 " =    0.841
peak=    3.271 closest distance to " OE2 GLU A   2 " =    1.846
peak=    3.270 closest distance to " O   HOH Z 213 " =    2.293
peak=    3.267 closest distance to " CG1 ILE A 263 " =    1.234
peak=    3.266 closest distance to " CB  ALA A 291 " =    1.369
peak=    3.265 closest distance to " O   HOH Z  21 " =    1.677
peak=    3.264 closest distance to " O   HOH Z 222 " =    2.280
peak=    3.262 closest distance to " O   HOH Z 148 " =    2.154
peak=    3.261 closest distance to " CG  MET A 185 " =    1.249
peak=    3.253 closest distance to " ND1 HIS A  81 " =    1.742
peak=    3.252 closest distance to " CG AARG A 275 " =    1.143
peak=    3.251 closest distance to " O   MET A 105 " =    1.714
peak=    3.249 closest distance to " CZ  PHE A 192 " =    0.975
peak=    3.249 closest distance to " OG  SER A  22 " =    2.843
peak=    3.240 closest distance to " CB  ALA A  10 " =    1.267
peak=    3.239 closest distance to " O   HOH Z 383 " =    1.791
peak=    3.239 closest distance to " CA  ILE A 106 " =    0.747
peak=    3.237 closest distance to " O   HOH Z 299 " =    3.977
peak=    3.235 closest distance to " CB  ALA A 104 " =    0.719
peak=    3.229 closest distance to " N   ARG A 156 " =    1.316
peak=    3.226 closest distance to " O   HOH Z 152 " =    2.717
peak=    3.226 closest distance to " CD  GLN A 240 " =    1.520
peak=    3.225 closest distance to " O   HOH Z 325 " =    3.707
peak=    3.224 closest distance to " O   HOH Z 435 " =    1.628
peak=    3.221 closest distance to " CG  LYS A 119 " =    1.098
peak=    3.220 closest distance to " CD2 LEU A 255 " =    1.421
peak=    3.217 closest distance to " O   ARG A 145 " =    1.754
peak=    3.212 closest distance to " NE  ARG A  56 " =    3.439
peak=    3.205 closest distance to " O   HOH Z 280 " =    3.071
peak=    3.203 closest distance to " O   HOH Z 423 " =    1.575
peak=    3.200 closest distance to " OD1BASN A 224 " =    2.344
peak=    3.196 closest distance to " N   GLN A 278 " =    1.094
peak=    3.193 closest distance to " CA  ALA A 248 " =    1.219
peak=    3.192 closest distance to " CD  ARG A  14 " =    1.393
peak=    3.188 closest distance to " CB  PHE A 225 " =    1.374
peak=    3.185 closest distance to " O   HOH Z 303 " =    3.125
peak=    3.185 closest distance to " O   HOH Z 423 " =    2.437
peak=    3.181 closest distance to " O   HOH Z 132 " =    1.300
peak=    3.181 closest distance to " CB  ALA A   1 " =    4.668
peak=    3.181 closest distance to " O   HOH Z  20 " =    1.529
peak=    3.180 closest distance to " O   HOH Z 133 " =    2.429
peak=    3.180 closest distance to " O   HOH Z 207 " =    2.004
peak=    3.179 closest distance to " O   HOH Z 119 " =    1.634
peak=    3.174 closest distance to " O   HOH Z 411 " =    1.823
peak=    3.171 closest distance to " CD1 ILE A 263 " =    1.284
peak=    3.170 closest distance to " N   VAL A 126 " =    1.268
peak=    3.167 closest distance to " O   HOH Z 196 " =    3.100
peak=    3.164 closest distance to " O   HOH Z 209 " =    2.331
peak=    3.163 closest distance to " OG BSER A  99 " =    2.068
peak=    3.163 closest distance to " CB  ASN A 110 " =    1.027
peak=    3.163 closest distance to " CA  ALA A 291 " =    0.938
peak=    3.162 closest distance to " CB  ASP A 140 " =    0.834
peak=    3.149 closest distance to " O   ALA A 158 " =    1.358
peak=    3.145 closest distance to " CD  ARG A 138 " =    1.149
peak=    3.144 closest distance to " O   HOH Z 132 " =    2.347
peak=    3.137 closest distance to " NZ  LYS A  76 " =    1.233
peak=    3.134 closest distance to " CB  PHE A 204 " =    0.787
peak=    3.134 closest distance to " O   HOH Z 271 " =    2.017
peak=    3.130 closest distance to " CB  ASN A 224 " =    1.007
peak=    3.129 closest distance to " O   HOH Z 217 " =    1.666
peak=    3.126 closest distance to " OG ASER A  99 " =    1.483
peak=    3.116 closest distance to " CG  GLN A 278 " =    1.328
peak=    3.113 closest distance to " CB  TRP A 150 " =    1.415
peak=    3.110 closest distance to " O  BHOH Z 338 " =    2.507
peak=    3.105 closest distance to " NZ  LYS A  48 " =    1.331
peak=    3.097 closest distance to " O   HOH Z 128 " =    2.146
peak=    3.094 closest distance to " O   HOH Z 433 " =    1.784
peak=    3.093 closest distance to " O   HOH Z 146 " =    1.672
peak=    3.092 closest distance to " CB  ILE A  20 " =    1.467
peak=    3.087 closest distance to " CZ3 TRP A  92 " =    1.307
peak=    3.087 closest distance to " CA  LYS A 290 " =    1.299
peak=    3.084 closest distance to " CB  TYR A  30 " =    1.597
peak=    3.080 closest distance to " CB  LEU A 300 " =    0.892
peak=    3.078 closest distance to " O   HOH Z 192 " =    2.073
peak=    3.076 closest distance to " O   HOH Z 110 " =    1.510
peak=    3.076 closest distance to " CB  ALA A   9 " =    1.533
peak=    3.073 closest distance to " CB  ILE A 120 " =    1.433
peak=    3.066 closest distance to " O   HOH Z 359 " =    3.964
peak=    3.061 closest distance to " O   HOH Z 173 " =    1.643
peak=    3.061 closest distance to " CZ3 TRP A 266 " =    1.082
peak=    3.060 closest distance to " N   SER A 135 " =    1.320
peak=    3.055 closest distance to " CA  ALA A 233 " =    1.012
peak=    3.051 closest distance to " CA  ARG A 102 " =    1.114
peak=    3.026 closest distance to " O   HOH Z 216 " =    1.914
peak=    3.007 closest distance to " O   HOH Z  59 " =    2.261

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.732 - 5.359
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 201
   mapped sites are within: 0.732 - 5.359

peak=   -5.077 closest distance to " CG2 VAL A 230 " =    0.822
peak=   -4.471 closest distance to " CB  PRO A 243 " =    2.626
peak=   -4.470 closest distance to " CD  ARG A  14 " =    3.091
peak=   -4.450 closest distance to " CD  ARG A 156 " =    2.006
peak=   -4.353 closest distance to " CD1 LEU A 255 " =    2.896
peak=   -4.237 closest distance to " O   HOH Z 290 " =    1.248
peak=   -4.142 closest distance to " O   PRO A 198 " =    1.192
peak=   -4.096 closest distance to " OG BSER A 134 " =    1.300
peak=   -4.021 closest distance to " NH2 ARG A  79 " =    1.937
peak=   -3.968 closest distance to " CG2 VAL A 296 " =    1.486
peak=   -3.939 closest distance to " O   HOH Z 266 " =    4.876
peak=   -3.936 closest distance to " O   HOH Z 231 " =    1.742
peak=   -3.922 closest distance to " OG  SER A  87 " =    1.353
peak=   -3.920 closest distance to " C   HIS A 108 " =    1.304
peak=   -3.918 closest distance to " CG2 VAL A 296 " =    0.913
peak=   -3.901 closest distance to " CD1 LEU A 101 " =    2.811
peak=   -3.863 closest distance to " O   HOH Z 185 " =    2.137
peak=   -3.851 closest distance to " O   HOH Z 140 " =    1.397
peak=   -3.829 closest distance to " O   HOH Z  11 " =    1.968
peak=   -3.807 closest distance to " O   VAL A  67 " =    2.517
peak=   -3.805 closest distance to " O   HOH Z 359 " =    3.341
peak=   -3.793 closest distance to " CB  PRO A 163 " =    2.454
peak=   -3.788 closest distance to " O   GLY A  80 " =    2.453
peak=   -3.777 closest distance to " CG1 VAL A 197 " =    2.244
peak=   -3.776 closest distance to " CE2 TYR A  30 " =    2.755
peak=   -3.771 closest distance to " CB  ALA A 248 " =    1.991
peak=   -3.759 closest distance to " O   HOH Z 211 " =    1.437
peak=   -3.758 closest distance to " CD1 LEU A 228 " =    2.249
peak=   -3.754 closest distance to " CD2 LEU A   5 " =    0.973
peak=   -3.750 closest distance to " O   HOH Z  43 " =    1.823
peak=   -3.732 closest distance to " O   SER A  22 " =    2.347
peak=   -3.721 closest distance to " CB  TYR A  15 " =    2.098
peak=   -3.702 closest distance to " N   GLN A  58 " =    2.009
peak=   -3.694 closest distance to " CZ3 TRP A 179 " =    1.225
peak=   -3.679 closest distance to " O   VAL A  67 " =    2.776
peak=   -3.678 closest distance to " O   PRO A 163 " =    1.944
peak=   -3.668 closest distance to " O   HOH Z 339 " =    1.870
peak=   -3.666 closest distance to " O   SER A 135 " =    1.538
peak=   -3.655 closest distance to " CB  ALA A 161 " =    2.522
peak=   -3.654 closest distance to " O   HOH Z 385 " =    2.165
peak=   -3.651 closest distance to " CG1 VAL A 112 " =    3.018
peak=   -3.649 closest distance to " ND2 ASN A 249 " =    2.411
peak=   -3.642 closest distance to " CA  GLY A  98 " =    1.849
peak=   -3.632 closest distance to " O   HOH Z 351 " =    1.532
peak=   -3.627 closest distance to " CG  GLN A 223 " =    1.957
peak=   -3.626 closest distance to " O   HOH Z 100 " =    1.326
peak=   -3.621 closest distance to " CD  LYS A 289 " =    2.442
peak=   -3.619 closest distance to " CE2 PHE A 218 " =    2.504
peak=   -3.617 closest distance to " O   PRO A 243 " =    2.514
peak=   -3.615 closest distance to " O   HOH Z  51 " =    1.110
peak=   -3.610 closest distance to " CG  PHE A 283 " =    2.582
peak=   -3.605 closest distance to " N   PHE A  59 " =    2.103
peak=   -3.591 closest distance to " O   HOH Z 394 " =    1.408
peak=   -3.591 closest distance to " O   HOH Z  65 " =    1.230
peak=   -3.585 closest distance to " O   HOH Z 377 " =    2.060
peak=   -3.584 closest distance to " C   ALA A 158 " =    1.372
peak=   -3.583 closest distance to " O   HOH Z  52 " =    1.175
peak=   -3.582 closest distance to " CD2 LEU A 237 " =    2.633
peak=   -3.573 closest distance to " CD1 LEU A 101 " =    2.305
peak=   -3.557 closest distance to " CA  GLY A 241 " =    2.239
peak=   -3.547 closest distance to " N   THR A 157 " =    1.453
peak=   -3.531 closest distance to " CG  TRP A 266 " =    1.812
peak=   -3.531 closest distance to " CE  MET A 105 " =    2.251
peak=   -3.526 closest distance to " CD1 PHE A  59 " =    1.988
peak=   -3.526 closest distance to " O   HOH Z 377 " =    0.838
peak=   -3.523 closest distance to " OG BSER A 134 " =    1.700
peak=   -3.510 closest distance to " O   PRO A 198 " =    1.230
peak=   -3.508 closest distance to " O   SER A 271 " =    2.060
peak=   -3.499 closest distance to " O   HOH Z 359 " =    1.623
peak=   -3.498 closest distance to " CG1 VAL A 250 " =    2.745
peak=   -3.495 closest distance to " OE1 GLN A  88 " =    1.187
peak=   -3.487 closest distance to " CZ  TYR A 172 " =    1.756
peak=   -3.483 closest distance to " CG  ASP A 231 " =    0.732
peak=   -3.482 closest distance to " CB  ALA A   7 " =    2.076
peak=   -3.474 closest distance to " OG1 THR A 178 " =    1.173
peak=   -3.474 closest distance to " CB  ALA A 248 " =    2.438
peak=   -3.469 closest distance to " CB  ASN A  39 " =    2.055
peak=   -3.467 closest distance to " O   HOH Z 350 " =    2.124
peak=   -3.464 closest distance to " CB  ASP A 132 " =    2.342
peak=   -3.460 closest distance to " O   HOH Z  60 " =    2.364
peak=   -3.457 closest distance to " O   ARG A 145 " =    1.519
peak=   -3.444 closest distance to " O   VAL A 189 " =    2.588
peak=   -3.441 closest distance to " O   ALA A 161 " =    1.768
peak=   -3.436 closest distance to " C   LEU A 222 " =    0.740
peak=   -3.432 closest distance to " C   LYS A  76 " =    1.635
peak=   -3.430 closest distance to " O   HOH Z 134 " =    2.867
peak=   -3.429 closest distance to " OD2 ASP A 171 " =    2.186
peak=   -3.428 closest distance to " O   HOH Z 198 " =    2.279
peak=   -3.423 closest distance to " CG  PRO A 163 " =    2.597
peak=   -3.417 closest distance to " O   HOH Z  90 " =    2.880
peak=   -3.415 closest distance to " CB  ALA A 244 " =    2.064
peak=   -3.411 closest distance to " O   HOH Z 131 " =    4.110
peak=   -3.409 closest distance to " O   HOH Z 166 " =    1.591
peak=   -3.408 closest distance to " OG  SER A 245 " =    1.147
peak=   -3.407 closest distance to " CD  GLN A  58 " =    1.047
peak=   -3.405 closest distance to " N   HIS A 115 " =    2.139
peak=   -3.394 closest distance to " CD1 TYR A 247 " =    2.620
peak=   -3.393 closest distance to " C   MET A 188 " =    1.618
peak=   -3.381 closest distance to " CE  LYS A  76 " =    2.944
peak=   -3.380 closest distance to " O   HOH Z 191 " =    5.359
peak=   -3.380 closest distance to " CA  GLY A 133 " =    2.014
peak=   -3.370 closest distance to " CG2 THR A 178 " =    2.128
peak=   -3.365 closest distance to " C   ASN A 285 " =    2.297
peak=   -3.364 closest distance to " C   ASN A 187 " =    1.784
peak=   -3.353 closest distance to " NH1 ARG A  56 " =    2.461
peak=   -3.352 closest distance to " NH2AARG A 275 " =    5.254
peak=   -3.352 closest distance to " CG  MET A 105 " =    0.951
peak=   -3.351 closest distance to " N   SER A 276 " =    1.293
peak=   -3.348 closest distance to " N   ALA A  43 " =    2.607
peak=   -3.347 closest distance to " O   HOH Z 388 " =    2.217
peak=   -3.338 closest distance to " OE1 GLU A 277 " =    2.156
peak=   -3.338 closest distance to " CB  ALA A  43 " =    2.417
peak=   -3.326 closest distance to " O   HOH Z 298 " =    1.177
peak=   -3.326 closest distance to " ND2 ASN A 187 " =    1.592
peak=   -3.321 closest distance to " C   ARG A 269 " =    1.404
peak=   -3.319 closest distance to " O   HOH Z 389 " =    1.469
peak=   -3.319 closest distance to " CE BMET A  47 " =    1.629
peak=   -3.318 closest distance to " O   HOH Z 414 " =    2.390
peak=   -3.313 closest distance to " CA  ASP A  27 " =    2.441
peak=   -3.308 closest distance to " O   HOH Z 389 " =    1.908
peak=   -3.307 closest distance to " CZ  PHE A  59 " =    1.481
peak=   -3.304 closest distance to " O   LYS A 289 " =    3.073
peak=   -3.301 closest distance to " OG ASER A 216 " =    1.098
peak=   -3.291 closest distance to " O   HOH Z 313 " =    1.551
peak=   -3.287 closest distance to " CG1 VAL A 296 " =    1.641
peak=   -3.286 closest distance to " O   HOH Z 426 " =    2.314
peak=   -3.286 closest distance to " O   MET A  40 " =    2.792
peak=   -3.283 closest distance to " O   HOH Z 243 " =    1.949
peak=   -3.281 closest distance to " C   GLN A 205 " =    2.032
peak=   -3.271 closest distance to " CB  ALA A 291 " =    2.069
peak=   -3.269 closest distance to " O   HOH Z 275 " =    1.560
peak=   -3.267 closest distance to " OG  SER A   3 " =    1.275
peak=   -3.267 closest distance to " CG  ASN A 301 " =    1.957
peak=   -3.253 closest distance to " CG2AVAL A  41 " =    2.830
peak=   -3.251 closest distance to " O   HOH Z 423 " =    2.217
peak=   -3.251 closest distance to " C   VAL A 265 " =    0.847
peak=   -3.242 closest distance to " O   HOH Z 281 " =    3.061
peak=   -3.240 closest distance to " N   THR A 235 " =    1.245
peak=   -3.238 closest distance to " O   HOH Z 152 " =    4.742
peak=   -3.237 closest distance to " CE1 PHE A  59 " =    2.078
peak=   -3.237 closest distance to " O   HOH Z 114 " =    2.973
peak=   -3.237 closest distance to " N   ALA A 248 " =    1.625
peak=   -3.233 closest distance to " CB  TRP A  85 " =    2.628
peak=   -3.229 closest distance to " CG2 VAL A 202 " =    2.688
peak=   -3.227 closest distance to " O   HOH Z 198 " =    1.537
peak=   -3.226 closest distance to " N   ALA A 226 " =    2.071
peak=   -3.219 closest distance to " C   LEU A 143 " =    1.243
peak=   -3.218 closest distance to " O   ALA A   1 " =    1.746
peak=   -3.218 closest distance to " O   GLY A 211 " =    1.274
peak=   -3.216 closest distance to " CA  GLY A 203 " =    2.318
peak=   -3.209 closest distance to " O   HOH Z  38 " =    1.821
peak=   -3.206 closest distance to " NH2BARG A 275 " =    1.639
peak=   -3.205 closest distance to " O   HOH Z 427 " =    1.575
peak=   -3.202 closest distance to " O   HOH Z 165 " =    2.171
peak=   -3.201 closest distance to " O   HOH Z 134 " =    3.404
peak=   -3.199 closest distance to " OG  SER A  97 " =    2.225
peak=   -3.198 closest distance to " CE  MET A  93 " =    1.061
peak=   -3.197 closest distance to " O   HOH Z 407 " =    3.118
peak=   -3.194 closest distance to " ND2 ASN A  60 " =    1.824
peak=   -3.192 closest distance to " O   HOH Z 103 " =    1.789
peak=   -3.189 closest distance to " O   HOH Z 318 " =    1.913
peak=   -3.188 closest distance to " O   HOH Z  13 " =    1.699
peak=   -3.186 closest distance to " ND2 ASN A 252 " =    1.818
peak=   -3.182 closest distance to " CB  CYS A 201 " =    2.245
peak=   -3.180 closest distance to " O   GLN A 240 " =    2.411
peak=   -3.178 closest distance to " ND2 ASN A  69 " =    1.818
peak=   -3.173 closest distance to " O   HOH Z 368 " =    1.352
peak=   -3.172 closest distance to " N   ALA A 248 " =    2.511
peak=   -3.170 closest distance to " O   HOH Z 166 " =    1.772
peak=   -3.169 closest distance to " O   HOH Z 281 " =    2.925
peak=   -3.165 closest distance to " CB  GLN A  11 " =    1.918
peak=   -3.158 closest distance to " O   GLN A 240 " =    2.150
peak=   -3.154 closest distance to " O   HOH Z 377 " =    1.319
peak=   -3.147 closest distance to " CE1 PHE A 208 " =    2.098
peak=   -3.147 closest distance to " OXT GLY A 302 " =    3.068
peak=   -3.147 closest distance to " O   HOH Z 435 " =    2.155
peak=   -3.144 closest distance to " CD2 TYR A 293 " =    1.965
peak=   -3.140 closest distance to " CB  PRO A  90 " =    1.601
peak=   -3.140 closest distance to " O   ILE A  49 " =    1.774
peak=   -3.138 closest distance to " O   HOH Z  63 " =    1.867
peak=   -3.135 closest distance to " O   HOH Z 189 " =    2.358
peak=   -3.128 closest distance to " O   PHE A 218 " =    1.513
peak=   -3.127 closest distance to " CE3 TRP A 123 " =    1.279
peak=   -3.122 closest distance to " CG  GLU A 152 " =    1.422
peak=   -3.109 closest distance to " O   HOH Z 393 " =    3.367
peak=   -3.108 closest distance to " O   HOH Z 423 " =    1.254
peak=   -3.106 closest distance to " O   HOH Z 228 " =    1.583
peak=   -3.101 closest distance to " CZ  TYR A 169 " =    1.616
peak=   -3.099 closest distance to " CG  ASP A  50 " =    2.177
peak=   -3.095 closest distance to " O   ASP A 270 " =    1.693
peak=   -3.093 closest distance to " OE2 GLU A 152 " =    1.106
peak=   -3.085 closest distance to " N   VAL A  72 " =    1.527
peak=   -3.083 closest distance to " O   HOH Z   2 " =    1.673
peak=   -3.070 closest distance to " NE BARG A 102 " =    2.470
peak=   -3.070 closest distance to " O   HOH Z 295 " =    1.558
peak=   -3.064 closest distance to " CG2 VAL A 296 " =    1.974
peak=   -3.051 closest distance to " OG  SER A 206 " =    1.791
peak=   -3.020 closest distance to " N   ALA A 248 " =    1.878
peak=   -3.018 closest distance to " O   HOH Z 132 " =    1.330

================= 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    :  0.4566 0.4422   6.257593e+00   6.239997e+00
   1_bss:  0.4476 0.4303   6.251197e+00   6.228775e+00
   1_xyz:  0.3544 0.3799   6.103554e+00   6.140897e+00
   1_adp:  0.3039 0.3496   5.992384e+00   6.088754e+00
   1_occ:  0.3035 0.3497   5.991494e+00   6.089238e+00
   2_bss:  0.2985 0.3430   5.989273e+00   6.083725e+00
   2_xyz:  0.2257 0.2792   5.750206e+00   5.898339e+00
   2_adp:  0.2077 0.2643   5.686280e+00   5.857420e+00
   2_occ:  0.2076 0.2642   5.686084e+00   5.857629e+00
   3_bss:  0.2068 0.2618   5.684057e+00   5.854086e+00
   3_xyz:  0.1577 0.2070   5.437104e+00   5.644859e+00
   3_adp:  0.1487 0.2012   5.391483e+00   5.612931e+00
   3_occ:  0.1486 0.2014   5.391485e+00   5.613055e+00
   4_bss:  0.1489 0.2008   5.391049e+00   5.611603e+00
   4_xyz:  0.1290 0.1814   5.276423e+00   5.521690e+00
   4_adp:  0.1205 0.1710   5.214447e+00   5.460310e+00
   4_occ:  0.1205 0.1709   5.213942e+00   5.459536e+00
   5_bss:  0.1204 0.1707   5.212871e+00   5.458778e+00
   5_xyz:  0.1121 0.1638   5.164817e+00   5.427120e+00
   5_adp:  0.1119 0.1587   5.149257e+00   5.397993e+00
   5_occ:  0.1118 0.1584   5.148108e+00   5.396372e+00
   5_bss:  0.1121 0.1586   5.149110e+00   5.395761e+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:  0.359   5.660   7.546  10.234   7.885   0.000   0.000   0.000
   1_xyz:  0.359   5.660   7.546  10.234   7.885   0.000   0.000   0.000
   1_adp:  0.359   5.660   7.546  10.234   7.885   0.000   0.000   0.000
   1_occ:  0.359   5.660   7.546  10.234   7.885   0.000   0.000   0.000
   2_bss:  0.347  33.141   3.930   5.551   4.650   0.000   0.000   0.000
   2_xyz:  0.347  33.141   3.930   5.551   4.650   0.000   0.000   0.000
   2_adp:  0.347  33.141   3.930   5.551   4.650   0.000   0.000   0.000
   2_occ:  0.347  33.141   3.930   5.551   4.650   0.000   0.000   0.000
   3_bss:  0.331  33.141   3.014   3.514   3.897   0.000   0.000   0.000
   3_xyz:  0.331  33.141   3.014   3.514   3.897   0.000   0.000   0.000
   3_adp:  0.331  33.141   3.014   3.514   3.897   0.000   0.000   0.000
   3_occ:  0.331  33.141   3.014   3.514   3.897   0.000   0.000   0.000
   4_bss:  0.327  36.727   2.681   2.679   3.649   0.000   0.000   0.000
   4_xyz:  0.327  36.727   2.681   2.679   3.649   0.000   0.000   0.000
   4_adp:  0.327  36.727   2.681   2.679   3.649   0.000   0.000   0.000
   4_occ:  0.327  36.727   2.681   2.679   3.649   0.000   0.000   0.000
   5_bss:  0.315  36.727   2.684   2.545   3.680   0.000   0.000   0.000
   5_xyz:  0.315  36.727   2.684   2.545   3.680   0.000   0.000   0.000
   5_adp:  0.315  36.727   2.684   2.545   3.680   0.000   0.000   0.000
   5_occ:  0.315  36.727   2.684   2.545   3.680   0.000   0.000   0.000
   5_bss:  0.315  39.656  -0.301  -0.481   0.782  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.384 0.4913  0.5663    60331.071
   1_bss:  52.302 0.4903  0.7203    57561.892
   1_xyz:  42.698 0.6091  0.8792    41477.369
   1_adp:  37.094 0.6775  1.0000    34439.514
   1_occ:  37.164 0.6767  0.9981    34466.512
   2_bss:  36.601 0.6832  0.8799    33669.951
   2_xyz:  28.044 0.7788  0.9692    20126.538
   2_adp:  26.022 0.8013  0.9889    18112.208
   2_occ:  26.033 0.8012  0.9884    18109.802
   3_bss:  25.838 0.8030  0.9467    17853.245
   3_xyz:  19.823 0.8631  0.9925    10852.948
   3_adp:  18.968 0.8715  0.9943    10211.642
   3_occ:  18.975 0.8714  0.9938    10213.086
   4_bss:  18.912 0.8719  0.9769    10165.905
   4_xyz:  16.911 0.8900  0.9853     8333.876
   4_adp:  15.614 0.9014  0.9823     7364.510
   4_occ:  15.599 0.9015  0.9823     7349.884
   5_bss:  15.577 0.9017  0.9812     7328.941
   5_xyz:  14.846 0.9079  0.9838     6846.597
   5_adp:  14.175 0.9136  0.9830     6505.953
   5_occ:  14.143 0.9138  0.9830     6471.342
   5_bss:  14.155 0.9137  0.9814     6476.658
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3485e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3485e+01
   1_xyz:   1.602  0.012  0.103 18.059  0.006  4.119   1.2891e-01
   1_adp:   1.602  0.012  0.103 18.059  0.006  4.119   1.2891e-01
   1_occ:   1.602  0.012  0.103 18.059  0.006  4.119   1.2891e-01
   2_bss:   1.602  0.012  0.103 18.059  0.006  4.119   1.2891e-01
   2_xyz:   1.003  0.007  0.071 15.690  0.004  4.117   6.5278e-02
   2_adp:   1.003  0.007  0.071 15.690  0.004  4.117   6.5278e-02
   2_occ:   1.003  0.007  0.071 15.690  0.004  4.117   6.5278e-02
   3_bss:   1.003  0.007  0.071 15.690  0.004  4.117   6.5278e-02
   3_xyz:   0.936  0.006  0.071 15.485  0.003  4.121   5.7337e-02
   3_adp:   0.936  0.006  0.071 15.485  0.003  4.121   5.7337e-02
   3_occ:   0.936  0.006  0.071 15.485  0.003  4.121   5.7337e-02
   4_bss:   0.936  0.006  0.071 15.485  0.003  4.121   5.7337e-02
   4_xyz:   0.996  0.007  0.077 15.709  0.003  4.114   6.1848e-02
   4_adp:   0.996  0.007  0.077 15.709  0.003  4.114   6.1848e-02
   4_occ:   0.996  0.007  0.077 15.709  0.003  4.114   6.1848e-02
   5_bss:   0.996  0.007  0.077 15.709  0.003  4.114   6.1848e-02
   5_xyz:   1.059  0.008  0.083 15.747  0.004  4.118   6.9737e-02
   5_adp:   1.059  0.008  0.083 15.747  0.004  4.118   6.9737e-02
   5_occ:   1.059  0.008  0.083 15.747  0.004  4.118   6.9737e-02
   5_bss:   1.059  0.008  0.083 15.747  0.004  4.118   6.9737e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9337e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9337e+00
   1_xyz:  12.774  0.159  0.416 88.528  0.033  2.225   9.3882e-02
   1_adp:  12.774  0.159  0.416 88.528  0.033  2.225   9.3882e-02
   1_occ:  12.774  0.159  0.416 88.528  0.033  2.225   9.3882e-02
   2_bss:  12.774  0.159  0.416 88.528  0.033  2.225   9.3882e-02
   2_xyz:   6.262  0.061  0.297 79.741  0.034  2.304   7.7741e-02
   2_adp:   6.262  0.061  0.297 79.741  0.034  2.304   7.7741e-02
   2_occ:   6.262  0.061  0.297 79.741  0.034  2.304   7.7741e-02
   3_bss:   6.262  0.061  0.297 79.741  0.034  2.304   7.7741e-02
   3_xyz:   6.427  0.044  0.345 80.497  0.031  2.350   9.7532e-02
   3_adp:   6.427  0.044  0.345 80.497  0.031  2.350   9.7532e-02
   3_occ:   6.427  0.044  0.345 80.497  0.031  2.350   9.7532e-02
   4_bss:   6.427  0.044  0.345 80.497  0.031  2.350   9.7532e-02
   4_xyz:   7.090  0.052  0.379 83.807  0.031  2.284   4.3365e-02
   4_adp:   7.090  0.052  0.379 83.807  0.031  2.284   4.3365e-02
   4_occ:   7.090  0.052  0.379 83.807  0.031  2.284   4.3365e-02
   5_bss:   7.090  0.052  0.379 83.807  0.031  2.284   4.3365e-02
   5_xyz:   7.111  0.051  0.456 84.083  0.040  2.290   5.8978e-02
   5_adp:   7.111  0.051  0.456 84.083  0.040  2.290   5.8978e-02
   5_occ:   7.111  0.051  0.456 84.083  0.040  2.290   5.8978e-02
   5_bss:   7.111  0.051  0.456 84.083  0.040  2.290   5.8978e-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:  75.55   0.00  12.00  74.86   0.00   9.38  75.55   0.00  26.23
   1_occ:  75.55   0.00  12.00  74.86   0.00   9.38  75.55   0.00  26.23
   2_bss:  75.55   0.00  12.00  74.86   0.00   9.38  75.55   0.00  26.23
   2_xyz:  75.55   0.00  12.00  74.86   0.00   9.38  75.55   0.00  26.23
   2_adp:  79.02   0.00  12.14  76.79   0.00   8.77  79.02   0.00  30.50
   2_occ:  79.02   0.00  12.14  76.79   0.00   8.77  79.02   0.00  30.50
   3_bss:  79.02   0.00  12.14  76.79   0.00   8.77  79.02   0.00  30.50
   3_xyz:  79.02   0.00  12.14  76.79   0.00   8.77  79.02   0.00  30.50
   3_adp:  86.64   0.00  12.13  86.64   0.00   8.55  79.37   1.04  31.61
   3_occ:  86.64   0.00  12.13  86.64   0.00   8.55  79.37   1.04  31.61
   4_bss:  86.64   0.00  12.13  86.64   0.00   8.55  79.37   1.04  31.61
   4_xyz:  86.64   0.00  12.13  86.64   0.00   8.55  79.37   1.04  31.61
   4_adp:  90.93   0.00  12.71  90.93   0.00   8.31  84.30   1.05  36.71
   4_occ:  90.93   0.00  12.71  90.93   0.00   8.31  84.30   1.05  36.71
   5_bss:  90.93   0.00  12.71  90.93   0.00   8.31  84.30   1.05  36.71
   5_xyz:  90.93   0.00  12.71  90.93   0.00   8.31  84.30   1.05  36.71
   5_adp:  90.27   0.00  12.15  90.27   0.00   7.95  82.19   1.67  34.99
   5_occ:  90.27   0.00  12.15  90.27   0.00   7.95  82.19   1.67  34.99
   5_bss:  93.20   2.93  15.08  93.20   2.93  10.88  85.12   4.60  37.92
------------------------------------------------------------------------
 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:    1.211    0.007    0.406
   1_adp:    1.211    0.007    0.406
   1_occ:    1.211    0.007    0.406
   2_bss:    1.211    0.007    0.406
   2_xyz:    1.474    0.024    0.524
   2_adp:    1.474    0.024    0.524
   2_occ:    1.474    0.024    0.524
   3_bss:    1.474    0.024    0.524
   3_xyz:    1.546    0.028    0.594
   3_adp:    1.546    0.028    0.594
   3_occ:    1.546    0.028    0.594
   4_bss:    1.546    0.028    0.594
   4_xyz:    1.756    0.058    0.636
   4_adp:    1.756    0.058    0.636
   4_occ:    1.756    0.058    0.636
   5_bss:    1.756    0.058    0.636
   5_xyz:    1.814    0.048    0.655
   5_adp:    1.814    0.048    0.655
   5_occ:    1.814    0.048    0.655
   5_bss:    1.814    0.048    0.655
------------------------------------------------------------------------

CPU time actual refinement: 318.64


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_752/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_752/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_752/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_752/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_752/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 318.49 
  Macro-tasks:
    bulk solvent and scale       = 41.10  
    individual site refinement   = 127.64 
    weights calculation          = 31.62  
    collect and process          = 6.40   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 206.86 
  Micro-tasks:
    mask                            = 2.25   
    f_calc                          = 96.57  
    alpha_beta                      = 7.88   
    target                          = 1.10   
    gradients_wrt_atomic_parameters = 106.71 
    fmodel                         = 7.04   
    r_factors                      = 0.21   
    phase_errors                   = 10.80  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 232.83 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.511 micro seconds
Total CPU time: 5.53 minutes
from_scatterers_fft:    638 calls, 96.17 s
gradients_fft:          582 calls, 93.63 s

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

# Date 2008-01-16 Time 02:20:32 PST -0800 (1200478832.11 s)
Start R-work = 0.4566, R-free = 0.4422 (no bulk solvent and anisotropic scale)
Final R-work = 0.1291, R-free = 0.1745 (no bulk solvent and anisotropic scale)

Start R-work = 0.4476, R-free = 0.4303
Final R-work = 0.1121, R-free = 0.1586