# Date 2008-01-16 Time 02:20:00 PST -0800 (1200478800.25 s)
#phil __OFF__

Command line arguments: "../784.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2184
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 784

-------------------------------------------------------------------------------
  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, 46.93, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.93, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.007 1.98109
Completeness in resolution range: 0.962983
Completeness with d_max=infinity: 0.96001

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0070
                             d_min =   1.9811

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, 46.93, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.007 1.98109
Completeness in resolution range: 0.962983
Completeness with d_max=infinity: 0.96001

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0074 -  4.2391 [2129/2157]  1918   211   9.9%
  bin  2:  4.2391 -  3.3773 [2051/2067]  1844   207  10.1%
  bin  3:  3.3773 -  2.9541 [2022/2041]  1818   204  10.1%
  bin  4:  2.9541 -  2.6857 [2017/2047]  1819   198   9.8%
  bin  5:  2.6857 -  2.4941 [1991/2010]  1792   199  10.0%
  bin  6:  2.4941 -  2.3476 [1981/2006]  1781   200  10.1%
  bin  7:  2.3476 -  2.2305 [1957/1990]  1764   193   9.9%
  bin  8:  2.2305 -  2.1337 [1974/2005]  1778   196   9.9%
  bin  9:  2.1337 -  2.0517 [1987/2029]  1785   202  10.2%
  bin 10:  2.0517 -  1.9811 [1480/1990]  1331   149  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_784/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: 10
        2.42 -     3.04: 2209
        3.04 -     3.66: 4683
        3.66 -     4.28: 9050
        4.28 -     4.90: 12389
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.170 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.182 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.259 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28336 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_784/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_784/model_refine_001.geo

CPU time processing inputs: 9.11


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.93 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4176   r_free= 0.4059   ksol= 0.00   Bsol= 0.00   scale= 0.832    |
|                                                                             |
| 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:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.204818                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.7280 0.99   1385  154 0.3585 0.3396      6.5049      6.4323|
|  2:  4.7280 -  3.7724 0.99   1340  146 0.3113 0.3160      6.6011      6.6326|
|  3:  3.7724 -  3.3013 0.99   1303  147 0.3589 0.3315      6.5206      6.5391|
|  4:  3.3013 -  3.0021 0.99   1306  147 0.3834 0.3654      6.4138      6.3377|
|  5:  3.0021 -  2.7884 0.99   1291  141 0.4316 0.4327      6.2877      6.3112|
|  6:  2.7884 -  2.6249 0.99   1281  147 0.4399 0.4780      6.2052      6.2203|
|  7:  2.6249 -  2.4941 0.99   1285  137 0.4655 0.4366      6.2101      6.1326|
|  8:  2.4941 -  2.3860 0.98   1267  147 0.4644 0.4439      6.1227      6.1184|
|  9:  2.3860 -  2.2945 0.98   1274  142 0.4702 0.4460      6.0815      6.0366|
| 10:  2.2945 -  2.2155 0.99   1262  135 0.4707 0.4849      6.0732      6.0648|
| 11:  2.2155 -  2.1465 0.99   1273  143 0.4806 0.4244      6.0151      5.9937|
| 12:  2.1465 -  2.0853 0.97   1244  138 0.4701 0.4629      5.9483      5.9793|
| 13:  2.0853 -  2.0305 0.99   1266  139 0.4941 0.5263      5.8693      5.8418|
| 14:  2.0305 -  1.9811 0.66    853   96 0.4946 0.4714      5.8146      5.7199|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0074 -  4.7280  1385   154  0.74  30.62   0.82     0.76      56882.75|
|  2:  4.7280 -  3.7724  1340   146  0.79  27.12   0.92     0.84      67591.87|
|  3:  3.7724 -  3.3013  1303   147  0.72  33.27   0.88     0.82      69409.10|
|  4:  3.3013 -  3.0021  1306   147  0.67  37.62   0.85     0.75      63253.05|
|  5:  3.0021 -  2.7884  1291   141  0.57  45.93   0.78     0.66      58013.79|
|  6:  2.7884 -  2.6249  1281   147  0.55  47.95   0.78     0.62      52704.33|
|  7:  2.6249 -  2.4941  1285   137  0.55  48.16   0.76     0.61      48193.51|
|  8:  2.4941 -  2.3860  1267   147  0.54  49.15   0.77     0.62      43117.85|
|  9:  2.3860 -  2.2945  1274   142  0.55  48.14   0.76     0.62      37906.27|
| 10:  2.2945 -  2.2155  1262   135  0.54  48.71   0.80     0.62      34616.25|
| 11:  2.2155 -  2.1465  1273   143  0.52  50.47   0.78     0.60      33025.89|
| 12:  2.1465 -  2.0853  1244   138  0.48  53.60   0.79     0.57      33962.21|
| 13:  2.0853 -  2.0305  1266   139  0.44  57.27   0.76     0.52      31071.17|
| 14:  2.0305 -  1.9811   853    96  0.45  55.92   0.74     0.50      25362.54|
|alpha:            min =        0.50 max =            0.84 mean =         0.65|
|beta:             min =    25362.54 max =        69409.10 mean =     47567.38|
|figures of merit: min =        0.00 max =            1.00 mean =         0.59|
|phase err.(work): min =        0.00 max =           89.92 mean =        44.81|
|phase err.(test): min =        0.00 max =           89.99 mean =        44.90|
|-----------------------------------------------------------------------------|

============================== 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 = 7.124397              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 73.352   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.551787              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.443   (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:       22 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      166 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      682 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1523 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2625 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3925 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5088 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6579 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7737 |
|-----------------------------------------------------------------------------|
|-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 |       53.676 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.664 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.869)------------------------------------------|
|    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 = 11.869)------------------------------------------|
|    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: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4272   r_free= 0.4150   ksol= 0.00   Bsol= 0.00   scale= 0.800    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.212431                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4096   r_free= 0.3963   ksol= 0.36   Bsol= 20.00   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.56,8.18,8.48,0.00,0.00,0.00); trace/3= 8.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.201528                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.495770              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.536   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.563000              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.176   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4096      final r-factor (work) = 0.2979          |
| start r-factor (free) = 0.3963      final r-factor (free) = 0.3262          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 73.8813 = 6.50 * 0.50 * 6.2212 + 1.00 * 53.6757                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.6960 = 6.50 * 0.50 * 6.0299 + 1.00 * 0.1116                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2979      final r-factor (work) = 0.2272          |
| start r-factor (free) = 0.3262      final r-factor (free) = 0.2648          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4095 = 0.56 * 1.00 * 6.0299 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2870 = 0.56 * 1.00 * 5.8192 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.869)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    67.64   10.35    None  None   None       |
|    all(noH): 2823   0      0.00    67.64   10.35    None  None   None       |
|    Sol.    : 438    0      0.00    67.64   28.08    None  None   None       |
|    Mac.    : 2385   0      0.00    63.54   7.10     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 -   6.764: 1530   |   5:    33.820 -  40.583:  103        |
|      1:     6.764 -  13.528:  658   |   6:    40.583 -  47.347:   58        |
|      2:    13.528 -  20.292:  190   |   7:    47.347 -  54.111:   14        |
|      3:    20.292 -  27.056:  133   |   8:    54.111 -  60.875:    6        |
|      4:    27.056 -  33.820:  128   |   9:    60.875 -  67.639:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2272 r_free = 0.2648             target_work(ml) = 5.725         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2266 r_free = 0.2652             target_work(ml) = 5.724         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2266   r_free= 0.2652   ksol= 0.36   Bsol= 20.00   scale= 1.090   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.56,8.18,8.48,0.00,0.00,0.00); trace/3= 8.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.724032                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2211   r_free= 0.2589   ksol= 0.34   Bsol= 39.39   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.03,4.21,5.36,0.00,0.00,0.00); trace/3= 4.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.721470                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.185879              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.524   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.282219              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.127  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2211      final r-factor (work) = 0.1572          |
| start r-factor (free) = 0.2589      final r-factor (free) = 0.1959          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4883 = 2.19 * 0.50 * 5.8349 + 1.00 * 0.1111                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1325 = 2.19 * 0.50 * 5.5619 + 1.00 * 0.0537                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1572      final r-factor (work) = 0.1461          |
| start r-factor (free) = 0.1959      final r-factor (free) = 0.1858          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5803 = 0.28 * 1.00 * 5.5619 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5304 = 0.28 * 1.00 * 5.3813 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.869)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.78   10.71    None  None   None       |
|    all(noH): 2823   0      0.00    66.78   10.71    None  None   None       |
|    Sol.    : 438    0      1.09    66.78   30.21    None  None   None       |
|    Mac.    : 2385   0      0.00    63.37   7.13     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 -   6.678: 1533   |   5:    33.392 -  40.070:  136        |
|      1:     6.678 -  13.357:  630   |   6:    40.070 -  46.749:   67        |
|      2:    13.357 -  20.035:  190   |   7:    46.749 -  53.427:   27        |
|      3:    20.035 -  26.714:  111   |   8:    53.427 -  60.106:    4        |
|      4:    26.714 -  33.392:  119   |   9:    60.106 -  66.784:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1461 r_free = 0.1858             target_work(ml) = 5.357         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1459 r_free = 0.1857             target_work(ml) = 5.356         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1459   r_free= 0.1857   ksol= 0.34   Bsol= 39.39   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.03,4.21,5.36,0.00,0.00,0.00); trace/3= 4.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.356441                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1458   r_free= 0.1853   ksol= 0.33   Bsol= 39.39   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.24,3.46,4.41,0.00,0.00,0.00); trace/3= 3.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.356730                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.604684              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.629  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.973181              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.934   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1458      final r-factor (work) = 0.1212          |
| start r-factor (free) = 0.1853      final r-factor (free) = 0.1622          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0671 = 2.60 * 0.50 * 5.3852 + 1.00 * 0.0537                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9284 = 2.60 * 0.50 * 5.2714 + 1.00 * 0.0632                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1212      final r-factor (work) = 0.1155          |
| start r-factor (free) = 0.1622      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1403 = 0.97 * 1.00 * 5.2714 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0489 = 0.97 * 1.00 * 5.1750 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.869)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.21   11.44    None  None   None       |
|    all(noH): 2823   0      0.00    76.21   11.44    None  None   None       |
|    Sol.    : 438    0      0.58    71.68   33.92    None  None   None       |
|    Mac.    : 2385   0      0.00    76.21   7.31     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 -   7.621: 1664   |   5:    38.104 -  45.725:   95        |
|      1:     7.621 -  15.242:  561   |   6:    45.725 -  53.346:   76        |
|      2:    15.242 -  22.863:  164   |   7:    53.346 -  60.967:   35        |
|      3:    22.863 -  30.483:  104   |   8:    60.967 -  68.588:   13        |
|      4:    30.483 -  38.104:  105   |   9:    68.588 -  76.208:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1155 r_free = 0.1584             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1154 r_free = 0.1583             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1583   ksol= 0.33   Bsol= 39.39   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.24,3.46,4.41,0.00,0.00,0.00); trace/3= 3.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.163637                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1587   ksol= 0.32   Bsol= 39.39   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.17,3.39,4.18,0.00,0.00,0.00); trace/3= 3.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.165113                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.083151              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.437  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.171990              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.264  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1158      final r-factor (work) = 0.1091          |
| start r-factor (free) = 0.1587      final r-factor (free) = 0.1564          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0413 = 3.08 * 0.50 * 5.1752 + 1.00 * 0.0633                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9971 = 3.08 * 0.50 * 5.1414 + 1.00 * 0.0713                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1091      final r-factor (work) = 0.1105          |
| start r-factor (free) = 0.1564      final r-factor (free) = 0.1555          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8968 = 0.17 * 1.00 * 5.1414 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8935 = 0.17 * 1.00 * 5.1403 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.869)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.10   10.95    None  None   None       |
|    all(noH): 2823   0      0.00    75.10   10.95    None  None   None       |
|    Sol.    : 438    0      0.92    63.50   31.63    None  None   None       |
|    Mac.    : 2385   0      0.00    75.10   7.15     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 -   7.510: 1676   |   5:    37.552 -  45.062:   86        |
|      1:     7.510 -  15.021:  577   |   6:    45.062 -  52.573:   69        |
|      2:    15.021 -  22.531:  152   |   7:    52.573 -  60.083:   19        |
|      3:    22.531 -  30.042:  119   |   8:    60.083 -  67.594:   10        |
|      4:    30.042 -  37.552:  111   |   9:    67.594 -  75.104:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1105 r_free = 0.1555             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1105 r_free = 0.1555             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1105   r_free= 0.1555   ksol= 0.32   Bsol= 39.39   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.17,3.39,4.18,0.00,0.00,0.00); trace/3= 3.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.134284                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1105   r_free= 0.1555   ksol= 0.32   Bsol= 39.39   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.17,3.39,4.18,0.00,0.00,0.00); trace/3= 3.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.134363                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.978757              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.669  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.294111              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.354  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1105      final r-factor (work) = 0.1116          |
| start r-factor (free) = 0.1555      final r-factor (free) = 0.1554          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1568 = 1.98 * 0.50 * 5.1401 + 1.00 * 0.0713                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1452 = 1.98 * 0.50 * 5.1388 + 1.00 * 0.0610                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1116      final r-factor (work) = 0.1108          |
| start r-factor (free) = 0.1554      final r-factor (free) = 0.1557          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5208 = 0.29 * 1.00 * 5.1388 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5209 = 0.29 * 1.00 * 5.1363 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.869)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.51   10.96    None  None   None       |
|    all(noH): 2823   0      0.00    75.51   10.96    None  None   None       |
|    Sol.    : 438    0      1.03    63.00   31.80    None  None   None       |
|    Mac.    : 2385   0      0.00    75.51   7.14     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 -   7.552: 1683   |   5:    37.757 -  45.309:   86        |
|      1:     7.552 -  15.103:  563   |   6:    45.309 -  52.860:   68        |
|      2:    15.103 -  22.654:  154   |   7:    52.860 -  60.411:   21        |
|      3:    22.654 -  30.206:  123   |   8:    60.411 -  67.963:    8        |
|      4:    30.206 -  37.757:  113   |   9:    67.963 -  75.514:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1108 r_free = 0.1557             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1108 r_free = 0.1558             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1558   ksol= 0.32   Bsol= 39.39   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.17,3.39,4.18,0.00,0.00,0.00); trace/3= 3.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138287                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.7280 0.99   1385  154 0.0995 0.1292      5.3802      5.5223|
|  2:  4.7280 -  3.7724 0.99   1340  146 0.0875 0.1105      5.4461      5.6371|
|  3:  3.7724 -  3.3013 0.99   1303  147 0.1045 0.1500      5.4663      5.8482|
|  4:  3.3013 -  3.0021 0.99   1306  147 0.1190 0.1515      5.4464      5.5721|
|  5:  3.0021 -  2.7884 0.99   1291  141 0.1304 0.1735      5.3177       5.553|
|  6:  2.7884 -  2.6249 0.99   1281  147 0.1175 0.1782      5.1973      5.4525|
|  7:  2.6249 -  2.4941 0.99   1285  137 0.1245 0.1628      5.1669      5.3659|
|  8:  2.4941 -  2.3860 0.98   1267  147 0.1170 0.1724      5.0683      5.3329|
|  9:  2.3860 -  2.2945 0.98   1274  142 0.1174 0.1775      5.0422      5.3288|
| 10:  2.2945 -  2.2155 0.99   1262  135 0.1102 0.1655      4.9472      5.1689|
| 11:  2.2155 -  2.1465 0.99   1273  143 0.1123 0.1778      4.9283      5.2892|
| 12:  2.1465 -  2.0853 0.97   1244  138 0.1095 0.1570      4.8718      5.1048|
| 13:  2.0853 -  2.0305 0.99   1266  139 0.1135 0.1772      4.7864      5.0987|
| 14:  2.0305 -  1.9811 0.66    853   96 0.1032 0.1703      4.6404      4.8903|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0074 -  4.7280  1385   154  0.94   8.84   0.98     0.96       6970.87|
|  2:  4.7280 -  3.7724  1340   146  0.95   7.84   1.02     1.00       8943.15|
|  3:  3.7724 -  3.3013  1303   147  0.93  11.20   1.02     1.01      10287.48|
|  4:  3.3013 -  3.0021  1306   147  0.92  13.44   1.00     0.99      10236.72|
|  5:  3.0021 -  2.7884  1291   141  0.90  15.95   0.99     0.96       8120.06|
|  6:  2.7884 -  2.6249  1281   147  0.90  15.60   0.98     0.95       6977.21|
|  7:  2.6249 -  2.4941  1285   137  0.91  15.23   0.99     0.96       6126.09|
|  8:  2.4941 -  2.3860  1267   147  0.91  15.24   0.99     0.97       5335.67|
|  9:  2.3860 -  2.2945  1274   142  0.91  15.29   1.01     0.98       5054.77|
| 10:  2.2945 -  2.2155  1262   135  0.91  15.19   1.00     0.97       4257.65|
| 11:  2.2155 -  2.1465  1273   143  0.90  16.20   1.00     0.96       4220.18|
| 12:  2.1465 -  2.0853  1244   138  0.92  14.52   1.01     1.00       3872.42|
| 13:  2.0853 -  2.0305  1266   139  0.90  15.97   1.01     1.01       3337.48|
| 14:  2.0305 -  1.9811   853    96  0.92  14.23   0.99     0.96       2391.45|
|alpha:            min =        0.95 max =            1.01 mean =         0.98|
|beta:             min =     2391.45 max =        10287.48 mean =      6280.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.91 mean =        13.84|
|phase err.(test): min =        0.00 max =           86.71 mean =        13.37|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1558   ksol= 0.32   Bsol= 43.63   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.41,-0.19,0.60,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138174                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1558   ksol= 0.32   Bsol= 43.63   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.41,-0.19,0.60,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138174                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.7280 0.99   1385  154 0.0996 0.1292      5.3799      5.5223|
|  2:  4.7280 -  3.7724 0.99   1340  146 0.0876 0.1106      5.4468      5.6377|
|  3:  3.7724 -  3.3013 0.99   1303  147 0.1046 0.1501      5.4666      5.8484|
|  4:  3.3013 -  3.0021 0.99   1306  147 0.1190 0.1515      5.4462      5.5719|
|  5:  3.0021 -  2.7884 0.99   1291  141 0.1304 0.1734      5.3174      5.5525|
|  6:  2.7884 -  2.6249 0.99   1281  147 0.1175 0.1782      5.1969      5.4522|
|  7:  2.6249 -  2.4941 0.99   1285  137 0.1244 0.1628      5.1666      5.3656|
|  8:  2.4941 -  2.3860 0.98   1267  147 0.1170 0.1723      5.0681      5.3326|
|  9:  2.3860 -  2.2945 0.98   1274  142 0.1174 0.1775       5.042      5.3289|
| 10:  2.2945 -  2.2155 0.99   1262  135 0.1102 0.1654       4.947      5.1686|
| 11:  2.2155 -  2.1465 0.99   1273  143 0.1122 0.1778      4.9281      5.2891|
| 12:  2.1465 -  2.0853 0.97   1244  138 0.1095 0.1569      4.8717      5.1045|
| 13:  2.0853 -  2.0305 0.99   1266  139 0.1135 0.1772      4.7862      5.0986|
| 14:  2.0305 -  1.9811 0.66    853   96 0.1032 0.1703      4.6402        4.89|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0074 -  4.7280  1385   154  0.94   8.83   0.98     0.96       6965.65|
|  2:  4.7280 -  3.7724  1340   146  0.95   7.84   1.02     1.00       8946.97|
|  3:  3.7724 -  3.3013  1303   147  0.93  11.20   1.02     1.01      10295.14|
|  4:  3.3013 -  3.0021  1306   147  0.92  13.44   1.00     0.99      10232.67|
|  5:  3.0021 -  2.7884  1291   141  0.90  15.95   0.99     0.96       8115.23|
|  6:  2.7884 -  2.6249  1281   147  0.90  15.59   0.98     0.95       6972.21|
|  7:  2.6249 -  2.4941  1285   137  0.91  15.22   0.99     0.96       6122.48|
|  8:  2.4941 -  2.3860  1267   147  0.91  15.23   0.99     0.97       5332.96|
|  9:  2.3860 -  2.2945  1274   142  0.91  15.29   1.01     0.98       5052.68|
| 10:  2.2945 -  2.2155  1262   135  0.91  15.18   1.00     0.97       4256.43|
| 11:  2.2155 -  2.1465  1273   143  0.90  16.20   1.00     0.96       4218.60|
| 12:  2.1465 -  2.0853  1244   138  0.92  14.52   1.01     1.00       3871.20|
| 13:  2.0853 -  2.0305  1266   139  0.90  15.97   1.01     1.01       3335.97|
| 14:  2.0305 -  1.9811   853    96  0.92  14.23   0.99     0.96       2390.34|
|alpha:            min =        0.95 max =            1.01 mean =         0.98|
|beta:             min =     2390.34 max =        10295.14 mean =      6279.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.89 mean =        13.84|
|phase err.(test): min =        0.00 max =           86.68 mean =        13.37|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.869)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.58    79.09   14.54    None  None   None       |
|    all(noH): 2823   0      3.58    79.09   14.54    None  None   None       |
|    Sol.    : 438    0      4.61    66.58   35.38    None  None   None       |
|    Mac.    : 2385   0      3.58    79.09   10.72    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.580 -  11.131: 1683   |   5:    41.337 -  48.889:   86        |
|      1:    11.131 -  18.683:  563   |   6:    48.889 -  56.440:   68        |
|      2:    18.683 -  26.234:  154   |   7:    56.440 -  63.991:   21        |
|      3:    26.234 -  33.786:  123   |   8:    63.991 -  71.543:    8        |
|      4:    33.786 -  41.337:  113   |   9:    71.543 -  79.094:    4        |
|                               =>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: 0.361 - 4.712
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 316 from: 320
   mapped sites are within: 0.728 - 4.712

peak=   10.640 closest distance to " CG2 VAL A 230 " =    1.391
peak=    6.882 closest distance to " CG2 VAL A 296 " =    1.096
peak=    6.335 closest distance to " CG  LEU A   5 " =    1.264
peak=    5.642 closest distance to " NH2 ARG A  56 " =    2.207
peak=    5.492 closest distance to " CD2 LEU A   5 " =    1.195
peak=    5.485 closest distance to " CG  LEU A 228 " =    1.183
peak=    5.473 closest distance to " CG  PRO A  54 " =    1.293
peak=    5.414 closest distance to " CB  GLN A 223 " =    1.432
peak=    5.333 closest distance to " CB  VAL A 296 " =    1.133
peak=    5.169 closest distance to " O   HOH Z 126 " =    1.914
peak=    5.088 closest distance to " CB  VAL A 230 " =    1.207
peak=    5.074 closest distance to " CB  SER A  63 " =    1.276
peak=    5.025 closest distance to " CB  PRO A  54 " =    0.953
peak=    4.924 closest distance to " NE2 GLN A  11 " =    1.141
peak=    4.888 closest distance to " CB  GLN A 183 " =    1.250
peak=    4.812 closest distance to " CB  ARG A 275 " =    0.865
peak=    4.766 closest distance to " O   HOH Z 232 " =    2.322
peak=    4.744 closest distance to " CG  PRO A 213 " =    1.223
peak=    4.723 closest distance to " O   HOH Z 272 " =    1.878
peak=    4.611 closest distance to " O   HOH Z 142 " =    1.660
peak=    4.590 closest distance to " C   PRO A 198 " =    1.533
peak=    4.573 closest distance to " CB  GLU A 152 " =    1.163
peak=    4.529 closest distance to " CG  PRO A 243 " =    1.116
peak=    4.520 closest distance to " OD1 ASN A  69 " =    2.620
peak=    4.485 closest distance to " O   HOH Z 209 " =    2.322
peak=    4.461 closest distance to " O   HOH Z 298 " =    1.800
peak=    4.435 closest distance to " O   HOH Z 369 " =    2.050
peak=    4.402 closest distance to " CB  SER A   3 " =    1.307
peak=    4.400 closest distance to " O   HOH Z 236 " =    1.931
peak=    4.400 closest distance to " O   HOH Z 193 " =    1.800
peak=    4.358 closest distance to " CD2 LEU A 228 " =    1.170
peak=    4.345 closest distance to " O   HOH Z 316 " =    3.029
peak=    4.292 closest distance to " O   HOH Z 368 " =    2.087
peak=    4.278 closest distance to " CB  ASN A 148 " =    1.367
peak=    4.275 closest distance to " CB  GLU A 128 " =    1.003
peak=    4.249 closest distance to " O   HOH Z 427 " =    2.972
peak=    4.188 closest distance to " O   HOH Z 303 " =    2.037
peak=    4.165 closest distance to " ND2 ASN A 187 " =    1.504
peak=    4.160 closest distance to " CB  VAL A 265 " =    1.300
peak=    4.155 closest distance to " O   HOH Z 203 " =    1.721
peak=    4.134 closest distance to " O   SER A  87 " =    2.279
peak=    4.132 closest distance to " O   HOH Z 263 " =    1.651
peak=    4.095 closest distance to " O   HOH Z 158 " =    3.138
peak=    4.085 closest distance to " O   HOH Z  78 " =    1.691
peak=    4.079 closest distance to " O   HOH Z 346 " =    1.594
peak=    4.078 closest distance to " O   HOH Z  61 " =    1.645
peak=    4.038 closest distance to " O   HOH Z 403 " =    1.683
peak=    4.017 closest distance to " CG  PRO A 198 " =    1.215
peak=    4.006 closest distance to " O   HOH Z 234 " =    3.624
peak=    4.006 closest distance to " CA  ASN A 215 " =    1.194
peak=    4.001 closest distance to " O   HOH Z 265 " =    2.454
peak=    3.979 closest distance to " CA  TYR A  30 " =    0.943
peak=    3.971 closest distance to " O   HOH Z 423 " =    1.756
peak=    3.968 closest distance to " CB  TRP A 266 " =    0.933
peak=    3.966 closest distance to " CB  ARG A  79 " =    1.393
peak=    3.948 closest distance to " CB  GLU A 277 " =    3.555
peak=    3.948 closest distance to " CG1BVAL A  72 " =    1.606
peak=    3.935 closest distance to " O   HOH Z 402 " =    1.473
peak=    3.933 closest distance to " CB  ASN A 187 " =    1.084
peak=    3.932 closest distance to " O   HOH Z 128 " =    2.047
peak=    3.925 closest distance to " OD2 ASP A 286 " =    2.811
peak=    3.916 closest distance to " O   HOH Z 389 " =    1.948
peak=    3.908 closest distance to " O   HOH Z 197 " =    3.159
peak=    3.897 closest distance to " CA  ALA A  21 " =    1.189
peak=    3.890 closest distance to " O   HOH Z 145 " =    2.058
peak=    3.889 closest distance to " O   HOH Z 280 " =    2.907
peak=    3.886 closest distance to " CB  ARG A 139 " =    0.933
peak=    3.885 closest distance to " O   HOH Z  43 " =    2.014
peak=    3.874 closest distance to " CB  ASN A  39 " =    0.861
peak=    3.861 closest distance to " O   HOH Z  68 " =    2.216
peak=    3.860 closest distance to " CB  TRP A 179 " =    1.365
peak=    3.846 closest distance to " CA  THR A 264 " =    0.777
peak=    3.845 closest distance to " O   HOH Z 344 " =    2.919
peak=    3.835 closest distance to " O   HOH Z  15 " =    2.201
peak=    3.812 closest distance to " O   HOH Z  88 " =    3.153
peak=    3.811 closest distance to " O   HOH Z 411 " =    3.769
peak=    3.795 closest distance to " CA  ALA A  51 " =    0.988
peak=    3.789 closest distance to " O   HOH Z 261 " =    2.267
peak=    3.785 closest distance to " O   HOH Z 193 " =    1.917
peak=    3.783 closest distance to " O   HOH Z  97 " =    2.562
peak=    3.770 closest distance to " O   HOH Z  97 " =    1.970
peak=    3.770 closest distance to " O   HOH Z 273 " =    2.598
peak=    3.768 closest distance to " CB  LEU A 143 " =    1.136
peak=    3.767 closest distance to " O   TRP A 274 " =    1.877
peak=    3.739 closest distance to " O   HOH Z 371 " =    3.102
peak=    3.739 closest distance to " CB  ALA A   9 " =    1.596
peak=    3.739 closest distance to " CG1 VAL A 296 " =    1.203
peak=    3.731 closest distance to " O   HOH Z 248 " =    1.728
peak=    3.728 closest distance to " CZ  PHE A 218 " =    1.070
peak=    3.726 closest distance to " NH2 ARG A 156 " =    1.141
peak=    3.724 closest distance to " O   HOH Z 250 " =    1.356
peak=    3.707 closest distance to " CG  ARG A  66 " =    2.671
peak=    3.704 closest distance to " CD1 LEU A 300 " =    1.183
peak=    3.703 closest distance to " O   HOH Z 189 " =    2.659
peak=    3.699 closest distance to " CB  SER A 216 " =    0.751
peak=    3.693 closest distance to " O   HOH Z 245 " =    1.401
peak=    3.677 closest distance to " CB  VAL A 202 " =    1.566
peak=    3.671 closest distance to " OG BSER A 164 " =    2.215
peak=    3.669 closest distance to " CB  ASP A 140 " =    0.887
peak=    3.667 closest distance to " CB  GLN A 278 " =    0.879
peak=    3.667 closest distance to " O   HOH Z 425 " =    1.331
peak=    3.666 closest distance to " CD  ARG A 159 " =    0.743
peak=    3.661 closest distance to " O   HOH Z  54 " =    1.600
peak=    3.658 closest distance to " CA  THR A 221 " =    0.940
peak=    3.651 closest distance to " O   HOH Z  59 " =    2.081
peak=    3.649 closest distance to " CB  LEU A 228 " =    1.278
peak=    3.640 closest distance to " CD BLYS A 290 " =    1.137
peak=    3.616 closest distance to " O   HOH Z 128 " =    2.110
peak=    3.599 closest distance to " CA  ALA A 158 " =    1.169
peak=    3.598 closest distance to " CB  ASN A 142 " =    1.006
peak=    3.597 closest distance to " O   MET A 105 " =    1.769
peak=    3.589 closest distance to " CG  LEU A 167 " =    1.182
peak=    3.587 closest distance to " O   HOH Z 132 " =    2.645
peak=    3.578 closest distance to " CB  SER A 212 " =    1.181
peak=    3.574 closest distance to " CA  LYS A 117 " =    1.207
peak=    3.567 closest distance to " CD1 ILE A 106 " =    1.019
peak=    3.562 closest distance to " CG2 VAL A 257 " =    0.900
peak=    3.555 closest distance to " N   PHE A 130 " =    1.274
peak=    3.551 closest distance to " CD  ARG A 269 " =    0.974
peak=    3.549 closest distance to " CA  VAL A  41 " =    0.839
peak=    3.542 closest distance to " CB  ALA A 248 " =    1.502
peak=    3.540 closest distance to " CG1 ILE A  33 " =    1.318
peak=    3.537 closest distance to " O   HOH Z 124 " =    1.380
peak=    3.531 closest distance to " O   HOH Z 426 " =    1.541
peak=    3.531 closest distance to " N   ASN A  39 " =    1.118
peak=    3.519 closest distance to " O   HOH Z  21 " =    1.712
peak=    3.519 closest distance to " CA  PHE A 283 " =    1.209
peak=    3.514 closest distance to " O   HOH Z 147 " =    1.713
peak=    3.513 closest distance to " CA  SER A  87 " =    0.998
peak=    3.512 closest distance to " O   HOH Z 207 " =    1.771
peak=    3.510 closest distance to " O   HOH Z 425 " =    2.010
peak=    3.510 closest distance to " CE1 TYR A 186 " =    1.319
peak=    3.509 closest distance to " O   HOH Z 193 " =    1.660
peak=    3.503 closest distance to " O   GLN A 278 " =    1.269
peak=    3.501 closest distance to " CG2 THR A 221 " =    1.180
peak=    3.499 closest distance to " N   VAL A 126 " =    1.332
peak=    3.497 closest distance to " O   HOH Z 368 " =    3.573
peak=    3.495 closest distance to " CB  GLN A  88 " =    1.218
peak=    3.495 closest distance to " NH1AARG A 145 " =    1.089
peak=    3.494 closest distance to " CD  LYS A 166 " =    1.306
peak=    3.493 closest distance to " O   HOH Z 214 " =    2.072
peak=    3.492 closest distance to " NH1BARG A 190 " =    1.986
peak=    3.491 closest distance to " CB  TRP A 150 " =    1.490
peak=    3.490 closest distance to " O   HOH Z  10 " =    1.822
peak=    3.488 closest distance to " CB  ALA A 291 " =    1.371
peak=    3.487 closest distance to " O   HOH Z 407 " =    2.416
peak=    3.487 closest distance to " CB  THR A  31 " =    1.646
peak=    3.481 closest distance to " CB  HIS A 108 " =    0.803
peak=    3.479 closest distance to " O   HOH Z 329 " =    3.824
peak=    3.475 closest distance to " O   HOH Z 291 " =    1.585
peak=    3.470 closest distance to " CE  LYS A  76 " =    0.895
peak=    3.469 closest distance to " CG  MET A 185 " =    1.196
peak=    3.465 closest distance to " NZ  LYS A 117 " =    3.196
peak=    3.463 closest distance to " O   HOH Z 359 " =    3.739
peak=    3.463 closest distance to " O   HOH Z  78 " =    2.083
peak=    3.462 closest distance to " O   HOH Z 133 " =    1.607
peak=    3.458 closest distance to " O   HOH Z   9 " =    2.021
peak=    3.456 closest distance to " CA  ARG A 195 " =    1.197
peak=    3.455 closest distance to " CG1 VAL A 153 " =    0.893
peak=    3.452 closest distance to " CA  ALA A 233 " =    1.361
peak=    3.449 closest distance to " O   HOH Z 345 " =    3.368
peak=    3.447 closest distance to " O   HOH Z  48 " =    1.740
peak=    3.446 closest distance to " O   HOH Z 411 " =    1.788
peak=    3.444 closest distance to " O   HOH Z 148 " =    3.277
peak=    3.441 closest distance to " O   HOH Z 227 " =    2.083
peak=    3.436 closest distance to " CZ  PHE A 192 " =    0.957
peak=    3.432 closest distance to " CB BVAL A  41 " =    1.157
peak=    3.428 closest distance to " O   HOH Z 112 " =    1.619
peak=    3.428 closest distance to " O   HOH Z 180 " =    2.099
peak=    3.427 closest distance to " CG1 ILE A  49 " =    1.390
peak=    3.423 closest distance to " CB  ARG A 190 " =    1.676
peak=    3.412 closest distance to " CB  MET A  40 " =    0.824
peak=    3.404 closest distance to " CD  LYS A 119 " =    1.508
peak=    3.389 closest distance to " CG  MET A 185 " =    1.111
peak=    3.389 closest distance to " CA  ASP A 140 " =    1.228
peak=    3.371 closest distance to " O   HOH Z 435 " =    1.977
peak=    3.370 closest distance to " CB  ILE A 120 " =    1.331
peak=    3.370 closest distance to " CD2 TRP A 179 " =    1.384
peak=    3.361 closest distance to " O   ASP A 124 " =    1.126
peak=    3.360 closest distance to " O   HOH Z 175 " =    2.139
peak=    3.359 closest distance to " CB  PRO A 198 " =    1.001
peak=    3.356 closest distance to " CB  THR A 157 " =    1.173
peak=    3.352 closest distance to " ND1 HIS A  81 " =    1.677
peak=    3.352 closest distance to " CB  ALA A 295 " =    1.181
peak=    3.351 closest distance to " OG  SER A  22 " =    2.801
peak=    3.350 closest distance to " O   HOH Z  40 " =    2.444
peak=    3.349 closest distance to " CA  ALA A 291 " =    0.970
peak=    3.349 closest distance to " CA  ASP A 162 " =    1.055
peak=    3.348 closest distance to " CG  GLN A  88 " =    1.035
peak=    3.346 closest distance to " O   HOH Z 417 " =    2.078
peak=    3.345 closest distance to " O   HOH Z 313 " =    1.773
peak=    3.345 closest distance to " CB  ALA A 114 " =    1.341
peak=    3.339 closest distance to " N   SER A 135 " =    1.348
peak=    3.336 closest distance to " O   HOH Z 135 " =    1.717
peak=    3.336 closest distance to " O   HOH Z 227 " =    1.636
peak=    3.333 closest distance to " CG2 ILE A 120 " =    1.278
peak=    3.331 closest distance to " CA  LEU A 282 " =    1.057
peak=    3.331 closest distance to " O   HOH Z 189 " =    2.804
peak=    3.330 closest distance to " CD1 LEU A  96 " =    0.728
peak=    3.327 closest distance to " NH2BARG A 145 " =    1.991
peak=    3.325 closest distance to " CA  MET A  40 " =    1.111
peak=    3.318 closest distance to " OG1 THR A 294 " =    1.742
peak=    3.315 closest distance to " OG1 THR A 294 " =    2.405
peak=    3.313 closest distance to " CB  SER A  26 " =    1.595
peak=    3.312 closest distance to " ND1 HIS A  86 " =    1.629
peak=    3.311 closest distance to " CG1 ILE A 151 " =    1.024
peak=    3.309 closest distance to " O   HOH Z 299 " =    4.288
peak=    3.305 closest distance to " CB  ASN A 224 " =    1.061
peak=    3.300 closest distance to " N   ARG A 190 " =    1.055
peak=    3.296 closest distance to " O   HOH Z 423 " =    2.930
peak=    3.292 closest distance to " CB  GLU A  46 " =    1.051
peak=    3.290 closest distance to " CA  ARG A  36 " =    1.072
peak=    3.288 closest distance to " O   HOH Z 337 " =    3.669
peak=    3.280 closest distance to " O   HOH Z 172 " =    3.711
peak=    3.279 closest distance to " O   HOH Z 130 " =    2.269
peak=    3.277 closest distance to " O   HOH Z  61 " =    1.587
peak=    3.276 closest distance to " O   HOH Z 171 " =    2.457
peak=    3.276 closest distance to " O   HOH Z  48 " =    1.413
peak=    3.273 closest distance to " N   ARG A 156 " =    1.326
peak=    3.265 closest distance to " CG BARG A 102 " =    1.787
peak=    3.263 closest distance to " O   HOH Z 286 " =    2.325
peak=    3.262 closest distance to " O   HOH Z 417 " =    3.292
peak=    3.259 closest distance to " C   ALA A 299 " =    0.964
peak=    3.256 closest distance to " NZ  LYS A  76 " =    1.280
peak=    3.253 closest distance to " O   HOH Z 305 " =    3.579
peak=    3.250 closest distance to " CA  GLN A 194 " =    1.265
peak=    3.248 closest distance to " CA  ASP A 191 " =    0.838
peak=    3.248 closest distance to " O   HOH Z 187 " =    2.263
peak=    3.246 closest distance to " O   HOH Z 357 " =    1.834
peak=    3.246 closest distance to " CD  PRO A 243 " =    1.428
peak=    3.244 closest distance to " O   HOH Z 216 " =    2.638
peak=    3.242 closest distance to " CD2 HIS A  81 " =    1.138
peak=    3.241 closest distance to " O   HOH Z 128 " =    1.683
peak=    3.236 closest distance to " CD2 LEU A 255 " =    1.567
peak=    3.232 closest distance to " O   HOH Z 108 " =    2.507
peak=    3.232 closest distance to " CA  VAL A 126 " =    0.854
peak=    3.232 closest distance to " O   HOH Z 280 " =    1.768
peak=    3.230 closest distance to " O   HOH Z 350 " =    1.592
peak=    3.227 closest distance to " O   HOH Z 166 " =    3.608
peak=    3.225 closest distance to " CB  VAL A 268 " =    0.818
peak=    3.224 closest distance to " CD1 ILE A  33 " =    1.593
peak=    3.224 closest distance to " O   HOH Z 250 " =    1.354
peak=    3.222 closest distance to " CA  LYS A 290 " =    1.238
peak=    3.219 closest distance to " CD1 LEU A   5 " =    1.372
peak=    3.215 closest distance to " CD1 LEU A 228 " =    1.869
peak=    3.213 closest distance to " O   HOH Z   1 " =    1.850
peak=    3.210 closest distance to " CG  GLN A  77 " =    2.103
peak=    3.207 closest distance to " CA  ALA A 154 " =    1.003
peak=    3.207 closest distance to " O   ALA A 158 " =    1.385
peak=    3.203 closest distance to " O   HOH Z 367 " =    3.474
peak=    3.201 closest distance to " OE1 GLU A   2 " =    2.111
peak=    3.201 closest distance to " CB  ALA A 248 " =    0.983
peak=    3.200 closest distance to " CB  LYS A 117 " =    1.167
peak=    3.197 closest distance to " CA  ILE A 106 " =    0.767
peak=    3.196 closest distance to " CB  ILE A  20 " =    1.446
peak=    3.194 closest distance to " NE2 HIS A 207 " =    1.377
peak=    3.192 closest distance to " O   HOH Z  19 " =    2.353
peak=    3.191 closest distance to " O   HOH Z 285 " =    3.059
peak=    3.191 closest distance to " O   HOH Z  90 " =    2.252
peak=    3.189 closest distance to " CG2 ILE A  20 " =    1.478
peak=    3.188 closest distance to " O   HOH Z 374 " =    2.601
peak=    3.187 closest distance to " O   ALA A   1 " =    1.521
peak=    3.186 closest distance to " CB  ASN A 110 " =    1.148
peak=    3.186 closest distance to " NZ  LYS A  48 " =    1.369
peak=    3.180 closest distance to " CA  GLY A 267 " =    0.782
peak=    3.179 closest distance to " OG  SER A 206 " =    1.254
peak=    3.178 closest distance to " OG BSER A 134 " =    2.985
peak=    3.178 closest distance to " CB  GLN A 205 " =    1.148
peak=    3.174 closest distance to " OD1BASN A 224 " =    2.255
peak=    3.170 closest distance to " CB  MET A  47 " =    1.064
peak=    3.170 closest distance to " CG BARG A 275 " =    1.397
peak=    3.169 closest distance to " CB  LEU A 255 " =    0.822
peak=    3.166 closest distance to " CA  ASN A 176 " =    1.041
peak=    3.165 closest distance to " O   HOH Z 417 " =    2.664
peak=    3.163 closest distance to " O   HOH Z 388 " =    1.974
peak=    3.163 closest distance to " CB  ALA A  71 " =    1.397
peak=    3.161 closest distance to " CG2 THR A 220 " =    0.903
peak=    3.160 closest distance to " O   HOH Z 258 " =    1.855
peak=    3.156 closest distance to " O   HOH Z 366 " =    3.065
peak=    3.154 closest distance to " O   HOH Z 234 " =    1.758
peak=    3.154 closest distance to " O   HOH Z 116 " =    1.711
peak=    3.153 closest distance to " O   HOH Z 302 " =    1.907
peak=    3.153 closest distance to " O   HOH Z 251 " =    1.714
peak=    3.153 closest distance to " CA  ALA A  84 " =    1.436
peak=    3.151 closest distance to " N   SER A  12 " =    1.571
peak=    3.151 closest distance to " O   HOH Z 294 " =    1.555
peak=    3.148 closest distance to " O   HOH Z  80 " =    1.584
peak=    3.145 closest distance to " CB  SER A  62 " =    1.240
peak=    3.142 closest distance to " CB  ALA A  34 " =    0.918
peak=    3.141 closest distance to " CB  ALA A   1 " =    4.712
peak=    3.136 closest distance to " CA  SER A 146 " =    1.770
peak=    3.130 closest distance to " O   HOH Z  49 " =    2.480
peak=    3.130 closest distance to " CZ2 TRP A 274 " =    1.572
peak=    3.127 closest distance to " CZ3 TRP A 123 " =    1.209
peak=    3.126 closest distance to " O   HOH Z 151 " =    1.752
peak=    3.122 closest distance to " CB  ASN A 215 " =    1.133
peak=    3.121 closest distance to " O   HOH Z  40 " =    1.767
peak=    3.117 closest distance to " O   HOH Z  85 " =    1.577
peak=    3.117 closest distance to " O   HOH Z 392 " =    1.463
peak=    3.116 closest distance to " OD1 ASN A 217 " =    1.687
peak=    3.115 closest distance to " OG1 THR A 279 " =    1.597
peak=    3.114 closest distance to " O   HOH Z 163 " =    1.857
peak=    3.110 closest distance to " O   HOH Z 409 " =    3.276
peak=    3.095 closest distance to " O   HOH Z 222 " =    2.538
peak=    3.093 closest distance to " CD1 LEU A 261 " =    1.195
peak=    3.092 closest distance to " O   HOH Z 353 " =    2.661
peak=    3.091 closest distance to " O   HOH Z 383 " =    2.012
peak=    3.086 closest distance to " O   HOH Z 154 " =    2.096
peak=    3.082 closest distance to " O   HOH Z 336 " =    1.811
peak=    3.078 closest distance to " CB  LYS A 290 " =    1.091
peak=    3.074 closest distance to " O   HOH Z 213 " =    1.887
peak=    3.073 closest distance to " O   HOH Z 341 " =    2.071
peak=    3.065 closest distance to " N   GLN A 278 " =    1.053
peak=    3.050 closest distance to " O   HOH Z  85 " =    2.161
peak=    3.047 closest distance to " CG  GLN A  89 " =    1.516
peak=    3.034 closest distance to " O   SER A 164 " =    1.186

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.533 - 5.426
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 204
   mapped sites are within: 0.741 - 5.426

peak=   -5.680 closest distance to " CG2 VAL A 230 " =    0.758
peak=   -4.561 closest distance to " O   HOH Z 290 " =    1.115
peak=   -4.439 closest distance to " CD  ARG A 156 " =    2.021
peak=   -4.294 closest distance to " SG  CYS A 254 " =    3.140
peak=   -4.220 closest distance to " CG  ASP A 231 " =    0.781
peak=   -4.212 closest distance to " O   ILE A 109 " =    2.582
peak=   -4.187 closest distance to " O   HOH Z 266 " =    4.789
peak=   -4.187 closest distance to " CB  PRO A 243 " =    2.633
peak=   -4.131 closest distance to " C   HIS A 108 " =    1.213
peak=   -4.078 closest distance to " N   GLN A  58 " =    1.700
peak=   -4.049 closest distance to " CG  GLN A 223 " =    1.968
peak=   -4.004 closest distance to " CG2BVAL A  41 " =    2.625
peak=   -3.973 closest distance to " CD2 LEU A 300 " =    2.793
peak=   -3.965 closest distance to " CG2 VAL A 296 " =    1.305
peak=   -3.927 closest distance to " O   HOH Z 351 " =    1.489
peak=   -3.874 closest distance to " OG BSER A 134 " =    1.202
peak=   -3.866 closest distance to " ND2 ASN A  45 " =    1.038
peak=   -3.834 closest distance to " O   PRO A 163 " =    2.100
peak=   -3.821 closest distance to " O   HOH Z 231 " =    1.820
peak=   -3.818 closest distance to " CE2 TYR A  30 " =    2.821
peak=   -3.801 closest distance to " O   HOH Z 389 " =    1.859
peak=   -3.799 closest distance to " CZ3 TRP A 179 " =    1.225
peak=   -3.793 closest distance to " CB  PRO A 163 " =    2.600
peak=   -3.779 closest distance to " CG  PHE A 283 " =    2.826
peak=   -3.777 closest distance to " O   HOH Z 114 " =    3.107
peak=   -3.776 closest distance to " N   ALA A 226 " =    2.090
peak=   -3.767 closest distance to " NH2AARG A 275 " =    5.178
peak=   -3.740 closest distance to " OXT GLY A 302 " =    2.804
peak=   -3.721 closest distance to " O   HOH Z  11 " =    1.909
peak=   -3.721 closest distance to " OG  SER A  97 " =    2.237
peak=   -3.717 closest distance to " O   HOH Z 103 " =    1.766
peak=   -3.717 closest distance to " CB  ALA A 248 " =    2.095
peak=   -3.712 closest distance to " CE  MET A 105 " =    2.083
peak=   -3.705 closest distance to " CD  GLN A  58 " =    1.093
peak=   -3.702 closest distance to " CD1 LEU A 101 " =    2.450
peak=   -3.695 closest distance to " CG1 VAL A 296 " =    1.280
peak=   -3.688 closest distance to " O   HOH Z 435 " =    2.784
peak=   -3.670 closest distance to " C   ALA A 158 " =    1.309
peak=   -3.668 closest distance to " O   VAL A  67 " =    2.687
peak=   -3.660 closest distance to " CG  LEU A 101 " =    2.491
peak=   -3.655 closest distance to " O   PRO A 198 " =    1.213
peak=   -3.655 closest distance to " CG1 VAL A 112 " =    2.864
peak=   -3.654 closest distance to " O   HOH Z 185 " =    2.352
peak=   -3.649 closest distance to " CG  TRP A 266 " =    1.896
peak=   -3.648 closest distance to " CB  PHE A 192 " =    1.843
peak=   -3.638 closest distance to " OG  SER A   3 " =    1.691
peak=   -3.636 closest distance to " CD  ARG A  14 " =    2.961
peak=   -3.633 closest distance to " NE2 GLN A  88 " =    2.029
peak=   -3.624 closest distance to " CD  ARG A 139 " =    1.553
peak=   -3.623 closest distance to " N   ALA A  43 " =    2.410
peak=   -3.595 closest distance to " O   HOH Z 211 " =    1.690
peak=   -3.594 closest distance to " NH2 ARG A  79 " =    1.941
peak=   -3.590 closest distance to " CD1 LEU A 101 " =    2.869
peak=   -3.576 closest distance to " CG  LEU A 228 " =    0.948
peak=   -3.574 closest distance to " O   HOH Z  52 " =    1.496
peak=   -3.569 closest distance to " CD  LYS A 289 " =    2.557
peak=   -3.564 closest distance to " OG BSER A 134 " =    1.722
peak=   -3.563 closest distance to " O   HOH Z 394 " =    1.509
peak=   -3.551 closest distance to " O   HOH Z 222 " =    1.453
peak=   -3.551 closest distance to " CD1 LEU A 228 " =    2.266
peak=   -3.551 closest distance to " O   HOH Z 196 " =    2.155
peak=   -3.536 closest distance to " CE2 PHE A 218 " =    2.616
peak=   -3.534 closest distance to " N   THR A 157 " =    1.491
peak=   -3.522 closest distance to " O   HOH Z 166 " =    1.987
peak=   -3.517 closest distance to " CB  ASP A 132 " =    2.327
peak=   -3.513 closest distance to " O   HOH Z 407 " =    3.061
peak=   -3.511 closest distance to " C   MET A 188 " =    1.418
peak=   -3.509 closest distance to " O   HOH Z  47 " =    1.596
peak=   -3.492 closest distance to " CG2 ILE A 263 " =    2.378
peak=   -3.491 closest distance to " O   HOH Z  13 " =    1.351
peak=   -3.486 closest distance to " CA  ASP A 298 " =    1.058
peak=   -3.484 closest distance to " CZ  TYR A 169 " =    1.649
peak=   -3.469 closest distance to " CB  ASP A 132 " =    2.270
peak=   -3.466 closest distance to " O   GLY A 196 " =    1.153
peak=   -3.466 closest distance to " N   ASP A 171 " =    2.393
peak=   -3.462 closest distance to " NZ  LYS A 119 " =    3.458
peak=   -3.457 closest distance to " C   ASP A 231 " =    2.624
peak=   -3.453 closest distance to " CG1 VAL A 112 " =    2.643
peak=   -3.452 closest distance to " O   HOH Z 198 " =    1.355
peak=   -3.451 closest distance to " O   HOH Z 102 " =    1.657
peak=   -3.447 closest distance to " CG1 VAL A 197 " =    2.248
peak=   -3.444 closest distance to " CG  ARG A 269 " =    2.336
peak=   -3.444 closest distance to " CG1 VAL A 250 " =    2.762
peak=   -3.429 closest distance to " ND2 ASN A 187 " =    1.618
peak=   -3.424 closest distance to " CB  VAL A 296 " =    1.136
peak=   -3.420 closest distance to " CG  GLU A 277 " =    1.123
peak=   -3.418 closest distance to " CZ  PHE A  59 " =    1.547
peak=   -3.412 closest distance to " N   THR A 235 " =    1.337
peak=   -3.412 closest distance to " OG  SER A  62 " =    1.562
peak=   -3.410 closest distance to " C   ASN A 187 " =    1.904
peak=   -3.409 closest distance to " O   HOH Z  60 " =    2.142
peak=   -3.408 closest distance to " O   VAL A 189 " =    2.552
peak=   -3.404 closest distance to " CB  PRO A 280 " =    2.067
peak=   -3.402 closest distance to " O   HOH Z  43 " =    1.743
peak=   -3.402 closest distance to " O   HOH Z 372 " =    2.385
peak=   -3.399 closest distance to " OG  SER A  87 " =    1.399
peak=   -3.396 closest distance to " OD1 ASN A 148 " =    1.509
peak=   -3.395 closest distance to " CB  ALA A 291 " =    2.237
peak=   -3.395 closest distance to " OG  SER A 206 " =    1.672
peak=   -3.391 closest distance to " CG  ASP A  50 " =    2.389
peak=   -3.391 closest distance to " O   HOH Z 417 " =    2.779
peak=   -3.387 closest distance to " CA  GLY A  98 " =    1.903
peak=   -3.382 closest distance to " N   SER A 212 " =    1.945
peak=   -3.367 closest distance to " CD1 PHE A  59 " =    1.910
peak=   -3.365 closest distance to " O   HOH Z 311 " =    3.710
peak=   -3.364 closest distance to " O   HOH Z  38 " =    1.646
peak=   -3.364 closest distance to " O   MET A  40 " =    2.650
peak=   -3.360 closest distance to " CZ3 TRP A 274 " =    1.013
peak=   -3.336 closest distance to " CA  GLY A 241 " =    3.031
peak=   -3.334 closest distance to " O   HOH Z  44 " =    2.190
peak=   -3.326 closest distance to " CG1 VAL A 230 " =    1.845
peak=   -3.325 closest distance to " CE BMET A  47 " =    1.839
peak=   -3.319 closest distance to " N   VAL A 230 " =    1.162
peak=   -3.315 closest distance to " OG  SER A  26 " =    1.198
peak=   -3.310 closest distance to " C   ASN A 285 " =    2.432
peak=   -3.308 closest distance to " O   HOH Z 165 " =    1.900
peak=   -3.308 closest distance to " OD2 ASP A 171 " =    2.242
peak=   -3.308 closest distance to " CD2 LEU A 237 " =    2.780
peak=   -3.307 closest distance to " O   HOH Z 262 " =    2.754
peak=   -3.300 closest distance to " C   LEU A 222 " =    0.788
peak=   -3.300 closest distance to " O   HOH Z 353 " =    2.071
peak=   -3.299 closest distance to " CB  ASN A  69 " =    1.164
peak=   -3.298 closest distance to " O   LYS A 117 " =    1.680
peak=   -3.297 closest distance to " O   HOH Z 166 " =    1.492
peak=   -3.296 closest distance to " O   HOH Z 241 " =    1.303
peak=   -3.292 closest distance to " O   HOH Z 436 " =    1.542
peak=   -3.292 closest distance to " CB  TYR A  15 " =    2.224
peak=   -3.292 closest distance to " O   HOH Z 134 " =    2.659
peak=   -3.288 closest distance to " O   HOH Z 388 " =    2.119
peak=   -3.283 closest distance to " CG  ARG A  66 " =    2.437
peak=   -3.281 closest distance to " OG1 THR A 246 " =    1.484
peak=   -3.278 closest distance to " CD2 LEU A 167 " =    1.751
peak=   -3.276 closest distance to " C   GLN A 205 " =    2.022
peak=   -3.276 closest distance to " O   SER A  22 " =    2.247
peak=   -3.274 closest distance to " CG  MET A 105 " =    0.935
peak=   -3.270 closest distance to " N   HIS A 115 " =    2.065
peak=   -3.265 closest distance to " CB  ALA A 291 " =    2.158
peak=   -3.261 closest distance to " OG ASER A 134 " =    1.269
peak=   -3.260 closest distance to " O   SER A  95 " =    1.577
peak=   -3.258 closest distance to " NE2 GLN A 103 " =    1.727
peak=   -3.255 closest distance to " C   LEU A 143 " =    1.042
peak=   -3.253 closest distance to " N   SER A 276 " =    1.253
peak=   -3.252 closest distance to " CD1 ILE A 239 " =    2.068
peak=   -3.250 closest distance to " CD  GLN A  88 " =    0.832
peak=   -3.248 closest distance to " O   HOH Z 210 " =    1.055
peak=   -3.247 closest distance to " CB  GLN A  11 " =    1.793
peak=   -3.245 closest distance to " NH2 ARG A  79 " =    1.591
peak=   -3.243 closest distance to " O   HOH Z 148 " =    1.799
peak=   -3.240 closest distance to " NH1 ARG A 195 " =    2.546
peak=   -3.239 closest distance to " O   HOH Z 191 " =    5.426
peak=   -3.233 closest distance to " N   ALA A 248 " =    1.619
peak=   -3.233 closest distance to " NH2 ARG A  66 " =    1.875
peak=   -3.232 closest distance to " O   HOH Z 423 " =    2.087
peak=   -3.232 closest distance to " O   HOH Z 295 " =    1.466
peak=   -3.232 closest distance to " CG1 VAL A 296 " =    1.281
peak=   -3.231 closest distance to " N   PHE A  59 " =    2.100
peak=   -3.230 closest distance to " OG1 THR A 178 " =    1.283
peak=   -3.229 closest distance to " O   HOH Z  90 " =    2.868
peak=   -3.228 closest distance to " O   HOH Z 313 " =    1.721
peak=   -3.226 closest distance to " O   HOH Z  22 " =    2.542
peak=   -3.226 closest distance to " CB  ASN A  39 " =    2.095
peak=   -3.223 closest distance to " NH1 ARG A  36 " =    2.073
peak=   -3.221 closest distance to " O   HOH Z  10 " =    1.488
peak=   -3.220 closest distance to " CG  GLU A  53 " =    1.507
peak=   -3.220 closest distance to " O   HOH Z 174 " =    2.409
peak=   -3.216 closest distance to " CE3 TRP A 150 " =    2.024
peak=   -3.215 closest distance to " O   ALA A 161 " =    1.614
peak=   -3.212 closest distance to " CB  ALA A 248 " =    2.419
peak=   -3.211 closest distance to " O   GLY A 211 " =    1.426
peak=   -3.207 closest distance to " O   HOH Z 369 " =    2.178
peak=   -3.203 closest distance to " O   PRO A 198 " =    1.317
peak=   -3.195 closest distance to " CA  GLY A 133 " =    2.002
peak=   -3.191 closest distance to " O   HOH Z 234 " =    4.166
peak=   -3.184 closest distance to " O   HOH Z  19 " =    2.359
peak=   -3.180 closest distance to " O   VAL A 125 " =    2.335
peak=   -3.179 closest distance to " O   HOH Z 426 " =    1.632
peak=   -3.174 closest distance to " O   HOH Z 222 " =    3.363
peak=   -3.172 closest distance to " N   GLN A  77 " =    1.555
peak=   -3.164 closest distance to " O   HOH Z 431 " =    1.710
peak=   -3.161 closest distance to " O   GLY A  80 " =    2.500
peak=   -3.159 closest distance to " O   HOH Z 377 " =    0.741
peak=   -3.154 closest distance to " ND2 ASN A  60 " =    1.466
peak=   -3.145 closest distance to " OXT GLY A 302 " =    3.493
peak=   -3.138 closest distance to " CA  GLY A 203 " =    2.335
peak=   -3.135 closest distance to " O   HOH Z 275 " =    1.511
peak=   -3.128 closest distance to " O   HOH Z 283 " =    1.976
peak=   -3.128 closest distance to " O   HOH Z 175 " =    4.283
peak=   -3.119 closest distance to " NE2 GLN A 278 " =    1.991
peak=   -3.118 closest distance to " O   GLY A  75 " =    1.929
peak=   -3.113 closest distance to " CD1 ILE A 199 " =    2.470
peak=   -3.095 closest distance to " ND2 ASN A 249 " =    2.381
peak=   -3.094 closest distance to " CD1 TYR A 247 " =    2.394
peak=   -3.091 closest distance to " O   VAL A 174 " =    2.036
peak=   -3.089 closest distance to " CD2 TYR A 293 " =    2.136
peak=   -3.086 closest distance to " O   HOH Z 111 " =    2.499
peak=   -3.078 closest distance to " O   GLY A  80 " =    2.480
peak=   -3.063 closest distance to " CD1 ILE A 239 " =    2.338
peak=   -3.041 closest distance to " O   HOH Z 281 " =    2.677
peak=   -3.032 closest distance to " O   HOH Z   6 " =    1.780
peak=   -3.031 closest distance to " N   ALA A 248 " =    1.884
peak=   -3.028 closest distance to " O   HOH Z 193 " =    1.905

================= 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    :  0.4176 0.4059   6.204818e+00   6.184251e+00
   1_bss:  0.4096 0.3963   6.201528e+00   6.170303e+00
   1_xyz:  0.2979 0.3262   5.965066e+00   6.022598e+00
   1_adp:  0.2272 0.2648   5.725421e+00   5.854350e+00
   1_occ:  0.2266 0.2652   5.724032e+00   5.854426e+00
   2_bss:  0.2211 0.2589   5.721470e+00   5.848301e+00
   2_xyz:  0.1572 0.1959   5.418346e+00   5.601447e+00
   2_adp:  0.1461 0.1858   5.356964e+00   5.552915e+00
   2_occ:  0.1459 0.1857   5.356441e+00   5.552531e+00
   3_bss:  0.1458 0.1853   5.356730e+00   5.552016e+00
   3_xyz:  0.1212 0.1622   5.197069e+00   5.421346e+00
   3_adp:  0.1155 0.1584   5.164013e+00   5.399694e+00
   3_occ:  0.1154 0.1583   5.163637e+00   5.399379e+00
   4_bss:  0.1158 0.1587   5.165113e+00   5.399932e+00
   4_xyz:  0.1091 0.1564   5.132884e+00   5.387610e+00
   4_adp:  0.1105 0.1555   5.134274e+00   5.379713e+00
   4_occ:  0.1105 0.1555   5.134284e+00   5.379976e+00
   5_bss:  0.1105 0.1555   5.134363e+00   5.380035e+00
   5_xyz:  0.1116 0.1554   5.140132e+00   5.382286e+00
   5_adp:  0.1108 0.1557   5.138302e+00   5.385022e+00
   5_occ:  0.1108 0.1558   5.138287e+00   5.385030e+00
   5_bss:  0.1108 0.1558   5.138174e+00   5.384922e+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:  0.356  20.001   7.562   8.180   8.479   0.000   0.000   0.000
   1_xyz:  0.356  20.001   7.562   8.180   8.479   0.000   0.000   0.000
   1_adp:  0.356  20.001   7.562   8.180   8.479   0.000   0.000   0.000
   1_occ:  0.356  20.001   7.562   8.180   8.479   0.000   0.000   0.000
   2_bss:  0.337  39.393   4.028   4.207   5.358   0.000   0.000   0.000
   2_xyz:  0.337  39.393   4.028   4.207   5.358   0.000   0.000   0.000
   2_adp:  0.337  39.393   4.028   4.207   5.358   0.000   0.000   0.000
   2_occ:  0.337  39.393   4.028   4.207   5.358   0.000   0.000   0.000
   3_bss:  0.329  39.393   3.240   3.456   4.407   0.000   0.000   0.000
   3_xyz:  0.329  39.393   3.240   3.456   4.407   0.000   0.000   0.000
   3_adp:  0.329  39.393   3.240   3.456   4.407   0.000   0.000   0.000
   3_occ:  0.329  39.393   3.240   3.456   4.407   0.000   0.000   0.000
   4_bss:  0.320  39.393   3.174   3.390   4.176   0.000   0.000   0.000
   4_xyz:  0.320  39.393   3.174   3.390   4.176   0.000   0.000   0.000
   4_adp:  0.320  39.393   3.174   3.390   4.176   0.000   0.000   0.000
   4_occ:  0.320  39.393   3.174   3.390   4.176   0.000   0.000   0.000
   5_bss:  0.322  39.393   3.174   3.390   4.176   0.000   0.000   0.000
   5_xyz:  0.322  39.393   3.174   3.390   4.176   0.000   0.000   0.000
   5_adp:  0.322  39.393   3.174   3.390   4.176   0.000   0.000   0.000
   5_occ:  0.322  39.393   3.174   3.390   4.176   0.000   0.000   0.000
   5_bss:  0.322  43.627  -0.406  -0.190   0.596   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  44.821 0.5863  0.6549    47569.042
   1_bss:  44.747 0.5847  0.8301    45015.349
   1_xyz:  34.411 0.7071  0.9776    28275.611
   1_adp:  26.015 0.8015  1.0694    17636.318
   1_occ:  26.016 0.8014  1.0689    17614.291
   2_bss:  25.772 0.8037  0.9424    17323.940
   2_xyz:  18.644 0.8745  0.9916     9723.086
   2_adp:  17.340 0.8869  1.0021     8834.265
   2_occ:  17.335 0.8870  1.0019     8822.591
   3_bss:  17.321 0.8870  0.9717     8812.631
   3_xyz:  14.638 0.9097  0.9831     6777.779
   3_adp:  14.207 0.9134  0.9842     6484.501
   3_occ:  14.198 0.9135  0.9842     6479.609
   4_bss:  14.214 0.9134  0.9790     6503.934
   4_xyz:  13.904 0.9160  0.9792     6306.709
   4_adp:  13.693 0.9177  0.9799     6223.262
   4_occ:  13.698 0.9177  0.9797     6226.319
   5_bss:  13.699 0.9177  0.9798     6228.300
   5_xyz:  13.730 0.9175  0.9793     6245.777
   5_adp:  13.794 0.9170  0.9774     6279.290
   5_occ:  13.794 0.9170  0.9773     6281.453
   5_bss:  13.792 0.9170  0.9773     6279.824
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.3676e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.3676e+01
   1_xyz:   1.470  0.011  0.099 17.741  0.006  4.121   1.1163e-01
   1_adp:   1.470  0.011  0.099 17.741  0.006  4.121   1.1163e-01
   1_occ:   1.470  0.011  0.099 17.741  0.006  4.121   1.1163e-01
   2_bss:   1.470  0.011  0.099 17.741  0.006  4.121   1.1163e-01
   2_xyz:   0.903  0.005  0.068 15.820  0.003  4.121   5.3678e-02
   2_adp:   0.903  0.005  0.068 15.820  0.003  4.121   5.3678e-02
   2_occ:   0.903  0.005  0.068 15.820  0.003  4.121   5.3678e-02
   3_bss:   0.903  0.005  0.068 15.820  0.003  4.121   5.3678e-02
   3_xyz:   1.025  0.007  0.083 15.726  0.004  4.127   6.3189e-02
   3_adp:   1.025  0.007  0.083 15.726  0.004  4.127   6.3189e-02
   3_occ:   1.025  0.007  0.083 15.726  0.004  4.127   6.3189e-02
   4_bss:   1.025  0.007  0.083 15.726  0.004  4.127   6.3189e-02
   4_xyz:   1.088  0.009  0.090 15.765  0.004  4.117   7.1339e-02
   4_adp:   1.088  0.009  0.090 15.765  0.004  4.117   7.1339e-02
   4_occ:   1.088  0.009  0.090 15.765  0.004  4.117   7.1339e-02
   5_bss:   1.088  0.009  0.090 15.765  0.004  4.117   7.1339e-02
   5_xyz:   0.994  0.007  0.082 15.466  0.004  4.116   6.1009e-02
   5_adp:   0.994  0.007  0.082 15.466  0.004  4.116   6.1009e-02
   5_occ:   0.994  0.007  0.082 15.466  0.004  4.116   6.1009e-02
   5_bss:   0.994  0.007  0.082 15.466  0.004  4.116   6.1009e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9597e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9597e+00
   1_xyz:  12.204  0.131  0.412 88.318  0.040  2.229   8.3286e-02
   1_adp:  12.204  0.131  0.412 88.318  0.040  2.229   8.3286e-02
   1_occ:  12.204  0.131  0.412 88.318  0.040  2.229   8.3286e-02
   2_bss:  12.204  0.131  0.412 88.318  0.040  2.229   8.3286e-02
   2_xyz:   6.094  0.043  0.291 81.254  0.034  2.365   3.5050e-02
   2_adp:   6.094  0.043  0.291 81.254  0.034  2.365   3.5050e-02
   2_occ:   6.094  0.043  0.291 81.254  0.034  2.365   3.5050e-02
   3_bss:   6.094  0.043  0.291 81.254  0.034  2.365   3.5050e-02
   3_xyz:   6.734  0.044  0.561 83.964  0.039  2.322   4.5033e-02
   3_adp:   6.734  0.044  0.561 83.964  0.039  2.322   4.5033e-02
   3_occ:   6.734  0.044  0.561 83.964  0.039  2.322   4.5033e-02
   4_bss:   6.734  0.044  0.561 83.964  0.039  2.322   4.5033e-02
   4_xyz:   6.884  0.046  0.672 82.757  0.040  2.295   5.6017e-02
   4_adp:   6.884  0.046  0.672 82.757  0.040  2.295   5.6017e-02
   4_occ:   6.884  0.046  0.672 82.757  0.040  2.295   5.6017e-02
   5_bss:   6.884  0.046  0.672 82.757  0.040  2.295   5.6017e-02
   5_xyz:   6.883  0.044  0.561 83.250  0.039  2.316   4.1205e-02
   5_adp:   6.883  0.044  0.561 83.250  0.039  2.316   4.1205e-02
   5_occ:   6.883  0.044  0.561 83.250  0.039  2.316   4.1205e-02
   5_bss:   6.883  0.044  0.561 83.250  0.039  2.316   4.1205e-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:  67.64   0.00  10.35  63.54   0.00   7.10  67.64   0.00  28.08
   1_occ:  67.64   0.00  10.35  63.54   0.00   7.10  67.64   0.00  28.08
   2_bss:  67.64   0.00  10.35  63.54   0.00   7.10  67.64   0.00  28.08
   2_xyz:  67.64   0.00  10.35  63.54   0.00   7.10  67.64   0.00  28.08
   2_adp:  66.78   0.00  10.71  63.37   0.00   7.13  66.78   1.09  30.21
   2_occ:  66.78   0.00  10.71  63.37   0.00   7.13  66.78   1.09  30.21
   3_bss:  66.78   0.00  10.71  63.37   0.00   7.13  66.78   1.09  30.21
   3_xyz:  66.78   0.00  10.71  63.37   0.00   7.13  66.78   1.09  30.21
   3_adp:  76.21   0.00  11.44  76.21   0.00   7.31  71.68   0.58  33.92
   3_occ:  76.21   0.00  11.44  76.21   0.00   7.31  71.68   0.58  33.92
   4_bss:  76.21   0.00  11.44  76.21   0.00   7.31  71.68   0.58  33.92
   4_xyz:  76.21   0.00  11.44  76.21   0.00   7.31  71.68   0.58  33.92
   4_adp:  75.10   0.00  10.95  75.10   0.00   7.15  63.50   0.92  31.63
   4_occ:  75.10   0.00  10.95  75.10   0.00   7.15  63.50   0.92  31.63
   5_bss:  75.10   0.00  10.95  75.10   0.00   7.15  63.50   0.92  31.63
   5_xyz:  75.10   0.00  10.95  75.10   0.00   7.15  63.50   0.92  31.63
   5_adp:  75.51   0.00  10.96  75.51   0.00   7.14  63.00   1.03  31.80
   5_occ:  75.51   0.00  10.96  75.51   0.00   7.14  63.00   1.03  31.80
   5_bss:  79.09   3.58  14.54  79.09   3.58  10.72  66.58   4.61  35.38
------------------------------------------------------------------------
 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:    1.158    0.012    0.400
   1_adp:    1.158    0.012    0.400
   1_occ:    1.158    0.012    0.400
   2_bss:    1.158    0.012    0.400
   2_xyz:    1.426    0.038    0.475
   2_adp:    1.426    0.038    0.475
   2_occ:    1.426    0.038    0.475
   3_bss:    1.426    0.038    0.475
   3_xyz:    1.417    0.032    0.510
   3_adp:    1.417    0.032    0.510
   3_occ:    1.417    0.032    0.510
   4_bss:    1.417    0.032    0.510
   4_xyz:    1.496    0.046    0.524
   4_adp:    1.496    0.046    0.524
   4_occ:    1.496    0.046    0.524
   5_bss:    1.496    0.046    0.524
   5_xyz:    1.536    0.047    0.529
   5_adp:    1.536    0.047    0.529
   5_occ:    1.536    0.047    0.529
   5_bss:    1.536    0.047    0.529
------------------------------------------------------------------------

CPU time actual refinement: 316.81


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_784/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_784/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_784/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_784/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_784/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 316.66 
  Macro-tasks:
    bulk solvent and scale       = 40.54  
    individual site refinement   = 128.53 
    weights calculation          = 31.59  
    collect and process          = 6.43   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 207.19 
  Micro-tasks:
    mask                            = 1.67   
    f_calc                          = 94.95  
    alpha_beta                      = 8.28   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 106.49 
    fmodel                         = 7.01   
    r_factors                      = 0.18   
    phase_errors                   = 10.90  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 230.91 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.445 micro seconds
Total CPU time: 5.50 minutes
from_scatterers_fft:    650 calls, 94.70 s
gradients_fft:          596 calls, 92.86 s

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

# Date 2008-01-16 Time 02:25:29 PST -0800 (1200479129.16 s)
Start R-work = 0.4176, R-free = 0.4059 (no bulk solvent and anisotropic scale)
Final R-work = 0.1283, R-free = 0.1717 (no bulk solvent and anisotropic scale)

Start R-work = 0.4096, R-free = 0.3963
Final R-work = 0.1108, R-free = 0.1558