# Date 2008-01-16 Time 00:45:39 PST -0800 (1200473139.35 s)
#phil __OFF__

Command line arguments: "../143.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 = 19243
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 143

-------------------------------------------------------------------------------
  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: (68.845, 46.2261, 84.2302, 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: 3.25, 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: (68.845, 46.2261, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6737 1.95106
Completeness in resolution range: 0.972545
Completeness with d_max=infinity: 0.969465

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.6737
                             d_min =   1.9511

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: (68.845, 46.2261, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6737 1.95106
Completeness in resolution range: 0.972545
Completeness with d_max=infinity: 0.969465

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.6741 -  4.1742 [2113/2140]  1902   211  10.0%
  bin  2:  4.1742 -  3.3259 [2029/2045]  1826   203  10.0%
  bin  3:  3.3259 -  2.9092 [2005/2024]  1802   203  10.1%
  bin  4:  2.9092 -  2.6449 [1991/2021]  1796   195   9.8%
  bin  5:  2.6449 -  2.4563 [1966/1985]  1767   199  10.1%
  bin  6:  2.4563 -  2.3120 [1958/1983]  1764   194   9.9%
  bin  7:  2.3120 -  2.1966 [1966/2000]  1769   197  10.0%
  bin  8:  2.1966 -  2.1013 [1937/1967]  1743   194  10.0%
  bin  9:  2.1013 -  2.0206 [1944/1986]  1748   196  10.1%
  bin 10:  2.0206 -  1.9511 [1680/1991]  1513   167   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_143/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        0.81 -     1.62: 7
        1.62 -     2.44: 84
        2.44 -     3.26: 3627
        3.26 -     4.08: 9727
        4.08 -     4.90: 15825
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  0.805 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.245 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.339 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.357 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.405 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 29265 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_143/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_143/model_refine_001.geo

CPU time processing inputs: 9.14


============================ 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 = 68.845 46.22605 84.23025 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: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5160   r_free= 0.5078   ksol= 0.00   Bsol= 0.00   scale= 0.785    |
|                                                                             |
| 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:   0.90 A                  |
| x-ray target function (ml) for work reflections: 6.305865                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6741 -  4.6554 0.99   1375  153 0.4280 0.4354      6.6413      6.6807|
|  2:  4.6554 -  3.7149 0.99   1320  145 0.4688 0.4490      6.8666      6.8637|
|  3:  3.7149 -  3.2511 0.99   1301  146 0.4888 0.4720      6.7416      6.8147|
|  4:  3.2511 -  2.9565 0.99   1285  144 0.5018 0.4824      6.5774      6.5208|
|  5:  2.9565 -  2.7461 0.99   1272  139 0.5472 0.5342      6.4109      6.3806|
|  6:  2.7461 -  2.5851 0.99   1278  143 0.5495 0.5680      6.3153      6.2855|
|  7:  2.5851 -  2.4563 0.99   1262  141 0.5344 0.4979      6.2609      6.1898|
|  8:  2.4563 -  2.3498 0.98   1265  140 0.5576 0.5740      6.2092      6.2149|
|  9:  2.3498 -  2.2597 0.98   1268  138 0.5505 0.5547       6.129      6.1553|
| 10:  2.2597 -  2.1819 0.98   1237  137 0.5667 0.5068      6.1394      6.1299|
| 11:  2.1819 -  2.1139 0.99   1267  147 0.5387 0.5853       6.056      6.1167|
| 12:  2.1139 -  2.0537 0.97   1249  130 0.5478 0.4941      5.9956      6.0157|
| 13:  2.0537 -  1.9997 0.99   1238  141 0.5547 0.5020      5.9026      5.8777|
| 14:  1.9997 -  1.9511 0.79   1013  115 0.5474 0.5300      5.8613      5.7664|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6741 -  4.6554  1375   153  0.59  43.20   0.79     0.64     102914.59|
|  2:  4.6554 -  3.7149  1320   145  0.60  43.95   0.84     0.69     150541.29|
|  3:  3.7149 -  3.2511  1301   146  0.49  52.60   0.84     0.64     154874.43|
|  4:  3.2511 -  2.9565  1285   144  0.42  58.44   0.80     0.54     127719.88|
|  5:  2.9565 -  2.7461  1272   139  0.34  64.43   0.72     0.43      96135.74|
|  6:  2.7461 -  2.5851  1278   143  0.30  67.52   0.72     0.36      82207.79|
|  7:  2.5851 -  2.4563  1262   141  0.23  72.85   0.74     0.27      76268.83|
|  8:  2.4563 -  2.3498  1265   140  0.21  74.16   0.73     0.26      70270.31|
|  9:  2.3498 -  2.2597  1268   138  0.20  75.11   0.72     0.25      64134.17|
| 10:  2.2597 -  2.1819  1237   137  0.23  72.86   0.75     0.28      56714.79|
| 11:  2.1819 -  2.1139  1267   147  0.18  76.22   0.78     0.24      54340.57|
| 12:  2.1139 -  2.0537  1249   130  0.20  74.98   0.75     0.26      49485.64|
| 13:  2.0537 -  1.9997  1238   141  0.21  74.44   0.75     0.28      42094.06|
| 14:  1.9997 -  1.9511  1013   115  0.28  69.23   0.73     0.33      32131.29|
|alpha:            min =        0.24 max =            0.69 mean =         0.39|
|beta:             min =    32131.29 max =       154874.43 mean =     84238.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.32|
|phase err.(work): min =        0.00 max =           90.00 mean =        65.39|
|phase err.(test): min =        0.00 max =           89.98 mean =        65.83|
|-----------------------------------------------------------------------------|

============================== 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 = 28.695524             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.210   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.656295              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 84.177   (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 |  0.428 -  0.875:        1 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  0.875 -  1.322:        3 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.322 -  1.769:       17 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  1.769 -  2.217:      155 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.217 -  2.664:      775 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.664 -  3.111:     2026 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.111 -  3.558:     3729 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.558 -  4.006:     5592 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.006 -  4.453:     7594 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.453 -  4.900:     9383 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       52.438 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.084    4.900  0.428 |       3.432 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.171)------------------------------------------|
|    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 = 11.171)------------------------------------------|
|    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: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5196   r_free= 0.5107   ksol= 0.00   Bsol= 0.00   scale= 0.755    |
|                                                                             |
| 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:   0.91 A                  |
| x-ray target function (ml) for work reflections: 6.306334                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5084   r_free= 0.4982   ksol= 0.42   Bsol= 20.00   scale= 0.962   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.15,8.22,8.19,0.00,0.00,0.00); trace/3= 7.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.91 A                  |
| x-ray target function (ml) for work reflections: 6.300761                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 21.363380             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.130   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.105156              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.256   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5084      final r-factor (work) = 0.4473          |
| start r-factor (free) = 0.4982      final r-factor (free) = 0.4652          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 119.7605 = 21.36 * 0.50 * 6.3026 + 1.00 * 52.4378                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 66.9628 = 21.36 * 0.50 * 6.2528 + 1.00 * 0.1724                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4473      final r-factor (work) = 0.4074          |
| start r-factor (free) = 0.4652      final r-factor (free) = 0.4605          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.1775 = 2.11 * 1.00 * 6.2528 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.0925 = 2.11 * 1.00 * 6.2080 + 1.00 * 0.0237                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.42   16.01    None  None   None       |
|    all(noH): 2823   0      0.00    83.42   16.01    None  None   None       |
|    Sol.    : 438    0      0.00    83.42   23.62    None  None   None       |
|    Mac.    : 2385   0      0.00    75.67   14.61    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.342:  920   |   5:    41.711 -  50.053:   79        |
|      1:     8.342 -  16.684:  766   |   6:    50.053 -  58.395:   38        |
|      2:    16.684 -  25.026:  546   |   7:    58.395 -  66.737:   13        |
|      3:    25.026 -  33.368:  276   |   8:    66.737 -  75.079:    5        |
|      4:    33.368 -  41.711:  176   |   9:    75.079 -  83.421:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4074 r_free = 0.4605             target_work(ml) = 6.197         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4068 r_free = 0.4616             target_work(ml) = 6.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4068   r_free= 0.4616   ksol= 0.42   Bsol= 20.00   scale= 1.104   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.15,8.22,8.19,0.00,0.00,0.00); trace/3= 7.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.196233                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4055   r_free= 0.4586   ksol= 0.36   Bsol= 28.61   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.50,4.81,5.82,0.00,0.00,0.00); trace/3= 4.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.196315                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.694496             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.705  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.814843              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.844  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4055      final r-factor (work) = 0.3452          |
| start r-factor (free) = 0.4586      final r-factor (free) = 0.4093          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.3434 = 10.69 * 0.50 * 6.2034 + 1.00 * 0.1724                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.9219 = 10.69 * 0.50 * 6.1386 + 1.00 * 0.0973                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3452      final r-factor (work) = 0.3278          |
| start r-factor (free) = 0.4093      final r-factor (free) = 0.3942          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0326 = 0.81 * 1.00 * 6.1386 + 1.00 * 0.0306                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9723 = 0.81 * 1.00 * 6.0652 + 1.00 * 0.0301                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.83   15.48    None  None   None       |
|    all(noH): 2823   0      0.00    83.83   15.48    None  None   None       |
|    Sol.    : 438    0      0.00    82.98   28.24    None  None   None       |
|    Mac.    : 2385   0      0.00    83.83   13.14    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 -   8.383:  965   |   5:    41.916 -  50.299:   64        |
|      1:     8.383 -  16.767:  858   |   6:    50.299 -  58.683:   25        |
|      2:    16.767 -  25.150:  475   |   7:    58.683 -  67.066:   16        |
|      3:    25.150 -  33.533:  260   |   8:    67.066 -  75.449:    4        |
|      4:    33.533 -  41.916:  150   |   9:    75.449 -  83.832:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3278 r_free = 0.3942             target_work(ml) = 6.049         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3273 r_free = 0.3945             target_work(ml) = 6.049         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3273   r_free= 0.3945   ksol= 0.36   Bsol= 28.61   scale= 1.087   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.50,4.81,5.82,0.00,0.00,0.00); trace/3= 4.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.048704                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3260   r_free= 0.3958   ksol= 0.32   Bsol= 28.61   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.78,2.51,3.50,0.00,0.00,0.00); trace/3= 2.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.048821                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.727849              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.342  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.446946              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.145   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3260      final r-factor (work) = 0.2531          |
| start r-factor (free) = 0.3958      final r-factor (free) = 0.3154          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.4924 = 6.73 * 0.50 * 6.0629 + 1.00 * 0.0973                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.1162 = 6.73 * 0.50 * 5.9531 + 1.00 * 0.0904                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2531      final r-factor (work) = 0.2220          |
| start r-factor (free) = 0.3154      final r-factor (free) = 0.2941          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.6287 = 1.45 * 1.00 * 5.9531 + 1.00 * 0.0149                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.3856 = 1.45 * 1.00 * 5.7833 + 1.00 * 0.0175                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.87  16.18    None  None   None       |
|    all(noH): 2823   0      0.00    108.87  16.18    None  None   None       |
|    Sol.    : 438    0      1.41    89.85   39.79    None  None   None       |
|    Mac.    : 2385   0      0.00    108.87  11.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.887: 1487   |   5:    54.433 -  65.320:   66        |
|      1:    10.887 -  21.773:  666   |   6:    65.320 -  76.207:   43        |
|      2:    21.773 -  32.660:  266   |   7:    76.207 -  87.093:   12        |
|      3:    32.660 -  43.547:  155   |   8:    87.093 -  97.980:    4        |
|      4:    43.547 -  54.433:  122   |   9:    97.980 - 108.867:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2220 r_free = 0.2941             target_work(ml) = 5.748         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2216 r_free = 0.2936             target_work(ml) = 5.747         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2216   r_free= 0.2936   ksol= 0.32   Bsol= 28.61   scale= 1.061   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.78,2.51,3.50,0.00,0.00,0.00); trace/3= 2.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.746540                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2207   r_free= 0.2937   ksol= 0.30   Bsol= 30.30   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.98,1.28,2.22,0.00,0.00,0.00); trace/3= 1.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.742975                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.925755              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.525   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.140018              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.125  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2207      final r-factor (work) = 0.1750          |
| start r-factor (free) = 0.2937      final r-factor (free) = 0.2368          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4426 = 3.93 * 0.50 * 5.7835 + 1.00 * 0.0904                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1653 = 3.93 * 0.50 * 5.6557 + 1.00 * 0.0639                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1750      final r-factor (work) = 0.1675          |
| start r-factor (free) = 0.2368      final r-factor (free) = 0.2169          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8099 = 0.14 * 1.00 * 5.6557 + 1.00 * 0.0180                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7851 = 0.14 * 1.00 * 5.5233 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.62  15.32    None  None   None       |
|    all(noH): 2823   0      0.00    104.62  15.32    None  None   None       |
|    Sol.    : 438    0      2.87    87.25   38.23    None  None   None       |
|    Mac.    : 2385   0      0.00    104.62  11.11    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.462: 1575   |   5:    52.309 -  62.771:   66        |
|      1:    10.462 -  20.924:  651   |   6:    62.771 -  73.233:   34        |
|      2:    20.924 -  31.386:  210   |   7:    73.233 -  83.695:   10        |
|      3:    31.386 -  41.847:  162   |   8:    83.695 -  94.156:    4        |
|      4:    41.847 -  52.309:  109   |   9:    94.156 - 104.618:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1675 r_free = 0.2169             target_work(ml) = 5.477         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1670 r_free = 0.2159             target_work(ml) = 5.474         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1670   r_free= 0.2159   ksol= 0.30   Bsol= 30.30   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.98,1.28,2.22,0.00,0.00,0.00); trace/3= 1.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.473611                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1665   r_free= 0.2142   ksol= 0.32   Bsol= 30.30   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.03,0.48,1.32,0.00,0.00,0.00); trace/3= 0.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.472517                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.106213              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.809  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.237090              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.651   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1665      final r-factor (work) = 0.1365          |
| start r-factor (free) = 0.2142      final r-factor (free) = 0.1807          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4058 = 4.11 * 0.50 * 5.5243 + 1.00 * 0.0639                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1225 = 4.11 * 0.50 * 5.3820 + 1.00 * 0.0727                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1365      final r-factor (work) = 0.1282          |
| start r-factor (free) = 0.1807      final r-factor (free) = 0.1723          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2882 = 0.24 * 1.00 * 5.3820 + 1.00 * 0.0122                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2567 = 0.24 * 1.00 * 5.2635 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.33   14.93    None  None   None       |
|    all(noH): 2823   0      0.00    99.33   14.93    None  None   None       |
|    Sol.    : 438    0      4.14    86.43   38.94    None  None   None       |
|    Mac.    : 2385   0      0.00    99.33   10.52    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.933: 1573   |   5:    49.663 -  59.595:   86        |
|      1:     9.933 -  19.865:  695   |   6:    59.595 -  69.528:   41        |
|      2:    19.865 -  29.798:  165   |   7:    69.528 -  79.460:   12        |
|      3:    29.798 -  39.730:  131   |   8:    79.460 -  89.393:    4        |
|      4:    39.730 -  49.663:  112   |   9:    89.393 -  99.325:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1282 r_free = 0.1723             target_work(ml) = 5.239         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1280 r_free = 0.1719             target_work(ml) = 5.238         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1280   r_free= 0.1719   ksol= 0.32   Bsol= 30.30   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.03,0.48,1.32,0.00,0.00,0.00); trace/3= 0.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.238287                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6741 -  4.6554 0.99   1375  153 0.1108 0.1335      5.4773      5.6034|
|  2:  4.6554 -  3.7149 0.99   1320  145 0.1003 0.1395       5.566      5.8389|
|  3:  3.7149 -  3.2511 0.99   1301  146 0.1243 0.1457      5.6115      5.8248|
|  4:  3.2511 -  2.9565 0.99   1285  144 0.1442 0.1874      5.5894      5.7802|
|  5:  2.9565 -  2.7461 0.99   1272  139 0.1459 0.1759      5.4111      5.5312|
|  6:  2.7461 -  2.5851 0.99   1278  143 0.1371 0.2013      5.2993      5.5068|
|  7:  2.5851 -  2.4563 0.99   1262  141 0.1352 0.1807      5.2348      5.4551|
|  8:  2.4563 -  2.3498 0.98   1265  140 0.1360 0.1877      5.1738      5.4411|
|  9:  2.3498 -  2.2597 0.98   1268  138 0.1337 0.1877      5.1138      5.3423|
| 10:  2.2597 -  2.1819 0.98   1237  137 0.1272 0.1935      5.0525      5.2741|
| 11:  2.1819 -  2.1139 0.99   1267  147 0.1304 0.1877      5.0263      5.3541|
| 12:  2.1139 -  2.0537 0.97   1249  130 0.1245 0.1729      4.9681      5.2541|
| 13:  2.0537 -  1.9997 0.99   1238  141 0.1252 0.1883      4.8783      5.1348|
| 14:  1.9997 -  1.9511 0.79   1013  115 0.1252 0.1838       4.774      5.0041|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6741 -  4.6554  1375   153  0.93  10.38   0.99     0.97       8709.16|
|  2:  4.6554 -  3.7149  1320   145  0.94   9.40   1.05     1.03      11005.96|
|  3:  3.7149 -  3.2511  1301   146  0.92  13.23   1.06     1.04      12987.88|
|  4:  3.2511 -  2.9565  1285   144  0.91  15.35   1.03     1.03      12541.19|
|  5:  2.9565 -  2.7461  1272   139  0.89  16.94   1.02     0.97       9296.00|
|  6:  2.7461 -  2.5851  1278   143  0.89  17.08   1.00     0.95       7979.00|
|  7:  2.5851 -  2.4563  1262   141  0.89  17.71   1.02     0.99       7329.28|
|  8:  2.4563 -  2.3498  1265   140  0.90  16.60   1.03     1.00       6201.34|
|  9:  2.3498 -  2.2597  1268   138  0.90  16.61   1.04     1.03       5654.75|
| 10:  2.2597 -  2.1819  1237   137  0.90  16.52   1.03     1.01       5089.88|
| 11:  2.1819 -  2.1139  1267   147  0.89  17.83   1.03     0.98       5082.75|
| 12:  2.1139 -  2.0537  1249   130  0.89  17.21   1.05     1.03       4713.13|
| 13:  2.0537 -  1.9997  1238   141  0.89  17.07   1.04     1.04       3871.68|
| 14:  1.9997 -  1.9511  1013   115  0.90  16.28   1.04     1.01       2978.29|
|alpha:            min =        0.95 max =            1.04 mean =         1.01|
|beta:             min =     2978.29 max =        12987.88 mean =      7500.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.52|
|phase err.(test): min =        0.00 max =           89.45 mean =        14.91|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1280   r_free= 0.1711   ksol= 0.32   Bsol= 30.54   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.52,-0.12,0.63,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.237648                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1280   r_free= 0.1711   ksol= 0.32   Bsol= 30.54   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.52,-0.12,0.63,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.237648                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6741 -  4.6554 0.99   1375  153 0.1102 0.1331      5.4717      5.5923|
|  2:  4.6554 -  3.7149 0.99   1320  145 0.1017 0.1385      5.5703      5.8312|
|  3:  3.7149 -  3.2511 0.99   1301  146 0.1248 0.1450      5.6141      5.8292|
|  4:  3.2511 -  2.9565 0.99   1285  144 0.1440 0.1893      5.5891      5.7853|
|  5:  2.9565 -  2.7461 0.99   1272  139 0.1454 0.1738      5.4076      5.5245|
|  6:  2.7461 -  2.5851 0.99   1278  143 0.1374 0.2008      5.2989      5.5076|
|  7:  2.5851 -  2.4563 0.99   1262  141 0.1351 0.1799      5.2344       5.456|
|  8:  2.4563 -  2.3498 0.98   1265  140 0.1359 0.1866      5.1722      5.4368|
|  9:  2.3498 -  2.2597 0.98   1268  138 0.1339 0.1869      5.1124      5.3421|
| 10:  2.2597 -  2.1819 0.98   1237  137 0.1269 0.1939      5.0505      5.2771|
| 11:  2.1819 -  2.1139 0.99   1267  147 0.1300 0.1874      5.0261      5.3525|
| 12:  2.1139 -  2.0537 0.97   1249  130 0.1246 0.1737      4.9679       5.256|
| 13:  2.0537 -  1.9997 0.99   1238  141 0.1246 0.1876      4.8776      5.1324|
| 14:  1.9997 -  1.9511 0.79   1013  115 0.1254 0.1840      4.7747      5.0046|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6741 -  4.6554  1375   153  0.93  10.09   0.99     0.97       8483.21|
|  2:  4.6554 -  3.7149  1320   145  0.94   9.37   1.04     1.02      10912.50|
|  3:  3.7149 -  3.2511  1301   146  0.92  13.24   1.05     1.04      13009.03|
|  4:  3.2511 -  2.9565  1285   144  0.91  15.29   1.02     1.02      12517.07|
|  5:  2.9565 -  2.7461  1272   139  0.89  16.90   1.00     0.96       9256.64|
|  6:  2.7461 -  2.5851  1278   143  0.89  17.02   0.99     0.94       7946.10|
|  7:  2.5851 -  2.4563  1262   141  0.89  17.65   1.00     0.97       7317.11|
|  8:  2.4563 -  2.3498  1265   140  0.90  16.56   1.01     0.99       6173.38|
|  9:  2.3498 -  2.2597  1268   138  0.90  16.58   1.02     1.01       5646.82|
| 10:  2.2597 -  2.1819  1237   137  0.90  16.52   1.02     0.99       5073.65|
| 11:  2.1819 -  2.1139  1267   147  0.89  17.83   1.01     0.96       5088.03|
| 12:  2.1139 -  2.0537  1249   130  0.89  17.20   1.03     1.01       4715.14|
| 13:  2.0537 -  1.9997  1238   141  0.89  17.09   1.02     1.02       3877.35|
| 14:  1.9997 -  1.9511  1013   115  0.90  16.28   1.01     0.99       2979.73|
|alpha:            min =        0.94 max =            1.04 mean =         0.99|
|beta:             min =     2979.73 max =        13009.03 mean =      7466.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.47|
|phase err.(test): min =        0.00 max =           88.27 mean =        14.88|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.24    99.57   15.17    None  None   None       |
|    all(noH): 2823   0      0.24    99.57   15.17    None  None   None       |
|    Sol.    : 438    0      4.38    86.67   39.18    None  None   None       |
|    Mac.    : 2385   0      0.24    99.57   10.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.241 -  10.173: 1573   |   5:    49.903 -  59.836:   86        |
|      1:    10.173 -  20.106:  695   |   6:    59.836 -  69.769:   41        |
|      2:    20.106 -  30.038:  165   |   7:    69.769 -  79.701:   12        |
|      3:    30.038 -  39.971:  131   |   8:    79.701 -  89.634:    4        |
|      4:    39.971 -  49.903:  112   |   9:    89.634 -  99.566:    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)= 335         
Filter by distance & map next to the model:
   mapped sites are within: 0.630 - 5.741
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 333 from: 335
   mapped sites are within: 0.748 - 5.741

peak=   10.483 closest distance to " CB  VAL A 230 " =    1.400
peak=   10.471 closest distance to " CB  VAL A 296 " =    1.514
peak=    6.719 closest distance to " O   HOH Z 199 " =    1.713
peak=    6.608 closest distance to " O   HOH Z 130 " =    1.382
peak=    6.528 closest distance to " O   HOH Z 381 " =    1.237
peak=    6.312 closest distance to " CD2 LEU A   5 " =    1.327
peak=    6.095 closest distance to " O   HOH Z 236 " =    1.734
peak=    5.836 closest distance to " CD1AILE A 234 " =    1.022
peak=    5.823 closest distance to " CG  ARG A 138 " =    1.065
peak=    5.813 closest distance to " O   HOH Z 193 " =    1.898
peak=    5.754 closest distance to " O   HOH Z 142 " =    1.926
peak=    5.698 closest distance to " O   HOH Z  65 " =    1.174
peak=    5.694 closest distance to " O   HOH Z 188 " =    1.544
peak=    5.600 closest distance to " O   HOH Z 205 " =    1.140
peak=    5.598 closest distance to " O   HOH Z 278 " =    2.300
peak=    5.543 closest distance to " O   HOH Z 124 " =    1.662
peak=    5.530 closest distance to " CG  ASN A  60 " =    1.258
peak=    5.472 closest distance to " O   HOH Z  69 " =    1.450
peak=    5.367 closest distance to " O   HOH Z 279 " =    1.175
peak=    5.336 closest distance to " O   HOH Z 385 " =    0.905
peak=    5.249 closest distance to " O   HOH Z  28 " =    2.007
peak=    5.223 closest distance to " NE2 GLN A  11 " =    1.131
peak=    5.126 closest distance to " O   HOH Z  78 " =    1.822
peak=    5.019 closest distance to " O   HOH Z 423 " =    1.623
peak=    4.999 closest distance to " CB  ASN A 187 " =    2.017
peak=    4.958 closest distance to " O   HOH Z 424 " =    1.326
peak=    4.927 closest distance to " NE2 GLN A  55 " =    1.509
peak=    4.903 closest distance to " CB  ARG A 275 " =    1.023
peak=    4.890 closest distance to " O   HOH Z 326 " =    1.520
peak=    4.885 closest distance to " O   HOH Z   7 " =    1.577
peak=    4.874 closest distance to " O   HOH Z 120 " =    1.162
peak=    4.819 closest distance to " O   HOH Z 260 " =    1.706
peak=    4.767 closest distance to " O   HOH Z 132 " =    1.485
peak=    4.750 closest distance to " O   HOH Z 347 " =    1.161
peak=    4.727 closest distance to " O   HOH Z 214 " =    1.496
peak=    4.721 closest distance to " O   HOH Z   9 " =    1.141
peak=    4.689 closest distance to " NH2 ARG A  56 " =    1.961
peak=    4.674 closest distance to " O   HOH Z 148 " =    2.114
peak=    4.660 closest distance to " O   HOH Z 276 " =    1.693
peak=    4.660 closest distance to " O   HOH Z  51 " =    1.698
peak=    4.603 closest distance to " O   HOH Z 410 " =    1.291
peak=    4.597 closest distance to " O   HOH Z 414 " =    1.536
peak=    4.590 closest distance to " CA  GLY A 241 " =    3.640
peak=    4.574 closest distance to " O   HOH Z 138 " =    0.955
peak=    4.553 closest distance to " O   HOH Z  97 " =    1.446
peak=    4.535 closest distance to " O   HOH Z 134 " =    1.603
peak=    4.528 closest distance to " CB  ASN A  60 " =    0.923
peak=    4.485 closest distance to " O   HOH Z 427 " =    2.373
peak=    4.477 closest distance to " O   HOH Z 202 " =    1.456
peak=    4.450 closest distance to " O   HOH Z 269 " =    1.405
peak=    4.449 closest distance to " CG  LEU A   5 " =    1.224
peak=    4.433 closest distance to " O   HOH Z 100 " =    1.311
peak=    4.408 closest distance to " O   HOH Z 344 " =    1.412
peak=    4.395 closest distance to " O   HOH Z 263 " =    1.489
peak=    4.322 closest distance to " O   HOH Z 373 " =    2.085
peak=    4.322 closest distance to " O   HOH Z 316 " =    2.482
peak=    4.321 closest distance to " O   HOH Z 117 " =    1.390
peak=    4.276 closest distance to " O   HOH Z 203 " =    1.424
peak=    4.262 closest distance to " O   HOH Z  59 " =    1.820
peak=    4.251 closest distance to " O   HOH Z 273 " =    1.111
peak=    4.193 closest distance to " CG  GLN A  88 " =    1.080
peak=    4.188 closest distance to " CG2 ILE A 234 " =    0.938
peak=    4.183 closest distance to " O   HOH Z 146 " =    1.675
peak=    4.182 closest distance to " CG  PRO A  54 " =    1.190
peak=    4.168 closest distance to " O   HOH Z 284 " =    1.655
peak=    4.158 closest distance to " CD2 LEU A 228 " =    1.231
peak=    4.156 closest distance to " O   PRO A 198 " =    1.286
peak=    4.145 closest distance to " O   HOH Z 194 " =    1.587
peak=    4.113 closest distance to " CB  SER A   3 " =    1.223
peak=    4.106 closest distance to " CD  GLN A  58 " =    5.556
peak=    4.094 closest distance to " O   HOH Z 249 " =    1.208
peak=    4.080 closest distance to " O   HOH Z 152 " =    2.644
peak=    4.073 closest distance to " O   HOH Z 357 " =    1.789
peak=    4.071 closest distance to " NH2BARG A 190 " =    1.568
peak=    4.064 closest distance to " O   HOH Z 375 " =    1.142
peak=    4.059 closest distance to " CB  PRO A  54 " =    0.999
peak=    4.050 closest distance to " CB  VAL A 230 " =    1.131
peak=    4.042 closest distance to " CB  VAL A 265 " =    1.281
peak=    4.020 closest distance to " O   HOH Z  11 " =    1.549
peak=    3.996 closest distance to " O   SER A  87 " =    2.362
peak=    3.989 closest distance to " CB  ASN A 148 " =    1.254
peak=    3.982 closest distance to " O   HOH Z 227 " =    2.086
peak=    3.975 closest distance to " O   HOH Z 423 " =    1.735
peak=    3.973 closest distance to " CB  GLN A 223 " =    1.540
peak=    3.946 closest distance to " O   HOH Z 217 " =    1.758
peak=    3.929 closest distance to " CG  PRO A 243 " =    1.310
peak=    3.917 closest distance to " O   HOH Z 366 " =    2.475
peak=    3.912 closest distance to " CE AMET A  47 " =    1.300
peak=    3.901 closest distance to " O   HOH Z 287 " =    1.626
peak=    3.893 closest distance to " O   HOH Z 272 " =    1.799
peak=    3.866 closest distance to " CG  PRO A 213 " =    1.194
peak=    3.864 closest distance to " NH1 ARG A  14 " =    0.951
peak=    3.859 closest distance to " O   HOH Z  58 " =    1.683
peak=    3.854 closest distance to " O   HOH Z  28 " =    1.714
peak=    3.852 closest distance to " NH1 ARG A 138 " =    1.140
peak=    3.850 closest distance to " O   HOH Z 156 " =    2.747
peak=    3.848 closest distance to " O   HOH Z 403 " =    2.110
peak=    3.839 closest distance to " O   HOH Z 108 " =    1.313
peak=    3.826 closest distance to " CA  ILE A 234 " =    0.927
peak=    3.814 closest distance to " O   HOH Z 406 " =    1.213
peak=    3.814 closest distance to " O   HOH Z 426 " =    1.219
peak=    3.811 closest distance to " O   HOH Z  89 " =    1.550
peak=    3.809 closest distance to " OG ASER A 134 " =    1.853
peak=    3.800 closest distance to " CB  GLN A 183 " =    1.188
peak=    3.787 closest distance to " CB  PRO A 198 " =    1.074
peak=    3.780 closest distance to " O   HOH Z 302 " =    1.444
peak=    3.778 closest distance to " O   HOH Z  44 " =    2.004
peak=    3.772 closest distance to " O   HOH Z  93 " =    2.078
peak=    3.769 closest distance to " O   HOH Z   1 " =    1.685
peak=    3.768 closest distance to " O   HOH Z 389 " =    1.449
peak=    3.760 closest distance to " O   HOH Z  43 " =    1.478
peak=    3.758 closest distance to " OD2 ASP A 286 " =    2.388
peak=    3.757 closest distance to " O   HOH Z 130 " =    2.024
peak=    3.752 closest distance to " O   HOH Z 251 " =    1.765
peak=    3.748 closest distance to " O   HOH Z  80 " =    1.974
peak=    3.746 closest distance to " O   HOH Z 143 " =    1.378
peak=    3.746 closest distance to " O   HOH Z 253 " =    1.611
peak=    3.742 closest distance to " CA  ASN A 284 " =    1.035
peak=    3.738 closest distance to " O   HOH Z  80 " =    1.981
peak=    3.730 closest distance to " CG  PRO A 163 " =    3.508
peak=    3.726 closest distance to " O   HOH Z 130 " =    2.075
peak=    3.718 closest distance to " CD  ARG A 269 " =    0.996
peak=    3.706 closest distance to " O   HOH Z  63 " =    1.318
peak=    3.700 closest distance to " O   HOH Z 112 " =    1.032
peak=    3.700 closest distance to " O   HOH Z 108 " =    1.670
peak=    3.699 closest distance to " CB  ARG A 102 " =    0.825
peak=    3.688 closest distance to " O   HOH Z 361 " =    1.651
peak=    3.680 closest distance to " O   HOH Z 366 " =    1.919
peak=    3.678 closest distance to " NE2 GLN A 223 " =    1.682
peak=    3.673 closest distance to " O   HOH Z  59 " =    2.080
peak=    3.666 closest distance to " O   HOH Z 232 " =    2.214
peak=    3.665 closest distance to " O   HOH Z 356 " =    1.577
peak=    3.654 closest distance to " CD1 LEU A   5 " =    1.873
peak=    3.649 closest distance to " O   HOH Z 291 " =    1.470
peak=    3.648 closest distance to " O   HOH Z 147 " =    1.432
peak=    3.644 closest distance to " O   HOH Z  95 " =    1.671
peak=    3.643 closest distance to " O   HOH Z 234 " =    3.181
peak=    3.638 closest distance to " O   HOH Z   6 " =    1.511
peak=    3.637 closest distance to " O   HOH Z 214 " =    1.699
peak=    3.628 closest distance to " O   HOH Z 153 " =    1.676
peak=    3.620 closest distance to " OE1 GLU A  44 " =    1.270
peak=    3.619 closest distance to " CG  LEU A 228 " =    1.010
peak=    3.614 closest distance to " N   PHE A 130 " =    1.343
peak=    3.607 closest distance to " CG  PRO A 198 " =    1.339
peak=    3.605 closest distance to " O   HOH Z 250 " =    1.479
peak=    3.604 closest distance to " O   HOH Z  24 " =    1.351
peak=    3.585 closest distance to " CE1 PHE A  61 " =    1.233
peak=    3.583 closest distance to " O   HOH Z 371 " =    1.604
peak=    3.581 closest distance to " O   HOH Z 233 " =    1.709
peak=    3.579 closest distance to " O   HOH Z 402 " =    1.651
peak=    3.579 closest distance to " O   HOH Z 189 " =    2.168
peak=    3.564 closest distance to " O   HOH Z 123 " =    1.182
peak=    3.560 closest distance to " NE BARG A 275 " =    1.099
peak=    3.560 closest distance to " CB  VAL A 202 " =    1.615
peak=    3.559 closest distance to " CG1BVAL A 121 " =    1.001
peak=    3.557 closest distance to " O   HOH Z 136 " =    1.012
peak=    3.557 closest distance to " CG  TRP A 179 " =    2.168
peak=    3.554 closest distance to " CB  ALA A   1 " =    1.026
peak=    3.554 closest distance to " O   HOH Z 145 " =    2.091
peak=    3.547 closest distance to " CD1 LEU A 228 " =    1.536
peak=    3.539 closest distance to " CB  ARG A  79 " =    1.523
peak=    3.527 closest distance to " CD1 ILE A  33 " =    1.599
peak=    3.521 closest distance to " CG1BVAL A  72 " =    1.195
peak=    3.520 closest distance to " OE1 GLN A  77 " =    1.327
peak=    3.520 closest distance to " CB  TRP A 179 " =    1.071
peak=    3.519 closest distance to " O   LYS A 290 " =    2.363
peak=    3.518 closest distance to " CG  LYS A 119 " =    1.091
peak=    3.512 closest distance to " O   HOH Z 327 " =    1.589
peak=    3.512 closest distance to " CG  ARG A  66 " =    1.122
peak=    3.510 closest distance to " O   HOH Z 395 " =    1.584
peak=    3.509 closest distance to " CB  GLN A 278 " =    0.769
peak=    3.509 closest distance to " O   HOH Z  61 " =    1.513
peak=    3.505 closest distance to " O   HOH Z 346 " =    1.512
peak=    3.503 closest distance to " CB  ASP A 200 " =    1.023
peak=    3.502 closest distance to " O   HOH Z 280 " =    1.641
peak=    3.501 closest distance to " O   HOH Z 419 " =    1.821
peak=    3.498 closest distance to " O   HOH Z  89 " =    2.353
peak=    3.493 closest distance to " O   HOH Z 191 " =    2.004
peak=    3.491 closest distance to " NH2 ARG A 219 " =    1.881
peak=    3.482 closest distance to " CG1 VAL A 153 " =    0.869
peak=    3.473 closest distance to " CA  VAL A 126 " =    1.042
peak=    3.473 closest distance to " O   HOH Z 134 " =    1.968
peak=    3.473 closest distance to " CA  ALA A  51 " =    0.967
peak=    3.468 closest distance to " O   HOH Z 435 " =    1.861
peak=    3.458 closest distance to " O   HOH Z 137 " =    1.576
peak=    3.456 closest distance to " O   HOH Z 305 " =    3.072
peak=    3.453 closest distance to " CA  ASN A 127 " =    1.019
peak=    3.453 closest distance to " NE1 TRP A 274 " =    0.946
peak=    3.453 closest distance to " O   HOH Z  37 " =    1.236
peak=    3.450 closest distance to " OE1 GLN A  58 " =    1.355
peak=    3.442 closest distance to " O   HOH Z 344 " =    2.805
peak=    3.441 closest distance to " O   HOH Z 128 " =    1.948
peak=    3.440 closest distance to " CB  LEU A 255 " =    0.846
peak=    3.438 closest distance to " O   HOH Z 261 " =    1.701
peak=    3.438 closest distance to " CA  LEU A 282 " =    1.332
peak=    3.433 closest distance to " OG  SER A  62 " =    3.123
peak=    3.432 closest distance to " O   HOH Z 380 " =    1.609
peak=    3.430 closest distance to " O   HOH Z 176 " =    1.633
peak=    3.415 closest distance to " CA  ARG A  66 " =    0.891
peak=    3.412 closest distance to " O   HOH Z 303 " =    1.823
peak=    3.409 closest distance to " OD1 ASN A  69 " =    2.947
peak=    3.409 closest distance to " CE  MET A  40 " =    1.078
peak=    3.402 closest distance to " O   HOH Z 183 " =    1.774
peak=    3.396 closest distance to " NE2 GLN A 278 " =    3.589
peak=    3.394 closest distance to " CA  TYR A 214 " =    1.394
peak=    3.393 closest distance to " O   HOH Z 366 " =    2.956
peak=    3.393 closest distance to " N   ASN A  60 " =    0.977
peak=    3.393 closest distance to " O   HOH Z  13 " =    1.767
peak=    3.383 closest distance to " O   HOH Z 269 " =    2.799
peak=    3.383 closest distance to " O   HOH Z 417 " =    2.973
peak=    3.381 closest distance to " CG2 VAL A 257 " =    0.929
peak=    3.375 closest distance to " CA  THR A 264 " =    0.835
peak=    3.375 closest distance to " CG2 THR A 221 " =    1.227
peak=    3.372 closest distance to " OE1 GLU A   2 " =    2.102
peak=    3.364 closest distance to " NH1BARG A 145 " =    1.608
peak=    3.364 closest distance to " O   HOH Z  88 " =    2.372
peak=    3.357 closest distance to " O   HOH Z 193 " =    1.860
peak=    3.355 closest distance to " NH2BARG A 145 " =    1.500
peak=    3.354 closest distance to " CA  TYR A  30 " =    1.124
peak=    3.352 closest distance to " CB  SER A  26 " =    1.477
peak=    3.350 closest distance to " CB  SER A  63 " =    1.221
peak=    3.347 closest distance to " CA  ALA A 299 " =    0.972
peak=    3.347 closest distance to " CA  ALA A  21 " =    1.111
peak=    3.346 closest distance to " CG  LYS A 166 " =    1.383
peak=    3.345 closest distance to " NH2BARG A 145 " =    2.348
peak=    3.344 closest distance to " O   HOH Z 438 " =    2.413
peak=    3.341 closest distance to " OG1 THR A 294 " =    1.769
peak=    3.340 closest distance to " O   HOH Z 433 " =    1.992
peak=    3.340 closest distance to " O   HOH Z 156 " =    2.321
peak=    3.339 closest distance to " O   HOH Z 390 " =    1.159
peak=    3.337 closest distance to " NE2 HIS A 115 " =    0.982
peak=    3.331 closest distance to " O   HOH Z   9 " =    2.145
peak=    3.331 closest distance to " O   HOH Z 422 " =    2.463
peak=    3.331 closest distance to " O   HOH Z 222 " =    1.220
peak=    3.328 closest distance to " CG  LYS A  76 " =    1.427
peak=    3.326 closest distance to " CE BLYS A 290 " =    1.019
peak=    3.326 closest distance to " CG  LEU A 167 " =    1.105
peak=    3.321 closest distance to " O   HOH Z 400 " =    0.758
peak=    3.316 closest distance to " O   HOH Z  88 " =    2.870
peak=    3.313 closest distance to " O   HOH Z  28 " =    1.704
peak=    3.310 closest distance to " SD BMET A  47 " =    1.595
peak=    3.310 closest distance to " CB  PHE A 225 " =    1.258
peak=    3.309 closest distance to " O   HOH Z 255 " =    1.935
peak=    3.308 closest distance to " O   HOH Z 392 " =    1.384
peak=    3.302 closest distance to " CD  LYS A 119 " =    1.747
peak=    3.299 closest distance to " NH2 ARG A 156 " =    1.053
peak=    3.296 closest distance to " O   HOH Z 180 " =    2.139
peak=    3.296 closest distance to " CD AARG A 145 " =    1.113
peak=    3.295 closest distance to " O   HOH Z 247 " =    1.278
peak=    3.293 closest distance to " CB  SER A 216 " =    0.831
peak=    3.288 closest distance to " NZ  LYS A  48 " =    1.757
peak=    3.287 closest distance to " CA  LYS A 117 " =    1.215
peak=    3.286 closest distance to " O   SER A  26 " =    1.640
peak=    3.286 closest distance to " CB  PHE A  61 " =    1.295
peak=    3.286 closest distance to " N   GLY A 111 " =    1.170
peak=    3.282 closest distance to " OG BSER A 134 " =    3.020
peak=    3.280 closest distance to " O   HOH Z 281 " =    1.985
peak=    3.278 closest distance to " O   HOH Z 142 " =    1.782
peak=    3.276 closest distance to " CB  ASN A 148 " =    1.881
peak=    3.275 closest distance to " O   HOH Z  69 " =    2.250
peak=    3.271 closest distance to " CB  ALA A 114 " =    1.423
peak=    3.265 closest distance to " CA  ASN A 176 " =    1.556
peak=    3.265 closest distance to " O   HOH Z  47 " =    1.558
peak=    3.260 closest distance to " O   HOH Z 329 " =    1.563
peak=    3.252 closest distance to " O   HOH Z 193 " =    1.973
peak=    3.250 closest distance to " O   HOH Z 332 " =    1.435
peak=    3.249 closest distance to " O   HOH Z 114 " =    2.114
peak=    3.249 closest distance to " O   GLY A 147 " =    1.511
peak=    3.244 closest distance to " O   HOH Z 364 " =    1.800
peak=    3.241 closest distance to " O   HOH Z 394 " =    1.493
peak=    3.240 closest distance to " O   HOH Z 234 " =    2.065
peak=    3.238 closest distance to " CB  TYR A 169 " =    0.975
peak=    3.234 closest distance to " CG  MET A 188 " =    1.091
peak=    3.233 closest distance to " CE BMET A  47 " =    0.894
peak=    3.229 closest distance to " OD1 ASP A 286 " =    1.231
peak=    3.228 closest distance to " CB  VAL A 121 " =    1.010
peak=    3.226 closest distance to " CD1 LEU A 228 " =    1.687
peak=    3.223 closest distance to " O   HOH Z 126 " =    2.105
peak=    3.223 closest distance to " CG  GLN A  77 " =    2.183
peak=    3.222 closest distance to " O   HOH Z 215 " =    1.548
peak=    3.221 closest distance to " O   PHE A  38 " =    2.079
peak=    3.218 closest distance to " O   HOH Z 367 " =    3.939
peak=    3.217 closest distance to " CB  GLU A 277 " =    3.577
peak=    3.216 closest distance to " O   HOH Z 328 " =    1.775
peak=    3.212 closest distance to " CB  ALA A   1 " =    4.272
peak=    3.212 closest distance to " NH2AARG A 190 " =    1.457
peak=    3.203 closest distance to " O   HOH Z 425 " =    1.557
peak=    3.202 closest distance to " O   HOH Z 389 " =    2.886
peak=    3.202 closest distance to " O   HOH Z 427 " =    1.271
peak=    3.202 closest distance to " CB  ASN A  69 " =    1.524
peak=    3.200 closest distance to " CA  ARG A 195 " =    1.130
peak=    3.199 closest distance to " CG  GLN A  89 " =    1.368
peak=    3.199 closest distance to " O   HOH Z 244 " =    1.590
peak=    3.197 closest distance to " O   HOH Z  94 " =    1.709
peak=    3.193 closest distance to " CB  ASN A 142 " =    1.064
peak=    3.191 closest distance to " O   SER A 164 " =    1.373
peak=    3.191 closest distance to " O   HOH Z 409 " =    1.722
peak=    3.190 closest distance to " N   PHE A  59 " =    0.986
peak=    3.190 closest distance to " O   HOH Z 133 " =    1.264
peak=    3.186 closest distance to " O   HOH Z 388 " =    1.000
peak=    3.186 closest distance to " O   HOH Z 184 " =    1.421
peak=    3.186 closest distance to " O   HOH Z   5 " =    1.272
peak=    3.185 closest distance to " N   ASN A 209 " =    1.608
peak=    3.184 closest distance to " CA  GLN A 194 " =    0.919
peak=    3.176 closest distance to " O   HOH Z 365 " =    5.741
peak=    3.174 closest distance to " O   HOH Z 245 " =    1.386
peak=    3.172 closest distance to " O   HOH Z 383 " =    2.001
peak=    3.168 closest distance to " O   HOH Z 222 " =    2.092
peak=    3.165 closest distance to " CB  MET A  40 " =    0.994
peak=    3.157 closest distance to " O   HOH Z 259 " =    1.520
peak=    3.157 closest distance to " O   HOH Z 272 " =    2.179
peak=    3.155 closest distance to " O   HOH Z 196 " =    1.513
peak=    3.133 closest distance to " O   HOH Z 284 " =    1.360
peak=    3.127 closest distance to " O   GLY A  57 " =    2.342
peak=    3.124 closest distance to " NH1 ARG A  66 " =    2.495
peak=    3.122 closest distance to " O   HOH Z 141 " =    1.559
peak=    3.121 closest distance to " NE2 GLN A  73 " =    1.789
peak=    3.114 closest distance to " O   HOH Z   1 " =    1.582
peak=    3.111 closest distance to " CE  LYS A 119 " =    1.248
peak=    3.111 closest distance to " O   HOH Z 222 " =    2.096
peak=    3.099 closest distance to " O   HOH Z 413 " =    1.424
peak=    3.094 closest distance to " O   HOH Z  43 " =    2.789
peak=    3.093 closest distance to " CZ2 TRP A 274 " =    1.857
peak=    3.088 closest distance to " O   HOH Z 213 " =    1.820
peak=    3.080 closest distance to " CB  TYR A  30 " =    1.689
peak=    3.068 closest distance to " CD2 LEU A 297 " =    1.017
peak=    3.063 closest distance to " NH1AARG A 145 " =    0.748
peak=    3.058 closest distance to " O   HOH Z 143 " =    2.248
peak=    3.052 closest distance to " O   HOH Z 417 " =    2.384
peak=    3.050 closest distance to " CB  THR A  52 " =    1.088
peak=    3.047 closest distance to " N   GLU A 236 " =    0.950
peak=    3.036 closest distance to " CG AARG A 102 " =    2.239
peak=    3.032 closest distance to " O   HOH Z  73 " =    3.368

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.534 - 5.285
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 198
   mapped sites are within: 0.714 - 5.285

peak=   -4.812 closest distance to " N   GLN A  58 " =    1.013
peak=   -4.473 closest distance to " NH2 ARG A  79 " =    1.846
peak=   -4.400 closest distance to " O   HOH Z 347 " =    0.818
peak=   -4.310 closest distance to " N   HIS A 115 " =    2.026
peak=   -4.268 closest distance to " SG  CYS A 254 " =    3.150
peak=   -4.263 closest distance to " CG  GLN A  88 " =    0.957
peak=   -4.215 closest distance to " C   HIS A 108 " =    1.268
peak=   -4.147 closest distance to " O   HOH Z 419 " =    0.908
peak=   -4.142 closest distance to " C   ASN A 285 " =    1.998
peak=   -4.105 closest distance to " O   HOH Z 164 " =    5.285
peak=   -4.104 closest distance to " CE2 TYR A  30 " =    2.835
peak=   -4.081 closest distance to " O   HOH Z  69 " =    1.475
peak=   -4.046 closest distance to " CD  ARG A 156 " =    2.058
peak=   -4.023 closest distance to " O   PRO A 163 " =    1.814
peak=   -3.952 closest distance to " CG2AVAL A  41 " =    2.908
peak=   -3.952 closest distance to " N   MET A 188 " =    1.724
peak=   -3.938 closest distance to " CA  GLY A  23 " =    1.763
peak=   -3.915 closest distance to " O   HOH Z 385 " =    1.314
peak=   -3.909 closest distance to " CD  GLU A 152 " =    2.525
peak=   -3.905 closest distance to " O   PRO A 198 " =    1.063
peak=   -3.880 closest distance to " OG BSER A 134 " =    1.240
peak=   -3.877 closest distance to " O   HOH Z  24 " =    1.302
peak=   -3.866 closest distance to " O   HOH Z  88 " =    2.350
peak=   -3.865 closest distance to " CB  ALA A 100 " =    2.507
peak=   -3.863 closest distance to " N   GLN A  58 " =    2.313
peak=   -3.851 closest distance to " N   THR A  52 " =    1.725
peak=   -3.824 closest distance to " O   HOH Z 290 " =    1.067
peak=   -3.824 closest distance to " CA  VAL A  67 " =    2.864
peak=   -3.802 closest distance to " O   HOH Z  93 " =    1.442
peak=   -3.788 closest distance to " O   HOH Z 193 " =    1.372
peak=   -3.765 closest distance to " O   HOH Z 407 " =    2.714
peak=   -3.755 closest distance to " CG  PHE A 283 " =    2.410
peak=   -3.741 closest distance to " CD  ARG A  14 " =    2.831
peak=   -3.737 closest distance to " O   HOH Z 266 " =    4.358
peak=   -3.716 closest distance to " CB  ALA A 248 " =    1.920
peak=   -3.699 closest distance to " CG2 THR A  52 " =    3.044
peak=   -3.694 closest distance to " OG  SER A   3 " =    1.283
peak=   -3.694 closest distance to " CG1 ILE A 234 " =    1.669
peak=   -3.687 closest distance to " CG  ARG A 138 " =    0.932
peak=   -3.683 closest distance to " CG2 THR A  52 " =    2.985
peak=   -3.651 closest distance to " O   HOH Z 385 " =    2.083
peak=   -3.643 closest distance to " O   HOH Z 365 " =    1.230
peak=   -3.641 closest distance to " OD1 ASN A  39 " =    2.074
peak=   -3.633 closest distance to " O   HOH Z 117 " =    1.139
peak=   -3.632 closest distance to " CD2 LEU A   5 " =    0.940
peak=   -3.616 closest distance to " O   HOH Z 250 " =    1.202
peak=   -3.604 closest distance to " O   ALA A 161 " =    1.586
peak=   -3.601 closest distance to " ND1 HIS A 115 " =    0.899
peak=   -3.597 closest distance to " O   SER A 273 " =    1.509
peak=   -3.596 closest distance to " CB  ALA A   7 " =    1.987
peak=   -3.576 closest distance to " CE2 PHE A 218 " =    2.635
peak=   -3.568 closest distance to " O   MET A  40 " =    2.885
peak=   -3.567 closest distance to " CB  ALA A 244 " =    2.125
peak=   -3.563 closest distance to " OD1 ASN A 301 " =    1.944
peak=   -3.562 closest distance to " O   HOH Z 131 " =    3.783
peak=   -3.540 closest distance to " CG2 THR A   4 " =    1.842
peak=   -3.534 closest distance to " O   HOH Z  98 " =    1.575
peak=   -3.525 closest distance to " O   ALA A  51 " =    1.260
peak=   -3.524 closest distance to " O   HOH Z 423 " =    2.395
peak=   -3.512 closest distance to " CG  PRO A 243 " =    1.080
peak=   -3.510 closest distance to " OG ASER A 134 " =    0.884
peak=   -3.510 closest distance to " O   SER A 135 " =    1.461
peak=   -3.509 closest distance to " NE2 GLN A  58 " =    1.737
peak=   -3.503 closest distance to " N   GLN A  88 " =    1.589
peak=   -3.497 closest distance to " O   HOH Z 426 " =    2.129
peak=   -3.495 closest distance to " O   HOH Z 308 " =    1.676
peak=   -3.494 closest distance to " CG1 VAL A 197 " =    1.724
peak=   -3.485 closest distance to " NE1 TRP A 274 " =    1.226
peak=   -3.484 closest distance to " O   PRO A 163 " =    1.340
peak=   -3.483 closest distance to " O   HOH Z 385 " =    1.419
peak=   -3.481 closest distance to " O   HOH Z  56 " =    1.731
peak=   -3.480 closest distance to " CD1 ILE A 239 " =    2.481
peak=   -3.479 closest distance to " O   HOH Z 211 " =    1.428
peak=   -3.477 closest distance to " C   ASP A 231 " =    2.345
peak=   -3.467 closest distance to " O   HOH Z 191 " =    4.896
peak=   -3.463 closest distance to " CG  LEU A 228 " =    0.980
peak=   -3.458 closest distance to " NH2AARG A 275 " =    4.791
peak=   -3.452 closest distance to " O   HOH Z 116 " =    1.214
peak=   -3.452 closest distance to " CD  LYS A 289 " =    2.553
peak=   -3.451 closest distance to " O   HOH Z  63 " =    1.113
peak=   -3.450 closest distance to " OE1 GLU A 277 " =    2.154
peak=   -3.446 closest distance to " O   HOH Z 138 " =    0.922
peak=   -3.439 closest distance to " N   GLN A  77 " =    1.536
peak=   -3.437 closest distance to " O   HOH Z 235 " =    1.084
peak=   -3.432 closest distance to " OG BSER A  99 " =    1.001
peak=   -3.425 closest distance to " CD1 LEU A 228 " =    1.965
peak=   -3.412 closest distance to " OG1 THR A 246 " =    1.206
peak=   -3.410 closest distance to " OD1 ASN A  60 " =    0.794
peak=   -3.410 closest distance to " CG  ARG A 219 " =    2.459
peak=   -3.408 closest distance to " O   HOH Z 166 " =    1.746
peak=   -3.401 closest distance to " OXT GLY A 302 " =    2.777
peak=   -3.399 closest distance to " CD1 LEU A 255 " =    2.790
peak=   -3.398 closest distance to " O   HOH Z 134 " =    2.523
peak=   -3.398 closest distance to " CG  PRO A 163 " =    2.716
peak=   -3.393 closest distance to " O   SER A 245 " =    1.376
peak=   -3.391 closest distance to " CG  ASP A  50 " =    2.224
peak=   -3.390 closest distance to " CD2 LEU A 237 " =    2.590
peak=   -3.389 closest distance to " C   ILE A 239 " =    2.078
peak=   -3.387 closest distance to " O   HOH Z 188 " =    4.099
peak=   -3.386 closest distance to " O   HOH Z 175 " =    1.053
peak=   -3.379 closest distance to " O   HOH Z 284 " =    0.741
peak=   -3.379 closest distance to " OG1 THR A 178 " =    1.075
peak=   -3.368 closest distance to " O   HOH Z 260 " =    0.929
peak=   -3.365 closest distance to " OD2 ASP A  50 " =    1.372
peak=   -3.364 closest distance to " O   HOH Z  70 " =    1.267
peak=   -3.363 closest distance to " CD  PRO A 198 " =    1.369
peak=   -3.362 closest distance to " O   HOH Z 388 " =    1.902
peak=   -3.359 closest distance to " O   HOH Z 393 " =    3.318
peak=   -3.356 closest distance to " O   HOH Z 137 " =    1.498
peak=   -3.354 closest distance to " O   HOH Z 205 " =    1.001
peak=   -3.352 closest distance to " CA  GLY A 133 " =    1.847
peak=   -3.345 closest distance to " OE2 GLU A   2 " =    0.990
peak=   -3.345 closest distance to " O   HOH Z   9 " =    1.398
peak=   -3.345 closest distance to " O   HOH Z 120 " =    0.994
peak=   -3.344 closest distance to " O   HOH Z 427 " =    1.607
peak=   -3.322 closest distance to " O   GLU A  44 " =    1.781
peak=   -3.320 closest distance to " O   SER A  22 " =    2.361
peak=   -3.308 closest distance to " CD  ARG A 219 " =    2.465
peak=   -3.305 closest distance to " N   THR A 235 " =    1.516
peak=   -3.302 closest distance to " O   HOH Z 220 " =    1.138
peak=   -3.295 closest distance to " O   HOH Z  37 " =    1.373
peak=   -3.294 closest distance to " O   ARG A 145 " =    1.369
peak=   -3.289 closest distance to " O   GLY A 118 " =    1.350
peak=   -3.288 closest distance to " O   VAL A 197 " =    1.270
peak=   -3.287 closest distance to " O   HOH Z 414 " =    1.044
peak=   -3.284 closest distance to " CE3 TRP A 274 " =    2.403
peak=   -3.278 closest distance to " OD2 ASP A 191 " =    1.374
peak=   -3.275 closest distance to " O   HOH Z 100 " =    1.082
peak=   -3.275 closest distance to " O   HOH Z 192 " =    2.383
peak=   -3.271 closest distance to " N   ALA A 248 " =    1.773
peak=   -3.270 closest distance to " CG2 THR A 220 " =    2.608
peak=   -3.269 closest distance to " O   HOH Z 350 " =    2.169
peak=   -3.264 closest distance to " O   HOH Z 313 " =    1.603
peak=   -3.263 closest distance to " C   LEU A 143 " =    1.197
peak=   -3.263 closest distance to " CG  ASP A 231 " =    0.830
peak=   -3.261 closest distance to " O   HOH Z 414 " =    2.535
peak=   -3.256 closest distance to " CB  TRP A 274 " =    2.680
peak=   -3.256 closest distance to " ND2 ASN A  45 " =    1.644
peak=   -3.255 closest distance to " O   HOH Z 429 " =    1.634
peak=   -3.254 closest distance to " O   ASP A 270 " =    1.801
peak=   -3.249 closest distance to " O   HOH Z 372 " =    2.370
peak=   -3.240 closest distance to " O   SER A 146 " =    0.880
peak=   -3.238 closest distance to " O   ASN A 187 " =    1.344
peak=   -3.235 closest distance to " C   GLN A 205 " =    1.908
peak=   -3.234 closest distance to " CA  GLY A  35 " =    2.073
peak=   -3.231 closest distance to " O   HOH Z 231 " =    1.573
peak=   -3.226 closest distance to " CB  ASP A  27 " =    2.381
peak=   -3.223 closest distance to " CD  GLU A 277 " =    0.893
peak=   -3.217 closest distance to " ND2 ASN A 209 " =    1.833
peak=   -3.216 closest distance to " O   HOH Z 366 " =    1.213
peak=   -3.215 closest distance to " N   PRO A 163 " =    1.472
peak=   -3.209 closest distance to " CG  PRO A 198 " =    1.666
peak=   -3.208 closest distance to " CE3 TRP A 150 " =    1.915
peak=   -3.202 closest distance to " O   HOH Z 145 " =    2.668
peak=   -3.202 closest distance to " O   HOH Z 130 " =    2.092
peak=   -3.200 closest distance to " O   HOH Z 153 " =    1.635
peak=   -3.197 closest distance to " CG  ASN A  45 " =    1.528
peak=   -3.196 closest distance to " CG BARG A 275 " =    0.952
peak=   -3.194 closest distance to " N   PHE A  59 " =    1.230
peak=   -3.187 closest distance to " O   HOH Z 234 " =    3.819
peak=   -3.182 closest distance to " OD1 ASP A 191 " =    1.883
peak=   -3.173 closest distance to " CZ3 TRP A 274 " =    1.047
peak=   -3.171 closest distance to " O   HOH Z 385 " =    1.078
peak=   -3.168 closest distance to " CG  GLN A 223 " =    1.452
peak=   -3.163 closest distance to " O   HOH Z 430 " =    1.972
peak=   -3.161 closest distance to " O   HOH Z 431 " =    1.327
peak=   -3.157 closest distance to " O   HOH Z 283 " =    1.213
peak=   -3.154 closest distance to " OD2 ASP A 270 " =    1.232
peak=   -3.152 closest distance to " CG2 THR A 264 " =    2.087
peak=   -3.148 closest distance to " OD1 ASP A 200 " =    1.084
peak=   -3.146 closest distance to " O   HOH Z 198 " =    1.625
peak=   -3.141 closest distance to " O   HOH Z  64 " =    0.946
peak=   -3.139 closest distance to " O   HOH Z 102 " =    1.771
peak=   -3.136 closest distance to " CA  SER A 245 " =    2.222
peak=   -3.129 closest distance to " O   ASN A 215 " =    1.469
peak=   -3.125 closest distance to " N   LYS A 166 " =    1.851
peak=   -3.116 closest distance to " O   HOH Z 122 " =    1.869
peak=   -3.113 closest distance to " CZ  PHE A 130 " =    2.185
peak=   -3.112 closest distance to " O   HOH Z 438 " =    0.849
peak=   -3.112 closest distance to " O   HOH Z 377 " =    0.887
peak=   -3.102 closest distance to " O   HOH Z  54 " =    0.967
peak=   -3.072 closest distance to " O   ASP A 191 " =    1.355
peak=   -3.069 closest distance to " CE1 TYR A 247 " =    2.285
peak=   -3.066 closest distance to " O   HOH Z 155 " =    1.100
peak=   -3.065 closest distance to " O   HOH Z 331 " =    1.044
peak=   -3.062 closest distance to " O   HOH Z 377 " =    0.714
peak=   -3.056 closest distance to " CB  ILE A  33 " =    2.841
peak=   -3.050 closest distance to " O   HOH Z  89 " =    1.024
peak=   -3.050 closest distance to " N   GLN A 223 " =    1.511
peak=   -3.047 closest distance to " O   ASN A 127 " =    1.523
peak=   -3.025 closest distance to " O   HOH Z  93 " =    1.912
peak=   -3.019 closest distance to " CG2 THR A 279 " =    2.146
peak=   -3.012 closest distance to " N   GLY A 302 " =    1.627

================= 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    :  0.5160 0.5078   6.305865e+00   6.300266e+00
   1_bss:  0.5084 0.4982   6.300761e+00   6.290262e+00
   1_xyz:  0.4473 0.4652   6.241234e+00   6.261851e+00
   1_adp:  0.4074 0.4605   6.196567e+00   6.255303e+00
   1_occ:  0.4068 0.4616   6.196233e+00   6.255588e+00
   2_bss:  0.4055 0.4586   6.196315e+00   6.253951e+00
   2_xyz:  0.3452 0.4093   6.080783e+00   6.187671e+00
   2_adp:  0.3278 0.3942   6.048829e+00   6.162533e+00
   2_occ:  0.3273 0.3945   6.048704e+00   6.163076e+00
   3_bss:  0.3260 0.3958   6.048821e+00   6.163374e+00
   3_xyz:  0.2531 0.3154   5.839823e+00   6.004448e+00
   3_adp:  0.2220 0.2941   5.747694e+00   5.950216e+00
   3_occ:  0.2216 0.2936   5.746540e+00   5.948876e+00
   4_bss:  0.2207 0.2937   5.742975e+00   5.945056e+00
   4_xyz:  0.1750 0.2368   5.537092e+00   5.761816e+00
   4_adp:  0.1675 0.2169   5.476608e+00   5.676480e+00
   4_occ:  0.1670 0.2159   5.473611e+00   5.672481e+00
   5_bss:  0.1665 0.2142   5.472517e+00   5.669704e+00
   5_xyz:  0.1365 0.1807   5.294238e+00   5.511551e+00
   5_adp:  0.1282 0.1723   5.239356e+00   5.464910e+00
   5_occ:  0.1280 0.1719   5.238287e+00   5.463673e+00
   5_bss:  0.1280 0.1711   5.237648e+00   5.462332e+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:  0.417  19.999   6.146   8.218   8.193   0.000   0.000   0.000
   1_xyz:  0.417  19.999   6.146   8.218   8.193   0.000   0.000   0.000
   1_adp:  0.417  19.999   6.146   8.218   8.193   0.000   0.000   0.000
   1_occ:  0.417  19.999   6.146   8.218   8.193   0.000   0.000   0.000
   2_bss:  0.364  28.608   3.499   4.812   5.820   0.000   0.000   0.000
   2_xyz:  0.364  28.608   3.499   4.812   5.820   0.000   0.000   0.000
   2_adp:  0.364  28.608   3.499   4.812   5.820   0.000   0.000   0.000
   2_occ:  0.364  28.608   3.499   4.812   5.820   0.000   0.000   0.000
   3_bss:  0.317  28.608   1.783   2.510   3.502   0.000   0.000   0.000
   3_xyz:  0.317  28.608   1.783   2.510   3.502   0.000   0.000   0.000
   3_adp:  0.317  28.608   1.783   2.510   3.502   0.000   0.000   0.000
   3_occ:  0.317  28.608   1.783   2.510   3.502   0.000   0.000   0.000
   4_bss:  0.301  30.300   0.976   1.278   2.216   0.000   0.000   0.000
   4_xyz:  0.301  30.300   0.976   1.278   2.216   0.000   0.000   0.000
   4_adp:  0.301  30.300   0.976   1.278   2.216   0.000   0.000   0.000
   4_occ:  0.301  30.300   0.976   1.278   2.216   0.000   0.000   0.000
   5_bss:  0.320  30.300   0.031   0.475   1.318   0.000   0.000   0.000
   5_xyz:  0.320  30.300   0.031   0.475   1.318   0.000   0.000   0.000
   5_adp:  0.320  30.300   0.031   0.475   1.318   0.000   0.000   0.000
   5_occ:  0.320  30.300   0.031   0.475   1.318   0.000   0.000   0.000
   5_bss:  0.320  30.540  -0.520  -0.115   0.635  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  65.433 0.3237  0.3942    84235.035
   1_bss:  65.432 0.3222  0.4803    81142.565
   1_xyz:  58.014 0.4179  0.6174    68969.819
   1_adp:  55.376 0.4522  0.7340    66465.964
   1_occ:  55.524 0.4503  0.7295    66551.695
   2_bss:  55.302 0.4529  0.6656    65886.917
   2_xyz:  45.958 0.5699  0.8354    48387.244
   2_adp:  43.071 0.6057  0.8969    44076.535
   2_occ:  43.062 0.6058  0.8962    44117.650
   3_bss:  42.992 0.6066  0.8316    44070.973
   3_xyz:  32.865 0.7254  0.9643    26510.674
   3_adp:  29.697 0.7612  0.9818    22542.674
   3_occ:  29.635 0.7619  0.9828    22464.101
   4_bss:  29.476 0.7634  0.9441    22164.939
   4_xyz:  23.089 0.8312  0.9993    14254.766
   4_adp:  20.292 0.8601  1.0237    12030.808
   4_occ:  20.186 0.8611  1.0241    11914.980
   5_bss:  20.101 0.8619  0.9905    11787.419
   5_xyz:  16.475 0.8945  1.0050     8251.899
   5_adp:  15.485 0.9031  1.0054     7530.347
   5_occ:  15.456 0.9033  1.0055     7500.428
   5_bss:  15.412 0.9037  0.9921     7466.814
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.084   5.2438e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.084   5.2438e+01
   1_xyz:   1.866  0.015  0.115 18.475  0.007  4.103   1.7239e-01
   1_adp:   1.866  0.015  0.115 18.475  0.007  4.103   1.7239e-01
   1_occ:   1.866  0.015  0.115 18.475  0.007  4.103   1.7239e-01
   2_bss:   1.866  0.015  0.115 18.475  0.007  4.103   1.7239e-01
   2_xyz:   1.251  0.009  0.082 16.857  0.005  4.103   9.7311e-02
   2_adp:   1.251  0.009  0.082 16.857  0.005  4.103   9.7311e-02
   2_occ:   1.251  0.009  0.082 16.857  0.005  4.103   9.7311e-02
   3_bss:   1.251  0.009  0.082 16.857  0.005  4.103   9.7311e-02
   3_xyz:   1.218  0.009  0.084 16.462  0.005  4.104   9.0363e-02
   3_adp:   1.218  0.009  0.084 16.462  0.005  4.104   9.0363e-02
   3_occ:   1.218  0.009  0.084 16.462  0.005  4.104   9.0363e-02
   4_bss:   1.218  0.009  0.084 16.462  0.005  4.104   9.0363e-02
   4_xyz:   1.008  0.006  0.067 15.780  0.003  4.110   6.3900e-02
   4_adp:   1.008  0.006  0.067 15.780  0.003  4.110   6.3900e-02
   4_occ:   1.008  0.006  0.067 15.780  0.003  4.110   6.3900e-02
   5_bss:   1.008  0.006  0.067 15.780  0.003  4.110   6.3900e-02
   5_xyz:   1.130  0.008  0.076 15.910  0.004  4.104   7.2711e-02
   5_adp:   1.130  0.008  0.076 15.910  0.004  4.104   7.2711e-02
   5_occ:   1.130  0.008  0.076 15.910  0.004  4.104   7.2711e-02
   5_bss:   1.130  0.008  0.076 15.910  0.004  4.104   7.2711e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.428   6.7856e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.428   6.7856e+00
   1_xyz:  16.048  0.181  0.540 83.678  0.058  2.096   1.1116e-01
   1_adp:  16.048  0.181  0.540 83.678  0.058  2.096   1.1116e-01
   1_occ:  16.048  0.181  0.540 83.678  0.058  2.096   1.1116e-01
   2_bss:  16.048  0.181  0.540 83.678  0.058  2.096   1.1116e-01
   2_xyz:   8.337  0.094  0.399 76.131  0.047  2.241   6.2610e-02
   2_adp:   8.337  0.094  0.399 76.131  0.047  2.241   6.2610e-02
   2_occ:   8.337  0.094  0.399 76.131  0.047  2.241   6.2610e-02
   3_bss:   8.337  0.094  0.399 76.131  0.047  2.241   6.2610e-02
   3_xyz:   8.459  0.098  0.280 80.350  0.038  2.192   1.0698e-01
   3_adp:   8.459  0.098  0.280 80.350  0.038  2.192   1.0698e-01
   3_occ:   8.459  0.098  0.280 80.350  0.038  2.192   1.0698e-01
   4_bss:   8.459  0.098  0.280 80.350  0.038  2.192   1.0698e-01
   4_xyz:   7.826  0.039  0.228 87.173  0.019  2.342   4.5757e-02
   4_adp:   7.826  0.039  0.228 87.173  0.019  2.342   4.5757e-02
   4_occ:   7.826  0.039  0.228 87.173  0.019  2.342   4.5757e-02
   5_bss:   7.826  0.039  0.228 87.173  0.019  2.342   4.5757e-02
   5_xyz:   7.770  0.049  0.241 84.561  0.040  2.264   5.8522e-02
   5_adp:   7.770  0.049  0.241 84.561  0.040  2.264   5.8522e-02
   5_occ:   7.770  0.049  0.241 84.561  0.040  2.264   5.8522e-02
   5_bss:   7.770  0.049  0.241 84.561  0.040  2.264   5.8522e-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:  83.42   0.00  16.01  75.67   0.00  14.61  83.42   0.00  23.62
   1_occ:  83.42   0.00  16.01  75.67   0.00  14.61  83.42   0.00  23.62
   2_bss:  83.42   0.00  16.01  75.67   0.00  14.61  83.42   0.00  23.62
   2_xyz:  83.42   0.00  16.01  75.67   0.00  14.61  83.42   0.00  23.62
   2_adp:  83.83   0.00  15.48  83.83   0.00  13.14  82.98   0.00  28.24
   2_occ:  83.83   0.00  15.48  83.83   0.00  13.14  82.98   0.00  28.24
   3_bss:  83.83   0.00  15.48  83.83   0.00  13.14  82.98   0.00  28.24
   3_xyz:  83.83   0.00  15.48  83.83   0.00  13.14  82.98   0.00  28.24
   3_adp: 108.87   0.00  16.18 108.87   0.00  11.85  89.85   1.41  39.79
   3_occ: 108.87   0.00  16.18 108.87   0.00  11.85  89.85   1.41  39.79
   4_bss: 108.87   0.00  16.18 108.87   0.00  11.85  89.85   1.41  39.79
   4_xyz: 108.87   0.00  16.18 108.87   0.00  11.85  89.85   1.41  39.79
   4_adp: 104.62   0.00  15.32 104.62   0.00  11.11  87.25   2.87  38.23
   4_occ: 104.62   0.00  15.32 104.62   0.00  11.11  87.25   2.87  38.23
   5_bss: 104.62   0.00  15.32 104.62   0.00  11.11  87.25   2.87  38.23
   5_xyz: 104.62   0.00  15.32 104.62   0.00  11.11  87.25   2.87  38.23
   5_adp:  99.33   0.00  14.93  99.33   0.00  10.52  86.43   4.14  38.94
   5_occ:  99.33   0.00  14.93  99.33   0.00  10.52  86.43   4.14  38.94
   5_bss:  99.57   0.24  15.17  99.57   0.24  10.76  86.67   4.38  39.18
------------------------------------------------------------------------
 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:    1.287    0.027    0.428
   1_adp:    1.287    0.027    0.428
   1_occ:    1.287    0.027    0.428
   2_bss:    1.287    0.027    0.428
   2_xyz:    1.656    0.034    0.573
   2_adp:    1.656    0.034    0.573
   2_occ:    1.656    0.034    0.573
   3_bss:    1.656    0.034    0.573
   3_xyz:    1.711    0.046    0.747
   3_adp:    1.711    0.046    0.747
   3_occ:    1.711    0.046    0.747
   4_bss:    1.711    0.046    0.747
   4_xyz:    1.735    0.030    0.821
   4_adp:    1.735    0.030    0.821
   4_occ:    1.735    0.030    0.821
   5_bss:    1.735    0.030    0.821
   5_xyz:    1.891    0.054    0.877
   5_adp:    1.891    0.054    0.877
   5_occ:    1.891    0.054    0.877
   5_bss:    1.891    0.054    0.877
------------------------------------------------------------------------

CPU time actual refinement: 363.48


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_143/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_143/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_143/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_143/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_143/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 363.33 
  Macro-tasks:
    bulk solvent and scale       = 41.77  
    individual site refinement   = 160.68 
    weights calculation          = 32.56  
    collect and process          = 6.52   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 241.66 
  Micro-tasks:
    mask                            = 2.99   
    f_calc                          = 115.26 
    alpha_beta                      = 8.39   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 127.23 
    fmodel                         = 7.44   
    r_factors                      = 0.24   
    phase_errors                   = 10.01  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 272.95 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.069 micro seconds
Total CPU time: 6.28 minutes
from_scatterers_fft:    653 calls, 114.92 s
gradients_fft:          598 calls, 113.73 s

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

# Date 2008-01-16 Time 00:51:56 PST -0800 (1200473516.75 s)
Start R-work = 0.5160, R-free = 0.5078 (no bulk solvent and anisotropic scale)
Final R-work = 0.1445, R-free = 0.1882 (no bulk solvent and anisotropic scale)

Start R-work = 0.5084, R-free = 0.4982
Final R-work = 0.1280, R-free = 0.1711