# Date 2008-01-16 Time 03:21:40 PST -0800 (1200482500.29 s)
#phil __OFF__

Command line arguments: "../1208.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17200
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1208

-------------------------------------------------------------------------------
  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: (71.655, 48.1033, 88.1178, 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: 3.34, per 1000 atoms: 1.18


================================== 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: (71.655, 48.1033, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2939 2.04045
Completeness in resolution range: 0.981757
Completeness with d_max=infinity: 0.978618

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2939
                             d_min =   2.0404

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: (71.655, 48.1033, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2939 2.04045
Completeness in resolution range: 0.981757
Completeness with d_max=infinity: 0.978618

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2943 -  4.3651 [2092/2116]  1883   209  10.0%
  bin  2:  4.3651 -  3.4781 [2025/2044]  1823   202  10.0%
  bin  3:  3.4781 -  3.0424 [1983/2002]  1784   199  10.0%
  bin  4:  3.0424 -  2.7660 [1955/1985]  1760   195  10.0%
  bin  5:  2.7660 -  2.5688 [1959/1978]  1763   196  10.0%
  bin  6:  2.5688 -  2.4179 [1950/1975]  1753   197  10.1%
  bin  7:  2.4179 -  2.2973 [1945/1973]  1755   190   9.8%
  bin  8:  2.2973 -  2.1976 [1938/1974]  1741   197  10.2%
  bin  9:  2.1976 -  2.1132 [1905/1947]  1714   191  10.0%
  bin 10:  2.1132 -  2.0404 [1837/1959]  1654   183  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1208/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.43 -     2.13: 4
        2.13 -     2.82: 843
        2.82 -     3.51: 4305
        3.51 -     4.21: 9038
        4.21 -     4.90: 13270
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.435 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.761 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG  SER A 245 " - " O   HOH Z 202 "  2.097 3.040 -x+1/2,-y+1,z-1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 27455 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_1208/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1208/model_refine_001.geo

CPU time processing inputs: 9.19


============================ 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 = 71.655 48.10325 88.1178 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: 2.04 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5287   r_free= 0.5137   ksol= 0.00   Bsol= 0.00   scale= 0.736    |
|                                                                             |
| 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:   1.06 A                  |
| x-ray target function (ml) for work reflections: 6.314322                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2943 -  4.8682 0.99   1370  153 0.4378 0.4349      6.6644       6.643|
|  2:  4.8682 -  3.8849 0.99   1303  145 0.4794 0.5126      6.9087      6.9714|
|  3:  3.8849 -  3.4000 0.99   1280  142 0.5169 0.4660       6.779      6.7449|
|  4:  3.4000 -  3.0919 0.99   1281  140 0.5328 0.4874      6.6041       6.539|
|  5:  3.0919 -  2.8718 0.99   1254  142 0.5469 0.5105      6.4158      6.4071|
|  6:  2.8718 -  2.7035 0.99   1276  140 0.5501 0.5346      6.3211      6.2805|
|  7:  2.7035 -  2.5688 0.99   1249  139 0.5492 0.4752      6.2651      6.1799|
|  8:  2.5688 -  2.4574 0.98   1256  140 0.5626 0.5228      6.2154      6.2281|
|  9:  2.4574 -  2.3632 0.98   1240  140 0.5466 0.6338      6.1353      6.1517|
| 10:  2.3632 -  2.2819 0.99   1235  137 0.5742 0.6150      6.1374      6.1651|
| 11:  2.2819 -  2.2108 0.98   1254  137 0.5576 0.5606      6.0628      6.0911|
| 12:  2.2108 -  2.1477 0.97   1233  137 0.5580 0.4957      6.0113      6.0491|
| 13:  2.1477 -  2.0914 1.00   1231  135 0.5459 0.4844      5.9073      5.8868|
| 14:  2.0914 -  2.0404 0.91   1168  132 0.5596 0.5445      5.8524      5.7837|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2943 -  4.8682  1370   153  0.62  41.48   0.76     0.65      99375.52|
|  2:  4.8682 -  3.8849  1303   145  0.60  43.63   0.82     0.65     146192.94|
|  3:  3.8849 -  3.4000  1280   142  0.49  52.47   0.75     0.58     152524.04|
|  4:  3.4000 -  3.0919  1281   140  0.38  60.93   0.75     0.47     131245.61|
|  5:  3.0919 -  2.8718  1254   142  0.33  65.17   0.68     0.39      96736.35|
|  6:  2.8718 -  2.7035  1276   140  0.31  66.44   0.67     0.36      80336.08|
|  7:  2.7035 -  2.5688  1249   139  0.29  67.95   0.68     0.32      71708.76|
|  8:  2.5688 -  2.4574  1256   140  0.21  74.43   0.71     0.24      69666.36|
|  9:  2.4574 -  2.3632  1240   140  0.11  81.57   0.67     0.13      66041.19|
| 10:  2.3632 -  2.2819  1235   137  0.07  85.02   0.66     0.08      62325.15|
| 11:  2.2819 -  2.2108  1254   137  0.12  80.81   0.71     0.15      56259.35|
| 12:  2.2108 -  2.1477  1233   137  0.19  76.16   0.71     0.23      50255.12|
| 13:  2.1477 -  2.0914  1231   135  0.16  77.80   0.69     0.19      42136.83|
| 14:  2.0914 -  2.0404  1168   132  0.17  77.50   0.66     0.19      35912.74|
|alpha:            min =        0.08 max =            0.65 mean =         0.33|
|beta:             min =    35912.74 max =       152524.04 mean =     83724.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.29|
|phase err.(work): min =        0.00 max =           90.00 mean =        67.58|
|phase err.(test): min =        0.00 max =           89.98 mean =        67.61|
|-----------------------------------------------------------------------------|

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

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 1
total                    = 1

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 28.697293             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.514   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.988375              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 85.305   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      165 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      669 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1461 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2548 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3797 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4914 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6373 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7526 |
|-----------------------------------------------------------------------------|
|-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 |       55.020 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.736 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.637)------------------------------------------|
|    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 = 12.637)------------------------------------------|
|    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: 2.04 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5322   r_free= 0.5188   ksol= 0.00   Bsol= 0.00   scale= 0.711    |
|                                                                             |
| 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:   1.06 A                  |
| x-ray target function (ml) for work reflections: 6.314884                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5240   r_free= 0.5115   ksol= 0.27   Bsol= 20.00   scale= 0.913   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.41,9.88,8.98,0.00,0.00,0.00); trace/3= 8.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.30 A                  |
| x-ray target function (ml) for work reflections: 5.882788                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 24.880766             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 86.066   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.405616              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.113   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5240      final r-factor (work) = 0.4721          |
| start r-factor (free) = 0.5115      final r-factor (free) = 0.4808          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 133.5540 = 24.88 * 0.50 * 6.3128 + 1.00 * 55.0199                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 72.8564 = 24.88 * 0.50 * 5.8427 + 1.00 * 0.1705                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4721      final r-factor (work) = 0.4303          |
| start r-factor (free) = 0.4808      final r-factor (free) = 0.4772          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.0702 = 2.41 * 1.00 * 5.8427 + 1.00 * 0.0148                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.0268 = 2.41 * 1.00 * 6.2332 + 1.00 * 0.0322                              |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    141.25  19.64    None  None   None       |
|    all(noH): 2823   0      0.00    141.25  19.64    None  None   None       |
|    Sol.    : 438    0      0.00    141.25  30.21    None  None   None       |
|    Mac.    : 2385   0      0.00    99.97   17.70    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 -  14.125: 1333   |   5:    70.626 -  84.751:   36        |
|      1:    14.125 -  28.251:  833   |   6:    84.751 -  98.877:   13        |
|      2:    28.251 -  42.376:  351   |   7:    98.877 - 113.002:    3        |
|      3:    42.376 -  56.501:  180   |   8:   113.002 - 127.127:    1        |
|      4:    56.501 -  70.626:   71   |   9:   127.127 - 141.252:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4303 r_free = 0.4772             target_work(ml) = 6.227         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4291 r_free = 0.4785             target_work(ml) = 6.227         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4291   r_free= 0.4785   ksol= 0.27   Bsol= 20.00   scale= 1.082   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.41,9.88,8.98,0.00,0.00,0.00); trace/3= 8.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.96 A                  |
| x-ray target function (ml) for work reflections: 6.227274                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4280   r_free= 0.4736   ksol= 0.33   Bsol= 80.00   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.02,6.13,5.97,0.00,0.00,0.00); trace/3= 5.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.96 A                  |
| x-ray target function (ml) for work reflections: 5.840787                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.811779             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.649  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.776394              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.329  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4280      final r-factor (work) = 0.3756          |
| start r-factor (free) = 0.4736      final r-factor (free) = 0.4475          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.3033 = 14.81 * 0.50 * 6.2293 + 1.00 * 0.1700                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.0105 = 14.81 * 0.50 * 5.7925 + 1.00 * 0.1122                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3756      final r-factor (work) = 0.3694          |
| start r-factor (free) = 0.4475      final r-factor (free) = 0.4349          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5319 = 0.78 * 1.00 * 5.7925 + 1.00 * 0.0347                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7879 = 0.78 * 1.00 * 6.1473 + 1.00 * 0.0152                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    143.89  16.63    None  None   None       |
|    all(noH): 2823   0      0.00    143.89  16.63    None  None   None       |
|    Sol.    : 438    0      0.00    143.89  28.33    None  None   None       |
|    Mac.    : 2385   0      0.00    79.08   14.48    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 -  14.390: 1545   |   5:    71.948 -  86.337:   18        |
|      1:    14.390 -  28.779:  878   |   6:    86.337 - 100.726:    1        |
|      2:    28.779 -  43.169:  271   |   7:   100.726 - 115.116:    2        |
|      3:    43.169 -  57.558:   85   |   8:   115.116 - 129.505:    1        |
|      4:    57.558 -  71.948:   21   |   9:   129.505 - 143.895:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3694 r_free = 0.4349             target_work(ml) = 6.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3693 r_free = 0.4352             target_work(ml) = 6.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3693   r_free= 0.4352   ksol= 0.33   Bsol= 80.00   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.02,6.13,5.97,0.00,0.00,0.00); trace/3= 5.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.135764                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3686   r_free= 0.4331   ksol= 0.32   Bsol= 80.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.35,4.43,3.77,0.00,0.00,0.00); trace/3= 3.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.136133                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.633166             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.300  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.620688              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.486   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3686      final r-factor (work) = 0.3081          |
| start r-factor (free) = 0.4331      final r-factor (free) = 0.3743          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.8603 = 11.63 * 0.50 * 6.1459 + 1.00 * 0.1122                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.4153 = 11.63 * 0.50 * 6.0694 + 1.00 * 0.1123                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3081      final r-factor (work) = 0.3062          |
| start r-factor (free) = 0.3743      final r-factor (free) = 0.3728          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8007 = 0.62 * 1.00 * 6.0694 + 1.00 * 0.0336                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8571 = 0.62 * 1.00 * 6.0013 + 1.00 * 0.1322                               |
|-----------------------------------------------------------------------------|
| number of iterations = 3       |    number of function evaluations = 4      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    143.84  16.64    None  None   None       |
|    all(noH): 2823   0      0.00    143.84  16.64    None  None   None       |
|    Sol.    : 438    0      0.00    143.84  28.52    None  None   None       |
|    Mac.    : 2385   0      0.00    79.01   14.46    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 -  14.384: 1553   |   5:    71.922 -  86.306:   19        |
|      1:    14.384 -  28.769:  867   |   6:    86.306 - 100.691:    1        |
|      2:    28.769 -  43.153:  272   |   7:   100.691 - 115.075:    2        |
|      3:    43.153 -  57.538:   86   |   8:   115.075 - 129.459:    1        |
|      4:    57.538 -  71.922:   21   |   9:   129.459 - 143.844:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3062 r_free = 0.3728             target_work(ml) = 6.000         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3059 r_free = 0.3727             target_work(ml) = 5.999         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3059   r_free= 0.3727   ksol= 0.32   Bsol= 80.00   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.35,4.43,3.77,0.00,0.00,0.00); trace/3= 3.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 5.998854                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3054   r_free= 0.3711   ksol= 0.33   Bsol= 69.90   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.58,3.35,2.81,0.00,0.00,0.00); trace/3= 2.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 5.997137                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.920020              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.014  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.493411              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.517   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3054      final r-factor (work) = 0.2639          |
| start r-factor (free) = 0.3711      final r-factor (free) = 0.3228          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.8717 = 8.92 * 0.50 * 5.9999 + 1.00 * 0.1123                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.5921 = 8.92 * 0.50 * 5.9396 + 1.00 * 0.1015                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2639      final r-factor (work) = 0.2246          |
| start r-factor (free) = 0.3228      final r-factor (free) = 0.2853          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 20.7942 = 3.49 * 1.00 * 5.9396 + 1.00 * 0.0449                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 20.3017 = 3.49 * 1.00 * 5.8027 + 1.00 * 0.0304                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    146.84  17.62    None  None   None       |
|    all(noH): 2823   0      0.00    146.84  17.62    None  None   None       |
|    Sol.    : 438    0      0.00    146.84  43.80    None  None   None       |
|    Mac.    : 2385   0      0.00    102.98  12.81    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 -  14.684: 1740   |   5:    73.422 -  88.106:   52        |
|      1:    14.684 -  29.369:  578   |   6:    88.106 - 102.791:   20        |
|      2:    29.369 -  44.053:  230   |   7:   102.791 - 117.475:    6        |
|      3:    44.053 -  58.738:  123   |   8:   117.475 - 132.159:    2        |
|      4:    58.738 -  73.422:   71   |   9:   132.159 - 146.844:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2246 r_free = 0.2853             target_work(ml) = 5.758         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2244 r_free = 0.2852             target_work(ml) = 5.757         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2244   r_free= 0.2852   ksol= 0.33   Bsol= 69.90   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.58,3.35,2.81,0.00,0.00,0.00); trace/3= 2.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.757414                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2242   r_free= 0.2857   ksol= 0.34   Bsol= 89.30   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.43,2.46,2.48,0.00,0.00,0.00); trace/3= 2.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.756611                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.685572              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.903  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.791269              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.273   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2242      final r-factor (work) = 0.1811          |
| start r-factor (free) = 0.2857      final r-factor (free) = 0.2413          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.4959 = 6.69 * 0.50 * 5.8019 + 1.00 * 0.1015                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.0561 = 6.69 * 0.50 * 5.6713 + 1.00 * 0.0981                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1811      final r-factor (work) = 0.1721          |
| start r-factor (free) = 0.2413      final r-factor (free) = 0.2314          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5134 = 0.79 * 1.00 * 5.6713 + 1.00 * 0.0259                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4251 = 0.79 * 1.00 * 5.5507 + 1.00 * 0.0330                               |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    146.45  17.19    None  None   None       |
|    all(noH): 2823   0      0.00    146.45  17.19    None  None   None       |
|    Sol.    : 438    0      0.00    146.45  44.16    None  None   None       |
|    Mac.    : 2385   0      0.00    103.15  12.24    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 -  14.645: 1816   |   5:    73.225 -  87.870:   54        |
|      1:    14.645 -  29.290:  520   |   6:    87.870 - 102.515:   19        |
|      2:    29.290 -  43.935:  214   |   7:   102.515 - 117.160:    6        |
|      3:    43.935 -  58.580:  125   |   8:   117.160 - 131.805:    2        |
|      4:    58.580 -  73.225:   66   |   9:   131.805 - 146.450:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1721 r_free = 0.2314             target_work(ml) = 5.529         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1720 r_free = 0.2317             target_work(ml) = 5.529         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1720   r_free= 0.2317   ksol= 0.34   Bsol= 89.30   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.43,2.46,2.48,0.00,0.00,0.00); trace/3= 2.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.528832                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2943 -  4.8682 0.99   1370  153 0.1144 0.1601      5.5494      5.7504|
|  2:  4.8682 -  3.8849 0.99   1303  145 0.1133 0.1457      5.7162      5.9235|
|  3:  3.8849 -  3.4000 0.99   1280  142 0.1510 0.2119      5.8244      6.1789|
|  4:  3.4000 -  3.0919 0.99   1281  140 0.1833 0.2264      5.8253      5.9797|
|  5:  3.0919 -  2.8718 0.99   1254  142 0.2039 0.2554      5.7074      5.9017|
|  6:  2.8718 -  2.7035 0.99   1276  140 0.1926 0.2780      5.6154       5.794|
|  7:  2.7035 -  2.5688 0.99   1249  139 0.1898 0.2727      5.5335      5.8023|
|  8:  2.5688 -  2.4574 0.98   1256  140 0.1930 0.2335      5.5255      5.7171|
|  9:  2.4574 -  2.3632 0.98   1240  140 0.2028 0.2885      5.4694      5.7572|
| 10:  2.3632 -  2.2819 0.99   1235  137 0.1876 0.2755      5.4336      5.6098|
| 11:  2.2819 -  2.2108 0.98   1254  137 0.2061 0.2518      5.4138      5.6049|
| 12:  2.2108 -  2.1477 0.97   1233  137 0.1916 0.2854      5.3166      5.7121|
| 13:  2.1477 -  2.0914 1.00   1231  135 0.1986 0.2528      5.2539      5.4011|
| 14:  2.0914 -  2.0404 0.91   1168  132 0.1931 0.2759      5.1599      5.3615|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2943 -  4.8682  1370   153  0.91  13.04   0.96     0.93      11773.36|
|  2:  4.8682 -  3.8849  1303   145  0.91  13.15   1.02     1.00      16967.17|
|  3:  3.8849 -  3.4000  1280   142  0.88  17.86   1.04     1.02      21905.51|
|  4:  3.4000 -  3.0919  1281   140  0.85  21.72   1.02     0.98      22679.16|
|  5:  3.0919 -  2.8718  1254   142  0.81  25.06   1.01     1.00      18870.18|
|  6:  2.8718 -  2.7035  1276   140  0.81  25.12   0.97     0.90      15634.15|
|  7:  2.7035 -  2.5688  1249   139  0.81  25.65   1.00     0.96      14291.54|
|  8:  2.5688 -  2.4574  1256   140  0.80  26.21   0.99     0.91      14119.16|
|  9:  2.4574 -  2.3632  1240   140  0.79  27.24   1.01     0.92      12657.78|
| 10:  2.3632 -  2.2819  1235   137  0.80  26.43   0.99     0.89      11473.67|
| 11:  2.2819 -  2.2108  1254   137  0.79  27.35   1.00     0.90      11095.78|
| 12:  2.2108 -  2.1477  1233   137  0.81  25.66   1.01     0.95       9570.44|
| 13:  2.1477 -  2.0914  1231   135  0.81  26.14   0.98     0.93       8366.96|
| 14:  2.0914 -  2.0404  1168   132  0.80  26.38   0.96     0.89       6973.66|
|alpha:            min =        0.89 max =            1.02 mean =         0.94|
|beta:             min =     6973.66 max =        22679.16 mean =     14098.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.83|
|phase err.(work): min =        0.00 max =           89.96 mean =        23.23|
|phase err.(test): min =        0.00 max =           89.97 mean =        21.85|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1723   r_free= 0.2314   ksol= 0.33   Bsol= 84.85   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.61,0.03,0.58,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.529202                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.04 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1723   r_free= 0.2314   ksol= 0.33   Bsol= 84.85   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.61,0.03,0.58,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.529202                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2943 -  4.8682 0.99   1370  153 0.1154 0.1609      5.5518      5.7521|
|  2:  4.8682 -  3.8849 0.99   1303  145 0.1141 0.1438      5.7175      5.9164|
|  3:  3.8849 -  3.4000 0.99   1280  142 0.1509 0.2100      5.8246      6.1784|
|  4:  3.4000 -  3.0919 0.99   1281  140 0.1830 0.2263      5.8254      5.9811|
|  5:  3.0919 -  2.8718 0.99   1254  142 0.2041 0.2554      5.7085       5.902|
|  6:  2.8718 -  2.7035 0.99   1276  140 0.1924 0.2768      5.6147      5.7918|
|  7:  2.7035 -  2.5688 0.99   1249  139 0.1899 0.2732      5.5335      5.8035|
|  8:  2.5688 -  2.4574 0.98   1256  140 0.1930 0.2337      5.5254      5.7165|
|  9:  2.4574 -  2.3632 0.98   1240  140 0.2025 0.2888       5.469      5.7573|
| 10:  2.3632 -  2.2819 0.99   1235  137 0.1874 0.2758      5.4341      5.6095|
| 11:  2.2819 -  2.2108 0.98   1254  137 0.2056 0.2523      5.4137      5.6066|
| 12:  2.2108 -  2.1477 0.97   1233  137 0.1914 0.2859      5.3172      5.7131|
| 13:  2.1477 -  2.0914 1.00   1231  135 0.1985 0.2529      5.2541      5.4026|
| 14:  2.0914 -  2.0404 0.91   1168  132 0.1932 0.2754      5.1598      5.3598|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2943 -  4.8682  1370   153  0.91  12.97   0.95     0.92      11574.44|
|  2:  4.8682 -  3.8849  1303   145  0.92  13.08   1.02     1.00      16833.36|
|  3:  3.8849 -  3.4000  1280   142  0.88  17.84   1.04     1.02      21876.64|
|  4:  3.4000 -  3.0919  1281   140  0.85  21.70   1.02     0.98      22682.91|
|  5:  3.0919 -  2.8718  1254   142  0.81  25.06   1.02     1.00      18877.98|
|  6:  2.8718 -  2.7035  1276   140  0.81  25.10   0.98     0.90      15634.08|
|  7:  2.7035 -  2.5688  1249   139  0.81  25.63   1.01     0.96      14269.50|
|  8:  2.5688 -  2.4574  1256   140  0.80  26.20   0.99     0.92      14109.29|
|  9:  2.4574 -  2.3632  1240   140  0.79  27.24   1.01     0.93      12652.14|
| 10:  2.3632 -  2.2819  1235   137  0.80  26.45   1.00     0.89      11489.35|
| 11:  2.2819 -  2.2108  1254   137  0.79  27.39   1.00     0.90      11124.27|
| 12:  2.2108 -  2.1477  1233   137  0.81  25.71   1.01     0.95       9606.51|
| 13:  2.1477 -  2.0914  1231   135  0.81  26.15   0.99     0.94       8375.97|
| 14:  2.0914 -  2.0404  1168   132  0.80  26.37   0.96     0.90       6960.62|
|alpha:            min =        0.89 max =            1.02 mean =         0.94|
|beta:             min =     6960.62 max =        22682.91 mean =     14074.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.83|
|phase err.(work): min =        0.00 max =           89.95 mean =        23.22|
|phase err.(test): min =        0.00 max =           89.55 mean =        21.81|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.26    148.71  19.45    None  None   None       |
|    all(noH): 2823   0      2.26    148.71  19.45    None  None   None       |
|    Sol.    : 438    0      2.26    148.71  46.42    None  None   None       |
|    Mac.    : 2385   0      2.26    105.40  14.50    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.258 -  16.902: 1816   |   5:    75.482 -  90.127:   54        |
|      1:    16.902 -  31.547:  520   |   6:    90.127 - 104.772:   19        |
|      2:    31.547 -  46.192:  214   |   7:   104.772 - 119.417:    6        |
|      3:    46.192 -  60.837:  125   |   8:   119.417 - 134.062:    2        |
|      4:    60.837 -  75.482:   66   |   9:   134.062 - 148.707:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 364         
Filter by distance & map next to the model:
   mapped sites are within: 0.115 - 5.747
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 346 from: 364
   mapped sites are within: 0.709 - 5.747

peak=    7.521 closest distance to " O   THR A  29 " =    0.832
peak=    7.020 closest distance to " O   HOH Z 103 " =    1.000
peak=    6.773 closest distance to " O   HOH Z  84 " =    1.232
peak=    6.658 closest distance to " O   HOH Z 159 " =    1.363
peak=    6.392 closest distance to " O   HOH Z 342 " =    1.025
peak=    6.361 closest distance to " ND2 ASN A  74 " =    0.830
peak=    6.007 closest distance to " O   HOH Z 102 " =    1.627
peak=    5.983 closest distance to " NH1 ARG A 138 " =    0.967
peak=    5.915 closest distance to " O   HOH Z  41 " =    1.095
peak=    5.842 closest distance to " O   GLN A  11 " =    1.101
peak=    5.746 closest distance to " NE  ARG A  36 " =    0.944
peak=    5.678 closest distance to " CB  SER A  26 " =    0.838
peak=    5.556 closest distance to " O   HOH Z 426 " =    1.239
peak=    5.400 closest distance to " O   HOH Z 411 " =    3.095
peak=    5.325 closest distance to " CG1 ILE A 234 " =    1.570
peak=    5.273 closest distance to " CB  SER A  63 " =    1.410
peak=    5.252 closest distance to " OD1 ASN A 301 " =    1.038
peak=    5.205 closest distance to " O   HOH Z 390 " =    0.887
peak=    5.126 closest distance to " CD  ARG A 138 " =    1.362
peak=    5.061 closest distance to " NH1 ARG A 269 " =    1.060
peak=    5.048 closest distance to " CG  GLN A  77 " =    0.976
peak=    5.030 closest distance to " O   HOH Z 139 " =    1.681
peak=    5.020 closest distance to " N   GLU A 277 " =    0.719
peak=    4.931 closest distance to " OD2 ASP A 270 " =    0.789
peak=    4.861 closest distance to " O   HOH Z 117 " =    2.240
peak=    4.845 closest distance to " O   HOH Z  57 " =    0.968
peak=    4.843 closest distance to " CA  VAL A 230 " =    1.321
peak=    4.819 closest distance to " O   SER A   3 " =    0.863
peak=    4.768 closest distance to " O  BHOH Z 338 " =    1.255
peak=    4.729 closest distance to " CG  LEU A   5 " =    1.169
peak=    4.704 closest distance to " O   HOH Z 422 " =    1.277
peak=    4.696 closest distance to " O   HOH Z 120 " =    1.638
peak=    4.676 closest distance to " O   HOH Z  54 " =    1.711
peak=    4.640 closest distance to " OH  TYR A  68 " =    0.993
peak=    4.622 closest distance to " CD ALYS A 290 " =    1.376
peak=    4.604 closest distance to " CD  ARG A 269 " =    0.790
peak=    4.548 closest distance to " O   HOH Z  53 " =    0.924
peak=    4.428 closest distance to " CG1 ILE A 120 " =    1.106
peak=    4.415 closest distance to " N   PHE A  59 " =    0.998
peak=    4.322 closest distance to " OD1 ASN A  60 " =    0.833
peak=    4.276 closest distance to " O   HOH Z 377 " =    1.951
peak=    4.274 closest distance to " CZ  PHE A 218 " =    1.218
peak=    4.260 closest distance to " O   LEU A  25 " =    0.878
peak=    4.243 closest distance to " CD1 LEU A 297 " =    1.059
peak=    4.240 closest distance to " O   HOH Z 131 " =    1.100
peak=    4.204 closest distance to " OD1 ASN A  69 " =    1.099
peak=    4.190 closest distance to " CG BARG A 275 " =    1.397
peak=    4.185 closest distance to " CB  TRP A 179 " =    1.252
peak=    4.168 closest distance to " O   HOH Z 286 " =    1.953
peak=    4.147 closest distance to " OG ASER A 134 " =    1.464
peak=    4.144 closest distance to " CA  ARG A  66 " =    1.020
peak=    4.125 closest distance to " O   HOH Z 174 " =    1.894
peak=    4.116 closest distance to " CG  ARG A 269 " =    0.788
peak=    4.103 closest distance to " NH1AARG A 145 " =    1.250
peak=    4.100 closest distance to " O   HOH Z 425 " =    2.070
peak=    4.061 closest distance to " CA  ARG A 195 " =    1.256
peak=    4.059 closest distance to " CG2 VAL A 230 " =    1.260
peak=    4.046 closest distance to " CA  THR A 246 " =    1.214
peak=    4.041 closest distance to " O   HOH Z 246 " =    1.722
peak=    4.037 closest distance to " O   HOH Z 417 " =    1.406
peak=    4.018 closest distance to " O   HOH Z 146 " =    2.430
peak=    4.017 closest distance to " O   THR A 251 " =    1.138
peak=    4.014 closest distance to " O   HOH Z  54 " =    1.838
peak=    4.007 closest distance to " O   GLN A  73 " =    0.974
peak=    3.998 closest distance to " CB  ALA A 137 " =    1.343
peak=    3.996 closest distance to " OG1 THR A  29 " =    0.953
peak=    3.982 closest distance to " O   HOH Z 248 " =    1.676
peak=    3.965 closest distance to " CD1 PHE A  16 " =    0.755
peak=    3.962 closest distance to " CB  GLN A  88 " =    1.393
peak=    3.950 closest distance to " ND2 ASN A 301 " =    1.043
peak=    3.941 closest distance to " O   HOH Z 379 " =    1.794
peak=    3.938 closest distance to " CB  PRO A 243 " =    1.267
peak=    3.931 closest distance to " OE1 GLU A   2 " =    1.057
peak=    3.921 closest distance to " CG1 VAL A 296 " =    1.966
peak=    3.918 closest distance to " O   HOH Z 350 " =    1.397
peak=    3.901 closest distance to " CB  THR A 235 " =    1.674
peak=    3.890 closest distance to " O   HOH Z  63 " =    1.898
peak=    3.884 closest distance to " CB  VAL A 202 " =    1.358
peak=    3.884 closest distance to " CB  SER A 273 " =    1.151
peak=    3.880 closest distance to " O   HOH Z  27 " =    1.288
peak=    3.879 closest distance to " O   HOH Z 107 " =    1.627
peak=    3.878 closest distance to " CD  GLN A  88 " =    1.106
peak=    3.876 closest distance to " N   ASP A 298 " =    0.788
peak=    3.866 closest distance to " NH1BARG A 102 " =    1.238
peak=    3.857 closest distance to " CG2 THR A  31 " =    1.077
peak=    3.848 closest distance to " O   HOH Z 128 " =    1.521
peak=    3.843 closest distance to " O   ASP A 298 " =    0.747
peak=    3.834 closest distance to " NE  ARG A 269 " =    1.158
peak=    3.819 closest distance to " O   PRO A  90 " =    1.669
peak=    3.815 closest distance to " O   ALA A 165 " =    1.285
peak=    3.811 closest distance to " O   HOH Z  67 " =    1.095
peak=    3.801 closest distance to " OE1 GLN A  73 " =    1.396
peak=    3.798 closest distance to " CA  PRO A  54 " =    0.839
peak=    3.792 closest distance to " CG1BVAL A 121 " =    1.312
peak=    3.791 closest distance to " O   HOH Z  65 " =    1.181
peak=    3.791 closest distance to " CA  TYR A  30 " =    0.951
peak=    3.789 closest distance to " CD2 LEU A 228 " =    1.473
peak=    3.787 closest distance to " O   HOH Z 174 " =    1.943
peak=    3.785 closest distance to " O   HOH Z 387 " =    2.934
peak=    3.782 closest distance to " CA  ARG A  36 " =    1.074
peak=    3.781 closest distance to " O   HOH Z 406 " =    1.968
peak=    3.776 closest distance to " CB  GLN A 183 " =    1.171
peak=    3.776 closest distance to " CG2 THR A 221 " =    1.235
peak=    3.774 closest distance to " CB  ALA A  34 " =    0.945
peak=    3.770 closest distance to " O   HOH Z 410 " =    1.045
peak=    3.757 closest distance to " CA  ARG A 102 " =    1.283
peak=    3.753 closest distance to " O   HOH Z 407 " =    2.430
peak=    3.748 closest distance to " CA  LEU A   5 " =    1.019
peak=    3.729 closest distance to " CD2 LEU A   5 " =    1.115
peak=    3.725 closest distance to " O   HOH Z 389 " =    1.975
peak=    3.711 closest distance to " O   HOH Z 185 " =    2.362
peak=    3.703 closest distance to " CB  VAL A 296 " =    0.822
peak=    3.701 closest distance to " O   VAL A 121 " =    0.771
peak=    3.694 closest distance to " CB  ARG A 275 " =    0.723
peak=    3.688 closest distance to " O   HOH Z 279 " =    1.094
peak=    3.664 closest distance to " CB  GLU A   2 " =    0.894
peak=    3.661 closest distance to " N   SER A  28 " =    0.844
peak=    3.651 closest distance to " CA  ALA A 154 " =    1.160
peak=    3.650 closest distance to " CG  GLN A  11 " =    0.999
peak=    3.631 closest distance to " O   THR A 294 " =    1.491
peak=    3.622 closest distance to " CG  ARG A 138 " =    1.732
peak=    3.620 closest distance to " CB  SER A 288 " =    1.624
peak=    3.616 closest distance to " O   HOH Z 152 " =    2.429
peak=    3.601 closest distance to " O   HOH Z 343 " =    1.669
peak=    3.598 closest distance to " CG2BVAL A  41 " =    1.261
peak=    3.598 closest distance to " O   HOH Z 133 " =    2.243
peak=    3.588 closest distance to " O   HOH Z 272 " =    1.945
peak=    3.587 closest distance to " NH2AARG A 145 " =    1.019
peak=    3.587 closest distance to " CG1 ILE A  20 " =    1.166
peak=    3.587 closest distance to " O   HOH Z 272 " =    1.292
peak=    3.586 closest distance to " CA  HIS A 115 " =    0.960
peak=    3.585 closest distance to " O   HOH Z 234 " =    3.828
peak=    3.584 closest distance to " OD2 ASP A 298 " =    3.168
peak=    3.582 closest distance to " CA  TYR A  30 " =    0.919
peak=    3.578 closest distance to " CD1 LEU A 167 " =    1.488
peak=    3.578 closest distance to " CA  ALA A 100 " =    1.150
peak=    3.574 closest distance to " O   HOH Z 394 " =    2.055
peak=    3.573 closest distance to " O   HOH Z 124 " =    1.313
peak=    3.572 closest distance to " O   HOH Z  61 " =    0.920
peak=    3.557 closest distance to " O   HOH Z   2 " =    3.641
peak=    3.555 closest distance to " O   HOH Z 134 " =    2.560
peak=    3.554 closest distance to " O   HOH Z 119 " =    1.648
peak=    3.548 closest distance to " N   SER A 164 " =    0.961
peak=    3.547 closest distance to " O   HOH Z 132 " =    2.814
peak=    3.544 closest distance to " CE3 TRP A  85 " =    1.041
peak=    3.543 closest distance to " O   HOH Z 435 " =    2.996
peak=    3.540 closest distance to " O   HOH Z 162 " =    2.430
peak=    3.538 closest distance to " OG  SER A 245 " =    1.662
peak=    3.533 closest distance to " CD  PRO A  54 " =    1.219
peak=    3.532 closest distance to " N   ALA A   1 " =    2.270
peak=    3.531 closest distance to " O   HOH Z 132 " =    2.909
peak=    3.520 closest distance to " O   HOH Z 388 " =    1.423
peak=    3.519 closest distance to " O   HOH Z  56 " =    2.037
peak=    3.518 closest distance to " O   HOH Z 137 " =    1.198
peak=    3.518 closest distance to " OE1 GLN A 240 " =    0.775
peak=    3.517 closest distance to " O   HOH Z 158 " =    2.978
peak=    3.515 closest distance to " O   HOH Z 413 " =    1.368
peak=    3.514 closest distance to " CB  TRP A 150 " =    1.475
peak=    3.513 closest distance to " O   HOH Z 277 " =    1.322
peak=    3.509 closest distance to " OXT GLY A 302 " =    3.667
peak=    3.508 closest distance to " O   HOH Z  88 " =    3.705
peak=    3.504 closest distance to " O   HOH Z 215 " =    1.530
peak=    3.495 closest distance to " O   HOH Z 359 " =    1.979
peak=    3.492 closest distance to " O   VAL A 265 " =    1.060
peak=    3.491 closest distance to " O   HOH Z 132 " =    2.792
peak=    3.485 closest distance to " CA  GLY A 287 " =    1.388
peak=    3.483 closest distance to " N   GLU A  53 " =    1.636
peak=    3.471 closest distance to " O   HOH Z 381 " =    2.067
peak=    3.470 closest distance to " O   HOH Z 106 " =    2.282
peak=    3.469 closest distance to " O   HOH Z  99 " =    1.666
peak=    3.468 closest distance to " N   SER A 271 " =    1.213
peak=    3.443 closest distance to " CA  LYS A 181 " =    0.846
peak=    3.442 closest distance to " ND2 ASN A 215 " =    0.735
peak=    3.439 closest distance to " CB  ARG A 259 " =    1.710
peak=    3.436 closest distance to " O   HOH Z 361 " =    2.644
peak=    3.436 closest distance to " O   HOH Z  80 " =    2.317
peak=    3.435 closest distance to " N   ASP A 162 " =    1.266
peak=    3.432 closest distance to " N   ASN A  74 " =    0.793
peak=    3.429 closest distance to " O   HOH Z 430 " =    5.747
peak=    3.427 closest distance to " O   HOH Z  14 " =    2.037
peak=    3.426 closest distance to " O   HOH Z 401 " =    1.398
peak=    3.426 closest distance to " O   PHE A 155 " =    1.389
peak=    3.426 closest distance to " O   HOH Z 186 " =    4.110
peak=    3.425 closest distance to " CE1 TYR A 186 " =    1.217
peak=    3.422 closest distance to " O   HOH Z   9 " =    2.168
peak=    3.421 closest distance to " CB  TRP A 179 " =    1.331
peak=    3.418 closest distance to " O   THR A 157 " =    1.320
peak=    3.415 closest distance to " O   HOH Z 193 " =    2.433
peak=    3.408 closest distance to " O   HOH Z 156 " =    4.758
peak=    3.408 closest distance to " OE1 GLN A  58 " =    1.066
peak=    3.407 closest distance to " OD2 ASP A  50 " =    1.306
peak=    3.400 closest distance to " N   ALA A 292 " =    1.101
peak=    3.398 closest distance to " O   HOH Z 344 " =    2.857
peak=    3.395 closest distance to " CB  TYR A  30 " =    0.885
peak=    3.394 closest distance to " O   HOH Z   1 " =    3.123
peak=    3.392 closest distance to " NH1BARG A 145 " =    1.164
peak=    3.392 closest distance to " OH  TYR A 247 " =    1.211
peak=    3.385 closest distance to " O   HOH Z 126 " =    1.883
peak=    3.385 closest distance to " O   HOH Z 368 " =    4.248
peak=    3.385 closest distance to " CG  ARG A  36 " =    1.001
peak=    3.384 closest distance to " O   GLU A   2 " =    1.750
peak=    3.381 closest distance to " CB  SER A  62 " =    4.141
peak=    3.380 closest distance to " O   HOH Z 431 " =    1.717
peak=    3.377 closest distance to " CA  GLY A   6 " =    0.759
peak=    3.377 closest distance to " O   HOH Z  47 " =    1.134
peak=    3.374 closest distance to " CA  ALA A 295 " =    0.785
peak=    3.369 closest distance to " CG  GLU A 277 " =    3.313
peak=    3.368 closest distance to " O   HOH Z 336 " =    1.622
peak=    3.367 closest distance to " OG  SER A 271 " =    2.184
peak=    3.366 closest distance to " CA  TRP A 274 " =    0.833
peak=    3.365 closest distance to " CG  LYS A  76 " =    1.047
peak=    3.362 closest distance to " O   ASP A 200 " =    1.401
peak=    3.355 closest distance to " CD2 TRP A 179 " =    1.269
peak=    3.354 closest distance to " O   HOH Z 148 " =    1.396
peak=    3.353 closest distance to " O   GLN A 103 " =    1.136
peak=    3.351 closest distance to " O   HOH Z 221 " =    1.598
peak=    3.347 closest distance to " CB  ASN A  39 " =    0.709
peak=    3.344 closest distance to " O   HOH Z 411 " =    1.768
peak=    3.342 closest distance to " CA  ALA A 227 " =    1.419
peak=    3.340 closest distance to " CD2 HIS A  81 " =    1.492
peak=    3.340 closest distance to " O   HOH Z 301 " =    2.227
peak=    3.339 closest distance to " O   HOH Z 191 " =    1.820
peak=    3.334 closest distance to " O   HOH Z 146 " =    1.938
peak=    3.328 closest distance to " CE3 TRP A 274 " =    0.950
peak=    3.328 closest distance to " CB  ALA A 154 " =    0.725
peak=    3.326 closest distance to " N   ASP A 132 " =    0.809
peak=    3.324 closest distance to " O   THR A 220 " =    1.106
peak=    3.318 closest distance to " CD  LYS A 289 " =    1.326
peak=    3.318 closest distance to " O   HOH Z 337 " =    1.760
peak=    3.313 closest distance to " OG  SER A  87 " =    1.653
peak=    3.312 closest distance to " NH1 ARG A  56 " =    1.065
peak=    3.308 closest distance to " NE2 HIS A 115 " =    1.212
peak=    3.302 closest distance to " NE2 HIS A  86 " =    1.190
peak=    3.302 closest distance to " CB  ASP A 253 " =    0.966
peak=    3.300 closest distance to " N   LYS A 119 " =    0.753
peak=    3.297 closest distance to " CB  TRP A 274 " =    1.015
peak=    3.296 closest distance to " O   HOH Z  68 " =    1.983
peak=    3.296 closest distance to " CA  ASP A 124 " =    0.907
peak=    3.295 closest distance to " O   HOH Z  18 " =    2.166
peak=    3.294 closest distance to " N   TYR A  30 " =    0.752
peak=    3.293 closest distance to " NH2 ARG A  56 " =    1.242
peak=    3.285 closest distance to " CB  LYS A 193 " =    1.031
peak=    3.285 closest distance to " O   HOH Z   5 " =    2.283
peak=    3.281 closest distance to " CG  GLN A 183 " =    1.154
peak=    3.280 closest distance to " CB  SER A  97 " =    1.111
peak=    3.275 closest distance to " NE2 GLN A  89 " =    1.059
peak=    3.273 closest distance to " N   VAL A  67 " =    1.309
peak=    3.273 closest distance to " O   GLY A  91 " =    1.345
peak=    3.265 closest distance to " O   HOH Z 210 " =    1.783
peak=    3.264 closest distance to " OG BSER A  99 " =    3.282
peak=    3.260 closest distance to " O   HOH Z 117 " =    2.032
peak=    3.256 closest distance to " CG  MET A 188 " =    0.898
peak=    3.253 closest distance to " O   HOH Z 293 " =    1.936
peak=    3.252 closest distance to " CE1 PHE A 155 " =    0.922
peak=    3.252 closest distance to " O   GLN A  55 " =    1.742
peak=    3.251 closest distance to " O   HOH Z 133 " =    1.830
peak=    3.248 closest distance to " OG  SER A  22 " =    2.559
peak=    3.246 closest distance to " O   HOH Z 194 " =    1.898
peak=    3.245 closest distance to " O   SER A  26 " =    1.290
peak=    3.245 closest distance to " O   HOH Z 116 " =    1.973
peak=    3.244 closest distance to " O   HOH Z 428 " =    3.671
peak=    3.242 closest distance to " OG ASER A  12 " =    1.368
peak=    3.241 closest distance to " CD  LYS A  48 " =    1.275
peak=    3.238 closest distance to " CB  TRP A 266 " =    1.196
peak=    3.237 closest distance to " O   HOH Z 251 " =    1.643
peak=    3.236 closest distance to " O   HOH Z 296 " =    1.811
peak=    3.232 closest distance to " O   HOH Z 120 " =    3.853
peak=    3.230 closest distance to " N   ARG A 275 " =    0.810
peak=    3.228 closest distance to " CA  THR A 235 " =    0.866
peak=    3.225 closest distance to " O   HOH Z 335 " =    1.131
peak=    3.223 closest distance to " CB  ALA A   1 " =    0.993
peak=    3.216 closest distance to " O   HOH Z 297 " =    2.809
peak=    3.215 closest distance to " O   HOH Z  51 " =    2.765
peak=    3.215 closest distance to " CB  THR A  31 " =    0.976
peak=    3.208 closest distance to " O   GLU A  37 " =    1.224
peak=    3.206 closest distance to " NE2 HIS A  81 " =    1.314
peak=    3.201 closest distance to " O   HOH Z  91 " =    2.648
peak=    3.201 closest distance to " CZ3 TRP A 274 " =    4.728
peak=    3.200 closest distance to " CZ3 TRP A  92 " =    1.791
peak=    3.197 closest distance to " O   HOH Z 327 " =    2.805
peak=    3.194 closest distance to " O   HOH Z 427 " =    3.558
peak=    3.191 closest distance to " O   HOH Z 392 " =    2.628
peak=    3.191 closest distance to " O   HOH Z 358 " =    3.057
peak=    3.190 closest distance to " O   HOH Z 261 " =    1.992
peak=    3.189 closest distance to " CA  ASN A  39 " =    1.141
peak=    3.188 closest distance to " O   HOH Z 145 " =    2.076
peak=    3.187 closest distance to " CD2 TYR A  68 " =    0.853
peak=    3.178 closest distance to " O   HOH Z 408 " =    3.136
peak=    3.175 closest distance to " CA  GLY A 147 " =    1.058
peak=    3.174 closest distance to " O   HOH Z 324 " =    1.472
peak=    3.172 closest distance to " O   HOH Z 285 " =    2.936
peak=    3.170 closest distance to " CA  CYS A 260 " =    0.969
peak=    3.168 closest distance to " O   HOH Z  95 " =    1.580
peak=    3.167 closest distance to " O   HOH Z 256 " =    1.893
peak=    3.167 closest distance to " O   HOH Z  33 " =    1.573
peak=    3.166 closest distance to " O   HOH Z  73 " =    2.642
peak=    3.166 closest distance to " N   ASN A  39 " =    1.536
peak=    3.165 closest distance to " CB  MET A  40 " =    0.880
peak=    3.163 closest distance to " OG1 THR A  31 " =    0.939
peak=    3.162 closest distance to " O   HOH Z 227 " =    1.725
peak=    3.160 closest distance to " CA  ILE A  33 " =    1.604
peak=    3.160 closest distance to " N   SER A   3 " =    0.711
peak=    3.160 closest distance to " O   HOH Z 223 " =    1.424
peak=    3.159 closest distance to " O   HOH Z 421 " =    3.209
peak=    3.155 closest distance to " CB  SER A  26 " =    2.135
peak=    3.155 closest distance to " CA  TRP A 274 " =    0.901
peak=    3.155 closest distance to " O   ASN A  69 " =    1.244
peak=    3.154 closest distance to " CD1 LEU A 222 " =    1.096
peak=    3.152 closest distance to " OE1 GLN A 194 " =    2.887
peak=    3.152 closest distance to " NH2 ARG A 156 " =    0.950
peak=    3.151 closest distance to " CG  LEU A 228 " =    1.455
peak=    3.151 closest distance to " O   HOH Z 365 " =    2.901
peak=    3.147 closest distance to " CA  ILE A 120 " =    1.472
peak=    3.143 closest distance to " O   ARG A 275 " =    1.873
peak=    3.143 closest distance to " C   ILE A 106 " =    1.830
peak=    3.143 closest distance to " CA  ALA A 160 " =    1.082
peak=    3.138 closest distance to " CA  LEU A  83 " =    1.245
peak=    3.137 closest distance to " CB  VAL A 121 " =    0.950
peak=    3.134 closest distance to " CB  ASN A 285 " =    0.969
peak=    3.129 closest distance to " NE2 GLN A 278 " =    2.132
peak=    3.128 closest distance to " CZ3 TRP A  85 " =    1.027
peak=    3.126 closest distance to " O   GLN A  58 " =    1.952
peak=    3.126 closest distance to " O   HOH Z  53 " =    1.543
peak=    3.125 closest distance to " O   HOH Z 158 " =    1.948
peak=    3.122 closest distance to " CG1 ILE A 120 " =    1.783
peak=    3.122 closest distance to " O   HOH Z 292 " =    2.290
peak=    3.122 closest distance to " O   HOH Z  68 " =    2.625
peak=    3.115 closest distance to " CB  PHE A 283 " =    0.895
peak=    3.099 closest distance to " OH  TYR A 293 " =    0.926
peak=    3.092 closest distance to " CB  ARG A 156 " =    1.455
peak=    3.091 closest distance to " CG2 ILE A 106 " =    0.860
peak=    3.087 closest distance to " CD2 PHE A  38 " =    1.050
peak=    3.085 closest distance to " CB  GLN A 103 " =    1.084
peak=    3.084 closest distance to " O   HOH Z  85 " =    2.241
peak=    3.081 closest distance to " O   HOH Z 191 " =    3.657
peak=    3.079 closest distance to " O   HOH Z 303 " =    2.119
peak=    3.073 closest distance to " O   HOH Z  68 " =    1.781
peak=    3.071 closest distance to " CG2 VAL A 257 " =    0.723
peak=    3.069 closest distance to " O   HOH Z 171 " =    3.849
peak=    3.067 closest distance to " CG2 THR A  29 " =    1.127
peak=    3.063 closest distance to " N   GLY A  80 " =    1.505
peak=    3.062 closest distance to " CG1 VAL A 153 " =    1.146
peak=    3.058 closest distance to " CD2 HIS A  86 " =    1.422
peak=    3.056 closest distance to " OG  SER A  62 " =    2.973
peak=    3.047 closest distance to " CA  ASP A 107 " =    1.207
peak=    3.034 closest distance to " O   PHE A 283 " =    1.313

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.091 - 5.858
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 218
   mapped sites are within: 0.722 - 5.858

peak=   -4.608 closest distance to " O   SER A  28 " =    1.248
peak=   -4.467 closest distance to " CB  ALA A 291 " =    2.274
peak=   -4.330 closest distance to " CD  GLN A 223 " =    1.503
peak=   -4.323 closest distance to " O   HOH Z 422 " =    1.629
peak=   -4.305 closest distance to " O   HOH Z 411 " =    4.787
peak=   -4.238 closest distance to " O   HOH Z 250 " =    1.360
peak=   -4.207 closest distance to " OG BSER A 164 " =    1.700
peak=   -4.184 closest distance to " O   SER A 276 " =    1.641
peak=   -4.140 closest distance to " OD1 ASP A 107 " =    1.428
peak=   -4.057 closest distance to " CG1 VAL A 112 " =    2.556
peak=   -4.042 closest distance to " O   HOH Z 109 " =    3.909
peak=   -4.020 closest distance to " CD  ARG A 138 " =    0.995
peak=   -3.960 closest distance to " C   TYR A  30 " =    1.063
peak=   -3.957 closest distance to " OG  SER A  32 " =    1.648
peak=   -3.942 closest distance to " N   ARG A 275 " =    1.109
peak=   -3.867 closest distance to " O   HOH Z 166 " =    1.339
peak=   -3.849 closest distance to " CG  LEU A   5 " =    1.125
peak=   -3.834 closest distance to " O   HOH Z  92 " =    1.479
peak=   -3.832 closest distance to " CA  GLY A  23 " =    3.127
peak=   -3.832 closest distance to " C   TRP A 274 " =    0.927
peak=   -3.822 closest distance to " CA  THR A 264 " =    1.460
peak=   -3.811 closest distance to " O   HOH Z 361 " =    4.129
peak=   -3.807 closest distance to " CA  ARG A  36 " =    1.260
peak=   -3.803 closest distance to " CD  ARG A 269 " =    2.428
peak=   -3.799 closest distance to " O   HOH Z 151 " =    1.319
peak=   -3.796 closest distance to " O   HOH Z  82 " =    0.800
peak=   -3.794 closest distance to " O   HOH Z 186 " =    1.960
peak=   -3.794 closest distance to " NZ  LYS A 119 " =    2.000
peak=   -3.790 closest distance to " O   HOH Z 150 " =    0.841
peak=   -3.789 closest distance to " O   HOH Z 174 " =    2.852
peak=   -3.784 closest distance to " CA  LEU A 143 " =    0.936
peak=   -3.770 closest distance to " C   SER A  28 " =    1.219
peak=   -3.770 closest distance to " N   SER A   3 " =    2.760
peak=   -3.764 closest distance to " CZ  TYR A 116 " =    1.430
peak=   -3.751 closest distance to " C   LEU A 101 " =    1.195
peak=   -3.749 closest distance to " CB  ARG A 269 " =    1.842
peak=   -3.738 closest distance to " O   SER A   3 " =    1.488
peak=   -3.737 closest distance to " CD  LYS A 289 " =    2.318
peak=   -3.732 closest distance to " O   PRO A 198 " =    1.266
peak=   -3.725 closest distance to " N   GLN A  58 " =    1.419
peak=   -3.722 closest distance to " O   HOH Z  64 " =    1.361
peak=   -3.721 closest distance to " CA  GLY A 241 " =    3.631
peak=   -3.717 closest distance to " OG  SER A 245 " =    0.824
peak=   -3.717 closest distance to " O   HOH Z 155 " =    1.592
peak=   -3.717 closest distance to " CZ  ARG A 138 " =    1.353
peak=   -3.714 closest distance to " N   ASP A 191 " =    1.488
peak=   -3.690 closest distance to " OD2 ASP A  27 " =    1.708
peak=   -3.689 closest distance to " O   ILE A 106 " =    2.007
peak=   -3.687 closest distance to " N   ALA A 184 " =    1.157
peak=   -3.675 closest distance to " ND2 ASN A  60 " =    2.531
peak=   -3.674 closest distance to " CG1BVAL A  72 " =    2.588
peak=   -3.671 closest distance to " O   THR A  31 " =    1.548
peak=   -3.670 closest distance to " OG  SER A  87 " =    1.620
peak=   -3.665 closest distance to " O   HOH Z 344 " =    2.042
peak=   -3.650 closest distance to " CB  ALA A 161 " =    2.555
peak=   -3.647 closest distance to " CD1 PHE A  59 " =    1.887
peak=   -3.644 closest distance to " SG BCYS A 201 " =    0.813
peak=   -3.633 closest distance to " OD1 ASN A 148 " =    1.880
peak=   -3.630 closest distance to " CA  GLY A 229 " =    2.261
peak=   -3.629 closest distance to " N   TYR A  68 " =    2.599
peak=   -3.626 closest distance to " O   HOH Z   6 " =    1.564
peak=   -3.620 closest distance to " O   HOH Z 179 " =    2.218
peak=   -3.605 closest distance to " O   HOH Z   9 " =    2.350
peak=   -3.605 closest distance to " O   HOH Z 384 " =    1.435
peak=   -3.603 closest distance to " O   HOH Z  41 " =    2.694
peak=   -3.603 closest distance to " CB  ASP A 286 " =    2.240
peak=   -3.598 closest distance to " CG  ASP A  50 " =    2.109
peak=   -3.596 closest distance to " NE2 HIS A  86 " =    0.928
peak=   -3.595 closest distance to " CA  GLY A 241 " =    2.328
peak=   -3.591 closest distance to " NH1 ARG A 219 " =    2.039
peak=   -3.588 closest distance to " CD  ARG A  14 " =    3.073
peak=   -3.582 closest distance to " OXT GLY A 302 " =    5.719
peak=   -3.578 closest distance to " N   MET A 185 " =    1.369
peak=   -3.577 closest distance to " CD  GLN A  11 " =    1.085
peak=   -3.576 closest distance to " CD1 ILE A 263 " =    2.520
peak=   -3.571 closest distance to " OG  SER A  26 " =    2.660
peak=   -3.558 closest distance to " CG  GLN A  73 " =    1.039
peak=   -3.553 closest distance to " NE2 HIS A 207 " =    2.224
peak=   -3.549 closest distance to " CG  LEU A  83 " =    2.183
peak=   -3.547 closest distance to " CG  LEU A  83 " =    1.787
peak=   -3.539 closest distance to " O   HOH Z  52 " =    2.118
peak=   -3.535 closest distance to " N   LEU A  25 " =    1.361
peak=   -3.535 closest distance to " CD2 PHE A  61 " =    2.279
peak=   -3.533 closest distance to " O   HOH Z 134 " =    2.681
peak=   -3.528 closest distance to " N   ALA A   1 " =    2.773
peak=   -3.527 closest distance to " O   HOH Z 351 " =    1.876
peak=   -3.518 closest distance to " CG2 THR A 235 " =    1.919
peak=   -3.514 closest distance to " CG2BVAL A  41 " =    2.320
peak=   -3.512 closest distance to " O   HOH Z 417 " =    1.545
peak=   -3.509 closest distance to " CG  TRP A 266 " =    1.930
peak=   -3.508 closest distance to " CG  MET A 105 " =    0.916
peak=   -3.508 closest distance to " O   HOH Z  58 " =    1.539
peak=   -3.504 closest distance to " O   ASN A 110 " =    1.540
peak=   -3.502 closest distance to " N   ALA A  34 " =    2.473
peak=   -3.497 closest distance to " CE3 TRP A  70 " =    1.558
peak=   -3.496 closest distance to " O   SER A 135 " =    1.781
peak=   -3.479 closest distance to " N   THR A   4 " =    1.439
peak=   -3.477 closest distance to " CG  PRO A 163 " =    4.747
peak=   -3.477 closest distance to " O   HOH Z 140 " =    0.777
peak=   -3.477 closest distance to " N   ALA A 242 " =    1.303
peak=   -3.475 closest distance to " OD1 ASN A  69 " =    1.157
peak=   -3.472 closest distance to " N   SER A 134 " =    1.262
peak=   -3.470 closest distance to " NH2AARG A 145 " =    1.710
peak=   -3.464 closest distance to " CG1 VAL A 296 " =    1.108
peak=   -3.463 closest distance to " NH2AARG A 275 " =    4.873
peak=   -3.459 closest distance to " CB  MET A  47 " =    1.216
peak=   -3.445 closest distance to " O   HOH Z 402 " =    1.470
peak=   -3.438 closest distance to " NE  ARG A  36 " =    1.564
peak=   -3.433 closest distance to " O   HOH Z 269 " =    1.306
peak=   -3.430 closest distance to " O   TYR A  15 " =    2.234
peak=   -3.423 closest distance to " O   HOH Z 199 " =    1.639
peak=   -3.420 closest distance to " CB  SER A 276 " =    1.124
peak=   -3.419 closest distance to " OE1 GLN A 122 " =    2.398
peak=   -3.418 closest distance to " N   SER A  32 " =    1.684
peak=   -3.417 closest distance to " CE  MET A 105 " =    2.500
peak=   -3.410 closest distance to " CG  PRO A 243 " =    1.701
peak=   -3.408 closest distance to " CG  ARG A 259 " =    2.392
peak=   -3.407 closest distance to " O   ASP A  27 " =    1.245
peak=   -3.405 closest distance to " O   HOH Z 388 " =    1.944
peak=   -3.398 closest distance to " CA  ASP A  27 " =    1.310
peak=   -3.390 closest distance to " O   HOH Z 265 " =    1.637
peak=   -3.389 closest distance to " N   ASP A 272 " =    1.504
peak=   -3.385 closest distance to " NH2 ARG A  66 " =    1.142
peak=   -3.379 closest distance to " O   HOH Z 100 " =    1.249
peak=   -3.366 closest distance to " O   HOH Z 138 " =    1.634
peak=   -3.366 closest distance to " O   HOH Z 137 " =    1.264
peak=   -3.359 closest distance to " CZ  ARG A 156 " =    1.988
peak=   -3.356 closest distance to " O   HOH Z 368 " =    1.393
peak=   -3.354 closest distance to " N   GLU A   2 " =    1.353
peak=   -3.353 closest distance to " O   HOH Z 438 " =    2.659
peak=   -3.349 closest distance to " O   HOH Z 183 " =    1.072
peak=   -3.348 closest distance to " CD1 ILE A 151 " =    1.876
peak=   -3.348 closest distance to " O   VAL A 121 " =    0.966
peak=   -3.347 closest distance to " O   HOH Z  40 " =    3.408
peak=   -3.347 closest distance to " CA  ALA A   8 " =    1.667
peak=   -3.340 closest distance to " CD2 LEU A 237 " =    2.671
peak=   -3.337 closest distance to " OD1 ASP A 231 " =    0.941
peak=   -3.332 closest distance to " CA  VAL A 197 " =    1.105
peak=   -3.329 closest distance to " O   HOH Z 216 " =    5.858
peak=   -3.327 closest distance to " N   GLY A  35 " =    1.452
peak=   -3.322 closest distance to " NE2 HIS A 115 " =    1.101
peak=   -3.317 closest distance to " O   HOH Z 265 " =    0.722
peak=   -3.314 closest distance to " O   HOH Z 263 " =    3.386
peak=   -3.311 closest distance to " O   HOH Z  43 " =    1.598
peak=   -3.310 closest distance to " OG  SER A  97 " =    2.063
peak=   -3.304 closest distance to " CB  PHE A 130 " =    1.197
peak=   -3.304 closest distance to " CD2 TYR A 293 " =    1.609
peak=   -3.304 closest distance to " O   HOH Z 228 " =    1.354
peak=   -3.300 closest distance to " O   HOH Z 392 " =    3.259
peak=   -3.283 closest distance to " O   ASP A 298 " =    1.415
peak=   -3.283 closest distance to " O   HOH Z  65 " =    1.871
peak=   -3.279 closest distance to " O   HOH Z 326 " =    3.178
peak=   -3.276 closest distance to " C   MET A 188 " =    1.195
peak=   -3.267 closest distance to " CG  LEU A 101 " =    2.540
peak=   -3.265 closest distance to " CD1 PHE A  16 " =    2.448
peak=   -3.264 closest distance to " N   ALA A 244 " =    1.383
peak=   -3.264 closest distance to " CE2 PHE A 283 " =    2.680
peak=   -3.263 closest distance to " O   LYS A 289 " =    2.723
peak=   -3.259 closest distance to " OG BSER A 164 " =    1.468
peak=   -3.257 closest distance to " O   VAL A 230 " =    2.328
peak=   -3.255 closest distance to " CB  ALA A  43 " =    2.965
peak=   -3.248 closest distance to " CG2 THR A  29 " =    1.113
peak=   -3.247 closest distance to " CG  ASN A 187 " =    0.935
peak=   -3.247 closest distance to " CG  LEU A 228 " =    1.140
peak=   -3.246 closest distance to " SG  CYS A 254 " =    2.875
peak=   -3.245 closest distance to " CE2 PHE A 218 " =    2.783
peak=   -3.238 closest distance to " O   HOH Z  31 " =    2.622
peak=   -3.238 closest distance to " O   HOH Z  53 " =    1.384
peak=   -3.237 closest distance to " OD1 ASP A 171 " =    1.437
peak=   -3.228 closest distance to " CG  ASP A 124 " =    1.134
peak=   -3.223 closest distance to " O   ASP A 171 " =    0.919
peak=   -3.212 closest distance to " O   HOH Z 394 " =    1.899
peak=   -3.211 closest distance to " OE2 GLU A 277 " =    2.528
peak=   -3.210 closest distance to " O   HOH Z 256 " =    1.507
peak=   -3.205 closest distance to " O   HOH Z  54 " =    1.316
peak=   -3.201 closest distance to " OD1 ASN A 301 " =    0.883
peak=   -3.199 closest distance to " CD2 PHE A  59 " =    2.006
peak=   -3.197 closest distance to " O   HOH Z 402 " =    1.136
peak=   -3.196 closest distance to " O   HOH Z 348 " =    1.814
peak=   -3.189 closest distance to " C   VAL A 265 " =    0.947
peak=   -3.188 closest distance to " O   HOH Z 210 " =    0.955
peak=   -3.186 closest distance to " O   ARG A 219 " =    1.528
peak=   -3.184 closest distance to " CA  GLU A 277 " =    0.862
peak=   -3.181 closest distance to " O   HOH Z 135 " =    1.343
peak=   -3.181 closest distance to " CB  SER A  26 " =    1.513
peak=   -3.175 closest distance to " CE3 TRP A 150 " =    2.033
peak=   -3.173 closest distance to " O   HOH Z 211 " =    1.491
peak=   -3.172 closest distance to " CD1 PHE A 225 " =    2.680
peak=   -3.160 closest distance to " CG2 THR A  31 " =    1.699
peak=   -3.158 closest distance to " CG  ARG A 219 " =    2.139
peak=   -3.156 closest distance to " OE1 GLN A  88 " =    2.650
peak=   -3.147 closest distance to " CB  ASP A 286 " =    1.586
peak=   -3.146 closest distance to " O   HOH Z 103 " =    1.573
peak=   -3.144 closest distance to " OE1 GLU A  53 " =    1.059
peak=   -3.144 closest distance to " C   SER A 273 " =    1.149
peak=   -3.133 closest distance to " O   SER A 212 " =    1.737
peak=   -3.118 closest distance to " O   HOH Z 365 " =    1.119
peak=   -3.117 closest distance to " O   HOH Z 135 " =    3.134
peak=   -3.111 closest distance to " CG2 VAL A 189 " =    2.465
peak=   -3.106 closest distance to " N   SER A 212 " =    1.793
peak=   -3.102 closest distance to " O   SER A  12 " =    1.715
peak=   -3.100 closest distance to " ND2 ASN A  74 " =    1.989
peak=   -3.097 closest distance to " NH1 ARG A 195 " =    0.960
peak=   -3.081 closest distance to " OG  SER A  87 " =    2.088
peak=   -3.081 closest distance to " CD  GLU A 236 " =    1.111
peak=   -3.066 closest distance to " C   ASN A  74 " =    2.093
peak=   -3.061 closest distance to " O   HOH Z 426 " =    1.388
peak=   -3.050 closest distance to " CD  LYS A 181 " =    1.891
peak=   -3.015 closest distance to " OH  TYR A 247 " =    1.383

================= 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    :  0.5287 0.5137   6.314322e+00   6.303071e+00
   1_bss:  0.5240 0.5115   5.882788e+00   5.867640e+00
   1_xyz:  0.4721 0.4808   6.267210e+00   6.274066e+00
   1_adp:  0.4303 0.4772   6.226792e+00   6.269035e+00
   1_occ:  0.4291 0.4785   6.227274e+00   6.269537e+00
   2_bss:  0.4280 0.4736   5.840787e+00   5.879584e+00
   2_xyz:  0.3756 0.4475   6.148601e+00   6.234100e+00
   2_adp:  0.3694 0.4349   6.135717e+00   6.220073e+00
   2_occ:  0.3693 0.4352   6.135764e+00   6.220483e+00
   3_bss:  0.3686 0.4331   6.136133e+00   6.219482e+00
   3_xyz:  0.3081 0.3743   6.004242e+00   6.127284e+00
   3_adp:  0.3062 0.3728   5.999997e+00   6.125075e+00
   3_occ:  0.3059 0.3727   5.998854e+00   6.124791e+00
   4_bss:  0.3054 0.3711   5.997137e+00   6.124077e+00
   4_xyz:  0.2639 0.3228   5.878763e+00   6.024079e+00
   4_adp:  0.2246 0.2853   5.758446e+00   5.940788e+00
   4_occ:  0.2244 0.2852   5.757414e+00   5.939920e+00
   5_bss:  0.2242 0.2857   5.756611e+00   5.939055e+00
   5_xyz:  0.1811 0.2413   5.572239e+00   5.787543e+00
   5_adp:  0.1721 0.2314   5.528583e+00   5.752449e+00
   5_occ:  0.1720 0.2317   5.528832e+00   5.753575e+00
   5_bss:  0.1723 0.2314   5.529202e+00   5.753321e+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:  0.267  20.001   6.414   9.880   8.978   0.000   0.000   0.000
   1_xyz:  0.267  20.001   6.414   9.880   8.978   0.000   0.000   0.000
   1_adp:  0.267  20.001   6.414   9.880   8.978   0.000   0.000   0.000
   1_occ:  0.267  20.001   6.414   9.880   8.978   0.000   0.000   0.000
   2_bss:  0.326  80.000   4.017   6.134   5.968   0.000   0.000   0.000
   2_xyz:  0.326  80.000   4.017   6.134   5.968   0.000   0.000   0.000
   2_adp:  0.326  80.000   4.017   6.134   5.968   0.000   0.000   0.000
   2_occ:  0.326  80.000   4.017   6.134   5.968   0.000   0.000   0.000
   3_bss:  0.322  80.000   2.355   4.426   3.772   0.000   0.000   0.000
   3_xyz:  0.322  80.000   2.355   4.426   3.772   0.000   0.000   0.000
   3_adp:  0.322  80.000   2.355   4.426   3.772   0.000   0.000   0.000
   3_occ:  0.322  80.000   2.355   4.426   3.772   0.000   0.000   0.000
   4_bss:  0.325  69.905   1.584   3.346   2.811   0.000   0.000   0.000
   4_xyz:  0.325  69.905   1.584   3.346   2.811   0.000   0.000   0.000
   4_adp:  0.325  69.905   1.584   3.346   2.811   0.000   0.000   0.000
   4_occ:  0.325  69.905   1.584   3.346   2.811   0.000   0.000   0.000
   5_bss:  0.337  89.299   1.433   2.459   2.484   0.000   0.000   0.000
   5_xyz:  0.337  89.299   1.433   2.459   2.484   0.000   0.000   0.000
   5_adp:  0.337  89.299   1.433   2.459   2.484   0.000   0.000   0.000
   5_occ:  0.337  89.299   1.433   2.459   2.484   0.000   0.000   0.000
   5_bss:  0.334  84.849  -0.610   0.029   0.581   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  67.581 0.2948  0.3349    83720.967
   1_bss:  67.011 0.3017  0.4321    82952.131
   1_xyz:  60.096 0.3911  0.5515    70949.250
   1_adp:  59.648 0.3967  0.6284    70248.258
   1_occ:  60.184 0.3897  0.6153    70838.952
   2_bss:  60.174 0.3897  0.5622    70454.745
   2_xyz:  53.576 0.4739  0.6886    59710.973
   2_adp:  50.203 0.5174  0.7480    55058.801
   2_occ:  50.223 0.5172  0.7474    55125.027
   3_bss:  50.103 0.5186  0.7042    54807.299
   3_xyz:  41.129 0.6291  0.8471    39804.755
   3_adp:  40.908 0.6318  0.8520    39479.277
   3_occ:  40.885 0.6320  0.8519    39341.198
   4_bss:  40.799 0.6329  0.8265    39065.763
   4_xyz:  34.171 0.7107  0.8996    28668.378
   4_adp:  30.017 0.7576  0.9068    22457.326
   4_occ:  29.958 0.7583  0.9068    22398.069
   5_bss:  29.913 0.7587  0.8932    22325.641
   5_xyz:  24.620 0.8145  0.9393    15307.283
   5_adp:  23.062 0.8312  0.9408    14059.555
   5_occ:  23.088 0.8309  0.9403    14097.407
   5_bss:  23.076 0.8310  0.9446    14073.523
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.5020e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.5020e+01
   1_xyz:   1.861  0.015  0.116 18.439  0.008  4.126   1.7054e-01
   1_adp:   1.861  0.015  0.116 18.439  0.008  4.126   1.7054e-01
   1_occ:   1.861  0.015  0.116 18.439  0.008  4.126   1.7054e-01
   2_bss:   1.861  0.015  0.116 18.439  0.008  4.126   1.7054e-01
   2_xyz:   1.370  0.010  0.093 17.320  0.006  4.109   1.1217e-01
   2_adp:   1.370  0.010  0.093 17.320  0.006  4.109   1.1217e-01
   2_occ:   1.370  0.010  0.093 17.320  0.006  4.109   1.1217e-01
   3_bss:   1.370  0.010  0.093 17.320  0.006  4.109   1.1217e-01
   3_xyz:   1.341  0.011  0.103 17.085  0.005  4.108   1.1229e-01
   3_adp:   1.341  0.011  0.103 17.085  0.005  4.108   1.1229e-01
   3_occ:   1.341  0.011  0.103 17.085  0.005  4.108   1.1229e-01
   4_bss:   1.341  0.011  0.103 17.085  0.005  4.108   1.1229e-01
   4_xyz:   1.291  0.011  0.089 16.259  0.005  4.111   1.0155e-01
   4_adp:   1.291  0.011  0.089 16.259  0.005  4.111   1.0155e-01
   4_occ:   1.291  0.011  0.089 16.259  0.005  4.111   1.0155e-01
   5_bss:   1.291  0.011  0.089 16.259  0.005  4.111   1.0155e-01
   5_xyz:   1.261  0.012  0.093 16.193  0.004  4.131   9.8114e-02
   5_adp:   1.261  0.012  0.093 16.193  0.004  4.131   9.8114e-02
   5_occ:   1.261  0.012  0.093 16.193  0.004  4.131   9.8114e-02
   5_bss:   1.261  0.012  0.093 16.193  0.004  4.131   9.8114e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.1333e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.1333e+00
   1_xyz:  15.912  0.127  0.482 87.746  0.055  2.121   1.1532e-01
   1_adp:  15.912  0.127  0.482 87.746  0.055  2.121   1.1532e-01
   1_occ:  15.912  0.127  0.482 87.746  0.055  2.121   1.1532e-01
   2_bss:  15.912  0.127  0.482 87.746  0.055  2.121   1.1532e-01
   2_xyz:   8.442  0.077  0.272 89.243  0.045  2.075   6.8196e-02
   2_adp:   8.442  0.077  0.272 89.243  0.045  2.075   6.8196e-02
   2_occ:   8.442  0.077  0.272 89.243  0.045  2.075   6.8196e-02
   3_bss:   8.442  0.077  0.272 89.243  0.045  2.075   6.8196e-02
   3_xyz:  10.761  0.078  0.397 85.897  0.027  2.013   1.1788e-01
   3_adp:  10.761  0.078  0.397 85.897  0.027  2.013   1.1788e-01
   3_occ:  10.761  0.078  0.397 85.897  0.027  2.013   1.1788e-01
   4_bss:  10.761  0.078  0.397 85.897  0.027  2.013   1.1788e-01
   4_xyz:   9.280  0.087  0.306 80.734  0.052  1.967   8.1373e-02
   4_adp:   9.280  0.087  0.306 80.734  0.052  1.967   8.1373e-02
   4_occ:   9.280  0.087  0.306 80.734  0.052  1.967   8.1373e-02
   5_bss:   9.280  0.087  0.306 80.734  0.052  1.967   8.1373e-02
   5_xyz:   8.413  0.066  0.315 83.735  0.042  2.170   6.9717e-02
   5_adp:   8.413  0.066  0.315 83.735  0.042  2.170   6.9717e-02
   5_occ:   8.413  0.066  0.315 83.735  0.042  2.170   6.9717e-02
   5_bss:   8.413  0.066  0.315 83.735  0.042  2.170   6.9717e-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: 141.25   0.00  19.64  99.97   0.00  17.70 141.25   0.00  30.21
   1_occ: 141.25   0.00  19.64  99.97   0.00  17.70 141.25   0.00  30.21
   2_bss: 141.25   0.00  19.64  99.97   0.00  17.70 141.25   0.00  30.21
   2_xyz: 141.25   0.00  19.64  99.97   0.00  17.70 141.25   0.00  30.21
   2_adp: 143.89   0.00  16.63  79.08   0.00  14.48 143.89   0.00  28.33
   2_occ: 143.89   0.00  16.63  79.08   0.00  14.48 143.89   0.00  28.33
   3_bss: 143.89   0.00  16.63  79.08   0.00  14.48 143.89   0.00  28.33
   3_xyz: 143.89   0.00  16.63  79.08   0.00  14.48 143.89   0.00  28.33
   3_adp: 143.84   0.00  16.64  79.01   0.00  14.46 143.84   0.00  28.52
   3_occ: 143.84   0.00  16.64  79.01   0.00  14.46 143.84   0.00  28.52
   4_bss: 143.84   0.00  16.64  79.01   0.00  14.46 143.84   0.00  28.52
   4_xyz: 143.84   0.00  16.64  79.01   0.00  14.46 143.84   0.00  28.52
   4_adp: 146.84   0.00  17.62 102.98   0.00  12.81 146.84   0.00  43.80
   4_occ: 146.84   0.00  17.62 102.98   0.00  12.81 146.84   0.00  43.80
   5_bss: 146.84   0.00  17.62 102.98   0.00  12.81 146.84   0.00  43.80
   5_xyz: 146.84   0.00  17.62 102.98   0.00  12.81 146.84   0.00  43.80
   5_adp: 146.45   0.00  17.19 103.15   0.00  12.24 146.45   0.00  44.16
   5_occ: 146.45   0.00  17.19 103.15   0.00  12.24 146.45   0.00  44.16
   5_bss: 148.71   2.26  19.45 105.40   2.26  14.50 148.71   2.26  46.42
------------------------------------------------------------------------
 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:    1.180    0.026    0.417
   1_adp:    1.180    0.026    0.417
   1_occ:    1.180    0.026    0.417
   2_bss:    1.180    0.026    0.417
   2_xyz:    1.579    0.055    0.581
   2_adp:    1.579    0.055    0.581
   2_occ:    1.579    0.055    0.581
   3_bss:    1.579    0.055    0.581
   3_xyz:    1.766    0.021    0.752
   3_adp:    1.766    0.021    0.752
   3_occ:    1.766    0.021    0.752
   4_bss:    1.766    0.021    0.752
   4_xyz:    2.089    0.051    0.880
   4_adp:    2.089    0.051    0.880
   4_occ:    2.089    0.051    0.880
   5_bss:    2.089    0.051    0.880
   5_xyz:    1.988    0.088    0.973
   5_adp:    1.988    0.088    0.973
   5_occ:    1.988    0.088    0.973
   5_bss:    1.988    0.088    0.973
------------------------------------------------------------------------

CPU time actual refinement: 371.15


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1208/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_1208/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1208/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1208/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1208/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 371.00 
  Macro-tasks:
    bulk solvent and scale       = 57.98  
    individual site refinement   = 166.63 
    weights calculation          = 32.44  
    collect and process          = 6.30   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 263.50 
  Micro-tasks:
    mask                            = 2.91   
    f_calc                          = 110.89 
    alpha_beta                      = 8.38   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 125.16 
    fmodel                         = 9.49   
    r_factors                      = 0.39   
    phase_errors                   = 9.24   
    foms                           = 0.30   
    TOTAL for micro-tasks          = 267.90 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.096 micro seconds
Total CPU time: 6.41 minutes
from_scatterers_fft:    627 calls, 110.49 s
gradients_fft:          572 calls, 111.12 s

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

# Date 2008-01-16 Time 03:28:05 PST -0800 (1200482885.14 s)
Start R-work = 0.5287, R-free = 0.5137 (no bulk solvent and anisotropic scale)
Final R-work = 0.1866, R-free = 0.2464 (no bulk solvent and anisotropic scale)

Start R-work = 0.5240, R-free = 0.5115
Final R-work = 0.1723, R-free = 0.2314