# Date 2008-01-16 Time 02:15:01 PST -0800 (1200478501.27 s)
#phil __OFF__

Command line arguments: "../753.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25805
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 753

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 46.2261, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.2261, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0485 1.97285
Completeness in resolution range: 0.956167
Completeness with d_max=infinity: 0.953282

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0485
                             d_min =   1.9729

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.2261, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0485 1.97285
Completeness in resolution range: 0.956167
Completeness with d_max=infinity: 0.953282

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0489 -  4.2220 [2153/2178]  1938   215  10.0%
  bin  2:  4.2220 -  3.3635 [2053/2073]  1848   205  10.0%
  bin  3:  3.3635 -  2.9419 [2059/2078]  1850   209  10.2%
  bin  4:  2.9419 -  2.6746 [2007/2037]  1810   197   9.8%
  bin  5:  2.6746 -  2.4838 [2022/2041]  1823   199   9.8%
  bin  6:  2.4838 -  2.3379 [2001/2026]  1794   207  10.3%
  bin  7:  2.3379 -  2.2212 [1979/2007]  1783   196   9.9%
  bin  8:  2.2212 -  2.1248 [1992/2028]  1796   196   9.8%
  bin  9:  2.1248 -  2.0432 [1960/2002]  1759   201  10.3%
  bin 10:  2.0432 -  1.9729 [1363/2017]  1229   134   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_753/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 25
        2.42 -     3.04: 2197
        3.04 -     3.66: 4728
        3.66 -     4.28: 9095
        4.28 -     4.90: 12366
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.113 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  2.132 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  2.148 3.040 x,y+1,z
  ... (remaining 28406 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_753/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_753/model_refine_001.geo

CPU time processing inputs: 9.09


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.22605 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4543   r_free= 0.4430   ksol= 0.00   Bsol= 0.00   scale= 0.812    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.255587                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7093 0.99   1397  155 0.3859 0.3728      6.5621      6.5501|
|  2:  4.7093 -  3.7571 0.99   1346  152 0.3586 0.3400      6.7275      6.6665|
|  3:  3.7571 -  3.2878 0.99   1319  141 0.3898 0.3539      6.6014      6.6063|
|  4:  3.2878 -  2.9898 0.99   1313  152 0.4348 0.4086      6.5022      6.4362|
|  5:  2.9898 -  2.7769 0.99   1306  147 0.4847 0.4678      6.3408      6.3547|
|  6:  2.7769 -  2.6141 0.99   1301  136 0.4794 0.5288      6.2554      6.1887|
|  7:  2.6141 -  2.4838 0.99   1287  142 0.5014 0.4764      6.2314      6.2136|
|  8:  2.4838 -  2.3761 0.98   1273  145 0.5115 0.4606      6.1678      6.1569|
|  9:  2.3761 -  2.2849 0.98   1265  147 0.4883 0.5065      6.0978      6.1423|
| 10:  2.2849 -  2.2063 1.00   1301  146 0.5095 0.4895      6.1009      6.0525|
| 11:  2.2063 -  2.1376 0.98   1273  135 0.5046 0.4850      6.0224      6.0298|
| 12:  2.1376 -  2.0766 0.98   1252  139 0.5106 0.5595      5.9766      6.0279|
| 13:  2.0766 -  2.0221 0.99   1283  141 0.5171 0.4948      5.8711      5.8053|
| 14:  2.0221 -  1.9729 0.55    714   81 0.5375 0.5192      5.8756      5.8048|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0489 -  4.7093  1397   155  0.71  33.76   0.80     0.75      68964.26|
|  2:  4.7093 -  3.7571  1346   152  0.76  30.23   0.89     0.82      84304.37|
|  3:  3.7571 -  3.2878  1319   141  0.68  37.49   0.88     0.79      87660.40|
|  4:  3.2878 -  2.9898  1313   152  0.61  43.18   0.82     0.69      79649.83|
|  5:  2.9898 -  2.7769  1306   147  0.50  52.24   0.76     0.59      70380.30|
|  6:  2.7769 -  2.6141  1301   136  0.46  54.93   0.74     0.52      63659.45|
|  7:  2.6141 -  2.4838  1287   142  0.42  58.01   0.76     0.48      60461.60|
|  8:  2.4838 -  2.3761  1273   145  0.40  59.66   0.74     0.47      55613.32|
|  9:  2.3761 -  2.2849  1265   147  0.43  57.65   0.74     0.49      49256.51|
| 10:  2.2849 -  2.2063  1301   146  0.42  58.13   0.77     0.50      43774.30|
| 11:  2.2063 -  2.1376  1273   135  0.41  59.52   0.77     0.50      43084.94|
| 12:  2.1376 -  2.0766  1252   139  0.36  63.19   0.79     0.44      41789.83|
| 13:  2.0766 -  2.0221  1283   141  0.31  66.58   0.72     0.39      37411.38|
| 14:  2.0221 -  1.9729   714    81  0.35  63.69   0.73     0.39      29678.09|
|alpha:            min =        0.39 max =            0.82 mean =         0.57|
|beta:             min =    29678.09 max =        87660.40 mean =     59500.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           90.00 mean =        52.11|
|phase err.(test): min =        0.00 max =           89.90 mean =        52.32|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.705467             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.555   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.965976              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.254   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       30 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      167 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      689 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1512 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2649 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3955 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5095 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6586 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7716 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.608 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       1.814 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4616   r_free= 0.4469   ksol= 0.00   Bsol= 0.00   scale= 0.781    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.259508                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4458   r_free= 0.4283   ksol= 0.38   Bsol= 20.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.21,10.00,7.69,0.00,0.00,0.00); trace/3= 8.30                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.249304                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.200590              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.155   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.898263              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.660   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4458      final r-factor (work) = 0.3511          |
| start r-factor (free) = 0.4283      final r-factor (free) = 0.3728          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 82.3909 = 9.20 * 0.50 * 6.2568 + 1.00 * 53.6080                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.3611 = 9.20 * 0.50 * 6.1376 + 1.00 * 0.1263                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3511      final r-factor (work) = 0.2966          |
| start r-factor (free) = 0.3728      final r-factor (free) = 0.3423          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5276 = 0.90 * 1.00 * 6.1376 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4163 = 0.90 * 1.00 * 6.0139 + 1.00 * 0.0143                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.01   12.12    None  None   None       |
|    all(noH): 2823   0      0.00    77.01   12.12    None  None   None       |
|    Sol.    : 438    0      0.00    77.01   26.93    None  None   None       |
|    Mac.    : 2385   0      0.00    70.57   9.40     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.701: 1277   |   5:    38.503 -  46.204:   63        |
|      1:     7.701 -  15.401:  757   |   6:    46.204 -  53.905:   34        |
|      2:    15.401 -  23.102:  377   |   7:    53.905 -  61.605:   11        |
|      3:    23.102 -  30.803:  180   |   8:    61.605 -  69.306:    2        |
|      4:    30.803 -  38.503:  120   |   9:    69.306 -  77.006:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2966 r_free = 0.3423             target_work(ml) = 5.980         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2963 r_free = 0.3425             target_work(ml) = 5.979         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2963   r_free= 0.3425   ksol= 0.38   Bsol= 20.00   scale= 1.104   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.21,10.00,7.69,0.00,0.00,0.00); trace/3= 8.30                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.978701                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2922   r_free= 0.3374   ksol= 0.35   Bsol= 37.06   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.86,5.55,4.61,0.00,0.00,0.00); trace/3= 4.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.978184                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.429828              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.925   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.418070              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.822  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2922      final r-factor (work) = 0.2144          |
| start r-factor (free) = 0.3374      final r-factor (free) = 0.2680          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4468 = 4.43 * 0.50 * 6.0140 + 1.00 * 0.1263                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.9885 = 4.43 * 0.50 * 5.8334 + 1.00 * 0.0680                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2144      final r-factor (work) = 0.1962          |
| start r-factor (free) = 0.2680      final r-factor (free) = 0.2532          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4532 = 0.42 * 1.00 * 5.8334 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4521 = 0.42 * 1.00 * 5.6624 + 1.00 * 0.0848                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.08   11.99    None  None   None       |
|    all(noH): 2823   0      0.00    79.08   11.99    None  None   None       |
|    Sol.    : 438    0      0.93    79.08   30.32    None  None   None       |
|    Mac.    : 2385   0      0.00    74.50   8.62     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.908: 1452   |   5:    39.540 -  47.447:   74        |
|      1:     7.908 -  15.816:  678   |   6:    47.447 -  55.355:   30        |
|      2:    15.816 -  23.724:  249   |   7:    55.355 -  63.263:    9        |
|      3:    23.724 -  31.632:  194   |   8:    63.263 -  71.171:    2        |
|      4:    31.632 -  39.540:  132   |   9:    71.171 -  79.079:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1962 r_free = 0.2532             target_work(ml) = 5.636         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1961 r_free = 0.2529             target_work(ml) = 5.635         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1961   r_free= 0.2529   ksol= 0.35   Bsol= 37.06   scale= 1.041   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.86,5.55,4.61,0.00,0.00,0.00); trace/3= 4.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.635278                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1956   r_free= 0.2502   ksol= 0.33   Bsol= 37.06   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,3.43,4.00,0.00,0.00,0.00); trace/3= 3.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.632765                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.966544              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.078  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.879137              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.047   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1956      final r-factor (work) = 0.1553          |
| start r-factor (free) = 0.2502      final r-factor (free) = 0.2028          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6377 = 1.97 * 0.50 * 5.6645 + 1.00 * 0.0680                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4900 = 1.97 * 0.50 * 5.5281 + 1.00 * 0.0544                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1553      final r-factor (work) = 0.1420          |
| start r-factor (free) = 0.2028      final r-factor (free) = 0.1939          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.4252 = 1.88 * 1.00 * 5.5281 + 1.00 * 0.0371                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.1264 = 1.88 * 1.00 * 5.3807 + 1.00 * 0.0153                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.64   13.05    None  None   None       |
|    all(noH): 2823   0      0.00    87.64   13.05    None  None   None       |
|    Sol.    : 438    0      1.26    87.39   37.55    None  None   None       |
|    Mac.    : 2385   0      0.00    87.64   8.55     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.764: 1645   |   5:    43.820 -  52.584:   95        |
|      1:     8.764 -  17.528:  578   |   6:    52.584 -  61.348:   66        |
|      2:    17.528 -  26.292:  164   |   7:    61.348 -  70.112:   28        |
|      3:    26.292 -  35.056:  118   |   8:    70.112 -  78.876:    9        |
|      4:    35.056 -  43.820:  116   |   9:    78.876 -  87.640:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1420 r_free = 0.1939             target_work(ml) = 5.354         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1420 r_free = 0.1938             target_work(ml) = 5.354         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1420   r_free= 0.1938   ksol= 0.33   Bsol= 37.06   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,3.43,4.00,0.00,0.00,0.00); trace/3= 3.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.353506                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1419   r_free= 0.1935   ksol= 0.33   Bsol= 46.93   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.58,2.58,3.72,0.00,0.00,0.00); trace/3= 2.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.352124                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.041131              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.917  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.300338              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.330  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1419      final r-factor (work) = 0.1198          |
| start r-factor (free) = 0.1935      final r-factor (free) = 0.1719          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.9289 = 4.04 * 0.50 * 5.3820 + 1.00 * 0.0542                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7446 = 4.04 * 0.50 * 5.2817 + 1.00 * 0.0726                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1198      final r-factor (work) = 0.1166          |
| start r-factor (free) = 0.1719      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6013 = 0.30 * 1.00 * 5.2817 + 1.00 * 0.0150                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5755 = 0.30 * 1.00 * 5.2076 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.10   12.33    None  None   None       |
|    all(noH): 2823   0      0.00    88.10   12.33    None  None   None       |
|    Sol.    : 438    0      1.66    82.96   35.36    None  None   None       |
|    Mac.    : 2385   0      0.00    88.10   8.10     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.810: 1730   |   5:    44.050 -  52.860:   89        |
|      1:     8.810 -  17.620:  547   |   6:    52.860 -  61.670:   47        |
|      2:    17.620 -  26.430:  156   |   7:    61.670 -  70.480:   20        |
|      3:    26.430 -  35.240:  125   |   8:    70.480 -  79.290:    9        |
|      4:    35.240 -  44.050:   98   |   9:    79.290 -  88.100:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1166 r_free = 0.1637             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1165 r_free = 0.1637             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1165   r_free= 0.1637   ksol= 0.33   Bsol= 46.93   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.58,2.58,3.72,0.00,0.00,0.00); trace/3= 2.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.179297                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1166   r_free= 0.1636   ksol= 0.33   Bsol= 46.93   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.51,2.39,3.71,0.00,0.00,0.00); trace/3= 2.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.179714                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.404759              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 141.218  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.387772              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.860  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1166      final r-factor (work) = 0.1172          |
| start r-factor (free) = 0.1636      final r-factor (free) = 0.1614          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7304 = 1.40 * 0.50 * 5.2077 + 1.00 * 0.0726                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6923 = 1.40 * 0.50 * 5.1845 + 1.00 * 0.0508                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1172      final r-factor (work) = 0.1164          |
| start r-factor (free) = 0.1614      final r-factor (free) = 0.1610          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0217 = 0.39 * 1.00 * 5.1845 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0188 = 0.39 * 1.00 * 5.1769 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.55   12.22    None  None   None       |
|    all(noH): 2823   0      0.00    88.55   12.22    None  None   None       |
|    Sol.    : 438    0      1.66    82.04   35.20    None  None   None       |
|    Mac.    : 2385   0      0.00    88.55   8.00     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:     0.000 -   8.855: 1749   |   5:    44.277 -  53.133:   87        |
|      1:     8.855 -  17.711:  536   |   6:    53.133 -  61.988:   47        |
|      2:    17.711 -  26.566:  148   |   7:    61.988 -  70.843:   18        |
|      3:    26.566 -  35.422:  124   |   8:    70.843 -  79.699:    8        |
|      4:    35.422 -  44.277:  104   |   9:    79.699 -  88.554:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1164 r_free = 0.1610             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1164 r_free = 0.1609             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1609   ksol= 0.33   Bsol= 46.93   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.51,2.39,3.71,0.00,0.00,0.00); trace/3= 2.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.176111                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7093 0.99   1397  155 0.1013 0.1246      5.3923      5.5158|
|  2:  4.7093 -  3.7571 0.99   1346  152 0.0894 0.1178      5.4665      5.6571|
|  3:  3.7571 -  3.2878 0.99   1319  141 0.1113 0.1497      5.5115      5.8658|
|  4:  3.2878 -  2.9898 0.99   1313  152 0.1261 0.1750      5.4888       5.631|
|  5:  2.9898 -  2.7769 0.99   1306  147 0.1381 0.1766      5.3571      5.5741|
|  6:  2.7769 -  2.6141 0.99   1301  136 0.1236 0.1857      5.2148      5.4585|
|  7:  2.6141 -  2.4838 0.99   1287  142 0.1323 0.1686      5.1985      5.3985|
|  8:  2.4838 -  2.3761 0.98   1273  145 0.1234 0.1750      5.1072      5.3458|
|  9:  2.3761 -  2.2849 0.98   1265  147 0.1243 0.1845      5.0842      5.3438|
| 10:  2.2849 -  2.2063 1.00   1301  146 0.1176 0.1709      4.9915       5.233|
| 11:  2.2063 -  2.1376 0.98   1273  135 0.1207 0.1829      4.9882      5.2979|
| 12:  2.1376 -  2.0766 0.98   1252  139 0.1157 0.1805      4.9112      5.2336|
| 13:  2.0766 -  2.0221 0.99   1283  141 0.1176 0.1694      4.8019       5.043|
| 14:  2.0221 -  1.9729 0.55    714   81 0.1021 0.1552      4.6633      4.8601|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0489 -  4.7093  1397   155  0.94   9.07   0.98     0.95       7077.85|
|  2:  4.7093 -  3.7571  1346   152  0.95   8.06   1.02     1.00       9225.13|
|  3:  3.7571 -  3.2878  1319   141  0.93  11.91   1.03     1.02      10999.51|
|  4:  3.2878 -  2.9898  1313   152  0.91  14.23   1.01     0.99      10926.30|
|  5:  2.9898 -  2.7769  1306   147  0.90  16.22   1.00     0.97       8638.32|
|  6:  2.7769 -  2.6141  1301   136  0.90  16.19   0.98     0.96       7069.92|
|  7:  2.6141 -  2.4838  1287   142  0.90  15.95   0.99     0.96       6407.99|
|  8:  2.4838 -  2.3761  1273   145  0.90  15.91   0.99     0.97       5635.78|
|  9:  2.3761 -  2.2849  1265   147  0.90  16.18   1.01     0.97       5528.82|
| 10:  2.2849 -  2.2063  1301   146  0.90  16.33   1.00     0.96       4694.53|
| 11:  2.2063 -  2.1376  1273   135  0.89  16.90   1.00     0.95       4680.33|
| 12:  2.1376 -  2.0766  1252   139  0.91  15.68   1.02     1.01       4221.85|
| 13:  2.0766 -  2.0221  1283   141  0.90  16.83   1.00     0.98       3436.46|
| 14:  2.0221 -  1.9729   714    81  0.92  13.78   0.99     0.96       2535.40|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2535.40 max =        10999.51 mean =      6671.87|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.48|
|phase err.(test): min =        0.00 max =           88.51 mean =        13.91|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1609   ksol= 0.33   Bsol= 49.80   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.36,-0.51,0.87,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.176073                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1609   ksol= 0.33   Bsol= 49.80   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.36,-0.51,0.87,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.176073                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7093 0.99   1397  155 0.1013 0.1246      5.3923      5.5159|
|  2:  4.7093 -  3.7571 0.99   1346  152 0.0894 0.1178      5.4666      5.6571|
|  3:  3.7571 -  3.2878 0.99   1319  141 0.1113 0.1497      5.5115      5.8657|
|  4:  3.2878 -  2.9898 0.99   1313  152 0.1261 0.1750      5.4887       5.631|
|  5:  2.9898 -  2.7769 0.99   1306  147 0.1381 0.1766       5.357      5.5741|
|  6:  2.7769 -  2.6141 0.99   1301  136 0.1236 0.1856      5.2146       5.458|
|  7:  2.6141 -  2.4838 0.99   1287  142 0.1323 0.1687      5.1984      5.3987|
|  8:  2.4838 -  2.3761 0.98   1273  145 0.1234 0.1750      5.1072      5.3457|
|  9:  2.3761 -  2.2849 0.98   1265  147 0.1243 0.1844      5.0841      5.3435|
| 10:  2.2849 -  2.2063 1.00   1301  146 0.1175 0.1709      4.9915      5.2335|
| 11:  2.2063 -  2.1376 0.98   1273  135 0.1207 0.1830      4.9884      5.2982|
| 12:  2.1376 -  2.0766 0.98   1252  139 0.1157 0.1806      4.9113      5.2339|
| 13:  2.0766 -  2.0221 0.99   1283  141 0.1176 0.1692      4.8017      5.0426|
| 14:  2.0221 -  1.9729 0.55    714   81 0.1021 0.1550      4.6627      4.8592|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0489 -  4.7093  1397   155  0.94   9.07   0.98     0.95       7077.77|
|  2:  4.7093 -  3.7571  1346   152  0.95   8.06   1.02     1.00       9225.65|
|  3:  3.7571 -  3.2878  1319   141  0.93  11.92   1.03     1.02      11000.72|
|  4:  3.2878 -  2.9898  1313   152  0.91  14.23   1.01     0.99      10924.43|
|  5:  2.9898 -  2.7769  1306   147  0.90  16.21   1.00     0.97       8633.79|
|  6:  2.7769 -  2.6141  1301   136  0.90  16.19   0.98     0.96       7068.38|
|  7:  2.6141 -  2.4838  1287   142  0.90  15.94   0.99     0.96       6406.17|
|  8:  2.4838 -  2.3761  1273   145  0.90  15.91   0.99     0.97       5634.93|
|  9:  2.3761 -  2.2849  1265   147  0.90  16.18   1.01     0.97       5527.71|
| 10:  2.2849 -  2.2063  1301   146  0.90  16.33   1.00     0.96       4696.46|
| 11:  2.2063 -  2.1376  1273   135  0.89  16.90   1.00     0.95       4683.80|
| 12:  2.1376 -  2.0766  1252   139  0.91  15.69   1.02     1.01       4223.82|
| 13:  2.0766 -  2.0221  1283   141  0.90  16.83   1.00     0.98       3435.08|
| 14:  2.0221 -  1.9729   714    81  0.92  13.76   0.99     0.96       2531.66|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2531.66 max =        11000.72 mean =      6671.41|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.48|
|phase err.(test): min =        0.00 max =           88.51 mean =        13.91|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.86    91.42   15.09    None  None   None       |
|    all(noH): 2823   0      2.86    91.42   15.09    None  None   None       |
|    Sol.    : 438    0      4.53    84.90   38.07    None  None   None       |
|    Mac.    : 2385   0      2.86    91.42   10.87    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:     2.864 -  11.720: 1749   |   5:    47.141 -  55.997:   87        |
|      1:    11.720 -  20.575:  536   |   6:    55.997 -  64.852:   47        |
|      2:    20.575 -  29.430:  148   |   7:    64.852 -  73.707:   18        |
|      3:    29.430 -  38.286:  124   |   8:    73.707 -  82.563:    8        |
|      4:    38.286 -  47.141:  104   |   9:    82.563 -  91.418:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 302         
Filter by distance & map next to the model:
   mapped sites are within: 0.326 - 4.653
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 300 from: 302
   mapped sites are within: 0.705 - 4.653

peak=   11.146 closest distance to " CB  VAL A 230 " =    1.470
peak=    9.037 closest distance to " CG2 VAL A 296 " =    1.349
peak=    6.749 closest distance to " CD2 LEU A   5 " =    1.305
peak=    6.276 closest distance to " O   HOH Z 130 " =    1.169
peak=    5.905 closest distance to " NE2 GLN A  11 " =    1.157
peak=    5.676 closest distance to " CG  PRO A  54 " =    1.417
peak=    5.660 closest distance to " CD1AILE A 234 " =    1.075
peak=    5.578 closest distance to " NH2 ARG A  56 " =    2.121
peak=    5.433 closest distance to " CG  LEU A   5 " =    1.204
peak=    5.354 closest distance to " O   HOH Z 144 " =    2.039
peak=    5.270 closest distance to " O   HOH Z 232 " =    2.315
peak=    5.267 closest distance to " CB  PRO A  54 " =    1.057
peak=    5.165 closest distance to " O   HOH Z   9 " =    1.482
peak=    5.091 closest distance to " CG  LEU A 228 " =    1.167
peak=    4.902 closest distance to " CB  SER A   3 " =    1.376
peak=    4.893 closest distance to " O   HOH Z 427 " =    2.468
peak=    4.808 closest distance to " CB  GLN A 223 " =    1.465
peak=    4.796 closest distance to " O   HOH Z  65 " =    0.984
peak=    4.761 closest distance to " CG  PRO A 198 " =    1.258
peak=    4.668 closest distance to " CB  ASN A 148 " =    1.349
peak=    4.617 closest distance to " O   HOH Z   7 " =    1.357
peak=    4.600 closest distance to " O   HOH Z  78 " =    1.652
peak=    4.599 closest distance to " CB  GLN A 183 " =    1.234
peak=    4.570 closest distance to " O   HOH Z 425 " =    1.525
peak=    4.551 closest distance to " O   HOH Z 126 " =    1.926
peak=    4.536 closest distance to " CD2 LEU A 228 " =    1.194
peak=    4.501 closest distance to " O   HOH Z 209 " =    2.345
peak=    4.469 closest distance to " CB  SER A  63 " =    1.292
peak=    4.462 closest distance to " O   HOH Z 298 " =    1.821
peak=    4.442 closest distance to " CB  VAL A 230 " =    1.138
peak=    4.412 closest distance to " CB  ARG A 275 " =    0.914
peak=    4.378 closest distance to " O   HOH Z 316 " =    2.989
peak=    4.372 closest distance to " CG  PRO A 213 " =    1.241
peak=    4.330 closest distance to " O   HOH Z   2 " =    1.765
peak=    4.322 closest distance to " CB  SER A 216 " =    0.880
peak=    4.298 closest distance to " O   HOH Z  55 " =    2.116
peak=    4.266 closest distance to " CG  LEU A 167 " =    1.216
peak=    4.265 closest distance to " O   HOH Z 287 " =    1.921
peak=    4.259 closest distance to " CB  TRP A 266 " =    0.997
peak=    4.255 closest distance to " CG  PRO A 243 " =    1.170
peak=    4.237 closest distance to " O   HOH Z 272 " =    1.807
peak=    4.199 closest distance to " CB  GLU A 128 " =    1.033
peak=    4.191 closest distance to " O   HOH Z 369 " =    2.121
peak=    4.176 closest distance to " CB  VAL A 265 " =    1.300
peak=    4.129 closest distance to " O   HOH Z  68 " =    2.106
peak=    4.109 closest distance to " O   HOH Z 423 " =    1.511
peak=    4.063 closest distance to " CA  VAL A 296 " =    1.114
peak=    4.063 closest distance to " ND2 ASN A 187 " =    1.631
peak=    4.042 closest distance to " O   HOH Z 234 " =    3.627
peak=    4.025 closest distance to " CG2 VAL A 257 " =    0.895
peak=    4.024 closest distance to " CB  ASN A 187 " =    1.093
peak=    4.005 closest distance to " O   HOH Z 346 " =    1.611
peak=    3.988 closest distance to " O   PRO A 198 " =    1.565
peak=    3.984 closest distance to " O   SER A  87 " =    2.295
peak=    3.968 closest distance to " O   HOH Z 263 " =    1.608
peak=    3.955 closest distance to " CB  ASN A  39 " =    0.933
peak=    3.945 closest distance to " CB  GLU A 152 " =    1.253
peak=    3.933 closest distance to " N   PHE A 130 " =    1.251
peak=    3.913 closest distance to " NH2AARG A 190 " =    1.763
peak=    3.910 closest distance to " O   HOH Z 193 " =    1.797
peak=    3.893 closest distance to " CA  ASN A 215 " =    1.125
peak=    3.888 closest distance to " O   HOH Z 380 " =    1.707
peak=    3.885 closest distance to " O   HOH Z 124 " =    1.376
peak=    3.881 closest distance to " O   HOH Z   1 " =    1.838
peak=    3.878 closest distance to " O   HOH Z  63 " =    1.346
peak=    3.877 closest distance to " O   HOH Z 203 " =    1.775
peak=    3.877 closest distance to " CB  ASP A 124 " =    0.719
peak=    3.871 closest distance to " O   HOH Z 419 " =    1.984
peak=    3.867 closest distance to " CB  ASN A 142 " =    0.971
peak=    3.867 closest distance to " O   HOH Z 193 " =    1.663
peak=    3.866 closest distance to " CB BVAL A  41 " =    1.223
peak=    3.837 closest distance to " O   HOH Z 368 " =    1.966
peak=    3.837 closest distance to " CB  TRP A 179 " =    1.445
peak=    3.833 closest distance to " O   HOH Z  40 " =    2.754
peak=    3.822 closest distance to " O   HOH Z 389 " =    1.861
peak=    3.819 closest distance to " O   HOH Z 303 " =    2.246
peak=    3.814 closest distance to " CB  ARG A  79 " =    1.395
peak=    3.807 closest distance to " O   HOH Z 261 " =    2.201
peak=    3.804 closest distance to " CA  TYR A  30 " =    0.977
peak=    3.797 closest distance to " CE3 TRP A 274 " =    2.529
peak=    3.789 closest distance to " CB  GLU A 277 " =    3.540
peak=    3.784 closest distance to " O   HOH Z 422 " =    2.599
peak=    3.783 closest distance to " CA  SER A  87 " =    0.948
peak=    3.781 closest distance to " OD1 ASN A  69 " =    2.595
peak=    3.780 closest distance to " CD  ARG A 159 " =    0.730
peak=    3.772 closest distance to " NH1AARG A 145 " =    1.114
peak=    3.754 closest distance to " O   HOH Z  30 " =    1.634
peak=    3.735 closest distance to " CA  THR A 264 " =    0.706
peak=    3.725 closest distance to " CA  ALA A  51 " =    1.014
peak=    3.722 closest distance to " CB  MET A  40 " =    0.851
peak=    3.720 closest distance to " O   HOH Z  61 " =    1.570
peak=    3.720 closest distance to " O   HOH Z 411 " =    3.599
peak=    3.720 closest distance to " CB  VAL A 202 " =    1.655
peak=    3.703 closest distance to " CB  LEU A 143 " =    1.114
peak=    3.701 closest distance to " O   HOH Z 222 " =    2.331
peak=    3.696 closest distance to " CA  ILE A 234 " =    0.971
peak=    3.693 closest distance to " CB  LYS A 117 " =    1.251
peak=    3.683 closest distance to " O   HOH Z 273 " =    2.678
peak=    3.681 closest distance to " ND1 HIS A  86 " =    1.759
peak=    3.678 closest distance to " O   HOH Z 371 " =    2.701
peak=    3.674 closest distance to " O   HOH Z 403 " =    1.632
peak=    3.660 closest distance to " N   GLN A 278 " =    1.061
peak=    3.650 closest distance to " O   HOH Z 189 " =    2.915
peak=    3.650 closest distance to " O   HOH Z 427 " =    1.186
peak=    3.648 closest distance to " O   HOH Z 437 " =    2.188
peak=    3.648 closest distance to " CG BARG A 102 " =    1.865
peak=    3.643 closest distance to " O   PRO A 198 " =    1.283
peak=    3.642 closest distance to " CB  SER A 210 " =    0.767
peak=    3.624 closest distance to " O   HOH Z 353 " =    2.567
peak=    3.620 closest distance to " N   ARG A 156 " =    1.298
peak=    3.619 closest distance to " O   HOH Z 128 " =    1.930
peak=    3.618 closest distance to " CB  VAL A 250 " =    1.096
peak=    3.618 closest distance to " O   HOH Z 214 " =    2.120
peak=    3.611 closest distance to " O   HOH Z 366 " =    2.900
peak=    3.604 closest distance to " CD  ARG A 269 " =    1.064
peak=    3.589 closest distance to " CG2 THR A 221 " =    1.112
peak=    3.586 closest distance to " O   HOH Z   3 " =    1.934
peak=    3.585 closest distance to " O   HOH Z 368 " =    3.573
peak=    3.582 closest distance to " O   HOH Z  88 " =    3.285
peak=    3.581 closest distance to " O   HOH Z 146 " =    1.607
peak=    3.576 closest distance to " NH1 ARG A  14 " =    0.940
peak=    3.573 closest distance to " O   HOH Z 410 " =    1.372
peak=    3.572 closest distance to " O   HOH Z  61 " =    1.596
peak=    3.571 closest distance to " CG  GLN A  88 " =    1.139
peak=    3.568 closest distance to " CZ  PHE A 192 " =    0.892
peak=    3.567 closest distance to " O   HOH Z  59 " =    1.705
peak=    3.563 closest distance to " CG  ARG A 138 " =    1.247
peak=    3.556 closest distance to " NZ  LYS A 117 " =    3.145
peak=    3.556 closest distance to " CA  ALA A 299 " =    0.958
peak=    3.554 closest distance to " CD1 ILE A  33 " =    1.695
peak=    3.548 closest distance to " CZ  PHE A 218 " =    1.085
peak=    3.548 closest distance to " O   HOH Z 193 " =    1.923
peak=    3.542 closest distance to " O   HOH Z 392 " =    1.298
peak=    3.537 closest distance to " CG1 VAL A 153 " =    0.927
peak=    3.535 closest distance to " CB  GLN A  88 " =    1.274
peak=    3.532 closest distance to " CB  SER A 212 " =    1.293
peak=    3.527 closest distance to " OG  SER A  62 " =    2.742
peak=    3.525 closest distance to " CD BLYS A 290 " =    1.087
peak=    3.519 closest distance to " O   HOH Z 158 " =    3.109
peak=    3.516 closest distance to " CB  THR A 157 " =    1.112
peak=    3.511 closest distance to " OG  SER A  62 " =    3.022
peak=    3.511 closest distance to " OD2 ASP A 286 " =    2.739
peak=    3.503 closest distance to " N   SER A 271 " =    0.993
peak=    3.499 closest distance to " CA  PHE A 283 " =    1.238
peak=    3.496 closest distance to " CB  LEU A 228 " =    1.240
peak=    3.495 closest distance to " O   HOH Z 425 " =    1.900
peak=    3.495 closest distance to " NH2BARG A 145 " =    2.002
peak=    3.494 closest distance to " O   HOH Z  97 " =    2.036
peak=    3.489 closest distance to " CG  LEU A 281 " =    1.100
peak=    3.483 closest distance to " O   HOH Z 128 " =    2.101
peak=    3.480 closest distance to " CB  ASP A 140 " =    0.857
peak=    3.479 closest distance to " CB  ALA A 291 " =    1.310
peak=    3.475 closest distance to " CG1 ILE A  33 " =    1.382
peak=    3.471 closest distance to " OG BSER A 212 " =    2.830
peak=    3.465 closest distance to " O   HOH Z 290 " =    1.094
peak=    3.455 closest distance to " O   HOH Z 195 " =    1.368
peak=    3.455 closest distance to " O   HOH Z 258 " =    2.299
peak=    3.454 closest distance to " CE3 TRP A 150 " =    0.981
peak=    3.453 closest distance to " O   HOH Z 175 " =    2.166
peak=    3.452 closest distance to " O   HOH Z  22 " =    2.116
peak=    3.452 closest distance to " OE2 GLU A  53 " =    1.953
peak=    3.451 closest distance to " CA  ASN A 127 " =    1.042
peak=    3.440 closest distance to " CB  SER A 276 " =    1.174
peak=    3.422 closest distance to " O   HOH Z 250 " =    1.344
peak=    3.422 closest distance to " O   HOH Z  43 " =    1.964
peak=    3.420 closest distance to " CA  LYS A 117 " =    1.174
peak=    3.420 closest distance to " O   HOH Z 184 " =    1.263
peak=    3.416 closest distance to " CG1BVAL A  72 " =    1.415
peak=    3.414 closest distance to " O   HOH Z   9 " =    1.778
peak=    3.412 closest distance to " O   HOH Z 303 " =    1.852
peak=    3.408 closest distance to " CD1 LEU A 300 " =    1.183
peak=    3.402 closest distance to " O   HOH Z  10 " =    1.721
peak=    3.399 closest distance to " O   TYR A 116 " =    1.297
peak=    3.397 closest distance to " CB  SER A  62 " =    1.178
peak=    3.376 closest distance to " NZ  LYS A  48 " =    1.356
peak=    3.374 closest distance to " O   HOH Z 359 " =    1.268
peak=    3.373 closest distance to " O   HOH Z 145 " =    1.790
peak=    3.371 closest distance to " O   HOH Z 344 " =    2.905
peak=    3.370 closest distance to " NE AARG A 275 " =    1.303
peak=    3.366 closest distance to " CD  LYS A 166 " =    1.384
peak=    3.365 closest distance to " O   HOH Z 153 " =    3.762
peak=    3.363 closest distance to " CB  ALA A 104 " =    0.717
peak=    3.359 closest distance to " CB  ILE A 234 " =    0.895
peak=    3.358 closest distance to " CB  LEU A 237 " =    0.876
peak=    3.354 closest distance to " CB  ASN A 110 " =    1.087
peak=    3.350 closest distance to " CB  GLU A 175 " =    1.049
peak=    3.348 closest distance to " CE1 TYR A 186 " =    1.321
peak=    3.347 closest distance to " CB  SER A  26 " =    1.585
peak=    3.344 closest distance to " OG BSER A 164 " =    2.281
peak=    3.343 closest distance to " O   CYS A 168 " =    1.193
peak=    3.342 closest distance to " O   HOH Z 207 " =    1.830
peak=    3.341 closest distance to " CE  LYS A  76 " =    0.872
peak=    3.340 closest distance to " OG BSER A 134 " =    3.013
peak=    3.338 closest distance to " OE2 GLU A   2 " =    1.887
peak=    3.338 closest distance to " CG1 ILE A 151 " =    1.092
peak=    3.333 closest distance to " CA  LYS A 290 " =    1.299
peak=    3.330 closest distance to " O   HOH Z 148 " =    2.209
peak=    3.327 closest distance to " O   HOH Z 213 " =    2.243
peak=    3.324 closest distance to " O   HOH Z 172 " =    2.935
peak=    3.322 closest distance to " O   HOH Z 305 " =    3.402
peak=    3.318 closest distance to " O   HOH Z 148 " =    3.460
peak=    3.318 closest distance to " O   HOH Z 227 " =    1.648
peak=    3.317 closest distance to " CB  HIS A 108 " =    0.844
peak=    3.317 closest distance to " CB  ARG A 139 " =    0.955
peak=    3.317 closest distance to " O   HOH Z  44 " =    1.729
peak=    3.315 closest distance to " O   HOH Z  40 " =    2.028
peak=    3.315 closest distance to " O   HOH Z 343 " =    3.371
peak=    3.310 closest distance to " CD1 LEU A   5 " =    1.472
peak=    3.306 closest distance to " O   HOH Z 133 " =    2.470
peak=    3.304 closest distance to " O   HOH Z 329 " =    3.843
peak=    3.303 closest distance to " O   HOH Z 145 " =    1.452
peak=    3.298 closest distance to " CB  ARG A 190 " =    1.675
peak=    3.297 closest distance to " CA  TYR A 116 " =    1.456
peak=    3.294 closest distance to " CA  THR A 221 " =    0.914
peak=    3.292 closest distance to " CG1 ILE A 120 " =    1.392
peak=    3.291 closest distance to " O   HOH Z 180 " =    2.061
peak=    3.282 closest distance to " CA  LEU A 282 " =    1.156
peak=    3.281 closest distance to " CA  ALA A 154 " =    0.983
peak=    3.281 closest distance to " O   HOH Z 334 " =    1.538
peak=    3.278 closest distance to " O   HOH Z 109 " =    2.426
peak=    3.271 closest distance to " O   HOH Z 145 " =    3.604
peak=    3.268 closest distance to " O   HOH Z   1 " =    1.770
peak=    3.267 closest distance to " CB  ALA A  34 " =    1.050
peak=    3.267 closest distance to " O   HOH Z 371 " =    1.730
peak=    3.259 closest distance to " O   HOH Z 405 " =    1.380
peak=    3.258 closest distance to " O   HOH Z 424 " =    2.513
peak=    3.257 closest distance to " O   HOH Z 227 " =    2.001
peak=    3.256 closest distance to " CB  ASN A 215 " =    1.110
peak=    3.251 closest distance to " NE1 TRP A 274 " =    0.999
peak=    3.249 closest distance to " CE3 TRP A  85 " =    1.162
peak=    3.249 closest distance to " CD  PRO A 243 " =    1.479
peak=    3.248 closest distance to " NH2BARG A 190 " =    1.525
peak=    3.246 closest distance to " CB  ASN A 224 " =    1.024
peak=    3.245 closest distance to " CA  VAL A  41 " =    0.801
peak=    3.245 closest distance to " CA  ILE A 106 " =    0.759
peak=    3.245 closest distance to " CG1AVAL A 121 " =    0.745
peak=    3.243 closest distance to " CB  ALA A 137 " =    1.135
peak=    3.236 closest distance to " O   HOH Z 133 " =    1.631
peak=    3.236 closest distance to " O   HOH Z 132 " =    2.422
peak=    3.233 closest distance to " CD  ARG A  14 " =    1.395
peak=    3.230 closest distance to " O   HOH Z  21 " =    1.731
peak=    3.229 closest distance to " N   SER A 135 " =    1.271
peak=    3.227 closest distance to " N   ASN A  39 " =    1.070
peak=    3.226 closest distance to " O   ASN A 209 " =    1.407
peak=    3.223 closest distance to " CG  GLN A 278 " =    1.286
peak=    3.221 closest distance to " CH2 TRP A 266 " =    1.101
peak=    3.220 closest distance to " CA  ARG A 102 " =    1.161
peak=    3.219 closest distance to " ND2 ASN A 249 " =    0.847
peak=    3.215 closest distance to " NZ BLYS A 290 " =    0.986
peak=    3.214 closest distance to " NE2 GLN A  58 " =    3.615
peak=    3.212 closest distance to " O   HOH Z  93 " =    2.527
peak=    3.206 closest distance to " CA  ARG A 195 " =    1.212
peak=    3.206 closest distance to " O   HOH Z 110 " =    1.620
peak=    3.204 closest distance to " CG  GLN A  89 " =    1.426
peak=    3.201 closest distance to " CB  ALA A  10 " =    0.842
peak=    3.201 closest distance to " O   HOH Z 280 " =    3.022
peak=    3.200 closest distance to " CA  GLY A 267 " =    0.996
peak=    3.195 closest distance to " N   TYR A  15 " =    0.905
peak=    3.188 closest distance to " NH1BARG A 145 " =    1.314
peak=    3.185 closest distance to " N   ASN A 127 " =    1.339
peak=    3.185 closest distance to " O   HOH Z 409 " =    2.749
peak=    3.181 closest distance to " O   HOH Z 383 " =    1.883
peak=    3.179 closest distance to " O   HOH Z  58 " =    1.737
peak=    3.174 closest distance to " O   HOH Z  59 " =    2.021
peak=    3.172 closest distance to " O   HOH Z 406 " =    1.554
peak=    3.165 closest distance to " CZ  PHE A  38 " =    1.145
peak=    3.156 closest distance to " CE  MET A  93 " =    1.486
peak=    3.156 closest distance to " CA  MET A 105 " =    0.893
peak=    3.151 closest distance to " CA  GLY A 136 " =    1.016
peak=    3.151 closest distance to " O   HOH Z 361 " =    1.314
peak=    3.150 closest distance to " CG  ARG A 159 " =    0.921
peak=    3.149 closest distance to " CA  ASN A 217 " =    1.277
peak=    3.141 closest distance to " CA  ARG A  36 " =    1.063
peak=    3.141 closest distance to " CA  ALA A 248 " =    1.202
peak=    3.139 closest distance to " CA  ALA A 158 " =    1.167
peak=    3.136 closest distance to " CA  LEU A 101 " =    1.697
peak=    3.129 closest distance to " NZ  LYS A  76 " =    1.489
peak=    3.126 closest distance to " O   HOH Z 248 " =    1.670
peak=    3.126 closest distance to " O  BHOH Z 338 " =    2.475
peak=    3.125 closest distance to " CB  ALA A 114 " =    1.199
peak=    3.124 closest distance to " CG2 ILE A 239 " =    0.705
peak=    3.123 closest distance to " O   HOH Z 389 " =    3.351
peak=    3.123 closest distance to " O   HOH Z  50 " =    1.514
peak=    3.115 closest distance to " CG2 ILE A  20 " =    1.661
peak=    3.114 closest distance to " CG2 ILE A  20 " =    1.145
peak=    3.108 closest distance to " N   SER A  12 " =    1.563
peak=    3.107 closest distance to " N   ALA A 233 " =    0.794
peak=    3.095 closest distance to " CB  TYR A  30 " =    1.633
peak=    3.094 closest distance to " N   VAL A 296 " =    1.726
peak=    3.091 closest distance to " NE2 HIS A 207 " =    1.249
peak=    3.082 closest distance to " CB  ALA A   1 " =    4.653
peak=    3.078 closest distance to " CB  TRP A 150 " =    1.381
peak=    3.074 closest distance to " O   HOH Z 219 " =    2.339
peak=    3.073 closest distance to " O   HOH Z 105 " =    1.598
peak=    3.071 closest distance to " O   HOH Z 390 " =    2.537
peak=    3.059 closest distance to " CB  PHE A 204 " =    0.760
peak=    3.056 closest distance to " O   HOH Z 272 " =    2.260
peak=    3.050 closest distance to " O   HOH Z 154 " =    1.882
peak=    3.032 closest distance to " O   ARG A 275 " =    1.410
peak=    3.028 closest distance to " CB  ALA A 180 " =    1.292

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 195         
Filter by distance & map next to the model:
   mapped sites are within: 0.737 - 5.366
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 195
   mapped sites are within: 0.737 - 5.366

peak=   -5.147 closest distance to " CG2 VAL A 230 " =    0.769
peak=   -4.527 closest distance to " CD  ARG A 156 " =    1.989
peak=   -4.391 closest distance to " CB  PRO A 243 " =    2.613
peak=   -4.159 closest distance to " CD1 LEU A 255 " =    2.933
peak=   -4.128 closest distance to " O   HOH Z 266 " =    5.007
peak=   -4.118 closest distance to " O   HOH Z 290 " =    1.137
peak=   -4.092 closest distance to " O   HOH Z 231 " =    1.683
peak=   -4.085 closest distance to " CD  ARG A  14 " =    3.163
peak=   -4.083 closest distance to " OG BSER A 134 " =    1.295
peak=   -4.061 closest distance to " O   PRO A 198 " =    1.157
peak=   -4.059 closest distance to " O   HOH Z 185 " =    2.185
peak=   -4.040 closest distance to " N   THR A 157 " =    1.445
peak=   -4.018 closest distance to " O   HOH Z 351 " =    1.442
peak=   -3.855 closest distance to " O   VAL A  67 " =    2.489
peak=   -3.838 closest distance to " CG2 VAL A 296 " =    1.761
peak=   -3.832 closest distance to " CZ3 TRP A 179 " =    1.227
peak=   -3.814 closest distance to " OG  SER A  87 " =    1.363
peak=   -3.814 closest distance to " OE1 GLN A  88 " =    1.113
peak=   -3.807 closest distance to " O   HOH Z 359 " =    1.629
peak=   -3.796 closest distance to " O   SER A 135 " =    1.438
peak=   -3.785 closest distance to " CB  ALA A  43 " =    2.456
peak=   -3.761 closest distance to " CE2 TYR A  30 " =    2.746
peak=   -3.757 closest distance to " O   HOH Z 231 " =    1.056
peak=   -3.757 closest distance to " CB  ALA A 248 " =    2.018
peak=   -3.746 closest distance to " O   HOH Z  65 " =    1.053
peak=   -3.744 closest distance to " NH2 ARG A  79 " =    1.976
peak=   -3.738 closest distance to " CB  ALA A 161 " =    2.566
peak=   -3.715 closest distance to " O   PRO A 163 " =    1.963
peak=   -3.714 closest distance to " O   HOH Z  43 " =    1.833
peak=   -3.707 closest distance to " O   HOH Z 140 " =    1.374
peak=   -3.694 closest distance to " C   HIS A 108 " =    1.187
peak=   -3.691 closest distance to " CG  GLN A 223 " =    2.045
peak=   -3.662 closest distance to " CG  MET A 105 " =    0.946
peak=   -3.659 closest distance to " CD2 LEU A   5 " =    0.950
peak=   -3.651 closest distance to " N   ALA A  43 " =    2.539
peak=   -3.645 closest distance to " O   HOH Z  11 " =    1.942
peak=   -3.635 closest distance to " O   HOH Z 191 " =    5.366
peak=   -3.628 closest distance to " O   TYR A 247 " =    2.860
peak=   -3.624 closest distance to " CD  GLN A  58 " =    1.023
peak=   -3.620 closest distance to " O   HOH Z 389 " =    2.009
peak=   -3.611 closest distance to " O   HOH Z 359 " =    3.438
peak=   -3.599 closest distance to " CE2 PHE A 218 " =    2.457
peak=   -3.592 closest distance to " N   GLN A  58 " =    1.889
peak=   -3.591 closest distance to " N   ALA A 226 " =    2.098
peak=   -3.590 closest distance to " O   ARG A 145 " =    1.487
peak=   -3.590 closest distance to " O   HOH Z 211 " =    1.389
peak=   -3.588 closest distance to " CB  TYR A  15 " =    2.109
peak=   -3.588 closest distance to " CE2 TYR A 116 " =    3.059
peak=   -3.583 closest distance to " C   MET A 188 " =    1.487
peak=   -3.581 closest distance to " C   LEU A 222 " =    0.842
peak=   -3.572 closest distance to " CG  TRP A 266 " =    1.843
peak=   -3.571 closest distance to " O   HOH Z 377 " =    1.978
peak=   -3.566 closest distance to " CA  GLY A 203 " =    2.337
peak=   -3.564 closest distance to " CD1 LEU A 228 " =    2.249
peak=   -3.563 closest distance to " ND2 ASN A 249 " =    2.530
peak=   -3.545 closest distance to " O   HOH Z  52 " =    1.543
peak=   -3.542 closest distance to " CG2 THR A 178 " =    2.216
peak=   -3.538 closest distance to " CG2 VAL A 296 " =    1.194
peak=   -3.537 closest distance to " O   HOH Z 198 " =    2.431
peak=   -3.536 closest distance to " CD  LYS A 289 " =    2.457
peak=   -3.533 closest distance to " O   HOH Z 394 " =    1.475
peak=   -3.533 closest distance to " O   SER A  22 " =    2.345
peak=   -3.523 closest distance to " O   HOH Z 350 " =    1.924
peak=   -3.522 closest distance to " O   HOH Z 377 " =    0.795
peak=   -3.518 closest distance to " CG1 VAL A 197 " =    2.341
peak=   -3.506 closest distance to " CA  GLY A 241 " =    2.227
peak=   -3.504 closest distance to " O   HOH Z 298 " =    1.164
peak=   -3.499 closest distance to " CZ2 TRP A 274 " =    0.956
peak=   -3.492 closest distance to " CG  ASP A 231 " =    0.737
peak=   -3.489 closest distance to " O   HOH Z 407 " =    3.135
peak=   -3.486 closest distance to " O   HOH Z  51 " =    0.975
peak=   -3.479 closest distance to " ND2 ASN A 187 " =    1.630
peak=   -3.475 closest distance to " CB  ALA A 244 " =    2.117
peak=   -3.472 closest distance to " C   ALA A 158 " =    1.425
peak=   -3.472 closest distance to " CB  PRO A 163 " =    2.446
peak=   -3.461 closest distance to " CA  GLY A 133 " =    1.990
peak=   -3.456 closest distance to " O   HOH Z 134 " =    2.960
peak=   -3.455 closest distance to " CA  GLY A  98 " =    1.894
peak=   -3.451 closest distance to " CG1 VAL A 112 " =    2.600
peak=   -3.446 closest distance to " O   HOH Z 166 " =    1.874
peak=   -3.444 closest distance to " CD2 TYR A 293 " =    1.946
peak=   -3.434 closest distance to " O   HOH Z 389 " =    1.438
peak=   -3.432 closest distance to " O   HOH Z  60 " =    2.365
peak=   -3.431 closest distance to " OG  SER A   3 " =    1.432
peak=   -3.426 closest distance to " CD1 TYR A 169 " =    2.541
peak=   -3.410 closest distance to " OG  SER A  63 " =    1.141
peak=   -3.404 closest distance to " O   VAL A  67 " =    2.732
peak=   -3.403 closest distance to " CD1 LEU A 101 " =    2.294
peak=   -3.399 closest distance to " ND2 ASN A  45 " =    1.084
peak=   -3.398 closest distance to " O   HOH Z 427 " =    1.626
peak=   -3.397 closest distance to " O   GLY A  80 " =    2.442
peak=   -3.381 closest distance to " CG1 VAL A 296 " =    1.428
peak=   -3.379 closest distance to " O   GLY A  17 " =    1.247
peak=   -3.370 closest distance to " O   ALA A 161 " =    1.632
peak=   -3.368 closest distance to " O   ILE A  49 " =    1.753
peak=   -3.368 closest distance to " CB  PHE A 192 " =    1.723
peak=   -3.366 closest distance to " O   PRO A 243 " =    2.550
peak=   -3.363 closest distance to " O   HOH Z 313 " =    1.519
peak=   -3.361 closest distance to " O   LEU A 101 " =    2.821
peak=   -3.361 closest distance to " CB  ASN A  39 " =    2.174
peak=   -3.351 closest distance to " CB  CYS A 201 " =    2.421
peak=   -3.343 closest distance to " O   HOH Z 201 " =    2.071
peak=   -3.339 closest distance to " O   HOH Z  90 " =    2.887
peak=   -3.336 closest distance to " OG  SER A  97 " =    2.158
peak=   -3.333 closest distance to " O   HOH Z 114 " =    2.977
peak=   -3.332 closest distance to " CB  ALA A 248 " =    2.439
peak=   -3.328 closest distance to " O   HOH Z 368 " =    1.342
peak=   -3.322 closest distance to " CB  ASP A 132 " =    2.321
peak=   -3.321 closest distance to " O   HOH Z 134 " =    3.629
peak=   -3.321 closest distance to " CE  LYS A  76 " =    2.782
peak=   -3.319 closest distance to " O   HOH Z 131 " =    4.084
peak=   -3.318 closest distance to " O   HOH Z 348 " =    1.785
peak=   -3.316 closest distance to " O   HOH Z  39 " =    1.188
peak=   -3.313 closest distance to " CB  ALA A 291 " =    2.137
peak=   -3.308 closest distance to " CE  LYS A 166 " =    1.238
peak=   -3.307 closest distance to " CD1 PHE A  59 " =    1.994
peak=   -3.307 closest distance to " C   GLU A 236 " =    0.859
peak=   -3.304 closest distance to " O   ALA A   1 " =    1.709
peak=   -3.303 closest distance to " CD  PRO A 243 " =    2.133
peak=   -3.296 closest distance to " N   ASP A 270 " =    1.446
peak=   -3.293 closest distance to " O   VAL A 189 " =    2.608
peak=   -3.285 closest distance to " O   GLY A 203 " =    2.486
peak=   -3.279 closest distance to " C   ASN A 187 " =    1.784
peak=   -3.277 closest distance to " O   GLY A 229 " =    1.966
peak=   -3.274 closest distance to " OD2 ASP A 191 " =    1.357
peak=   -3.268 closest distance to " CG  PRO A 163 " =    2.547
peak=   -3.250 closest distance to " CZ  PHE A  59 " =    1.433
peak=   -3.248 closest distance to " CE  MET A 105 " =    2.354
peak=   -3.243 closest distance to " O   HOH Z 243 " =    1.974
peak=   -3.238 closest distance to " CG  GLN A 278 " =    2.162
peak=   -3.238 closest distance to " OD1 ASN A 148 " =    1.436
peak=   -3.238 closest distance to " O   SER A 271 " =    2.201
peak=   -3.236 closest distance to " CA  ASP A  27 " =    2.366
peak=   -3.231 closest distance to " O   HOH Z  24 " =    1.272
peak=   -3.231 closest distance to " O   HOH Z 292 " =    1.647
peak=   -3.228 closest distance to " O   HOH Z 165 " =    2.170
peak=   -3.226 closest distance to " O   HOH Z 423 " =    2.271
peak=   -3.220 closest distance to " CG  PHE A 283 " =    2.624
peak=   -3.214 closest distance to " CZ  TYR A 172 " =    1.825
peak=   -3.213 closest distance to " O   HOH Z   9 " =    1.646
peak=   -3.212 closest distance to " ND2 ASN A  45 " =    1.971
peak=   -3.207 closest distance to " O   HOH Z 309 " =    2.297
peak=   -3.206 closest distance to " N   ALA A 248 " =    1.588
peak=   -3.206 closest distance to " CG  GLN A  88 " =    0.910
peak=   -3.205 closest distance to " CZ  TYR A 169 " =    1.563
peak=   -3.200 closest distance to " CB  TYR A 172 " =    2.377
peak=   -3.199 closest distance to " O   HOH Z 437 " =    2.006
peak=   -3.196 closest distance to " O   HOH Z 346 " =    1.766
peak=   -3.194 closest distance to " O   HOH Z 166 " =    1.438
peak=   -3.189 closest distance to " O   HOH Z 357 " =    2.011
peak=   -3.188 closest distance to " O   HOH Z 100 " =    1.248
peak=   -3.177 closest distance to " CG2 VAL A 202 " =    2.707
peak=   -3.176 closest distance to " OE2 GLU A 152 " =    1.067
peak=   -3.171 closest distance to " O   SER A 210 " =    1.957
peak=   -3.167 closest distance to " CB  ALA A 114 " =    2.340
peak=   -3.165 closest distance to " O   HOH Z 377 " =    1.221
peak=   -3.165 closest distance to " OG BSER A 134 " =    1.791
peak=   -3.161 closest distance to " O   HOH Z 340 " =    1.893
peak=   -3.161 closest distance to " O   ASN A 301 " =    1.513
peak=   -3.159 closest distance to " O   HOH Z   2 " =    1.832
peak=   -3.157 closest distance to " CB  ALA A 291 " =    2.240
peak=   -3.156 closest distance to " O   HOH Z 102 " =    1.646
peak=   -3.150 closest distance to " CE BMET A  47 " =    1.576
peak=   -3.149 closest distance to " O   HOH Z 111 " =    4.283
peak=   -3.146 closest distance to " CG2 VAL A 296 " =    1.963
peak=   -3.141 closest distance to " O   HOH Z 417 " =    2.928
peak=   -3.139 closest distance to " ND2BASN A 224 " =    1.571
peak=   -3.138 closest distance to " CG1 VAL A 230 " =    1.897
peak=   -3.135 closest distance to " O   HOH Z   2 " =    1.705
peak=   -3.134 closest distance to " CB  TRP A  85 " =    2.491
peak=   -3.131 closest distance to " ND2 ASN A 285 " =    2.063
peak=   -3.131 closest distance to " O   HOH Z  67 " =    3.131
peak=   -3.129 closest distance to " O   HOH Z 286 " =    1.826
peak=   -3.117 closest distance to " CG  ASN A 301 " =    1.980
peak=   -3.117 closest distance to " OG ASER A 216 " =    1.068
peak=   -3.114 closest distance to " NH2 ARG A 219 " =    1.689
peak=   -3.112 closest distance to " CD  LYS A 166 " =    2.493
peak=   -3.110 closest distance to " O   HOH Z 111 " =    1.114
peak=   -3.103 closest distance to " CB  ALA A 129 " =    2.436
peak=   -3.100 closest distance to " ND2 ASN A  45 " =    1.454
peak=   -3.098 closest distance to " O   MET A  40 " =    2.764
peak=   -3.091 closest distance to " OG  SER A 206 " =    1.690
peak=   -3.088 closest distance to " CD  ARG A 139 " =    1.605
peak=   -3.085 closest distance to " CD2 LEU A 297 " =    1.899
peak=   -3.085 closest distance to " OE1 GLU A 277 " =    2.236
peak=   -3.082 closest distance to " O   LYS A 289 " =    3.035
peak=   -3.078 closest distance to " O   HOH Z 353 " =    1.717
peak=   -3.078 closest distance to " O   HOH Z 412 " =    4.115
peak=   -3.078 closest distance to " O   PRO A 198 " =    1.349
peak=   -3.073 closest distance to " N   VAL A  72 " =    1.607
peak=   -3.072 closest distance to " CD1 TYR A 247 " =    2.703
peak=   -3.068 closest distance to " O   HOH Z 435 " =    2.064
peak=   -3.047 closest distance to " NE2 GLN A  11 " =    1.118
peak=   -3.004 closest distance to " CD1 PHE A  61 " =    2.917

================= 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    :  0.4543 0.4430   6.255587e+00   6.236064e+00
   1_bss:  0.4458 0.4283   6.249304e+00   6.223982e+00
   1_xyz:  0.3511 0.3728   6.097910e+00   6.132503e+00
   1_adp:  0.2966 0.3423   5.979510e+00   6.078770e+00
   1_occ:  0.2963 0.3425   5.978701e+00   6.079613e+00
   2_bss:  0.2922 0.3374   5.978184e+00   6.075790e+00
   2_xyz:  0.2144 0.2680   5.706540e+00   5.862914e+00
   2_adp:  0.1962 0.2532   5.635742e+00   5.813430e+00
   2_occ:  0.1961 0.2529   5.635278e+00   5.813262e+00
   3_bss:  0.1956 0.2502   5.632765e+00   5.808461e+00
   3_xyz:  0.1553 0.2028   5.423396e+00   5.629325e+00
   3_adp:  0.1420 0.1939   5.353709e+00   5.577232e+00
   3_occ:  0.1420 0.1938   5.353506e+00   5.577049e+00
   4_bss:  0.1419 0.1935   5.352124e+00   5.575405e+00
   4_xyz:  0.1198 0.1719   5.215741e+00   5.468871e+00
   4_adp:  0.1166 0.1637   5.179681e+00   5.421420e+00
   4_occ:  0.1165 0.1637   5.179297e+00   5.420931e+00
   5_bss:  0.1166 0.1636   5.179714e+00   5.419988e+00
   5_xyz:  0.1172 0.1614   5.180174e+00   5.411340e+00
   5_adp:  0.1164 0.1610   5.176452e+00   5.410629e+00
   5_occ:  0.1164 0.1609   5.176111e+00   5.410050e+00
   5_bss:  0.1164 0.1609   5.176073e+00   5.410004e+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:  0.377  20.001   7.214  10.004   7.690   0.000   0.000   0.000
   1_xyz:  0.377  20.001   7.214  10.004   7.690   0.000   0.000   0.000
   1_adp:  0.377  20.001   7.214  10.004   7.690   0.000   0.000   0.000
   1_occ:  0.377  20.001   7.214  10.004   7.690   0.000   0.000   0.000
   2_bss:  0.349  37.059   3.865   5.553   4.610   0.000   0.000   0.000
   2_xyz:  0.349  37.059   3.865   5.553   4.610   0.000   0.000   0.000
   2_adp:  0.349  37.059   3.865   5.553   4.610   0.000   0.000   0.000
   2_occ:  0.349  37.059   3.865   5.553   4.610   0.000   0.000   0.000
   3_bss:  0.333  37.059   2.982   3.428   4.002   0.000   0.000   0.000
   3_xyz:  0.333  37.059   2.982   3.428   4.002   0.000   0.000   0.000
   3_adp:  0.333  37.059   2.982   3.428   4.002   0.000   0.000   0.000
   3_occ:  0.333  37.059   2.982   3.428   4.002   0.000   0.000   0.000
   4_bss:  0.326  46.934   2.585   2.576   3.723   0.000   0.000   0.000
   4_xyz:  0.326  46.934   2.585   2.576   3.723   0.000   0.000   0.000
   4_adp:  0.326  46.934   2.585   2.576   3.723   0.000   0.000   0.000
   4_occ:  0.326  46.934   2.585   2.576   3.723   0.000   0.000   0.000
   5_bss:  0.327  46.934   2.505   2.386   3.709   0.000   0.000   0.000
   5_xyz:  0.327  46.934   2.505   2.386   3.709   0.000   0.000   0.000
   5_adp:  0.327  46.934   2.505   2.386   3.709   0.000   0.000   0.000
   5_occ:  0.327  46.934   2.505   2.386   3.709   0.000   0.000   0.000
   5_bss:  0.327  49.798  -0.356  -0.513   0.869   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.127 0.4943  0.5689    59499.970
   1_bss:  52.088 0.4928  0.7199    56901.614
   1_xyz:  42.046 0.6170  0.8828    40247.698
   1_adp:  36.507 0.6843  0.9981    33288.975
   1_occ:  36.580 0.6834  0.9960    33313.106
   2_bss:  36.207 0.6876  0.8799    32774.333
   2_xyz:  26.942 0.7906  0.9763    18579.401
   2_adp:  24.784 0.8141  0.9936    16447.837
   2_occ:  24.779 0.8141  0.9933    16429.367
   3_bss:  24.551 0.8162  0.9527    16141.928
   3_xyz:  19.463 0.8665  0.9890    10552.611
   3_adp:  18.133 0.8793  0.9896     9496.904
   3_occ:  18.126 0.8793  0.9894     9485.391
   4_bss:  18.081 0.8798  0.9717     9457.843
   4_xyz:  15.833 0.8993  0.9825     7508.776
   4_adp:  14.763 0.9085  0.9843     6869.105
   4_occ:  14.752 0.9086  0.9841     6852.602
   5_bss:  14.743 0.9087  0.9806     6847.284
   5_xyz:  14.494 0.9110  0.9797     6700.306
   5_adp:  14.429 0.9117  0.9766     6684.017
   5_occ:  14.420 0.9118  0.9765     6672.175
   5_bss:  14.420 0.9118  0.9765     6671.715
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3608e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3608e+01
   1_xyz:   1.582  0.012  0.102 18.088  0.006  4.109   1.2631e-01
   1_adp:   1.582  0.012  0.102 18.088  0.006  4.109   1.2631e-01
   1_occ:   1.582  0.012  0.102 18.088  0.006  4.109   1.2631e-01
   2_bss:   1.582  0.012  0.102 18.088  0.006  4.109   1.2631e-01
   2_xyz:   1.021  0.007  0.075 15.883  0.004  4.120   6.8003e-02
   2_adp:   1.021  0.007  0.075 15.883  0.004  4.120   6.8003e-02
   2_occ:   1.021  0.007  0.075 15.883  0.004  4.120   6.8003e-02
   3_bss:   1.021  0.007  0.075 15.883  0.004  4.120   6.8003e-02
   3_xyz:   0.910  0.006  0.069 15.572  0.003  4.122   5.4366e-02
   3_adp:   0.910  0.006  0.069 15.572  0.003  4.122   5.4366e-02
   3_occ:   0.910  0.006  0.069 15.572  0.003  4.122   5.4366e-02
   4_bss:   0.910  0.006  0.069 15.572  0.003  4.122   5.4366e-02
   4_xyz:   1.091  0.009  0.085 15.985  0.004  4.117   7.2578e-02
   4_adp:   1.091  0.009  0.085 15.985  0.004  4.117   7.2578e-02
   4_occ:   1.091  0.009  0.085 15.985  0.004  4.117   7.2578e-02
   5_bss:   1.091  0.009  0.085 15.985  0.004  4.117   7.2578e-02
   5_xyz:   0.878  0.005  0.070 15.327  0.003  4.113   5.0825e-02
   5_adp:   0.878  0.005  0.070 15.327  0.003  4.113   5.0825e-02
   5_occ:   0.878  0.005  0.070 15.327  0.003  4.113   5.0825e-02
   5_bss:   0.878  0.005  0.070 15.327  0.003  4.113   5.0825e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9498e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9498e+00
   1_xyz:  12.509  0.170  0.419 89.106  0.032  2.220   9.1371e-02
   1_adp:  12.509  0.170  0.419 89.106  0.032  2.220   9.1371e-02
   1_occ:  12.509  0.170  0.419 89.106  0.032  2.220   9.1371e-02
   2_bss:  12.509  0.170  0.419 89.106  0.032  2.220   9.1371e-02
   2_xyz:   6.400  0.075  0.305 82.737  0.038  2.300   6.2902e-02
   2_adp:   6.400  0.075  0.305 82.737  0.038  2.300   6.2902e-02
   2_occ:   6.400  0.075  0.305 82.737  0.038  2.300   6.2902e-02
   3_bss:   6.400  0.075  0.305 82.737  0.038  2.300   6.2902e-02
   3_xyz:   6.677  0.043  0.317 81.213  0.029  2.334   4.5521e-02
   3_adp:   6.677  0.043  0.317 81.213  0.029  2.334   4.5521e-02
   3_occ:   6.677  0.043  0.317 81.213  0.029  2.334   4.5521e-02
   4_bss:   6.677  0.043  0.317 81.213  0.029  2.334   4.5521e-02
   4_xyz:   9.605  0.065  0.454 83.731  0.040  2.293   5.8620e-02
   4_adp:   9.605  0.065  0.454 83.731  0.040  2.293   5.8620e-02
   4_occ:   9.605  0.065  0.454 83.731  0.040  2.293   5.8620e-02
   5_bss:   9.605  0.065  0.454 83.731  0.040  2.293   5.8620e-02
   5_xyz:   7.148  0.040  0.351 83.994  0.038  2.375   3.1437e-02
   5_adp:   7.148  0.040  0.351 83.994  0.038  2.375   3.1437e-02
   5_occ:   7.148  0.040  0.351 83.994  0.038  2.375   3.1437e-02
   5_bss:   7.148  0.040  0.351 83.994  0.038  2.375   3.1437e-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:  77.01   0.00  12.12  70.57   0.00   9.40  77.01   0.00  26.93
   1_occ:  77.01   0.00  12.12  70.57   0.00   9.40  77.01   0.00  26.93
   2_bss:  77.01   0.00  12.12  70.57   0.00   9.40  77.01   0.00  26.93
   2_xyz:  77.01   0.00  12.12  70.57   0.00   9.40  77.01   0.00  26.93
   2_adp:  79.08   0.00  11.99  74.50   0.00   8.62  79.08   0.93  30.32
   2_occ:  79.08   0.00  11.99  74.50   0.00   8.62  79.08   0.93  30.32
   3_bss:  79.08   0.00  11.99  74.50   0.00   8.62  79.08   0.93  30.32
   3_xyz:  79.08   0.00  11.99  74.50   0.00   8.62  79.08   0.93  30.32
   3_adp:  87.64   0.00  13.05  87.64   0.00   8.55  87.39   1.26  37.55
   3_occ:  87.64   0.00  13.05  87.64   0.00   8.55  87.39   1.26  37.55
   4_bss:  87.64   0.00  13.05  87.64   0.00   8.55  87.39   1.26  37.55
   4_xyz:  87.64   0.00  13.05  87.64   0.00   8.55  87.39   1.26  37.55
   4_adp:  88.10   0.00  12.33  88.10   0.00   8.10  82.96   1.66  35.36
   4_occ:  88.10   0.00  12.33  88.10   0.00   8.10  82.96   1.66  35.36
   5_bss:  88.10   0.00  12.33  88.10   0.00   8.10  82.96   1.66  35.36
   5_xyz:  88.10   0.00  12.33  88.10   0.00   8.10  82.96   1.66  35.36
   5_adp:  88.55   0.00  12.22  88.55   0.00   8.00  82.04   1.66  35.20
   5_occ:  88.55   0.00  12.22  88.55   0.00   8.00  82.04   1.66  35.20
   5_bss:  91.42   2.86  15.09  91.42   2.86  10.87  84.90   4.53  38.07
------------------------------------------------------------------------
 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:    1.221    0.019    0.404
   1_adp:    1.221    0.019    0.404
   1_occ:    1.221    0.019    0.404
   2_bss:    1.221    0.019    0.404
   2_xyz:    1.406    0.024    0.535
   2_adp:    1.406    0.024    0.535
   2_occ:    1.406    0.024    0.535
   3_bss:    1.406    0.024    0.535
   3_xyz:    1.573    0.038    0.587
   3_adp:    1.573    0.038    0.587
   3_occ:    1.573    0.038    0.587
   4_bss:    1.573    0.038    0.587
   4_xyz:    1.735    0.030    0.634
   4_adp:    1.735    0.030    0.634
   4_occ:    1.735    0.030    0.634
   5_bss:    1.735    0.030    0.634
   5_xyz:    1.789    0.047    0.640
   5_adp:    1.789    0.047    0.640
   5_occ:    1.789    0.047    0.640
   5_bss:    1.789    0.047    0.640
------------------------------------------------------------------------

CPU time actual refinement: 336.36


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_753/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_753/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_753/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_753/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_753/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.21 
  Macro-tasks:
    bulk solvent and scale       = 40.39  
    individual site refinement   = 143.32 
    weights calculation          = 33.08  
    collect and process          = 6.68   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 223.59 
  Micro-tasks:
    mask                            = 2.40   
    f_calc                          = 102.38 
    alpha_beta                      = 8.52   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 114.33 
    fmodel                         = 7.43   
    r_factors                      = 0.30   
    phase_errors                   = 10.79  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 247.55 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.656 micro seconds
Total CPU time: 5.83 minutes
from_scatterers_fft:    651 calls, 101.84 s
gradients_fft:          597 calls, 100.08 s

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

# Date 2008-01-16 Time 02:20:50 PST -0800 (1200478850.52 s)
Start R-work = 0.4543, R-free = 0.4430 (no bulk solvent and anisotropic scale)
Final R-work = 0.1334, R-free = 0.1776 (no bulk solvent and anisotropic scale)

Start R-work = 0.4458, R-free = 0.4283
Final R-work = 0.1164, R-free = 0.1609