# Date 2008-01-16 Time 02:33:33 PST -0800 (1200479613.36 s)
#phil __OFF__

Command line arguments: "../881.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8912
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 881

-------------------------------------------------------------------------------
  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: (70.9525, 46.4607, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.4607, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.96111
Completeness in resolution range: 0.948482
Completeness with d_max=infinity: 0.945643

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0179
                             d_min =   1.9611

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: (70.9525, 46.4607, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.96111
Completeness in resolution range: 0.948482
Completeness with d_max=infinity: 0.945643

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0183 -  4.1972 [2161/2190]  1948   213   9.9%
  bin  2:  4.1972 -  3.3435 [2088/2104]  1879   209  10.0%
  bin  3:  3.3435 -  2.9244 [2041/2060]  1832   209  10.2%
  bin  4:  2.9244 -  2.6587 [2047/2077]  1850   197   9.6%
  bin  5:  2.6587 -  2.4690 [2038/2057]  1831   207  10.2%
  bin  6:  2.4690 -  2.3240 [2006/2031]  1801   205  10.2%
  bin  7:  2.3240 -  2.2080 [1991/2025]  1796   195   9.8%
  bin  8:  2.2080 -  2.1121 [2008/2038]  1806   202  10.1%
  bin  9:  2.1121 -  2.0310 [1988/2030]  1790   198  10.0%
  bin 10:  2.0310 -  1.9611 [1221/2041]  1097   124  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_881/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: 0.12 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: 34
        2.42 -     3.04: 2231
        3.04 -     3.66: 4761
        3.66 -     4.28: 9115
        4.28 -     4.90: 12429
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.867 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.905 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.912 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.925 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28565 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_881/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_881/model_refine_001.geo

CPU time processing inputs: 8.74


============================ 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 = 70.9525 46.4607 84.6622 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: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4760   r_free= 0.4611   ksol= 0.00   Bsol= 0.00   scale= 0.802    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.274086                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6818 0.99   1402  158 0.3959 0.4079      6.5781      6.6087|
|  2:  4.6818 -  3.7349 0.99   1358  143 0.3932 0.3786      6.7786      6.7449|
|  3:  3.7349 -  3.2683 0.99   1327  151 0.4365 0.3884      6.6574      6.7342|
|  4:  3.2683 -  2.9720 0.99   1332  154 0.4563 0.4191      6.5187       6.465|
|  5:  2.9720 -  2.7604 0.99   1306  142 0.5042 0.4867      6.3618      6.3415|
|  6:  2.7604 -  2.5985 0.99   1303  148 0.5022 0.5283      6.2708      6.2807|
|  7:  2.5985 -  2.4690 0.99   1312  139 0.5155 0.4495      6.2588      6.1795|
|  8:  2.4690 -  2.3620 0.98   1276  147 0.5349 0.4904      6.1701      6.1779|
|  9:  2.3620 -  2.2713 0.98   1294  148 0.5041 0.4911        6.11      6.0786|
| 10:  2.2713 -  2.1932 0.99   1290  138 0.5215 0.5535      6.0986        6.12|
| 11:  2.1932 -  2.1248 0.99   1281  137 0.5246 0.4929      6.0394      6.0302|
| 12:  2.1248 -  2.0643 0.97   1264  146 0.5053 0.5370      5.9527      5.9943|
| 13:  2.0643 -  2.0100 0.97   1269  137 0.5425 0.5233      5.8851      5.8165|
| 14:  2.0100 -  1.9611 0.47    616   71 0.5606 0.5800      5.8452       5.822|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.6818  1402   158  0.67  36.53   0.80     0.72      77577.51|
|  2:  4.6818 -  3.7349  1358   143  0.71  34.40   0.88     0.79     104626.68|
|  3:  3.7349 -  3.2683  1327   151  0.61  43.15   0.84     0.75     110239.67|
|  4:  3.2683 -  2.9720  1332   154  0.54  48.78   0.82     0.66      97627.53|
|  5:  2.9720 -  2.7604  1306   142  0.43  57.29   0.74     0.53      81349.79|
|  6:  2.7604 -  2.5985  1303   148  0.41  58.71   0.73     0.49      70694.73|
|  7:  2.5985 -  2.4690  1312   139  0.41  59.48   0.76     0.46      61417.07|
|  8:  2.4690 -  2.3620  1276   147  0.41  59.31   0.71     0.49      55381.73|
|  9:  2.3620 -  2.2713  1294   148  0.41  59.30   0.75     0.47      49626.79|
| 10:  2.2713 -  2.1932  1290   138  0.38  61.33   0.75     0.46      47981.48|
| 11:  2.1932 -  2.1248  1281   137  0.34  64.44   0.78     0.43      45725.41|
| 12:  2.1248 -  2.0643  1264   146  0.31  66.68   0.76     0.39      43870.69|
| 13:  2.0643 -  2.0100  1269   137  0.26  70.73   0.74     0.34      39208.61|
| 14:  2.0100 -  1.9611   616    71  0.22  73.39   0.69     0.26      33722.03|
|alpha:            min =        0.26 max =            0.79 mean =         0.53|
|beta:             min =    33722.03 max =       110239.67 mean =     67353.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           89.98 mean =        55.75|
|phase err.(test): min =        0.00 max =           89.98 mean =        55.92|
|-----------------------------------------------------------------------------|

============================== 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 = 13.238694             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.476   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.196854              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.643   (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:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      174 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      710 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1524 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2670 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3956 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5120 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6648 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7777 |
|-----------------------------------------------------------------------------|
|-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 |       53.307 |
| 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 |       1.854 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    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 = 11.686)------------------------------------------|
|    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: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4812   r_free= 0.4659   ksol= 0.00   Bsol= 0.00   scale= 0.771    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.276829                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4670   r_free= 0.4501   ksol= 0.38   Bsol= 20.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.27,8.26,8.82,0.00,0.00,0.00); trace/3= 8.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.269096                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.846748             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.867   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.048821              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.277   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4670      final r-factor (work) = 0.3848          |
| start r-factor (free) = 0.4501      final r-factor (free) = 0.4061          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 87.3226 = 10.85 * 0.50 * 6.2721 + 1.00 * 53.3069                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.6613 = 10.85 * 0.50 * 6.1817 + 1.00 * 0.1355                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3848      final r-factor (work) = 0.3413          |
| start r-factor (free) = 0.4061      final r-factor (free) = 0.3948          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4979 = 1.05 * 1.00 * 6.1817 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4028 = 1.05 * 1.00 * 6.0904 + 1.00 * 0.0150                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.77  12.93    None  None   None       |
|    all(noH): 2823   0      0.00    101.77  12.93    None  None   None       |
|    Sol.    : 438    0      0.00    83.73   26.84    None  None   None       |
|    Mac.    : 2385   0      0.00    101.77  10.37    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.177: 1493   |   5:    50.885 -  61.062:   27        |
|      1:    10.177 -  20.354:  776   |   6:    61.062 -  71.239:    6        |
|      2:    20.354 -  30.531:  313   |   7:    71.239 -  81.416:    3        |
|      3:    30.531 -  40.708:  128   |   8:    81.416 -  91.593:    2        |
|      4:    40.708 -  50.885:   73   |   9:    91.593 - 101.769:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3413 r_free = 0.3948             target_work(ml) = 6.074         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3409 r_free = 0.3953             target_work(ml) = 6.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3409   r_free= 0.3953   ksol= 0.38   Bsol= 20.00   scale= 1.102   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.27,8.26,8.82,0.00,0.00,0.00); trace/3= 8.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.073667                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3376   r_free= 0.3913   ksol= 0.34   Bsol= 37.64   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.71,4.03,5.58,0.00,0.00,0.00); trace/3= 4.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.073326                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.781461              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.410   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.493976              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.002  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3376      final r-factor (work) = 0.2521          |
| start r-factor (free) = 0.3913      final r-factor (free) = 0.3062          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6904 = 4.78 * 0.50 * 6.0881 + 1.00 * 0.1355                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.3014 = 4.78 * 0.50 * 5.9519 + 1.00 * 0.0720                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2521      final r-factor (work) = 0.2315          |
| start r-factor (free) = 0.3062      final r-factor (free) = 0.2902          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9551 = 0.49 * 1.00 * 5.9519 + 1.00 * 0.0150                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8761 = 0.49 * 1.00 * 5.7992 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.60   13.09    None  None   None       |
|    all(noH): 2823   0      0.00    99.60   13.09    None  None   None       |
|    Sol.    : 438    0      0.00    82.37   31.82    None  None   None       |
|    Mac.    : 2385   0      0.00    99.60   9.66     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.960: 1608   |   5:    49.799 -  59.759:   34        |
|      1:     9.960 -  19.920:  633   |   6:    59.759 -  69.719:    5        |
|      2:    19.920 -  29.880:  250   |   7:    69.719 -  79.679:    3        |
|      3:    29.880 -  39.839:  204   |   8:    79.679 -  89.639:    1        |
|      4:    39.839 -  49.799:   82   |   9:    89.639 -  99.598:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2315 r_free = 0.2902             target_work(ml) = 5.776         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2312 r_free = 0.2899             target_work(ml) = 5.775         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2312   r_free= 0.2899   ksol= 0.34   Bsol= 37.64   scale= 1.055   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.71,4.03,5.58,0.00,0.00,0.00); trace/3= 4.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.774867                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2305   r_free= 0.2875   ksol= 0.34   Bsol= 42.97   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.33,2.05,3.56,0.00,0.00,0.00); trace/3= 2.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.774969                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.894859              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.116  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.571784              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.172  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2305      final r-factor (work) = 0.1708          |
| start r-factor (free) = 0.2875      final r-factor (free) = 0.2231          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4714 = 2.89 * 0.50 * 5.8030 + 1.00 * 0.0720                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2491 = 2.89 * 0.50 * 5.6574 + 1.00 * 0.0604                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1708      final r-factor (work) = 0.1539          |
| start r-factor (free) = 0.2231      final r-factor (free) = 0.2099          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 20.2183 = 3.57 * 1.00 * 5.6574 + 1.00 * 0.0114                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 19.5275 = 3.57 * 1.00 * 5.4628 + 1.00 * 0.0155                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.23  14.37    None  None   None       |
|    all(noH): 2823   0      0.00    106.23  14.37    None  None   None       |
|    Sol.    : 438    0      2.05    88.02   40.40    None  None   None       |
|    Mac.    : 2385   0      0.00    106.23  9.59     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.624: 1718   |   5:    53.117 -  63.741:   90        |
|      1:    10.624 -  21.247:  549   |   6:    63.741 -  74.364:   36        |
|      2:    21.247 -  31.870:  165   |   7:    74.364 -  84.987:    7        |
|      3:    31.870 -  42.494:  134   |   8:    84.987 -  95.611:    4        |
|      4:    42.494 -  53.117:  118   |   9:    95.611 - 106.234:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1539 r_free = 0.2099             target_work(ml) = 5.431         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1537 r_free = 0.2096             target_work(ml) = 5.431         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1537   r_free= 0.2096   ksol= 0.34   Bsol= 42.97   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.33,2.05,3.56,0.00,0.00,0.00); trace/3= 2.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.430520                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1537   r_free= 0.2093   ksol= 0.33   Bsol= 44.87   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.92,1.57,2.60,0.00,0.00,0.00); trace/3= 2.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.428661                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.916312              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.297   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.327852              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.253  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1537      final r-factor (work) = 0.1337          |
| start r-factor (free) = 0.2093      final r-factor (free) = 0.1827          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2972 = 1.92 * 0.50 * 5.4654 + 1.00 * 0.0604                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2004 = 1.92 * 0.50 * 5.3731 + 1.00 * 0.0521                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1337      final r-factor (work) = 0.1290          |
| start r-factor (free) = 0.1827      final r-factor (free) = 0.1766          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.5232 = 2.33 * 1.00 * 5.3731 + 1.00 * 0.0155                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.3176 = 2.33 * 1.00 * 5.2850 + 1.00 * 0.0148                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.37  14.29    None  None   None       |
|    all(noH): 2823   0      0.00    112.37  14.29    None  None   None       |
|    Sol.    : 438    0      3.03    95.98   40.72    None  None   None       |
|    Mac.    : 2385   0      0.00    112.37  9.43     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 -  11.237: 1821   |   5:    56.187 -  67.424:   62        |
|      1:    11.237 -  22.475:  503   |   6:    67.424 -  78.662:   34        |
|      2:    22.475 -  33.712:  147   |   7:    78.662 -  89.899:   10        |
|      3:    33.712 -  44.949:  125   |   8:    89.899 - 101.136:    5        |
|      4:    44.949 -  56.187:  114   |   9:   101.136 - 112.374:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1290 r_free = 0.1766             target_work(ml) = 5.267         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1289 r_free = 0.1764             target_work(ml) = 5.266         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1289   r_free= 0.1764   ksol= 0.33   Bsol= 44.87   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.92,1.57,2.60,0.00,0.00,0.00); trace/3= 2.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.266485                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1289   r_free= 0.1764   ksol= 0.32   Bsol= 44.31   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.79,1.49,2.31,0.00,0.00,0.00); trace/3= 1.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.266107                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.065330              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.536  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.994364              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.092  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1289      final r-factor (work) = 0.1192          |
| start r-factor (free) = 0.1764      final r-factor (free) = 0.1676          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5097 = 2.07 * 0.50 * 5.2849 + 1.00 * 0.0521                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4623 = 2.07 * 0.50 * 5.2335 + 1.00 * 0.0579                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1192      final r-factor (work) = 0.1177          |
| start r-factor (free) = 0.1676      final r-factor (free) = 0.1647          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2187 = 0.99 * 1.00 * 5.2335 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1839 = 0.99 * 1.00 * 5.1998 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.90  13.92    None  None   None       |
|    all(noH): 2823   0      0.00    113.90  13.92    None  None   None       |
|    Sol.    : 438    0      2.50    96.96   39.39    None  None   None       |
|    Mac.    : 2385   0      0.00    113.90  9.24     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.390: 1874   |   5:    56.951 -  68.341:   52        |
|      1:    11.390 -  22.780:  472   |   6:    68.341 -  79.731:   26        |
|      2:    22.780 -  34.171:  151   |   7:    79.731 -  91.122:   11        |
|      3:    34.171 -  45.561:  124   |   8:    91.122 - 102.512:    3        |
|      4:    45.561 -  56.951:  108   |   9:   102.512 - 113.902:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1177 r_free = 0.1647             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1176 r_free = 0.1644             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1644   ksol= 0.32   Bsol= 44.31   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.79,1.49,2.31,0.00,0.00,0.00); trace/3= 1.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.187507                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6818 0.99   1402  158 0.0992 0.1290      5.3813      5.5463|
|  2:  4.6818 -  3.7349 0.99   1358  143 0.0885 0.1193      5.4632      5.6938|
|  3:  3.7349 -  3.2683 0.99   1327  151 0.1125 0.1548      5.5239      5.8518|
|  4:  3.2683 -  2.9720 0.99   1332  154 0.1292 0.1673      5.5017        5.66|
|  5:  2.9720 -  2.7604 0.99   1306  142 0.1377 0.1721      5.3521      5.5236|
|  6:  2.7604 -  2.5985 0.99   1303  148 0.1270 0.1827      5.2435      5.4957|
|  7:  2.5985 -  2.4690 0.99   1312  139 0.1334 0.1835       5.225      5.4434|
|  8:  2.4690 -  2.3620 0.98   1276  147 0.1200 0.1794      5.0776      5.3808|
|  9:  2.3620 -  2.2713 0.98   1294  148 0.1204 0.1936      5.0576      5.3679|
| 10:  2.2713 -  2.1932 0.99   1290  138 0.1183 0.1791      4.9853      5.2146|
| 11:  2.1932 -  2.1248 0.99   1281  137 0.1254 0.1939      5.0088      5.3858|
| 12:  2.1248 -  2.0643 0.97   1264  146 0.1165 0.1685      4.9285      5.1303|
| 13:  2.0643 -  2.0100 0.97   1269  137 0.1296 0.1816      4.8579      5.0715|
| 14:  2.0100 -  1.9611 0.47    616   71 0.1109 0.1774      4.6937      4.9804|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.6818  1402   158  0.94   8.97   0.98     0.96       7089.44|
|  2:  4.6818 -  3.7349  1358   143  0.95   8.23   1.02     1.01       9388.26|
|  3:  3.7349 -  3.2683  1327   151  0.93  12.21   1.04     1.03      11460.85|
|  4:  3.2683 -  2.9720  1332   154  0.91  14.37   1.02     1.00      11102.46|
|  5:  2.9720 -  2.7604  1306   142  0.89  16.52   1.00     0.97       8627.08|
|  6:  2.7604 -  2.5985  1303   148  0.90  16.64   0.99     0.97       7600.44|
|  7:  2.5985 -  2.4690  1312   139  0.90  16.49   1.00     0.97       7000.98|
|  8:  2.4690 -  2.3620  1276   147  0.90  16.14   0.99     0.94       5324.51|
|  9:  2.3620 -  2.2713  1294   148  0.91  15.56   1.01     1.00       5278.75|
| 10:  2.2713 -  2.1932  1290   138  0.90  15.85   1.01     0.97       4557.37|
| 11:  2.1932 -  2.1248  1281   137  0.88  17.90   1.00     0.96       4996.52|
| 12:  2.1248 -  2.0643  1264   146  0.91  16.19   1.01     1.00       4478.99|
| 13:  2.0643 -  2.0100  1269   137  0.89  17.34   1.00     0.99       3700.52|
| 14:  2.0100 -  1.9611   616    71  0.90  15.86   0.99     0.97       2772.03|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2772.03 max =        11460.85 mean =      6863.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.77|
|phase err.(test): min =        0.00 max =           89.16 mean =        14.11|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1648   ksol= 0.32   Bsol= 46.28   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.07,-0.33,0.40,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.188878                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1648   ksol= 0.32   Bsol= 46.28   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.07,-0.33,0.40,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.188878                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6818 0.99   1402  158 0.0992 0.1312      5.3852      5.5594|
|  2:  4.6818 -  3.7349 0.99   1358  143 0.0899 0.1194      5.4754      5.7016|
|  3:  3.7349 -  3.2683 0.99   1327  151 0.1128 0.1552      5.5281      5.8499|
|  4:  3.2683 -  2.9720 0.99   1332  154 0.1300 0.1671       5.504      5.6611|
|  5:  2.9720 -  2.7604 0.99   1306  142 0.1377 0.1714      5.3522      5.5221|
|  6:  2.7604 -  2.5985 0.99   1303  148 0.1269 0.1825      5.2434      5.4941|
|  7:  2.5985 -  2.4690 0.99   1312  139 0.1335 0.1836      5.2252      5.4436|
|  8:  2.4690 -  2.3620 0.98   1276  147 0.1199 0.1796      5.0773      5.3823|
|  9:  2.3620 -  2.2713 0.98   1294  148 0.1202 0.1928      5.0561      5.3663|
| 10:  2.2713 -  2.1932 0.99   1290  138 0.1181 0.1789      4.9836       5.214|
| 11:  2.1932 -  2.1248 0.99   1281  137 0.1252 0.1936      5.0079      5.3843|
| 12:  2.1248 -  2.0643 0.97   1264  146 0.1164 0.1686      4.9278      5.1301|
| 13:  2.0643 -  2.0100 0.97   1269  137 0.1295 0.1812      4.8574      5.0697|
| 14:  2.0100 -  1.9611 0.47    616   71 0.1110 0.1779       4.694      4.9826|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.6818  1402   158  0.94   9.14   0.98     0.96       7329.58|
|  2:  4.6818 -  3.7349  1358   143  0.95   8.44   1.02     1.01       9646.05|
|  3:  3.7349 -  3.2683  1327   151  0.93  12.28   1.04     1.04      11601.97|
|  4:  3.2683 -  2.9720  1332   154  0.91  14.42   1.02     1.00      11110.85|
|  5:  2.9720 -  2.7604  1306   142  0.89  16.47   1.00     0.97       8595.77|
|  6:  2.7604 -  2.5985  1303   148  0.90  16.65   0.99     0.97       7597.91|
|  7:  2.5985 -  2.4690  1312   139  0.90  16.47   1.00     0.97       6993.96|
|  8:  2.4690 -  2.3620  1276   147  0.90  16.16   0.99     0.94       5335.81|
|  9:  2.3620 -  2.2713  1294   148  0.91  15.56   1.01     1.00       5272.04|
| 10:  2.2713 -  2.1932  1290   138  0.90  15.84   1.01     0.97       4546.17|
| 11:  2.1932 -  2.1248  1281   137  0.89  17.88   1.00     0.96       4988.32|
| 12:  2.1248 -  2.0643  1264   146  0.91  16.17   1.01     1.00       4470.87|
| 13:  2.0643 -  2.0100  1269   137  0.89  17.34   1.01     0.99       3697.97|
| 14:  2.0100 -  1.9611   616    71  0.90  15.86   0.99     0.97       2773.22|
|alpha:            min =        0.94 max =            1.04 mean =         0.98|
|beta:             min =     2773.22 max =        11601.97 mean =      6909.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.80|
|phase err.(test): min =        0.00 max =           89.28 mean =        14.14|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.87    115.77  15.78    None  None   None       |
|    all(noH): 2823   0      1.87    115.77  15.78    None  None   None       |
|    Sol.    : 438    0      4.37    98.82   41.26    None  None   None       |
|    Mac.    : 2385   0      1.87    115.77  11.10    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:     1.866 -  13.256: 1874   |   5:    58.817 -  70.207:   52        |
|      1:    13.256 -  24.647:  472   |   6:    70.207 -  81.598:   26        |
|      2:    24.647 -  36.037:  151   |   7:    81.598 -  92.988:   11        |
|      3:    36.037 -  47.427:  124   |   8:    92.988 - 104.378:    3        |
|      4:    47.427 -  58.817:  108   |   9:   104.378 - 115.768:    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)= 323         
Filter by distance & map next to the model:
   mapped sites are within: 0.423 - 5.463
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 320 from: 323
   mapped sites are within: 0.713 - 5.463

peak=   10.718 closest distance to " CB  VAL A 230 " =    1.442
peak=    8.893 closest distance to " CG2 VAL A 296 " =    1.298
peak=    7.534 closest distance to " CG  ARG A 138 " =    1.186
peak=    6.600 closest distance to " CD1AILE A 234 " =    1.139
peak=    6.107 closest distance to " O   HOH Z 278 " =    1.321
peak=    5.864 closest distance to " CD2 LEU A   5 " =    1.210
peak=    5.844 closest distance to " NH2 ARG A  56 " =    2.165
peak=    5.617 closest distance to " O   HOH Z  37 " =    1.370
peak=    5.532 closest distance to " O   HOH Z 132 " =    1.178
peak=    5.326 closest distance to " CG  LEU A   5 " =    1.216
peak=    5.241 closest distance to " CG  PRO A 198 " =    1.279
peak=    5.214 closest distance to " NE2 GLN A  11 " =    1.172
peak=    5.194 closest distance to " O   HOH Z 124 " =    1.467
peak=    5.128 closest distance to " O   HOH Z   7 " =    1.354
peak=    5.098 closest distance to " CG  PRO A 213 " =    1.275
peak=    4.958 closest distance to " O   HOH Z 202 " =    1.375
peak=    4.935 closest distance to " O   HOH Z 144 " =    1.883
peak=    4.865 closest distance to " O   HOH Z 427 " =    2.797
peak=    4.842 closest distance to " CB  ASN A 148 " =    1.386
peak=    4.694 closest distance to " CB  GLN A 223 " =    1.381
peak=    4.628 closest distance to " NH1 ARG A 138 " =    1.018
peak=    4.628 closest distance to " O   HOH Z 263 " =    1.550
peak=    4.627 closest distance to " NH2BARG A 102 " =    0.963
peak=    4.623 closest distance to " O   HOH Z 316 " =    2.827
peak=    4.618 closest distance to " CG  LEU A 228 " =    1.239
peak=    4.614 closest distance to " O   HOH Z 232 " =    2.234
peak=    4.591 closest distance to " O   HOH Z 126 " =    1.903
peak=    4.569 closest distance to " O   HOH Z 260 " =    1.337
peak=    4.558 closest distance to " O   HOH Z   3 " =    2.112
peak=    4.514 closest distance to " CB  GLN A 183 " =    1.269
peak=    4.499 closest distance to " CA  GLY A 241 " =    3.769
peak=    4.472 closest distance to " CB  VAL A 230 " =    1.113
peak=    4.459 closest distance to " CB  SER A   3 " =    1.463
peak=    4.450 closest distance to " O   HOH Z 247 " =    1.278
peak=    4.440 closest distance to " O   HOH Z 193 " =    1.746
peak=    4.423 closest distance to " O   HOH Z 134 " =    1.468
peak=    4.419 closest distance to " O   HOH Z 117 " =    1.896
peak=    4.402 closest distance to " O   HOH Z 298 " =    1.818
peak=    4.385 closest distance to " O   HOH Z 214 " =    1.140
peak=    4.346 closest distance to " O   HOH Z  97 " =    1.205
peak=    4.305 closest distance to " O   HOH Z 369 " =    1.957
peak=    4.281 closest distance to " CB  ARG A 275 " =    0.877
peak=    4.268 closest distance to " O   HOH Z 227 " =    1.679
peak=    4.235 closest distance to " CG  LEU A 167 " =    1.116
peak=    4.209 closest distance to " CD2 LEU A 228 " =    1.206
peak=    4.196 closest distance to " O   HOH Z 287 " =    1.896
peak=    4.168 closest distance to " CB  SER A  63 " =    1.349
peak=    4.166 closest distance to " CB  TYR A 169 " =    0.906
peak=    4.159 closest distance to " CB  VAL A 265 " =    1.196
peak=    4.149 closest distance to " O   HOH Z 183 " =    1.319
peak=    4.144 closest distance to " O   PRO A 198 " =    1.233
peak=    4.138 closest distance to " NZ  LYS A 117 " =    3.220
peak=    4.127 closest distance to " O   HOH Z 425 " =    1.390
peak=    4.122 closest distance to " O   HOH Z 126 " =    1.538
peak=    4.116 closest distance to " O   HOH Z 344 " =    1.192
peak=    4.073 closest distance to " CB  TRP A 179 " =    1.342
peak=    4.072 closest distance to " O   HOH Z 236 " =    1.558
peak=    4.068 closest distance to " O   SER A  87 " =    2.395
peak=    4.061 closest distance to " CB  GLU A 152 " =    1.325
peak=    4.057 closest distance to " O   HOH Z  97 " =    1.643
peak=    4.032 closest distance to " O   HOH Z 272 " =    1.897
peak=    4.024 closest distance to " O   HOH Z 108 " =    1.429
peak=    4.012 closest distance to " O   HOH Z 193 " =    1.625
peak=    4.010 closest distance to " O   HOH Z 126 " =    1.650
peak=    4.000 closest distance to " OD2 ASP A 286 " =    2.681
peak=    3.992 closest distance to " O   HOH Z 143 " =    0.984
peak=    3.976 closest distance to " O   HOH Z  48 " =    1.563
peak=    3.975 closest distance to " O   HOH Z 280 " =    2.940
peak=    3.975 closest distance to " CB  VAL A 202 " =    1.648
peak=    3.973 closest distance to " CD  ARG A 138 " =    1.096
peak=    3.972 closest distance to " CG  GLN A  88 " =    1.078
peak=    3.969 closest distance to " O   PRO A 198 " =    1.496
peak=    3.964 closest distance to " O   HOH Z   9 " =    2.124
peak=    3.954 closest distance to " O   HOH Z 368 " =    2.079
peak=    3.954 closest distance to " O   HOH Z  78 " =    2.359
peak=    3.926 closest distance to " O   HOH Z 371 " =    2.774
peak=    3.895 closest distance to " CG2 THR A 221 " =    1.210
peak=    3.879 closest distance to " CG1BVAL A 121 " =    1.208
peak=    3.876 closest distance to " O   HOH Z 189 " =    2.486
peak=    3.865 closest distance to " CG2 VAL A 257 " =    0.919
peak=    3.865 closest distance to " CB  PRO A  54 " =    0.843
peak=    3.844 closest distance to " O   HOH Z   2 " =    1.796
peak=    3.838 closest distance to " O   HOH Z  59 " =    1.735
peak=    3.836 closest distance to " CB  GLU A 128 " =    1.154
peak=    3.821 closest distance to " O   HOH Z 303 " =    2.357
peak=    3.816 closest distance to " O   HOH Z  92 " =    0.791
peak=    3.813 closest distance to " O   HOH Z 284 " =    1.528
peak=    3.790 closest distance to " CD1 LEU A 300 " =    1.214
peak=    3.781 closest distance to " CA  TYR A  30 " =    1.012
peak=    3.781 closest distance to " O   HOH Z 374 " =    1.125
peak=    3.776 closest distance to " NH1AARG A 145 " =    1.064
peak=    3.773 closest distance to " O   HOH Z 180 " =    2.147
peak=    3.762 closest distance to " CA  LEU A 282 " =    1.121
peak=    3.760 closest distance to " CB  LEU A 143 " =    1.081
peak=    3.739 closest distance to " OD1 ASN A  69 " =    2.739
peak=    3.727 closest distance to " O   HOH Z 371 " =    1.585
peak=    3.725 closest distance to " O   MET A 105 " =    1.711
peak=    3.718 closest distance to " O   HOH Z 133 " =    1.631
peak=    3.718 closest distance to " OD1 ASN A 217 " =    1.631
peak=    3.711 closest distance to " CG  PRO A 243 " =    1.171
peak=    3.700 closest distance to " CG  ARG A  66 " =    2.707
peak=    3.698 closest distance to " CE1 TYR A 186 " =    1.284
peak=    3.691 closest distance to " O   HOH Z  78 " =    1.796
peak=    3.688 closest distance to " O   HOH Z 345 " =    3.273
peak=    3.686 closest distance to " O   HOH Z 133 " =    2.378
peak=    3.682 closest distance to " O   HOH Z 128 " =    1.877
peak=    3.680 closest distance to " CG BARG A 102 " =    1.851
peak=    3.667 closest distance to " O   HOH Z  89 " =    1.565
peak=    3.666 closest distance to " CB  ILE A 234 " =    0.940
peak=    3.665 closest distance to " CA  VAL A 126 " =    1.217
peak=    3.648 closest distance to " O   HOH Z  44 " =    1.751
peak=    3.646 closest distance to " CA  VAL A  41 " =    0.916
peak=    3.645 closest distance to " CG  PRO A 280 " =    0.830
peak=    3.645 closest distance to " CB  LEU A 228 " =    1.365
peak=    3.639 closest distance to " CD  ARG A 269 " =    1.041
peak=    3.638 closest distance to " O   HOH Z 234 " =    3.623
peak=    3.634 closest distance to " O   HOH Z 147 " =    1.317
peak=    3.633 closest distance to " CB  GLU A 277 " =    3.565
peak=    3.631 closest distance to " O   HOH Z  58 " =    1.564
peak=    3.626 closest distance to " O   SER A  26 " =    1.563
peak=    3.624 closest distance to " CA  ALA A 295 " =    1.030
peak=    3.624 closest distance to " O   HOH Z 295 " =    1.587
peak=    3.624 closest distance to " CB  VAL A 296 " =    1.096
peak=    3.622 closest distance to " CB  ARG A 138 " =    1.641
peak=    3.622 closest distance to " CB  SER A 216 " =    0.984
peak=    3.614 closest distance to " CG1 VAL A 153 " =    0.931
peak=    3.613 closest distance to " CD BLYS A 290 " =    1.055
peak=    3.612 closest distance to " CB  LEU A 255 " =    0.851
peak=    3.604 closest distance to " CB  MET A  40 " =    0.885
peak=    3.599 closest distance to " CD1 ILE A  33 " =    1.575
peak=    3.597 closest distance to " O   HOH Z 158 " =    2.699
peak=    3.592 closest distance to " OG  SER A  62 " =    3.165
peak=    3.592 closest distance to " O   HOH Z 357 " =    1.499
peak=    3.586 closest distance to " ND2 ASN A 187 " =    1.640
peak=    3.585 closest distance to " O   HOH Z  43 " =    1.925
peak=    3.583 closest distance to " O   HOH Z 281 " =    1.702
peak=    3.582 closest distance to " CA  ASN A  74 " =    1.310
peak=    3.573 closest distance to " C   LYS A 290 " =    1.296
peak=    3.573 closest distance to " CA  ALA A 154 " =    1.162
peak=    3.572 closest distance to " O   HOH Z 108 " =    1.812
peak=    3.571 closest distance to " O   HOH Z 290 " =    1.026
peak=    3.567 closest distance to " CB  GLN A  88 " =    1.353
peak=    3.561 closest distance to " CB  LEU A 237 " =    0.990
peak=    3.553 closest distance to " CA  ILE A 234 " =    0.925
peak=    3.553 closest distance to " CG1 ILE A  33 " =    1.319
peak=    3.551 closest distance to " O   HOH Z  61 " =    1.628
peak=    3.551 closest distance to " O   HOH Z 276 " =    1.296
peak=    3.547 closest distance to " CA  LEU A 101 " =    1.515
peak=    3.541 closest distance to " O   HOH Z 145 " =    1.529
peak=    3.539 closest distance to " O   HOH Z 427 " =    1.337
peak=    3.538 closest distance to " CA  ALA A  51 " =    1.043
peak=    3.534 closest distance to " O   HOH Z  49 " =    1.869
peak=    3.532 closest distance to " O   HOH Z 151 " =    1.598
peak=    3.528 closest distance to " O   HOH Z 271 " =    1.868
peak=    3.526 closest distance to " OE1 GLU A   2 " =    2.037
peak=    3.525 closest distance to " O   HOH Z 123 " =    1.031
peak=    3.519 closest distance to " CB  TRP A 266 " =    1.008
peak=    3.518 closest distance to " NE2 GLN A  58 " =    5.463
peak=    3.509 closest distance to " O   HOH Z  80 " =    1.672
peak=    3.509 closest distance to " O   HOH Z  68 " =    2.076
peak=    3.508 closest distance to " O   HOH Z 184 " =    1.456
peak=    3.504 closest distance to " O   HOH Z 278 " =    1.313
peak=    3.504 closest distance to " CA  ALA A  21 " =    1.166
peak=    3.497 closest distance to " O   HOH Z 151 " =    1.512
peak=    3.494 closest distance to " O   HOH Z 344 " =    2.800
peak=    3.492 closest distance to " ND1 HIS A  86 " =    1.778
peak=    3.491 closest distance to " O   HOH Z 132 " =    2.478
peak=    3.491 closest distance to " O   HOH Z 389 " =    1.765
peak=    3.484 closest distance to " C   ALA A 299 " =    0.927
peak=    3.482 closest distance to " CB  SER A 273 " =    0.870
peak=    3.469 closest distance to " O   HOH Z 193 " =    1.785
peak=    3.462 closest distance to " CB BVAL A  41 " =    1.363
peak=    3.461 closest distance to " O   HOH Z 373 " =    1.524
peak=    3.461 closest distance to " O   HOH Z 280 " =    1.673
peak=    3.459 closest distance to " OG  SER A  62 " =    2.929
peak=    3.455 closest distance to " CA  ALA A 248 " =    1.219
peak=    3.453 closest distance to " O   HOH Z 214 " =    1.943
peak=    3.447 closest distance to " O   HOH Z 289 " =    1.417
peak=    3.442 closest distance to " N   PHE A 130 " =    1.330
peak=    3.439 closest distance to " CB  ARG A 139 " =    1.011
peak=    3.436 closest distance to " CB  ARG A  79 " =    1.447
peak=    3.432 closest distance to " O   HOH Z 209 " =    2.250
peak=    3.428 closest distance to " CG1BVAL A  72 " =    1.373
peak=    3.427 closest distance to " O   HOH Z  93 " =    2.567
peak=    3.421 closest distance to " CB  ASP A 124 " =    0.832
peak=    3.421 closest distance to " O   HOH Z 281 " =    4.443
peak=    3.420 closest distance to " O   HOH Z 410 " =    1.511
peak=    3.418 closest distance to " CH2 TRP A 150 " =    1.018
peak=    3.415 closest distance to " O   HOH Z 265 " =    2.208
peak=    3.411 closest distance to " O   HOH Z  30 " =    1.337
peak=    3.408 closest distance to " CA  GLY A 267 " =    1.071
peak=    3.408 closest distance to " NH1 ARG A  56 " =    1.007
peak=    3.403 closest distance to " CB  THR A 157 " =    0.985
peak=    3.398 closest distance to " OE2 GLU A  53 " =    2.083
peak=    3.393 closest distance to " NH2BARG A 190 " =    1.548
peak=    3.392 closest distance to " CB  THR A  82 " =    1.205
peak=    3.392 closest distance to " O   HOH Z 148 " =    1.596
peak=    3.388 closest distance to " CA  ALA A 160 " =    0.794
peak=    3.385 closest distance to " O   HOH Z 130 " =    2.155
peak=    3.385 closest distance to " CA  LYS A  48 " =    1.438
peak=    3.384 closest distance to " CA  ASN A 127 " =    1.061
peak=    3.384 closest distance to " O   GLN A  58 " =    1.498
peak=    3.383 closest distance to " O   HOH Z 426 " =    3.092
peak=    3.382 closest distance to " CB  ALA A 291 " =    1.457
peak=    3.381 closest distance to " O   HOH Z 403 " =    1.350
peak=    3.379 closest distance to " O   HOH Z 189 " =    3.026
peak=    3.379 closest distance to " O   HOH Z  88 " =    3.046
peak=    3.375 closest distance to " O   HOH Z 244 " =    1.532
peak=    3.373 closest distance to " O   HOH Z 209 " =    2.550
peak=    3.369 closest distance to " CD1 LEU A 228 " =    1.532
peak=    3.367 closest distance to " O   HOH Z 437 " =    2.425
peak=    3.365 closest distance to " CA  ASN A 215 " =    1.131
peak=    3.361 closest distance to " CA  THR A 264 " =    0.783
peak=    3.355 closest distance to " O   HOH Z 302 " =    1.814
peak=    3.355 closest distance to " O   HOH Z 326 " =    1.292
peak=    3.354 closest distance to " O   ALA A 165 " =    1.248
peak=    3.350 closest distance to " C   GLU A 277 " =    1.278
peak=    3.349 closest distance to " O   HOH Z  10 " =    1.704
peak=    3.347 closest distance to " O   HOH Z 374 " =    2.545
peak=    3.344 closest distance to " O   HOH Z 118 " =    1.780
peak=    3.341 closest distance to " CB  ALA A 161 " =    0.930
peak=    3.340 closest distance to " O   HOH Z 403 " =    1.577
peak=    3.339 closest distance to " O   HOH Z  64 " =    2.429
peak=    3.333 closest distance to " CB  ARG A 102 " =    0.713
peak=    3.331 closest distance to " O   HOH Z 207 " =    2.095
peak=    3.328 closest distance to " NZ BLYS A 290 " =    1.042
peak=    3.321 closest distance to " OD1 ASN A  45 " =    1.401
peak=    3.318 closest distance to " O   HOH Z 194 " =    2.158
peak=    3.315 closest distance to " CA  PHE A 283 " =    1.309
peak=    3.313 closest distance to " NZ  LYS A  76 " =    1.265
peak=    3.311 closest distance to " N   ARG A 156 " =    1.307
peak=    3.309 closest distance to " O   HOH Z 181 " =    2.184
peak=    3.307 closest distance to " O   HOH Z 261 " =    2.041
peak=    3.301 closest distance to " NH1 ARG A  14 " =    1.032
peak=    3.300 closest distance to " O   HOH Z 380 " =    1.599
peak=    3.296 closest distance to " O   HOH Z  61 " =    1.623
peak=    3.283 closest distance to " O   HOH Z   1 " =    1.701
peak=    3.282 closest distance to " CB  LYS A 117 " =    1.196
peak=    3.282 closest distance to " O   HOH Z 329 " =    3.493
peak=    3.281 closest distance to " CD2 LEU A 255 " =    1.522
peak=    3.280 closest distance to " CE  MET A  93 " =    1.466
peak=    3.278 closest distance to " CG2 ILE A 120 " =    1.308
peak=    3.278 closest distance to " O   HOH Z  63 " =    1.141
peak=    3.277 closest distance to " CA  LYS A 117 " =    1.182
peak=    3.275 closest distance to " O   HOH Z 406 " =    1.664
peak=    3.274 closest distance to " CE AMET A  47 " =    1.448
peak=    3.271 closest distance to " O   HOH Z 391 " =    3.085
peak=    3.271 closest distance to " N   TYR A  15 " =    1.009
peak=    3.269 closest distance to " O   HOH Z 172 " =    3.596
peak=    3.265 closest distance to " NH2 ARG A 219 " =    1.834
peak=    3.265 closest distance to " O   HOH Z 305 " =    3.308
peak=    3.263 closest distance to " O   HOH Z 217 " =    1.380
peak=    3.262 closest distance to " O   HOH Z 211 " =    2.281
peak=    3.262 closest distance to " O   HOH Z 350 " =    1.342
peak=    3.261 closest distance to " CB  ALA A 295 " =    1.420
peak=    3.261 closest distance to " O   HOH Z 140 " =    2.406
peak=    3.260 closest distance to " O   HOH Z 115 " =    2.247
peak=    3.259 closest distance to " OG ASER A 134 " =    1.358
peak=    3.257 closest distance to " O   HOH Z 109 " =    2.613
peak=    3.255 closest distance to " CB  GLU A 236 " =    1.313
peak=    3.254 closest distance to " CE  LYS A  76 " =    0.972
peak=    3.249 closest distance to " OG BSER A 164 " =    2.175
peak=    3.243 closest distance to " O   ALA A 158 " =    1.345
peak=    3.238 closest distance to " CA  ARG A  36 " =    1.092
peak=    3.235 closest distance to " O   HOH Z  59 " =    2.054
peak=    3.234 closest distance to " O   HOH Z 423 " =    1.561
peak=    3.229 closest distance to " OD1 ASP A 231 " =    1.845
peak=    3.222 closest distance to " CA  SER A  87 " =    0.960
peak=    3.221 closest distance to " O   HOH Z 195 " =    1.275
peak=    3.220 closest distance to " CD  GLU A 152 " =    0.766
peak=    3.213 closest distance to " O   HOH Z 374 " =    3.071
peak=    3.212 closest distance to " CB  ASN A 142 " =    0.911
peak=    3.211 closest distance to " CA  TYR A 116 " =    1.572
peak=    3.205 closest distance to " NE AARG A 275 " =    1.351
peak=    3.205 closest distance to " CA  ASN A 217 " =    1.240
peak=    3.203 closest distance to " O   HOH Z 116 " =    3.169
peak=    3.203 closest distance to " CH2 TRP A 274 " =    2.402
peak=    3.201 closest distance to " CG  MET A 188 " =    1.682
peak=    3.192 closest distance to " CA  ALA A 158 " =    1.168
peak=    3.192 closest distance to " O   HOH Z 222 " =    2.319
peak=    3.191 closest distance to " O   HOH Z 392 " =    1.179
peak=    3.189 closest distance to " CG  LYS A  76 " =    1.507
peak=    3.185 closest distance to " O   HOH Z 419 " =    1.821
peak=    3.182 closest distance to " CA  GLN A 194 " =    1.180
peak=    3.182 closest distance to " O   HOH Z 258 " =    2.194
peak=    3.180 closest distance to " O   HOH Z 285 " =    1.845
peak=    3.180 closest distance to " CA  MET A  40 " =    1.053
peak=    3.179 closest distance to " O   HOH Z 203 " =    1.682
peak=    3.174 closest distance to " CB  SER A 212 " =    1.140
peak=    3.171 closest distance to " CB  TYR A  30 " =    1.654
peak=    3.170 closest distance to " O   HOH Z 411 " =    1.942
peak=    3.169 closest distance to " O   HOH Z 204 " =    1.551
peak=    3.161 closest distance to " O   HOH Z 313 " =    1.804
peak=    3.159 closest distance to " O   HOH Z 119 " =    1.496
peak=    3.158 closest distance to " O   HOH Z 422 " =    2.597
peak=    3.157 closest distance to " O   ALA A  10 " =    1.525
peak=    3.156 closest distance to " OD1BASN A 224 " =    2.120
peak=    3.150 closest distance to " N   GLY A 133 " =    3.723
peak=    3.149 closest distance to " CD  LYS A 166 " =    1.395
peak=    3.148 closest distance to " O   HOH Z 273 " =    2.684
peak=    3.148 closest distance to " O   HOH Z 409 " =    2.963
peak=    3.143 closest distance to " O   HOH Z 116 " =    1.667
peak=    3.141 closest distance to " OG BSER A 134 " =    2.928
peak=    3.140 closest distance to " N   GLN A 278 " =    1.014
peak=    3.137 closest distance to " O   HOH Z 405 " =    1.220
peak=    3.136 closest distance to " O   TRP A 274 " =    1.840
peak=    3.128 closest distance to " O   HOH Z 145 " =    3.351
peak=    3.124 closest distance to " CD2 HIS A  81 " =    1.103
peak=    3.120 closest distance to " NH2BARG A 145 " =    2.022
peak=    3.096 closest distance to " O   HOH Z 148 " =    2.480
peak=    3.093 closest distance to " O   GLY A  57 " =    2.530
peak=    3.090 closest distance to " OE2 GLU A   2 " =    1.639
peak=    3.088 closest distance to " O   HOH Z 222 " =    2.369
peak=    3.085 closest distance to " CB  ASN A 187 " =    1.113
peak=    3.074 closest distance to " O   HOH Z 271 " =    2.144
peak=    3.068 closest distance to " O   HOH Z 359 " =    3.770
peak=    3.059 closest distance to " O   HOH Z 102 " =    1.971
peak=    3.049 closest distance to " O   HOH Z 148 " =    1.957
peak=    3.028 closest distance to " O   HOH Z  66 " =    2.223
peak=    3.020 closest distance to " CB  ALA A 104 " =    0.775

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 196         
Filter by distance & map next to the model:
   mapped sites are within: 0.647 - 5.389
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 196
   mapped sites are within: 0.804 - 5.389

peak=   -4.985 closest distance to " CG2 VAL A 230 " =    0.871
peak=   -4.691 closest distance to " CD  ARG A 138 " =    1.168
peak=   -4.500 closest distance to " CD  ARG A 156 " =    1.925
peak=   -4.445 closest distance to " O   HOH Z 377 " =    1.643
peak=   -4.427 closest distance to " OG ASER A 134 " =    1.093
peak=   -4.408 closest distance to " O   HOH Z 198 " =    2.330
peak=   -4.360 closest distance to " O   HOH Z 231 " =    1.544
peak=   -4.255 closest distance to " O   HOH Z 266 " =    4.599
peak=   -4.209 closest distance to " O   HOH Z 388 " =    1.951
peak=   -4.174 closest distance to " CG  ARG A 138 " =    0.859
peak=   -4.103 closest distance to " CB  ASP A  27 " =    2.398
peak=   -4.081 closest distance to " O   PRO A 198 " =    1.270
peak=   -4.080 closest distance to " O   HOH Z  92 " =    1.616
peak=   -4.036 closest distance to " O   PRO A 163 " =    1.914
peak=   -4.024 closest distance to " CG  GLN A  88 " =    0.821
peak=   -3.996 closest distance to " CD  ARG A  14 " =    3.325
peak=   -3.941 closest distance to " CB  PRO A 243 " =    2.696
peak=   -3.933 closest distance to " OG BSER A 134 " =    1.107
peak=   -3.922 closest distance to " CD  LYS A 289 " =    2.570
peak=   -3.880 closest distance to " O   HOH Z  98 " =    1.831
peak=   -3.829 closest distance to " O   HOH Z 166 " =    1.470
peak=   -3.822 closest distance to " OG1 THR A   4 " =    1.914
peak=   -3.819 closest distance to " OD2 ASP A  50 " =    1.473
peak=   -3.778 closest distance to " CG  PRO A 163 " =    2.503
peak=   -3.767 closest distance to " O   HOH Z 298 " =    1.160
peak=   -3.761 closest distance to " OE1 GLN A  88 " =    0.938
peak=   -3.756 closest distance to " O   ASP A 231 " =    2.547
peak=   -3.755 closest distance to " O   HOH Z  43 " =    1.805
peak=   -3.742 closest distance to " CD1 LEU A 101 " =    2.504
peak=   -3.727 closest distance to " O   HOH Z 350 " =    1.996
peak=   -3.716 closest distance to " O   HOH Z 389 " =    1.855
peak=   -3.710 closest distance to " O   HOH Z 111 " =    1.042
peak=   -3.705 closest distance to " NH2AARG A 275 " =    5.389
peak=   -3.700 closest distance to " CB  TYR A  15 " =    2.095
peak=   -3.696 closest distance to " CB  ALA A 100 " =    2.478
peak=   -3.693 closest distance to " O   HOH Z 143 " =    1.036
peak=   -3.684 closest distance to " O   HOH Z 365 " =    1.215
peak=   -3.679 closest distance to " CB  PRO A 163 " =    2.561
peak=   -3.673 closest distance to " C   ASN A 285 " =    2.349
peak=   -3.671 closest distance to " N   SER A 276 " =    1.240
peak=   -3.663 closest distance to " N   GLN A  58 " =    1.932
peak=   -3.656 closest distance to " O   HOH Z 410 " =    2.035
peak=   -3.645 closest distance to " O   ALA A 161 " =    1.743
peak=   -3.643 closest distance to " CG2 VAL A 296 " =    1.652
peak=   -3.628 closest distance to " O   HOH Z 290 " =    1.123
peak=   -3.623 closest distance to " O   HOH Z  44 " =    2.021
peak=   -3.622 closest distance to " O   ALA A  51 " =    1.514
peak=   -3.599 closest distance to " O   HOH Z 274 " =    2.789
peak=   -3.592 closest distance to " O   HOH Z  13 " =    1.433
peak=   -3.592 closest distance to " O   GLY A  80 " =    2.405
peak=   -3.587 closest distance to " C   HIS A 108 " =    1.127
peak=   -3.580 closest distance to " OG  SER A 245 " =    1.159
peak=   -3.577 closest distance to " CG  GLN A 223 " =    2.231
peak=   -3.575 closest distance to " CG  MET A 105 " =    0.940
peak=   -3.571 closest distance to " CA  GLY A 133 " =    1.900
peak=   -3.571 closest distance to " O   ILE A 109 " =    2.582
peak=   -3.555 closest distance to " CZ  PHE A  59 " =    1.596
peak=   -3.552 closest distance to " C   ALA A 158 " =    1.138
peak=   -3.550 closest distance to " OG  SER A  87 " =    1.337
peak=   -3.544 closest distance to " NH2 ARG A  79 " =    1.900
peak=   -3.544 closest distance to " O   HOH Z  63 " =    1.074
peak=   -3.525 closest distance to " O   HOH Z 427 " =    1.531
peak=   -3.513 closest distance to " O   HOH Z 407 " =    3.042
peak=   -3.506 closest distance to " CE2 TYR A  30 " =    2.777
peak=   -3.505 closest distance to " CB  ALA A 244 " =    2.018
peak=   -3.502 closest distance to " CE2 PHE A 218 " =    2.564
peak=   -3.500 closest distance to " O   HOH Z 111 " =    4.208
peak=   -3.492 closest distance to " CG2 VAL A 112 " =    2.521
peak=   -3.482 closest distance to " O   HOH Z  11 " =    1.955
peak=   -3.482 closest distance to " OG  SER A 206 " =    1.729
peak=   -3.466 closest distance to " CG  ASN A  45 " =    1.827
peak=   -3.462 closest distance to " CB  ALA A 227 " =    2.325
peak=   -3.462 closest distance to " O   THR A  18 " =    1.692
peak=   -3.457 closest distance to " O   HOH Z 392 " =    0.804
peak=   -3.454 closest distance to " O   HOH Z 205 " =    0.937
peak=   -3.444 closest distance to " O   HOH Z  93 " =    2.070
peak=   -3.440 closest distance to " CD1 LEU A 228 " =    2.225
peak=   -3.438 closest distance to " CE  MET A 105 " =    2.114
peak=   -3.437 closest distance to " C   ASN A 187 " =    1.771
peak=   -3.435 closest distance to " CB  ALA A 248 " =    1.911
peak=   -3.433 closest distance to " NE BARG A 102 " =    2.158
peak=   -3.424 closest distance to " O   PRO A 198 " =    1.333
peak=   -3.421 closest distance to " CD1 LEU A 255 " =    2.835
peak=   -3.421 closest distance to " O   ILE A  49 " =    1.714
peak=   -3.420 closest distance to " O   HOH Z 435 " =    2.001
peak=   -3.418 closest distance to " CG1 VAL A 197 " =    2.426
peak=   -3.413 closest distance to " N   HIS A 115 " =    2.002
peak=   -3.403 closest distance to " CG  TRP A 266 " =    1.644
peak=   -3.397 closest distance to " O   GLY A 211 " =    1.338
peak=   -3.394 closest distance to " O   HOH Z  60 " =    2.252
peak=   -3.388 closest distance to " O   HOH Z  90 " =    2.885
peak=   -3.387 closest distance to " CD2 LEU A   5 " =    1.144
peak=   -3.383 closest distance to " O   HOH Z  90 " =    1.716
peak=   -3.382 closest distance to " N   ALA A 248 " =    1.656
peak=   -3.377 closest distance to " O   VAL A 197 " =    1.401
peak=   -3.374 closest distance to " ND2 ASN A  60 " =    1.393
peak=   -3.370 closest distance to " O   HOH Z 207 " =    1.860
peak=   -3.364 closest distance to " CG  LYS A 193 " =    2.386
peak=   -3.361 closest distance to " O   GLY A  98 " =    2.033
peak=   -3.351 closest distance to " O   GLY A  57 " =    1.248
peak=   -3.350 closest distance to " CB  ASN A  39 " =    2.035
peak=   -3.348 closest distance to " O   HOH Z 132 " =    0.890
peak=   -3.345 closest distance to " O   HOH Z 345 " =    1.943
peak=   -3.344 closest distance to " O   HOH Z 103 " =    1.740
peak=   -3.343 closest distance to " CG  PHE A 283 " =    2.568
peak=   -3.341 closest distance to " N   THR A 157 " =    1.466
peak=   -3.337 closest distance to " O   HOH Z 313 " =    1.642
peak=   -3.336 closest distance to " O   SER A 135 " =    1.537
peak=   -3.333 closest distance to " OG BSER A 134 " =    1.747
peak=   -3.317 closest distance to " OG  SER A  97 " =    2.094
peak=   -3.306 closest distance to " CA  GLY A  35 " =    2.032
peak=   -3.302 closest distance to " OH  TYR A 214 " =    1.176
peak=   -3.302 closest distance to " CB  ALA A  43 " =    2.423
peak=   -3.296 closest distance to " CG  ASP A 231 " =    0.849
peak=   -3.293 closest distance to " O   HOH Z  97 " =    2.289
peak=   -3.290 closest distance to " O   HOH Z  88 " =    4.484
peak=   -3.287 closest distance to " N   GLN A  58 " =    1.277
peak=   -3.287 closest distance to " CA  TYR A  68 " =    2.713
peak=   -3.283 closest distance to " NH2 ARG A  66 " =    3.023
peak=   -3.283 closest distance to " O   HOH Z 189 " =    2.672
peak=   -3.277 closest distance to " OG  SER A  87 " =    1.554
peak=   -3.272 closest distance to " OD1 ASN A 249 " =    1.185
peak=   -3.272 closest distance to " CG  ARG A 259 " =    2.878
peak=   -3.267 closest distance to " OE1 GLN A  73 " =    2.354
peak=   -3.267 closest distance to " O   HOH Z 168 " =    2.012
peak=   -3.266 closest distance to " CB  ALA A   1 " =    1.559
peak=   -3.264 closest distance to " O   TRP A  70 " =    1.465
peak=   -3.262 closest distance to " CA  ARG A  56 " =    1.335
peak=   -3.260 closest distance to " O   HOH Z 357 " =    2.029
peak=   -3.257 closest distance to " O   HOH Z 275 " =    1.554
peak=   -3.251 closest distance to " O   VAL A  67 " =    2.636
peak=   -3.249 closest distance to " O   HOH Z 351 " =    1.422
peak=   -3.246 closest distance to " CB  TYR A 172 " =    2.271
peak=   -3.245 closest distance to " O   HOH Z 411 " =    3.747
peak=   -3.243 closest distance to " ND2BASN A 224 " =    1.583
peak=   -3.240 closest distance to " O   HOH Z 426 " =    1.685
peak=   -3.240 closest distance to " O   TYR A  30 " =    2.854
peak=   -3.237 closest distance to " CB  ALA A  51 " =    1.690
peak=   -3.236 closest distance to " N   ALA A   9 " =    1.421
peak=   -3.232 closest distance to " CD1 PHE A  59 " =    1.953
peak=   -3.224 closest distance to " CD2 LEU A 237 " =    2.664
peak=   -3.218 closest distance to " CG  GLU A 277 " =    1.246
peak=   -3.217 closest distance to " C   GLN A 240 " =    2.353
peak=   -3.211 closest distance to " OD2 ASP A 171 " =    1.792
peak=   -3.209 closest distance to " O   MET A  40 " =    2.763
peak=   -3.209 closest distance to " O   HOH Z  98 " =    1.541
peak=   -3.207 closest distance to " CD  PRO A 198 " =    1.452
peak=   -3.206 closest distance to " O   HOH Z  71 " =    1.127
peak=   -3.199 closest distance to " CG2 VAL A 257 " =    2.943
peak=   -3.197 closest distance to " CG1 VAL A 296 " =    2.173
peak=   -3.190 closest distance to " O   HOH Z 396 " =    1.528
peak=   -3.190 closest distance to " ND2 ASN A  39 " =    1.604
peak=   -3.188 closest distance to " O   HOH Z 210 " =    1.109
peak=   -3.186 closest distance to " CD2 LEU A 237 " =    2.732
peak=   -3.186 closest distance to " O   HOH Z  40 " =    3.862
peak=   -3.184 closest distance to " O   HOH Z 152 " =    4.937
peak=   -3.183 closest distance to " O   HOH Z 339 " =    1.789
peak=   -3.182 closest distance to " O   HOH Z 165 " =    2.152
peak=   -3.175 closest distance to " O   GLU A  44 " =    1.703
peak=   -3.168 closest distance to " OG1 THR A 178 " =    1.133
peak=   -3.154 closest distance to " C   LEU A 143 " =    1.371
peak=   -3.152 closest distance to " O   HOH Z 222 " =    3.032
peak=   -3.152 closest distance to " OD1 ASP A 200 " =    1.274
peak=   -3.151 closest distance to " O   HOH Z 423 " =    2.110
peak=   -3.143 closest distance to " CB  PHE A 192 " =    1.753
peak=   -3.139 closest distance to " O   HOH Z 231 " =    1.179
peak=   -3.137 closest distance to " CB  ASP A 132 " =    2.280
peak=   -3.136 closest distance to " O   HOH Z 234 " =    4.113
peak=   -3.136 closest distance to " O   PRO A 243 " =    2.498
peak=   -3.135 closest distance to " CB  CYS A 254 " =    1.952
peak=   -3.133 closest distance to " C   MET A 188 " =    1.699
peak=   -3.133 closest distance to " O   GLN A  11 " =    1.507
peak=   -3.130 closest distance to " N   GLN A  77 " =    1.560
peak=   -3.128 closest distance to " CE3 TRP A 150 " =    1.984
peak=   -3.127 closest distance to " O   ALA A   1 " =    1.309
peak=   -3.127 closest distance to " O   HOH Z 309 " =    2.324
peak=   -3.119 closest distance to " OD1 ASN A 187 " =    1.574
peak=   -3.116 closest distance to " O   HOH Z 423 " =    1.275
peak=   -3.115 closest distance to " O   HOH Z 124 " =    3.184
peak=   -3.115 closest distance to " OG  SER A  26 " =    1.118
peak=   -3.107 closest distance to " O   HOH Z 228 " =    1.469
peak=   -3.105 closest distance to " N   LYS A 166 " =    1.954
peak=   -3.104 closest distance to " NH2 ARG A  66 " =    2.233
peak=   -3.098 closest distance to " CG2 VAL A 296 " =    1.086
peak=   -3.096 closest distance to " CA  SER A 146 " =    2.322
peak=   -3.087 closest distance to " O   GLY A 196 " =    1.155
peak=   -3.084 closest distance to " ND2 ASN A  45 " =    0.990
peak=   -3.076 closest distance to " CD1 ILE A 199 " =    2.432
peak=   -3.073 closest distance to " O   SER A  22 " =    2.445
peak=   -3.072 closest distance to " N   GLY A  23 " =    2.127
peak=   -3.068 closest distance to " CG  LEU A 228 " =    1.018
peak=   -3.066 closest distance to " CG1 VAL A 296 " =    1.368
peak=   -3.036 closest distance to " O   HOH Z 266 " =    4.795
peak=   -3.008 closest distance to " CD  LYS A 166 " =    2.547

================= 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    :  0.4760 0.4611   6.274086e+00   6.265453e+00
   1_bss:  0.4670 0.4501   6.269096e+00   6.257416e+00
   1_xyz:  0.3848 0.4061   6.154525e+00   6.188768e+00
   1_adp:  0.3413 0.3948   6.074364e+00   6.164977e+00
   1_occ:  0.3409 0.3953   6.073667e+00   6.164901e+00
   2_bss:  0.3376 0.3913   6.073326e+00   6.162798e+00
   2_xyz:  0.2521 0.3062   5.836007e+00   5.988492e+00
   2_adp:  0.2315 0.2902   5.775933e+00   5.946338e+00
   2_occ:  0.2312 0.2899   5.774867e+00   5.945986e+00
   3_bss:  0.2305 0.2875   5.774969e+00   5.945199e+00
   3_xyz:  0.1708 0.2231   5.511497e+00   5.715478e+00
   3_adp:  0.1539 0.2099   5.431126e+00   5.659910e+00
   3_occ:  0.1537 0.2096   5.430520e+00   5.659334e+00
   4_bss:  0.1537 0.2093   5.428661e+00   5.656715e+00
   4_xyz:  0.1337 0.1827   5.299439e+00   5.539118e+00
   4_adp:  0.1290 0.1766   5.266789e+00   5.504208e+00
   4_occ:  0.1289 0.1764   5.266485e+00   5.503840e+00
   5_bss:  0.1289 0.1764   5.266107e+00   5.503764e+00
   5_xyz:  0.1192 0.1676   5.204098e+00   5.451355e+00
   5_adp:  0.1177 0.1647   5.187907e+00   5.432089e+00
   5_occ:  0.1176 0.1644   5.187507e+00   5.431593e+00
   5_bss:  0.1180 0.1648   5.188878e+00   5.432723e+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:  0.379  20.000   7.267   8.261   8.823   0.000   0.000   0.000
   1_xyz:  0.379  20.000   7.267   8.261   8.823   0.000   0.000   0.000
   1_adp:  0.379  20.000   7.267   8.261   8.823   0.000   0.000   0.000
   1_occ:  0.379  20.000   7.267   8.261   8.823   0.000   0.000   0.000
   2_bss:  0.339  37.645   3.715   4.034   5.578   0.000   0.000   0.000
   2_xyz:  0.339  37.645   3.715   4.034   5.578   0.000   0.000   0.000
   2_adp:  0.339  37.645   3.715   4.034   5.578   0.000   0.000   0.000
   2_occ:  0.339  37.645   3.715   4.034   5.578   0.000   0.000   0.000
   3_bss:  0.336  42.968   2.330   2.046   3.564   0.000   0.000   0.000
   3_xyz:  0.336  42.968   2.330   2.046   3.564   0.000   0.000   0.000
   3_adp:  0.336  42.968   2.330   2.046   3.564   0.000   0.000   0.000
   3_occ:  0.336  42.968   2.330   2.046   3.564   0.000   0.000   0.000
   4_bss:  0.325  44.868   1.917   1.566   2.601   0.000   0.000   0.000
   4_xyz:  0.325  44.868   1.917   1.566   2.601   0.000   0.000   0.000
   4_adp:  0.325  44.868   1.917   1.566   2.601   0.000   0.000   0.000
   4_occ:  0.325  44.868   1.917   1.566   2.601   0.000   0.000   0.000
   5_bss:  0.320  44.314   1.786   1.493   2.310   0.000   0.000   0.000
   5_xyz:  0.320  44.314   1.786   1.493   2.310   0.000   0.000   0.000
   5_adp:  0.320  44.314   1.786   1.493   2.310   0.000   0.000   0.000
   5_occ:  0.320  44.314   1.786   1.493   2.310   0.000   0.000   0.000
   5_bss:  0.320  46.281  -0.065  -0.330   0.396   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.765 0.4484  0.5306    67356.234
   1_bss:  56.033 0.4428  0.6568    64453.307
   1_xyz:  46.355 0.5643  0.8247    48178.114
   1_adp:  42.986 0.6063  0.9331    43858.358
   1_occ:  43.106 0.6048  0.9302    43973.948
   2_bss:  42.830 0.6080  0.8212    43518.027
   2_xyz:  32.284 0.7312  0.9546    25194.817
   2_adp:  30.026 0.7572  0.9859    22716.868
   2_occ:  29.987 0.7576  0.9861    22651.192
   3_bss:  29.826 0.7591  0.9256    22458.236
   3_xyz:  21.816 0.8440  0.9903    12929.736
   3_adp:  20.157 0.8605  0.9968    11442.172
   3_occ:  20.137 0.8607  0.9967    11410.199
   4_bss:  20.040 0.8616  0.9745    11320.990
   4_xyz:  17.078 0.8887  0.9882     8547.911
   4_adp:  16.251 0.8965  0.9864     7992.067
   4_occ:  16.239 0.8966  0.9863     7978.856
   5_bss:  16.231 0.8966  0.9803     7974.106
   5_xyz:  15.200 0.9052  0.9848     7133.259
   5_adp:  14.715 0.9094  0.9832     6876.524
   5_occ:  14.701 0.9095  0.9831     6864.659
   5_bss:  14.732 0.9093  0.9830     6909.988
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3307e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3307e+01
   1_xyz:   1.642  0.013  0.104 18.421  0.006  4.109   1.3546e-01
   1_adp:   1.642  0.013  0.104 18.421  0.006  4.109   1.3546e-01
   1_occ:   1.642  0.013  0.104 18.421  0.006  4.109   1.3546e-01
   2_bss:   1.642  0.013  0.104 18.421  0.006  4.109   1.3546e-01
   2_xyz:   1.050  0.007  0.073 16.293  0.005  4.109   7.2008e-02
   2_adp:   1.050  0.007  0.073 16.293  0.005  4.109   7.2008e-02
   2_occ:   1.050  0.007  0.073 16.293  0.005  4.109   7.2008e-02
   3_bss:   1.050  0.007  0.073 16.293  0.005  4.109   7.2008e-02
   3_xyz:   0.985  0.006  0.072 15.714  0.004  4.120   6.0425e-02
   3_adp:   0.985  0.006  0.072 15.714  0.004  4.120   6.0425e-02
   3_occ:   0.985  0.006  0.072 15.714  0.004  4.120   6.0425e-02
   4_bss:   0.985  0.006  0.072 15.714  0.004  4.120   6.0425e-02
   4_xyz:   0.889  0.005  0.068 15.397  0.003  4.121   5.2127e-02
   4_adp:   0.889  0.005  0.068 15.397  0.003  4.121   5.2127e-02
   4_occ:   0.889  0.005  0.068 15.397  0.003  4.121   5.2127e-02
   5_bss:   0.889  0.005  0.068 15.397  0.003  4.121   5.2127e-02
   5_xyz:   0.969  0.006  0.074 15.623  0.003  4.110   5.7872e-02
   5_adp:   0.969  0.006  0.074 15.623  0.003  4.110   5.7872e-02
   5_occ:   0.969  0.006  0.074 15.623  0.003  4.110   5.7872e-02
   5_bss:   0.969  0.006  0.074 15.623  0.003  4.110   5.7872e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9104e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9104e+00
   1_xyz:  13.370  0.165  0.443 84.655  0.042  2.279   9.4713e-02
   1_adp:  13.370  0.165  0.443 84.655  0.042  2.279   9.4713e-02
   1_occ:  13.370  0.165  0.443 84.655  0.042  2.279   9.4713e-02
   2_bss:  13.370  0.165  0.443 84.655  0.042  2.279   9.4713e-02
   2_xyz:   6.983  0.048  0.254 85.723  0.040  2.302   5.2523e-02
   2_adp:   6.983  0.048  0.254 85.723  0.040  2.302   5.2523e-02
   2_occ:   6.983  0.048  0.254 85.723  0.040  2.302   5.2523e-02
   3_bss:   6.983  0.048  0.254 85.723  0.040  2.302   5.2523e-02
   3_xyz:   7.185  0.048  0.336 88.367  0.040  2.364   6.8207e-02
   3_adp:   7.185  0.048  0.336 88.367  0.040  2.364   6.8207e-02
   3_occ:   7.185  0.048  0.336 88.367  0.040  2.364   6.8207e-02
   4_bss:   7.185  0.048  0.336 88.367  0.040  2.364   6.8207e-02
   4_xyz:   7.151  0.051  0.321 85.688  0.032  2.369   3.6711e-02
   4_adp:   7.151  0.051  0.321 85.688  0.032  2.369   3.6711e-02
   4_occ:   7.151  0.051  0.321 85.688  0.032  2.369   3.6711e-02
   5_bss:   7.151  0.051  0.321 85.688  0.032  2.369   3.6711e-02
   5_xyz:   7.542  0.052  0.432 83.781  0.025  2.324   3.7357e-02
   5_adp:   7.542  0.052  0.432 83.781  0.025  2.324   3.7357e-02
   5_occ:   7.542  0.052  0.432 83.781  0.025  2.324   3.7357e-02
   5_bss:   7.542  0.052  0.432 83.781  0.025  2.324   3.7357e-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: 101.77   0.00  12.93 101.77   0.00  10.37  83.73   0.00  26.84
   1_occ: 101.77   0.00  12.93 101.77   0.00  10.37  83.73   0.00  26.84
   2_bss: 101.77   0.00  12.93 101.77   0.00  10.37  83.73   0.00  26.84
   2_xyz: 101.77   0.00  12.93 101.77   0.00  10.37  83.73   0.00  26.84
   2_adp:  99.60   0.00  13.09  99.60   0.00   9.66  82.37   0.00  31.82
   2_occ:  99.60   0.00  13.09  99.60   0.00   9.66  82.37   0.00  31.82
   3_bss:  99.60   0.00  13.09  99.60   0.00   9.66  82.37   0.00  31.82
   3_xyz:  99.60   0.00  13.09  99.60   0.00   9.66  82.37   0.00  31.82
   3_adp: 106.23   0.00  14.37 106.23   0.00   9.59  88.02   2.05  40.40
   3_occ: 106.23   0.00  14.37 106.23   0.00   9.59  88.02   2.05  40.40
   4_bss: 106.23   0.00  14.37 106.23   0.00   9.59  88.02   2.05  40.40
   4_xyz: 106.23   0.00  14.37 106.23   0.00   9.59  88.02   2.05  40.40
   4_adp: 112.37   0.00  14.29 112.37   0.00   9.43  95.98   3.03  40.72
   4_occ: 112.37   0.00  14.29 112.37   0.00   9.43  95.98   3.03  40.72
   5_bss: 112.37   0.00  14.29 112.37   0.00   9.43  95.98   3.03  40.72
   5_xyz: 112.37   0.00  14.29 112.37   0.00   9.43  95.98   3.03  40.72
   5_adp: 113.90   0.00  13.92 113.90   0.00   9.24  96.96   2.50  39.39
   5_occ: 113.90   0.00  13.92 113.90   0.00   9.24  96.96   2.50  39.39
   5_bss: 115.77   1.87  15.78 115.77   1.87  11.10  98.82   4.37  41.26
------------------------------------------------------------------------
 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:    1.232    0.019    0.407
   1_adp:    1.232    0.019    0.407
   1_occ:    1.232    0.019    0.407
   2_bss:    1.232    0.019    0.407
   2_xyz:    1.510    0.051    0.556
   2_adp:    1.510    0.051    0.556
   2_occ:    1.510    0.051    0.556
   3_bss:    1.510    0.051    0.556
   3_xyz:    1.536    0.066    0.633
   3_adp:    1.536    0.066    0.633
   3_occ:    1.536    0.066    0.633
   4_bss:    1.536    0.066    0.633
   4_xyz:    1.777    0.056    0.675
   4_adp:    1.777    0.056    0.675
   4_occ:    1.777    0.056    0.675
   5_bss:    1.777    0.056    0.675
   5_xyz:    1.886    0.026    0.694
   5_adp:    1.886    0.026    0.694
   5_occ:    1.886    0.026    0.694
   5_bss:    1.886    0.026    0.694
------------------------------------------------------------------------

CPU time actual refinement: 345.97


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_881/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_881/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_881/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_881/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_881/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 345.83 
  Macro-tasks:
    bulk solvent and scale       = 43.82  
    individual site refinement   = 142.85 
    weights calculation          = 32.07  
    collect and process          = 6.61   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 225.45 
  Micro-tasks:
    mask                            = 2.32   
    f_calc                          = 109.82 
    alpha_beta                      = 8.49   
    target                          = 1.27   
    gradients_wrt_atomic_parameters = 114.31 
    fmodel                         = 7.38   
    r_factors                      = 0.17   
    phase_errors                   = 11.26  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 255.30 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.895 micro seconds
Total CPU time: 5.98 minutes
from_scatterers_fft:    627 calls, 109.29 s
gradients_fft:          573 calls, 103.01 s

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

# Date 2008-01-16 Time 02:39:32 PST -0800 (1200479972.76 s)
Start R-work = 0.4760, R-free = 0.4611 (no bulk solvent and anisotropic scale)
Final R-work = 0.1338, R-free = 0.1809 (no bulk solvent and anisotropic scale)

Start R-work = 0.4670, R-free = 0.4501
Final R-work = 0.1180, R-free = 0.1648