# Date 2008-01-16 Time 03:33:21 PST -0800 (1200483201.05 s)
#phil __OFF__

Command line arguments: "../1284.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7215
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1284

-------------------------------------------------------------------------------
  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: (72.0062, 47.1647, 87.6859, 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: (72.0062, 47.1647, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3277 2.01276
Completeness in resolution range: 0.961754
Completeness with d_max=infinity: 0.958835

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3277
                             d_min =   2.0128

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: (72.0062, 47.1647, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3277 2.01276
Completeness in resolution range: 0.961754
Completeness with d_max=infinity: 0.958835

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3282 -  4.3073 [2137/2162]  1924   213  10.0%
  bin  2:  4.3073 -  3.4314 [2049/2069]  1844   205  10.0%
  bin  3:  3.4314 -  3.0014 [2041/2060]  1836   205  10.0%
  bin  4:  3.0014 -  2.7287 [2004/2034]  1805   199   9.9%
  bin  5:  2.7287 -  2.5340 [2007/2026]  1810   197   9.8%
  bin  6:  2.5340 -  2.3852 [1985/2010]  1779   206  10.4%
  bin  7:  2.3852 -  2.2661 [1968/1996]  1772   196  10.0%
  bin  8:  2.2661 -  2.1678 [1977/2013]  1780   197  10.0%
  bin  9:  2.1678 -  2.0845 [1969/2011]  1776   193   9.8%
  bin 10:  2.0845 -  2.0128 [1452/1987]  1304   148  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1284/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.64 -     2.30: 4
        2.30 -     2.95: 1593
        2.95 -     3.60: 4394
        3.60 -     4.25: 9001
        4.25 -     4.90: 12746
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.644 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.238 3.040 -x+1/2,-y+1,z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 27733 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_1284/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1284/model_refine_001.geo

CPU time processing inputs: 9.19


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 72.00625 47.16465 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4806   r_free= 0.4714   ksol= 0.00   Bsol= 0.00   scale= 0.778    |
|                                                                             |
| 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: 6.281496                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3282 -  4.8044 0.99   1390  155 0.3921 0.3625      6.5945      6.5181|
|  2:  4.8044 -  3.8330 0.99   1335  150 0.3970 0.4210      6.7938      6.8371|
|  3:  3.8330 -  3.3543 0.99   1317  141 0.4379 0.4029      6.6675      6.6828|
|  4:  3.3543 -  3.0502 0.99   1303  151 0.4656 0.4151      6.5355      6.4272|
|  5:  3.0502 -  2.8331 0.99   1297  144 0.5050 0.5138      6.3712      6.4213|
|  6:  2.8331 -  2.6669 0.99   1296  137 0.5066 0.5356      6.2831      6.1964|
|  7:  2.6669 -  2.5340 0.99   1281  141 0.5315 0.5176       6.248       6.267|
|  8:  2.5340 -  2.4241 0.98   1272  147 0.5404 0.4906      6.1874       6.147|
|  9:  2.4241 -  2.3312 0.98   1259  144 0.5065 0.5862      6.1178      6.1847|
| 10:  2.3312 -  2.2510 1.00   1291  139 0.5313 0.4786      6.1141      6.0861|
| 11:  2.2510 -  2.1808 0.98   1266  139 0.5224 0.5211      6.0379      6.0699|
| 12:  2.1808 -  2.1186 0.98   1249  140 0.5214 0.5368      5.9933      6.0209|
| 13:  2.1186 -  2.0630 0.99   1278  141 0.5386 0.4761       5.892      5.8122|
| 14:  2.0630 -  2.0128 0.62    796   90 0.5334 0.4953      5.8724      5.7793|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3282 -  4.8044  1390   155  0.72  32.89   0.79     0.75      66587.86|
|  2:  4.8044 -  3.8330  1335   150  0.72  33.63   0.87     0.77      97912.37|
|  3:  3.8330 -  3.3543  1317   141  0.63  41.59   0.81     0.71     105240.91|
|  4:  3.3543 -  3.0502  1303   151  0.54  49.05   0.79     0.62      96083.00|
|  5:  3.0502 -  2.8331  1297   144  0.43  57.23   0.72     0.51      80666.82|
|  6:  2.8331 -  2.6669  1296   137  0.39  60.98   0.72     0.44      72430.85|
|  7:  2.6669 -  2.5340  1281   141  0.33  65.23   0.71     0.37      67868.07|
|  8:  2.5340 -  2.4241  1272   147  0.30  67.26   0.69     0.35      63305.77|
|  9:  2.4241 -  2.3312  1259   144  0.31  66.76   0.72     0.35      57480.04|
| 10:  2.3312 -  2.2510  1291   139  0.33  65.53   0.72     0.38      51078.81|
| 11:  2.2510 -  2.1808  1266   139  0.34  64.86   0.74     0.41      46741.02|
| 12:  2.1808 -  2.1186  1249   140  0.36  63.17   0.73     0.43      42950.65|
| 13:  2.1186 -  2.0630  1278   141  0.37  62.20   0.69     0.45      34743.74|
| 14:  2.0630 -  2.0128   796    90  0.47  54.55   0.70     0.48      23878.93|
|alpha:            min =        0.35 max =            0.77 mean =         0.50|
|beta:             min =    23878.93 max =       105240.91 mean =     66226.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           90.00 mean =        55.83|
|phase err.(test): min =        0.00 max =           89.99 mean =        55.51|
|-----------------------------------------------------------------------------|

============================== 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 = 14.367899             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.304   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.188721              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.220   (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:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      160 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      676 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1468 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2566 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3847 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4960 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6456 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7548 |
|-----------------------------------------------------------------------------|
|-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 |       54.658 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.604 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.428)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.428)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4851   r_free= 0.4744   ksol= 0.00   Bsol= 0.00   scale= 0.751    |
|                                                                             |
| 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: 6.282085                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4723   r_free= 0.4596   ksol= 0.30   Bsol= 50.00   scale= 0.965   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.25,6.67,9.21,0.00,0.00,0.00); trace/3= 8.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.276683                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.107901             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.240   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.114910              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.108   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4723      final r-factor (work) = 0.3806          |
| start r-factor (free) = 0.4596      final r-factor (free) = 0.4073          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 95.8184 = 13.11 * 0.50 * 6.2802 + 1.00 * 54.6580                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.6433 = 13.11 * 0.50 * 6.1779 + 1.00 * 0.1539                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3806      final r-factor (work) = 0.3369          |
| start r-factor (free) = 0.4073      final r-factor (free) = 0.3845          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9022 = 1.11 * 1.00 * 6.1779 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8053 = 1.11 * 1.00 * 6.0894 + 1.00 * 0.0161                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.428)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.33   12.55    None  None   None       |
|    all(noH): 2823   0      0.00    97.33   12.55    None  None   None       |
|    Sol.    : 438    0      0.00    97.33   28.04    None  None   None       |
|    Mac.    : 2385   0      0.00    75.49   9.70     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.733: 1534   |   5:    48.665 -  58.398:   56        |
|      1:     9.733 -  19.466:  720   |   6:    58.398 -  68.132:   11        |
|      2:    19.466 -  29.199:  281   |   7:    68.132 -  77.865:    6        |
|      3:    29.199 -  38.932:  143   |   8:    77.865 -  87.598:    2        |
|      4:    38.932 -  48.665:   69   |   9:    87.598 -  97.331:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3369 r_free = 0.3845             target_work(ml) = 6.065         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3365 r_free = 0.3855             target_work(ml) = 6.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3365   r_free= 0.3855   ksol= 0.30   Bsol= 50.00   scale= 1.057   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.25,6.67,9.21,0.00,0.00,0.00); trace/3= 8.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.064536                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3353   r_free= 0.3829   ksol= 0.31   Bsol= 56.89   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.37,4.38,6.42,0.00,0.00,0.00); trace/3= 5.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.065608                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.317990              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.714   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.559026              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.280  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3353      final r-factor (work) = 0.2515          |
| start r-factor (free) = 0.3829      final r-factor (free) = 0.3051          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.3305 = 5.32 * 0.50 * 6.0837 + 1.00 * 0.1539                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.9166 = 5.32 * 0.50 * 5.9522 + 1.00 * 0.0898                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2515      final r-factor (work) = 0.2297          |
| start r-factor (free) = 0.3051      final r-factor (free) = 0.2791          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3606 = 0.56 * 1.00 * 5.9522 + 1.00 * 0.0331                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3097 = 0.56 * 1.00 * 5.7891 + 1.00 * 0.0734                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.428)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.32  12.75    None  None   None       |
|    all(noH): 2823   0      0.00    101.32  12.75    None  None   None       |
|    Sol.    : 438    0      0.00    101.32  33.85    None  None   None       |
|    Mac.    : 2385   0      0.00    75.33   8.87     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.132: 1688   |   5:    50.659 -  60.791:   62        |
|      1:    10.132 -  20.264:  606   |   6:    60.791 -  70.923:   23        |
|      2:    20.264 -  30.396:  212   |   7:    70.923 -  81.055:    7        |
|      3:    30.396 -  40.527:  141   |   8:    81.055 -  91.187:    0        |
|      4:    40.527 -  50.659:   83   |   9:    91.187 - 101.319:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2297 r_free = 0.2791             target_work(ml) = 5.758         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2294 r_free = 0.2793             target_work(ml) = 5.758         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2294   r_free= 0.2793   ksol= 0.31   Bsol= 56.89   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.37,4.38,6.42,0.00,0.00,0.00); trace/3= 5.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.757814                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2282   r_free= 0.2784   ksol= 0.34   Bsol= 73.02   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.97,3.09,4.52,0.00,0.00,0.00); trace/3= 3.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.759062                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.707400              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.927   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.940026              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.730   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2282      final r-factor (work) = 0.1606          |
| start r-factor (free) = 0.2784      final r-factor (free) = 0.2085          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.5121 = 6.71 * 0.50 * 5.7913 + 1.00 * 0.0898                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.9541 = 6.71 * 0.50 * 5.6240 + 1.00 * 0.0929                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1606      final r-factor (work) = 0.1426          |
| start r-factor (free) = 0.2085      final r-factor (free) = 0.1977          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 22.1735 = 3.94 * 1.00 * 5.6240 + 1.00 * 0.0148                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.2549 = 3.94 * 1.00 * 5.3899 + 1.00 * 0.0186                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.428)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.77   14.00    None  None   None       |
|    all(noH): 2823   0      0.00    96.77   14.00    None  None   None       |
|    Sol.    : 438    0      0.00    96.77   41.81    None  None   None       |
|    Mac.    : 2385   0      0.00    87.58   8.89     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 -   9.677: 1675   |   5:    48.385 -  58.062:   82        |
|      1:     9.677 -  19.354:  580   |   6:    58.062 -  67.739:   68        |
|      2:    19.354 -  29.031:  161   |   7:    67.739 -  77.416:   36        |
|      3:    29.031 -  38.708:   99   |   8:    77.416 -  87.093:   12        |
|      4:    38.708 -  48.385:   99   |   9:    87.093 -  96.770:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1426 r_free = 0.1977             target_work(ml) = 5.366         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1425 r_free = 0.1977             target_work(ml) = 5.366         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1425   r_free= 0.1977   ksol= 0.34   Bsol= 73.02   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.97,3.09,4.52,0.00,0.00,0.00); trace/3= 3.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.365926                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1426   r_free= 0.1970   ksol= 0.33   Bsol= 73.02   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,2.51,3.90,0.00,0.00,0.00); trace/3= 3.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.365182                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.922923              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.628  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.226085              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.454  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1426      final r-factor (work) = 0.1310          |
| start r-factor (free) = 0.1970      final r-factor (free) = 0.1860          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9757 = 2.92 * 0.50 * 5.3938 + 1.00 * 0.0929                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8717 = 2.92 * 0.50 * 5.3340 + 1.00 * 0.0763                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1310      final r-factor (work) = 0.1303          |
| start r-factor (free) = 0.1860      final r-factor (free) = 0.1790          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2243 = 0.23 * 1.00 * 5.3340 + 1.00 * 0.0183                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2137 = 0.23 * 1.00 * 5.3007 + 1.00 * 0.0153                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.428)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.56   13.30    None  None   None       |
|    all(noH): 2823   0      0.00    93.56   13.30    None  None   None       |
|    Sol.    : 438    0      1.33    93.56   39.28    None  None   None       |
|    Mac.    : 2385   0      0.00    85.53   8.53     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 -   9.356: 1738   |   5:    46.782 -  56.138:   78        |
|      1:     9.356 -  18.713:  540   |   6:    56.138 -  65.495:   61        |
|      2:    18.713 -  28.069:  159   |   7:    65.495 -  74.851:   34        |
|      3:    28.069 -  37.425:  103   |   8:    74.851 -  84.207:   11        |
|      4:    37.425 -  46.782:   90   |   9:    84.207 -  93.564:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1303 r_free = 0.1790             target_work(ml) = 5.277         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1301 r_free = 0.1788             target_work(ml) = 5.276         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1301   r_free= 0.1788   ksol= 0.33   Bsol= 73.02   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,2.51,3.90,0.00,0.00,0.00); trace/3= 3.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.276029                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1301   r_free= 0.1787   ksol= 0.33   Bsol= 69.93   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.61,2.38,3.72,0.00,0.00,0.00); trace/3= 2.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.275928                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.969374              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.562  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.166296              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.247   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1301      final r-factor (work) = 0.1270          |
| start r-factor (free) = 0.1787      final r-factor (free) = 0.1746          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2945 = 1.97 * 0.50 * 5.2994 + 1.00 * 0.0763                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2556 = 1.97 * 0.50 * 5.2662 + 1.00 * 0.0701                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1270      final r-factor (work) = 0.1281          |
| start r-factor (free) = 0.1746      final r-factor (free) = 0.1736          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8914 = 0.17 * 1.00 * 5.2662 + 1.00 * 0.0157                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8901 = 0.17 * 1.00 * 5.2600 + 1.00 * 0.0153                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.428)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.70   12.39    None  None   None       |
|    all(noH): 2823   0      0.00    90.70   12.39    None  None   None       |
|    Sol.    : 438    0      1.66    90.70   34.76    None  None   None       |
|    Mac.    : 2385   0      0.00    79.69   8.28     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 -   9.070: 1722   |   5:    45.351 -  54.421:   80        |
|      1:     9.070 -  18.140:  574   |   6:    54.421 -  63.491:   35        |
|      2:    18.140 -  27.211:  160   |   7:    63.491 -  72.561:   10        |
|      3:    27.211 -  36.281:  127   |   8:    72.561 -  81.631:   12        |
|      4:    36.281 -  45.351:   99   |   9:    81.631 -  90.702:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1281 r_free = 0.1736             target_work(ml) = 5.256         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1279 r_free = 0.1735             target_work(ml) = 5.255         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1279   r_free= 0.1735   ksol= 0.33   Bsol= 69.93   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.61,2.38,3.72,0.00,0.00,0.00); trace/3= 2.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.255360                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3282 -  4.8044 0.99   1390  155 0.1107 0.1409      5.4671      5.6077|
|  2:  4.8044 -  3.8330 0.99   1335  150 0.0947 0.1271       5.529      5.7346|
|  3:  3.8330 -  3.3543 0.99   1317  141 0.1168 0.1561       5.562      5.8844|
|  4:  3.3543 -  3.0502 0.99   1303  151 0.1359 0.1703      5.5387      5.6651|
|  5:  3.0502 -  2.8331 0.99   1297  144 0.1580 0.1965      5.4653      5.6833|
|  6:  2.8331 -  2.6669 0.99   1296  137 0.1410 0.2266      5.3293      5.5914|
|  7:  2.6669 -  2.5340 0.99   1281  141 0.1482 0.1718      5.3005       5.422|
|  8:  2.5340 -  2.4241 0.98   1272  147 0.1370 0.1841      5.1908      5.4156|
|  9:  2.4241 -  2.3312 0.98   1259  144 0.1364 0.2012      5.1527      5.3901|
| 10:  2.3312 -  2.2510 1.00   1291  139 0.1361 0.1869      5.0825      5.3098|
| 11:  2.2510 -  2.1808 0.98   1266  139 0.1341 0.1955      5.0652      5.3248|
| 12:  2.1808 -  2.1186 0.98   1249  140 0.1275 0.1903      4.9828      5.2682|
| 13:  2.1186 -  2.0630 0.99   1278  141 0.1348 0.1937      4.9003      5.1443|
| 14:  2.0630 -  2.0128 0.62    796   90 0.1206 0.1721      4.7665      4.9746|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3282 -  4.8044  1390   155  0.94   9.88   0.96     0.94       8387.87|
|  2:  4.8044 -  3.8330  1335   150  0.95   8.94   0.99     0.97      10638.00|
|  3:  3.8330 -  3.3543  1317   141  0.92  12.68   1.00     1.00      12352.67|
|  4:  3.3543 -  3.0502  1303   151  0.91  14.96   0.99     0.97      11897.26|
|  5:  3.0502 -  2.8331  1297   144  0.88  18.00   0.99     0.97      10411.75|
|  6:  2.8331 -  2.6669  1296   137  0.89  17.83   0.97     0.95       8740.37|
|  7:  2.6669 -  2.5340  1281   141  0.89  17.55   0.98     0.95       7695.76|
|  8:  2.5340 -  2.4241  1272   147  0.89  17.08   0.98     0.96       6469.29|
|  9:  2.4241 -  2.3312  1259   144  0.89  17.32   1.00     0.95       6181.86|
| 10:  2.3312 -  2.2510  1291   139  0.89  17.17   0.99     0.95       5215.49|
| 11:  2.2510 -  2.1808  1266   139  0.89  17.78   0.99     0.93       5178.65|
| 12:  2.1808 -  2.1186  1249   140  0.90  16.45   1.00     0.99       4731.26|
| 13:  2.1186 -  2.0630  1278   141  0.88  18.35   0.98     0.96       4044.91|
| 14:  2.0630 -  2.0128   796    90  0.90  15.92   0.97     0.93       2998.59|
|alpha:            min =        0.93 max =            1.00 mean =         0.96|
|beta:             min =     2998.59 max =        12352.67 mean =      7662.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.64|
|phase err.(test): min =        0.00 max =           87.51 mean =        15.01|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1280   r_free= 0.1727   ksol= 0.33   Bsol= 72.58   scale= 0.979   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.32,-0.51,0.83,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.253992                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1280   r_free= 0.1727   ksol= 0.33   Bsol= 72.58   scale= 0.979   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.32,-0.51,0.83,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.253992                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3282 -  4.8044 0.99   1390  155 0.1108 0.1327      5.4546      5.5664|
|  2:  4.8044 -  3.8330 0.99   1335  150 0.0944 0.1248      5.5204      5.7295|
|  3:  3.8330 -  3.3543 0.99   1317  141 0.1169 0.1570      5.5617      5.8876|
|  4:  3.3543 -  3.0502 0.99   1303  151 0.1359 0.1715      5.5399      5.6698|
|  5:  3.0502 -  2.8331 0.99   1297  144 0.1580 0.1962      5.4671      5.6821|
|  6:  2.8331 -  2.6669 0.99   1296  137 0.1409 0.2266      5.3294      5.5918|
|  7:  2.6669 -  2.5340 0.99   1281  141 0.1484 0.1717      5.3011      5.4226|
|  8:  2.5340 -  2.4241 0.98   1272  147 0.1370 0.1839      5.1909      5.4157|
|  9:  2.4241 -  2.3312 0.98   1259  144 0.1363 0.2011      5.1526      5.3897|
| 10:  2.3312 -  2.2510 1.00   1291  139 0.1361 0.1870      5.0826      5.3106|
| 11:  2.2510 -  2.1808 0.98   1266  139 0.1341 0.1954      5.0651      5.3244|
| 12:  2.1808 -  2.1186 0.98   1249  140 0.1275 0.1903       4.983      5.2685|
| 13:  2.1186 -  2.0630 0.99   1278  141 0.1348 0.1938      4.9004      5.1448|
| 14:  2.0630 -  2.0128 0.62    796   90 0.1206 0.1722      4.7666       4.975|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3282 -  4.8044  1390   155  0.94   9.62   0.96     0.94       7826.76|
|  2:  4.8044 -  3.8330  1335   150  0.95   8.73   0.99     0.97      10247.82|
|  3:  3.8330 -  3.3543  1317   141  0.92  12.63   1.00     1.00      12280.06|
|  4:  3.3543 -  3.0502  1303   151  0.91  15.00   0.99     0.96      11941.05|
|  5:  3.0502 -  2.8331  1297   144  0.88  18.03   0.98     0.96      10469.60|
|  6:  2.8331 -  2.6669  1296   137  0.89  17.83   0.96     0.94       8744.10|
|  7:  2.6669 -  2.5340  1281   141  0.89  17.56   0.98     0.94       7702.55|
|  8:  2.5340 -  2.4241  1272   147  0.89  17.09   0.97     0.95       6475.44|
|  9:  2.4241 -  2.3312  1259   144  0.89  17.32   0.99     0.94       6179.45|
| 10:  2.3312 -  2.2510  1291   139  0.89  17.17   0.98     0.94       5215.37|
| 11:  2.2510 -  2.1808  1266   139  0.89  17.78   0.98     0.92       5180.27|
| 12:  2.1808 -  2.1186  1249   140  0.90  16.45   0.99     0.98       4733.36|
| 13:  2.1186 -  2.0630  1278   141  0.88  18.35   0.97     0.95       4047.31|
| 14:  2.0630 -  2.0128   796    90  0.90  15.92   0.95     0.92       3000.22|
|alpha:            min =        0.92 max =            1.00 mean =         0.95|
|beta:             min =     3000.22 max =        12280.06 mean =      7592.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.60|
|phase err.(test): min =        0.00 max =           87.55 mean =        14.97|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.428)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.65    93.35   15.04    None  None   None       |
|    all(noH): 2823   0      2.65    93.35   15.04    None  None   None       |
|    Sol.    : 438    0      4.31    93.35   37.41    None  None   None       |
|    Mac.    : 2385   0      2.65    82.34   10.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.651 -  11.721: 1722   |   5:    48.002 -  57.072:   80        |
|      1:    11.721 -  20.791:  574   |   6:    57.072 -  66.142:   35        |
|      2:    20.791 -  29.862:  160   |   7:    66.142 -  75.212:   10        |
|      3:    29.862 -  38.932:  127   |   8:    75.212 -  84.283:   12        |
|      4:    38.932 -  48.002:   99   |   9:    84.283 -  93.353:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 329         
Filter by distance & map next to the model:
   mapped sites are within: 0.360 - 4.960
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 320 from: 329
   mapped sites are within: 0.719 - 4.960

peak=    9.950 closest distance to " CB  VAL A 230 " =    1.495
peak=    7.692 closest distance to " CG2 VAL A 296 " =    1.253
peak=    6.207 closest distance to " CG  ARG A 138 " =    1.205
peak=    5.800 closest distance to " NH1 ARG A 138 " =    1.081
peak=    5.671 closest distance to " CB  GLN A 223 " =    1.434
peak=    5.585 closest distance to " CG  LEU A   5 " =    1.308
peak=    5.174 closest distance to " CD2 LEU A   5 " =    1.192
peak=    5.134 closest distance to " O   HOH Z 111 " =    2.038
peak=    4.995 closest distance to " O   HOH Z 232 " =    2.227
peak=    4.871 closest distance to " O   HOH Z 102 " =    1.406
peak=    4.821 closest distance to " CB  SER A  63 " =    1.341
peak=    4.812 closest distance to " CG  LEU A 228 " =    1.267
peak=    4.760 closest distance to " CB  ASP A 124 " =    0.784
peak=    4.738 closest distance to " CZ  PHE A 218 " =    1.137
peak=    4.705 closest distance to " CG  PRO A 198 " =    1.340
peak=    4.704 closest distance to " CB  GLN A 183 " =    1.201
peak=    4.669 closest distance to " CD1AILE A 234 " =    1.089
peak=    4.652 closest distance to " O   HOH Z 369 " =    1.986
peak=    4.621 closest distance to " CB  TRP A 266 " =    0.976
peak=    4.598 closest distance to " O   HOH Z 265 " =    2.258
peak=    4.571 closest distance to " O   HOH Z 368 " =    2.212
peak=    4.564 closest distance to " CG  PRO A 243 " =    1.139
peak=    4.509 closest distance to " NH1AARG A 145 " =    1.197
peak=    4.508 closest distance to " CA  VAL A 230 " =    1.218
peak=    4.459 closest distance to " O   HOH Z 303 " =    2.206
peak=    4.369 closest distance to " O   HOH Z 425 " =    1.600
peak=    4.367 closest distance to " NE2 GLN A  11 " =    1.125
peak=    4.342 closest distance to " O   HOH Z 236 " =    2.161
peak=    4.341 closest distance to " O   HOH Z 184 " =    1.662
peak=    4.323 closest distance to " CD  ARG A 138 " =    1.236
peak=    4.261 closest distance to " CD2 LEU A 228 " =    1.201
peak=    4.258 closest distance to " O   HOH Z 298 " =    2.153
peak=    4.254 closest distance to " CB  ASN A 148 " =    1.349
peak=    4.225 closest distance to " CD  LYS A 166 " =    1.264
peak=    4.225 closest distance to " CZ  PHE A 192 " =    1.034
peak=    4.192 closest distance to " O   PRO A 198 " =    1.562
peak=    4.189 closest distance to " ND2 ASN A 187 " =    1.442
peak=    4.188 closest distance to " CG  PRO A 213 " =    1.310
peak=    4.177 closest distance to " CB  GLU A 152 " =    1.178
peak=    4.168 closest distance to " O   HOH Z 183 " =    1.401
peak=    4.162 closest distance to " O   HOH Z 261 " =    1.967
peak=    4.150 closest distance to " O   HOH Z 411 " =    3.542
peak=    4.122 closest distance to " CG2 THR A 221 " =    0.978
peak=    4.112 closest distance to " CB  GLU A  46 " =    0.933
peak=    4.061 closest distance to " CB  ASN A  39 " =    0.857
peak=    4.010 closest distance to " O   HOH Z 272 " =    1.980
peak=    4.009 closest distance to " N   PHE A 130 " =    1.255
peak=    3.977 closest distance to " CD1 LEU A   5 " =    1.284
peak=    3.960 closest distance to " CG  MET A 185 " =    1.342
peak=    3.921 closest distance to " O   HOH Z 193 " =    2.201
peak=    3.921 closest distance to " N   ASN A  39 " =    1.215
peak=    3.918 closest distance to " NH1 ARG A  56 " =    1.095
peak=    3.912 closest distance to " CB  ASP A 140 " =    0.777
peak=    3.910 closest distance to " O   HOH Z 234 " =    3.909
peak=    3.903 closest distance to " CD1 LEU A 300 " =    1.178
peak=    3.901 closest distance to " CB  ARG A 275 " =    0.886
peak=    3.900 closest distance to " O   HOH Z 410 " =    1.369
peak=    3.887 closest distance to " CD  ARG A 159 " =    0.777
peak=    3.880 closest distance to " CA  ARG A 195 " =    1.206
peak=    3.880 closest distance to " N   SER A 135 " =    1.411
peak=    3.857 closest distance to " CB  LEU A 143 " =    1.282
peak=    3.856 closest distance to " CB  GLU A 128 " =    0.992
peak=    3.854 closest distance to " O   HOH Z 427 " =    3.382
peak=    3.845 closest distance to " O   SER A  87 " =    2.408
peak=    3.842 closest distance to " O   HOH Z 214 " =    2.190
peak=    3.836 closest distance to " O   HOH Z  57 " =    1.565
peak=    3.829 closest distance to " CA  SER A  87 " =    0.870
peak=    3.822 closest distance to " CB  VAL A 202 " =    1.548
peak=    3.818 closest distance to " O   HOH Z 346 " =    1.555
peak=    3.796 closest distance to " CD  ARG A  66 " =    2.351
peak=    3.792 closest distance to " CB  ASN A 142 " =    1.011
peak=    3.785 closest distance to " O   HOH Z 290 " =    1.494
peak=    3.779 closest distance to " CA  ALA A 295 " =    1.153
peak=    3.779 closest distance to " O   HOH Z  78 " =    2.312
peak=    3.774 closest distance to " CB  ILE A 120 " =    1.323
peak=    3.766 closest distance to " CB  ALA A 104 " =    0.835
peak=    3.764 closest distance to " CB  ALA A 291 " =    1.236
peak=    3.763 closest distance to " O   HOH Z 188 " =    2.958
peak=    3.761 closest distance to " O   HOH Z  88 " =    3.477
peak=    3.759 closest distance to " CB  SER A 210 " =    0.904
peak=    3.757 closest distance to " O   HOH Z 316 " =    3.237
peak=    3.755 closest distance to " O   HOH Z   4 " =    1.839
peak=    3.744 closest distance to " CD  ARG A 269 " =    0.897
peak=    3.743 closest distance to " CG1 ILE A  33 " =    1.336
peak=    3.739 closest distance to " CD ALYS A 290 " =    1.048
peak=    3.733 closest distance to " O   HOH Z 247 " =    1.528
peak=    3.728 closest distance to " CD1 LEU A  96 " =    0.819
peak=    3.722 closest distance to " CB  GLU A 277 " =    3.723
peak=    3.717 closest distance to " NE2 HIS A 207 " =    1.112
peak=    3.717 closest distance to " CB  ARG A 190 " =    1.458
peak=    3.717 closest distance to " CG AARG A 275 " =    1.312
peak=    3.716 closest distance to " CB  LEU A 228 " =    1.150
peak=    3.711 closest distance to " CG BARG A 275 " =    1.522
peak=    3.711 closest distance to " CB  ARG A  79 " =    1.488
peak=    3.710 closest distance to " CB  ALA A   9 " =    1.636
peak=    3.690 closest distance to " CB  ASN A 187 " =    1.994
peak=    3.688 closest distance to " CA  ALA A  51 " =    0.978
peak=    3.677 closest distance to " O   HOH Z  49 " =    1.139
peak=    3.673 closest distance to " O   HOH Z  53 " =    2.538
peak=    3.665 closest distance to " CB  ALA A 242 " =    0.819
peak=    3.659 closest distance to " O   HOH Z 171 " =    3.961
peak=    3.658 closest distance to " O   HOH Z 142 " =    1.635
peak=    3.653 closest distance to " CB  LEU A  83 " =    0.798
peak=    3.651 closest distance to " CA  VAL A 112 " =    1.112
peak=    3.650 closest distance to " O   ASP A 124 " =    1.179
peak=    3.641 closest distance to " CA  LEU A 282 " =    0.985
peak=    3.635 closest distance to " CB  SER A 212 " =    1.280
peak=    3.635 closest distance to " CA  ALA A 184 " =    1.071
peak=    3.634 closest distance to " CB  SER A   3 " =    1.543
peak=    3.624 closest distance to " O   HOH Z 258 " =    2.261
peak=    3.623 closest distance to " O   HOH Z 215 " =    1.459
peak=    3.617 closest distance to " CG  LEU A 167 " =    1.206
peak=    3.612 closest distance to " OD1 ASN A 217 " =    1.591
peak=    3.610 closest distance to " CG  GLU A  37 " =    0.918
peak=    3.610 closest distance to " O   HOH Z 156 " =    2.895
peak=    3.603 closest distance to " CA  GLY A 267 " =    0.824
peak=    3.594 closest distance to " CB  ASN A 187 " =    1.017
peak=    3.594 closest distance to " O   HOH Z  78 " =    1.923
peak=    3.587 closest distance to " CG2 ILE A 234 " =    0.899
peak=    3.579 closest distance to " O   HOH Z 158 " =    3.012
peak=    3.573 closest distance to " CG  GLN A  88 " =    1.059
peak=    3.572 closest distance to " CB  PRO A  54 " =    0.901
peak=    3.570 closest distance to " OG  SER A  28 " =    1.589
peak=    3.561 closest distance to " CB  VAL A 265 " =    1.367
peak=    3.559 closest distance to " O   HOH Z 128 " =    2.259
peak=    3.551 closest distance to " O   HOH Z  80 " =    1.946
peak=    3.550 closest distance to " CG1 ILE A 120 " =    1.137
peak=    3.550 closest distance to " ND2 ASN A 249 " =    2.010
peak=    3.546 closest distance to " O   HOH Z  48 " =    1.827
peak=    3.543 closest distance to " CA  GLN A 223 " =    0.947
peak=    3.543 closest distance to " O   HOH Z   9 " =    1.317
peak=    3.541 closest distance to " O   HOH Z 126 " =    1.709
peak=    3.539 closest distance to " CA  TYR A  30 " =    0.971
peak=    3.536 closest distance to " CG1 VAL A 153 " =    0.991
peak=    3.534 closest distance to " CD2 LEU A 237 " =    0.997
peak=    3.532 closest distance to " CB  SER A 216 " =    0.855
peak=    3.527 closest distance to " O   HOH Z 403 " =    1.699
peak=    3.516 closest distance to " CA  ILE A  33 " =    1.718
peak=    3.512 closest distance to " O   HOH Z 350 " =    1.700
peak=    3.506 closest distance to " CB  THR A  82 " =    1.406
peak=    3.503 closest distance to " CG BARG A 102 " =    1.825
peak=    3.499 closest distance to " CZ3 TRP A 266 " =    1.109
peak=    3.482 closest distance to " O   HOH Z 185 " =    2.285
peak=    3.477 closest distance to " CZ  PHE A  38 " =    1.193
peak=    3.477 closest distance to " O   HOH Z 213 " =    1.941
peak=    3.476 closest distance to " CA  ILE A 234 " =    0.973
peak=    3.474 closest distance to " CB  GLN A 103 " =    1.026
peak=    3.473 closest distance to " CB  ALA A 161 " =    0.928
peak=    3.473 closest distance to " CE2 TYR A 186 " =    0.987
peak=    3.472 closest distance to " OH  TYR A 247 " =    1.079
peak=    3.460 closest distance to " CE  LYS A  76 " =    0.910
peak=    3.459 closest distance to " O   HOH Z 437 " =    1.608
peak=    3.452 closest distance to " O   HOH Z 163 " =    1.758
peak=    3.447 closest distance to " CG  ARG A 269 " =    1.767
peak=    3.447 closest distance to " OG  SER A 276 " =    1.464
peak=    3.445 closest distance to " O   HOH Z  21 " =    1.766
peak=    3.445 closest distance to " O   HOH Z 201 " =    2.822
peak=    3.444 closest distance to " O   HOH Z 193 " =    1.755
peak=    3.444 closest distance to " CD1 ILE A 106 " =    0.961
peak=    3.441 closest distance to " CA  GLU A 152 " =    0.949
peak=    3.441 closest distance to " CG2BVAL A  41 " =    1.289
peak=    3.439 closest distance to " O   HOH Z 112 " =    1.561
peak=    3.431 closest distance to " O   HOH Z  43 " =    1.857
peak=    3.428 closest distance to " O   HOH Z 182 " =    1.522
peak=    3.426 closest distance to " CZ3 TRP A 274 " =    4.960
peak=    3.424 closest distance to " CB  ALA A 248 " =    1.178
peak=    3.423 closest distance to " O   HOH Z 313 " =    1.864
peak=    3.422 closest distance to " CB  MET A  47 " =    1.035
peak=    3.418 closest distance to " O   HOH Z 406 " =    1.576
peak=    3.411 closest distance to " CB  TRP A 150 " =    1.511
peak=    3.411 closest distance to " CA  ASP A 124 " =    0.742
peak=    3.411 closest distance to " CA  ASN A 127 " =    1.066
peak=    3.411 closest distance to " CA  ASP A 162 " =    0.937
peak=    3.409 closest distance to " CB  ALA A  10 " =    0.929
peak=    3.408 closest distance to " CB  ALA A  34 " =    0.924
peak=    3.406 closest distance to " O   HOH Z 353 " =    2.604
peak=    3.403 closest distance to " CG1 ILE A  49 " =    1.650
peak=    3.398 closest distance to " CA  ARG A  36 " =    1.163
peak=    3.394 closest distance to " O   HOH Z 423 " =    1.670
peak=    3.389 closest distance to " NH2AARG A 145 " =    1.280
peak=    3.389 closest distance to " CB  PRO A 198 " =    0.946
peak=    3.384 closest distance to " CG2 VAL A 257 " =    0.937
peak=    3.378 closest distance to " CE3 TRP A  85 " =    1.131
peak=    3.374 closest distance to " CA  ASN A 284 " =    0.851
peak=    3.374 closest distance to " NE2 GLN A 278 " =    2.431
peak=    3.371 closest distance to " CB  GLN A  88 " =    1.230
peak=    3.366 closest distance to " CB  PRO A 243 " =    1.233
peak=    3.363 closest distance to " O   HOH Z 215 " =    2.891
peak=    3.351 closest distance to " CA  ASP A 140 " =    1.396
peak=    3.351 closest distance to " O   HOH Z  10 " =    1.845
peak=    3.350 closest distance to " CB  PHE A 204 " =    0.962
peak=    3.349 closest distance to " OG1 THR A 264 " =    0.850
peak=    3.347 closest distance to " N   TYR A  15 " =    0.719
peak=    3.345 closest distance to " O   MET A 105 " =    1.756
peak=    3.344 closest distance to " CG2 ILE A 106 " =    0.899
peak=    3.339 closest distance to " CA  GLN A  88 " =    1.462
peak=    3.336 closest distance to " CD  PRO A  54 " =    0.856
peak=    3.333 closest distance to " CA  ALA A  21 " =    1.198
peak=    3.333 closest distance to " NE1 TRP A 274 " =    0.890
peak=    3.331 closest distance to " O   HOH Z  63 " =    1.925
peak=    3.330 closest distance to " O   HOH Z 132 " =    2.614
peak=    3.321 closest distance to " O   HOH Z 128 " =    2.430
peak=    3.321 closest distance to " O   HOH Z 285 " =    2.608
peak=    3.316 closest distance to " CA  ILE A 106 " =    0.840
peak=    3.315 closest distance to " CD1 ILE A  33 " =    1.801
peak=    3.315 closest distance to " O   HOH Z 109 " =    2.730
peak=    3.311 closest distance to " NH1 ARG A  14 " =    0.985
peak=    3.309 closest distance to " O   HOH Z 197 " =    2.722
peak=    3.309 closest distance to " CA  GLY A 211 " =    1.333
peak=    3.307 closest distance to " O   HOH Z 180 " =    2.111
peak=    3.306 closest distance to " N   ALA A 256 " =    0.992
peak=    3.305 closest distance to " NH2 ARG A 156 " =    1.143
peak=    3.304 closest distance to " OD2 ASP A 286 " =    2.932
peak=    3.304 closest distance to " CB  ALA A 137 " =    1.009
peak=    3.303 closest distance to " O   HOH Z 293 " =    1.935
peak=    3.302 closest distance to " O   HOH Z 422 " =    2.669
peak=    3.302 closest distance to " O   HOH Z 250 " =    1.363
peak=    3.301 closest distance to " O   HOH Z 227 " =    1.737
peak=    3.301 closest distance to " CG1 ILE A 151 " =    1.294
peak=    3.300 closest distance to " O   HOH Z 197 " =    1.832
peak=    3.299 closest distance to " CA  ASP A 191 " =    0.770
peak=    3.299 closest distance to " O   ASP A 200 " =    1.502
peak=    3.295 closest distance to " O   HOH Z 291 " =    1.695
peak=    3.287 closest distance to " C   ALA A 299 " =    0.943
peak=    3.287 closest distance to " OG BSER A 212 " =    2.284
peak=    3.277 closest distance to " CD2 TRP A 179 " =    1.304
peak=    3.273 closest distance to " ND1 HIS A  81 " =    1.642
peak=    3.272 closest distance to " CB  MET A  40 " =    0.757
peak=    3.267 closest distance to " CA  ALA A 154 " =    1.026
peak=    3.267 closest distance to " O   HOH Z 368 " =    3.606
peak=    3.261 closest distance to " O   THR A 294 " =    1.117
peak=    3.257 closest distance to " O   HOH Z 332 " =    1.540
peak=    3.256 closest distance to " O   HOH Z 148 " =    2.026
peak=    3.256 closest distance to " OG1 THR A 279 " =    1.513
peak=    3.251 closest distance to " CA  ASN A 217 " =    1.598
peak=    3.250 closest distance to " O   HOH Z 173 " =    1.651
peak=    3.247 closest distance to " O   HOH Z 235 " =    1.620
peak=    3.245 closest distance to " OE1 GLN A  11 " =    2.036
peak=    3.240 closest distance to " O   PRO A 198 " =    1.397
peak=    3.232 closest distance to " CB  ARG A 259 " =    1.930
peak=    3.231 closest distance to " OD1 ASN A  69 " =    2.491
peak=    3.231 closest distance to " O   PHE A 192 " =    1.493
peak=    3.228 closest distance to " O   HOH Z 188 " =    2.009
peak=    3.220 closest distance to " O   GLN A 278 " =    1.263
peak=    3.220 closest distance to " CD1 LEU A 101 " =    1.043
peak=    3.218 closest distance to " CG  ASP A 231 " =    1.135
peak=    3.217 closest distance to " OG  SER A 135 " =    1.309
peak=    3.217 closest distance to " O   HOH Z   9 " =    1.866
peak=    3.216 closest distance to " CB  ALA A   1 " =    4.795
peak=    3.215 closest distance to " O   HOH Z 302 " =    1.911
peak=    3.214 closest distance to " O   TYR A 116 " =    1.162
peak=    3.213 closest distance to " CB  ALA A 100 " =    1.449
peak=    3.212 closest distance to " CB  LYS A 193 " =    1.217
peak=    3.212 closest distance to " CA  THR A 264 " =    0.819
peak=    3.211 closest distance to " O   HOH Z  59 " =    2.095
peak=    3.207 closest distance to " O   HOH Z 200 " =    3.398
peak=    3.199 closest distance to " O   ASN A 209 " =    1.384
peak=    3.198 closest distance to " O   HOH Z 294 " =    1.586
peak=    3.198 closest distance to " O   TRP A 274 " =    1.823
peak=    3.195 closest distance to " CD  ARG A 219 " =    1.058
peak=    3.195 closest distance to " CZ3 TRP A  92 " =    1.450
peak=    3.193 closest distance to " CB  ARG A 138 " =    1.481
peak=    3.193 closest distance to " CB  GLU A 236 " =    1.004
peak=    3.192 closest distance to " CB  LYS A 117 " =    1.158
peak=    3.187 closest distance to " CG2 ILE A 263 " =    1.003
peak=    3.186 closest distance to " CB  ASN A 173 " =    0.916
peak=    3.184 closest distance to " CB  GLN A  89 " =    1.183
peak=    3.181 closest distance to " CZ3 TRP A  85 " =    1.109
peak=    3.179 closest distance to " O   HOH Z 148 " =    3.304
peak=    3.175 closest distance to " OH  TYR A 186 " =    0.978
peak=    3.171 closest distance to " CA  TYR A 116 " =    1.536
peak=    3.169 closest distance to " CB  SER A  62 " =    0.961
peak=    3.167 closest distance to " ND1 HIS A  86 " =    1.643
peak=    3.167 closest distance to " O   HOH Z 218 " =    4.736
peak=    3.163 closest distance to " O   HOH Z 221 " =    1.464
peak=    3.162 closest distance to " N   ARG A 156 " =    1.494
peak=    3.161 closest distance to " O   HOH Z 394 " =    1.926
peak=    3.160 closest distance to " O   HOH Z 116 " =    1.907
peak=    3.158 closest distance to " CA  ARG A 139 " =    1.151
peak=    3.155 closest distance to " CA  ALA A 160 " =    1.089
peak=    3.154 closest distance to " CB  THR A  31 " =    1.482
peak=    3.154 closest distance to " ND2 ASN A 249 " =    0.878
peak=    3.150 closest distance to " CA  TYR A 186 " =    1.472
peak=    3.149 closest distance to " CA  LYS A 290 " =    1.327
peak=    3.146 closest distance to " O  BHOH Z  74 " =    1.162
peak=    3.144 closest distance to " O   HOH Z 327 " =    1.972
peak=    3.143 closest distance to " O   HOH Z 134 " =    2.614
peak=    3.139 closest distance to " CB  ILE A 199 " =    0.903
peak=    3.137 closest distance to " CG1 VAL A 174 " =    0.994
peak=    3.135 closest distance to " CE  MET A 113 " =    1.733
peak=    3.131 closest distance to " O   HOH Z 344 " =    3.096
peak=    3.128 closest distance to " CG2 ILE A  49 " =    1.321
peak=    3.127 closest distance to " CB  PHE A  61 " =    0.723
peak=    3.125 closest distance to " CE2 PHE A 204 " =    0.852
peak=    3.123 closest distance to " CA  GLY A 147 " =    0.846
peak=    3.117 closest distance to " OE1 GLN A  55 " =    1.317
peak=    3.113 closest distance to " O   HOH Z 391 " =    2.907
peak=    3.113 closest distance to " O   HOH Z  89 " =    1.918
peak=    3.112 closest distance to " O   HOH Z   1 " =    1.844
peak=    3.112 closest distance to " O   HOH Z 172 " =    3.840
peak=    3.112 closest distance to " O   HOH Z 124 " =    1.935
peak=    3.112 closest distance to " O   HOH Z 435 " =    2.023
peak=    3.111 closest distance to " O   HOH Z 298 " =    2.416
peak=    3.110 closest distance to " CB  ALA A 248 " =    1.310
peak=    3.098 closest distance to " CG  MET A 185 " =    0.974
peak=    3.094 closest distance to " CA  ALA A 158 " =    1.111
peak=    3.089 closest distance to " CA  ALA A 291 " =    0.933
peak=    3.088 closest distance to " CE3 TRP A 274 " =    1.189
peak=    3.082 closest distance to " O   HOH Z 185 " =    2.068
peak=    3.077 closest distance to " CE2 PHE A  16 " =    0.928
peak=    3.077 closest distance to " O   HOH Z 423 " =    1.669
peak=    3.076 closest distance to " N   ASN A 127 " =    1.301
peak=    3.068 closest distance to " CD2 LEU A 255 " =    1.676
peak=    3.065 closest distance to " CB  ALA A 227 " =    1.081
peak=    3.055 closest distance to " O   THR A 251 " =    1.299
peak=    3.053 closest distance to " O   HOH Z 392 " =    1.783
peak=    3.046 closest distance to " O   HOH Z  49 " =    3.317
peak=    3.017 closest distance to " CA  GLY A  98 " =    1.037
peak=    3.013 closest distance to " O   HOH Z 359 " =    4.177
peak=    3.009 closest distance to " O   HOH Z 413 " =    1.796

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.490 - 5.556
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 195 from: 203
   mapped sites are within: 0.702 - 5.556

peak=   -5.700 closest distance to " CG2 VAL A 230 " =    0.731
peak=   -4.762 closest distance to " O   HOH Z 211 " =    0.702
peak=   -4.509 closest distance to " O   HOH Z 231 " =    0.893
peak=   -4.396 closest distance to " CD  ARG A 138 " =    1.211
peak=   -4.269 closest distance to " OE1 GLN A  88 " =    0.909
peak=   -4.255 closest distance to " CG1 VAL A 296 " =    1.324
peak=   -4.228 closest distance to " CG1 VAL A 112 " =    2.605
peak=   -4.096 closest distance to " CG  ARG A 138 " =    0.866
peak=   -4.070 closest distance to " O   HOH Z 102 " =    1.246
peak=   -4.027 closest distance to " O   PRO A 198 " =    1.267
peak=   -4.015 closest distance to " O   HOH Z 231 " =    1.890
peak=   -3.988 closest distance to " CD2 LEU A 237 " =    2.717
peak=   -3.980 closest distance to " O   HOH Z 394 " =    1.429
peak=   -3.956 closest distance to " CA  GLY A 241 " =    2.381
peak=   -3.952 closest distance to " CD  GLN A  55 " =    0.929
peak=   -3.951 closest distance to " CG  ASP A 231 " =    0.740
peak=   -3.946 closest distance to " CD  GLN A  58 " =    0.845
peak=   -3.935 closest distance to " O   HOH Z  19 " =    2.373
peak=   -3.923 closest distance to " OE1 GLN A 223 " =    2.268
peak=   -3.915 closest distance to " CB  PRO A 243 " =    2.718
peak=   -3.904 closest distance to " CG  MET A 105 " =    1.009
peak=   -3.899 closest distance to " O   HOH Z 118 " =    1.348
peak=   -3.891 closest distance to " CD1 LEU A 101 " =    2.888
peak=   -3.883 closest distance to " C   ALA A 158 " =    1.353
peak=   -3.872 closest distance to " O   HOH Z 216 " =    1.165
peak=   -3.856 closest distance to " O   HOH Z 196 " =    2.424
peak=   -3.836 closest distance to " O   ILE A 109 " =    2.673
peak=   -3.834 closest distance to " CD  ARG A 156 " =    2.141
peak=   -3.829 closest distance to " O   HOH Z  73 " =    2.101
peak=   -3.811 closest distance to " NH2 ARG A  66 " =    2.147
peak=   -3.797 closest distance to " O   HOH Z 290 " =    1.396
peak=   -3.783 closest distance to " CE2 TYR A  30 " =    2.824
peak=   -3.782 closest distance to " OG  SER A  97 " =    2.300
peak=   -3.778 closest distance to " O   HOH Z 351 " =    1.462
peak=   -3.753 closest distance to " CG  HIS A  86 " =    1.140
peak=   -3.746 closest distance to " OE1 GLN A  88 " =    1.168
peak=   -3.730 closest distance to " CD1 LEU A   5 " =    2.628
peak=   -3.726 closest distance to " CZ2 TRP A  92 " =    2.877
peak=   -3.721 closest distance to " N   THR A  18 " =    1.317
peak=   -3.701 closest distance to " O   HOH Z  38 " =    1.077
peak=   -3.693 closest distance to " OD2 ASP A  50 " =    2.260
peak=   -3.688 closest distance to " O   GLY A 203 " =    2.478
peak=   -3.677 closest distance to " CD  ARG A  14 " =    3.168
peak=   -3.663 closest distance to " NE2 GLN A  55 " =    2.527
peak=   -3.662 closest distance to " O   HOH Z 113 " =    2.213
peak=   -3.652 closest distance to " O   HOH Z 166 " =    1.819
peak=   -3.651 closest distance to " O   VAL A 189 " =    2.565
peak=   -3.645 closest distance to " O   HOH Z 177 " =    1.656
peak=   -3.642 closest distance to " CB  ARG A  79 " =    2.592
peak=   -3.641 closest distance to " NE2 GLN A  88 " =    0.878
peak=   -3.637 closest distance to " CG  LEU A   5 " =    0.889
peak=   -3.637 closest distance to " CZ2 TRP A 274 " =    0.951
peak=   -3.628 closest distance to " CD1 PHE A  59 " =    1.967
peak=   -3.627 closest distance to " O   HOH Z 377 " =    0.987
peak=   -3.610 closest distance to " CD1 LEU A 228 " =    2.513
peak=   -3.610 closest distance to " CG2BVAL A  41 " =    2.474
peak=   -3.610 closest distance to " CD2 TYR A 293 " =    1.887
peak=   -3.606 closest distance to " CB  TRP A  85 " =    2.667
peak=   -3.602 closest distance to " CE3 TRP A  70 " =    1.788
peak=   -3.599 closest distance to " CD2 LEU A 237 " =    2.887
peak=   -3.593 closest distance to " CA  GLY A 241 " =    3.105
peak=   -3.584 closest distance to " CG2 VAL A 296 " =    1.486
peak=   -3.576 closest distance to " CD2 LEU A 167 " =    1.878
peak=   -3.566 closest distance to " O   PRO A 163 " =    2.128
peak=   -3.563 closest distance to " CD1 ILE A  33 " =    2.558
peak=   -3.556 closest distance to " CG2 VAL A 296 " =    0.878
peak=   -3.556 closest distance to " O   HOH Z 241 " =    1.043
peak=   -3.554 closest distance to " O   HOH Z 133 " =    1.158
peak=   -3.530 closest distance to " CG  TRP A 266 " =    1.892
peak=   -3.529 closest distance to " O   HOH Z 359 " =    3.066
peak=   -3.526 closest distance to " O   HOH Z 179 " =    2.250
peak=   -3.524 closest distance to " O   HOH Z 411 " =    5.230
peak=   -3.517 closest distance to " NH2AARG A 275 " =    5.556
peak=   -3.481 closest distance to " O   HOH Z  10 " =    1.588
peak=   -3.479 closest distance to " O   HOH Z  44 " =    2.245
peak=   -3.466 closest distance to " CG1 VAL A 265 " =    2.426
peak=   -3.464 closest distance to " CD1 LEU A 101 " =    2.509
peak=   -3.461 closest distance to " O   HOH Z 183 " =    1.103
peak=   -3.456 closest distance to " O   GLY A 211 " =    1.470
peak=   -3.451 closest distance to " O   HOH Z  17 " =    1.334
peak=   -3.450 closest distance to " C   ALA A 165 " =    2.018
peak=   -3.450 closest distance to " CG  ARG A 269 " =    2.303
peak=   -3.443 closest distance to " CD2 PHE A 225 " =    2.845
peak=   -3.440 closest distance to " CG1 VAL A 112 " =    2.865
peak=   -3.434 closest distance to " O   HOH Z 236 " =    1.203
peak=   -3.434 closest distance to " CG  GLU A 277 " =    1.307
peak=   -3.433 closest distance to " CB  PHE A 225 " =    2.289
peak=   -3.432 closest distance to " O   HOH Z   9 " =    1.512
peak=   -3.431 closest distance to " CB  PRO A 163 " =    2.564
peak=   -3.426 closest distance to " O   ASP A  27 " =    1.877
peak=   -3.424 closest distance to " CA  ASP A 298 " =    1.095
peak=   -3.420 closest distance to " CZ  PHE A 218 " =    1.221
peak=   -3.418 closest distance to " N   THR A 157 " =    1.637
peak=   -3.415 closest distance to " O   HOH Z 357 " =    2.095
peak=   -3.410 closest distance to " O   HOH Z 255 " =    0.724
peak=   -3.408 closest distance to " O   HOH Z 407 " =    3.403
peak=   -3.407 closest distance to " CB  ALA A  43 " =    2.564
peak=   -3.407 closest distance to " O   HOH Z 435 " =    2.773
peak=   -3.406 closest distance to " O   HOH Z 198 " =    0.807
peak=   -3.399 closest distance to " O   HOH Z 177 " =    1.085
peak=   -3.398 closest distance to " OG ASER A 134 " =    1.600
peak=   -3.394 closest distance to " O   HOH Z 275 " =    1.639
peak=   -3.393 closest distance to " OG  SER A  87 " =    1.650
peak=   -3.386 closest distance to " O   HOH Z 136 " =    0.813
peak=   -3.381 closest distance to " ND2 ASN A  45 " =    2.338
peak=   -3.381 closest distance to " CG  GLU A 152 " =    0.771
peak=   -3.377 closest distance to " O   HOH Z  92 " =    1.207
peak=   -3.376 closest distance to " N   ALA A  43 " =    2.442
peak=   -3.375 closest distance to " OE1 GLN A 278 " =    0.989
peak=   -3.373 closest distance to " O   HOH Z 114 " =    1.555
peak=   -3.363 closest distance to " O   HOH Z 380 " =    1.292
peak=   -3.355 closest distance to " O   HOH Z 232 " =    1.799
peak=   -3.352 closest distance to " CZ3 TRP A 179 " =    1.112
peak=   -3.350 closest distance to " O   HOH Z 317 " =    2.190
peak=   -3.346 closest distance to " SD  MET A 113 " =    2.955
peak=   -3.338 closest distance to " NH2 ARG A  79 " =    2.032
peak=   -3.337 closest distance to " CA  GLY A 133 " =    2.248
peak=   -3.336 closest distance to " CD  GLN A  88 " =    0.803
peak=   -3.336 closest distance to " O   HOH Z  44 " =    1.115
peak=   -3.335 closest distance to " O   HOH Z 185 " =    2.479
peak=   -3.330 closest distance to " N   THR A  52 " =    1.680
peak=   -3.326 closest distance to " O   HOH Z 201 " =    2.062
peak=   -3.326 closest distance to " CD  GLN A  88 " =    0.806
peak=   -3.322 closest distance to " CE BMET A  47 " =    1.809
peak=   -3.321 closest distance to " C   MET A 188 " =    1.439
peak=   -3.318 closest distance to " O   HOH Z 177 " =    1.491
peak=   -3.315 closest distance to " CG  PHE A 130 " =    1.297
peak=   -3.315 closest distance to " OG BSER A 134 " =    1.373
peak=   -3.315 closest distance to " CB  ASN A  69 " =    1.414
peak=   -3.314 closest distance to " NE2 GLN A 240 " =    1.620
peak=   -3.313 closest distance to " O   HOH Z  13 " =    1.425
peak=   -3.310 closest distance to " N   ASP A 191 " =    1.094
peak=   -3.305 closest distance to " O   HOH Z 390 " =    2.169
peak=   -3.300 closest distance to " O   HOH Z  52 " =    1.619
peak=   -3.300 closest distance to " N   SER A 212 " =    1.776
peak=   -3.287 closest distance to " CD  PRO A 213 " =    2.149
peak=   -3.285 closest distance to " CA  GLY A  98 " =    2.180
peak=   -3.276 closest distance to " O   LEU A 167 " =    1.500
peak=   -3.269 closest distance to " O   HOH Z 103 " =    1.998
peak=   -3.269 closest distance to " CG  TYR A 186 " =    2.342
peak=   -3.265 closest distance to " CG1 VAL A  67 " =    2.794
peak=   -3.263 closest distance to " O   HOH Z 113 " =    2.293
peak=   -3.261 closest distance to " O   HOH Z  11 " =    1.821
peak=   -3.255 closest distance to " N   SER A   3 " =    2.128
peak=   -3.243 closest distance to " ND2 ASN A  60 " =    1.895
peak=   -3.236 closest distance to " CB  ALA A   9 " =    2.648
peak=   -3.233 closest distance to " OD1 ASN A 148 " =    1.356
peak=   -3.222 closest distance to " O   HOH Z  43 " =    1.579
peak=   -3.220 closest distance to " C   LEU A 222 " =    0.967
peak=   -3.214 closest distance to " O   HOH Z 411 " =    1.643
peak=   -3.214 closest distance to " O   HOH Z  38 " =    1.681
peak=   -3.213 closest distance to " OG1 THR A  82 " =    2.043
peak=   -3.212 closest distance to " OG  SER A 206 " =    1.699
peak=   -3.212 closest distance to " OH  TYR A 247 " =    2.240
peak=   -3.203 closest distance to " NH2 ARG A  79 " =    1.597
peak=   -3.198 closest distance to " O   HOH Z 396 " =    2.081
peak=   -3.194 closest distance to " CE  LYS A  76 " =    2.607
peak=   -3.191 closest distance to " CA  GLY A 203 " =    2.484
peak=   -3.190 closest distance to " O   HOH Z  60 " =    2.352
peak=   -3.187 closest distance to " OE1 GLN A  77 " =    0.938
peak=   -3.179 closest distance to " CD1 LEU A   5 " =    1.756
peak=   -3.179 closest distance to " O   HOH Z  60 " =    1.458
peak=   -3.174 closest distance to " OG1 THR A 246 " =    1.579
peak=   -3.173 closest distance to " O   HOH Z 177 " =    0.758
peak=   -3.173 closest distance to " O   HOH Z 186 " =    0.927
peak=   -3.172 closest distance to " NE2 GLN A 103 " =    1.930
peak=   -3.172 closest distance to " ND2 ASN A 249 " =    2.298
peak=   -3.155 closest distance to " C   GLY A  13 " =    0.879
peak=   -3.144 closest distance to " CG  LEU A 101 " =    2.492
peak=   -3.141 closest distance to " CB  SER A 276 " =    1.116
peak=   -3.125 closest distance to " O   HOH Z 285 " =    1.639
peak=   -3.125 closest distance to " O   HOH Z  49 " =    1.261
peak=   -3.119 closest distance to " O   THR A  31 " =    1.447
peak=   -3.119 closest distance to " OD1 ASP A 171 " =    1.676
peak=   -3.118 closest distance to " C   PHE A  59 " =    1.174
peak=   -3.118 closest distance to " N   ALA A 248 " =    2.346
peak=   -3.111 closest distance to " CD2 TRP A 274 " =    2.446
peak=   -3.111 closest distance to " O   HOH Z 165 " =    1.794
peak=   -3.110 closest distance to " CG  PHE A 283 " =    2.814
peak=   -3.106 closest distance to " CG  PRO A 163 " =    2.277
peak=   -3.096 closest distance to " O   HOH Z 100 " =    1.097
peak=   -3.091 closest distance to " O   HOH Z 105 " =    2.083
peak=   -3.089 closest distance to " NH2 ARG A  66 " =    1.710
peak=   -3.086 closest distance to " O   HOH Z 380 " =    4.928
peak=   -3.077 closest distance to " C   ASP A 270 " =    1.315
peak=   -3.077 closest distance to " CG2 VAL A 112 " =    2.641
peak=   -3.074 closest distance to " CD  PRO A 243 " =    1.985
peak=   -3.073 closest distance to " CD2 TYR A 169 " =    2.260
peak=   -3.072 closest distance to " O   HOH Z 438 " =    3.110
peak=   -3.068 closest distance to " O   HOH Z 166 " =    1.914
peak=   -3.067 closest distance to " CA  SER A  62 " =    2.704
peak=   -3.065 closest distance to " O   HOH Z 251 " =    4.849
peak=   -3.058 closest distance to " OG  SER A  63 " =    1.100
peak=   -3.052 closest distance to " CD1 TYR A 247 " =    2.186
peak=   -3.039 closest distance to " CA  SER A 135 " =    1.270

================= 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    :  0.4806 0.4714   6.281496e+00   6.264609e+00
   1_bss:  0.4723 0.4596   6.276683e+00   6.257705e+00
   1_xyz:  0.3806 0.4073   6.149683e+00   6.187616e+00
   1_adp:  0.3369 0.3845   6.065428e+00   6.151337e+00
   1_occ:  0.3365 0.3855   6.064536e+00   6.152073e+00
   2_bss:  0.3353 0.3829   6.065608e+00   6.151124e+00
   2_xyz:  0.2515 0.3051   5.830080e+00   5.974802e+00
   2_adp:  0.2297 0.2791   5.757819e+00   5.917604e+00
   2_occ:  0.2294 0.2793   5.757814e+00   5.918096e+00
   3_bss:  0.2282 0.2784   5.759062e+00   5.918226e+00
   3_xyz:  0.1606 0.2085   5.443064e+00   5.647657e+00
   3_adp:  0.1426 0.1977   5.366325e+00   5.602118e+00
   3_occ:  0.1425 0.1977   5.365926e+00   5.601906e+00
   4_bss:  0.1426 0.1970   5.365182e+00   5.599848e+00
   4_xyz:  0.1310 0.1860   5.298999e+00   5.542177e+00
   4_adp:  0.1303 0.1790   5.276651e+00   5.502366e+00
   4_occ:  0.1301 0.1788   5.276029e+00   5.501927e+00
   5_bss:  0.1301 0.1787   5.275928e+00   5.502066e+00
   5_xyz:  0.1270 0.1746   5.253987e+00   5.478453e+00
   5_adp:  0.1281 0.1736   5.256478e+00   5.475365e+00
   5_occ:  0.1279 0.1735   5.255360e+00   5.474488e+00
   5_bss:  0.1280 0.1727   5.253992e+00   5.471498e+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:  0.300  50.000   9.248   6.667   9.213   0.000   0.000   0.000
   1_xyz:  0.300  50.000   9.248   6.667   9.213   0.000   0.000   0.000
   1_adp:  0.300  50.000   9.248   6.667   9.213   0.000   0.000   0.000
   1_occ:  0.300  50.000   9.248   6.667   9.213   0.000   0.000   0.000
   2_bss:  0.308  56.895   6.372   4.380   6.425   0.000   0.000   0.000
   2_xyz:  0.308  56.895   6.372   4.380   6.425   0.000   0.000   0.000
   2_adp:  0.308  56.895   6.372   4.380   6.425   0.000   0.000   0.000
   2_occ:  0.308  56.895   6.372   4.380   6.425   0.000   0.000   0.000
   3_bss:  0.340  73.016   3.972   3.090   4.519   0.000   0.000   0.000
   3_xyz:  0.340  73.016   3.972   3.090   4.519   0.000   0.000   0.000
   3_adp:  0.340  73.016   3.972   3.090   4.519   0.000   0.000   0.000
   3_occ:  0.340  73.016   3.972   3.090   4.519   0.000   0.000   0.000
   4_bss:  0.333  73.016   2.985   2.513   3.896   0.000   0.000   0.000
   4_xyz:  0.333  73.016   2.985   2.513   3.896   0.000   0.000   0.000
   4_adp:  0.333  73.016   2.985   2.513   3.896   0.000   0.000   0.000
   4_occ:  0.333  73.016   2.985   2.513   3.896   0.000   0.000   0.000
   5_bss:  0.325  69.929   2.612   2.380   3.716   0.000   0.000   0.000
   5_xyz:  0.325  69.929   2.612   2.380   3.716   0.000   0.000   0.000
   5_adp:  0.325  69.929   2.612   2.380   3.716   0.000   0.000   0.000
   5_occ:  0.325  69.929   2.612   2.380   3.716   0.000   0.000   0.000
   5_bss:  0.329  72.580  -0.317  -0.512   0.829   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.796 0.4476  0.5043    66224.538
   1_bss:  55.106 0.4557  0.6574    64594.290
   1_xyz:  47.506 0.5498  0.7683    48282.027
   1_adp:  43.300 0.6023  0.8621    42684.700
   1_occ:  43.333 0.6018  0.8608    42760.846
   2_bss:  43.247 0.6028  0.7875    42620.914
   2_xyz:  31.908 0.7360  0.9409    25037.941
   2_adp:  28.770 0.7717  0.9729    21353.563
   2_occ:  28.830 0.7710  0.9715    21375.330
   3_bss:  28.806 0.7713  0.9099    21410.291
   3_xyz:  20.049 0.8610  0.9815    11151.142
   3_adp:  18.894 0.8721  0.9828    10031.425
   3_occ:  18.889 0.8721  0.9827    10024.714
   4_bss:  18.848 0.8724  0.9573     9954.908
   4_xyz:  17.345 0.8864  0.9622     8733.518
   4_adp:  16.322 0.8960  0.9655     8103.494
   4_occ:  16.315 0.8960  0.9653     8092.764
   5_bss:  16.317 0.8960  0.9574     8091.899
   5_xyz:  15.736 0.9013  0.9610     7685.744
   5_adp:  15.595 0.9027  0.9609     7678.019
   5_occ:  15.573 0.9029  0.9608     7662.084
   5_bss:  15.540 0.9030  0.9523     7591.895
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4658e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4658e+01
   1_xyz:   1.769  0.015  0.113 18.278  0.007  4.112   1.5387e-01
   1_adp:   1.769  0.015  0.113 18.278  0.007  4.112   1.5387e-01
   1_occ:   1.769  0.015  0.113 18.278  0.007  4.112   1.5387e-01
   2_bss:   1.769  0.015  0.113 18.278  0.007  4.112   1.5387e-01
   2_xyz:   1.139  0.009  0.077 16.618  0.005  4.112   8.9764e-02
   2_adp:   1.139  0.009  0.077 16.618  0.005  4.112   8.9764e-02
   2_occ:   1.139  0.009  0.077 16.618  0.005  4.112   8.9764e-02
   3_bss:   1.139  0.009  0.077 16.618  0.005  4.112   8.9764e-02
   3_xyz:   1.268  0.011  0.094 16.555  0.004  4.140   9.2942e-02
   3_adp:   1.268  0.011  0.094 16.555  0.004  4.140   9.2942e-02
   3_occ:   1.268  0.011  0.094 16.555  0.004  4.140   9.2942e-02
   4_bss:   1.268  0.011  0.094 16.555  0.004  4.140   9.2942e-02
   4_xyz:   1.106  0.010  0.084 16.017  0.004  4.117   7.6266e-02
   4_adp:   1.106  0.010  0.084 16.017  0.004  4.117   7.6266e-02
   4_occ:   1.106  0.010  0.084 16.017  0.004  4.117   7.6266e-02
   5_bss:   1.106  0.010  0.084 16.017  0.004  4.117   7.6266e-02
   5_xyz:   1.072  0.009  0.083 15.804  0.004  4.121   7.0103e-02
   5_adp:   1.072  0.009  0.083 15.804  0.004  4.121   7.0103e-02
   5_occ:   1.072  0.009  0.083 15.804  0.004  4.121   7.0103e-02
   5_bss:   1.072  0.009  0.083 15.804  0.004  4.121   7.0103e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0875e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0875e+00
   1_xyz:  14.754  0.171  0.477 85.714  0.049  2.160   1.1381e-01
   1_adp:  14.754  0.171  0.477 85.714  0.049  2.160   1.1381e-01
   1_occ:  14.754  0.171  0.477 85.714  0.049  2.160   1.1381e-01
   2_bss:  14.754  0.171  0.477 85.714  0.049  2.160   1.1381e-01
   2_xyz:   7.025  0.098  0.264 81.094  0.043  2.254   2.1328e-01
   2_adp:   7.025  0.098  0.264 81.094  0.043  2.254   2.1328e-01
   2_occ:   7.025  0.098  0.264 81.094  0.043  2.254   2.1328e-01
   3_bss:   7.025  0.098  0.264 81.094  0.043  2.254   2.1328e-01
   3_xyz:   9.471  0.083  0.461 88.326  0.045  2.292   7.1441e-02
   3_adp:   9.471  0.083  0.461 88.326  0.045  2.292   7.1441e-02
   3_occ:   9.471  0.083  0.461 88.326  0.045  2.292   7.1441e-02
   4_bss:   9.471  0.083  0.461 88.326  0.045  2.292   7.1441e-02
   4_xyz:   8.378  0.063  0.445 81.925  0.041  2.304   4.4775e-02
   4_adp:   8.378  0.063  0.445 81.925  0.041  2.304   4.4775e-02
   4_occ:   8.378  0.063  0.445 81.925  0.041  2.304   4.4775e-02
   5_bss:   8.378  0.063  0.445 81.925  0.041  2.304   4.4775e-02
   5_xyz:   8.795  0.060  0.416 82.291  0.040  2.377   3.8420e-02
   5_adp:   8.795  0.060  0.416 82.291  0.040  2.377   3.8420e-02
   5_occ:   8.795  0.060  0.416 82.291  0.040  2.377   3.8420e-02
   5_bss:   8.795  0.060  0.416 82.291  0.040  2.377   3.8420e-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:  97.33   0.00  12.55  75.49   0.00   9.70  97.33   0.00  28.04
   1_occ:  97.33   0.00  12.55  75.49   0.00   9.70  97.33   0.00  28.04
   2_bss:  97.33   0.00  12.55  75.49   0.00   9.70  97.33   0.00  28.04
   2_xyz:  97.33   0.00  12.55  75.49   0.00   9.70  97.33   0.00  28.04
   2_adp: 101.32   0.00  12.75  75.33   0.00   8.87 101.32   0.00  33.85
   2_occ: 101.32   0.00  12.75  75.33   0.00   8.87 101.32   0.00  33.85
   3_bss: 101.32   0.00  12.75  75.33   0.00   8.87 101.32   0.00  33.85
   3_xyz: 101.32   0.00  12.75  75.33   0.00   8.87 101.32   0.00  33.85
   3_adp:  96.77   0.00  14.00  87.58   0.00   8.89  96.77   0.00  41.81
   3_occ:  96.77   0.00  14.00  87.58   0.00   8.89  96.77   0.00  41.81
   4_bss:  96.77   0.00  14.00  87.58   0.00   8.89  96.77   0.00  41.81
   4_xyz:  96.77   0.00  14.00  87.58   0.00   8.89  96.77   0.00  41.81
   4_adp:  93.56   0.00  13.30  85.53   0.00   8.53  93.56   1.33  39.28
   4_occ:  93.56   0.00  13.30  85.53   0.00   8.53  93.56   1.33  39.28
   5_bss:  93.56   0.00  13.30  85.53   0.00   8.53  93.56   1.33  39.28
   5_xyz:  93.56   0.00  13.30  85.53   0.00   8.53  93.56   1.33  39.28
   5_adp:  90.70   0.00  12.39  79.69   0.00   8.28  90.70   1.66  34.76
   5_occ:  90.70   0.00  12.39  79.69   0.00   8.28  90.70   1.66  34.76
   5_bss:  93.35   2.65  15.04  82.34   2.65  10.93  93.35   4.31  37.41
------------------------------------------------------------------------
 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:    1.272    0.020    0.419
   1_adp:    1.272    0.020    0.419
   1_occ:    1.272    0.020    0.419
   2_bss:    1.272    0.020    0.419
   2_xyz:    1.691    0.038    0.571
   2_adp:    1.691    0.038    0.571
   2_occ:    1.691    0.038    0.571
   3_bss:    1.691    0.038    0.571
   3_xyz:    1.670    0.063    0.677
   3_adp:    1.670    0.063    0.677
   3_occ:    1.670    0.063    0.677
   4_bss:    1.670    0.063    0.677
   4_xyz:    1.701    0.074    0.699
   4_adp:    1.701    0.074    0.699
   4_occ:    1.701    0.074    0.699
   5_bss:    1.701    0.074    0.699
   5_xyz:    1.778    0.057    0.717
   5_adp:    1.778    0.057    0.717
   5_occ:    1.778    0.057    0.717
   5_bss:    1.778    0.057    0.717
------------------------------------------------------------------------

CPU time actual refinement: 326.21


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1284/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_1284/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1284/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1284/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1284/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 326.06 
  Macro-tasks:
    bulk solvent and scale       = 34.68  
    individual site refinement   = 138.76 
    weights calculation          = 30.60  
    collect and process          = 6.41   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 210.58 
  Micro-tasks:
    mask                            = 2.32   
    f_calc                          = 102.32 
    alpha_beta                      = 8.21   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 113.74 
    fmodel                         = 6.31   
    r_factors                      = 0.26   
    phase_errors                   = 10.57  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 245.10 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.560 micro seconds
Total CPU time: 5.66 minutes
from_scatterers_fft:    665 calls, 101.92 s
gradients_fft:          609 calls,  99.89 s

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

# Date 2008-01-16 Time 03:38:59 PST -0800 (1200483539.82 s)
Start R-work = 0.4806, R-free = 0.4714 (no bulk solvent and anisotropic scale)
Final R-work = 0.1434, R-free = 0.1886 (no bulk solvent and anisotropic scale)

Start R-work = 0.4723, R-free = 0.4596
Final R-work = 0.1280, R-free = 0.1727