# Date 2008-01-16 Time 02:02:37 PST -0800 (1200477757.20 s)
#phil __OFF__

Command line arguments: "../666.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 = 25555
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 666

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.93, 86.822, 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: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.93, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0142 2.00009
Completeness in resolution range: 0.981364
Completeness with d_max=infinity: 0.978227

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0142
                             d_min =   2.0001

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.93, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0142 2.00009
Completeness in resolution range: 0.981364
Completeness with d_max=infinity: 0.978227

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0146 -  4.2789 [2096/2119]  1886   210  10.0%
  bin  2:  4.2789 -  3.4094 [2023/2043]  1821   202  10.0%
  bin  3:  3.4094 -  2.9823 [1990/2009]  1792   198   9.9%
  bin  4:  2.9823 -  2.7113 [1953/1983]  1757   196  10.0%
  bin  5:  2.7113 -  2.5180 [1970/1989]  1773   197  10.0%
  bin  6:  2.5180 -  2.3701 [1951/1976]  1754   197  10.1%
  bin  7:  2.3701 -  2.2518 [1926/1954]  1734   192  10.0%
  bin  8:  2.2518 -  2.1541 [1934/1970]  1740   194  10.0%
  bin  9:  2.1541 -  2.0714 [1920/1962]  1730   190   9.9%
  bin 10:  2.0714 -  2.0001 [1826/1956]  1643   183  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_666/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:
        1.81 -     2.42: 9
        2.42 -     3.04: 2200
        3.04 -     3.66: 4608
        3.66 -     4.28: 9049
        4.28 -     4.90: 12314
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.258 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.268 3.040 -x+1,y+1/2,-z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 28175 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_666/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_666/model_refine_001.geo

CPU time processing inputs: 9.14


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.93 86.82195 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: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4062   r_free= 0.3918   ksol= 0.00   Bsol= 0.00   scale= 0.835    |
|                                                                             |
| 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:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.188069                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.7721 0.99   1371  152 0.3484 0.3236      6.4922      6.4052|
|  2:  4.7721 -  3.8081 0.99   1299  146 0.2912 0.2958      6.5478      6.5749|
|  3:  3.8081 -  3.3327 0.99   1286  141 0.3410 0.3138      6.4862      6.4811|
|  4:  3.3327 -  3.0308 0.99   1281  142 0.3782 0.3440      6.4017      6.2987|
|  5:  3.0308 -  2.8151 0.99   1260  141 0.4155 0.4322      6.2676      6.2993|
|  6:  2.8151 -  2.6500 0.99   1268  141 0.4272 0.4659      6.1971      6.1859|
|  7:  2.6500 -  2.5180 0.99   1264  140 0.4547 0.4639      6.1838      6.1447|
|  8:  2.5180 -  2.4088 0.98   1249  137 0.4595 0.4364      6.1359      6.1149|
|  9:  2.4088 -  2.3164 0.98   1241  141 0.4494 0.4496      6.0589      6.0408|
| 10:  2.3164 -  2.2368 1.00   1243  138 0.4772 0.4274      6.0939      5.9988|
| 11:  2.2368 -  2.1670 0.97   1249  138 0.4692 0.4007      6.0021      5.9488|
| 12:  2.1670 -  2.1053 0.98   1240  139 0.4716 0.4459      5.9581      5.9828|
| 13:  2.1053 -  2.0500 0.99   1247  137 0.4702 0.4905      5.8719      5.8831|
| 14:  2.0500 -  2.0001 0.91   1132  126 0.4749 0.4241      5.8407      5.6829|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0146 -  4.7721  1371   152  0.76  29.05   0.82     0.78      51833.53|
|  2:  4.7721 -  3.8081  1299   146  0.81  25.28   0.93     0.85      60139.76|
|  3:  3.8081 -  3.3327  1286   141  0.76  30.28   0.89     0.82      61060.65|
|  4:  3.3327 -  3.0308  1281   142  0.71  34.67   0.85     0.75      55205.93|
|  5:  3.0308 -  2.8151  1260   141  0.62  42.69   0.79     0.67      52195.26|
|  6:  2.8151 -  2.6500  1268   141  0.58  45.66   0.77     0.64      49635.32|
|  7:  2.6500 -  2.5180  1264   140  0.55  48.16   0.77     0.62      47394.50|
|  8:  2.5180 -  2.4088  1249   137  0.55  48.09   0.78     0.62      42334.43|
|  9:  2.4088 -  2.3164  1241   141  0.58  45.88   0.76     0.64      35973.58|
| 10:  2.3164 -  2.2368  1243   138  0.59  44.86   0.78     0.66      31262.92|
| 11:  2.2368 -  2.1670  1249   138  0.58  45.84   0.78     0.65      29285.42|
| 12:  2.1670 -  2.1053  1240   139  0.54  49.20   0.80     0.63      29656.79|
| 13:  2.1053 -  2.0500  1247   137  0.53  49.66   0.78     0.60      26209.55|
| 14:  2.0500 -  2.0001  1132   126  0.59  45.63   0.76     0.61      19358.96|
|alpha:            min =        0.60 max =            0.85 mean =         0.68|
|beta:             min =    19358.96 max =        61060.65 mean =     42618.64|
|figures of merit: min =        0.00 max =            1.00 mean =         0.63|
|phase err.(work): min =        0.00 max =           89.99 mean =        41.59|
|phase err.(test): min =        0.00 max =           89.90 mean =        41.83|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.815357              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 71.882   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.456267              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.748   (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:       22 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      164 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      683 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1489 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2612 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3935 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5036 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6528 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7753 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.863 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.645 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    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: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4163   r_free= 0.3975   ksol= 0.00   Bsol= 0.00   scale= 0.803    |
|                                                                             |
| 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:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.199124                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3988   r_free= 0.3785   ksol= 0.35   Bsol= 20.00   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.31,8.17,8.89,0.00,0.00,0.00); trace/3= 8.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.185396                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.507827              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.035   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.448479              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 74.466   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3988      final r-factor (work) = 0.2797          |
| start r-factor (free) = 0.3785      final r-factor (free) = 0.2974          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 70.9796 = 5.51 * 0.50 * 6.2155 + 1.00 * 53.8628                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.5782 = 5.51 * 0.50 * 5.9819 + 1.00 * 0.1045                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2797      final r-factor (work) = 0.1986          |
| start r-factor (free) = 0.2974      final r-factor (free) = 0.2256          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6975 = 0.45 * 1.00 * 5.9819 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5771 = 0.45 * 1.00 * 5.7237 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    54.69   10.01    None  None   None       |
|    all(noH): 2823   0      0.00    54.69   10.01    None  None   None       |
|    Sol.    : 438    0      0.00    54.29   27.69    None  None   None       |
|    Mac.    : 2385   0      0.00    54.69   6.76     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.469: 1310   |   5:    27.343 -  32.812:  110        |
|      1:     5.469 -  10.937:  732   |   6:    32.812 -  38.281:  102        |
|      2:    10.937 -  16.406:  260   |   7:    38.281 -  43.750:   51        |
|      3:    16.406 -  21.875:  120   |   8:    43.750 -  49.218:   33        |
|      4:    21.875 -  27.343:   96   |   9:    49.218 -  54.687:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1986 r_free = 0.2256             target_work(ml) = 5.586         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1979 r_free = 0.2257             target_work(ml) = 5.584         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1979   r_free= 0.2257   ksol= 0.35   Bsol= 20.00   scale= 1.089   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.31,8.17,8.89,0.00,0.00,0.00); trace/3= 8.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.584394                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1912   r_free= 0.2188   ksol= 0.35   Bsol= 50.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.84,4.41,5.59,0.00,0.00,0.00); trace/3= 4.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.580391                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.239602              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.603   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.221611              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.317  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1912      final r-factor (work) = 0.1343          |
| start r-factor (free) = 0.2188      final r-factor (free) = 0.1694          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4168 = 3.24 * 0.50 * 5.7494 + 1.00 * 0.1040                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8221 = 3.24 * 0.50 * 5.4055 + 1.00 * 0.0662                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1343      final r-factor (work) = 0.1243          |
| start r-factor (free) = 0.1694      final r-factor (free) = 0.1620          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2080 = 0.22 * 1.00 * 5.4055 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1695 = 0.22 * 1.00 * 5.2294 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    59.21   10.39    None  None   None       |
|    all(noH): 2823   0      0.00    59.21   10.39    None  None   None       |
|    Sol.    : 438    0      0.00    56.63   30.53    None  None   None       |
|    Mac.    : 2385   0      0.00    59.21   6.69     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 -   5.921: 1474   |   5:    29.606 -  35.527:   90        |
|      1:     5.921 -  11.842:  645   |   6:    35.527 -  41.448:   93        |
|      2:    11.842 -  17.763:  210   |   7:    41.448 -  47.369:   79        |
|      3:    17.763 -  23.685:   94   |   8:    47.369 -  53.290:   29        |
|      4:    23.685 -  29.606:  102   |   9:    53.290 -  59.211:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1243 r_free = 0.1620             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1242 r_free = 0.1620             target_work(ml) = 5.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1242   r_free= 0.1620   ksol= 0.35   Bsol= 50.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.84,4.41,5.59,0.00,0.00,0.00); trace/3= 4.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.204333                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1240   r_free= 0.1616   ksol= 0.33   Bsol= 47.23   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.37,3.83,5.00,0.00,0.00,0.00); trace/3= 4.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.204181                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.163393              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 131.263  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.478474              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.615  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1240      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1616      final r-factor (free) = 0.1553          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7233 = 2.16 * 0.50 * 5.2298 + 1.00 * 0.0662                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6585 = 2.16 * 0.50 * 5.1712 + 1.00 * 0.0648                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1154      final r-factor (work) = 0.1129          |
| start r-factor (free) = 0.1553      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4865 = 0.48 * 1.00 * 5.1712 + 1.00 * 0.0122                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4853 = 0.48 * 1.00 * 5.1417 + 1.00 * 0.0252                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.55   10.81    None  None   None       |
|    all(noH): 2823   0      0.00    69.55   10.81    None  None   None       |
|    Sol.    : 438    0      0.42    63.41   32.41    None  None   None       |
|    Mac.    : 2385   0      0.00    69.55   6.84     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 -   6.955: 1655   |   5:    34.773 -  41.728:   80        |
|      1:     6.955 -  13.909:  545   |   6:    41.728 -  48.682:   90        |
|      2:    13.909 -  20.864:  171   |   7:    48.682 -  55.637:   53        |
|      3:    20.864 -  27.819:  101   |   8:    55.637 -  62.592:   16        |
|      4:    27.819 -  34.773:  106   |   9:    62.592 -  69.546:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1129 r_free = 0.1547             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1128 r_free = 0.1547             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1128   r_free= 0.1547   ksol= 0.33   Bsol= 47.23   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.37,3.83,5.00,0.00,0.00,0.00); trace/3= 4.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.140659                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1128   r_free= 0.1547   ksol= 0.33   Bsol= 47.23   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.37,3.83,5.00,0.00,0.00,0.00); trace/3= 4.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.140659                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.883533              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.046  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.488342              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.425   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1128      final r-factor (work) = 0.1119          |
| start r-factor (free) = 0.1547      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9065 = 1.88 * 0.50 * 5.1411 + 1.00 * 0.0648                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8996 = 1.88 * 0.50 * 5.1375 + 1.00 * 0.0613                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1119      final r-factor (work) = 0.1116          |
| start r-factor (free) = 0.1556      final r-factor (free) = 0.1555          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5328 = 0.49 * 1.00 * 5.1375 + 1.00 * 0.0239                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5220 = 0.49 * 1.00 * 5.1394 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.01   10.81    None  None   None       |
|    all(noH): 2823   0      0.00    76.01   10.81    None  None   None       |
|    Sol.    : 438    0      0.64    65.68   32.39    None  None   None       |
|    Mac.    : 2385   0      0.00    76.01   6.85     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.601: 1730   |   5:    38.003 -  45.603:   94        |
|      1:     7.601 -  15.201:  519   |   6:    45.603 -  53.204:   69        |
|      2:    15.201 -  22.802:  149   |   7:    53.204 -  60.804:   28        |
|      3:    22.802 -  30.402:  107   |   8:    60.804 -  68.405:   12        |
|      4:    30.402 -  38.003:  112   |   9:    68.405 -  76.005:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1116 r_free = 0.1555             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1116 r_free = 0.1556             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1116   r_free= 0.1556   ksol= 0.33   Bsol= 47.23   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.37,3.83,5.00,0.00,0.00,0.00); trace/3= 4.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.140579                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1116   r_free= 0.1556   ksol= 0.33   Bsol= 47.23   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.42,3.84,5.01,0.00,0.00,0.00); trace/3= 4.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.140554                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.212947              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 163.225  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.916497              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.901  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1116      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1556      final r-factor (free) = 0.1551          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7480 = 2.21 * 0.50 * 5.1395 + 1.00 * 0.0613                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7461 = 2.21 * 0.50 * 5.1342 + 1.00 * 0.0653                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1100      final r-factor (work) = 0.1097          |
| start r-factor (free) = 0.1551      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7177 = 0.92 * 1.00 * 5.1342 + 1.00 * 0.0122                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7153 = 0.92 * 1.00 * 5.1307 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.32   10.82    None  None   None       |
|    all(noH): 2823   0      0.00    77.32   10.82    None  None   None       |
|    Sol.    : 438    0      0.39    67.06   32.64    None  None   None       |
|    Mac.    : 2385   0      0.00    77.32   6.81     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.732: 1736   |   5:    38.660 -  46.391:   93        |
|      1:     7.732 -  15.464:  516   |   6:    46.391 -  54.123:   66        |
|      2:    15.464 -  23.196:  145   |   7:    54.123 -  61.855:   26        |
|      3:    23.196 -  30.928:  114   |   8:    61.855 -  69.587:   12        |
|      4:    30.928 -  38.660:  112   |   9:    69.587 -  77.319:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1097 r_free = 0.1556             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1097 r_free = 0.1556             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1097   r_free= 0.1556   ksol= 0.33   Bsol= 47.23   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.42,3.84,5.01,0.00,0.00,0.00); trace/3= 4.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.134062                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.7721 0.99   1371  152 0.1001 0.1302      5.3883      5.5193|
|  2:  4.7721 -  3.8081 0.99   1299  146 0.0842 0.1132      5.4337      5.6462|
|  3:  3.8081 -  3.3327 0.99   1286  141 0.1038 0.1424      5.4681      5.8105|
|  4:  3.3327 -  3.0308 0.99   1281  142 0.1171 0.1560      5.4319      5.6051|
|  5:  3.0308 -  2.8151 0.99   1260  141 0.1275 0.1733      5.3182      5.5405|
|  6:  2.8151 -  2.6500 0.99   1268  141 0.1173 0.1793      5.1992      5.4803|
|  7:  2.6500 -  2.5180 0.99   1264  140 0.1232 0.1555      5.1567       5.325|
|  8:  2.5180 -  2.4088 0.98   1249  137 0.1137 0.1772      5.0728      5.3871|
|  9:  2.4088 -  2.3164 0.98   1241  141 0.1148 0.1747      5.0337      5.2587|
| 10:  2.3164 -  2.2368 1.00   1243  138 0.1111 0.1709      4.9731      5.2617|
| 11:  2.2368 -  2.1670 0.97   1249  138 0.1121 0.1611       4.937      5.2002|
| 12:  2.1670 -  2.1053 0.98   1240  139 0.1117 0.1751      4.8742      5.2633|
| 13:  2.1053 -  2.0500 0.99   1247  137 0.1123 0.1628      4.8068      5.0394|
| 14:  2.0500 -  2.0001 0.91   1132  126 0.1038 0.1845      4.6795      4.9837|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0146 -  4.7721  1371   152  0.94   9.20   0.98     0.96       7314.10|
|  2:  4.7721 -  3.8081  1299   146  0.95   7.88   1.01     1.00       9065.01|
|  3:  3.8081 -  3.3327  1286   141  0.94  10.91   1.02     1.02      10197.68|
|  4:  3.3327 -  3.0308  1281   142  0.93  12.79   1.00     0.99       9767.28|
|  5:  3.0308 -  2.8151  1260   141  0.90  15.50   0.99     0.97       8271.24|
|  6:  2.8151 -  2.6500  1268   141  0.90  15.64   0.98     0.95       6913.81|
|  7:  2.6500 -  2.5180  1264   140  0.91  15.26   0.98     0.96       6063.98|
|  8:  2.5180 -  2.4088  1249   137  0.91  14.59   0.99     0.97       5302.84|
|  9:  2.4088 -  2.3164  1241   141  0.91  15.53   1.00     0.97       5099.69|
| 10:  2.3164 -  2.2368  1243   138  0.90  15.51   1.00     0.95       4410.88|
| 11:  2.2368 -  2.1670  1249   138  0.90  15.96   1.00     0.96       4424.90|
| 12:  2.1670 -  2.1053  1240   139  0.91  15.33   1.01     0.99       3887.68|
| 13:  2.1053 -  2.0500  1247   137  0.91  15.44   1.00     0.98       3411.49|
| 14:  2.0500 -  2.0001  1132   126  0.91  14.86   0.98     0.94       2660.66|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2660.66 max =        10197.68 mean =      6258.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.82|
|phase err.(test): min =        0.00 max =           89.53 mean =        13.37|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1097   r_free= 0.1556   ksol= 0.33   Bsol= 51.40   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.65,-0.27,0.92,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.134068                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1097   r_free= 0.1556   ksol= 0.33   Bsol= 51.40   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.65,-0.27,0.92,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.134068                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.7721 0.99   1371  152 0.1001 0.1303      5.3886      5.5198|
|  2:  4.7721 -  3.8081 0.99   1299  146 0.0842 0.1132      5.4339      5.6462|
|  3:  3.8081 -  3.3327 0.99   1286  141 0.1038 0.1425      5.4682      5.8107|
|  4:  3.3327 -  3.0308 0.99   1281  142 0.1171 0.1560      5.4319      5.6052|
|  5:  3.0308 -  2.8151 0.99   1260  141 0.1275 0.1733      5.3181      5.5403|
|  6:  2.8151 -  2.6500 0.99   1268  141 0.1173 0.1793      5.1991      5.4801|
|  7:  2.6500 -  2.5180 0.99   1264  140 0.1232 0.1555      5.1568      5.3252|
|  8:  2.5180 -  2.4088 0.98   1249  137 0.1137 0.1771      5.0729      5.3871|
|  9:  2.4088 -  2.3164 0.98   1241  141 0.1148 0.1746      5.0337      5.2585|
| 10:  2.3164 -  2.2368 1.00   1243  138 0.1111 0.1710       4.973      5.2621|
| 11:  2.2368 -  2.1670 0.97   1249  138 0.1120 0.1611      4.9369         5.2|
| 12:  2.1670 -  2.1053 0.98   1240  139 0.1118 0.1751      4.8741      5.2632|
| 13:  2.1053 -  2.0500 0.99   1247  137 0.1123 0.1628      4.8067      5.0393|
| 14:  2.0500 -  2.0001 0.91   1132  126 0.1038 0.1844      4.6793      4.9835|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0146 -  4.7721  1371   152  0.94   9.21   0.98     0.96       7320.71|
|  2:  4.7721 -  3.8081  1299   146  0.95   7.88   1.01     1.00       9070.08|
|  3:  3.8081 -  3.3327  1286   141  0.94  10.91   1.02     1.02      10200.37|
|  4:  3.3327 -  3.0308  1281   142  0.93  12.79   1.01     0.99       9766.67|
|  5:  3.0308 -  2.8151  1260   141  0.90  15.50   1.00     0.97       8268.79|
|  6:  2.8151 -  2.6500  1268   141  0.90  15.64   0.99     0.95       6912.28|
|  7:  2.6500 -  2.5180  1264   140  0.91  15.26   0.99     0.96       6064.42|
|  8:  2.5180 -  2.4088  1249   137  0.91  14.59   1.00     0.97       5303.11|
|  9:  2.4088 -  2.3164  1241   141  0.91  15.53   1.01     0.97       5101.22|
| 10:  2.3164 -  2.2368  1243   138  0.90  15.51   1.00     0.96       4409.40|
| 11:  2.2368 -  2.1670  1249   138  0.90  15.96   1.00     0.97       4424.30|
| 12:  2.1670 -  2.1053  1240   139  0.91  15.33   1.01     1.00       3886.70|
| 13:  2.1053 -  2.0500  1247   137  0.91  15.44   1.00     0.98       3410.53|
| 14:  2.0500 -  2.0001  1132   126  0.91  14.85   0.98     0.95       2658.86|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2658.86 max =        10200.37 mean =      6258.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.82|
|phase err.(test): min =        0.00 max =           89.53 mean =        13.37|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      4.17    81.49   15.00    None  None   None       |
|    all(noH): 2823   0      4.17    81.49   15.00    None  None   None       |
|    Sol.    : 438    0      4.57    71.24   36.82    None  None   None       |
|    Mac.    : 2385   0      4.17    81.49   10.99    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:     4.174 -  11.906: 1736   |   5:    42.833 -  50.565:   93        |
|      1:    11.906 -  19.637:  516   |   6:    50.565 -  58.297:   66        |
|      2:    19.637 -  27.369:  145   |   7:    58.297 -  66.029:   26        |
|      3:    27.369 -  35.101:  114   |   8:    66.029 -  73.761:   12        |
|      4:    35.101 -  42.833:  112   |   9:    73.761 -  81.493:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 307         
Filter by distance & map next to the model:
   mapped sites are within: 0.286 - 4.779
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 299 from: 307
   mapped sites are within: 0.706 - 4.779

peak=   10.546 closest distance to " CG2 VAL A 230 " =    1.358
peak=    6.870 closest distance to " CG2 VAL A 296 " =    1.101
peak=    6.199 closest distance to " CG  LEU A   5 " =    1.223
peak=    5.779 closest distance to " CG  LEU A 228 " =    1.168
peak=    5.733 closest distance to " NH2 ARG A  56 " =    2.253
peak=    5.637 closest distance to " CD2 LEU A   5 " =    1.198
peak=    5.378 closest distance to " CB  VAL A 296 " =    1.095
peak=    5.235 closest distance to " CB  GLN A 223 " =    1.455
peak=    5.180 closest distance to " NE2 GLN A  11 " =    1.151
peak=    5.080 closest distance to " CB  VAL A 230 " =    1.159
peak=    4.981 closest distance to " O   HOH Z 142 " =    1.718
peak=    4.952 closest distance to " O   HOH Z 232 " =    2.364
peak=    4.920 closest distance to " CB  GLN A 183 " =    1.289
peak=    4.873 closest distance to " CB  ARG A 275 " =    0.913
peak=    4.738 closest distance to " O   HOH Z 126 " =    1.920
peak=    4.721 closest distance to " CG  PRO A 213 " =    1.211
peak=    4.665 closest distance to " CB  SER A  63 " =    1.266
peak=    4.573 closest distance to " O   HOH Z 209 " =    2.265
peak=    4.440 closest distance to " C   PRO A 198 " =    1.490
peak=    4.419 closest distance to " O   HOH Z  61 " =    1.645
peak=    4.419 closest distance to " O   HOH Z  43 " =    1.989
peak=    4.356 closest distance to " O   HOH Z 427 " =    3.032
peak=    4.309 closest distance to " O   SER A  87 " =    2.224
peak=    4.304 closest distance to " CB  GLU A 152 " =    1.208
peak=    4.303 closest distance to " ND2 ASN A 187 " =    1.514
peak=    4.295 closest distance to " O   HOH Z 346 " =    1.643
peak=    4.287 closest distance to " O   HOH Z 423 " =    1.816
peak=    4.269 closest distance to " O   HOH Z 236 " =    1.945
peak=    4.245 closest distance to " O   HOH Z 369 " =    2.162
peak=    4.204 closest distance to " CZ  PHE A 218 " =    1.108
peak=    4.201 closest distance to " O   HOH Z 316 " =    3.112
peak=    4.201 closest distance to " CG  PRO A 198 " =    1.231
peak=    4.194 closest distance to " O   HOH Z 272 " =    1.895
peak=    4.170 closest distance to " O   HOH Z 158 " =    3.192
peak=    4.170 closest distance to " O   HOH Z 265 " =    2.365
peak=    4.167 closest distance to " CG  PRO A 243 " =    1.091
peak=    4.160 closest distance to " CB  ASN A 148 " =    1.383
peak=    4.145 closest distance to " CB  ARG A  79 " =    1.403
peak=    4.128 closest distance to " O   HOH Z 193 " =    1.813
peak=    4.125 closest distance to " O   HOH Z 368 " =    2.147
peak=    4.121 closest distance to " CA  TYR A  30 " =    0.947
peak=    4.071 closest distance to " O   HOH Z 298 " =    1.783
peak=    4.061 closest distance to " OD1 ASN A  69 " =    2.628
peak=    4.045 closest distance to " CB  TRP A 266 " =    0.984
peak=    4.044 closest distance to " O   HOH Z 248 " =    1.599
peak=    4.035 closest distance to " CD2 LEU A 228 " =    1.128
peak=    4.035 closest distance to " O   HOH Z 189 " =    2.782
peak=    4.027 closest distance to " CB  ASP A 140 " =    0.996
peak=    4.022 closest distance to " O   HOH Z 261 " =    2.008
peak=    4.018 closest distance to " O   HOH Z  15 " =    2.183
peak=    4.011 closest distance to " O   HOH Z 303 " =    2.080
peak=    4.008 closest distance to " O   HOH Z  78 " =    1.687
peak=    3.992 closest distance to " O   HOH Z 203 " =    1.697
peak=    3.974 closest distance to " CB  ALA A   9 " =    1.586
peak=    3.959 closest distance to " CB  VAL A 265 " =    1.339
peak=    3.956 closest distance to " CB  SER A   3 " =    1.263
peak=    3.938 closest distance to " CB  ARG A 190 " =    1.642
peak=    3.933 closest distance to " O   HOH Z 234 " =    3.619
peak=    3.917 closest distance to " O   HOH Z 403 " =    1.654
peak=    3.908 closest distance to " O   HOH Z  59 " =    2.096
peak=    3.885 closest distance to " CB  GLU A 128 " =    1.010
peak=    3.883 closest distance to " O   HOH Z 280 " =    2.939
peak=    3.875 closest distance to " CB  ASN A  39 " =    0.920
peak=    3.851 closest distance to " O   HOH Z 250 " =    1.378
peak=    3.832 closest distance to " O   HOH Z 402 " =    1.399
peak=    3.829 closest distance to " CB  TRP A 179 " =    1.424
peak=    3.821 closest distance to " O   HOH Z 371 " =    3.080
peak=    3.820 closest distance to " O   HOH Z  92 " =    2.409
peak=    3.799 closest distance to " CG1BVAL A  72 " =    1.672
peak=    3.791 closest distance to " CB  GLU A 277 " =    3.612
peak=    3.784 closest distance to " O   HOH Z 411 " =    3.763
peak=    3.778 closest distance to " O   HOH Z  97 " =    2.013
peak=    3.774 closest distance to " O   HOH Z 313 " =    1.826
peak=    3.768 closest distance to " CB  PRO A  54 " =    0.797
peak=    3.762 closest distance to " O   HOH Z 425 " =    2.087
peak=    3.757 closest distance to " CB  ASN A 142 " =    1.141
peak=    3.748 closest distance to " O   HOH Z 389 " =    1.895
peak=    3.745 closest distance to " CB  THR A  31 " =    1.628
peak=    3.742 closest distance to " O   HOH Z 145 " =    2.186
peak=    3.712 closest distance to " CB  VAL A 202 " =    1.584
peak=    3.710 closest distance to " CB  HIS A 108 " =    0.813
peak=    3.707 closest distance to " O   HOH Z 214 " =    2.161
peak=    3.704 closest distance to " O   HOH Z 197 " =    3.098
peak=    3.699 closest distance to " CA  ALA A  21 " =    1.143
peak=    3.695 closest distance to " N   ASN A  39 " =    1.253
peak=    3.693 closest distance to " O   HOH Z 435 " =    1.959
peak=    3.691 closest distance to " CB  ASP A 124 " =    0.768
peak=    3.690 closest distance to " O   HOH Z 147 " =    1.756
peak=    3.681 closest distance to " CG2 VAL A 257 " =    0.847
peak=    3.674 closest distance to " CG1 VAL A 153 " =    0.955
peak=    3.662 closest distance to " O   HOH Z 193 " =    1.939
peak=    3.655 closest distance to " CD2 TRP A 179 " =    1.363
peak=    3.654 closest distance to " CA  ASN A 215 " =    1.195
peak=    3.646 closest distance to " NH1AARG A 145 " =    1.155
peak=    3.646 closest distance to " CA  ALA A  51 " =    0.917
peak=    3.644 closest distance to " O   HOH Z  66 " =    2.160
peak=    3.637 closest distance to " CG2 ILE A  20 " =    1.582
peak=    3.636 closest distance to " CA  ALA A 158 " =    1.260
peak=    3.623 closest distance to " CB  SER A 212 " =    1.180
peak=    3.622 closest distance to " CB  ASN A 148 " =    1.937
peak=    3.621 closest distance to " OG BSER A 164 " =    2.246
peak=    3.620 closest distance to " CD BLYS A 290 " =    1.088
peak=    3.619 closest distance to " CD  ARG A 159 " =    0.706
peak=    3.609 closest distance to " CB  ALA A 291 " =    1.389
peak=    3.607 closest distance to " NE2 GLN A  77 " =    3.220
peak=    3.601 closest distance to " CA  PHE A 283 " =    1.279
peak=    3.595 closest distance to " CB  ARG A 139 " =    0.887
peak=    3.594 closest distance to " CG1 ILE A  49 " =    1.458
peak=    3.587 closest distance to " CB  ARG A  79 " =    0.896
peak=    3.585 closest distance to " NH2 ARG A 156 " =    1.135
peak=    3.584 closest distance to " O   HOH Z 417 " =    3.191
peak=    3.582 closest distance to " NZ  LYS A 117 " =    3.174
peak=    3.580 closest distance to " CD1 LEU A 300 " =    1.281
peak=    3.575 closest distance to " CA  ARG A 195 " =    1.173
peak=    3.570 closest distance to " CB  THR A 157 " =    1.165
peak=    3.565 closest distance to " O   HOH Z 273 " =    2.790
peak=    3.564 closest distance to " O   HOH Z 285 " =    2.795
peak=    3.557 closest distance to " O   HOH Z 193 " =    1.628
peak=    3.554 closest distance to " CB  LEU A 143 " =    1.181
peak=    3.550 closest distance to " N   PHE A 130 " =    1.270
peak=    3.548 closest distance to " O   HOH Z 172 " =    3.515
peak=    3.545 closest distance to " O   HOH Z 245 " =    1.330
peak=    3.542 closest distance to " OD2 ASP A 286 " =    2.826
peak=    3.541 closest distance to " CE  LYS A  76 " =    0.885
peak=    3.541 closest distance to " O   HOH Z 261 " =    1.580
peak=    3.536 closest distance to " CG2 THR A 221 " =    1.253
peak=    3.533 closest distance to " O   HOH Z 325 " =    2.149
peak=    3.532 closest distance to " CB  ASN A 224 " =    1.010
peak=    3.531 closest distance to " O   HOH Z 403 " =    1.407
peak=    3.520 closest distance to " CG  ARG A  66 " =    2.770
peak=    3.519 closest distance to " CB  ASN A 110 " =    1.115
peak=    3.509 closest distance to " CB  GLU A  46 " =    0.974
peak=    3.495 closest distance to " O   HOH Z 145 " =    3.867
peak=    3.494 closest distance to " CG  LEU A 167 " =    1.198
peak=    3.482 closest distance to " O   HOH Z 305 " =    3.637
peak=    3.473 closest distance to " O   HOH Z 128 " =    2.205
peak=    3.472 closest distance to " O   HOH Z  48 " =    1.602
peak=    3.463 closest distance to " CB  ALA A 248 " =    1.444
peak=    3.462 closest distance to " O   HOH Z 251 " =    1.541
peak=    3.460 closest distance to " O   ASP A 124 " =    1.086
peak=    3.458 closest distance to " CA  GLY A 267 " =    0.749
peak=    3.456 closest distance to " CA  ALA A 291 " =    0.872
peak=    3.456 closest distance to " CB AVAL A  41 " =    1.163
peak=    3.452 closest distance to " CA  ARG A  36 " =    1.030
peak=    3.449 closest distance to " OG1 THR A 294 " =    2.418
peak=    3.449 closest distance to " O   HOH Z  97 " =    2.536
peak=    3.441 closest distance to " CA  LYS A 117 " =    1.252
peak=    3.432 closest distance to " CD1 LEU A 228 " =    2.036
peak=    3.432 closest distance to " O   HOH Z  21 " =    1.702
peak=    3.425 closest distance to " O   HOH Z 437 " =    1.846
peak=    3.423 closest distance to " CD  LYS A 166 " =    1.311
peak=    3.421 closest distance to " CB  MET A  40 " =    0.827
peak=    3.420 closest distance to " CA  THR A 264 " =    0.748
peak=    3.418 closest distance to " O   HOH Z 426 " =    1.616
peak=    3.416 closest distance to " O   HOH Z 112 " =    1.684
peak=    3.416 closest distance to " CA  SER A  87 " =    0.980
peak=    3.409 closest distance to " O  BHOH Z 338 " =    2.419
peak=    3.407 closest distance to " N   SER A 135 " =    1.363
peak=    3.404 closest distance to " CG  MET A 185 " =    1.183
peak=    3.402 closest distance to " O   HOH Z  80 " =    1.607
peak=    3.399 closest distance to " CE1 TYR A 186 " =    1.342
peak=    3.398 closest distance to " NZ  LYS A  48 " =    1.272
peak=    3.398 closest distance to " O   HOH Z 422 " =    2.633
peak=    3.397 closest distance to " CB  THR A  82 " =    1.346
peak=    3.397 closest distance to " O   HOH Z  88 " =    2.959
peak=    3.389 closest distance to " CD  LYS A 119 " =    1.600
peak=    3.386 closest distance to " CD  ARG A 269 " =    0.973
peak=    3.383 closest distance to " CA  THR A 221 " =    0.985
peak=    3.381 closest distance to " CA  VAL A  41 " =    0.812
peak=    3.376 closest distance to " O   HOH Z  10 " =    1.763
peak=    3.375 closest distance to " CB  GLN A  89 " =    1.204
peak=    3.372 closest distance to " N   ARG A 156 " =    1.373
peak=    3.372 closest distance to " O   HOH Z 180 " =    2.148
peak=    3.370 closest distance to " CB  GLN A  88 " =    1.173
peak=    3.368 closest distance to " O   HOH Z 344 " =    2.978
peak=    3.368 closest distance to " O   TRP A 274 " =    1.839
peak=    3.367 closest distance to " O   HOH Z 291 " =    1.573
peak=    3.364 closest distance to " CB  SER A 216 " =    0.811
peak=    3.360 closest distance to " CG2 ILE A 120 " =    1.274
peak=    3.358 closest distance to " O   HOH Z 126 " =    1.589
peak=    3.356 closest distance to " O   HOH Z 187 " =    2.305
peak=    3.353 closest distance to " CG  MET A 185 " =    1.079
peak=    3.352 closest distance to " O   HOH Z   1 " =    1.953
peak=    3.351 closest distance to " CB  LEU A 228 " =    1.281
peak=    3.349 closest distance to " O   HOH Z 148 " =    3.343
peak=    3.348 closest distance to " CB  SER A  26 " =    1.745
peak=    3.348 closest distance to " CB  TRP A 150 " =    1.376
peak=    3.348 closest distance to " O   HOH Z 313 " =    1.631
peak=    3.335 closest distance to " O   HOH Z  40 " =    1.603
peak=    3.331 closest distance to " O   HOH Z 407 " =    2.414
peak=    3.329 closest distance to " O   HOH Z 250 " =    1.358
peak=    3.328 closest distance to " CD1 ILE A  33 " =    1.731
peak=    3.328 closest distance to " CG1 VAL A 296 " =    1.209
peak=    3.327 closest distance to " CB  VAL A 268 " =    0.807
peak=    3.322 closest distance to " CG BARG A 275 " =    1.435
peak=    3.321 closest distance to " CB  ALA A 295 " =    1.216
peak=    3.314 closest distance to " O   HOH Z 359 " =    3.821
peak=    3.306 closest distance to " CG1 ILE A  33 " =    1.286
peak=    3.300 closest distance to " CB  GLN A 278 " =    0.843
peak=    3.299 closest distance to " CB  MET A  47 " =    1.111
peak=    3.298 closest distance to " N   VAL A 126 " =    1.454
peak=    3.296 closest distance to " NZ  LYS A  76 " =    1.540
peak=    3.289 closest distance to " CD1 LEU A   5 " =    1.363
peak=    3.284 closest distance to " O   HOH Z 368 " =    3.542
peak=    3.283 closest distance to " CD2 LEU A   5 " =    0.721
peak=    3.274 closest distance to " O   HOH Z 365 " =    3.034
peak=    3.272 closest distance to " O   MET A 105 " =    1.867
peak=    3.270 closest distance to " O   HOH Z 234 " =    1.838
peak=    3.269 closest distance to " O   HOH Z  85 " =    2.149
peak=    3.269 closest distance to " O   HOH Z 133 " =    2.475
peak=    3.261 closest distance to " O   HOH Z 128 " =    1.952
peak=    3.259 closest distance to " CD2 LEU A 297 " =    0.914
peak=    3.258 closest distance to " CB  SER A 273 " =    0.838
peak=    3.256 closest distance to " CB  ALA A 242 " =    0.821
peak=    3.254 closest distance to " CA  MET A 105 " =    0.983
peak=    3.253 closest distance to " OG  SER A  22 " =    2.788
peak=    3.251 closest distance to " CA  TYR A 116 " =    1.424
peak=    3.249 closest distance to " O   HOH Z 109 " =    2.609
peak=    3.248 closest distance to " O   HOH Z 132 " =    2.715
peak=    3.246 closest distance to " O   ARG A  56 " =    2.863
peak=    3.245 closest distance to " N   ASN A 127 " =    1.266
peak=    3.243 closest distance to " CA  SER A 146 " =    1.723
peak=    3.243 closest distance to " O   HOH Z 383 " =    1.896
peak=    3.238 closest distance to " O   HOH Z 353 " =    2.649
peak=    3.236 closest distance to " O   HOH Z 425 " =    1.310
peak=    3.230 closest distance to " O   HOH Z 290 " =    1.075
peak=    3.224 closest distance to " CB  PRO A  90 " =    1.210
peak=    3.224 closest distance to " O   HOH Z 162 " =    2.098
peak=    3.223 closest distance to " ND1 HIS A  81 " =    1.740
peak=    3.219 closest distance to " CA  ASP A 191 " =    1.098
peak=    3.217 closest distance to " ND2 ASN A 110 " =    1.598
peak=    3.216 closest distance to " CB  GLN A 205 " =    1.125
peak=    3.216 closest distance to " O   HOH Z 171 " =    2.299
peak=    3.215 closest distance to " O   HOH Z 411 " =    1.741
peak=    3.215 closest distance to " CG  GLN A  88 " =    1.061
peak=    3.215 closest distance to " N   ASP A 162 " =    1.236
peak=    3.215 closest distance to " NH2BARG A 145 " =    2.013
peak=    3.211 closest distance to " O   HOH Z 173 " =    2.253
peak=    3.209 closest distance to " CB  LYS A 290 " =    0.974
peak=    3.209 closest distance to " O   HOH Z 227 " =    2.103
peak=    3.205 closest distance to " OE2 GLU A  53 " =    1.999
peak=    3.203 closest distance to " O   HOH Z 263 " =    1.657
peak=    3.200 closest distance to " O   HOH Z 329 " =    4.001
peak=    3.197 closest distance to " O   HOH Z 141 " =    1.594
peak=    3.192 closest distance to " O   HOH Z 128 " =    2.169
peak=    3.192 closest distance to " O   HOH Z  96 " =    2.185
peak=    3.191 closest distance to " CB  ILE A  20 " =    1.438
peak=    3.190 closest distance to " CE  LYS A  48 " =    1.178
peak=    3.189 closest distance to " OG  SER A 245 " =    1.588
peak=    3.188 closest distance to " CB  ALA A   1 " =    4.778
peak=    3.185 closest distance to " CA  ALA A 154 " =    0.969
peak=    3.185 closest distance to " CA  ILE A 106 " =    0.749
peak=    3.180 closest distance to " CB  ASN A 215 " =    1.196
peak=    3.174 closest distance to " O   HOH Z  61 " =    1.522
peak=    3.169 closest distance to " N   GLN A 278 " =    1.258
peak=    3.168 closest distance to " CD1 ILE A 263 " =    1.264
peak=    3.165 closest distance to " CB  TYR A 116 " =    0.846
peak=    3.163 closest distance to " CA  ASP A 162 " =    1.025
peak=    3.157 closest distance to " CZ  PHE A  38 " =    1.184
peak=    3.152 closest distance to " CD2 LEU A 255 " =    1.649
peak=    3.152 closest distance to " CB  LYS A 117 " =    1.219
peak=    3.152 closest distance to " O   HOH Z 133 " =    1.538
peak=    3.149 closest distance to " ND1 HIS A  86 " =    1.698
peak=    3.143 closest distance to " O   HOH Z 298 " =    2.689
peak=    3.137 closest distance to " CG1 VAL A 174 " =    1.118
peak=    3.137 closest distance to " O   HOH Z   9 " =    1.921
peak=    3.137 closest distance to " O   HOH Z 406 " =    1.484
peak=    3.135 closest distance to " O   PHE A  61 " =    1.394
peak=    3.133 closest distance to " O   HOH Z 421 " =    1.766
peak=    3.132 closest distance to " CA  ASN A 127 " =    1.042
peak=    3.129 closest distance to " O   HOH Z 302 " =    1.986
peak=    3.125 closest distance to " O   HOH Z 409 " =    3.240
peak=    3.120 closest distance to " O   GLN A  88 " =    1.664
peak=    3.118 closest distance to " CD1 ILE A 106 " =    0.986
peak=    3.116 closest distance to " OE2 GLU A   2 " =    1.839
peak=    3.114 closest distance to " O   HOH Z 359 " =    1.338
peak=    3.106 closest distance to " CB  ALA A 248 " =    1.001
peak=    3.106 closest distance to " NE2 HIS A 207 " =    1.337
peak=    3.106 closest distance to " O   HOH Z 336 " =    1.806
peak=    3.097 closest distance to " CG  GLN A  77 " =    2.229
peak=    3.096 closest distance to " CA  ASN A 176 " =    1.136
peak=    3.090 closest distance to " OE1 GLU A   2 " =    2.096
peak=    3.082 closest distance to " CA  LYS A 290 " =    1.209
peak=    3.079 closest distance to " CG2 ILE A 234 " =    0.800
peak=    3.069 closest distance to " CA  GLY A 211 " =    1.368
peak=    3.062 closest distance to " O   HOH Z 345 " =    3.362
peak=    3.060 closest distance to " CB  ALA A 114 " =    1.266
peak=    3.058 closest distance to " O   HOH Z   1 " =    4.779
peak=    3.056 closest distance to " O   HOH Z 423 " =    3.002
peak=    3.055 closest distance to " CG  ARG A 159 " =    0.958
peak=    3.055 closest distance to " O   GLN A 278 " =    1.506
peak=    3.054 closest distance to " O   ALA A 292 " =    1.763
peak=    3.043 closest distance to " O   SER A 164 " =    1.194
peak=    3.035 closest distance to " O   ALA A 158 " =    1.343
peak=    3.026 closest distance to " O   HOH Z 438 " =    2.968
peak=    3.025 closest distance to " CB  GLU A 277 " =    3.747
peak=    3.022 closest distance to " O   HOH Z 213 " =    1.848
peak=    3.021 closest distance to " O   HOH Z 201 " =    3.080
peak=    3.018 closest distance to " O   HOH Z 419 " =    1.837

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.565 - 5.472
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 204
   mapped sites are within: 0.764 - 5.472

peak=   -5.301 closest distance to " CG2 VAL A 230 " =    0.764
peak=   -4.496 closest distance to " CD  ARG A 156 " =    2.014
peak=   -4.480 closest distance to " SG  CYS A 254 " =    3.337
peak=   -4.337 closest distance to " CB  PRO A 243 " =    2.693
peak=   -4.307 closest distance to " CD  GLN A  58 " =    1.057
peak=   -4.297 closest distance to " OG BSER A 134 " =    1.225
peak=   -4.220 closest distance to " O   HOH Z 266 " =    5.192
peak=   -4.175 closest distance to " C   HIS A 108 " =    1.203
peak=   -4.139 closest distance to " CG  GLN A 223 " =    2.079
peak=   -4.139 closest distance to " CG2 VAL A 296 " =    1.295
peak=   -4.076 closest distance to " CB  PHE A 192 " =    2.039
peak=   -4.026 closest distance to " O   HOH Z 114 " =    3.039
peak=   -4.024 closest distance to " CA  ASN A 110 " =    2.595
peak=   -3.956 closest distance to " O   HOH Z 196 " =    2.148
peak=   -3.940 closest distance to " O   HOH Z 231 " =    2.083
peak=   -3.938 closest distance to " O   HOH Z 290 " =    1.196
peak=   -3.928 closest distance to " O   VAL A  67 " =    2.803
peak=   -3.906 closest distance to " CG2BVAL A  41 " =    2.656
peak=   -3.901 closest distance to " OXT GLY A 302 " =    2.832
peak=   -3.889 closest distance to " CE2 TYR A  30 " =    2.745
peak=   -3.879 closest distance to " O   HOH Z 166 " =    1.970
peak=   -3.870 closest distance to " O   PRO A 163 " =    2.153
peak=   -3.854 closest distance to " N   ALA A  43 " =    2.550
peak=   -3.815 closest distance to " CZ3 TRP A 179 " =    1.196
peak=   -3.794 closest distance to " O   HOH Z 351 " =    1.518
peak=   -3.784 closest distance to " CG1 VAL A 112 " =    2.629
peak=   -3.783 closest distance to " CB  ALA A 291 " =    2.314
peak=   -3.762 closest distance to " CB  ALA A  43 " =    2.526
peak=   -3.760 closest distance to " CG1 VAL A 112 " =    2.807
peak=   -3.750 closest distance to " O   HOH Z 389 " =    1.939
peak=   -3.745 closest distance to " O   HOH Z 185 " =    2.442
peak=   -3.740 closest distance to " ND2 ASN A  45 " =    1.369
peak=   -3.723 closest distance to " CG1 VAL A 250 " =    2.750
peak=   -3.701 closest distance to " O   HOH Z 394 " =    1.542
peak=   -3.692 closest distance to " CE  MET A 105 " =    2.209
peak=   -3.680 closest distance to " ND2 ASN A 187 " =    1.452
peak=   -3.680 closest distance to " CB  ALA A 248 " =    2.338
peak=   -3.679 closest distance to " CB  ALA A 248 " =    2.142
peak=   -3.678 closest distance to " C   ILE A 239 " =    2.130
peak=   -3.674 closest distance to " OG  SER A  97 " =    2.286
peak=   -3.657 closest distance to " CG  ASP A 231 " =    0.791
peak=   -3.648 closest distance to " CE2 PHE A 218 " =    2.527
peak=   -3.646 closest distance to " CB  ALA A 291 " =    2.190
peak=   -3.643 closest distance to " NH2AARG A 275 " =    5.209
peak=   -3.638 closest distance to " CA  ASP A 298 " =    1.066
peak=   -3.633 closest distance to " OD1 ASN A 187 " =    1.654
peak=   -3.628 closest distance to " CA  GLY A 241 " =    3.105
peak=   -3.627 closest distance to " NE2 GLN A  88 " =    1.881
peak=   -3.627 closest distance to " N   ALA A 226 " =    2.123
peak=   -3.620 closest distance to " O   HOH Z 211 " =    1.626
peak=   -3.610 closest distance to " CB  ASP A 132 " =    2.321
peak=   -3.593 closest distance to " O   HOH Z 435 " =    2.765
peak=   -3.589 closest distance to " O   HOH Z  11 " =    1.876
peak=   -3.585 closest distance to " O   HOH Z 426 " =    1.577
peak=   -3.558 closest distance to " OD1 ASN A 148 " =    1.469
peak=   -3.554 closest distance to " O   HOH Z  73 " =    2.149
peak=   -3.547 closest distance to " NE2 GLN A 278 " =    1.958
peak=   -3.544 closest distance to " O   HOH Z  44 " =    2.274
peak=   -3.535 closest distance to " C   ALA A 158 " =    1.254
peak=   -3.535 closest distance to " CB  PRO A 163 " =    2.557
peak=   -3.533 closest distance to " O   PRO A 198 " =    1.226
peak=   -3.529 closest distance to " CG2 ILE A 263 " =    2.315
peak=   -3.527 closest distance to " CG  TRP A 266 " =    1.807
peak=   -3.526 closest distance to " O   HOH Z  38 " =    1.617
peak=   -3.523 closest distance to " O   HOH Z 103 " =    1.869
peak=   -3.506 closest distance to " CD2 LEU A 300 " =    2.719
peak=   -3.506 closest distance to " CE BMET A  47 " =    1.684
peak=   -3.504 closest distance to " N   THR A 157 " =    1.498
peak=   -3.497 closest distance to " O   HOH Z 407 " =    3.045
peak=   -3.490 closest distance to " NE2 GLN A 194 " =    1.791
peak=   -3.489 closest distance to " CG1 VAL A 296 " =    1.401
peak=   -3.487 closest distance to " C   MET A 188 " =    1.380
peak=   -3.460 closest distance to " CZ  PHE A 192 " =    2.868
peak=   -3.458 closest distance to " O   HOH Z 292 " =    4.626
peak=   -3.457 closest distance to " O   HOH Z  52 " =    1.502
peak=   -3.456 closest distance to " CB  ASP A 171 " =    2.237
peak=   -3.452 closest distance to " NH2 ARG A  79 " =    2.029
peak=   -3.444 closest distance to " C   LEU A 143 " =    1.039
peak=   -3.434 closest distance to " O   HOH Z 359 " =    3.216
peak=   -3.434 closest distance to " O   MET A  40 " =    2.762
peak=   -3.430 closest distance to " O   HOH Z  10 " =    1.479
peak=   -3.429 closest distance to " CG  PHE A 283 " =    2.636
peak=   -3.427 closest distance to " O   VAL A 189 " =    2.622
peak=   -3.409 closest distance to " O   HOH Z 166 " =    1.571
peak=   -3.407 closest distance to " O   HOH Z 139 " =    3.120
peak=   -3.403 closest distance to " N   ALA A 248 " =    1.733
peak=   -3.401 closest distance to " CD  ARG A 139 " =    1.590
peak=   -3.399 closest distance to " O   HOH Z 102 " =    1.562
peak=   -3.398 closest distance to " CG1 VAL A 112 " =    2.924
peak=   -3.397 closest distance to " CE3 TRP A 150 " =    2.123
peak=   -3.392 closest distance to " N   THR A 235 " =    1.295
peak=   -3.389 closest distance to " C   PHE A  59 " =    1.321
peak=   -3.385 closest distance to " CD1 LEU A 101 " =    2.277
peak=   -3.382 closest distance to " O   HOH Z 295 " =    1.608
peak=   -3.373 closest distance to " O   HOH Z  60 " =    1.982
peak=   -3.372 closest distance to " O   HOH Z 198 " =    2.234
peak=   -3.370 closest distance to " O   HOH Z 175 " =    4.304
peak=   -3.365 closest distance to " CD2 LEU A 167 " =    1.800
peak=   -3.359 closest distance to " O   GLY A 196 " =    1.248
peak=   -3.359 closest distance to " CZ  PHE A  59 " =    1.545
peak=   -3.356 closest distance to " O   HOH Z 313 " =    1.130
peak=   -3.351 closest distance to " CB  VAL A 296 " =    1.097
peak=   -3.351 closest distance to " O   SER A 271 " =    2.156
peak=   -3.349 closest distance to " CB  VAL A 230 " =    1.031
peak=   -3.346 closest distance to " OG  SER A  62 " =    1.657
peak=   -3.339 closest distance to " O   HOH Z 417 " =    2.867
peak=   -3.339 closest distance to " O   HOH Z  13 " =    1.584
peak=   -3.333 closest distance to " N   GLN A  58 " =    1.763
peak=   -3.327 closest distance to " ND2 ASN A 249 " =    2.414
peak=   -3.325 closest distance to " CG1 VAL A 230 " =    1.940
peak=   -3.323 closest distance to " OG  SER A 206 " =    1.709
peak=   -3.322 closest distance to " CB  ASN A  39 " =    2.310
peak=   -3.322 closest distance to " CD1 LEU A 228 " =    2.238
peak=   -3.318 closest distance to " CD  ARG A 195 " =    5.176
peak=   -3.317 closest distance to " O   HOH Z 123 " =    2.446
peak=   -3.315 closest distance to " CG1 VAL A 197 " =    2.239
peak=   -3.315 closest distance to " N   SER A 276 " =    1.329
peak=   -3.311 closest distance to " O   HOH Z 357 " =    2.230
peak=   -3.308 closest distance to " N   ASP A 171 " =    2.314
peak=   -3.307 closest distance to " O   HOH Z 311 " =    3.815
peak=   -3.303 closest distance to " O   SER A  22 " =    2.250
peak=   -3.302 closest distance to " CB  ASP A 132 " =    2.368
peak=   -3.296 closest distance to " O   HOH Z 136 " =    2.306
peak=   -3.292 closest distance to " CA  GLY A 241 " =    2.306
peak=   -3.287 closest distance to " O   ALA A  10 " =    1.697
peak=   -3.283 closest distance to " CZ  TYR A 169 " =    1.689
peak=   -3.281 closest distance to " NZ  LYS A 119 " =    3.580
peak=   -3.271 closest distance to " CD2 TYR A 247 " =    2.301
peak=   -3.268 closest distance to " N   THR A  52 " =    1.683
peak=   -3.262 closest distance to " CA  GLY A  98 " =    1.913
peak=   -3.258 closest distance to " O   LEU A 101 " =    2.877
peak=   -3.256 closest distance to " O   HOH Z 313 " =    1.631
peak=   -3.254 closest distance to " CD1 PHE A  59 " =    1.982
peak=   -3.253 closest distance to " NH2 ARG A  79 " =    1.575
peak=   -3.248 closest distance to " O   LYS A 117 " =    1.729
peak=   -3.242 closest distance to " O   HOH Z  43 " =    1.781
peak=   -3.242 closest distance to " O   HOH Z 310 " =    1.900
peak=   -3.237 closest distance to " CD2 TYR A 293 " =    2.080
peak=   -3.233 closest distance to " CG  ARG A 269 " =    2.341
peak=   -3.232 closest distance to " O   HOH Z 174 " =    2.451
peak=   -3.229 closest distance to " C   LEU A 222 " =    0.767
peak=   -3.228 closest distance to " CD1 ILE A 239 " =    2.160
peak=   -3.227 closest distance to " N   MET A 188 " =    1.879
peak=   -3.225 closest distance to " CA  GLY A 133 " =    1.960
peak=   -3.225 closest distance to " O   SER A  95 " =    1.589
peak=   -3.224 closest distance to " CB  GLN A  11 " =    1.845
peak=   -3.223 closest distance to " CD  PRO A 213 " =    2.169
peak=   -3.221 closest distance to " CZ  PHE A 155 " =    1.257
peak=   -3.220 closest distance to " O   HOH Z 134 " =    3.067
peak=   -3.217 closest distance to " CB  ALA A  10 " =    2.279
peak=   -3.211 closest distance to " OG  SER A  87 " =    1.457
peak=   -3.210 closest distance to " CG  GLU A 277 " =    1.200
peak=   -3.209 closest distance to " N   GLN A  77 " =    1.676
peak=   -3.206 closest distance to " O   ALA A 161 " =    1.685
peak=   -3.206 closest distance to " CD2 LEU A 237 " =    2.867
peak=   -3.202 closest distance to " CB  ASN A 252 " =    1.799
peak=   -3.201 closest distance to " CG1 VAL A  67 " =    3.063
peak=   -3.199 closest distance to " O   GLY A  17 " =    1.297
peak=   -3.195 closest distance to " CD2 LEU A 300 " =    2.861
peak=   -3.192 closest distance to " O   HOH Z 252 " =    4.166
peak=   -3.189 closest distance to " O   HOH Z 256 " =    1.335
peak=   -3.187 closest distance to " CD1 ILE A 199 " =    2.486
peak=   -3.182 closest distance to " OD2 ASP A  50 " =    2.250
peak=   -3.180 closest distance to " CZ2 TRP A  92 " =    2.823
peak=   -3.179 closest distance to " O   HOH Z   6 " =    1.637
peak=   -3.175 closest distance to " O   HOH Z 191 " =    5.472
peak=   -3.173 closest distance to " O   SER A 276 " =    1.643
peak=   -3.168 closest distance to " CD  GLN A 223 " =    0.776
peak=   -3.167 closest distance to " N   VAL A 230 " =    1.127
peak=   -3.165 closest distance to " O   HOH Z 253 " =    3.883
peak=   -3.164 closest distance to " CB  PRO A  54 " =    2.391
peak=   -3.160 closest distance to " O   HOH Z 309 " =    2.606
peak=   -3.159 closest distance to " N   SER A   3 " =    1.964
peak=   -3.153 closest distance to " N   ALA A 248 " =    2.388
peak=   -3.153 closest distance to " CA  PRO A 243 " =    2.274
peak=   -3.149 closest distance to " CB  ASN A  69 " =    1.197
peak=   -3.148 closest distance to " ND2 ASN A  60 " =    1.363
peak=   -3.146 closest distance to " CA  GLY A 203 " =    2.462
peak=   -3.137 closest distance to " O   HOH Z  41 " =    2.449
peak=   -3.137 closest distance to " CB  TYR A  15 " =    2.200
peak=   -3.136 closest distance to " O   ALA A  51 " =    1.383
peak=   -3.124 closest distance to " O   PRO A 198 " =    1.337
peak=   -3.123 closest distance to " CG  LEU A 228 " =    1.009
peak=   -3.115 closest distance to " O   GLN A 240 " =    2.155
peak=   -3.114 closest distance to " O   HOH Z 339 " =    1.775
peak=   -3.113 closest distance to " ND2 ASN A 252 " =    1.857
peak=   -3.109 closest distance to " O   HOH Z 350 " =    1.880
peak=   -3.108 closest distance to " O   HOH Z 165 " =    1.857
peak=   -3.104 closest distance to " O   HOH Z 281 " =    2.715
peak=   -3.090 closest distance to " CG  GLU A 152 " =    1.625
peak=   -3.088 closest distance to " O   HOH Z 371 " =    2.036
peak=   -3.084 closest distance to " CG2 VAL A 189 " =    2.016
peak=   -3.081 closest distance to " O   HOH Z 222 " =    1.472
peak=   -3.078 closest distance to " CE1 HIS A  81 " =    1.397
peak=   -3.062 closest distance to " O   HOH Z 193 " =    1.773
peak=   -3.051 closest distance to " NE2 GLN A  58 " =    2.554
peak=   -3.047 closest distance to " O   VAL A 125 " =    2.321
peak=   -3.046 closest distance to " OG BSER A 134 " =    1.785
peak=   -3.044 closest distance to " CG  PRO A 163 " =    2.623
peak=   -3.043 closest distance to " O   HOH Z 128 " =    2.592
peak=   -3.039 closest distance to " OE2 GLU A 152 " =    1.218
peak=   -3.028 closest distance to " C   ASP A 270 " =    1.277

================= 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    :  0.4062 0.3918   6.188069e+00   6.153321e+00
   1_bss:  0.3988 0.3785   6.185396e+00   6.134802e+00
   1_xyz:  0.2797 0.2974   5.908358e+00   5.952115e+00
   1_adp:  0.1986 0.2256   5.586287e+00   5.711604e+00
   1_occ:  0.1979 0.2257   5.584394e+00   5.712798e+00
   2_bss:  0.1912 0.2188   5.580391e+00   5.704749e+00
   2_xyz:  0.1343 0.1694   5.267919e+00   5.459563e+00
   2_adp:  0.1243 0.1620   5.204581e+00   5.410595e+00
   2_occ:  0.1242 0.1620   5.204333e+00   5.410693e+00
   3_bss:  0.1240 0.1616   5.204181e+00   5.410241e+00
   3_xyz:  0.1154 0.1553   5.152673e+00   5.378878e+00
   3_adp:  0.1129 0.1547   5.141263e+00   5.376362e+00
   3_occ:  0.1128 0.1547   5.140659e+00   5.376085e+00
   4_bss:  0.1128 0.1547   5.140659e+00   5.376085e+00
   4_xyz:  0.1119 0.1556   5.141282e+00   5.382679e+00
   4_adp:  0.1116 0.1555   5.140580e+00   5.383798e+00
   4_occ:  0.1116 0.1556   5.140579e+00   5.384048e+00
   5_bss:  0.1116 0.1556   5.140554e+00   5.384053e+00
   5_xyz:  0.1100 0.1551   5.132455e+00   5.381838e+00
   5_adp:  0.1097 0.1556   5.134153e+00   5.386030e+00
   5_occ:  0.1097 0.1556   5.134062e+00   5.385966e+00
   5_bss:  0.1097 0.1556   5.134068e+00   5.385986e+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:  0.347  20.002   7.315   8.173   8.887   0.000   0.000   0.000
   1_xyz:  0.347  20.002   7.315   8.173   8.887   0.000   0.000   0.000
   1_adp:  0.347  20.002   7.315   8.173   8.887   0.000   0.000   0.000
   1_occ:  0.347  20.002   7.315   8.173   8.887   0.000   0.000   0.000
   2_bss:  0.347  50.001   3.839   4.414   5.589   0.000   0.000   0.000
   2_xyz:  0.347  50.001   3.839   4.414   5.589   0.000   0.000   0.000
   2_adp:  0.347  50.001   3.839   4.414   5.589   0.000   0.000   0.000
   2_occ:  0.347  50.001   3.839   4.414   5.589   0.000   0.000   0.000
   3_bss:  0.332  47.229   3.368   3.831   4.997   0.000   0.000   0.000
   3_xyz:  0.332  47.229   3.368   3.831   4.997   0.000   0.000   0.000
   3_adp:  0.332  47.229   3.368   3.831   4.997   0.000   0.000   0.000
   3_occ:  0.332  47.229   3.368   3.831   4.997   0.000   0.000   0.000
   4_bss:  0.332  47.229   3.368   3.831   4.997   0.000   0.000   0.000
   4_xyz:  0.332  47.229   3.368   3.831   4.997   0.000   0.000   0.000
   4_adp:  0.332  47.229   3.368   3.831   4.997   0.000   0.000   0.000
   4_occ:  0.332  47.229   3.368   3.831   4.997   0.000   0.000   0.000
   5_bss:  0.332  47.229   3.419   3.840   5.007   0.000   0.000   0.000
   5_xyz:  0.332  47.229   3.419   3.840   5.007   0.000   0.000   0.000
   5_adp:  0.332  47.229   3.419   3.840   5.007   0.000   0.000   0.000
   5_occ:  0.332  47.229   3.419   3.840   5.007   0.000   0.000   0.000
   5_bss:  0.332  51.403  -0.650  -0.267   0.917   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  41.611 0.6259  0.6826    42618.199
   1_bss:  41.003 0.6313  0.8805    39839.345
   1_xyz:  31.028 0.7457  1.0050    23300.654
   1_adp:  21.313 0.8501  1.0844    12503.674
   1_occ:  21.338 0.8498  1.0837    12523.048
   2_bss:  21.076 0.8523  0.9556    12240.081
   2_xyz:  15.529 0.9021  0.9905     7277.381
   2_adp:  14.407 0.9117  0.9974     6642.750
   2_occ:  14.410 0.9116  0.9974     6640.187
   3_bss:  14.424 0.9115  0.9765     6640.978
   3_xyz:  13.667 0.9179  0.9773     6189.980
   3_adp:  13.610 0.9184  0.9757     6138.182
   3_occ:  13.606 0.9184  0.9756     6138.027
   4_bss:  13.606 0.9184  0.9756     6138.027
   4_xyz:  13.723 0.9176  0.9753     6231.398
   4_adp:  13.738 0.9175  0.9735     6228.626
   4_occ:  13.741 0.9175  0.9735     6231.946
   5_bss:  13.741 0.9175  0.9743     6232.193
   5_xyz:  13.688 0.9179  0.9745     6219.542
   5_adp:  13.779 0.9172  0.9717     6259.037
   5_occ:  13.778 0.9172  0.9717     6258.034
   5_bss:  13.778 0.9172  0.9747     6258.547
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.3863e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.3863e+01
   1_xyz:   1.404  0.010  0.098 17.879  0.005  4.123   1.0448e-01
   1_adp:   1.404  0.010  0.098 17.879  0.005  4.123   1.0448e-01
   1_occ:   1.404  0.010  0.098 17.879  0.005  4.123   1.0448e-01
   2_bss:   1.404  0.010  0.098 17.879  0.005  4.123   1.0448e-01
   2_xyz:   1.029  0.008  0.081 16.217  0.004  4.128   6.6218e-02
   2_adp:   1.029  0.008  0.081 16.217  0.004  4.128   6.6218e-02
   2_occ:   1.029  0.008  0.081 16.217  0.004  4.128   6.6218e-02
   3_bss:   1.029  0.008  0.081 16.217  0.004  4.128   6.6218e-02
   3_xyz:   1.018  0.008  0.084 15.956  0.004  4.133   6.4786e-02
   3_adp:   1.018  0.008  0.084 15.956  0.004  4.133   6.4786e-02
   3_occ:   1.018  0.008  0.084 15.956  0.004  4.133   6.4786e-02
   4_bss:   1.018  0.008  0.084 15.956  0.004  4.133   6.4786e-02
   4_xyz:   0.982  0.007  0.081 15.737  0.004  4.135   6.1251e-02
   4_adp:   0.982  0.007  0.081 15.737  0.004  4.135   6.1251e-02
   4_occ:   0.982  0.007  0.081 15.737  0.004  4.135   6.1251e-02
   5_bss:   0.982  0.007  0.081 15.737  0.004  4.135   6.1251e-02
   5_xyz:   1.022  0.008  0.085 15.752  0.004  4.136   6.5261e-02
   5_adp:   1.022  0.008  0.085 15.752  0.004  4.136   6.5261e-02
   5_occ:   1.022  0.008  0.085 15.752  0.004  4.136   6.5261e-02
   5_bss:   1.022  0.008  0.085 15.752  0.004  4.136   6.5261e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9840e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9840e+00
   1_xyz:  10.800  0.118  0.420 88.280  0.034  2.244   7.5510e-02
   1_adp:  10.800  0.118  0.420 88.280  0.034  2.244   7.5510e-02
   1_occ:  10.800  0.118  0.420 88.280  0.034  2.244   7.5510e-02
   2_bss:  10.800  0.118  0.420 88.280  0.034  2.244   7.5510e-02
   2_xyz:   6.875  0.046  0.498 83.915  0.037  2.252   4.4275e-02
   2_adp:   6.875  0.046  0.498 83.915  0.037  2.252   4.4275e-02
   2_occ:   6.875  0.046  0.498 83.915  0.037  2.252   4.4275e-02
   3_bss:   6.875  0.046  0.498 83.915  0.037  2.252   4.4275e-02
   3_xyz:   6.735  0.045  0.599 83.599  0.036  2.342   4.3626e-02
   3_adp:   6.735  0.045  0.599 83.599  0.036  2.342   4.3626e-02
   3_occ:   6.735  0.045  0.599 83.599  0.036  2.342   4.3626e-02
   4_bss:   6.735  0.045  0.599 83.599  0.036  2.342   4.3626e-02
   4_xyz:   6.517  0.043  0.543 83.032  0.037  2.370   3.8956e-02
   4_adp:   6.517  0.043  0.543 83.032  0.037  2.370   3.8956e-02
   4_occ:   6.517  0.043  0.543 83.032  0.037  2.370   3.8956e-02
   5_bss:   6.517  0.043  0.543 83.032  0.037  2.370   3.8956e-02
   5_xyz:   6.771  0.047  0.602 82.986  0.036  2.328   4.2830e-02
   5_adp:   6.771  0.047  0.602 82.986  0.036  2.328   4.2830e-02
   5_occ:   6.771  0.047  0.602 82.986  0.036  2.328   4.2830e-02
   5_bss:   6.771  0.047  0.602 82.986  0.036  2.328   4.2830e-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:  54.69   0.00  10.01  54.69   0.00   6.76  54.29   0.00  27.69
   1_occ:  54.69   0.00  10.01  54.69   0.00   6.76  54.29   0.00  27.69
   2_bss:  54.69   0.00  10.01  54.69   0.00   6.76  54.29   0.00  27.69
   2_xyz:  54.69   0.00  10.01  54.69   0.00   6.76  54.29   0.00  27.69
   2_adp:  59.21   0.00  10.39  59.21   0.00   6.69  56.63   0.00  30.53
   2_occ:  59.21   0.00  10.39  59.21   0.00   6.69  56.63   0.00  30.53
   3_bss:  59.21   0.00  10.39  59.21   0.00   6.69  56.63   0.00  30.53
   3_xyz:  59.21   0.00  10.39  59.21   0.00   6.69  56.63   0.00  30.53
   3_adp:  69.55   0.00  10.81  69.55   0.00   6.84  63.41   0.42  32.41
   3_occ:  69.55   0.00  10.81  69.55   0.00   6.84  63.41   0.42  32.41
   4_bss:  69.55   0.00  10.81  69.55   0.00   6.84  63.41   0.42  32.41
   4_xyz:  69.55   0.00  10.81  69.55   0.00   6.84  63.41   0.42  32.41
   4_adp:  76.01   0.00  10.81  76.01   0.00   6.85  65.68   0.64  32.39
   4_occ:  76.01   0.00  10.81  76.01   0.00   6.85  65.68   0.64  32.39
   5_bss:  76.01   0.00  10.81  76.01   0.00   6.85  65.68   0.64  32.39
   5_xyz:  76.01   0.00  10.81  76.01   0.00   6.85  65.68   0.64  32.39
   5_adp:  77.32   0.00  10.82  77.32   0.00   6.81  67.06   0.39  32.64
   5_occ:  77.32   0.00  10.82  77.32   0.00   6.81  67.06   0.39  32.64
   5_bss:  81.49   4.17  15.00  81.49   4.17  10.99  71.24   4.57  36.82
------------------------------------------------------------------------
 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:    1.165    0.025    0.395
   1_adp:    1.165    0.025    0.395
   1_occ:    1.165    0.025    0.395
   2_bss:    1.165    0.025    0.395
   2_xyz:    1.349    0.036    0.466
   2_adp:    1.349    0.036    0.466
   2_occ:    1.349    0.036    0.466
   3_bss:    1.349    0.036    0.466
   3_xyz:    1.307    0.038    0.480
   3_adp:    1.307    0.038    0.480
   3_occ:    1.307    0.038    0.480
   4_bss:    1.307    0.038    0.480
   4_xyz:    1.376    0.035    0.488
   4_adp:    1.376    0.035    0.488
   4_occ:    1.376    0.035    0.488
   5_bss:    1.376    0.035    0.488
   5_xyz:    1.426    0.042    0.492
   5_adp:    1.426    0.042    0.492
   5_occ:    1.426    0.042    0.492
   5_bss:    1.426    0.042    0.492
------------------------------------------------------------------------

CPU time actual refinement: 314.06


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_666/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_666/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_666/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_666/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_666/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 313.91 
  Macro-tasks:
    bulk solvent and scale       = 41.71  
    individual site refinement   = 123.49 
    weights calculation          = 31.58  
    collect and process          = 6.55   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 203.45 
  Micro-tasks:
    mask                            = 1.16   
    f_calc                          = 93.96  
    alpha_beta                      = 8.05   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 103.97 
    fmodel                         = 7.29   
    r_factors                      = 0.14   
    phase_errors                   = 11.12  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 227.08 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.485 micro seconds
Total CPU time: 5.46 minutes
from_scatterers_fft:    633 calls, 93.66 s
gradients_fft:          579 calls, 91.24 s

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

# Date 2008-01-16 Time 02:08:04 PST -0800 (1200478084.13 s)
Start R-work = 0.4062, R-free = 0.3918 (no bulk solvent and anisotropic scale)
Final R-work = 0.1277, R-free = 0.1719 (no bulk solvent and anisotropic scale)

Start R-work = 0.3988, R-free = 0.3785
Final R-work = 0.1097, R-free = 0.1556