# Date 2008-01-16 Time 02:22:31 PST -0800 (1200478951.99 s)
#phil __OFF__

Command line arguments: "../811.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 20260
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 811

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.3993, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.34, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.3993, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1092 2.01058
Completeness in resolution range: 0.972642
Completeness with d_max=infinity: 0.96956

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1092
                             d_min =   2.0106

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.3993, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1092 2.01058
Completeness in resolution range: 0.972642
Completeness with d_max=infinity: 0.96956

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1096 -  4.3015 [2117/2141]  1903   214  10.1%
  bin  2:  4.3015 -  3.4273 [2037/2056]  1836   201   9.9%
  bin  3:  3.4273 -  2.9979 [2007/2026]  1808   199   9.9%
  bin  4:  2.9979 -  2.7256 [1980/2010]  1776   204  10.3%
  bin  5:  2.7256 -  2.5312 [1982/2001]  1787   195   9.8%
  bin  6:  2.5312 -  2.3826 [1963/1988]  1767   196  10.0%
  bin  7:  2.3826 -  2.2636 [1954/1982]  1759   195  10.0%
  bin  8:  2.2636 -  2.1654 [1946/1982]  1751   195  10.0%
  bin  9:  2.1654 -  2.0823 [1929/1971]  1735   194  10.1%
  bin 10:  2.0823 -  2.0106 [1674/1983]  1508   166   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_811/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 13
        2.42 -     3.04: 2152
        3.04 -     3.66: 4591
        3.66 -     4.28: 8880
        4.28 -     4.90: 12249
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.930 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.024 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.135 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.135 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27880 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_811/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_811/model_refine_001.geo

CPU time processing inputs: 9.66


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 47.3993 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4590   r_free= 0.4439   ksol= 0.00   Bsol= 0.00   scale= 0.797    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.256261                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7973 0.99   1380  153 0.3732 0.3415      6.5549       6.457|
|  2:  4.7973 -  3.8281 0.99   1311  149 0.3604 0.3987      6.7109       6.847|
|  3:  3.8281 -  3.3503 0.99   1306  145 0.4126 0.3857       6.644      6.5969|
|  4:  3.3503 -  3.0467 0.99   1288  136 0.4437 0.3890      6.5051      6.3994|
|  5:  3.0467 -  2.8298 0.99   1269  144 0.4816 0.4582      6.3542      6.3611|
|  6:  2.8298 -  2.6640 0.99   1276  145 0.4837 0.5222        6.27      6.1972|
|  7:  2.6640 -  2.5312 0.99   1280  141 0.4953 0.4592      6.2224      6.1604|
|  8:  2.5312 -  2.4215 0.98   1261  137 0.5010 0.4326      6.1765      6.1264|
|  9:  2.4215 -  2.3286 0.98   1251  143 0.5031 0.5504      6.1071      6.1501|
| 10:  2.3286 -  2.2485 0.99   1264  136 0.5250 0.4813      6.1271      6.0768|
| 11:  2.2485 -  2.1784 0.98   1259  142 0.5054 0.4998      6.0253      6.0695|
| 12:  2.1784 -  2.1163 0.97   1231  139 0.5233 0.5007      5.9806      6.0228|
| 13:  2.1163 -  2.0607 1.00   1261  137 0.5202 0.4881      5.8954      5.8357|
| 14:  2.0607 -  2.0106 0.78    993  112 0.5256 0.5014      5.8556       5.773|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1096 -  4.7973  1380   153  0.74  31.13   0.80     0.75      58852.33|
|  2:  4.7973 -  3.8281  1311   149  0.75  30.89   0.89     0.79      85737.84|
|  3:  3.8281 -  3.3503  1306   145  0.67  38.08   0.84     0.75      90692.92|
|  4:  3.3503 -  3.0467  1288   136  0.60  44.20   0.81     0.65      80010.49|
|  5:  3.0467 -  2.8298  1269   144  0.51  51.17   0.75     0.58      67708.40|
|  6:  2.8298 -  2.6640  1276   145  0.49  53.03   0.74     0.54      61534.03|
|  7:  2.6640 -  2.5312  1280   141  0.46  55.03   0.73     0.52      56615.58|
|  8:  2.5312 -  2.4215  1261   137  0.46  55.38   0.75     0.52      51014.84|
|  9:  2.4215 -  2.3286  1251   143  0.45  55.92   0.72     0.52      47180.13|
| 10:  2.3286 -  2.2485  1264   136  0.44  56.91   0.73     0.51      44181.83|
| 11:  2.2485 -  2.1784  1259   142  0.41  58.81   0.75     0.49      41769.03|
| 12:  2.1784 -  2.1163  1231   139  0.40  60.25   0.75     0.48      38873.55|
| 13:  2.1163 -  2.0607  1261   137  0.39  60.51   0.73     0.46      33432.39|
| 14:  2.0607 -  2.0106   993   112  0.42  58.45   0.71     0.45      27038.39|
|alpha:            min =        0.45 max =            0.79 mean =         0.58|
|beta:             min =    27038.39 max =        90692.92 mean =     56759.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           89.95 mean =        50.34|
|phase err.(test): min =        0.00 max =           89.55 mean =        50.41|
|-----------------------------------------------------------------------------|

============================== 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 = 9.949604              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.044   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.899499              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.079   (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:       25 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      160 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      673 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1479 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2576 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3843 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5007 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6471 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7638 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.399 |
| 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 |       1.663 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4650   r_free= 0.4437   ksol= 0.00   Bsol= 0.00   scale= 0.769    |
|                                                                             |
| 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:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.260401                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4503   r_free= 0.4318   ksol= 0.30   Bsol= 20.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.71,8.85,10.25,0.00,0.00,0.00); trace/3= 8.60                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.249603                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.085219              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.358   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.821126              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.029   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4503      final r-factor (work) = 0.3471          |
| start r-factor (free) = 0.4318      final r-factor (free) = 0.3687          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 82.8463 = 9.09 * 0.50 * 6.2624 + 1.00 * 54.3986                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.9308 = 9.09 * 0.50 * 6.1190 + 1.00 * 0.1346                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3471      final r-factor (work) = 0.2950          |
| start r-factor (free) = 0.3687      final r-factor (free) = 0.3381          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0389 = 0.82 * 1.00 * 6.1190 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9297 = 0.82 * 1.00 * 5.9867 + 1.00 * 0.0139                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.24   11.49    None  None   None       |
|    all(noH): 2823   0      0.00    98.24   11.49    None  None   None       |
|    Sol.    : 438    0      0.00    98.24   27.68    None  None   None       |
|    Mac.    : 2385   0      0.00    65.40   8.51     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.824: 1694   |   5:    49.122 -  58.947:   28        |
|      1:     9.824 -  19.649:  629   |   6:    58.947 -  68.771:   11        |
|      2:    19.649 -  29.473:  236   |   7:    68.771 -  78.595:    1        |
|      3:    29.473 -  39.298:  141   |   8:    78.595 -  88.420:    0        |
|      4:    39.298 -  49.122:   82   |   9:    88.420 -  98.244:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2950 r_free = 0.3381             target_work(ml) = 5.951         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2945 r_free = 0.3387             target_work(ml) = 5.950         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2945   r_free= 0.3387   ksol= 0.30   Bsol= 20.00   scale= 1.076   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.71,8.85,10.25,0.00,0.00,0.00); trace/3= 8.60                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.950013                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2909   r_free= 0.3345   ksol= 0.32   Bsol= 50.00   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.62,5.51,6.60,0.00,0.00,0.00); trace/3= 5.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.950673                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.360501              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.627   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.398906              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.792  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2909      final r-factor (work) = 0.2086          |
| start r-factor (free) = 0.3345      final r-factor (free) = 0.2505          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1928 = 3.36 * 0.50 * 5.9862 + 1.00 * 0.1346                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8119 = 3.36 * 0.50 * 5.7998 + 1.00 * 0.0668                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2086      final r-factor (work) = 0.1916          |
| start r-factor (free) = 0.2505      final r-factor (free) = 0.2339          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3473 = 0.40 * 1.00 * 5.7998 + 1.00 * 0.0338                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3507 = 0.40 * 1.00 * 5.6199 + 1.00 * 0.1089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.41   11.49    None  None   None       |
|    all(noH): 2823   0      0.00    97.41   11.49    None  None   None       |
|    Sol.    : 438    0      0.00    97.41   31.54    None  None   None       |
|    Mac.    : 2385   0      0.00    67.75   7.81     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 -   9.742: 1823   |   5:    48.707 -  58.449:   44        |
|      1:     9.742 -  19.483:  497   |   6:    58.449 -  68.190:   12        |
|      2:    19.483 -  29.225:  171   |   7:    68.190 -  77.932:    1        |
|      3:    29.225 -  38.966:  176   |   8:    77.932 -  87.673:    0        |
|      4:    38.966 -  48.707:   98   |   9:    87.673 -  97.415:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1916 r_free = 0.2339             target_work(ml) = 5.593         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1913 r_free = 0.2344             target_work(ml) = 5.593         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1913   r_free= 0.2344   ksol= 0.32   Bsol= 50.00   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.62,5.51,6.60,0.00,0.00,0.00); trace/3= 5.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.593278                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1909   r_free= 0.2341   ksol= 0.33   Bsol= 61.08   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.90,4.09,4.97,0.00,0.00,0.00); trace/3= 3.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.594099                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.249250              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.907  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.677282              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.968   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1909      final r-factor (work) = 0.1390          |
| start r-factor (free) = 0.2341      final r-factor (free) = 0.1795          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0130 = 4.25 * 0.50 * 5.6227 + 1.00 * 0.0669                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6789 = 4.25 * 0.50 * 5.4612 + 1.00 * 0.0760                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1390      final r-factor (work) = 0.1280          |
| start r-factor (free) = 0.1795      final r-factor (free) = 0.1733          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.6383 = 2.68 * 1.00 * 5.4612 + 1.00 * 0.0172                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.1252 = 2.68 * 1.00 * 5.2700 + 1.00 * 0.0159                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.12   12.40    None  None   None       |
|    all(noH): 2823   0      0.00    90.12   12.40    None  None   None       |
|    Sol.    : 438    0      0.00    90.12   37.39    None  None   None       |
|    Mac.    : 2385   0      0.00    77.81   7.81     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 -   9.012: 1752   |   5:    45.059 -  54.070:  101        |
|      1:     9.012 -  18.023:  521   |   6:    54.070 -  63.082:   66        |
|      2:    18.023 -  27.035:  142   |   7:    63.082 -  72.094:   24        |
|      3:    27.035 -  36.047:  120   |   8:    72.094 -  81.105:   11        |
|      4:    36.047 -  45.059:   85   |   9:    81.105 -  90.117:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1280 r_free = 0.1733             target_work(ml) = 5.252         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1279 r_free = 0.1733             target_work(ml) = 5.252         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1279   r_free= 0.1733   ksol= 0.33   Bsol= 61.08   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.90,4.09,4.97,0.00,0.00,0.00); trace/3= 3.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.252211                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1282   r_free= 0.1734   ksol= 0.33   Bsol= 67.18   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.79,3.53,4.60,0.00,0.00,0.00); trace/3= 3.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.252010                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.131158              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.142  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.323759              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.568  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1282      final r-factor (work) = 0.1177          |
| start r-factor (free) = 0.1734      final r-factor (free) = 0.1656          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3281 = 3.13 * 0.50 * 5.2710 + 1.00 * 0.0760                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2467 = 3.13 * 0.50 * 5.2169 + 1.00 * 0.0792                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1177      final r-factor (work) = 0.1169          |
| start r-factor (free) = 0.1656      final r-factor (free) = 0.1622          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7049 = 0.32 * 1.00 * 5.2169 + 1.00 * 0.0159                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6999 = 0.32 * 1.00 * 5.1900 + 1.00 * 0.0196                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.36   11.77    None  None   None       |
|    all(noH): 2823   0      0.00    83.36   11.77    None  None   None       |
|    Sol.    : 438    0      0.64    83.36   35.11    None  None   None       |
|    Mac.    : 2385   0      0.00    79.77   7.49     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.336: 1736   |   5:    41.682 -  50.018:   87        |
|      1:     8.336 -  16.673:  525   |   6:    50.018 -  58.355:   62        |
|      2:    16.673 -  25.009:  159   |   7:    58.355 -  66.691:   28        |
|      3:    25.009 -  33.346:  105   |   8:    66.691 -  75.028:   11        |
|      4:    33.346 -  41.682:  105   |   9:    75.028 -  83.364:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1169 r_free = 0.1622             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1168 r_free = 0.1621             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1621   ksol= 0.33   Bsol= 67.18   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.79,3.53,4.60,0.00,0.00,0.00); trace/3= 3.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.178979                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1621   ksol= 0.33   Bsol= 67.18   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.79,3.53,4.60,0.00,0.00,0.00); trace/3= 3.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.178979                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.493780              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.947  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.575886              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.260   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1168      final r-factor (work) = 0.1192          |
| start r-factor (free) = 0.1621      final r-factor (free) = 0.1631          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9554 = 1.49 * 0.50 * 5.1897 + 1.00 * 0.0792                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9371 = 1.49 * 0.50 * 5.1892 + 1.00 * 0.0613                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1192      final r-factor (work) = 0.1188          |
| start r-factor (free) = 0.1631      final r-factor (free) = 0.1635          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0037 = 0.58 * 1.00 * 5.1892 + 1.00 * 0.0153                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0392 = 0.58 * 1.00 * 5.1901 + 1.00 * 0.0503                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.93   11.76    None  None   None       |
|    all(noH): 2823   0      0.00    81.93   11.76    None  None   None       |
|    Sol.    : 438    0      0.61    81.93   35.17    None  None   None       |
|    Mac.    : 2385   0      0.00    80.73   7.47     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.194: 1718   |   5:    40.967 -  49.161:   84        |
|      1:     8.194 -  16.387:  535   |   6:    49.161 -  57.354:   72        |
|      2:    16.387 -  24.580:  158   |   7:    57.354 -  65.548:   26        |
|      3:    24.580 -  32.774:  106   |   8:    65.548 -  73.741:   16        |
|      4:    32.774 -  40.967:  103   |   9:    73.741 -  81.935:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1188 r_free = 0.1635             target_work(ml) = 5.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1187 r_free = 0.1635             target_work(ml) = 5.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1635   ksol= 0.33   Bsol= 67.18   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.79,3.53,4.60,0.00,0.00,0.00); trace/3= 3.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.193317                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7973 0.99   1380  153 0.1047 0.1320      5.4239      5.5378|
|  2:  4.7973 -  3.8281 0.99   1311  149 0.0882 0.1129       5.464      5.6687|
|  3:  3.8281 -  3.3503 0.99   1306  145 0.1096 0.1513      5.5071      5.8476|
|  4:  3.3503 -  3.0467 0.99   1288  136 0.1247 0.1550      5.4702      5.6019|
|  5:  3.0467 -  2.8298 0.99   1269  144 0.1417 0.1773      5.3901      5.5663|
|  6:  2.8298 -  2.6640 0.99   1276  145 0.1293 0.2070      5.2742      5.5656|
|  7:  2.6640 -  2.5312 0.99   1280  141 0.1382 0.1783      5.2422      5.4078|
|  8:  2.5312 -  2.4215 0.98   1261  137 0.1285 0.1770      5.1561      5.4184|
|  9:  2.4215 -  2.3286 0.98   1251  143 0.1248 0.1972      5.0954      5.3661|
| 10:  2.3286 -  2.2485 0.99   1264  136 0.1240 0.1733      5.0403      5.2473|
| 11:  2.2485 -  2.1784 0.98   1259  142 0.1238 0.1804      4.9988      5.2475|
| 12:  2.1784 -  2.1163 0.97   1231  139 0.1233 0.1730      4.9383      5.2515|
| 13:  2.1163 -  2.0607 1.00   1261  137 0.1191 0.1808      4.8383      5.1005|
| 14:  2.0607 -  2.0106 0.78    993  112 0.1097 0.1825      4.7042      4.9906|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1096 -  4.7973  1380   153  0.94   9.49   0.97     0.94       7749.51|
|  2:  4.7973 -  3.8281  1311   149  0.95   8.12   1.00     0.98       9286.82|
|  3:  3.8281 -  3.3503  1306   145  0.93  11.29   1.01     1.01      10732.70|
|  4:  3.3503 -  3.0467  1288   136  0.92  13.41   1.00     0.98      10213.14|
|  5:  3.0467 -  2.8298  1269   144  0.89  16.54   0.99     0.97       9090.58|
|  6:  2.8298 -  2.6640  1276   145  0.89  16.86   0.98     0.95       7948.16|
|  7:  2.6640 -  2.5312  1280   141  0.89  16.88   0.98     0.95       7123.69|
|  8:  2.5312 -  2.4215  1261   137  0.90  16.07   0.98     0.96       6111.46|
|  9:  2.4215 -  2.3286  1251   143  0.90  16.52   1.00     0.96       5715.49|
| 10:  2.3286 -  2.2485  1264   136  0.89  16.87   0.99     0.94       4922.48|
| 11:  2.2485 -  2.1784  1259   142  0.90  16.60   0.99     0.94       4765.11|
| 12:  2.1784 -  2.1163  1231   139  0.90  16.33   1.00     0.98       4332.80|
| 13:  2.1163 -  2.0607  1261   137  0.90  16.25   0.98     0.96       3593.02|
| 14:  2.0607 -  2.0106   993   112  0.91  14.83   0.96     0.92       2656.57|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2656.57 max =        10732.70 mean =      6830.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.85 mean =        14.65|
|phase err.(test): min =        0.00 max =           89.16 mean =        14.15|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1634   ksol= 0.32   Bsol= 62.62   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.77,-0.20,0.97,-0.00,0.00,0.00); trace/3= -0.00                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.192927                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1634   ksol= 0.32   Bsol= 62.62   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.77,-0.20,0.97,-0.00,0.00,0.00); trace/3= -0.00                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.192927                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7973 0.99   1380  153 0.1043 0.1316      5.4185      5.5335|
|  2:  4.7973 -  3.8281 0.99   1311  149 0.0878 0.1122      5.4597      5.6625|
|  3:  3.8281 -  3.3503 0.99   1306  145 0.1094 0.1513      5.5054      5.8481|
|  4:  3.3503 -  3.0467 0.99   1288  136 0.1249 0.1551      5.4716      5.6026|
|  5:  3.0467 -  2.8298 0.99   1269  144 0.1420 0.1777      5.3923      5.5683|
|  6:  2.8298 -  2.6640 0.99   1276  145 0.1294 0.2072      5.2758      5.5669|
|  7:  2.6640 -  2.5312 0.99   1280  141 0.1384 0.1788      5.2438      5.4098|
|  8:  2.5312 -  2.4215 0.98   1261  137 0.1287 0.1771      5.1568       5.419|
|  9:  2.4215 -  2.3286 0.98   1251  143 0.1247 0.1970      5.0957       5.366|
| 10:  2.3286 -  2.2485 0.99   1264  136 0.1240 0.1736      5.0403      5.2484|
| 11:  2.2485 -  2.1784 0.98   1259  142 0.1239 0.1803      4.9987       5.247|
| 12:  2.1784 -  2.1163 0.97   1231  139 0.1233 0.1726      4.9382      5.2508|
| 13:  2.1163 -  2.0607 1.00   1261  137 0.1192 0.1807      4.8378      5.1008|
| 14:  2.0607 -  2.0106 0.78    993  112 0.1098 0.1820      4.7035      4.9891|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1096 -  4.7973  1380   153  0.94   9.44   0.97     0.94       7660.30|
|  2:  4.7973 -  3.8281  1311   149  0.95   8.05   1.00     0.98       9201.95|
|  3:  3.8281 -  3.3503  1306   145  0.93  11.25   1.01     1.01      10678.16|
|  4:  3.3503 -  3.0467  1288   136  0.92  13.43   1.00     0.98      10232.25|
|  5:  3.0467 -  2.8298  1269   144  0.89  16.57   0.99     0.97       9129.47|
|  6:  2.8298 -  2.6640  1276   145  0.89  16.91   0.98     0.95       7979.45|
|  7:  2.6640 -  2.5312  1280   141  0.89  16.91   0.98     0.95       7151.63|
|  8:  2.5312 -  2.4215  1261   137  0.90  16.09   0.98     0.96       6120.02|
|  9:  2.4215 -  2.3286  1251   143  0.90  16.54   1.00     0.96       5724.12|
| 10:  2.3286 -  2.2485  1264   136  0.89  16.86   0.99     0.94       4920.57|
| 11:  2.2485 -  2.1784  1259   142  0.90  16.59   0.99     0.95       4765.81|
| 12:  2.1784 -  2.1163  1231   139  0.90  16.32   1.00     0.99       4330.63|
| 13:  2.1163 -  2.0607  1261   137  0.90  16.24   0.98     0.96       3587.49|
| 14:  2.0607 -  2.0106   993   112  0.91  14.79   0.96     0.92       2648.53|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2648.53 max =        10678.16 mean =      6821.54|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        14.65|
|phase err.(test): min =        0.00 max =           89.07 mean =        14.14|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.66    85.60   15.42    None  None   None       |
|    all(noH): 2823   0      3.66    85.60   15.42    None  None   None       |
|    Sol.    : 438    0      4.27    85.60   38.83    None  None   None       |
|    Mac.    : 2385   0      3.66    84.39   11.13    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:     3.661 -  11.854: 1718   |   5:    44.628 -  52.821:   84        |
|      1:    11.854 -  20.048:  535   |   6:    52.821 -  61.015:   72        |
|      2:    20.048 -  28.241:  158   |   7:    61.015 -  69.208:   26        |
|      3:    28.241 -  36.435:  106   |   8:    69.208 -  77.402:   16        |
|      4:    36.435 -  44.628:  103   |   9:    77.402 -  85.595:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 339         
Filter by distance & map next to the model:
   mapped sites are within: 0.255 - 4.525
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 329 from: 339
   mapped sites are within: 0.720 - 4.525

peak=   10.333 closest distance to " CB  VAL A 230 " =    1.477
peak=    6.039 closest distance to " CG  LEU A   5 " =    1.244
peak=    6.009 closest distance to " NH2 ARG A  56 " =    2.250
peak=    5.837 closest distance to " CB  GLN A 223 " =    1.452
peak=    5.497 closest distance to " CG  LEU A 228 " =    1.234
peak=    5.458 closest distance to " CG2 VAL A 296 " =    1.045
peak=    5.267 closest distance to " CG  PRO A  54 " =    1.376
peak=    5.232 closest distance to " CB  VAL A 296 " =    1.093
peak=    5.085 closest distance to " CG  PRO A 198 " =    1.308
peak=    4.951 closest distance to " CB  PRO A  54 " =    0.989
peak=    4.887 closest distance to " CD2 LEU A   5 " =    1.101
peak=    4.817 closest distance to " CG1 VAL A 296 " =    1.154
peak=    4.808 closest distance to " CZ  PHE A 218 " =    1.125
peak=    4.757 closest distance to " O   HOH Z 232 " =    2.287
peak=    4.688 closest distance to " CB  GLN A 183 " =    1.262
peak=    4.560 closest distance to " CB  SER A  63 " =    1.230
peak=    4.505 closest distance to " CB  VAL A 230 " =    1.240
peak=    4.483 closest distance to " CB  ARG A 275 " =    0.932
peak=    4.446 closest distance to " CB  ARG A 190 " =    1.606
peak=    4.444 closest distance to " CG  PRO A 213 " =    1.236
peak=    4.421 closest distance to " O   HOH Z 265 " =    2.132
peak=    4.393 closest distance to " NE2 GLN A  11 " =    1.075
peak=    4.371 closest distance to " CB  GLU A 128 " =    1.046
peak=    4.285 closest distance to " O   HOH Z 369 " =    2.167
peak=    4.259 closest distance to " C   PRO A 198 " =    1.546
peak=    4.259 closest distance to " CA  TYR A  30 " =    0.970
peak=    4.244 closest distance to " CG  PRO A 243 " =    1.162
peak=    4.242 closest distance to " CA  ALA A  51 " =    0.974
peak=    4.232 closest distance to " O   HOH Z 248 " =    1.529
peak=    4.189 closest distance to " O   HOH Z 298 " =    1.869
peak=    4.160 closest distance to " O   HOH Z 234 " =    3.750
peak=    4.156 closest distance to " CB  ASP A 124 " =    0.752
peak=    4.126 closest distance to " O   HOH Z 142 " =    1.692
peak=    4.123 closest distance to " CD2 LEU A 228 " =    1.370
peak=    4.113 closest distance to " CB  TRP A 266 " =    1.037
peak=    4.098 closest distance to " O   HOH Z 411 " =    3.896
peak=    4.089 closest distance to " CD  LYS A 166 " =    1.322
peak=    4.078 closest distance to " O   HOH Z 188 " =    3.012
peak=    4.072 closest distance to " O   HOH Z  43 " =    1.996
peak=    4.065 closest distance to " CB  ASN A 148 " =    1.385
peak=    4.053 closest distance to " CB  VAL A 202 " =    1.580
peak=    4.053 closest distance to " CG  MET A 185 " =    1.225
peak=    4.052 closest distance to " O   SER A  87 " =    2.324
peak=    4.025 closest distance to " CB BVAL A  41 " =    1.114
peak=    4.023 closest distance to " CB  ARG A  79 " =    1.444
peak=    4.013 closest distance to " O   HOH Z 427 " =    3.069
peak=    3.999 closest distance to " N   ASN A  39 " =    1.215
peak=    3.991 closest distance to " O   HOH Z 346 " =    1.581
peak=    3.990 closest distance to " O   HOH Z 126 " =    1.603
peak=    3.989 closest distance to " CB  GLU A 277 " =    3.733
peak=    3.987 closest distance to " CB  ASN A 142 " =    1.119
peak=    3.981 closest distance to " O   HOH Z 126 " =    1.988
peak=    3.972 closest distance to " O   HOH Z  78 " =    1.642
peak=    3.967 closest distance to " O   HOH Z 368 " =    2.358
peak=    3.961 closest distance to " O   HOH Z 236 " =    1.995
peak=    3.951 closest distance to " O   HOH Z 402 " =    1.485
peak=    3.944 closest distance to " O   HOH Z 303 " =    2.161
peak=    3.922 closest distance to " ND2 ASN A 187 " =    1.553
peak=    3.919 closest distance to " CB  ASP A 140 " =    1.012
peak=    3.919 closest distance to " OG BSER A 164 " =    2.215
peak=    3.906 closest distance to " CA  ARG A 195 " =    1.243
peak=    3.906 closest distance to " O   HOH Z 422 " =    2.671
peak=    3.905 closest distance to " CB  GLU A 152 " =    1.171
peak=    3.903 closest distance to " CD  ARG A 269 " =    0.965
peak=    3.898 closest distance to " CG1 VAL A 153 " =    1.010
peak=    3.891 closest distance to " CD1 LEU A  96 " =    0.756
peak=    3.886 closest distance to " CB  GLU A  46 " =    0.960
peak=    3.878 closest distance to " CZ3 TRP A 266 " =    1.128
peak=    3.870 closest distance to " O   HOH Z 313 " =    1.764
peak=    3.856 closest distance to " CB  ASN A  39 " =    0.899
peak=    3.847 closest distance to " O   HOH Z 251 " =    1.499
peak=    3.847 closest distance to " CE  LYS A  76 " =    0.849
peak=    3.842 closest distance to " CA  ALA A 295 " =    1.060
peak=    3.841 closest distance to " O   HOH Z 214 " =    2.579
peak=    3.838 closest distance to " O   HOH Z 280 " =    2.925
peak=    3.833 closest distance to " CB  VAL A 265 " =    1.282
peak=    3.832 closest distance to " O   HOH Z 403 " =    1.627
peak=    3.823 closest distance to " CZ  PHE A  38 " =    1.176
peak=    3.820 closest distance to " O   HOH Z  40 " =    1.849
peak=    3.809 closest distance to " CD2 TRP A 179 " =    1.340
peak=    3.778 closest distance to " O   HOH Z  48 " =    1.695
peak=    3.776 closest distance to " CA  THR A 264 " =    0.739
peak=    3.775 closest distance to " O   HOH Z  59 " =    2.339
peak=    3.773 closest distance to " O   HOH Z 423 " =    1.775
peak=    3.767 closest distance to " O   HOH Z 273 " =    2.881
peak=    3.767 closest distance to " OD1 ASN A  69 " =    2.536
peak=    3.753 closest distance to " O   HOH Z 359 " =    1.511
peak=    3.747 closest distance to " ND2 ASN A 249 " =    1.910
peak=    3.746 closest distance to " O   HOH Z  44 " =    2.163
peak=    3.744 closest distance to " O   HOH Z 158 " =    3.107
peak=    3.738 closest distance to " O   HOH Z 316 " =    3.164
peak=    3.738 closest distance to " CA  ARG A  36 " =    1.082
peak=    3.725 closest distance to " O   HOH Z 285 " =    2.540
peak=    3.724 closest distance to " O   ASP A 124 " =    1.140
peak=    3.715 closest distance to " O   HOH Z  63 " =    1.871
peak=    3.713 closest distance to " CD  ARG A  66 " =    2.701
peak=    3.712 closest distance to " CA  SER A  87 " =    1.046
peak=    3.684 closest distance to " NH1AARG A 145 " =    1.270
peak=    3.681 closest distance to " O   HOH Z  80 " =    1.864
peak=    3.680 closest distance to " CA  TYR A  30 " =    1.074
peak=    3.674 closest distance to " O   HOH Z 272 " =    1.919
peak=    3.674 closest distance to " O   HOH Z 353 " =    2.571
peak=    3.670 closest distance to " O   HOH Z  19 " =    2.030
peak=    3.665 closest distance to " NE2 GLN A  77 " =    3.366
peak=    3.661 closest distance to " O   HOH Z 238 " =    2.242
peak=    3.659 closest distance to " CZ  PHE A 192 " =    1.004
peak=    3.655 closest distance to " CG2 VAL A 257 " =    0.879
peak=    3.651 closest distance to " O   HOH Z 261 " =    1.928
peak=    3.642 closest distance to " CB  ALA A   9 " =    1.620
peak=    3.636 closest distance to " CA  ILE A 106 " =    0.760
peak=    3.632 closest distance to " CE1 TYR A 186 " =    1.282
peak=    3.631 closest distance to " CB  LEU A  83 " =    0.754
peak=    3.630 closest distance to " CD  ARG A 159 " =    0.763
peak=    3.620 closest distance to " CB  GLN A  89 " =    1.184
peak=    3.616 closest distance to " O   HOH Z 128 " =    1.504
peak=    3.615 closest distance to " O   HOH Z  61 " =    1.671
peak=    3.613 closest distance to " O   HOH Z 425 " =    1.396
peak=    3.602 closest distance to " CD ALYS A 290 " =    1.071
peak=    3.599 closest distance to " O   HOH Z 171 " =    3.916
peak=    3.594 closest distance to " O   HOH Z  21 " =    1.803
peak=    3.592 closest distance to " CG1 ILE A  49 " =    1.614
peak=    3.591 closest distance to " O   MET A 105 " =    1.858
peak=    3.587 closest distance to " CA  ALA A  21 " =    1.139
peak=    3.587 closest distance to " N   PHE A 130 " =    1.247
peak=    3.585 closest distance to " CB  ALA A 104 " =    0.753
peak=    3.574 closest distance to " CB  THR A  31 " =    1.567
peak=    3.561 closest distance to " CB  ARG A  79 " =    0.938
peak=    3.560 closest distance to " CB  LEU A 143 " =    1.209
peak=    3.554 closest distance to " NH2 ARG A 156 " =    1.100
peak=    3.553 closest distance to " O   HOH Z 130 " =    2.265
peak=    3.550 closest distance to " CB  TRP A 179 " =    1.372
peak=    3.546 closest distance to " O   HOH Z 130 " =    1.061
peak=    3.537 closest distance to " CA  MET A 105 " =    0.975
peak=    3.532 closest distance to " CA  VAL A  41 " =    0.743
peak=    3.532 closest distance to " O   HOH Z 102 " =    1.306
peak=    3.525 closest distance to " CB  SER A   3 " =    1.300
peak=    3.519 closest distance to " O   HOH Z 227 " =    1.687
peak=    3.517 closest distance to " O   HOH Z 247 " =    1.447
peak=    3.506 closest distance to " O   HOH Z 403 " =    1.443
peak=    3.504 closest distance to " O   HOH Z  49 " =    0.991
peak=    3.504 closest distance to " CB  ALA A 291 " =    1.230
peak=    3.503 closest distance to " O   PRO A 213 " =    1.511
peak=    3.500 closest distance to " O   HOH Z 172 " =    3.843
peak=    3.497 closest distance to " CG  LEU A 167 " =    1.127
peak=    3.496 closest distance to " CG  MET A 185 " =    1.012
peak=    3.492 closest distance to " O  BHOH Z 338 " =    2.379
peak=    3.491 closest distance to " CA  GLY A 211 " =    1.352
peak=    3.491 closest distance to " CG  PHE A 204 " =    0.917
peak=    3.490 closest distance to " O   HOH Z 371 " =    2.894
peak=    3.490 closest distance to " O   HOH Z 147 " =    1.791
peak=    3.481 closest distance to " O   ALA A 165 " =    1.456
peak=    3.481 closest distance to " CZ3 TRP A  85 " =    0.999
peak=    3.481 closest distance to " O   HOH Z 368 " =    3.525
peak=    3.478 closest distance to " CB  ASN A 187 " =    1.198
peak=    3.477 closest distance to " O   HOH Z  97 " =    2.321
peak=    3.475 closest distance to " CZ3 TRP A 274 " =    4.525
peak=    3.475 closest distance to " O   ASN A  74 " =    1.477
peak=    3.474 closest distance to " NE2 HIS A 207 " =    1.128
peak=    3.470 closest distance to " CG2AVAL A  72 " =    1.879
peak=    3.464 closest distance to " CA  ALA A 154 " =    0.987
peak=    3.455 closest distance to " CB  PRO A 243 " =    1.212
peak=    3.451 closest distance to " O   HOH Z 406 " =    1.548
peak=    3.447 closest distance to " NZ  LYS A  48 " =    1.296
peak=    3.445 closest distance to " CB  TRP A 150 " =    1.417
peak=    3.443 closest distance to " CD1 ILE A 199 " =    0.863
peak=    3.439 closest distance to " CB  TYR A 247 " =    1.024
peak=    3.436 closest distance to " CD1 LEU A 300 " =    1.176
peak=    3.433 closest distance to " CG2 ILE A 234 " =    0.859
peak=    3.432 closest distance to " O   HOH Z 128 " =    2.323
peak=    3.431 closest distance to " O   HOH Z 203 " =    1.787
peak=    3.431 closest distance to " O   HOH Z  97 " =    2.095
peak=    3.428 closest distance to " CG2 THR A 221 " =    1.075
peak=    3.427 closest distance to " CA  LEU A 282 " =    1.077
peak=    3.424 closest distance to " CD1 LEU A   5 " =    1.369
peak=    3.423 closest distance to " OG  SER A 276 " =    1.342
peak=    3.421 closest distance to " CA  ASP A 191 " =    1.010
peak=    3.418 closest distance to " NH1 ARG A  14 " =    0.988
peak=    3.408 closest distance to " O   GLN A  88 " =    1.661
peak=    3.405 closest distance to " CB  MET A  40 " =    0.823
peak=    3.397 closest distance to " CA  ALA A 160 " =    0.947
peak=    3.397 closest distance to " CB  SER A 273 " =    0.921
peak=    3.394 closest distance to " CG  GLU A  37 " =    0.896
peak=    3.393 closest distance to " CA  VAL A 125 " =    1.239
peak=    3.392 closest distance to " O   HOH Z  68 " =    2.030
peak=    3.386 closest distance to " O   HOH Z 383 " =    2.023
peak=    3.381 closest distance to " ND2 ASN A 249 " =    0.879
peak=    3.378 closest distance to " CA  TYR A 116 " =    1.477
peak=    3.376 closest distance to " O   THR A 220 " =    1.220
peak=    3.374 closest distance to " O   TRP A 274 " =    1.815
peak=    3.372 closest distance to " CB  GLN A 103 " =    1.023
peak=    3.372 closest distance to " NZ  LYS A 117 " =    3.206
peak=    3.371 closest distance to " O   HOH Z 145 " =    2.175
peak=    3.370 closest distance to " O   HOH Z 294 " =    1.576
peak=    3.364 closest distance to " CA  ASN A 215 " =    1.122
peak=    3.360 closest distance to " CB  LYS A 117 " =    1.224
peak=    3.355 closest distance to " O   HOH Z 193 " =    2.088
peak=    3.354 closest distance to " CG1 ILE A  33 " =    1.288
peak=    3.351 closest distance to " CG  ARG A 138 " =    1.241
peak=    3.348 closest distance to " CA  LYS A 117 " =    1.257
peak=    3.343 closest distance to " O   HOH Z   9 " =    2.087
peak=    3.339 closest distance to " CA  ASN A 217 " =    1.271
peak=    3.339 closest distance to " O   HOH Z 329 " =    4.143
peak=    3.338 closest distance to " CA  LYS A 181 " =    1.028
peak=    3.337 closest distance to " CD2 LEU A 297 " =    0.851
peak=    3.337 closest distance to " CB  MET A  47 " =    0.980
peak=    3.337 closest distance to " CG2 ILE A 263 " =    0.971
peak=    3.337 closest distance to " N   SER A 135 " =    1.521
peak=    3.334 closest distance to " O   HOH Z 258 " =    2.125
peak=    3.333 closest distance to " CB  ASN A 110 " =    1.139
peak=    3.332 closest distance to " CG2 ILE A  49 " =    1.461
peak=    3.327 closest distance to " CD  ARG A  66 " =    2.012
peak=    3.327 closest distance to " CB  ALA A 248 " =    1.113
peak=    3.326 closest distance to " CA  THR A 221 " =    0.907
peak=    3.325 closest distance to " CB  ALA A 242 " =    0.830
peak=    3.323 closest distance to " O   ASN A  74 " =    2.083
peak=    3.320 closest distance to " O   LYS A 290 " =    2.438
peak=    3.312 closest distance to " CB  ASN A 173 " =    1.090
peak=    3.311 closest distance to " O   HOH Z 417 " =    3.128
peak=    3.303 closest distance to " O   PHE A  61 " =    1.345
peak=    3.299 closest distance to " CB  ASN A 215 " =    1.176
peak=    3.296 closest distance to " O   HOH Z 187 " =    2.397
peak=    3.294 closest distance to " O   HOH Z 128 " =    2.161
peak=    3.293 closest distance to " O   HOH Z 290 " =    1.084
peak=    3.293 closest distance to " O   HOH Z 313 " =    1.597
peak=    3.291 closest distance to " CA  ALA A 291 " =    0.877
peak=    3.279 closest distance to " O   HOH Z 261 " =    1.570
peak=    3.275 closest distance to " O   HOH Z 437 " =    1.666
peak=    3.275 closest distance to " CB  SER A  26 " =    1.812
peak=    3.273 closest distance to " CA  PHE A 283 " =    1.112
peak=    3.272 closest distance to " O   HOH Z  88 " =    3.211
peak=    3.270 closest distance to " O   HOH Z 193 " =    1.736
peak=    3.270 closest distance to " CB  SER A 210 " =    0.886
peak=    3.269 closest distance to " O   HOH Z 180 " =    2.154
peak=    3.268 closest distance to " CA  ALA A 158 " =    1.267
peak=    3.267 closest distance to " O   HOH Z 250 " =    1.352
peak=    3.265 closest distance to " CD  ARG A  66 " =    2.431
peak=    3.264 closest distance to " O   HOH Z 201 " =    2.987
peak=    3.261 closest distance to " N   ASP A 162 " =    1.272
peak=    3.256 closest distance to " CA  ASP A 162 " =    0.969
peak=    3.252 closest distance to " CB  GLN A  88 " =    1.215
peak=    3.250 closest distance to " CB  GLN A 205 " =    1.058
peak=    3.247 closest distance to " CB  LEU A 228 " =    1.244
peak=    3.241 closest distance to " N   VAL A 126 " =    1.404
peak=    3.238 closest distance to " CB  ALA A 248 " =    1.379
peak=    3.234 closest distance to " O   HOH Z 407 " =    2.516
peak=    3.234 closest distance to " O   HOH Z 365 " =    2.906
peak=    3.234 closest distance to " O   HOH Z 291 " =    1.523
peak=    3.233 closest distance to " O   HOH Z 199 " =    1.644
peak=    3.232 closest distance to " CG  ARG A 269 " =    1.806
peak=    3.232 closest distance to " CD1 LEU A 281 " =    1.103
peak=    3.231 closest distance to " CA  GLU A 152 " =    0.921
peak=    3.225 closest distance to " CG1 ILE A 151 " =    1.082
peak=    3.224 closest distance to " OG  SER A 245 " =    1.596
peak=    3.223 closest distance to " CB  THR A  52 " =    0.892
peak=    3.223 closest distance to " O   HOH Z 245 " =    1.348
peak=    3.219 closest distance to " CB  PRO A  90 " =    1.205
peak=    3.216 closest distance to " O   HOH Z  44 " =    2.634
peak=    3.212 closest distance to " O   THR A 182 " =    1.385
peak=    3.212 closest distance to " OG BSER A 134 " =    2.785
peak=    3.212 closest distance to " CA  ASN A 127 " =    1.110
peak=    3.206 closest distance to " CG2 THR A 220 " =    0.816
peak=    3.204 closest distance to " O   HOH Z 344 " =    2.955
peak=    3.204 closest distance to " O   HOH Z 293 " =    1.848
peak=    3.202 closest distance to " CG2 ILE A 120 " =    1.031
peak=    3.202 closest distance to " O   HOH Z   4 " =    1.660
peak=    3.199 closest distance to " CB  SER A 212 " =    1.295
peak=    3.198 closest distance to " O   HOH Z 141 " =    1.657
peak=    3.197 closest distance to " O   HOH Z 163 " =    1.566
peak=    3.195 closest distance to " CG BARG A 275 " =    1.298
peak=    3.188 closest distance to " OG1 THR A 279 " =    1.521
peak=    3.186 closest distance to " CG BARG A 102 " =    1.804
peak=    3.182 closest distance to " OD1 ASN A 217 " =    1.617
peak=    3.177 closest distance to " O   TYR A 116 " =    1.333
peak=    3.176 closest distance to " O   HOH Z 305 " =    3.734
peak=    3.176 closest distance to " O   HOH Z 325 " =    2.219
peak=    3.175 closest distance to " O   ALA A 158 " =    1.342
peak=    3.174 closest distance to " O   ASP A 200 " =    1.624
peak=    3.172 closest distance to " CB  ALA A  43 " =    0.884
peak=    3.169 closest distance to " CB  VAL A 268 " =    0.832
peak=    3.168 closest distance to " O   HOH Z 188 " =    1.901
peak=    3.168 closest distance to " N   GLY A  98 " =    1.122
peak=    3.168 closest distance to " O   HOH Z 421 " =    3.125
peak=    3.167 closest distance to " CG  GLN A  11 " =    1.483
peak=    3.166 closest distance to " CH2 TRP A  70 " =    0.986
peak=    3.165 closest distance to " N   ARG A 156 " =    1.489
peak=    3.159 closest distance to " O   HOH Z 271 " =    2.430
peak=    3.156 closest distance to " CG2 ILE A  20 " =    1.428
peak=    3.155 closest distance to " N   ALA A 256 " =    1.141
peak=    3.154 closest distance to " O   HOH Z 166 " =    3.647
peak=    3.148 closest distance to " CG2 VAL A 197 " =    1.098
peak=    3.142 closest distance to " O   GLY A  91 " =    1.225
peak=    3.142 closest distance to " CB  ALA A 114 " =    1.055
peak=    3.141 closest distance to " NH2AARG A 275 " =    3.506
peak=    3.139 closest distance to " CB  PHE A 204 " =    0.902
peak=    3.137 closest distance to " CB  SER A 216 " =    0.794
peak=    3.135 closest distance to " CD  PRO A  54 " =    1.077
peak=    3.134 closest distance to " CD1 ILE A  33 " =    1.744
peak=    3.132 closest distance to " O   ASP A 124 " =    1.776
peak=    3.131 closest distance to " O   HOH Z   1 " =    2.420
peak=    3.129 closest distance to " CB  LEU A  96 " =    1.285
peak=    3.123 closest distance to " CB  PHE A 204 " =    0.890
peak=    3.121 closest distance to " O   HOH Z 112 " =    1.652
peak=    3.115 closest distance to " O   HOH Z 435 " =    2.063
peak=    3.115 closest distance to " O   HOH Z 148 " =    3.282
peak=    3.113 closest distance to " OG  SER A  22 " =    2.806
peak=    3.108 closest distance to " CA  GLN A  88 " =    1.249
peak=    3.106 closest distance to " CE3 TRP A 150 " =    1.081
peak=    3.100 closest distance to " CG  GLN A  58 " =    2.963
peak=    3.099 closest distance to " O   HOH Z  47 " =    1.818
peak=    3.098 closest distance to " CB  LEU A 300 " =    0.844
peak=    3.096 closest distance to " CG  GLN A 205 " =    0.876
peak=    3.095 closest distance to " CB  ALA A 100 " =    1.287
peak=    3.094 closest distance to " CB  ARG A 145 " =    0.838
peak=    3.093 closest distance to " O   HOH Z 213 " =    1.812
peak=    3.090 closest distance to " CG1 ILE A  20 " =    1.261
peak=    3.090 closest distance to " CB  ASN A 285 " =    0.949
peak=    3.085 closest distance to " O   HOH Z 195 " =    4.234
peak=    3.084 closest distance to " CB  PHE A 283 " =    0.720
peak=    3.073 closest distance to " N   GLY A 133 " =    3.740
peak=    3.073 closest distance to " CB  ALA A 227 " =    1.074
peak=    3.069 closest distance to " O   HOH Z 124 " =    1.925
peak=    3.058 closest distance to " CB  ILE A 120 " =    1.318
peak=    3.054 closest distance to " CB  VAL A 257 " =    0.739
peak=    3.049 closest distance to " O   HOH Z 172 " =    3.333
peak=    3.045 closest distance to " ND1 HIS A  81 " =    1.673
peak=    3.043 closest distance to " CA  ALA A 233 " =    1.604
peak=    3.038 closest distance to " CA  LYS A 290 " =    1.154
peak=    3.025 closest distance to " O   GLN A 278 " =    1.535
peak=    3.017 closest distance to " O   GLU A   2 " =    1.517

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.765 - 5.574
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 203
   mapped sites are within: 0.765 - 5.574

peak=   -5.483 closest distance to " CG2 VAL A 230 " =    0.765
peak=   -4.814 closest distance to " CD  GLN A  58 " =    1.009
peak=   -4.471 closest distance to " CB  PRO A 243 " =    2.722
peak=   -4.422 closest distance to " CD  ARG A  14 " =    3.284
peak=   -4.299 closest distance to " CG1 VAL A 296 " =    1.139
peak=   -4.282 closest distance to " CD  ARG A 156 " =    2.077
peak=   -4.187 closest distance to " O   VAL A  67 " =    2.721
peak=   -4.146 closest distance to " O   HOH Z 196 " =    2.336
peak=   -4.118 closest distance to " CG1 VAL A 112 " =    2.662
peak=   -4.095 closest distance to " O   HOH Z 266 " =    5.524
peak=   -4.088 closest distance to " CA  ASP A 298 " =    1.060
peak=   -4.058 closest distance to " CG1 VAL A 112 " =    2.767
peak=   -4.049 closest distance to " C   HIS A 108 " =    1.127
peak=   -4.046 closest distance to " O   HOH Z 166 " =    1.750
peak=   -4.000 closest distance to " CG1 VAL A 250 " =    2.780
peak=   -3.996 closest distance to " O   HOH Z 351 " =    1.556
peak=   -3.953 closest distance to " CE2 TYR A  30 " =    2.743
peak=   -3.948 closest distance to " OG  SER A  97 " =    2.340
peak=   -3.929 closest distance to " CB  PHE A 192 " =    2.022
peak=   -3.920 closest distance to " CA  VAL A  67 " =    2.808
peak=   -3.894 closest distance to " O   HOH Z  73 " =    2.346
peak=   -3.860 closest distance to " O   HOH Z 290 " =    1.190
peak=   -3.854 closest distance to " O   ILE A 109 " =    2.634
peak=   -3.845 closest distance to " CE3 TRP A 150 " =    2.212
peak=   -3.835 closest distance to " O   HOH Z 231 " =    2.285
peak=   -3.830 closest distance to " CG  ARG A 269 " =    2.369
peak=   -3.809 closest distance to " OE1 GLN A 223 " =    2.120
peak=   -3.800 closest distance to " CG  ASP A 231 " =    0.785
peak=   -3.794 closest distance to " O   HOH Z 211 " =    1.402
peak=   -3.784 closest distance to " O   HOH Z 394 " =    1.548
peak=   -3.781 closest distance to " CZ3 TRP A 179 " =    1.199
peak=   -3.777 closest distance to " O   HOH Z  10 " =    1.537
peak=   -3.759 closest distance to " OD1 ASN A 148 " =    1.389
peak=   -3.751 closest distance to " CD2 TYR A 293 " =    1.978
peak=   -3.729 closest distance to " O   SER A 271 " =    2.147
peak=   -3.688 closest distance to " O   HOH Z 128 " =    2.638
peak=   -3.677 closest distance to " O   PRO A 163 " =    2.206
peak=   -3.667 closest distance to " CG2 ILE A  49 " =    2.847
peak=   -3.660 closest distance to " O   HOH Z 177 " =    1.854
peak=   -3.657 closest distance to " N   ALA A 226 " =    2.129
peak=   -3.654 closest distance to " O   HOH Z  37 " =    1.900
peak=   -3.648 closest distance to " OXT GLY A 302 " =    2.950
peak=   -3.638 closest distance to " C   ALA A 158 " =    1.327
peak=   -3.633 closest distance to " C   GLY A  17 " =    1.323
peak=   -3.630 closest distance to " ND2 ASN A  45 " =    1.126
peak=   -3.627 closest distance to " CD1 LEU A 101 " =    2.447
peak=   -3.624 closest distance to " O   HOH Z 114 " =    3.083
peak=   -3.612 closest distance to " CD2 PHE A  61 " =    2.603
peak=   -3.610 closest distance to " OG BSER A 134 " =    1.308
peak=   -3.602 closest distance to " O   HOH Z  52 " =    1.714
peak=   -3.600 closest distance to " O   HOH Z 210 " =    1.013
peak=   -3.599 closest distance to " CB  ALA A 248 " =    2.341
peak=   -3.597 closest distance to " NE2 GLN A 194 " =    1.912
peak=   -3.589 closest distance to " O   HOH Z 133 " =    1.269
peak=   -3.583 closest distance to " N   ALA A  43 " =    2.611
peak=   -3.569 closest distance to " CA  GLY A 241 " =    2.374
peak=   -3.568 closest distance to " NH2AARG A 275 " =    5.155
peak=   -3.563 closest distance to " O   HOH Z 216 " =    1.254
peak=   -3.554 closest distance to " O   PRO A 198 " =    1.232
peak=   -3.549 closest distance to " O   HOH Z 185 " =    2.387
peak=   -3.517 closest distance to " CZ  TYR A 169 " =    1.742
peak=   -3.510 closest distance to " CG  GLU A 277 " =    1.188
peak=   -3.509 closest distance to " N   THR A  52 " =    1.587
peak=   -3.509 closest distance to " CE2 TRP A  70 " =    2.111
peak=   -3.493 closest distance to " CA  GLY A 241 " =    3.152
peak=   -3.491 closest distance to " O   HOH Z 241 " =    1.262
peak=   -3.490 closest distance to " OE1 GLN A  88 " =    0.892
peak=   -3.489 closest distance to " O   HOH Z 113 " =    2.398
peak=   -3.476 closest distance to " O   HOH Z 123 " =    2.554
peak=   -3.468 closest distance to " CE BMET A  47 " =    1.945
peak=   -3.468 closest distance to " O   HOH Z 431 " =    1.966
peak=   -3.456 closest distance to " O   HOH Z 222 " =    1.606
peak=   -3.455 closest distance to " CB  ALA A 248 " =    2.159
peak=   -3.452 closest distance to " C   MET A 188 " =    1.409
peak=   -3.446 closest distance to " CD  GLN A 223 " =    1.274
peak=   -3.444 closest distance to " O   HOH Z  38 " =    1.551
peak=   -3.439 closest distance to " O   HOH Z 102 " =    1.708
peak=   -3.438 closest distance to " C   LEU A 143 " =    1.033
peak=   -3.437 closest distance to " CD2 LEU A 167 " =    1.797
peak=   -3.427 closest distance to " CG  HIS A  86 " =    1.145
peak=   -3.424 closest distance to " CG  LEU A   5 " =    1.513
peak=   -3.417 closest distance to " ND2 ASN A  45 " =    1.909
peak=   -3.411 closest distance to " O   HOH Z 435 " =    2.630
peak=   -3.411 closest distance to " O   VAL A 189 " =    2.615
peak=   -3.408 closest distance to " NE2 GLN A  88 " =    1.006
peak=   -3.407 closest distance to " NE2 GLN A 103 " =    1.848
peak=   -3.405 closest distance to " O   HOH Z 407 " =    3.131
peak=   -3.400 closest distance to " CB  ALA A  10 " =    2.263
peak=   -3.396 closest distance to " O   HOH Z 238 " =    0.997
peak=   -3.396 closest distance to " O   HOH Z  11 " =    1.872
peak=   -3.394 closest distance to " OD1 ASN A 249 " =    2.436
peak=   -3.394 closest distance to " CD1 LEU A   5 " =    2.502
peak=   -3.389 closest distance to " CG  GLN A  11 " =    1.640
peak=   -3.381 closest distance to " CE3 TRP A  70 " =    1.776
peak=   -3.379 closest distance to " CD1 ILE A 199 " =    2.575
peak=   -3.376 closest distance to " O   HOH Z 136 " =    2.452
peak=   -3.375 closest distance to " O   HOH Z 285 " =    1.819
peak=   -3.366 closest distance to " CG  TRP A 266 " =    1.863
peak=   -3.364 closest distance to " O   HOH Z 251 " =    4.942
peak=   -3.350 closest distance to " O   HOH Z  44 " =    2.250
peak=   -3.347 closest distance to " CD  PRO A 243 " =    1.975
peak=   -3.346 closest distance to " NE2 GLN A  88 " =    2.065
peak=   -3.339 closest distance to " CD1 PHE A  59 " =    2.043
peak=   -3.336 closest distance to " CG1 VAL A 112 " =    2.836
peak=   -3.332 closest distance to " CG1 VAL A 265 " =    2.420
peak=   -3.331 closest distance to " O   HOH Z 234 " =    4.431
peak=   -3.329 closest distance to " O   GLY A  80 " =    2.567
peak=   -3.327 closest distance to " O   SER A 210 " =    1.893
peak=   -3.326 closest distance to " CB  ALA A  43 " =    2.590
peak=   -3.319 closest distance to " O   HOH Z 252 " =    3.821
peak=   -3.317 closest distance to " C   ASN A 285 " =    2.381
peak=   -3.316 closest distance to " ND2 ASN A 187 " =    1.671
peak=   -3.312 closest distance to " CB  ASP A 171 " =    2.327
peak=   -3.310 closest distance to " OE2 GLU A 277 " =    2.980
peak=   -3.309 closest distance to " O   HOH Z 377 " =    1.442
peak=   -3.303 closest distance to " O   HOH Z  60 " =    1.809
peak=   -3.302 closest distance to " CG  MET A 105 " =    0.959
peak=   -3.301 closest distance to " O   HOH Z 165 " =    1.841
peak=   -3.301 closest distance to " O   HOH Z 434 " =    1.737
peak=   -3.298 closest distance to " O   HOH Z 106 " =    1.932
peak=   -3.298 closest distance to " CD  PRO A 213 " =    2.140
peak=   -3.296 closest distance to " O   HOH Z 198 " =    2.391
peak=   -3.294 closest distance to " CG2 VAL A 189 " =    2.091
peak=   -3.287 closest distance to " CD1 ILE A 151 " =    2.411
peak=   -3.283 closest distance to " O   HOH Z  17 " =    1.385
peak=   -3.280 closest distance to " OG1 THR A  82 " =    1.417
peak=   -3.279 closest distance to " CG1 VAL A  67 " =    2.856
peak=   -3.278 closest distance to " NH2 ARG A  79 " =    1.567
peak=   -3.275 closest distance to " CG1 VAL A 125 " =    1.964
peak=   -3.272 closest distance to " CA  GLY A 133 " =    2.353
peak=   -3.270 closest distance to " O   GLY A 203 " =    2.362
peak=   -3.268 closest distance to " CB  VAL A 230 " =    1.106
peak=   -3.267 closest distance to " ND2 ASN A  69 " =    1.881
peak=   -3.266 closest distance to " CG2 VAL A 296 " =    1.140
peak=   -3.263 closest distance to " CE  LYS A  76 " =    2.667
peak=   -3.263 closest distance to " CG  LYS A 166 " =    2.146
peak=   -3.258 closest distance to " O   HOH Z 265 " =    2.451
peak=   -3.254 closest distance to " O   ARG A  24 " =    2.152
peak=   -3.251 closest distance to " O   HOH Z 231 " =    1.801
peak=   -3.244 closest distance to " C   PHE A  59 " =    1.290
peak=   -3.236 closest distance to " CA  GLY A  98 " =    2.046
peak=   -3.234 closest distance to " OD2 ASP A  50 " =    2.286
peak=   -3.232 closest distance to " CG  ASP A 132 " =    2.371
peak=   -3.228 closest distance to " N   THR A 157 " =    1.539
peak=   -3.222 closest distance to " O   HOH Z 348 " =    2.268
peak=   -3.221 closest distance to " O   HOH Z 193 " =    1.615
peak=   -3.220 closest distance to " O   HOH Z 368 " =    1.826
peak=   -3.216 closest distance to " NH2 ARG A 159 " =    2.339
peak=   -3.215 closest distance to " O   HOH Z   6 " =    1.619
peak=   -3.214 closest distance to " O   HOH Z 377 " =    2.014
peak=   -3.213 closest distance to " OG1 THR A  82 " =    1.377
peak=   -3.212 closest distance to " O   HOH Z 275 " =    1.517
peak=   -3.210 closest distance to " CG  GLU A  53 " =    1.557
peak=   -3.210 closest distance to " O   HOH Z 411 " =    1.705
peak=   -3.203 closest distance to " CA  SER A  62 " =    2.510
peak=   -3.201 closest distance to " O   ALA A 227 " =    1.527
peak=   -3.191 closest distance to " CE  MET A 105 " =    2.212
peak=   -3.190 closest distance to " CB  TRP A  85 " =    2.569
peak=   -3.187 closest distance to " NH2 ARG A  66 " =    1.901
peak=   -3.187 closest distance to " NE2 GLN A 194 " =    2.005
peak=   -3.183 closest distance to " CD2 LEU A 300 " =    2.621
peak=   -3.181 closest distance to " O   HOH Z 340 " =    1.648
peak=   -3.179 closest distance to " O   HOH Z  19 " =    2.237
peak=   -3.173 closest distance to " N   SER A   3 " =    2.132
peak=   -3.166 closest distance to " O   HOH Z 426 " =    1.695
peak=   -3.163 closest distance to " CA  GLY A 203 " =    2.451
peak=   -3.160 closest distance to " O   HOH Z 176 " =    0.829
peak=   -3.157 closest distance to " O   HOH Z  13 " =    1.646
peak=   -3.156 closest distance to " O   HOH Z 392 " =    1.854
peak=   -3.149 closest distance to " OG  SER A  87 " =    1.587
peak=   -3.149 closest distance to " OD1 ASN A 173 " =    1.413
peak=   -3.147 closest distance to " CA  ASN A 127 " =    1.108
peak=   -3.142 closest distance to " O   HOH Z   9 " =    1.708
peak=   -3.142 closest distance to " O   HOH Z  49 " =    1.143
peak=   -3.140 closest distance to " O   GLY A 196 " =    1.186
peak=   -3.139 closest distance to " CB  PRO A 163 " =    2.557
peak=   -3.128 closest distance to " CG  PRO A 243 " =    1.643
peak=   -3.124 closest distance to " O   HOH Z 421 " =    3.316
peak=   -3.122 closest distance to " OG  SER A  63 " =    1.201
peak=   -3.116 closest distance to " O   HOH Z 236 " =    1.493
peak=   -3.115 closest distance to " O   HOH Z 191 " =    5.574
peak=   -3.115 closest distance to " O   HOH Z  44 " =    1.024
peak=   -3.114 closest distance to " CB  ASN A  39 " =    2.313
peak=   -3.112 closest distance to " O   GLY A 211 " =    1.342
peak=   -3.103 closest distance to " CB  ALA A 291 " =    2.331
peak=   -3.097 closest distance to " OG BSER A 210 " =    1.547
peak=   -3.093 closest distance to " NH2 ARG A  36 " =    2.427
peak=   -3.089 closest distance to " O   HOH Z 429 " =    2.070
peak=   -3.088 closest distance to " C   ASP A 270 " =    1.097
peak=   -3.086 closest distance to " OG  SER A 206 " =    1.756
peak=   -3.085 closest distance to " O   HOH Z 423 " =    2.161
peak=   -3.084 closest distance to " CH2 TRP A 150 " =    1.141
peak=   -3.080 closest distance to " CD  GLN A  88 " =    0.822
peak=   -3.076 closest distance to " O   HOH Z 357 " =    2.056
peak=   -3.073 closest distance to " CD2 PHE A  61 " =    2.126
peak=   -3.072 closest distance to " O   HOH Z 395 " =    1.417
peak=   -3.067 closest distance to " O   SER A  95 " =    1.869
peak=   -3.050 closest distance to " CD2 TYR A 247 " =    2.289
peak=   -3.044 closest distance to " N   PHE A  59 " =    2.319
peak=   -3.040 closest distance to " CD2 PHE A 225 " =    1.080
peak=   -3.033 closest distance to " O   HOH Z 227 " =    1.316
peak=   -3.028 closest distance to " CG1 VAL A  78 " =    2.675
peak=   -3.019 closest distance to " O   HOH Z 110 " =    1.442

================= 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    :  0.4590 0.4439   6.256261e+00   6.232027e+00
   1_bss:  0.4503 0.4318   6.249603e+00   6.220916e+00
   1_xyz:  0.3471 0.3687   6.078999e+00   6.111652e+00
   1_adp:  0.2950 0.3381   5.950731e+00   6.041587e+00
   1_occ:  0.2945 0.3387   5.950013e+00   6.043222e+00
   2_bss:  0.2909 0.3345   5.950673e+00   6.041189e+00
   2_xyz:  0.2086 0.2505   5.660291e+00   5.811691e+00
   2_adp:  0.1916 0.2339   5.593464e+00   5.755300e+00
   2_occ:  0.1913 0.2344   5.593278e+00   5.756115e+00
   3_bss:  0.1909 0.2341   5.594099e+00   5.756465e+00
   3_xyz:  0.1390 0.1795   5.309879e+00   5.517419e+00
   3_adp:  0.1280 0.1733   5.252495e+00   5.482309e+00
   3_occ:  0.1279 0.1733   5.252211e+00   5.481900e+00
   4_bss:  0.1282 0.1734   5.252010e+00   5.479522e+00
   4_xyz:  0.1177 0.1656   5.191252e+00   5.433280e+00
   4_adp:  0.1169 0.1622   5.179759e+00   5.416178e+00
   4_occ:  0.1168 0.1621   5.178979e+00   5.415418e+00
   5_bss:  0.1168 0.1621   5.178979e+00   5.415418e+00
   5_xyz:  0.1192 0.1631   5.193057e+00   5.422019e+00
   5_adp:  0.1188 0.1635   5.193676e+00   5.425902e+00
   5_occ:  0.1187 0.1635   5.193317e+00   5.425655e+00
   5_bss:  0.1187 0.1634   5.192927e+00   5.425286e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000   6.711   8.853  10.247   0.000   0.000   0.000
   1_xyz:  0.300  20.000   6.711   8.853  10.247   0.000   0.000   0.000
   1_adp:  0.300  20.000   6.711   8.853  10.247   0.000   0.000   0.000
   1_occ:  0.300  20.000   6.711   8.853  10.247   0.000   0.000   0.000
   2_bss:  0.321  50.000   3.616   5.510   6.601   0.000   0.000   0.000
   2_xyz:  0.321  50.000   3.616   5.510   6.601   0.000   0.000   0.000
   2_adp:  0.321  50.000   3.616   5.510   6.601   0.000   0.000   0.000
   2_occ:  0.321  50.000   3.616   5.510   6.601   0.000   0.000   0.000
   3_bss:  0.327  61.079   2.904   4.085   4.975   0.000   0.000   0.000
   3_xyz:  0.327  61.079   2.904   4.085   4.975   0.000   0.000   0.000
   3_adp:  0.327  61.079   2.904   4.085   4.975   0.000   0.000   0.000
   3_occ:  0.327  61.079   2.904   4.085   4.975   0.000   0.000   0.000
   4_bss:  0.335  67.185   2.790   3.529   4.601   0.000   0.000   0.000
   4_xyz:  0.335  67.185   2.790   3.529   4.601   0.000   0.000   0.000
   4_adp:  0.335  67.185   2.790   3.529   4.601   0.000   0.000   0.000
   4_occ:  0.335  67.185   2.790   3.529   4.601   0.000   0.000   0.000
   5_bss:  0.335  67.185   2.790   3.529   4.601   0.000   0.000   0.000
   5_xyz:  0.335  67.185   2.790   3.529   4.601   0.000   0.000   0.000
   5_adp:  0.335  67.185   2.790   3.529   4.601   0.000   0.000   0.000
   5_occ:  0.335  67.185   2.790   3.529   4.601   0.000   0.000   0.000
   5_bss:  0.324  62.616  -0.772  -0.200   0.973  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.345 0.5174  0.5751    56757.582
   1_bss:  49.350 0.5291  0.7614    54817.128
   1_xyz:  40.548 0.6352  0.8836    37352.544
   1_adp:  35.211 0.6990  0.9690    30032.440
   1_occ:  35.304 0.6979  0.9674    30166.297
   2_bss:  35.109 0.7001  0.8624    29932.289
   2_xyz:  25.442 0.8065  0.9663    16402.648
   2_adp:  23.185 0.8305  0.9804    14319.681
   2_occ:  23.214 0.8302  0.9799    14337.632
   3_bss:  23.171 0.8308  0.9376    14349.369
   3_xyz:  16.835 0.8909  0.9774     8306.227
   3_adp:  15.960 0.8986  0.9760     7687.231
   3_occ:  15.951 0.8987  0.9760     7681.762
   4_bss:  15.909 0.8990  0.9640     7642.602
   4_xyz:  14.871 0.9081  0.9675     6923.063
   4_adp:  14.454 0.9117  0.9647     6711.141
   4_occ:  14.439 0.9118  0.9648     6702.959
   5_bss:  14.439 0.9118  0.9648     6702.959
   5_xyz:  14.520 0.9114  0.9641     6777.723
   5_adp:  14.608 0.9107  0.9598     6830.128
   5_occ:  14.603 0.9107  0.9597     6829.886
   5_bss:  14.598 0.9108  0.9605     6821.167
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4399e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4399e+01
   1_xyz:   1.650  0.013  0.107 17.912  0.006  4.113   1.3455e-01
   1_adp:   1.650  0.013  0.107 17.912  0.006  4.113   1.3455e-01
   1_occ:   1.650  0.013  0.107 17.912  0.006  4.113   1.3455e-01
   2_bss:   1.650  0.013  0.107 17.912  0.006  4.113   1.3455e-01
   2_xyz:   1.064  0.008  0.072 16.098  0.004  4.129   6.6815e-02
   2_adp:   1.064  0.008  0.072 16.098  0.004  4.129   6.6815e-02
   2_occ:   1.064  0.008  0.072 16.098  0.004  4.129   6.6815e-02
   3_bss:   1.064  0.008  0.072 16.098  0.004  4.129   6.6815e-02
   3_xyz:   1.135  0.009  0.087 15.948  0.004  4.138   7.5961e-02
   3_adp:   1.135  0.009  0.087 15.948  0.004  4.138   7.5961e-02
   3_occ:   1.135  0.009  0.087 15.948  0.004  4.138   7.5961e-02
   4_bss:   1.135  0.009  0.087 15.948  0.004  4.138   7.5961e-02
   4_xyz:   1.137  0.011  0.091 15.616  0.004  4.120   7.9235e-02
   4_adp:   1.137  0.011  0.091 15.616  0.004  4.120   7.9235e-02
   4_occ:   1.137  0.011  0.091 15.616  0.004  4.120   7.9235e-02
   5_bss:   1.137  0.011  0.091 15.616  0.004  4.120   7.9235e-02
   5_xyz:   0.993  0.008  0.079 15.290  0.003  4.120   6.1284e-02
   5_adp:   0.993  0.008  0.079 15.290  0.003  4.120   6.1284e-02
   5_occ:   0.993  0.008  0.079 15.290  0.003  4.120   6.1284e-02
   5_bss:   0.993  0.008  0.079 15.290  0.003  4.120   6.1284e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0533e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0533e+00
   1_xyz:  14.741  0.158  0.461 87.920  0.039  2.246   1.0211e-01
   1_adp:  14.741  0.158  0.461 87.920  0.039  2.246   1.0211e-01
   1_occ:  14.741  0.158  0.461 87.920  0.039  2.246   1.0211e-01
   2_bss:  14.741  0.158  0.461 87.920  0.039  2.246   1.0211e-01
   2_xyz:   6.685  0.068  0.235 85.902  0.021  2.180   4.9547e-02
   2_adp:   6.685  0.068  0.235 85.902  0.021  2.180   4.9547e-02
   2_occ:   6.685  0.068  0.235 85.902  0.021  2.180   4.9547e-02
   3_bss:   6.685  0.068  0.235 85.902  0.021  2.180   4.9547e-02
   3_xyz:   7.283  0.053  0.451 83.448  0.046  2.308   5.5244e-02
   3_adp:   7.283  0.053  0.451 83.448  0.046  2.308   5.5244e-02
   3_occ:   7.283  0.053  0.451 83.448  0.046  2.308   5.5244e-02
   4_bss:   7.283  0.053  0.451 83.448  0.046  2.308   5.5244e-02
   4_xyz:   7.811  0.053  0.537 82.579  0.043  2.326   6.7988e-02
   4_adp:   7.811  0.053  0.537 82.579  0.043  2.326   6.7988e-02
   4_occ:   7.811  0.053  0.537 82.579  0.043  2.326   6.7988e-02
   5_bss:   7.811  0.053  0.537 82.579  0.043  2.326   6.7988e-02
   5_xyz:   7.123  0.046  0.388 81.665  0.040  2.399   3.4481e-02
   5_adp:   7.123  0.046  0.388 81.665  0.040  2.399   3.4481e-02
   5_occ:   7.123  0.046  0.388 81.665  0.040  2.399   3.4481e-02
   5_bss:   7.123  0.046  0.388 81.665  0.040  2.399   3.4481e-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:  98.24   0.00  11.49  65.40   0.00   8.51  98.24   0.00  27.68
   1_occ:  98.24   0.00  11.49  65.40   0.00   8.51  98.24   0.00  27.68
   2_bss:  98.24   0.00  11.49  65.40   0.00   8.51  98.24   0.00  27.68
   2_xyz:  98.24   0.00  11.49  65.40   0.00   8.51  98.24   0.00  27.68
   2_adp:  97.41   0.00  11.49  67.75   0.00   7.81  97.41   0.00  31.54
   2_occ:  97.41   0.00  11.49  67.75   0.00   7.81  97.41   0.00  31.54
   3_bss:  97.41   0.00  11.49  67.75   0.00   7.81  97.41   0.00  31.54
   3_xyz:  97.41   0.00  11.49  67.75   0.00   7.81  97.41   0.00  31.54
   3_adp:  90.12   0.00  12.40  77.81   0.00   7.81  90.12   0.00  37.39
   3_occ:  90.12   0.00  12.40  77.81   0.00   7.81  90.12   0.00  37.39
   4_bss:  90.12   0.00  12.40  77.81   0.00   7.81  90.12   0.00  37.39
   4_xyz:  90.12   0.00  12.40  77.81   0.00   7.81  90.12   0.00  37.39
   4_adp:  83.36   0.00  11.77  79.77   0.00   7.49  83.36   0.64  35.11
   4_occ:  83.36   0.00  11.77  79.77   0.00   7.49  83.36   0.64  35.11
   5_bss:  83.36   0.00  11.77  79.77   0.00   7.49  83.36   0.64  35.11
   5_xyz:  83.36   0.00  11.77  79.77   0.00   7.49  83.36   0.64  35.11
   5_adp:  81.93   0.00  11.76  80.73   0.00   7.47  81.93   0.61  35.17
   5_occ:  81.93   0.00  11.76  80.73   0.00   7.47  81.93   0.61  35.17
   5_bss:  85.60   3.66  15.42  84.39   3.66  11.13  85.60   4.27  38.83
------------------------------------------------------------------------
 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:    1.252    0.029    0.411
   1_adp:    1.252    0.029    0.411
   1_occ:    1.252    0.029    0.411
   2_bss:    1.252    0.029    0.411
   2_xyz:    1.741    0.032    0.533
   2_adp:    1.741    0.032    0.533
   2_occ:    1.741    0.032    0.533
   3_bss:    1.741    0.032    0.533
   3_xyz:    1.660    0.042    0.604
   3_adp:    1.660    0.042    0.604
   3_occ:    1.660    0.042    0.604
   4_bss:    1.660    0.042    0.604
   4_xyz:    1.772    0.032    0.631
   4_adp:    1.772    0.032    0.631
   4_occ:    1.772    0.032    0.631
   5_bss:    1.772    0.032    0.631
   5_xyz:    1.844    0.031    0.635
   5_adp:    1.844    0.031    0.635
   5_occ:    1.844    0.031    0.635
   5_bss:    1.844    0.031    0.635
------------------------------------------------------------------------

CPU time actual refinement: 330.66


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_811/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_811/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_811/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_811/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_811/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 330.51 
  Macro-tasks:
    bulk solvent and scale       = 41.43  
    individual site refinement   = 134.87 
    weights calculation          = 31.64  
    collect and process          = 6.62   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 214.71 
  Micro-tasks:
    mask                            = 1.81   
    f_calc                          = 101.30 
    alpha_beta                      = 8.34   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 111.99 
    fmodel                         = 6.89   
    r_factors                      = 0.40   
    phase_errors                   = 10.59  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 242.72 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.665 micro seconds
Total CPU time: 5.74 minutes
from_scatterers_fft:    649 calls, 100.92 s
gradients_fft:          593 calls,  98.60 s

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

# Date 2008-01-16 Time 02:28:16 PST -0800 (1200479296.50 s)
Start R-work = 0.4590, R-free = 0.4439 (no bulk solvent and anisotropic scale)
Final R-work = 0.1350, R-free = 0.1789 (no bulk solvent and anisotropic scale)

Start R-work = 0.4503, R-free = 0.4318
Final R-work = 0.1187, R-free = 0.1634