# Date 2008-01-16 Time 02:41:04 PST -0800 (1200480064.77 s)
#phil __OFF__

Command line arguments: "../932.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 = 29843
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 932

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 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: 3.31, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.3993, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1641 2.02009
Completeness in resolution range: 0.981364
Completeness with d_max=infinity: 0.978227

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1641
                             d_min =   2.0201

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.3993, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1641 2.02009
Completeness in resolution range: 0.981364
Completeness with d_max=infinity: 0.978227

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1645 -  4.3217 [2096/2119]  1886   210  10.0%
  bin  2:  4.3217 -  3.4435 [2023/2043]  1821   202  10.0%
  bin  3:  3.4435 -  3.0121 [1990/2009]  1792   198   9.9%
  bin  4:  3.0121 -  2.7384 [1953/1983]  1757   196  10.0%
  bin  5:  2.7384 -  2.5431 [1970/1989]  1773   197  10.0%
  bin  6:  2.5431 -  2.3938 [1951/1976]  1754   197  10.1%
  bin  7:  2.3938 -  2.2743 [1925/1953]  1733   192  10.0%
  bin  8:  2.2743 -  2.1756 [1933/1969]  1739   194  10.0%
  bin  9:  2.1756 -  2.0921 [1922/1964]  1732   190   9.9%
  bin 10:  2.0921 -  2.0201 [1826/1956]  1643   183  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_932/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 11
        2.42 -     3.04: 2150
        3.04 -     3.66: 4585
        3.66 -     4.28: 8845
        4.28 -     4.90: 12230
  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 207 " - " O   HOH Z 341 "  1.879 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.084 3.040 -x+1,y+1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.228 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27816 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_932/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_932/model_refine_001.geo

CPU time processing inputs: 9.56


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 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: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4640   r_free= 0.4509   ksol= 0.00   Bsol= 0.00   scale= 0.792    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.262351                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1645 -  4.8198 0.99   1371  152 0.3784 0.3487      6.5653       6.461|
|  2:  4.8198 -  3.8462 0.99   1299  146 0.3681 0.3993      6.7296      6.8365|
|  3:  3.8462 -  3.3661 0.99   1286  141 0.4178 0.3959      6.6552      6.6306|
|  4:  3.3661 -  3.0611 0.99   1280  142 0.4490 0.4005      6.5208      6.4165|
|  5:  3.0611 -  2.8432 0.99   1261  141 0.4831 0.4585      6.3591      6.3473|
|  6:  2.8432 -  2.6765 0.99   1268  141 0.4957 0.5309       6.282      6.2357|
|  7:  2.6765 -  2.5431 0.99   1264  140 0.4997 0.4617        6.23      6.1835|
|  8:  2.5431 -  2.4329 0.98   1247  137 0.5067 0.4536      6.1939      6.1466|
|  9:  2.4329 -  2.3396 0.98   1243  141 0.5081 0.5471       6.112      6.1376|
| 10:  2.3396 -  2.2591 1.00   1243  138 0.5238 0.5111      6.1259      6.1249|
| 11:  2.2591 -  2.1887 0.97   1249  138 0.5044 0.4983      6.0257      6.0787|
| 12:  2.1887 -  2.1263 0.98   1239  139 0.5249 0.4889      6.0005       6.023|
| 13:  2.1263 -  2.0705 0.99   1247  137 0.5206 0.4906      5.9029      5.8647|
| 14:  2.0705 -  2.0201 0.91   1133  126 0.5345 0.5118      5.8613      5.7539|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1645 -  4.8198  1371   152  0.73  31.41   0.80     0.75      59844.54|
|  2:  4.8198 -  3.8462  1299   146  0.74  31.39   0.88     0.78      88177.51|
|  3:  3.8462 -  3.3661  1286   141  0.66  38.52   0.83     0.74      93124.75|
|  4:  3.3661 -  3.0611  1280   142  0.59  44.87   0.81     0.65      82673.17|
|  5:  3.0611 -  2.8432  1261   141  0.51  51.51   0.74     0.57      69072.39|
|  6:  2.8432 -  2.6765  1268   141  0.47  54.26   0.72     0.53      63646.29|
|  7:  2.6765 -  2.5431  1264   140  0.44  56.52   0.73     0.49      59051.61|
|  8:  2.5431 -  2.4329  1247   137  0.42  58.05   0.75     0.48      54549.33|
|  9:  2.4329 -  2.3396  1243   141  0.41  58.99   0.71     0.47      50373.72|
| 10:  2.3396 -  2.2591  1243   138  0.41  58.88   0.72     0.47      46378.97|
| 11:  2.2591 -  2.1887  1249   138  0.40  60.05   0.74     0.46      42921.17|
| 12:  2.1887 -  2.1263  1239   139  0.39  60.63   0.75     0.47      39460.22|
| 13:  2.1263 -  2.0705  1247   137  0.39  60.56   0.72     0.45      33960.72|
| 14:  2.0705 -  2.0201  1133   126  0.41  59.35   0.70     0.44      27354.84|
|alpha:            min =        0.44 max =            0.78 mean =         0.56|
|beta:             min =    27354.84 max =        93124.75 mean =     58351.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.50|
|phase err.(work): min =        0.00 max =           89.99 mean =        51.49|
|phase err.(test): min =        0.00 max =           89.97 mean =        51.52|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.623103             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.772   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.989363              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.299   (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:      161 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      670 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1478 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2569 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3837 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4992 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6454 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7636 |
|-----------------------------------------------------------------------------|
|-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 |       54.474 |
| 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 |       1.643 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.313)------------------------------------------|
|    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 = 12.313)------------------------------------------|
|    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: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4694   r_free= 0.4521   ksol= 0.00   Bsol= 0.00   scale= 0.764    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.265385                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4560   r_free= 0.4394   ksol= 0.30   Bsol= 20.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.18,8.69,10.14,0.00,0.00,0.00); trace/3= 8.67                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.256480                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.782640              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.908   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.880752              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.467   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4560      final r-factor (work) = 0.3552          |
| start r-factor (free) = 0.4394      final r-factor (free) = 0.3787          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 85.1356 = 9.78 * 0.50 * 6.2685 + 1.00 * 54.4744                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.1355 = 9.78 * 0.50 * 6.1326 + 1.00 * 0.1390                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3552      final r-factor (work) = 0.3061          |
| start r-factor (free) = 0.3787      final r-factor (free) = 0.3511          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4157 = 0.88 * 1.00 * 6.1326 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3101 = 0.88 * 1.00 * 6.0125 + 1.00 * 0.0146                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.313)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.26  11.67    None  None   None       |
|    all(noH): 2823   0      0.00    103.26  11.67    None  None   None       |
|    Sol.    : 438    0      0.00    103.26  27.59    None  None   None       |
|    Mac.    : 2385   0      0.00    69.23   8.75     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.327: 1707   |   5:    51.632 -  61.959:   18        |
|      1:    10.327 -  20.653:  662   |   6:    61.959 -  72.285:   13        |
|      2:    20.653 -  30.979:  223   |   7:    72.285 -  82.612:    0        |
|      3:    30.979 -  41.306:  127   |   8:    82.612 -  92.938:    0        |
|      4:    41.306 -  51.632:   72   |   9:    92.938 - 103.264:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3061 r_free = 0.3511             target_work(ml) = 5.979         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3056 r_free = 0.3518             target_work(ml) = 5.979         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3056   r_free= 0.3518   ksol= 0.30   Bsol= 20.00   scale= 1.075   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.18,8.69,10.14,0.00,0.00,0.00); trace/3= 8.67                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.978508                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3022   r_free= 0.3461   ksol= 0.33   Bsol= 59.55   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.02,5.41,6.49,0.00,0.00,0.00); trace/3= 5.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.978528                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.213006              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.868   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.446387              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.895  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3022      final r-factor (work) = 0.2076          |
| start r-factor (free) = 0.3461      final r-factor (free) = 0.2516          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.8014 = 5.21 * 0.50 * 6.0090 + 1.00 * 0.1390                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.2445 = 5.21 * 0.50 * 5.8199 + 1.00 * 0.0750                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2076      final r-factor (work) = 0.1863          |
| start r-factor (free) = 0.2516      final r-factor (free) = 0.2314          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6225 = 0.45 * 1.00 * 5.8199 + 1.00 * 0.0246                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5808 = 0.45 * 1.00 * 5.6027 + 1.00 * 0.0798                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.313)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.09  11.69    None  None   None       |
|    all(noH): 2823   0      0.00    102.09  11.69    None  None   None       |
|    Sol.    : 438    0      0.00    102.09  32.44    None  None   None       |
|    Mac.    : 2385   0      0.00    83.40   7.88     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.209: 1855   |   5:    51.044 -  61.252:   35        |
|      1:    10.209 -  20.418:  477   |   6:    61.252 -  71.461:    8        |
|      2:    20.418 -  30.626:  173   |   7:    71.461 -  81.670:    0        |
|      3:    30.626 -  40.835:  172   |   8:    81.670 -  91.879:    1        |
|      4:    40.835 -  51.044:  101   |   9:    91.879 - 102.087:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1863 r_free = 0.2314             target_work(ml) = 5.567         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1860 r_free = 0.2319             target_work(ml) = 5.566         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1860   r_free= 0.2319   ksol= 0.33   Bsol= 59.55   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.02,5.41,6.49,0.00,0.00,0.00); trace/3= 5.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.566096                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1852   r_free= 0.2318   ksol= 0.32   Bsol= 67.59   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.05,3.84,4.82,0.00,0.00,0.00); trace/3= 3.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.567993                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.071384              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.618  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.477639              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.467   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1852      final r-factor (work) = 0.1420          |
| start r-factor (free) = 0.2318      final r-factor (free) = 0.1825          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6869 = 3.07 * 0.50 * 5.6077 + 1.00 * 0.0752                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4511 = 3.07 * 0.50 * 5.4568 + 1.00 * 0.0712                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1420      final r-factor (work) = 0.1317          |
| start r-factor (free) = 0.1825      final r-factor (free) = 0.1777          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0810 = 1.48 * 1.00 * 5.4568 + 1.00 * 0.0179                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8397 = 1.48 * 1.00 * 5.2897 + 1.00 * 0.0234                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.313)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.03   12.63    None  None   None       |
|    all(noH): 2823   0      0.00    94.03   12.63    None  None   None       |
|    Sol.    : 438    0      0.00    94.03   37.94    None  None   None       |
|    Mac.    : 2385   0      0.00    78.99   7.99     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.403: 1777   |   5:    47.014 -  56.416:   99        |
|      1:     9.403 -  18.806:  506   |   6:    56.416 -  65.819:   56        |
|      2:    18.806 -  28.208:  141   |   7:    65.819 -  75.222:   23        |
|      3:    28.208 -  37.611:  122   |   8:    75.222 -  84.625:    6        |
|      4:    37.611 -  47.014:   92   |   9:    84.625 -  94.027:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1317 r_free = 0.1777             target_work(ml) = 5.276         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1316 r_free = 0.1776             target_work(ml) = 5.275         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1316   r_free= 0.1776   ksol= 0.32   Bsol= 67.59   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.05,3.84,4.82,0.00,0.00,0.00); trace/3= 3.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.275331                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1318   r_free= 0.1779   ksol= 0.33   Bsol= 67.59   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.79,3.31,4.43,0.00,0.00,0.00); trace/3= 3.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.275781                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.938629              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.893  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.233141              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 104.341  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1318      final r-factor (work) = 0.1241          |
| start r-factor (free) = 0.1779      final r-factor (free) = 0.1705          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2000 = 1.94 * 0.50 * 5.2906 + 1.00 * 0.0717                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1519 = 1.94 * 0.50 * 5.2495 + 1.00 * 0.0634                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1241      final r-factor (work) = 0.1245          |
| start r-factor (free) = 0.1705      final r-factor (free) = 0.1671          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2474 = 0.23 * 1.00 * 5.2495 + 1.00 * 0.0235                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2349 = 0.23 * 1.00 * 5.2329 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.313)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.34   11.85    None  None   None       |
|    all(noH): 2823   0      0.00    88.34   11.85    None  None   None       |
|    Sol.    : 438    0      0.66    88.34   35.10    None  None   None       |
|    Mac.    : 2385   0      0.00    78.36   7.58     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 -   8.834: 1778   |   5:    44.169 -  53.002:   92        |
|      1:     8.834 -  17.668:  512   |   6:    53.002 -  61.836:   42        |
|      2:    17.668 -  26.501:  149   |   7:    61.836 -  70.670:   24        |
|      3:    26.501 -  35.335:  129   |   8:    70.670 -  79.504:    6        |
|      4:    35.335 -  44.169:   89   |   9:    79.504 -  88.337:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1245 r_free = 0.1671             target_work(ml) = 5.223         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1244 r_free = 0.1670             target_work(ml) = 5.223         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1244   r_free= 0.1670   ksol= 0.33   Bsol= 67.59   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.79,3.31,4.43,0.00,0.00,0.00); trace/3= 3.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.222611                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1244   r_free= 0.1670   ksol= 0.33   Bsol= 67.59   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.79,3.31,4.43,0.00,0.00,0.00); trace/3= 3.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.222606                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.961974              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.954  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.784860              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.345   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1244      final r-factor (work) = 0.1195          |
| start r-factor (free) = 0.1670      final r-factor (free) = 0.1639          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1967 = 1.96 * 0.50 * 5.2326 + 1.00 * 0.0636                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1728 = 1.96 * 0.50 * 5.2036 + 1.00 * 0.0682                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1195      final r-factor (work) = 0.1183          |
| start r-factor (free) = 0.1639      final r-factor (free) = 0.1647          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0958 = 0.78 * 1.00 * 5.2036 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0879 = 0.78 * 1.00 * 5.1870 + 1.00 * 0.0169                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.313)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.64   11.83    None  None   None       |
|    all(noH): 2823   0      0.00    87.64   11.83    None  None   None       |
|    Sol.    : 438    0      0.83    87.64   35.31    None  None   None       |
|    Mac.    : 2385   0      0.00    78.79   7.52     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.764: 1762   |   5:    43.821 -  52.586:   93        |
|      1:     8.764 -  17.529:  518   |   6:    52.586 -  61.350:   44        |
|      2:    17.529 -  26.293:  153   |   7:    61.350 -  70.114:   28        |
|      3:    26.293 -  35.057:  123   |   8:    70.114 -  78.879:    6        |
|      4:    35.057 -  43.821:   94   |   9:    78.879 -  87.643:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1183 r_free = 0.1647             target_work(ml) = 5.192         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1183 r_free = 0.1647             target_work(ml) = 5.192         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1183   r_free= 0.1647   ksol= 0.33   Bsol= 67.59   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.79,3.31,4.43,0.00,0.00,0.00); trace/3= 3.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.192091                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1645 -  4.8198 0.99   1371  152 0.1045 0.1369      5.4287      5.5528|
|  2:  4.8198 -  3.8462 0.99   1299  146 0.0877 0.1148      5.4647      5.6671|
|  3:  3.8462 -  3.3661 0.99   1286  141 0.1101 0.1457      5.5177      5.8224|
|  4:  3.3661 -  3.0611 0.99   1280  142 0.1241 0.1656      5.4747      5.6676|
|  5:  3.0611 -  2.8432 0.99   1261  141 0.1396 0.1822        5.39      5.5777|
|  6:  2.8432 -  2.6765 0.99   1268  141 0.1309 0.1995      5.2822      5.5583|
|  7:  2.6765 -  2.5431 0.99   1264  140 0.1378 0.1746      5.2442      5.4053|
|  8:  2.5431 -  2.4329 0.98   1247  137 0.1272 0.1861      5.1564       5.446|
|  9:  2.4329 -  2.3396 0.98   1243  141 0.1242 0.1847      5.0934      5.3136|
| 10:  2.3396 -  2.2591 1.00   1243  138 0.1238 0.1817      5.0444      5.3004|
| 11:  2.2591 -  2.1887 0.97   1249  138 0.1236 0.1737      4.9995      5.2387|
| 12:  2.1887 -  2.1263 0.98   1239  139 0.1228 0.1882      4.9465      5.3042|
| 13:  2.1263 -  2.0705 0.99   1247  137 0.1186 0.1749      4.8456      5.0919|
| 14:  2.0705 -  2.0201 0.91   1133  126 0.1092 0.1815      4.6968      4.9846|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1645 -  4.8198  1371   152  0.94   9.57   0.96     0.94       7934.82|
|  2:  4.8198 -  3.8462  1299   146  0.95   8.27   1.00     0.98       9506.23|
|  3:  3.8462 -  3.3661  1286   141  0.93  11.53   1.01     1.01      11021.58|
|  4:  3.3661 -  3.0611  1280   142  0.92  13.47   0.99     0.97      10461.20|
|  5:  3.0611 -  2.8432  1261   141  0.90  16.51   0.99     0.97       9282.71|
|  6:  2.8432 -  2.6765  1268   141  0.89  16.92   0.98     0.94       7985.77|
|  7:  2.6765 -  2.5431  1264   140  0.89  16.81   0.98     0.95       7120.28|
|  8:  2.5431 -  2.4329  1247   137  0.90  16.11   0.98     0.95       6187.54|
|  9:  2.4329 -  2.3396  1243   141  0.90  16.46   0.99     0.95       5635.74|
| 10:  2.3396 -  2.2591  1243   138  0.90  16.51   0.99     0.94       4957.07|
| 11:  2.2591 -  2.1887  1249   138  0.90  16.67   0.98     0.94       4776.41|
| 12:  2.1887 -  2.1263  1239   139  0.90  16.51   0.99     0.97       4412.52|
| 13:  2.1263 -  2.0705  1247   137  0.90  16.12   0.98     0.96       3650.22|
| 14:  2.0705 -  2.0201  1133   126  0.91  14.90   0.96     0.91       2613.51|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2613.51 max =        11021.58 mean =      6888.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.68|
|phase err.(test): min =        0.00 max =           88.58 mean =        14.14|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1183   r_free= 0.1646   ksol= 0.32   Bsol= 63.59   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.66,-0.26,0.92,-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: 5.191846                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1183   r_free= 0.1646   ksol= 0.32   Bsol= 63.59   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.66,-0.26,0.92,-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: 5.191846                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1645 -  4.8198 0.99   1371  152 0.1042 0.1367       5.424      5.5498|
|  2:  4.8198 -  3.8462 0.99   1299  146 0.0873 0.1141      5.4613      5.6621|
|  3:  3.8462 -  3.3661 0.99   1286  141 0.1099 0.1458      5.5164      5.8219|
|  4:  3.3661 -  3.0611 0.99   1280  142 0.1243 0.1657       5.476      5.6687|
|  5:  3.0611 -  2.8432 0.99   1261  141 0.1399 0.1825       5.392      5.5796|
|  6:  2.8432 -  2.6765 0.99   1268  141 0.1311 0.1997      5.2837      5.5592|
|  7:  2.6765 -  2.5431 0.99   1264  140 0.1380 0.1751      5.2457      5.4073|
|  8:  2.5431 -  2.4329 0.98   1247  137 0.1273 0.1862      5.1572      5.4466|
|  9:  2.4329 -  2.3396 0.98   1243  141 0.1241 0.1846      5.0937      5.3133|
| 10:  2.3396 -  2.2591 1.00   1243  138 0.1238 0.1819      5.0445      5.3018|
| 11:  2.2591 -  2.1887 0.97   1249  138 0.1236 0.1736      4.9995      5.2382|
| 12:  2.1887 -  2.1263 0.98   1239  139 0.1228 0.1881      4.9465       5.304|
| 13:  2.1263 -  2.0705 0.99   1247  137 0.1186 0.1748      4.8453      5.0918|
| 14:  2.0705 -  2.0201 0.91   1133  126 0.1093 0.1813      4.6962      4.9838|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1645 -  4.8198  1371   152  0.94   9.54   0.96     0.94       7872.35|
|  2:  4.8198 -  3.8462  1299   146  0.95   8.22   1.00     0.98       9442.30|
|  3:  3.8462 -  3.3661  1286   141  0.93  11.51   1.01     1.01      10977.00|
|  4:  3.3661 -  3.0611  1280   142  0.92  13.49   1.00     0.98      10478.03|
|  5:  3.0611 -  2.8432  1261   141  0.90  16.53   0.99     0.97       9315.65|
|  6:  2.8432 -  2.6765  1268   141  0.89  16.95   0.98     0.94       8012.57|
|  7:  2.6765 -  2.5431  1264   140  0.89  16.84   0.98     0.96       7143.27|
|  8:  2.5431 -  2.4329  1247   137  0.90  16.13   0.98     0.96       6196.60|
|  9:  2.4329 -  2.3396  1243   141  0.90  16.47   0.99     0.95       5643.98|
| 10:  2.3396 -  2.2591  1243   138  0.90  16.51   0.99     0.94       4955.01|
| 11:  2.2591 -  2.1887  1249   138  0.90  16.66   0.98     0.94       4777.16|
| 12:  2.1887 -  2.1263  1239   139  0.90  16.50   1.00     0.98       4413.02|
| 13:  2.1263 -  2.0705  1247   137  0.90  16.11   0.98     0.96       3647.46|
| 14:  2.0705 -  2.0201  1133   126  0.91  14.88   0.96     0.92       2606.88|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2606.88 max =        10977.00 mean =      6883.78|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.83 mean =        14.68|
|phase err.(test): min =        0.00 max =           88.51 mean =        14.13|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.313)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.57    91.22   15.40    None  None   None       |
|    all(noH): 2823   0      3.57    91.22   15.40    None  None   None       |
|    Sol.    : 438    0      4.40    91.22   38.88    None  None   None       |
|    Mac.    : 2385   0      3.57    82.37   11.09    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:     3.573 -  12.338: 1762   |   5:    47.395 -  56.159:   93        |
|      1:    12.338 -  21.102:  518   |   6:    56.159 -  64.923:   44        |
|      2:    21.102 -  29.866:  153   |   7:    64.923 -  73.688:   28        |
|      3:    29.866 -  38.630:  123   |   8:    73.688 -  82.452:    6        |
|      4:    38.630 -  47.395:   94   |   9:    82.452 -  91.216:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 340         
Filter by distance & map next to the model:
   mapped sites are within: 0.264 - 5.941
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 331 from: 340
   mapped sites are within: 0.714 - 5.941

peak=   10.192 closest distance to " CG2 VAL A 230 " =    1.465
peak=    6.100 closest distance to " NH2 ARG A  56 " =    2.265
peak=    5.813 closest distance to " CG  LEU A   5 " =    1.230
peak=    5.813 closest distance to " CB  GLN A 223 " =    1.462
peak=    5.517 closest distance to " CG  LEU A 228 " =    1.212
peak=    5.191 closest distance to " CG2 VAL A 296 " =    1.026
peak=    5.144 closest distance to " CG  PRO A  54 " =    1.358
peak=    5.126 closest distance to " CB  VAL A 296 " =    1.071
peak=    4.975 closest distance to " CD2 LEU A   5 " =    1.146
peak=    4.884 closest distance to " CB  PRO A  54 " =    0.983
peak=    4.789 closest distance to " CG  PRO A 198 " =    1.324
peak=    4.733 closest distance to " CB  GLN A 183 " =    1.272
peak=    4.700 closest distance to " O   HOH Z 232 " =    2.283
peak=    4.692 closest distance to " CB  SER A  63 " =    1.234
peak=    4.620 closest distance to " CZ  PHE A 218 " =    1.120
peak=    4.600 closest distance to " CB  VAL A 230 " =    1.239
peak=    4.516 closest distance to " CB  ARG A 190 " =    1.582
peak=    4.492 closest distance to " CG  PRO A 213 " =    1.222
peak=    4.482 closest distance to " NE2 GLN A  11 " =    1.115
peak=    4.420 closest distance to " O   HOH Z 369 " =    2.081
peak=    4.419 closest distance to " CG1 VAL A 296 " =    1.166
peak=    4.391 closest distance to " O   HOH Z 265 " =    2.126
peak=    4.373 closest distance to " CB  ARG A 275 " =    0.898
peak=    4.301 closest distance to " CG  PRO A 243 " =    1.152
peak=    4.269 closest distance to " O   HOH Z 298 " =    1.958
peak=    4.230 closest distance to " CB  ASP A 124 " =    0.734
peak=    4.222 closest distance to " O   HOH Z 303 " =    2.149
peak=    4.219 closest distance to " CA  ALA A  51 " =    0.967
peak=    4.202 closest distance to " CB  GLU A 128 " =    1.094
peak=    4.158 closest distance to " O   SER A  87 " =    2.320
peak=    4.149 closest distance to " O   HOH Z 234 " =    3.726
peak=    4.138 closest distance to " O   PRO A 198 " =    1.579
peak=    4.129 closest distance to " CB  TRP A 266 " =    1.035
peak=    4.118 closest distance to " O   HOH Z 427 " =    3.136
peak=    4.115 closest distance to " CB  TYR A 169 " =    0.717
peak=    4.114 closest distance to " CD  LYS A 166 " =    1.333
peak=    4.110 closest distance to " CG  MET A 185 " =    1.263
peak=    4.101 closest distance to " CB  ARG A  79 " =    1.458
peak=    4.086 closest distance to " O   HOH Z 368 " =    2.357
peak=    4.084 closest distance to " CA  TYR A  30 " =    0.972
peak=    4.065 closest distance to " CB  GLU A 152 " =    1.147
peak=    4.064 closest distance to " CD2 LEU A 228 " =    1.354
peak=    4.058 closest distance to " CB  GLU A 277 " =    3.720
peak=    4.052 closest distance to " CB  ASN A 142 " =    1.065
peak=    4.048 closest distance to " CB  ASN A 148 " =    1.370
peak=    4.041 closest distance to " O   HOH Z 248 " =    1.647
peak=    4.038 closest distance to " CB  ASP A 140 " =    1.024
peak=    4.029 closest distance to " O   HOH Z 126 " =    2.074
peak=    4.005 closest distance to " O   HOH Z 411 " =    3.847
peak=    4.004 closest distance to " O   ASP A 124 " =    1.144
peak=    4.002 closest distance to " O   HOH Z 425 " =    1.456
peak=    4.000 closest distance to " NH1AARG A 145 " =    1.290
peak=    3.996 closest distance to " CB  GLU A  46 " =    0.960
peak=    3.988 closest distance to " O   HOH Z 236 " =    1.976
peak=    3.986 closest distance to " O   HOH Z 142 " =    1.675
peak=    3.982 closest distance to " O   HOH Z  61 " =    1.677
peak=    3.978 closest distance to " ND2 ASN A 187 " =    1.555
peak=    3.973 closest distance to " O   HOH Z 188 " =    3.096
peak=    3.964 closest distance to " CA  ARG A 195 " =    1.231
peak=    3.932 closest distance to " O   HOH Z 214 " =    2.558
peak=    3.932 closest distance to " CB AVAL A  41 " =    1.250
peak=    3.911 closest distance to " OG BSER A 164 " =    2.256
peak=    3.909 closest distance to " CB  VAL A 202 " =    1.601
peak=    3.897 closest distance to " CD1 LEU A  96 " =    0.732
peak=    3.886 closest distance to " O   HOH Z 422 " =    2.683
peak=    3.884 closest distance to " O   HOH Z  78 " =    1.652
peak=    3.880 closest distance to " O   HOH Z 126 " =    1.661
peak=    3.876 closest distance to " O   HOH Z 423 " =    1.763
peak=    3.873 closest distance to " O   HOH Z 402 " =    1.503
peak=    3.854 closest distance to " O   HOH Z 313 " =    1.784
peak=    3.848 closest distance to " N   ASN A  39 " =    1.242
peak=    3.844 closest distance to " CG2 VAL A 257 " =    0.872
peak=    3.842 closest distance to " O   HOH Z  63 " =    1.870
peak=    3.835 closest distance to " O   HOH Z  44 " =    2.090
peak=    3.826 closest distance to " O   HOH Z 261 " =    1.774
peak=    3.778 closest distance to " O   HOH Z 280 " =    2.927
peak=    3.771 closest distance to " O   HOH Z  19 " =    2.061
peak=    3.769 closest distance to " CD  ARG A 269 " =    0.923
peak=    3.769 closest distance to " O   HOH Z  48 " =    1.703
peak=    3.765 closest distance to " O   HOH Z  80 " =    1.800
peak=    3.760 closest distance to " O   HOH Z 346 " =    1.552
peak=    3.759 closest distance to " O   HOH Z 272 " =    1.934
peak=    3.758 closest distance to " O   HOH Z  43 " =    2.003
peak=    3.755 closest distance to " CB  VAL A 265 " =    1.317
peak=    3.753 closest distance to " CG2 ILE A 234 " =    0.899
peak=    3.752 closest distance to " O   HOH Z 158 " =    3.098
peak=    3.745 closest distance to " O   HOH Z  59 " =    2.284
peak=    3.733 closest distance to " CA  ALA A 295 " =    1.124
peak=    3.730 closest distance to " CB  ALA A 104 " =    0.791
peak=    3.729 closest distance to " CZ  PHE A 192 " =    0.970
peak=    3.719 closest distance to " CD  ARG A 159 " =    0.765
peak=    3.717 closest distance to " O   HOH Z  40 " =    1.829
peak=    3.717 closest distance to " CA  SER A  87 " =    1.040
peak=    3.712 closest distance to " ND2 ASN A 249 " =    1.889
peak=    3.704 closest distance to " CG1 VAL A 153 " =    0.944
peak=    3.703 closest distance to " CB  ALA A   9 " =    1.642
peak=    3.695 closest distance to " O   HOH Z 316 " =    3.156
peak=    3.690 closest distance to " O   HOH Z 285 " =    2.561
peak=    3.689 closest distance to " O   HOH Z 359 " =    1.575
peak=    3.682 closest distance to " CD1 LEU A   5 " =    1.305
peak=    3.668 closest distance to " CG2 THR A 221 " =    1.085
peak=    3.662 closest distance to " CB  TRP A 150 " =    1.400
peak=    3.656 closest distance to " CB  LEU A  83 " =    0.789
peak=    3.656 closest distance to " O   HOH Z 227 " =    1.761
peak=    3.651 closest distance to " CA  ARG A  36 " =    1.119
peak=    3.646 closest distance to " CB  ASN A  39 " =    0.882
peak=    3.645 closest distance to " O   HOH Z 171 " =    3.935
peak=    3.632 closest distance to " CB  THR A  31 " =    1.590
peak=    3.628 closest distance to " O   HOH Z 102 " =    1.365
peak=    3.623 closest distance to " CZ3 TRP A 266 " =    1.149
peak=    3.622 closest distance to " OD1 ASN A  69 " =    2.618
peak=    3.621 closest distance to " CD2 TRP A 179 " =    1.294
peak=    3.609 closest distance to " O   HOH Z 273 " =    2.898
peak=    3.593 closest distance to " CE  LYS A  76 " =    0.853
peak=    3.590 closest distance to " CB  LEU A 143 " =    1.221
peak=    3.589 closest distance to " CG1 ILE A  49 " =    1.575
peak=    3.584 closest distance to " O   HOH Z  21 " =    1.752
peak=    3.584 closest distance to " O  BHOH Z 338 " =    2.375
peak=    3.580 closest distance to " CD  ARG A  66 " =    2.616
peak=    3.570 closest distance to " O   MET A 105 " =    1.882
peak=    3.563 closest distance to " CZ  PHE A  38 " =    1.172
peak=    3.560 closest distance to " CA  VAL A 125 " =    1.294
peak=    3.560 closest distance to " CB  GLN A  89 " =    1.179
peak=    3.559 closest distance to " O   HOH Z 261 " =    1.797
peak=    3.558 closest distance to " O   HOH Z 403 " =    1.626
peak=    3.557 closest distance to " O   ALA A 165 " =    1.407
peak=    3.548 closest distance to " CA  THR A 264 " =    0.714
peak=    3.547 closest distance to " CB  SER A   3 " =    1.329
peak=    3.546 closest distance to " CA  LEU A 282 " =    1.113
peak=    3.543 closest distance to " N   PHE A 130 " =    1.268
peak=    3.537 closest distance to " CG  LEU A 167 " =    1.149
peak=    3.530 closest distance to " CA  MET A 105 " =    0.986
peak=    3.522 closest distance to " CB  GLN A  88 " =    1.233
peak=    3.521 closest distance to " NH2 ARG A 156 " =    1.112
peak=    3.520 closest distance to " O   HOH Z 247 " =    1.509
peak=    3.514 closest distance to " O   HOH Z 251 " =    1.456
peak=    3.509 closest distance to " O   HOH Z 184 " =    1.412
peak=    3.507 closest distance to " CB  ALA A 291 " =    1.293
peak=    3.506 closest distance to " CA  TYR A  30 " =    1.059
peak=    3.500 closest distance to " O   HOH Z 128 " =    1.871
peak=    3.499 closest distance to " CB  ASN A 187 " =    1.146
peak=    3.498 closest distance to " CB  MET A  47 " =    0.986
peak=    3.496 closest distance to " CB  TRP A 179 " =    1.375
peak=    3.495 closest distance to " CG  PHE A 204 " =    0.931
peak=    3.495 closest distance to " CA  ALA A  21 " =    1.206
peak=    3.488 closest distance to " CA  ILE A 106 " =    0.774
peak=    3.487 closest distance to " O   HOH Z 193 " =    2.112
peak=    3.483 closest distance to " CD1 ILE A 199 " =    0.823
peak=    3.478 closest distance to " O   HOH Z 353 " =    2.617
peak=    3.461 closest distance to " O   PRO A 213 " =    1.565
peak=    3.459 closest distance to " O   HOH Z 172 " =    3.858
peak=    3.458 closest distance to " CB  LYS A 117 " =    1.197
peak=    3.445 closest distance to " O   HOH Z 406 " =    1.534
peak=    3.441 closest distance to " NE2 GLN A  77 " =    3.387
peak=    3.437 closest distance to " CA  TYR A 116 " =    1.499
peak=    3.437 closest distance to " O   HOH Z 193 " =    1.717
peak=    3.434 closest distance to " N   SER A 135 " =    1.338
peak=    3.433 closest distance to " CB  LEU A 228 " =    1.199
peak=    3.425 closest distance to " CD1 LEU A 300 " =    1.211
peak=    3.424 closest distance to " CB  TYR A 247 " =    1.024
peak=    3.423 closest distance to " CD ALYS A 290 " =    1.093
peak=    3.422 closest distance to " CB  THR A  82 " =    1.419
peak=    3.422 closest distance to " CZ3 TRP A  85 " =    0.966
peak=    3.420 closest distance to " CG1BVAL A  72 " =    1.854
peak=    3.412 closest distance to " O   HOH Z 213 " =    1.905
peak=    3.411 closest distance to " CG BARG A 275 " =    1.416
peak=    3.411 closest distance to " O   HOH Z  49 " =    1.018
peak=    3.407 closest distance to " O   HOH Z  97 " =    2.098
peak=    3.405 closest distance to " O   GLN A  88 " =    1.641
peak=    3.403 closest distance to " O   HOH Z 147 " =    1.796
peak=    3.402 closest distance to " O   HOH Z 193 " =    1.986
peak=    3.400 closest distance to " O   HOH Z 368 " =    3.552
peak=    3.398 closest distance to " O   HOH Z  78 " =    1.835
peak=    3.395 closest distance to " CA  ASP A 191 " =    1.020
peak=    3.393 closest distance to " CG2 THR A 220 " =    0.867
peak=    3.391 closest distance to " CE1 TYR A 186 " =    1.269
peak=    3.389 closest distance to " CB  ALA A 242 " =    0.806
peak=    3.389 closest distance to " CD  ARG A  66 " =    2.436
peak=    3.385 closest distance to " OD1 ASN A 217 " =    1.551
peak=    3.379 closest distance to " CB  MET A  40 " =    0.752
peak=    3.375 closest distance to " O   HOH Z 437 " =    1.672
peak=    3.374 closest distance to " CD2 LEU A 297 " =    0.915
peak=    3.372 closest distance to " CB  PRO A 243 " =    1.371
peak=    3.371 closest distance to " CZ3 TRP A 274 " =    4.572
peak=    3.371 closest distance to " CA  ALA A 158 " =    1.253
peak=    3.368 closest distance to " CB  VAL A 268 " =    0.821
peak=    3.365 closest distance to " NE2 HIS A 207 " =    1.166
peak=    3.364 closest distance to " CB  SER A 212 " =    1.272
peak=    3.363 closest distance to " CA  ALA A 154 " =    1.010
peak=    3.363 closest distance to " CG  MET A 185 " =    0.999
peak=    3.362 closest distance to " CB  SER A 273 " =    0.883
peak=    3.361 closest distance to " CB  ASN A 110 " =    1.221
peak=    3.358 closest distance to " O   HOH Z 371 " =    2.928
peak=    3.358 closest distance to " O   HOH Z 294 " =    1.571
peak=    3.353 closest distance to " OG  SER A  22 " =    2.835
peak=    3.353 closest distance to " CB  SER A  26 " =    1.806
peak=    3.349 closest distance to " NH1 ARG A  14 " =    0.928
peak=    3.339 closest distance to " CA  ASN A 217 " =    1.308
peak=    3.338 closest distance to " O   HOH Z 329 " =    4.105
peak=    3.338 closest distance to " CB  ALA A 248 " =    1.111
peak=    3.333 closest distance to " NZ  LYS A  48 " =    1.308
peak=    3.333 closest distance to " CG1 ILE A 151 " =    1.080
peak=    3.332 closest distance to " O   ASN A  74 " =    1.469
peak=    3.329 closest distance to " O   HOH Z   9 " =    2.123
peak=    3.325 closest distance to " N   VAL A 126 " =    1.384
peak=    3.323 closest distance to " O   HOH Z 163 " =    1.607
peak=    3.321 closest distance to " O   PHE A  61 " =    1.337
peak=    3.319 closest distance to " O   HOH Z 365 " =    2.889
peak=    3.311 closest distance to " CB  THR A 157 " =    1.165
peak=    3.309 closest distance to " CG1 ILE A  33 " =    1.276
peak=    3.308 closest distance to " O   TRP A 274 " =    1.839
peak=    3.307 closest distance to " CA  ASN A 215 " =    1.182
peak=    3.305 closest distance to " CA  LYS A 181 " =    1.064
peak=    3.305 closest distance to " O   HOH Z 201 " =    2.983
peak=    3.304 closest distance to " CB  HIS A 108 " =    0.773
peak=    3.304 closest distance to " O   HOH Z 271 " =    2.488
peak=    3.302 closest distance to " ND2 ASN A 249 " =    0.820
peak=    3.301 closest distance to " O   HOH Z 146 " =    2.269
peak=    3.298 closest distance to " CB  GLN A 205 " =    1.053
peak=    3.296 closest distance to " CA  VAL A  41 " =    0.797
peak=    3.296 closest distance to " CH2 TRP A  70 " =    1.015
peak=    3.290 closest distance to " O   HOH Z 125 " =    3.823
peak=    3.289 closest distance to " O   LYS A 290 " =    2.426
peak=    3.288 closest distance to " O   HOH Z  68 " =    2.030
peak=    3.287 closest distance to " O   ALA A 158 " =    1.382
peak=    3.287 closest distance to " O   HOH Z 238 " =    2.227
peak=    3.285 closest distance to " N   ASP A 162 " =    1.254
peak=    3.284 closest distance to " O   HOH Z 130 " =    2.274
peak=    3.284 closest distance to " O   HOH Z 305 " =    3.650
peak=    3.283 closest distance to " O   HOH Z 293 " =    1.845
peak=    3.283 closest distance to " CA  GLY A 211 " =    1.353
peak=    3.281 closest distance to " O   HOH Z  88 " =    3.104
peak=    3.279 closest distance to " ND1 HIS A  81 " =    1.667
peak=    3.276 closest distance to " O   HOH Z 180 " =    2.133
peak=    3.274 closest distance to " CA  ALA A 291 " =    0.864
peak=    3.269 closest distance to " CG  GLU A  37 " =    0.877
peak=    3.268 closest distance to " CB  THR A  52 " =    0.914
peak=    3.268 closest distance to " CE2 TYR A  30 " =    0.731
peak=    3.265 closest distance to " NZ  LYS A 117 " =    3.204
peak=    3.263 closest distance to " CA  THR A 221 " =    0.880
peak=    3.254 closest distance to " CG2 ILE A  20 " =    1.360
peak=    3.248 closest distance to " CE3 TRP A 150 " =    1.066
peak=    3.248 closest distance to " O   HOH Z 141 " =    1.668
peak=    3.247 closest distance to " CB  ALA A  43 " =    0.862
peak=    3.246 closest distance to " O   HOH Z 258 " =    2.117
peak=    3.246 closest distance to " OG  SER A 245 " =    1.619
peak=    3.243 closest distance to " CB  ASP A 298 " =    1.189
peak=    3.242 closest distance to " O   PRO A  90 " =    1.388
peak=    3.240 closest distance to " O   HOH Z 383 " =    2.166
peak=    3.235 closest distance to " O   HOH Z 197 " =    2.766
peak=    3.234 closest distance to " CA  LYS A 117 " =    1.280
peak=    3.231 closest distance to " O   HOH Z 325 " =    2.262
peak=    3.227 closest distance to " O   HOH Z 261 " =    1.362
peak=    3.226 closest distance to " O   ASN A 284 " =    1.788
peak=    3.222 closest distance to " NH2 ARG A  79 " =    1.341
peak=    3.222 closest distance to " O   HOH Z 403 " =    1.422
peak=    3.220 closest distance to " O   HOH Z 130 " =    1.039
peak=    3.217 closest distance to " O   HOH Z 332 " =    1.549
peak=    3.216 closest distance to " O   HOH Z 187 " =    2.348
peak=    3.214 closest distance to " O   HOH Z 146 " =    1.432
peak=    3.212 closest distance to " CA  ALA A 160 " =    0.938
peak=    3.210 closest distance to " CB  SER A 210 " =    0.908
peak=    3.209 closest distance to " CB  ALA A 100 " =    1.269
peak=    3.208 closest distance to " O   HOH Z 203 " =    1.845
peak=    3.207 closest distance to " CG  LEU A 281 " =    1.097
peak=    3.203 closest distance to " CD  ARG A  66 " =    1.964
peak=    3.200 closest distance to " O   HOH Z 148 " =    3.222
peak=    3.199 closest distance to " O   HOH Z   4 " =    1.720
peak=    3.198 closest distance to " CB  ASN A 285 " =    0.962
peak=    3.196 closest distance to " CG2 ILE A 151 " =    0.836
peak=    3.193 closest distance to " O   HOH Z 199 " =    1.678
peak=    3.190 closest distance to " CG BARG A 102 " =    1.813
peak=    3.188 closest distance to " O   HOH Z 391 " =    2.986
peak=    3.188 closest distance to " CB  PRO A  90 " =    1.183
peak=    3.186 closest distance to " CE2 PHE A 204 " =    0.801
peak=    3.185 closest distance to " O   PHE A 192 " =    1.489
peak=    3.181 closest distance to " N   ALA A 256 " =    1.058
peak=    3.181 closest distance to " O   HOH Z  10 " =    1.785
peak=    3.180 closest distance to " C   ALA A 299 " =    0.918
peak=    3.180 closest distance to " CG2 ILE A 263 " =    0.927
peak=    3.175 closest distance to " O   HOH Z 327 " =    2.414
peak=    3.174 closest distance to " CB  ILE A 120 " =    1.334
peak=    3.173 closest distance to " CB  GLN A 103 " =    0.936
peak=    3.170 closest distance to " O   HOH Z 188 " =    1.935
peak=    3.169 closest distance to " O   ASP A 200 " =    1.685
peak=    3.164 closest distance to " O   HOH Z 435 " =    2.035
peak=    3.164 closest distance to " CA  LYS A 290 " =    1.193
peak=    3.163 closest distance to " CA  ARG A 139 " =    1.133
peak=    3.162 closest distance to " CB  SER A  62 " =    0.726
peak=    3.147 closest distance to " NH1 ARG A 138 " =    1.071
peak=    3.146 closest distance to " CB  SER A 216 " =    0.797
peak=    3.145 closest distance to " CB  ALA A   1 " =    4.920
peak=    3.144 closest distance to " O   HOH Z 133 " =    2.522
peak=    3.142 closest distance to " CZ3 TRP A  92 " =    1.396
peak=    3.139 closest distance to " OH  TYR A 214 " =    1.226
peak=    3.138 closest distance to " CG  GLN A  11 " =    1.523
peak=    3.137 closest distance to " O   HOH Z 417 " =    3.197
peak=    3.136 closest distance to " CB  ASN A 173 " =    1.100
peak=    3.131 closest distance to " CA  ASP A 162 " =    1.037
peak=    3.131 closest distance to " CD1 ILE A  33 " =    1.761
peak=    3.126 closest distance to " O   HOH Z 112 " =    1.664
peak=    3.125 closest distance to " O   HOH Z 109 " =    2.718
peak=    3.124 closest distance to " O   HOH Z 313 " =    1.603
peak=    3.122 closest distance to " O   HOH Z 421 " =    1.998
peak=    3.119 closest distance to " N   GLY A  98 " =    1.130
peak=    3.119 closest distance to " CB  PHE A 204 " =    0.885
peak=    3.113 closest distance to " O   HOH Z 421 " =    3.125
peak=    3.111 closest distance to " CG  ARG A 159 " =    0.976
peak=    3.108 closest distance to " O   HOH Z 344 " =    2.971
peak=    3.105 closest distance to " CG  GLN A  58 " =    2.993
peak=    3.104 closest distance to " O   HOH Z 256 " =    2.218
peak=    3.098 closest distance to " CB  LEU A 300 " =    0.867
peak=    3.098 closest distance to " CB  ASN A 215 " =    1.237
peak=    3.093 closest distance to " OG BSER A 134 " =    2.796
peak=    3.087 closest distance to " O   THR A 182 " =    1.419
peak=    3.086 closest distance to " O   GLU A   2 " =    1.515
peak=    3.084 closest distance to " CD  PRO A  54 " =    1.135
peak=    3.081 closest distance to " CA  ALA A 233 " =    1.573
peak=    3.080 closest distance to " CB  ARG A 145 " =    0.795
peak=    3.080 closest distance to " CB  ALA A 114 " =    1.161
peak=    3.068 closest distance to " N   GLY A 133 " =    3.748
peak=    3.068 closest distance to " O   HOH Z 420 " =    5.941
peak=    3.061 closest distance to " N   ILE A  20 " =    2.246
peak=    3.059 closest distance to " O   GLN A 278 " =    1.540
peak=    3.057 closest distance to " O   HOH Z 116 " =    1.865
peak=    3.051 closest distance to " CE  MET A  40 " =    1.102
peak=    3.048 closest distance to " CB  TYR A 116 " =    0.915
peak=    3.044 closest distance to " CB  ARG A 138 " =    1.002
peak=    3.042 closest distance to " CB  ALA A 227 " =    1.041
peak=    3.037 closest distance to " O   HOH Z 433 " =    4.235
peak=    3.034 closest distance to " O   THR A  31 " =    1.568

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 217         
Filter by distance & map next to the model:
   mapped sites are within: 0.761 - 5.516
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 217 from: 217
   mapped sites are within: 0.761 - 5.516

peak=   -5.601 closest distance to " CG2 VAL A 230 " =    0.761
peak=   -4.722 closest distance to " CD  GLN A  58 " =    0.973
peak=   -4.317 closest distance to " CG1 VAL A 112 " =    2.649
peak=   -4.282 closest distance to " O   HOH Z 196 " =    2.365
peak=   -4.252 closest distance to " CB  PRO A 243 " =    2.688
peak=   -4.229 closest distance to " CD  ARG A 156 " =    2.098
peak=   -4.146 closest distance to " CG1 VAL A 296 " =    1.144
peak=   -4.138 closest distance to " CA  ASP A 298 " =    1.055
peak=   -4.131 closest distance to " CB  ALA A 161 " =    2.604
peak=   -4.122 closest distance to " O   HOH Z 266 " =    5.516
peak=   -4.114 closest distance to " CD  ARG A  14 " =    3.267
peak=   -4.083 closest distance to " O   HOH Z 211 " =    1.302
peak=   -4.052 closest distance to " O   HOH Z  73 " =    2.326
peak=   -4.025 closest distance to " OG  SER A  97 " =    2.346
peak=   -4.016 closest distance to " CG1 VAL A 250 " =    2.800
peak=   -4.012 closest distance to " O   VAL A  67 " =    2.794
peak=   -3.968 closest distance to " O   HOH Z 166 " =    1.762
peak=   -3.961 closest distance to " O   HOH Z  37 " =    1.875
peak=   -3.910 closest distance to " CG  ASP A 231 " =    0.796
peak=   -3.909 closest distance to " O   HOH Z 394 " =    1.615
peak=   -3.896 closest distance to " CG  ARG A 269 " =    2.452
peak=   -3.881 closest distance to " NH2AARG A 275 " =    5.262
peak=   -3.863 closest distance to " OE1 GLN A 223 " =    2.132
peak=   -3.863 closest distance to " O   HOH Z 351 " =    1.549
peak=   -3.857 closest distance to " O   VAL A  67 " =    2.732
peak=   -3.856 closest distance to " C   HIS A 108 " =    1.127
peak=   -3.833 closest distance to " O   HOH Z  52 " =    1.661
peak=   -3.826 closest distance to " O   HOH Z 290 " =    1.211
peak=   -3.824 closest distance to " CE3 TRP A 150 " =    2.246
peak=   -3.813 closest distance to " O   HOH Z  10 " =    1.509
peak=   -3.807 closest distance to " CE2 TYR A  30 " =    2.721
peak=   -3.794 closest distance to " O   HOH Z 231 " =    2.177
peak=   -3.792 closest distance to " CB  PHE A 192 " =    1.976
peak=   -3.786 closest distance to " CG2 ILE A  49 " =    2.847
peak=   -3.749 closest distance to " CD2 TYR A 293 " =    1.965
peak=   -3.736 closest distance to " N   ALA A  43 " =    2.574
peak=   -3.730 closest distance to " N   ALA A 226 " =    2.173
peak=   -3.726 closest distance to " CA  GLY A 241 " =    2.408
peak=   -3.725 closest distance to " C   ALA A 158 " =    1.295
peak=   -3.721 closest distance to " CZ3 TRP A 179 " =    1.201
peak=   -3.696 closest distance to " CB  ALA A 248 " =    2.172
peak=   -3.674 closest distance to " OG BSER A 134 " =    1.287
peak=   -3.667 closest distance to " CG1 VAL A 112 " =    2.822
peak=   -3.655 closest distance to " NE2 GLN A 194 " =    1.953
peak=   -3.647 closest distance to " CG  GLU A 277 " =    1.223
peak=   -3.643 closest distance to " O   HOH Z 241 " =    1.162
peak=   -3.643 closest distance to " O   HOH Z 128 " =    2.654
peak=   -3.637 closest distance to " O   SER A 271 " =    2.189
peak=   -3.616 closest distance to " O   HOH Z 177 " =    1.880
peak=   -3.608 closest distance to " O   HOH Z 216 " =    1.250
peak=   -3.603 closest distance to " CE3 TRP A  70 " =    1.783
peak=   -3.598 closest distance to " OXT GLY A 302 " =    3.028
peak=   -3.595 closest distance to " O   HOH Z 113 " =    2.371
peak=   -3.577 closest distance to " OD1 ASN A 148 " =    1.393
peak=   -3.572 closest distance to " C   LEU A 143 " =    1.017
peak=   -3.559 closest distance to " O   PRO A 163 " =    2.227
peak=   -3.553 closest distance to " O   HOH Z 114 " =    3.109
peak=   -3.552 closest distance to " CD2 LEU A 167 " =    1.852
peak=   -3.551 closest distance to " CD1 PHE A  59 " =    2.064
peak=   -3.546 closest distance to " O   VAL A 189 " =    2.625
peak=   -3.537 closest distance to " CG  HIS A  86 " =    1.103
peak=   -3.528 closest distance to " OD1 ASN A 249 " =    2.406
peak=   -3.520 closest distance to " O   HOH Z 407 " =    3.292
peak=   -3.514 closest distance to " CB  ALA A 248 " =    2.331
peak=   -3.512 closest distance to " O   ARG A  24 " =    2.165
peak=   -3.508 closest distance to " CD  GLN A 223 " =    1.235
peak=   -3.508 closest distance to " CB  ALA A 114 " =    2.592
peak=   -3.486 closest distance to " O   HOH Z 431 " =    2.004
peak=   -3.484 closest distance to " CA  GLY A 241 " =    3.160
peak=   -3.484 closest distance to " C   ASN A 285 " =    2.462
peak=   -3.479 closest distance to " O   PRO A 198 " =    1.252
peak=   -3.468 closest distance to " CD1 LEU A 101 " =    2.460
peak=   -3.467 closest distance to " CE2 PHE A  61 " =    2.571
peak=   -3.465 closest distance to " O   GLY A  17 " =    1.314
peak=   -3.461 closest distance to " CG  TRP A 266 " =    1.862
peak=   -3.458 closest distance to " O   HOH Z  17 " =    1.376
peak=   -3.449 closest distance to " O   HOH Z 185 " =    2.440
peak=   -3.433 closest distance to " O   HOH Z 435 " =    2.612
peak=   -3.431 closest distance to " NE2 GLN A  88 " =    0.945
peak=   -3.424 closest distance to " OD2 ASP A  50 " =    2.282
peak=   -3.421 closest distance to " CD1 LEU A   5 " =    2.563
peak=   -3.421 closest distance to " NE2 GLN A 103 " =    1.861
peak=   -3.420 closest distance to " N   THR A  52 " =    1.634
peak=   -3.416 closest distance to " CE BMET A  47 " =    2.032
peak=   -3.413 closest distance to " ND2 ASN A  45 " =    1.180
peak=   -3.412 closest distance to " CD1 ILE A 151 " =    2.457
peak=   -3.397 closest distance to " O   HOH Z 251 " =    4.931
peak=   -3.396 closest distance to " O   HOH Z 236 " =    1.431
peak=   -3.394 closest distance to " O   GLY A  80 " =    2.607
peak=   -3.392 closest distance to " CG2BVAL A  41 " =    1.795
peak=   -3.384 closest distance to " O   HOH Z 434 " =    1.786
peak=   -3.382 closest distance to " CG2 VAL A 296 " =    1.124
peak=   -3.379 closest distance to " O   HOH Z 133 " =    1.363
peak=   -3.373 closest distance to " OG  SER A 206 " =    1.783
peak=   -3.366 closest distance to " O   HOH Z 102 " =    1.699
peak=   -3.366 closest distance to " CZ  TYR A 169 " =    1.775
peak=   -3.365 closest distance to " O   HOH Z 222 " =    1.581
peak=   -3.365 closest distance to " C   MET A 188 " =    1.420
peak=   -3.357 closest distance to " O   HOH Z  38 " =    1.510
peak=   -3.353 closest distance to " O   HOH Z 252 " =    3.879
peak=   -3.352 closest distance to " OD1 ASN A 173 " =    1.366
peak=   -3.347 closest distance to " CG  GLU A  53 " =    1.561
peak=   -3.345 closest distance to " O   GLY A 203 " =    2.344
peak=   -3.343 closest distance to " CG2 ILE A 263 " =    2.468
peak=   -3.340 closest distance to " CG1 VAL A  67 " =    2.849
peak=   -3.340 closest distance to " O   HOH Z  94 " =    2.124
peak=   -3.335 closest distance to " O   HOH Z 234 " =    4.426
peak=   -3.334 closest distance to " O   HOH Z  44 " =    2.250
peak=   -3.325 closest distance to " CA  GLY A 133 " =    2.314
peak=   -3.323 closest distance to " O   HOH Z  60 " =    1.822
peak=   -3.317 closest distance to " O   HOH Z 136 " =    2.415
peak=   -3.306 closest distance to " CD  GLN A  88 " =    0.783
peak=   -3.306 closest distance to " N   ASN A  60 " =    1.288
peak=   -3.306 closest distance to " CD  PRO A 243 " =    2.020
peak=   -3.305 closest distance to " O   HOH Z 426 " =    1.670
peak=   -3.300 closest distance to " O   HOH Z 377 " =    1.951
peak=   -3.298 closest distance to " O   HOH Z 285 " =    1.798
peak=   -3.296 closest distance to " CD2 LEU A 300 " =    2.758
peak=   -3.294 closest distance to " O   HOH Z 359 " =    2.920
peak=   -3.292 closest distance to " O   HOH Z 292 " =    4.684
peak=   -3.292 closest distance to " CD1 ILE A 199 " =    2.576
peak=   -3.290 closest distance to " O   HOH Z   6 " =    1.619
peak=   -3.283 closest distance to " NH2 ARG A  79 " =    1.597
peak=   -3.282 closest distance to " CD  PRO A 213 " =    2.174
peak=   -3.277 closest distance to " CB  ALA A  43 " =    2.623
peak=   -3.275 closest distance to " O   HOH Z  11 " =    1.887
peak=   -3.273 closest distance to " CE  MET A 105 " =    2.203
peak=   -3.272 closest distance to " O   HOH Z 429 " =    2.087
peak=   -3.272 closest distance to " O   HOH Z 232 " =    1.722
peak=   -3.265 closest distance to " OE2 GLU A 277 " =    2.970
peak=   -3.262 closest distance to " O   HOH Z 111 " =    1.397
peak=   -3.259 closest distance to " O   HOH Z 380 " =    1.350
peak=   -3.257 closest distance to " NH2 ARG A 159 " =    2.358
peak=   -3.256 closest distance to " O   HOH Z 106 " =    1.899
peak=   -3.250 closest distance to " O   HOH Z   9 " =    1.681
peak=   -3.249 closest distance to " O   HOH Z 165 " =    1.796
peak=   -3.247 closest distance to " O   GLY A 211 " =    1.394
peak=   -3.246 closest distance to " O   HOH Z  43 " =    1.634
peak=   -3.245 closest distance to " N   SER A   3 " =    2.107
peak=   -3.242 closest distance to " OG1 THR A  82 " =    1.427
peak=   -3.240 closest distance to " O   HOH Z 368 " =    1.828
peak=   -3.240 closest distance to " ND2 ASN A 187 " =    1.598
peak=   -3.239 closest distance to " O   HOH Z  44 " =    1.037
peak=   -3.237 closest distance to " N   PHE A  59 " =    2.140
peak=   -3.231 closest distance to " CB  GLN A  11 " =    1.633
peak=   -3.229 closest distance to " O   HOH Z  49 " =    1.198
peak=   -3.229 closest distance to " O   HOH Z  19 " =    2.210
peak=   -3.221 closest distance to " O   ILE A 234 " =    1.223
peak=   -3.219 closest distance to " OG1 THR A  82 " =    1.548
peak=   -3.219 closest distance to " C   SER A 206 " =    1.448
peak=   -3.215 closest distance to " CG  MET A 105 " =    0.942
peak=   -3.213 closest distance to " CD  GLN A 223 " =    0.781
peak=   -3.211 closest distance to " O   HOH Z 396 " =    2.061
peak=   -3.205 closest distance to " CB  ALA A  10 " =    2.232
peak=   -3.202 closest distance to " CB  ALA A 291 " =    2.244
peak=   -3.199 closest distance to " OG BSER A 210 " =    1.557
peak=   -3.196 closest distance to " CE2 TRP A  70 " =    2.178
peak=   -3.195 closest distance to " CA  GLY A  98 " =    2.066
peak=   -3.193 closest distance to " CG  PHE A 283 " =    2.756
peak=   -3.192 closest distance to " CG1 VAL A 125 " =    1.963
peak=   -3.191 closest distance to " O   HOH Z  13 " =    1.537
peak=   -3.187 closest distance to " CG  LYS A 166 " =    2.132
peak=   -3.184 closest distance to " O   HOH Z 231 " =    1.710
peak=   -3.181 closest distance to " O   HOH Z 411 " =    1.704
peak=   -3.179 closest distance to " O   HOH Z 166 " =    1.836
peak=   -3.177 closest distance to " O   HOH Z 377 " =    1.335
peak=   -3.171 closest distance to " ND2 ASN A  69 " =    1.931
peak=   -3.169 closest distance to " CG  ASP A 132 " =    2.338
peak=   -3.163 closest distance to " O   HOH Z 313 " =    1.244
peak=   -3.161 closest distance to " CD1 ILE A 239 " =    2.116
peak=   -3.159 closest distance to " CG1 VAL A 112 " =    2.847
peak=   -3.159 closest distance to " OE1 GLN A  88 " =    0.999
peak=   -3.150 closest distance to " OG  SER A  87 " =    1.578
peak=   -3.147 closest distance to " O   HOH Z 264 " =    1.670
peak=   -3.140 closest distance to " O   HOH Z 409 " =    4.813
peak=   -3.140 closest distance to " CG2 VAL A 112 " =    2.549
peak=   -3.139 closest distance to " CG2 VAL A 189 " =    2.048
peak=   -3.137 closest distance to " CB  LEU A  83 " =    2.349
peak=   -3.136 closest distance to " CB  PRO A 163 " =    2.541
peak=   -3.136 closest distance to " O   HOH Z 149 " =    2.203
peak=   -3.135 closest distance to " O   GLY A  80 " =    2.328
peak=   -3.134 closest distance to " OG BSER A 134 " =    1.990
peak=   -3.128 closest distance to " CB  ASP A 171 " =    2.328
peak=   -3.126 closest distance to " CG1 VAL A 197 " =    2.287
peak=   -3.126 closest distance to " O   HOH Z 110 " =    1.458
peak=   -3.126 closest distance to " O   ALA A 227 " =    1.495
peak=   -3.124 closest distance to " O   HOH Z 275 " =    1.554
peak=   -3.123 closest distance to " CD1 LEU A 228 " =    2.328
peak=   -3.119 closest distance to " CB  ALA A 291 " =    2.299
peak=   -3.117 closest distance to " O   HOH Z 262 " =    2.857
peak=   -3.117 closest distance to " CG  PRO A 243 " =    1.721
peak=   -3.115 closest distance to " O   HOH Z 392 " =    1.896
peak=   -3.113 closest distance to " O   HOH Z 298 " =    2.731
peak=   -3.112 closest distance to " CA  ASN A 127 " =    1.093
peak=   -3.108 closest distance to " CG  PRO A 163 " =    2.393
peak=   -3.108 closest distance to " O   HOH Z 193 " =    1.806
peak=   -3.106 closest distance to " O   HOH Z 421 " =    3.292
peak=   -3.103 closest distance to " C   ASP A 270 " =    1.173
peak=   -3.100 closest distance to " O   GLY A 196 " =    1.231
peak=   -3.098 closest distance to " CD1 ILE A 263 " =    2.020
peak=   -3.095 closest distance to " CA  ALA A 248 " =    2.577
peak=   -3.093 closest distance to " NH2 ARG A  66 " =    1.976
peak=   -3.087 closest distance to " OD1 ASP A 171 " =    1.609
peak=   -3.087 closest distance to " CD2 LEU A 237 " =    2.820
peak=   -3.077 closest distance to " NE2 GLN A 194 " =    1.999
peak=   -3.076 closest distance to " O   HOH Z 176 " =    0.834
peak=   -3.075 closest distance to " N   SER A 276 " =    1.424
peak=   -3.067 closest distance to " O   HOH Z 423 " =    2.092
peak=   -3.067 closest distance to " CD1 LEU A 101 " =    2.798
peak=   -3.064 closest distance to " CG1 VAL A  78 " =    2.696
peak=   -3.061 closest distance to " CE  LYS A  76 " =    2.661
peak=   -3.061 closest distance to " O   HOH Z 145 " =    1.311
peak=   -3.060 closest distance to " CG1AVAL A  41 " =    2.909
peak=   -3.041 closest distance to " O   HOH Z  60 " =    2.094
peak=   -3.040 closest distance to " CA  SER A  62 " =    2.514
peak=   -3.037 closest distance to " O   HOH Z 326 " =    5.049
peak=   -3.024 closest distance to " CG1 VAL A 197 " =    2.399

================= 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    :  0.4640 0.4509   6.262351e+00   6.239606e+00
   1_bss:  0.4560 0.4394   6.256480e+00   6.229708e+00
   1_xyz:  0.3552 0.3787   6.095337e+00   6.129558e+00
   1_adp:  0.3061 0.3511   5.979319e+00   6.068717e+00
   1_occ:  0.3056 0.3518   5.978508e+00   6.070224e+00
   2_bss:  0.3022 0.3461   5.978528e+00   6.067582e+00
   2_xyz:  0.2076 0.2516   5.655080e+00   5.811365e+00
   2_adp:  0.1863 0.2314   5.566561e+00   5.739978e+00
   2_occ:  0.1860 0.2319   5.566096e+00   5.740516e+00
   3_bss:  0.1852 0.2318   5.567993e+00   5.741970e+00
   3_xyz:  0.1420 0.1825   5.325998e+00   5.531347e+00
   3_adp:  0.1317 0.1777   5.275712e+00   5.502525e+00
   3_occ:  0.1316 0.1776   5.275331e+00   5.502057e+00
   4_bss:  0.1318 0.1779   5.275781e+00   5.500609e+00
   4_xyz:  0.1241 0.1705   5.229049e+00   5.459385e+00
   4_adp:  0.1245 0.1671   5.223417e+00   5.442824e+00
   4_occ:  0.1244 0.1670   5.222611e+00   5.441966e+00
   5_bss:  0.1244 0.1670   5.222606e+00   5.441935e+00
   5_xyz:  0.1195 0.1639   5.192837e+00   5.423330e+00
   5_adp:  0.1183 0.1647   5.192119e+00   5.429519e+00
   5_occ:  0.1183 0.1647   5.192091e+00   5.429684e+00
   5_bss:  0.1183 0.1646   5.191846e+00   5.429484e+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   7.177   8.687  10.138   0.000   0.000   0.000
   1_xyz:  0.300  20.000   7.177   8.687  10.138   0.000   0.000   0.000
   1_adp:  0.300  20.000   7.177   8.687  10.138   0.000   0.000   0.000
   1_occ:  0.300  20.000   7.177   8.687  10.138   0.000   0.000   0.000
   2_bss:  0.329  59.548   4.024   5.415   6.495   0.000   0.000   0.000
   2_xyz:  0.329  59.548   4.024   5.415   6.495   0.000   0.000   0.000
   2_adp:  0.329  59.548   4.024   5.415   6.495   0.000   0.000   0.000
   2_occ:  0.329  59.548   4.024   5.415   6.495   0.000   0.000   0.000
   3_bss:  0.319  67.589   3.048   3.843   4.820   0.000   0.000   0.000
   3_xyz:  0.319  67.589   3.048   3.843   4.820   0.000   0.000   0.000
   3_adp:  0.319  67.589   3.048   3.843   4.820   0.000   0.000   0.000
   3_occ:  0.319  67.589   3.048   3.843   4.820   0.000   0.000   0.000
   4_bss:  0.331  67.589   2.794   3.311   4.429   0.000   0.000   0.000
   4_xyz:  0.331  67.589   2.794   3.311   4.429   0.000   0.000   0.000
   4_adp:  0.331  67.589   2.794   3.311   4.429   0.000   0.000   0.000
   4_occ:  0.331  67.589   2.794   3.311   4.429   0.000   0.000   0.000
   5_bss:  0.332  67.589   2.794   3.311   4.429   0.000   0.000   0.000
   5_xyz:  0.332  67.589   2.794   3.311   4.429   0.000   0.000   0.000
   5_adp:  0.332  67.589   2.794   3.311   4.429   0.000   0.000   0.000
   5_occ:  0.332  67.589   2.794   3.311   4.429   0.000   0.000   0.000
   5_bss:  0.321  63.592  -0.657  -0.263   0.920  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.494 0.5028  0.5570    58351.507
   1_bss:  50.531 0.5142  0.7397    56616.748
   1_xyz:  41.983 0.6179  0.8602    39538.318
   1_adp:  36.808 0.6804  0.9514    32472.741
   1_occ:  36.862 0.6797  0.9503    32581.606
   2_bss:  36.680 0.6818  0.8472    32312.852
   2_xyz:  25.476 0.8060  0.9731    16407.440
   2_adp:  22.677 0.8357  0.9899    13797.533
   2_occ:  22.713 0.8353  0.9891    13814.564
   3_bss:  22.715 0.8354  0.9402    13882.654
   3_xyz:  16.993 0.8897  0.9746     8531.071
   3_adp:  16.241 0.8965  0.9729     7989.439
   3_occ:  16.234 0.8966  0.9728     7986.841
   4_bss:  16.216 0.8967  0.9593     7974.248
   4_xyz:  15.327 0.9044  0.9622     7267.650
   4_adp:  14.899 0.9082  0.9593     7060.736
   4_occ:  14.881 0.9084  0.9593     7051.201
   5_bss:  14.880 0.9084  0.9594     7050.287
   5_xyz:  14.486 0.9117  0.9620     6807.466
   5_adp:  14.624 0.9106  0.9569     6886.984
   5_occ:  14.626 0.9106  0.9569     6888.807
   5_bss:  14.623 0.9106  0.9590     6883.684
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4474e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4474e+01
   1_xyz:   1.683  0.013  0.109 17.940  0.006  4.113   1.3899e-01
   1_adp:   1.683  0.013  0.109 17.940  0.006  4.113   1.3899e-01
   1_occ:   1.683  0.013  0.109 17.940  0.006  4.113   1.3899e-01
   2_bss:   1.683  0.013  0.109 17.940  0.006  4.113   1.3899e-01
   2_xyz:   1.133  0.009  0.077 16.335  0.004  4.134   7.4979e-02
   2_adp:   1.133  0.009  0.077 16.335  0.004  4.134   7.4979e-02
   2_occ:   1.133  0.009  0.077 16.335  0.004  4.134   7.4979e-02
   3_bss:   1.133  0.009  0.077 16.335  0.004  4.134   7.4979e-02
   3_xyz:   1.098  0.009  0.085 15.993  0.004  4.137   7.1174e-02
   3_adp:   1.098  0.009  0.085 15.993  0.004  4.137   7.1174e-02
   3_occ:   1.098  0.009  0.085 15.993  0.004  4.137   7.1174e-02
   4_bss:   1.098  0.009  0.085 15.993  0.004  4.137   7.1174e-02
   4_xyz:   1.011  0.008  0.080 15.527  0.003  4.128   6.3414e-02
   4_adp:   1.011  0.008  0.080 15.527  0.003  4.128   6.3414e-02
   4_occ:   1.011  0.008  0.080 15.527  0.003  4.128   6.3414e-02
   5_bss:   1.011  0.008  0.080 15.527  0.003  4.128   6.3414e-02
   5_xyz:   1.063  0.009  0.084 15.279  0.004  4.132   6.8217e-02
   5_adp:   1.063  0.009  0.084 15.279  0.004  4.132   6.8217e-02
   5_occ:   1.063  0.009  0.084 15.279  0.004  4.132   6.8217e-02
   5_bss:   1.063  0.009  0.084 15.279  0.004  4.132   6.8217e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0633e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0633e+00
   1_xyz:  14.227  0.167  0.452 86.074  0.041  2.271   1.0529e-01
   1_adp:  14.227  0.167  0.452 86.074  0.041  2.271   1.0529e-01
   1_occ:  14.227  0.167  0.452 86.074  0.041  2.271   1.0529e-01
   2_bss:  14.227  0.167  0.452 86.074  0.041  2.271   1.0529e-01
   2_xyz:   7.164  0.068  0.260 88.345  0.023  2.212   5.3717e-02
   2_adp:   7.164  0.068  0.260 88.345  0.023  2.212   5.3717e-02
   2_occ:   7.164  0.068  0.260 88.345  0.023  2.212   5.3717e-02
   3_bss:   7.164  0.068  0.260 88.345  0.023  2.212   5.3717e-02
   3_xyz:   8.819  0.053  0.386 81.867  0.047  2.376   4.7346e-02
   3_adp:   8.819  0.053  0.386 81.867  0.047  2.376   4.7346e-02
   3_occ:   8.819  0.053  0.386 81.867  0.047  2.376   4.7346e-02
   4_bss:   8.819  0.053  0.386 81.867  0.047  2.376   4.7346e-02
   4_xyz:   7.399  0.039  0.393 82.911  0.038  2.439   3.8744e-02
   4_adp:   7.399  0.039  0.393 82.911  0.038  2.439   3.8744e-02
   4_occ:   7.399  0.039  0.393 82.911  0.038  2.439   3.8744e-02
   5_bss:   7.399  0.039  0.393 82.911  0.038  2.439   3.8744e-02
   5_xyz:   7.544  0.050  0.437 81.454  0.040  2.376   4.2989e-02
   5_adp:   7.544  0.050  0.437 81.454  0.040  2.376   4.2989e-02
   5_occ:   7.544  0.050  0.437 81.454  0.040  2.376   4.2989e-02
   5_bss:   7.544  0.050  0.437 81.454  0.040  2.376   4.2989e-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: 103.26   0.00  11.67  69.23   0.00   8.75 103.26   0.00  27.59
   1_occ: 103.26   0.00  11.67  69.23   0.00   8.75 103.26   0.00  27.59
   2_bss: 103.26   0.00  11.67  69.23   0.00   8.75 103.26   0.00  27.59
   2_xyz: 103.26   0.00  11.67  69.23   0.00   8.75 103.26   0.00  27.59
   2_adp: 102.09   0.00  11.69  83.40   0.00   7.88 102.09   0.00  32.44
   2_occ: 102.09   0.00  11.69  83.40   0.00   7.88 102.09   0.00  32.44
   3_bss: 102.09   0.00  11.69  83.40   0.00   7.88 102.09   0.00  32.44
   3_xyz: 102.09   0.00  11.69  83.40   0.00   7.88 102.09   0.00  32.44
   3_adp:  94.03   0.00  12.63  78.99   0.00   7.99  94.03   0.00  37.94
   3_occ:  94.03   0.00  12.63  78.99   0.00   7.99  94.03   0.00  37.94
   4_bss:  94.03   0.00  12.63  78.99   0.00   7.99  94.03   0.00  37.94
   4_xyz:  94.03   0.00  12.63  78.99   0.00   7.99  94.03   0.00  37.94
   4_adp:  88.34   0.00  11.85  78.36   0.00   7.58  88.34   0.66  35.10
   4_occ:  88.34   0.00  11.85  78.36   0.00   7.58  88.34   0.66  35.10
   5_bss:  88.34   0.00  11.85  78.36   0.00   7.58  88.34   0.66  35.10
   5_xyz:  88.34   0.00  11.85  78.36   0.00   7.58  88.34   0.66  35.10
   5_adp:  87.64   0.00  11.83  78.79   0.00   7.52  87.64   0.83  35.31
   5_occ:  87.64   0.00  11.83  78.79   0.00   7.52  87.64   0.83  35.31
   5_bss:  91.22   3.57  15.40  82.37   3.57  11.09  91.22   4.40  38.88
------------------------------------------------------------------------
 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:    1.262    0.019    0.413
   1_adp:    1.262    0.019    0.413
   1_occ:    1.262    0.019    0.413
   2_bss:    1.262    0.019    0.413
   2_xyz:    1.662    0.015    0.561
   2_adp:    1.662    0.015    0.561
   2_occ:    1.662    0.015    0.561
   3_bss:    1.662    0.015    0.561
   3_xyz:    1.642    0.032    0.616
   3_adp:    1.642    0.032    0.616
   3_occ:    1.642    0.032    0.616
   4_bss:    1.642    0.032    0.616
   4_xyz:    1.769    0.026    0.639
   4_adp:    1.769    0.026    0.639
   4_occ:    1.769    0.026    0.639
   5_bss:    1.769    0.026    0.639
   5_xyz:    1.812    0.025    0.654
   5_adp:    1.812    0.025    0.654
   5_occ:    1.812    0.025    0.654
   5_bss:    1.812    0.025    0.654
------------------------------------------------------------------------

CPU time actual refinement: 319.03


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_932/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_932/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_932/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_932/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_932/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 318.87 
  Macro-tasks:
    bulk solvent and scale       = 41.70  
    individual site refinement   = 127.63 
    weights calculation          = 32.46  
    collect and process          = 6.44   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 208.35 
  Micro-tasks:
    mask                            = 1.80   
    f_calc                          = 95.57  
    alpha_beta                      = 8.07   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 106.19 
    fmodel                         = 7.31   
    r_factors                      = 0.24   
    phase_errors                   = 10.56  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 231.16 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.542 micro seconds
Total CPU time: 5.55 minutes
from_scatterers_fft:    631 calls, 95.21 s
gradients_fft:          576 calls, 93.04 s

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

# Date 2008-01-16 Time 02:46:36 PST -0800 (1200480396.80 s)
Start R-work = 0.4640, R-free = 0.4509 (no bulk solvent and anisotropic scale)
Final R-work = 0.1345, R-free = 0.1796 (no bulk solvent and anisotropic scale)

Start R-work = 0.4560, R-free = 0.4394
Final R-work = 0.1183, R-free = 0.1646