# Date 2008-01-16 Time 01:44:20 PST -0800 (1200476660.25 s)
#phil __OFF__

Command line arguments: "../533.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3039
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 533

-------------------------------------------------------------------------------
  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: (69.8988, 46.6953, 86.39, 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: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.6953, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9392 1.99009
Completeness in resolution range: 0.981314
Completeness with d_max=infinity: 0.978178

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9392
                             d_min =   1.9901

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: (69.8988, 46.6953, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9392 1.99009
Completeness in resolution range: 0.981314
Completeness with d_max=infinity: 0.978178

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9396 -  4.2575 [2096/2119]  1886   210  10.0%
  bin  2:  4.2575 -  3.3923 [2024/2044]  1822   202  10.0%
  bin  3:  3.3923 -  2.9673 [1989/2008]  1791   198  10.0%
  bin  4:  2.9673 -  2.6978 [1953/1983]  1757   196  10.0%
  bin  5:  2.6978 -  2.5054 [1971/1990]  1774   197  10.0%
  bin  6:  2.5054 -  2.3583 [1950/1975]  1753   197  10.1%
  bin  7:  2.3583 -  2.2406 [1927/1955]  1735   192  10.0%
  bin  8:  2.2406 -  2.1433 [1933/1969]  1739   194  10.0%
  bin  9:  2.1433 -  2.0610 [1921/1963]  1731   190   9.9%
  bin 10:  2.0610 -  1.9901 [1825/1956]  1642   183  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_533/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 11
        2.42 -     3.04: 2217
        3.04 -     3.66: 4688
        3.66 -     4.28: 9110
        4.28 -     4.90: 12378
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.229 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  2.258 3.040 -x+1,y+1/2,-z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 28399 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_533/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_533/model_refine_001.geo

CPU time processing inputs: 9.04


============================ 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 = 69.89875 46.69535 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4127   r_free= 0.3988   ksol= 0.00   Bsol= 0.00   scale= 0.837    |
|                                                                             |
| 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:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.199325                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7482 0.99   1371  152 0.3525 0.3378      6.4927      6.4511|
|  2:  4.7482 -  3.7891 0.99   1299  146 0.3033 0.3020       6.576      6.5756|
|  3:  3.7891 -  3.3161 0.99   1286  141 0.3434 0.3228      6.4987      6.5088|
|  4:  3.3161 -  3.0156 0.99   1282  142 0.3860 0.3565      6.4151      6.3262|
|  5:  3.0156 -  2.8010 0.99   1259  141 0.4288 0.4526      6.2822      6.3214|
|  6:  2.8010 -  2.6368 0.99   1268  141 0.4310 0.4982      6.2104      6.2196|
|  7:  2.6368 -  2.5054 0.99   1265  140 0.4566 0.4314      6.1899      6.1397|
|  8:  2.5054 -  2.3968 0.98   1248  137 0.4643 0.4448       6.143      6.1458|
|  9:  2.3968 -  2.3049 0.98   1241  141 0.4555 0.4534      6.0655      6.0474|
| 10:  2.3049 -  2.2256 1.00   1243  138 0.4810 0.4379      6.1055      6.0134|
| 11:  2.2256 -  2.1562 0.97   1249  139 0.4759 0.3929      6.0211      5.9372|
| 12:  2.1562 -  2.0947 0.98   1241  138 0.4713 0.4470       5.972      5.9924|
| 13:  2.0947 -  2.0397 0.99   1246  137 0.4778 0.4727      5.8828      5.8715|
| 14:  2.0397 -  1.9901 0.91   1132  126 0.4910 0.4544      5.8392      5.7245|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9396 -  4.7482  1371   152  0.74  30.77   0.82     0.77      57514.06|
|  2:  4.7482 -  3.7891  1299   146  0.80  26.49   0.93     0.84      65474.54|
|  3:  3.7891 -  3.3161  1286   141  0.74  31.66   0.90     0.82      66070.19|
|  4:  3.3161 -  3.0156  1282   142  0.69  36.59   0.85     0.74      60000.13|
|  5:  3.0156 -  2.8010  1259   141  0.58  45.12   0.79     0.65      56609.55|
|  6:  2.8010 -  2.6368  1268   141  0.55  47.89   0.77     0.61      53555.38|
|  7:  2.6368 -  2.5054  1265   140  0.53  49.85   0.77     0.60      50404.39|
|  8:  2.5054 -  2.3968  1248   137  0.53  49.45   0.78     0.61      44577.79|
|  9:  2.3968 -  2.3049  1241   141  0.57  46.84   0.76     0.63      37085.67|
| 10:  2.3049 -  2.2256  1243   138  0.59  45.19   0.79     0.66      31617.31|
| 11:  2.2256 -  2.1562  1249   139  0.59  45.22   0.78     0.66      29022.34|
| 12:  2.1562 -  2.0947  1241   138  0.54  48.89   0.81     0.63      29891.07|
| 13:  2.0947 -  2.0397  1246   137  0.51  51.24   0.78     0.59      27261.26|
| 14:  2.0397 -  1.9901  1132   126  0.53  50.12   0.75     0.56      21516.53|
|alpha:            min =        0.56 max =            0.84 mean =         0.67|
|beta:             min =    21516.53 max =        66070.19 mean =     45454.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.61|
|phase err.(work): min =        0.00 max =           90.00 mean =        43.03|
|phase err.(test): min =        0.00 max =           89.90 mean =        43.19|
|-----------------------------------------------------------------------------|

============================== 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 = 6.231612              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 72.934   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.495313              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.753   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      167 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      683 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1514 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2658 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3931 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5119 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6575 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7765 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.546 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.717 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.790)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.790)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4226   r_free= 0.4095   ksol= 0.00   Bsol= 0.00   scale= 0.804    |
|                                                                             |
| 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:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.206720                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4048   r_free= 0.3908   ksol= 0.36   Bsol= 20.00   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.36,8.56,8.18,0.00,0.00,0.00); trace/3= 8.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.192933                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.880392              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.980   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.497501              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.554   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4048      final r-factor (work) = 0.2902          |
| start r-factor (free) = 0.3908      final r-factor (free) = 0.3100          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 71.8413 = 5.88 * 0.50 * 6.2225 + 1.00 * 53.5460                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.7848 = 5.88 * 0.50 * 6.0126 + 1.00 * 0.1065                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2902      final r-factor (work) = 0.2137          |
| start r-factor (free) = 0.3100      final r-factor (free) = 0.2436          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0060 = 0.50 * 1.00 * 6.0126 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8824 = 0.50 * 1.00 * 5.7728 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.790)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    58.42   10.17    None  None   None       |
|    all(noH): 2823   0      0.00    58.42   10.17    None  None   None       |
|    Sol.    : 438    0      0.00    56.56   27.49    None  None   None       |
|    Mac.    : 2385   0      0.00    58.42   6.99     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 -   5.842: 1343   |   5:    29.208 -  35.050:  104        |
|      1:     5.842 -  11.683:  734   |   6:    35.050 -  40.891:   79        |
|      2:    11.683 -  17.525:  231   |   7:    40.891 -  46.733:   41        |
|      3:    17.525 -  23.366:  138   |   8:    46.733 -  52.574:   18        |
|      4:    23.366 -  29.208:  132   |   9:    52.574 -  58.416:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2137 r_free = 0.2436             target_work(ml) = 5.659         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2130 r_free = 0.2430             target_work(ml) = 5.657         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2130   r_free= 0.2430   ksol= 0.36   Bsol= 20.00   scale= 1.093   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.36,8.56,8.18,0.00,0.00,0.00); trace/3= 8.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.656802                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2067   r_free= 0.2360   ksol= 0.34   Bsol= 34.58   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.90,4.59,5.24,0.00,0.00,0.00); trace/3= 4.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.652316                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.305003              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.696   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.249655              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.237  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2067      final r-factor (work) = 0.1455          |
| start r-factor (free) = 0.2360      final r-factor (free) = 0.1803          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7809 = 2.31 * 0.50 * 5.7916 + 1.00 * 0.1060                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3698 = 2.31 * 0.50 * 5.4769 + 1.00 * 0.0576                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1455      final r-factor (work) = 0.1349          |
| start r-factor (free) = 0.1803      final r-factor (free) = 0.1721          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3776 = 0.25 * 1.00 * 5.4769 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3321 = 0.25 * 1.00 * 5.2967 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.790)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    60.38   10.49    None  None   None       |
|    all(noH): 2823   0      0.00    60.38   10.49    None  None   None       |
|    Sol.    : 438    0      0.71    57.85   30.22    None  None   None       |
|    Mac.    : 2385   0      0.00    60.38   6.87     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.039: 1459   |   5:    30.192 -  36.231:  115        |
|      1:     6.039 -  12.077:  647   |   6:    36.231 -  42.269:  105        |
|      2:    12.077 -  18.116:  218   |   7:    42.269 -  48.308:   51        |
|      3:    18.116 -  24.154:   96   |   8:    48.308 -  54.346:   19        |
|      4:    24.154 -  30.192:  110   |   9:    54.346 -  60.385:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1349 r_free = 0.1721             target_work(ml) = 5.274         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1348 r_free = 0.1720             target_work(ml) = 5.273         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1348   r_free= 0.1720   ksol= 0.34   Bsol= 34.58   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.90,4.59,5.24,0.00,0.00,0.00); trace/3= 4.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.273353                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1347   r_free= 0.1719   ksol= 0.32   Bsol= 34.58   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.30,3.74,4.79,0.00,0.00,0.00); trace/3= 3.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.273470                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.625158              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.641  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.236281              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.916  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1347      final r-factor (work) = 0.1204          |
| start r-factor (free) = 0.1719      final r-factor (free) = 0.1590          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3635 = 1.63 * 0.50 * 5.2991 + 1.00 * 0.0576                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2939 = 1.63 * 0.50 * 5.2172 + 1.00 * 0.0545                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1204      final r-factor (work) = 0.1168          |
| start r-factor (free) = 0.1590      final r-factor (free) = 0.1586          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.6767 = 2.24 * 1.00 * 5.2172 + 1.00 * 0.0097                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.5682 = 2.24 * 1.00 * 5.1670 + 1.00 * 0.0133                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.790)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.01   10.95    None  None   None       |
|    all(noH): 2823   0      0.00    66.01   10.95    None  None   None       |
|    Sol.    : 438    0      0.42    61.36   32.60    None  None   None       |
|    Mac.    : 2385   0      0.00    66.01   6.97     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.601: 1550   |   5:    33.006 -  39.607:  103        |
|      1:     6.601 -  13.202:  581   |   6:    39.607 -  46.208:  105        |
|      2:    13.202 -  19.803:  212   |   7:    46.208 -  52.809:   53        |
|      3:    19.803 -  26.405:   96   |   8:    52.809 -  59.410:   21        |
|      4:    26.405 -  33.006:   98   |   9:    59.410 -  66.011:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1168 r_free = 0.1586             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1168 r_free = 0.1585             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1585   ksol= 0.32   Bsol= 34.58   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.30,3.74,4.79,0.00,0.00,0.00); trace/3= 3.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.168013                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1585   ksol= 0.32   Bsol= 34.58   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.30,3.74,4.79,0.00,0.00,0.00); trace/3= 3.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.167629                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.826761              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.292  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 16.298216             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.107   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1168      final r-factor (work) = 0.1095          |
| start r-factor (free) = 0.1585      final r-factor (free) = 0.1565          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3571 = 2.83 * 0.50 * 5.1667 + 1.00 * 0.0545                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3329 = 2.83 * 0.50 * 5.1394 + 1.00 * 0.0690                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1095      final r-factor (work) = 0.1083          |
| start r-factor (free) = 0.1565      final r-factor (free) = 0.1569          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 83.7778 = 16.30 * 1.00 * 5.1394 + 1.00 * 0.0147                             |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 83.5946 = 16.30 * 1.00 * 5.1262 + 1.00 * 0.0469                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.790)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.71   11.34    None  None   None       |
|    all(noH): 2823   0      0.00    82.71   11.34    None  None   None       |
|    Sol.    : 438    0      0.00    78.05   34.55    None  None   None       |
|    Mac.    : 2385   0      0.00    82.71   7.08     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 -   8.271: 1791   |   5:    41.355 -  49.625:   91        |
|      1:     8.271 -  16.542:  470   |   6:    49.625 -  57.896:   61        |
|      2:    16.542 -  24.813:  146   |   7:    57.896 -  66.167:   30        |
|      3:    24.813 -  33.084:  122   |   8:    66.167 -  74.438:   12        |
|      4:    33.084 -  41.355:   97   |   9:    74.438 -  82.709:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1083 r_free = 0.1569             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1082 r_free = 0.1568             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1082   r_free= 0.1568   ksol= 0.32   Bsol= 34.58   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.30,3.74,4.79,0.00,0.00,0.00); trace/3= 3.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.126673                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1084   r_free= 0.1567   ksol= 0.31   Bsol= 34.58   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.43,3.77,4.92,0.00,0.00,0.00); trace/3= 4.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.127057                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.363553              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 159.147  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.961628              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.602   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1084      final r-factor (work) = 0.1115          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5641 = 1.36 * 0.50 * 5.1266 + 1.00 * 0.0690                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5563 = 1.36 * 0.50 * 5.1403 + 1.00 * 0.0517                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1115      final r-factor (work) = 0.1114          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1578          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.1011 = 1.96 * 1.00 * 5.1403 + 1.00 * 0.0176                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.1068 = 1.96 * 1.00 * 5.1448 + 1.00 * 0.0146                              |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.790)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.50   11.21    None  None   None       |
|    all(noH): 2823   0      0.00    84.50   11.21    None  None   None       |
|    Sol.    : 438    0      0.00    79.23   34.20    None  None   None       |
|    Mac.    : 2385   0      0.00    84.50   6.99     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 -   8.450: 1817   |   5:    42.250 -  50.700:   88        |
|      1:     8.450 -  16.900:  456   |   6:    50.700 -  59.150:   57        |
|      2:    16.900 -  25.350:  146   |   7:    59.150 -  67.601:   23        |
|      3:    25.350 -  33.800:  125   |   8:    67.601 -  76.051:   10        |
|      4:    33.800 -  42.250:   98   |   9:    76.051 -  84.501:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1114 r_free = 0.1578             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1113 r_free = 0.1578             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1578   ksol= 0.31   Bsol= 34.58   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.43,3.77,4.92,0.00,0.00,0.00); trace/3= 4.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.144166                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7482 0.99   1371  152 0.0997 0.1266      5.3894       5.513|
|  2:  4.7482 -  3.7891 0.99   1299  146 0.0847 0.1119      5.4288      5.6099|
|  3:  3.7891 -  3.3161 0.99   1286  141 0.1031 0.1427      5.4632      5.8158|
|  4:  3.3161 -  3.0156 0.99   1282  142 0.1174 0.1604      5.4422      5.6224|
|  5:  3.0156 -  2.8010 0.99   1259  141 0.1280 0.1760      5.3264      5.5574|
|  6:  2.8010 -  2.6368 0.99   1268  141 0.1201 0.1833      5.2148      5.4923|
|  7:  2.6368 -  2.5054 0.99   1265  140 0.1254 0.1593      5.1733       5.345|
|  8:  2.5054 -  2.3968 0.98   1248  137 0.1179 0.1826      5.0999      5.4088|
|  9:  2.3968 -  2.3049 0.98   1241  141 0.1177 0.1755      5.0487      5.2529|
| 10:  2.3049 -  2.2256 1.00   1243  138 0.1115 0.1699      4.9743      5.2575|
| 11:  2.2256 -  2.1562 0.97   1249  139 0.1146 0.1671      4.9419      5.2327|
| 12:  2.1562 -  2.0947 0.98   1241  138 0.1134 0.1725      4.8892      5.2484|
| 13:  2.0947 -  2.0397 0.99   1246  137 0.1156 0.1661       4.828      5.0601|
| 14:  2.0397 -  1.9901 0.91   1132  126 0.1058 0.1858      4.6967      4.9916|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9396 -  4.7482  1371   152  0.94   9.17   0.98     0.95       7235.54|
|  2:  4.7482 -  3.7891  1299   146  0.95   7.76   1.02     1.01       8820.00|
|  3:  3.7891 -  3.3161  1286   141  0.94  10.81   1.04     1.03      10060.28|
|  4:  3.3161 -  3.0156  1282   142  0.93  12.99   1.01     1.00      10080.62|
|  5:  3.0156 -  2.8010  1259   141  0.90  15.71   1.00     0.97       8480.28|
|  6:  2.8010 -  2.6368  1268   141  0.90  15.90   0.99     0.96       7166.46|
|  7:  2.6368 -  2.5054  1265   140  0.90  15.72   0.99     0.96       6319.06|
|  8:  2.5054 -  2.3968  1248   137  0.91  15.00   1.00     0.97       5537.49|
|  9:  2.3968 -  2.3049  1241   141  0.91  15.70   1.01     0.98       5234.14|
| 10:  2.3049 -  2.2256  1243   138  0.90  15.37   1.00     0.96       4402.84|
| 11:  2.2256 -  2.1562  1249   139  0.90  16.04   1.00     0.97       4416.05|
| 12:  2.1562 -  2.0947  1241   138  0.91  15.47   1.02     1.00       3989.11|
| 13:  2.0947 -  2.0397  1246   137  0.91  15.71   1.00     0.98       3521.47|
| 14:  2.0397 -  1.9901  1132   126  0.91  15.07   0.99     0.95       2745.77|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2745.77 max =        10080.62 mean =      6343.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.97|
|phase err.(test): min =        0.00 max =           88.67 mean =        13.63|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1577   ksol= 0.32   Bsol= 44.33   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.61,-0.29,0.90,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.143755                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1577   ksol= 0.32   Bsol= 44.33   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.61,-0.29,0.90,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.143755                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7482 0.99   1371  152 0.1000 0.1269      5.3919      5.5158|
|  2:  4.7482 -  3.7891 0.99   1299  146 0.0851 0.1121      5.4321      5.6138|
|  3:  3.7891 -  3.3161 0.99   1286  141 0.1034 0.1431      5.4647      5.8171|
|  4:  3.3161 -  3.0156 0.99   1282  142 0.1171 0.1602      5.4411      5.6204|
|  5:  3.0156 -  2.8010 0.99   1259  141 0.1277 0.1759      5.3241      5.5556|
|  6:  2.8010 -  2.6368 0.99   1268  141 0.1198 0.1826      5.2125      5.4901|
|  7:  2.6368 -  2.5054 0.99   1265  140 0.1252 0.1592      5.1711       5.343|
|  8:  2.5054 -  2.3968 0.98   1248  137 0.1178 0.1824      5.0987       5.407|
|  9:  2.3968 -  2.3049 0.98   1241  141 0.1176 0.1756      5.0481      5.2533|
| 10:  2.3049 -  2.2256 1.00   1243  138 0.1115 0.1699      4.9741      5.2564|
| 11:  2.2256 -  2.1562 0.97   1249  139 0.1145 0.1671       4.941      5.2323|
| 12:  2.1562 -  2.0947 0.98   1241  138 0.1134 0.1722      4.8888      5.2474|
| 13:  2.0947 -  2.0397 0.99   1246  137 0.1157 0.1661      4.8272       5.059|
| 14:  2.0397 -  1.9901 0.91   1132  126 0.1058 0.1855      4.6953      4.9898|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9396 -  4.7482  1371   152  0.94   9.22   0.98     0.95       7288.25|
|  2:  4.7482 -  3.7891  1299   146  0.95   7.82   1.02     1.01       8872.77|
|  3:  3.7891 -  3.3161  1286   141  0.94  10.85   1.04     1.03      10094.14|
|  4:  3.3161 -  3.0156  1282   142  0.93  12.97   1.01     1.00      10060.71|
|  5:  3.0156 -  2.8010  1259   141  0.90  15.69   1.00     0.98       8446.68|
|  6:  2.8010 -  2.6368  1268   141  0.90  15.86   0.99     0.96       7134.28|
|  7:  2.6368 -  2.5054  1265   140  0.90  15.68   0.99     0.96       6287.16|
|  8:  2.5054 -  2.3968  1248   137  0.91  14.98   1.00     0.98       5521.33|
|  9:  2.3968 -  2.3049  1241   141  0.91  15.68   1.01     0.98       5225.35|
| 10:  2.3049 -  2.2256  1243   138  0.90  15.37   1.01     0.96       4400.04|
| 11:  2.2256 -  2.1562  1249   139  0.90  16.02   1.00     0.97       4408.07|
| 12:  2.1562 -  2.0947  1241   138  0.91  15.44   1.02     1.00       3979.75|
| 13:  2.0947 -  2.0397  1246   137  0.91  15.69   1.00     0.99       3509.90|
| 14:  2.0397 -  1.9901  1132   126  0.91  15.04   0.99     0.95       2734.69|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2734.69 max =        10094.14 mean =      6340.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.75 mean =        13.96|
|phase err.(test): min =        0.00 max =           88.74 mean =        13.61|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.790)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      4.07    88.58   15.29    None  None   None       |
|    all(noH): 2823   0      4.07    88.58   15.29    None  None   None       |
|    Sol.    : 438    0      4.07    83.31   38.28    None  None   None       |
|    Mac.    : 2385   0      4.07    88.58   11.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     4.075 -  12.525: 1817   |   5:    46.325 -  54.775:   88        |
|      1:    12.525 -  20.975:  456   |   6:    54.775 -  63.225:   57        |
|      2:    20.975 -  29.425:  146   |   7:    63.225 -  71.675:   23        |
|      3:    29.425 -  37.875:  125   |   8:    71.675 -  80.125:   10        |
|      4:    37.875 -  46.325:   98   |   9:    80.125 -  88.575:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 309         
Filter by distance & map next to the model:
   mapped sites are within: 0.292 - 3.926
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 299 from: 309
   mapped sites are within: 0.716 - 3.926

peak=   11.302 closest distance to " CB  VAL A 230 " =    1.443
peak=    8.885 closest distance to " CG2 VAL A 296 " =    1.261
peak=    6.252 closest distance to " CG  LEU A   5 " =    1.200
peak=    6.043 closest distance to " NH2 ARG A  56 " =    2.183
peak=    5.981 closest distance to " CG  PRO A  54 " =    1.317
peak=    5.852 closest distance to " CD2 LEU A   5 " =    1.163
peak=    5.482 closest distance to " NE2 GLN A  11 " =    1.156
peak=    5.465 closest distance to " CG  LEU A 228 " =    1.144
peak=    5.315 closest distance to " CB  PRO A  54 " =    1.025
peak=    5.223 closest distance to " CB  GLN A 223 " =    1.457
peak=    5.206 closest distance to " O   HOH Z 142 " =    1.845
peak=    5.107 closest distance to " CB  ARG A 275 " =    0.933
peak=    5.017 closest distance to " CB  GLN A 183 " =    1.264
peak=    4.993 closest distance to " CG  PRO A 213 " =    1.242
peak=    4.822 closest distance to " CB  VAL A 296 " =    1.031
peak=    4.766 closest distance to " CG  PRO A 198 " =    1.233
peak=    4.702 closest distance to " O   HOH Z 232 " =    2.325
peak=    4.636 closest distance to " O   HOH Z 427 " =    2.962
peak=    4.633 closest distance to " O   HOH Z 209 " =    2.283
peak=    4.563 closest distance to " O   HOH Z 126 " =    1.943
peak=    4.531 closest distance to " CG  PRO A 243 " =    1.133
peak=    4.529 closest distance to " ND2 ASN A 187 " =    1.493
peak=    4.518 closest distance to " OG ASER A 258 " =    3.095
peak=    4.496 closest distance to " CB  VAL A 230 " =    1.150
peak=    4.495 closest distance to " CB  SER A  63 " =    1.281
peak=    4.422 closest distance to " O   HOH Z 369 " =    2.159
peak=    4.402 closest distance to " O   HOH Z  61 " =    1.689
peak=    4.395 closest distance to " O   SER A  87 " =    2.331
peak=    4.374 closest distance to " O   HOH Z  78 " =    1.707
peak=    4.357 closest distance to " O   HOH Z 346 " =    1.615
peak=    4.336 closest distance to " O   HOH Z 272 " =    1.857
peak=    4.333 closest distance to " O   HOH Z 298 " =    1.767
peak=    4.331 closest distance to " O   HOH Z 203 " =    1.702
peak=    4.306 closest distance to " C   PRO A 198 " =    1.518
peak=    4.300 closest distance to " CB  SER A   3 " =    1.292
peak=    4.292 closest distance to " O   HOH Z  43 " =    1.969
peak=    4.277 closest distance to " CB  GLU A 128 " =    0.987
peak=    4.256 closest distance to " O   HOH Z 189 " =    2.873
peak=    4.219 closest distance to " CB  ASN A 148 " =    1.326
peak=    4.185 closest distance to " O   HOH Z 236 " =    2.028
peak=    4.134 closest distance to " CB  VAL A 265 " =    1.305
peak=    4.126 closest distance to " O   HOH Z 193 " =    1.668
peak=    4.096 closest distance to " O   HOH Z 368 " =    2.128
peak=    4.094 closest distance to " CZ  PHE A 218 " =    1.122
peak=    4.086 closest distance to " CG1BVAL A  72 " =    1.581
peak=    4.074 closest distance to " CB  GLU A 152 " =    1.250
peak=    4.068 closest distance to " CB  TRP A 266 " =    1.007
peak=    4.058 closest distance to " OD1 ASN A  69 " =    2.559
peak=    4.057 closest distance to " CA  TYR A  30 " =    0.979
peak=    4.029 closest distance to " CB  ARG A  79 " =    1.388
peak=    4.007 closest distance to " O   HOH Z 261 " =    1.963
peak=    4.006 closest distance to " CA  PHE A 283 " =    1.066
peak=    3.998 closest distance to " O   HOH Z  66 " =    2.241
peak=    3.967 closest distance to " O   HOH Z 126 " =    1.977
peak=    3.965 closest distance to " N   ASN A  39 " =    1.171
peak=    3.963 closest distance to " O   HOH Z 234 " =    3.587
peak=    3.951 closest distance to " O   HOH Z 403 " =    1.692
peak=    3.942 closest distance to " O   HOH Z 248 " =    1.592
peak=    3.922 closest distance to " CA  VAL A  41 " =    0.716
peak=    3.920 closest distance to " CB  ASN A 142 " =    1.088
peak=    3.914 closest distance to " CG2 VAL A 257 " =    0.817
peak=    3.910 closest distance to " O   HOH Z 124 " =    1.373
peak=    3.908 closest distance to " O   HOH Z   9 " =    2.226
peak=    3.903 closest distance to " O   HOH Z 313 " =    1.784
peak=    3.889 closest distance to " CB  VAL A 202 " =    1.653
peak=    3.884 closest distance to " CD2 LEU A 228 " =    1.133
peak=    3.879 closest distance to " O   HOH Z 303 " =    2.114
peak=    3.866 closest distance to " O   HOH Z 158 " =    3.169
peak=    3.856 closest distance to " CB  ALA A 248 " =    1.476
peak=    3.848 closest distance to " CB  ALA A   9 " =    1.554
peak=    3.841 closest distance to " O   HOH Z 423 " =    1.754
peak=    3.822 closest distance to " CB  GLU A 277 " =    3.568
peak=    3.814 closest distance to " O   HOH Z  59 " =    1.817
peak=    3.810 closest distance to " O   HOH Z 402 " =    1.381
peak=    3.794 closest distance to " O   HOH Z 261 " =    1.532
peak=    3.789 closest distance to " CD BLYS A 290 " =    1.101
peak=    3.783 closest distance to " CB  LEU A 143 " =    1.174
peak=    3.773 closest distance to " CB  THR A 157 " =    1.098
peak=    3.765 closest distance to " O   HOH Z 411 " =    3.732
peak=    3.745 closest distance to " O   HOH Z 371 " =    2.935
peak=    3.738 closest distance to " O   HOH Z  54 " =    2.438
peak=    3.737 closest distance to " CG  ARG A  66 " =    2.764
peak=    3.734 closest distance to " CB  TRP A 179 " =    1.345
peak=    3.727 closest distance to " CB  ASN A  39 " =    0.913
peak=    3.721 closest distance to " CB  ARG A 190 " =    1.628
peak=    3.712 closest distance to " O   HOH Z 425 " =    1.377
peak=    3.705 closest distance to " O   HOH Z 290 " =    1.012
peak=    3.683 closest distance to " OG BSER A 164 " =    2.162
peak=    3.682 closest distance to " CB  ALA A 291 " =    1.412
peak=    3.679 closest distance to " CB BVAL A  41 " =    1.226
peak=    3.664 closest distance to " O   HOH Z  44 " =    1.621
peak=    3.664 closest distance to " O   HOH Z 435 " =    2.019
peak=    3.656 closest distance to " O   HOH Z 353 " =    2.589
peak=    3.654 closest distance to " CB  ASP A 140 " =    0.935
peak=    3.650 closest distance to " CA  ALA A  21 " =    1.071
peak=    3.643 closest distance to " O   HOH Z 250 " =    1.391
peak=    3.639 closest distance to " CB  SER A 216 " =    0.801
peak=    3.629 closest distance to " CA  ASN A 215 " =    1.119
peak=    3.622 closest distance to " CG1 VAL A 153 " =    0.937
peak=    3.611 closest distance to " O   HOH Z  97 " =    1.992
peak=    3.606 closest distance to " CG  LEU A 167 " =    1.181
peak=    3.606 closest distance to " CD  ARG A 269 " =    1.017
peak=    3.603 closest distance to " NH1AARG A 145 " =    1.047
peak=    3.599 closest distance to " O   HOH Z 366 " =    2.902
peak=    3.573 closest distance to " CA  ALA A  51 " =    0.920
peak=    3.566 closest distance to " CB  ARG A  79 " =    0.881
peak=    3.563 closest distance to " O   HOH Z 145 " =    2.105
peak=    3.561 closest distance to " O   HOH Z 417 " =    3.113
peak=    3.560 closest distance to " O   HOH Z 214 " =    2.096
peak=    3.554 closest distance to " O   ASP A 124 " =    0.961
peak=    3.551 closest distance to " CE  LYS A  76 " =    0.864
peak=    3.550 closest distance to " CB  HIS A 108 " =    0.842
peak=    3.549 closest distance to " NZ  LYS A 117 " =    3.164
peak=    3.548 closest distance to " O   HOH Z  10 " =    1.752
peak=    3.547 closest distance to " CA  THR A 264 " =    0.730
peak=    3.547 closest distance to " CB  THR A  31 " =    1.636
peak=    3.544 closest distance to " CD1 LEU A 300 " =    1.304
peak=    3.542 closest distance to " O   HOH Z 392 " =    3.128
peak=    3.537 closest distance to " CA  ALA A 158 " =    1.318
peak=    3.534 closest distance to " CB  ARG A 139 " =    0.863
peak=    3.533 closest distance to " O   HOH Z 128 " =    2.032
peak=    3.532 closest distance to " CG1 ILE A  33 " =    1.326
peak=    3.532 closest distance to " CD  LYS A 166 " =    1.310
peak=    3.523 closest distance to " CA  ARG A  36 " =    1.019
peak=    3.523 closest distance to " O   HOH Z  85 " =    1.272
peak=    3.522 closest distance to " O   HOH Z  40 " =    1.421
peak=    3.522 closest distance to " OD2 ASP A 286 " =    2.735
peak=    3.521 closest distance to " O   HOH Z 280 " =    2.970
peak=    3.520 closest distance to " O   HOH Z 147 " =    1.722
peak=    3.518 closest distance to " CD2 TRP A 179 " =    1.400
peak=    3.518 closest distance to " CG  MET A 185 " =    1.264
peak=    3.517 closest distance to " CA  ASN A 127 " =    1.024
peak=    3.513 closest distance to " CA  LYS A 117 " =    1.239
peak=    3.509 closest distance to " N   PHE A 130 " =    1.315
peak=    3.506 closest distance to " O  BHOH Z 338 " =    2.432
peak=    3.503 closest distance to " O   HOH Z   3 " =    1.855
peak=    3.502 closest distance to " O   HOH Z 193 " =    1.643
peak=    3.501 closest distance to " O   HOH Z 345 " =    3.248
peak=    3.498 closest distance to " O   HOH Z 389 " =    1.783
peak=    3.482 closest distance to " O   HOH Z 193 " =    1.932
peak=    3.477 closest distance to " O   HOH Z 422 " =    2.631
peak=    3.472 closest distance to " O   HOH Z 263 " =    1.604
peak=    3.470 closest distance to " CB  SER A 273 " =    0.875
peak=    3.460 closest distance to " O   HOH Z  97 " =    2.561
peak=    3.457 closest distance to " CB  SER A 212 " =    1.188
peak=    3.456 closest distance to " O   HOH Z 172 " =    3.502
peak=    3.448 closest distance to " CG2 ILE A 120 " =    1.193
peak=    3.445 closest distance to " CB  GLN A  89 " =    1.351
peak=    3.443 closest distance to " O   HOH Z 344 " =    2.875
peak=    3.442 closest distance to " O   HOH Z 305 " =    3.586
peak=    3.440 closest distance to " CE1 TYR A 186 " =    1.342
peak=    3.439 closest distance to " O   HOH Z 180 " =    2.181
peak=    3.435 closest distance to " O   HOH Z 128 " =    2.147
peak=    3.434 closest distance to " O   HOH Z 145 " =    3.649
peak=    3.429 closest distance to " N   GLN A 278 " =    1.178
peak=    3.428 closest distance to " O   HOH Z 273 " =    2.736
peak=    3.428 closest distance to " O   HOH Z 227 " =    2.151
peak=    3.426 closest distance to " CB  VAL A 268 " =    0.812
peak=    3.426 closest distance to " NH2 ARG A 156 " =    1.106
peak=    3.423 closest distance to " O   HOH Z 112 " =    1.648
peak=    3.423 closest distance to " O   HOH Z 329 " =    3.926
peak=    3.423 closest distance to " O   HOH Z 407 " =    2.419
peak=    3.421 closest distance to " O   HOH Z 132 " =    2.591
peak=    3.419 closest distance to " O   HOH Z   1 " =    1.694
peak=    3.410 closest distance to " N   ARG A 156 " =    1.337
peak=    3.408 closest distance to " O   HOH Z 437 " =    1.877
peak=    3.403 closest distance to " CA  ARG A 195 " =    1.177
peak=    3.397 closest distance to " C   ILE A 106 " =    1.899
peak=    3.396 closest distance to " CA  LYS A 290 " =    1.185
peak=    3.392 closest distance to " CD1 LEU A 228 " =    2.018
peak=    3.389 closest distance to " CB  ASN A 110 " =    1.078
peak=    3.389 closest distance to " O   HOH Z 291 " =    1.540
peak=    3.388 closest distance to " O   HOH Z 417 " =    2.225
peak=    3.378 closest distance to " CD2 LEU A 297 " =    0.966
peak=    3.373 closest distance to " CG  GLN A  77 " =    2.387
peak=    3.371 closest distance to " ND2 ASN A 249 " =    0.845
peak=    3.370 closest distance to " O   HOH Z 380 " =    1.634
peak=    3.364 closest distance to " CA  TYR A  30 " =    1.074
peak=    3.358 closest distance to " CB  THR A  82 " =    1.354
peak=    3.354 closest distance to " O   HOH Z 368 " =    3.635
peak=    3.346 closest distance to " O   GLN A 278 " =    1.305
peak=    3.339 closest distance to " O   HOH Z 247 " =    1.352
peak=    3.339 closest distance to " O   HOH Z 258 " =    2.291
peak=    3.337 closest distance to " CB  LYS A 117 " =    1.243
peak=    3.336 closest distance to " CB  SER A  26 " =    1.677
peak=    3.329 closest distance to " O   HOH Z 337 " =    3.543
peak=    3.329 closest distance to " CG2 ILE A  20 " =    1.527
peak=    3.328 closest distance to " NH1BARG A 190 " =    2.115
peak=    3.323 closest distance to " O   HOH Z 251 " =    1.478
peak=    3.321 closest distance to " CB  TRP A 150 " =    1.443
peak=    3.320 closest distance to " O   HOH Z 148 " =    3.405
peak=    3.318 closest distance to " O   HOH Z 426 " =    1.685
peak=    3.318 closest distance to " NE2 GLN A  77 " =    3.210
peak=    3.317 closest distance to " CB  ASN A 215 " =    1.095
peak=    3.314 closest distance to " O   HOH Z 286 " =    2.457
peak=    3.311 closest distance to " O   TRP A 274 " =    1.875
peak=    3.310 closest distance to " CA  ASP A 162 " =    1.067
peak=    3.306 closest distance to " OE2 GLU A  53 " =    1.978
peak=    3.299 closest distance to " O   HOH Z 425 " =    2.057
peak=    3.293 closest distance to " CA  GLN A 194 " =    1.171
peak=    3.292 closest distance to " N   SER A 135 " =    1.379
peak=    3.291 closest distance to " O   HOH Z   1 " =    1.842
peak=    3.290 closest distance to " CA  ASP A 140 " =    1.202
peak=    3.289 closest distance to " O   HOH Z 109 " =    2.605
peak=    3.289 closest distance to " O   HOH Z 357 " =    1.949
peak=    3.289 closest distance to " CG2 THR A 221 " =    1.235
peak=    3.285 closest distance to " O   HOH Z 227 " =    1.620
peak=    3.284 closest distance to " NH2BARG A 145 " =    2.072
peak=    3.284 closest distance to " CG1 ILE A  49 " =    1.336
peak=    3.284 closest distance to " O   HOH Z 189 " =    2.747
peak=    3.283 closest distance to " CB  LEU A 255 " =    0.725
peak=    3.282 closest distance to " CD  LYS A 119 " =    1.399
peak=    3.282 closest distance to " CA  MET A 105 " =    1.001
peak=    3.280 closest distance to " ND2 ASN A 110 " =    1.736
peak=    3.278 closest distance to " CD  LYS A  76 " =    1.949
peak=    3.276 closest distance to " O   HOH Z  88 " =    2.905
peak=    3.275 closest distance to " CD1 LEU A  96 " =    0.747
peak=    3.274 closest distance to " CA  SER A 146 " =    1.796
peak=    3.274 closest distance to " CB  THR A  52 " =    0.908
peak=    3.272 closest distance to " CG1 ILE A 151 " =    1.007
peak=    3.271 closest distance to " O   LYS A 290 " =    2.403
peak=    3.271 closest distance to " O   HOH Z 245 " =    1.341
peak=    3.267 closest distance to " CA  ILE A 234 " =    0.805
peak=    3.267 closest distance to " NZ  LYS A  48 " =    1.265
peak=    3.266 closest distance to " CG1 VAL A 296 " =    1.213
peak=    3.266 closest distance to " O   HOH Z  92 " =    2.390
peak=    3.264 closest distance to " CA  ALA A 154 " =    1.034
peak=    3.264 closest distance to " O   HOH Z 234 " =    1.833
peak=    3.261 closest distance to " CD1 LEU A 261 " =    1.175
peak=    3.260 closest distance to " O   HOH Z 146 " =    1.440
peak=    3.258 closest distance to " O   HOH Z 222 " =    2.448
peak=    3.252 closest distance to " C   PHE A  59 " =    0.927
peak=    3.252 closest distance to " O   HOH Z 126 " =    1.509
peak=    3.251 closest distance to " N   SER A 271 " =    0.978
peak=    3.251 closest distance to " CB  GLN A  88 " =    1.180
peak=    3.247 closest distance to " CA  ALA A 291 " =    0.873
peak=    3.245 closest distance to " CG AARG A 275 " =    1.127
peak=    3.233 closest distance to " CB  LEU A 228 " =    1.334
peak=    3.230 closest distance to " O   HOH Z  21 " =    1.735
peak=    3.228 closest distance to " CA  MET A  40 " =    1.036
peak=    3.227 closest distance to " CZ3 TRP A 266 " =    1.124
peak=    3.227 closest distance to " CB  LEU A 300 " =    0.890
peak=    3.218 closest distance to " NH1 ARG A  14 " =    1.061
peak=    3.217 closest distance to " CB  ASN A 224 " =    0.998
peak=    3.213 closest distance to " CB  GLN A 205 " =    1.098
peak=    3.212 closest distance to " CB  LYS A 290 " =    0.990
peak=    3.212 closest distance to " O   HOH Z  48 " =    1.564
peak=    3.211 closest distance to " CD2 HIS A  81 " =    1.073
peak=    3.209 closest distance to " CZ  PHE A  38 " =    1.182
peak=    3.207 closest distance to " O   HOH Z 285 " =    2.885
peak=    3.207 closest distance to " CG2 THR A 294 " =    1.672
peak=    3.205 closest distance to " CB  GLN A 278 " =    0.932
peak=    3.199 closest distance to " O   HOH Z 336 " =    1.789
peak=    3.198 closest distance to " O   HOH Z 384 " =    3.164
peak=    3.198 closest distance to " CB  MET A  40 " =    0.793
peak=    3.198 closest distance to " O   ASN A  74 " =    1.642
peak=    3.192 closest distance to " O   HOH Z 173 " =    2.184
peak=    3.189 closest distance to " CB  PRO A  90 " =    1.196
peak=    3.179 closest distance to " CE1 HIS A 108 " =    1.131
peak=    3.177 closest distance to " CD2 LEU A 255 " =    1.616
peak=    3.175 closest distance to " CD1 ILE A  33 " =    1.666
peak=    3.175 closest distance to " O   ARG A  56 " =    2.782
peak=    3.174 closest distance to " O   HOH Z 359 " =    3.665
peak=    3.173 closest distance to " O   HOH Z 187 " =    2.328
peak=    3.173 closest distance to " O   ALA A   1 " =    1.670
peak=    3.172 closest distance to " CG  MET A 113 " =    1.061
peak=    3.166 closest distance to " CD1 ILE A 106 " =    0.962
peak=    3.166 closest distance to " O   HOH Z   2 " =    1.489
peak=    3.165 closest distance to " CB  MET A  47 " =    1.005
peak=    3.164 closest distance to " O   HOH Z  66 " =    2.108
peak=    3.164 closest distance to " CA  ALA A 233 " =    1.129
peak=    3.163 closest distance to " CB  ILE A  20 " =    1.426
peak=    3.157 closest distance to " O   HOH Z 325 " =    2.148
peak=    3.157 closest distance to " O   HOH Z 303 " =    1.658
peak=    3.152 closest distance to " O   ALA A 292 " =    1.743
peak=    3.150 closest distance to " CA  ARG A 102 " =    1.127
peak=    3.147 closest distance to " CG  GLN A 205 " =    0.802
peak=    3.146 closest distance to " O   HOH Z 409 " =    3.268
peak=    3.146 closest distance to " OD1BASN A 224 " =    2.242
peak=    3.146 closest distance to " O   HOH Z 279 " =    2.194
peak=    3.141 closest distance to " CD1 ILE A 263 " =    1.258
peak=    3.139 closest distance to " N   GLY A 133 " =    3.685
peak=    3.133 closest distance to " O   HOH Z 419 " =    1.879
peak=    3.130 closest distance to " CG  GLN A  88 " =    1.049
peak=    3.129 closest distance to " CA  LEU A 282 " =    1.151
peak=    3.129 closest distance to " OG  SER A  22 " =    2.791
peak=    3.127 closest distance to " C   ALA A 299 " =    0.927
peak=    3.127 closest distance to " CG  MET A 185 " =    1.040
peak=    3.119 closest distance to " CD2 TYR A  30 " =    0.944
peak=    3.119 closest distance to " CE AMET A  47 " =    1.504
peak=    3.096 closest distance to " OD2 ASP A 200 " =    1.388
peak=    3.089 closest distance to " CG  LYS A  76 " =    0.997
peak=    3.073 closest distance to " N   ALA A 256 " =    1.170
peak=    3.068 closest distance to " CG  ARG A 159 " =    0.935
peak=    3.054 closest distance to " CG  LEU A 281 " =    1.034
peak=    3.050 closest distance to " O   HOH Z  40 " =    2.377
peak=    3.048 closest distance to " O   HOH Z 423 " =    2.905
peak=    3.034 closest distance to " O   HOH Z 148 " =    2.143
peak=    3.014 closest distance to " O   HOH Z 424 " =    1.462

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.772 - 5.469
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 206
   mapped sites are within: 0.772 - 5.469

peak=   -4.882 closest distance to " CG2 VAL A 230 " =    0.772
peak=   -4.706 closest distance to " SG  CYS A 254 " =    3.343
peak=   -4.467 closest distance to " CD  ARG A 156 " =    2.024
peak=   -4.465 closest distance to " OG BSER A 134 " =    1.164
peak=   -4.445 closest distance to " O   HOH Z 266 " =    5.119
peak=   -4.250 closest distance to " CG  GLN A 223 " =    2.145
peak=   -4.187 closest distance to " CB  PHE A 192 " =    1.930
peak=   -4.178 closest distance to " CB  PRO A 243 " =    2.653
peak=   -4.120 closest distance to " CG2 VAL A 296 " =    1.618
peak=   -4.111 closest distance to " CD  GLN A  58 " =    1.164
peak=   -4.103 closest distance to " O   HOH Z 231 " =    2.105
peak=   -4.062 closest distance to " C   HIS A 108 " =    1.191
peak=   -4.036 closest distance to " O   VAL A  67 " =    2.613
peak=   -3.988 closest distance to " CB  ALA A 161 " =    2.573
peak=   -3.916 closest distance to " CB  ALA A 248 " =    2.055
peak=   -3.912 closest distance to " O   PRO A 163 " =    2.073
peak=   -3.910 closest distance to " O   HOH Z 351 " =    1.490
peak=   -3.905 closest distance to " O   HOH Z 166 " =    2.058
peak=   -3.890 closest distance to " O   HOH Z 114 " =    2.978
peak=   -3.888 closest distance to " CA  VAL A  67 " =    2.905
peak=   -3.878 closest distance to " CE  MET A 105 " =    2.268
peak=   -3.871 closest distance to " O   HOH Z 196 " =    2.226
peak=   -3.849 closest distance to " O   PRO A 198 " =    1.190
peak=   -3.849 closest distance to " ND2 ASN A 187 " =    1.521
peak=   -3.818 closest distance to " CE2 TYR A  30 " =    2.769
peak=   -3.808 closest distance to " CG1 VAL A 112 " =    2.829
peak=   -3.796 closest distance to " ND2 ASN A  45 " =    1.342
peak=   -3.791 closest distance to " OD1 ASN A 187 " =    1.685
peak=   -3.787 closest distance to " CG  ASP A 231 " =    0.800
peak=   -3.760 closest distance to " OXT GLY A 302 " =    2.890
peak=   -3.715 closest distance to " O   HOH Z  11 " =    1.887
peak=   -3.712 closest distance to " O   HOH Z 185 " =    2.325
peak=   -3.711 closest distance to " O   HOH Z 198 " =    2.173
peak=   -3.708 closest distance to " CG  TRP A 266 " =    1.864
peak=   -3.702 closest distance to " O   HOH Z 435 " =    2.849
peak=   -3.701 closest distance to " O   HOH Z 394 " =    1.548
peak=   -3.641 closest distance to " ND2 ASN A 249 " =    2.392
peak=   -3.639 closest distance to " C   MET A 188 " =    1.452
peak=   -3.632 closest distance to " CB  ALA A 248 " =    2.395
peak=   -3.629 closest distance to " O   HOH Z 211 " =    1.580
peak=   -3.598 closest distance to " N   ALA A 248 " =    1.717
peak=   -3.594 closest distance to " CG2 VAL A 296 " =    0.950
peak=   -3.576 closest distance to " O   HOH Z 290 " =    1.172
peak=   -3.574 closest distance to " O   HOH Z 102 " =    1.660
peak=   -3.564 closest distance to " CB  ALA A 291 " =    2.199
peak=   -3.561 closest distance to " N   GLN A  58 " =    1.999
peak=   -3.558 closest distance to " CA  GLY A 203 " =    2.427
peak=   -3.558 closest distance to " O   HOH Z 388 " =    2.110
peak=   -3.557 closest distance to " CZ  PHE A  59 " =    1.457
peak=   -3.546 closest distance to " O   HOH Z  13 " =    1.708
peak=   -3.544 closest distance to " CE BMET A  47 " =    1.548
peak=   -3.542 closest distance to " O   MET A  40 " =    2.698
peak=   -3.542 closest distance to " N   ALA A 226 " =    2.053
peak=   -3.534 closest distance to " CZ3 TRP A 179 " =    1.212
peak=   -3.507 closest distance to " CB  ASN A  39 " =    2.257
peak=   -3.505 closest distance to " CG2 ILE A 263 " =    2.322
peak=   -3.497 closest distance to " O   HOH Z 165 " =    1.971
peak=   -3.497 closest distance to " CE3 TRP A 150 " =    2.023
peak=   -3.494 closest distance to " NE2 GLN A  88 " =    1.866
peak=   -3.488 closest distance to " CG1 VAL A 296 " =    1.319
peak=   -3.484 closest distance to " C   ALA A 158 " =    1.283
peak=   -3.467 closest distance to " O   ALA A 161 " =    1.683
peak=   -3.465 closest distance to " O   HOH Z 389 " =    1.994
peak=   -3.465 closest distance to " CB  PRO A 280 " =    2.107
peak=   -3.460 closest distance to " N   THR A 157 " =    1.435
peak=   -3.459 closest distance to " CD  ARG A 139 " =    1.643
peak=   -3.459 closest distance to " CB  ALA A 291 " =    2.296
peak=   -3.457 closest distance to " N   ASP A 171 " =    2.323
peak=   -3.454 closest distance to " OH  TYR A 169 " =    0.960
peak=   -3.452 closest distance to " O   HOH Z  60 " =    2.120
peak=   -3.451 closest distance to " O   HOH Z  44 " =    2.233
peak=   -3.450 closest distance to " OXT GLY A 302 " =    3.624
peak=   -3.447 closest distance to " O   HOH Z 407 " =    2.970
peak=   -3.444 closest distance to " CB  ASP A 132 " =    2.351
peak=   -3.440 closest distance to " NH2 ARG A  79 " =    2.040
peak=   -3.436 closest distance to " O   ALA A  51 " =    1.352
peak=   -3.434 closest distance to " CE2 PHE A 218 " =    2.510
peak=   -3.433 closest distance to " CA  GLY A 241 " =    2.293
peak=   -3.425 closest distance to " O   HOH Z 313 " =    1.612
peak=   -3.417 closest distance to " CA  GLY A 241 " =    3.049
peak=   -3.415 closest distance to " CG1 VAL A 250 " =    2.671
peak=   -3.405 closest distance to " O   HOH Z 372 " =    2.308
peak=   -3.405 closest distance to " CA  ASP A 298 " =    1.047
peak=   -3.403 closest distance to " C   LEU A 222 " =    0.813
peak=   -3.398 closest distance to " CZ  TYR A 169 " =    1.700
peak=   -3.397 closest distance to " OG  SER A  97 " =    2.200
peak=   -3.383 closest distance to " O   HOH Z 243 " =    1.925
peak=   -3.383 closest distance to " O   HOH Z 377 " =    0.944
peak=   -3.370 closest distance to " CD  LYS A 289 " =    2.473
peak=   -3.368 closest distance to " CD1 LEU A 228 " =    2.113
peak=   -3.364 closest distance to " OD2 ASP A 171 " =    2.266
peak=   -3.356 closest distance to " OD2 ASP A 191 " =    1.370
peak=   -3.355 closest distance to " O   SER A  22 " =    2.266
peak=   -3.351 closest distance to " CG1 VAL A 230 " =    1.901
peak=   -3.349 closest distance to " O   HOH Z 350 " =    2.102
peak=   -3.344 closest distance to " CA  ASN A 127 " =    1.291
peak=   -3.342 closest distance to " NH2AARG A 275 " =    5.126
peak=   -3.335 closest distance to " CG  LEU A 228 " =    1.028
peak=   -3.327 closest distance to " CB  ASN A  69 " =    1.155
peak=   -3.322 closest distance to " O   HOH Z 256 " =    1.302
peak=   -3.320 closest distance to " O   SER A 271 " =    2.092
peak=   -3.316 closest distance to " O   HOH Z 103 " =    1.746
peak=   -3.314 closest distance to " N   SER A 276 " =    1.215
peak=   -3.313 closest distance to " O   SER A 135 " =    1.464
peak=   -3.305 closest distance to " N   THR A 235 " =    1.299
peak=   -3.304 closest distance to " C   LEU A 143 " =    1.031
peak=   -3.301 closest distance to " CZ  PHE A 192 " =    2.780
peak=   -3.297 closest distance to " CD1 LEU A 101 " =    2.308
peak=   -3.295 closest distance to " CB  TYR A  15 " =    2.207
peak=   -3.295 closest distance to " O   PRO A 198 " =    1.357
peak=   -3.292 closest distance to " O   HOH Z 210 " =    1.193
peak=   -3.290 closest distance to " O   HOH Z 191 " =    5.469
peak=   -3.290 closest distance to " CG  PHE A 283 " =    2.598
peak=   -3.287 closest distance to " O   HOH Z 140 " =    1.548
peak=   -3.287 closest distance to " CD1 PHE A  59 " =    1.912
peak=   -3.286 closest distance to " O   VAL A 189 " =    2.554
peak=   -3.282 closest distance to " CB  GLN A  11 " =    1.910
peak=   -3.280 closest distance to " O   HOH Z 359 " =    3.236
peak=   -3.278 closest distance to " ND2 ASN A  69 " =    1.770
peak=   -3.277 closest distance to " N   SER A 212 " =    1.954
peak=   -3.277 closest distance to " CB  ALA A   7 " =    2.171
peak=   -3.276 closest distance to " CD1 LEU A 101 " =    2.846
peak=   -3.275 closest distance to " C   GLY A  17 " =    1.251
peak=   -3.271 closest distance to " O   ALA A  10 " =    1.699
peak=   -3.271 closest distance to " OG  SER A  63 " =    1.176
peak=   -3.270 closest distance to " O   HOH Z 281 " =    2.762
peak=   -3.269 closest distance to " O   HOH Z  52 " =    1.456
peak=   -3.269 closest distance to " CD1 ILE A 239 " =    2.337
peak=   -3.266 closest distance to " N   ALA A  43 " =    2.563
peak=   -3.263 closest distance to " O   HOH Z 411 " =    3.897
peak=   -3.258 closest distance to " CB  ALA A  43 " =    2.481
peak=   -3.258 closest distance to " CD2 LEU A 300 " =    2.849
peak=   -3.257 closest distance to " NZ  LYS A 119 " =    3.509
peak=   -3.254 closest distance to " O   HOH Z 427 " =    1.487
peak=   -3.253 closest distance to " OG  SER A  62 " =    1.678
peak=   -3.253 closest distance to " NH2 ARG A  79 " =    1.543
peak=   -3.253 closest distance to " CB  PRO A 163 " =    2.577
peak=   -3.252 closest distance to " CD1 TRP A 274 " =    0.953
peak=   -3.249 closest distance to " O   SER A  95 " =    1.570
peak=   -3.246 closest distance to " SG BCYS A 201 " =    2.002
peak=   -3.246 closest distance to " CB  ALA A  10 " =    2.271
peak=   -3.244 closest distance to " O   HOH Z   9 " =    1.518
peak=   -3.242 closest distance to " CA  ASP A  27 " =    2.401
peak=   -3.238 closest distance to " CZ2 TRP A 274 " =    0.897
peak=   -3.237 closest distance to " O   HOH Z 423 " =    2.072
peak=   -3.236 closest distance to " O   HOH Z  19 " =    2.501
peak=   -3.235 closest distance to " C   ASN A 187 " =    1.841
peak=   -3.234 closest distance to " CB  TYR A 172 " =    2.392
peak=   -3.231 closest distance to " O   HOH Z 193 " =    1.935
peak=   -3.230 closest distance to " OG  SER A  87 " =    1.363
peak=   -3.218 closest distance to " N   GLN A  77 " =    1.549
peak=   -3.211 closest distance to " O   HOH Z  47 " =    1.576
peak=   -3.206 closest distance to " CG1 VAL A 112 " =    2.651
peak=   -3.206 closest distance to " O   GLY A  80 " =    2.447
peak=   -3.200 closest distance to " CD1 TYR A 247 " =    2.461
peak=   -3.196 closest distance to " O   LYS A 117 " =    1.703
peak=   -3.195 closest distance to " O   HOH Z 111 " =    4.657
peak=   -3.191 closest distance to " CD2 LEU A   5 " =    1.197
peak=   -3.189 closest distance to " N   ASN A  60 " =    1.352
peak=   -3.189 closest distance to " O   VAL A 197 " =    1.378
peak=   -3.188 closest distance to " O   HOH Z  38 " =    1.743
peak=   -3.186 closest distance to " CG1 VAL A 125 " =    2.035
peak=   -3.179 closest distance to " O   GLU A  44 " =    1.683
peak=   -3.175 closest distance to " O   PHE A 218 " =    1.556
peak=   -3.173 closest distance to " C   VAL A 265 " =    0.877
peak=   -3.173 closest distance to " OE1 GLN A  88 " =    1.138
peak=   -3.172 closest distance to " O   HOH Z 139 " =    5.138
peak=   -3.171 closest distance to " CG  GLN A 278 " =    2.107
peak=   -3.169 closest distance to " O   HOH Z  89 " =    2.794
peak=   -3.166 closest distance to " NE2 GLN A 278 " =    1.919
peak=   -3.166 closest distance to " O   HOH Z 353 " =    2.075
peak=   -3.164 closest distance to " N   ALA A 248 " =    2.261
peak=   -3.164 closest distance to " O   HOH Z 423 " =    1.180
peak=   -3.163 closest distance to " CA  GLY A  98 " =    1.881
peak=   -3.162 closest distance to " OG ASER A 134 " =    1.232
peak=   -3.160 closest distance to " O   ALA A 180 " =    1.362
peak=   -3.158 closest distance to " O   HOH Z 166 " =    1.546
peak=   -3.158 closest distance to " CD2 LEU A 237 " =    2.816
peak=   -3.157 closest distance to " OH  TYR A 214 " =    1.229
peak=   -3.152 closest distance to " O   HOH Z 139 " =    3.017
peak=   -3.150 closest distance to " O   HOH Z 148 " =    3.538
peak=   -3.148 closest distance to " CG2 VAL A 202 " =    2.633
peak=   -3.135 closest distance to " O   ILE A 106 " =    2.049
peak=   -3.134 closest distance to " CG  ASP A  50 " =    2.418
peak=   -3.132 closest distance to " CG  GLU A   2 " =    1.972
peak=   -3.132 closest distance to " CB  ASP A 132 " =    2.362
peak=   -3.129 closest distance to " NH1 ARG A 195 " =    2.602
peak=   -3.123 closest distance to " CA  VAL A 296 " =    0.934
peak=   -3.117 closest distance to " CG1 VAL A 197 " =    2.232
peak=   -3.113 closest distance to " CZ2 TRP A  92 " =    2.801
peak=   -3.112 closest distance to " O   HOH Z  10 " =    1.409
peak=   -3.110 closest distance to " NH1 ARG A  36 " =    1.981
peak=   -3.108 closest distance to " CD2 TYR A 293 " =    2.092
peak=   -3.106 closest distance to " CA  GLY A 133 " =    1.941
peak=   -3.106 closest distance to " O   ARG A  24 " =    1.943
peak=   -3.103 closest distance to " O   HOH Z 389 " =    1.476
peak=   -3.098 closest distance to " ND2 ASN A  60 " =    1.376
peak=   -3.092 closest distance to " OE2 GLU A 152 " =    1.316
peak=   -3.092 closest distance to " CB  VAL A 296 " =    1.274
peak=   -3.088 closest distance to " O   HOH Z 311 " =    3.687
peak=   -3.083 closest distance to " O   TRP A  70 " =    1.425
peak=   -3.083 closest distance to " O   HOH Z 250 " =    1.343
peak=   -3.074 closest distance to " O   HOH Z 111 " =    2.360
peak=   -3.044 closest distance to " O   HOH Z 193 " =    1.746
peak=   -3.034 closest distance to " O   HOH Z 216 " =    1.776

================= 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    :  0.4127 0.3988   6.199325e+00   6.169937e+00
   1_bss:  0.4048 0.3908   6.192933e+00   6.153941e+00
   1_xyz:  0.2902 0.3100   5.938278e+00   5.982888e+00
   1_adp:  0.2137 0.2436   5.658547e+00   5.780461e+00
   1_occ:  0.2130 0.2430   5.656802e+00   5.780493e+00
   2_bss:  0.2067 0.2360   5.652316e+00   5.771921e+00
   2_xyz:  0.1455 0.1803   5.336869e+00   5.515680e+00
   2_adp:  0.1349 0.1721   5.273922e+00   5.465603e+00
   2_occ:  0.1348 0.1720   5.273353e+00   5.464850e+00
   3_bss:  0.1347 0.1719   5.273470e+00   5.464374e+00
   3_xyz:  0.1204 0.1590   5.182660e+00   5.398929e+00
   3_adp:  0.1168 0.1586   5.167805e+00   5.398155e+00
   3_occ:  0.1168 0.1585   5.168013e+00   5.398477e+00
   4_bss:  0.1168 0.1585   5.167629e+00   5.398084e+00
   4_xyz:  0.1095 0.1565   5.131454e+00   5.386610e+00
   4_adp:  0.1083 0.1569   5.127083e+00   5.385511e+00
   4_occ:  0.1082 0.1568   5.126673e+00   5.385317e+00
   5_bss:  0.1084 0.1567   5.127057e+00   5.384096e+00
   5_xyz:  0.1115 0.1581   5.146139e+00   5.393784e+00
   5_adp:  0.1114 0.1578   5.144219e+00   5.391941e+00
   5_occ:  0.1113 0.1578   5.144166e+00   5.391905e+00
   5_bss:  0.1113 0.1577   5.143755e+00   5.391474e+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:  0.362  20.001   7.357   8.564   8.184   0.000   0.000   0.000
   1_xyz:  0.362  20.001   7.357   8.564   8.184   0.000   0.000   0.000
   1_adp:  0.362  20.001   7.357   8.564   8.184   0.000   0.000   0.000
   1_occ:  0.362  20.001   7.357   8.564   8.184   0.000   0.000   0.000
   2_bss:  0.340  34.584   3.896   4.591   5.243   0.000   0.000   0.000
   2_xyz:  0.340  34.584   3.896   4.591   5.243   0.000   0.000   0.000
   2_adp:  0.340  34.584   3.896   4.591   5.243   0.000   0.000   0.000
   2_occ:  0.340  34.584   3.896   4.591   5.243   0.000   0.000   0.000
   3_bss:  0.325  34.584   3.297   3.740   4.792   0.000   0.000   0.000
   3_xyz:  0.325  34.584   3.297   3.740   4.792   0.000   0.000   0.000
   3_adp:  0.325  34.584   3.297   3.740   4.792   0.000   0.000   0.000
   3_occ:  0.325  34.584   3.297   3.740   4.792   0.000   0.000   0.000
   4_bss:  0.317  34.584   3.297   3.740   4.792   0.000   0.000   0.000
   4_xyz:  0.317  34.584   3.297   3.740   4.792   0.000   0.000   0.000
   4_adp:  0.317  34.584   3.297   3.740   4.792   0.000   0.000   0.000
   4_occ:  0.317  34.584   3.297   3.740   4.792   0.000   0.000   0.000
   5_bss:  0.313  34.584   3.425   3.767   4.923   0.000   0.000   0.000
   5_xyz:  0.313  34.584   3.425   3.767   4.923   0.000   0.000   0.000
   5_adp:  0.313  34.584   3.425   3.767   4.923   0.000   0.000   0.000
   5_occ:  0.313  34.584   3.425   3.767   4.923   0.000   0.000   0.000
   5_bss:  0.321  44.332  -0.609  -0.286   0.895   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.043 0.6087  0.6714    45453.422
   1_bss:  43.391 0.6018  0.8466    43135.930
   1_xyz:  32.380 0.7308  0.9966    25457.373
   1_adp:  23.223 0.8313  1.0827    14847.789
   1_occ:  23.224 0.8312  1.0818    14797.999
   2_bss:  22.921 0.8340  0.9550    14402.955
   2_xyz:  16.707 0.8921  0.9958     8203.579
   2_adp:  15.494 0.9029  1.0023     7466.275
   2_occ:  15.481 0.9030  1.0022     7446.632
   3_bss:  15.454 0.9032  0.9785     7424.212
   3_xyz:  14.127 0.9140  0.9832     6443.632
   3_adp:  14.095 0.9144  0.9810     6414.882
   3_occ:  14.102 0.9144  0.9809     6417.178
   4_bss:  14.095 0.9144  0.9808     6407.988
   4_xyz:  13.826 0.9166  0.9819     6269.639
   4_adp:  13.810 0.9168  0.9776     6251.882
   4_occ:  13.803 0.9169  0.9776     6253.831
   5_bss:  13.807 0.9168  0.9808     6245.073
   5_xyz:  13.969 0.9157  0.9799     6366.372
   5_adp:  13.935 0.9159  0.9773     6343.651
   5_occ:  13.934 0.9159  0.9773     6343.449
   5_bss:  13.923 0.9160  0.9789     6340.741
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3546e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3546e+01
   1_xyz:   1.432  0.010  0.098 17.698  0.005  4.120   1.0654e-01
   1_adp:   1.432  0.010  0.098 17.698  0.005  4.120   1.0654e-01
   1_occ:   1.432  0.010  0.098 17.698  0.005  4.120   1.0654e-01
   2_bss:   1.432  0.010  0.098 17.698  0.005  4.120   1.0654e-01
   2_xyz:   0.944  0.006  0.073 15.945  0.004  4.118   5.7594e-02
   2_adp:   0.944  0.006  0.073 15.945  0.004  4.118   5.7594e-02
   2_occ:   0.944  0.006  0.073 15.945  0.004  4.118   5.7594e-02
   3_bss:   0.944  0.006  0.073 15.945  0.004  4.118   5.7594e-02
   3_xyz:   0.928  0.006  0.075 15.513  0.003  4.122   5.4497e-02
   3_adp:   0.928  0.006  0.075 15.513  0.003  4.122   5.4497e-02
   3_occ:   0.928  0.006  0.075 15.513  0.003  4.122   5.4497e-02
   4_bss:   0.928  0.006  0.075 15.513  0.003  4.122   5.4497e-02
   4_xyz:   1.066  0.008  0.087 15.717  0.004  4.114   6.8969e-02
   4_adp:   1.066  0.008  0.087 15.717  0.004  4.114   6.8969e-02
   4_occ:   1.066  0.008  0.087 15.717  0.004  4.114   6.8969e-02
   5_bss:   1.066  0.008  0.087 15.717  0.004  4.114   6.8969e-02
   5_xyz:   0.892  0.005  0.072 15.299  0.003  4.114   5.1736e-02
   5_adp:   0.892  0.005  0.072 15.299  0.003  4.114   5.1736e-02
   5_occ:   0.892  0.005  0.072 15.299  0.003  4.114   5.1736e-02
   5_bss:   0.892  0.005  0.072 15.299  0.003  4.114   5.1736e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9424e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9424e+00
   1_xyz:  11.377  0.127  0.438 88.376  0.033  2.257   7.7681e-02
   1_adp:  11.377  0.127  0.438 88.376  0.033  2.257   7.7681e-02
   1_occ:  11.377  0.127  0.438 88.376  0.033  2.257   7.7681e-02
   2_bss:  11.377  0.127  0.438 88.376  0.033  2.257   7.7681e-02
   2_xyz:   7.133  0.052  0.384 85.426  0.037  2.277   4.2229e-02
   2_adp:   7.133  0.052  0.384 85.426  0.037  2.277   4.2229e-02
   2_occ:   7.133  0.052  0.384 85.426  0.037  2.277   4.2229e-02
   3_bss:   7.133  0.052  0.384 85.426  0.037  2.277   4.2229e-02
   3_xyz:   6.310  0.037  0.441 83.808  0.032  2.324   3.6010e-02
   3_adp:   6.310  0.037  0.441 83.808  0.032  2.324   3.6010e-02
   3_occ:   6.310  0.037  0.441 83.808  0.032  2.324   3.6010e-02
   4_bss:   6.310  0.037  0.441 83.808  0.032  2.324   3.6010e-02
   4_xyz:   6.552  0.043  0.589 83.924  0.039  2.289   5.1597e-02
   4_adp:   6.552  0.043  0.589 83.924  0.039  2.289   5.1597e-02
   4_occ:   6.552  0.043  0.589 83.924  0.039  2.289   5.1597e-02
   5_bss:   6.552  0.043  0.589 83.924  0.039  2.289   5.1597e-02
   5_xyz:   6.135  0.040  0.415 83.112  0.034  2.375   2.8943e-02
   5_adp:   6.135  0.040  0.415 83.112  0.034  2.375   2.8943e-02
   5_occ:   6.135  0.040  0.415 83.112  0.034  2.375   2.8943e-02
   5_bss:   6.135  0.040  0.415 83.112  0.034  2.375   2.8943e-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:  58.42   0.00  10.17  58.42   0.00   6.99  56.56   0.00  27.49
   1_occ:  58.42   0.00  10.17  58.42   0.00   6.99  56.56   0.00  27.49
   2_bss:  58.42   0.00  10.17  58.42   0.00   6.99  56.56   0.00  27.49
   2_xyz:  58.42   0.00  10.17  58.42   0.00   6.99  56.56   0.00  27.49
   2_adp:  60.38   0.00  10.49  60.38   0.00   6.87  57.85   0.71  30.22
   2_occ:  60.38   0.00  10.49  60.38   0.00   6.87  57.85   0.71  30.22
   3_bss:  60.38   0.00  10.49  60.38   0.00   6.87  57.85   0.71  30.22
   3_xyz:  60.38   0.00  10.49  60.38   0.00   6.87  57.85   0.71  30.22
   3_adp:  66.01   0.00  10.95  66.01   0.00   6.97  61.36   0.42  32.60
   3_occ:  66.01   0.00  10.95  66.01   0.00   6.97  61.36   0.42  32.60
   4_bss:  66.01   0.00  10.95  66.01   0.00   6.97  61.36   0.42  32.60
   4_xyz:  66.01   0.00  10.95  66.01   0.00   6.97  61.36   0.42  32.60
   4_adp:  82.71   0.00  11.34  82.71   0.00   7.08  78.05   0.00  34.55
   4_occ:  82.71   0.00  11.34  82.71   0.00   7.08  78.05   0.00  34.55
   5_bss:  82.71   0.00  11.34  82.71   0.00   7.08  78.05   0.00  34.55
   5_xyz:  82.71   0.00  11.34  82.71   0.00   7.08  78.05   0.00  34.55
   5_adp:  84.50   0.00  11.21  84.50   0.00   6.99  79.23   0.00  34.20
   5_occ:  84.50   0.00  11.21  84.50   0.00   6.99  79.23   0.00  34.20
   5_bss:  88.58   4.07  15.29  88.58   4.07  11.06  83.31   4.07  38.28
------------------------------------------------------------------------
 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:    1.163    0.015    0.396
   1_adp:    1.163    0.015    0.396
   1_occ:    1.163    0.015    0.396
   2_bss:    1.163    0.015    0.396
   2_xyz:    1.355    0.025    0.463
   2_adp:    1.355    0.025    0.463
   2_occ:    1.355    0.025    0.463
   3_bss:    1.355    0.025    0.463
   3_xyz:    1.427    0.049    0.487
   3_adp:    1.427    0.049    0.487
   3_occ:    1.427    0.049    0.487
   4_bss:    1.427    0.049    0.487
   4_xyz:    1.465    0.048    0.503
   4_adp:    1.465    0.048    0.503
   4_occ:    1.465    0.048    0.503
   5_bss:    1.465    0.048    0.503
   5_xyz:    1.527    0.055    0.507
   5_adp:    1.527    0.055    0.507
   5_occ:    1.527    0.055    0.507
   5_bss:    1.527    0.055    0.507
------------------------------------------------------------------------

CPU time actual refinement: 315.95


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_533/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_533/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_533/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_533/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_533/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 315.80 
  Macro-tasks:
    bulk solvent and scale       = 40.32  
    individual site refinement   = 125.17 
    weights calculation          = 31.39  
    collect and process          = 6.52   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 203.50 
  Micro-tasks:
    mask                            = 1.72   
    f_calc                          = 95.51  
    alpha_beta                      = 8.18   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 106.26 
    fmodel                         = 6.91   
    r_factors                      = 0.29   
    phase_errors                   = 11.18  
    foms                           = 0.17   
    TOTAL for micro-tasks          = 231.41 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.465 micro seconds
Total CPU time: 5.49 minutes
from_scatterers_fft:    651 calls, 95.16 s
gradients_fft:          595 calls, 92.75 s

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

# Date 2008-01-16 Time 01:49:48 PST -0800 (1200476988.14 s)
Start R-work = 0.4127, R-free = 0.3988 (no bulk solvent and anisotropic scale)
Final R-work = 0.1290, R-free = 0.1739 (no bulk solvent and anisotropic scale)

Start R-work = 0.4048, R-free = 0.3908
Final R-work = 0.1113, R-free = 0.1577