# Date 2008-01-16 Time 02:02:37 PST -0800 (1200477757.28 s)
#phil __OFF__

Command line arguments: "../665.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 = 13655
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 665

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.93, 86.39, 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: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.93, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 2
Completeness in resolution range: 0.985412
Completeness with d_max=infinity: 0.982249

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9940
                             d_min =   2.0000

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.93, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 2
Completeness in resolution range: 0.985412
Completeness with d_max=infinity: 0.982249

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9944 -  4.2786 [2087/2110]  1878   209  10.0%
  bin  2:  4.2786 -  3.4092 [2015/2035]  1813   202  10.0%
  bin  3:  3.4092 -  2.9821 [1978/1997]  1781   197  10.0%
  bin  4:  2.9821 -  2.7112 [1933/1963]  1740   193  10.0%
  bin  5:  2.7112 -  2.5179 [1963/1982]  1766   197  10.0%
  bin  6:  2.5179 -  2.3700 [1940/1965]  1747   193   9.9%
  bin  7:  2.3700 -  2.2517 [1926/1954]  1733   193  10.0%
  bin  8:  2.2517 -  2.1540 [1926/1962]  1734   192  10.0%
  bin  9:  2.1540 -  2.0713 [1921/1963]  1728   193  10.0%
  bin 10:  2.0713 -  2.0000 [1900/1948]  1710   190  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_665/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: 0.15 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: 8
        2.42 -     3.04: 2210
        3.04 -     3.66: 4624
        3.66 -     4.28: 9065
        4.28 -     4.90: 12352
  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
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.343 3.040 -x+1/2,-y+1,z+1/2
  " NH2BARG A 275 " - " O   HOH Z 335 "  2.406 3.120
  ... (remaining 28254 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_665/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_665/model_refine_001.geo

CPU time processing inputs: 9.13


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.93 86.39 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: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4012   r_free= 0.3869   ksol= 0.00   Bsol= 0.00   scale= 0.839    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.179790                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7717 0.99   1363  152 0.3476 0.3277      6.4846      6.4134|
|  2:  4.7717 -  3.8079 0.99   1299  144 0.2888 0.2918      6.5381      6.5579|
|  3:  3.8079 -  3.3326 0.99   1272  141 0.3314 0.3084      6.4716      6.4704|
|  4:  3.3326 -  3.0306 0.99   1277  142 0.3727 0.3310      6.3952      6.2697|
|  5:  3.0306 -  2.8149 0.99   1255  140 0.4055 0.4273      6.2541      6.3101|
|  6:  2.8149 -  2.6499 0.99   1266  140 0.4181 0.4557       6.189      6.1953|
|  7:  2.6499 -  2.5179 0.99   1246  139 0.4549 0.4442       6.185      6.1034|
|  8:  2.5179 -  2.4087 0.98   1249  138 0.4493 0.4466      6.1252      6.1331|
|  9:  2.4087 -  2.3163 0.98   1233  137 0.4446 0.4469      6.0559      6.0385|
| 10:  2.3163 -  2.2367 1.00   1237  138 0.4660 0.4354      6.0866      6.0052|
| 11:  2.2367 -  2.1669 0.97   1250  139 0.4645 0.3806      6.0067      5.9346|
| 12:  2.1669 -  2.1052 0.97   1224  136 0.4636 0.4290      5.9604      5.9576|
| 13:  2.1052 -  2.0499 0.99   1229  136 0.4656 0.5090      5.8699      5.9046|
| 14:  2.0499 -  2.0000 0.97   1230  137 0.4731 0.4291      5.8251      5.7225|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9944 -  4.7717  1363   152  0.75  29.52   0.82     0.77      53128.10|
|  2:  4.7717 -  3.8079  1299   144  0.81  25.14   0.93     0.85      59271.46|
|  3:  3.8079 -  3.3326  1272   141  0.76  29.67   0.90     0.83      59051.25|
|  4:  3.3326 -  3.0306  1277   142  0.72  33.89   0.86     0.76      53163.57|
|  5:  3.0306 -  2.8149  1255   140  0.62  42.00   0.80     0.68      50789.75|
|  6:  2.8149 -  2.6499  1266   140  0.59  44.94   0.78     0.64      48395.30|
|  7:  2.6499 -  2.5179  1246   139  0.56  46.99   0.77     0.62      45994.47|
|  8:  2.5179 -  2.4087  1249   138  0.57  46.86   0.79     0.64      41207.77|
|  9:  2.4087 -  2.3163  1233   137  0.59  44.78   0.77     0.65      34675.94|
| 10:  2.3163 -  2.2367  1237   138  0.61  43.38   0.78     0.67      29940.61|
| 11:  2.2367 -  2.1669  1250   139  0.60  44.46   0.79     0.67      28152.25|
| 12:  2.1669 -  2.1052  1224   136  0.55  48.37   0.81     0.63      29385.44|
| 13:  2.1052 -  2.0499  1229   136  0.52  50.46   0.78     0.59      26950.82|
| 14:  2.0499 -  2.0000  1230   137  0.55  48.12   0.76     0.58      20774.16|
|alpha:            min =        0.58 max =            0.85 mean =         0.69|
|beta:             min =    20774.16 max =        59271.46 mean =     41736.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.63|
|phase err.(work): min =        0.00 max =           89.98 mean =        41.15|
|phase err.(test): min =        0.00 max =           89.80 mean =        41.35|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.890422              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 71.149   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.441039              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.133   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       22 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      163 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      685 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1502 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2619 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3930 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5063 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6559 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7729 |
|-----------------------------------------------------------------------------|
|-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 |       53.787 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.647 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    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 = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4110   r_free= 0.3955   ksol= 0.00   Bsol= 0.00   scale= 0.807    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.190748                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3931   r_free= 0.3765   ksol= 0.35   Bsol= 20.00   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.36,8.27,8.28,0.00,0.00,0.00); trace/3= 7.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.177375                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.509395              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 73.357   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.454536              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.021   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3931      final r-factor (work) = 0.2749          |
| start r-factor (free) = 0.3765      final r-factor (free) = 0.2961          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 70.8918 = 5.51 * 0.50 * 6.2092 + 1.00 * 53.7874                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.5561 = 5.51 * 0.50 * 5.9731 + 1.00 * 0.1021                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2749      final r-factor (work) = 0.1908          |
| start r-factor (free) = 0.2961      final r-factor (free) = 0.2172          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7297 = 0.45 * 1.00 * 5.9731 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6042 = 0.45 * 1.00 * 5.7070 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    55.12   9.88     None  None   None       |
|    all(noH): 2823   0      0.00    55.12   9.88     None  None   None       |
|    Sol.    : 438    0      0.00    53.21   27.65    None  None   None       |
|    Mac.    : 2385   0      0.00    55.12   6.61     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 -   5.512: 1358   |   5:    27.560 -  33.072:  100        |
|      1:     5.512 -  11.024:  719   |   6:    33.072 -  38.584:  102        |
|      2:    11.024 -  16.536:  227   |   7:    38.584 -  44.096:   58        |
|      3:    16.536 -  22.048:  113   |   8:    44.096 -  49.608:   26        |
|      4:    22.048 -  27.560:  111   |   9:    49.608 -  55.120:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1908 r_free = 0.2172             target_work(ml) = 5.549         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1902 r_free = 0.2171             target_work(ml) = 5.547         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1902   r_free= 0.2171   ksol= 0.35   Bsol= 20.00   scale= 1.086   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.36,8.27,8.28,0.00,0.00,0.00); trace/3= 7.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.547310                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1836   r_free= 0.2094   ksol= 0.34   Bsol= 39.16   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.12,4.59,5.46,0.00,0.00,0.00); trace/3= 4.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.541718                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.109025              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.854   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.210568              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 111.068  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1836      final r-factor (work) = 0.1317          |
| start r-factor (free) = 0.2094      final r-factor (free) = 0.1658          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0063 = 3.11 * 0.50 * 5.7283 + 1.00 * 0.1017                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4182 = 3.11 * 0.50 * 5.3729 + 1.00 * 0.0660                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1317      final r-factor (work) = 0.1232          |
| start r-factor (free) = 0.1658      final r-factor (free) = 0.1594          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1413 = 0.21 * 1.00 * 5.3729 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1073 = 0.21 * 1.00 * 5.2140 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    57.91   10.18    None  None   None       |
|    all(noH): 2823   0      0.00    57.91   10.18    None  None   None       |
|    Sol.    : 438    0      0.67    53.84   29.78    None  None   None       |
|    Mac.    : 2385   0      0.00    57.91   6.59     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 -   5.792: 1465   |   5:    28.958 -  34.749:   98        |
|      1:     5.792 -  11.583:  644   |   6:    34.749 -  40.540:   96        |
|      2:    11.583 -  17.375:  214   |   7:    40.540 -  46.332:   79        |
|      3:    17.375 -  23.166:   97   |   8:    46.332 -  52.123:   25        |
|      4:    23.166 -  28.958:   97   |   9:    52.123 -  57.915:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1232 r_free = 0.1594             target_work(ml) = 5.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1231 r_free = 0.1594             target_work(ml) = 5.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1231   r_free= 0.1594   ksol= 0.34   Bsol= 39.16   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.12,4.59,5.46,0.00,0.00,0.00); trace/3= 4.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.193284                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1229   r_free= 0.1594   ksol= 0.33   Bsol= 39.32   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.51,3.93,4.91,0.00,0.00,0.00); trace/3= 4.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.193894                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.402859              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.526  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.378478              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.235  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1229      final r-factor (work) = 0.1182          |
| start r-factor (free) = 0.1594      final r-factor (free) = 0.1562          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7244 = 1.40 * 0.50 * 5.2157 + 1.00 * 0.0660                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6860 = 1.40 * 0.50 * 5.1765 + 1.00 * 0.0551                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1182      final r-factor (work) = 0.1148          |
| start r-factor (free) = 0.1562      final r-factor (free) = 0.1559          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1451 = 1.38 * 1.00 * 5.1765 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1182 = 1.38 * 1.00 * 5.1519 + 1.00 * 0.0164                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.72   10.90    None  None   None       |
|    all(noH): 2823   0      0.00    70.72   10.90    None  None   None       |
|    Sol.    : 438    0      0.18    68.45   33.13    None  None   None       |
|    Mac.    : 2385   0      0.00    70.72   6.82     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:     0.000 -   7.072: 1657   |   5:    35.359 -  42.431:   93        |
|      1:     7.072 -  14.144:  543   |   6:    42.431 -  49.502:   79        |
|      2:    14.144 -  21.215:  166   |   7:    49.502 -  56.574:   59        |
|      3:    21.215 -  28.287:  104   |   8:    56.574 -  63.646:   15        |
|      4:    28.287 -  35.359:  100   |   9:    63.646 -  70.718:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1148 r_free = 0.1559             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1148 r_free = 0.1559             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1559   ksol= 0.33   Bsol= 39.32   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.51,3.93,4.91,0.00,0.00,0.00); trace/3= 4.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.153926                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1559   ksol= 0.32   Bsol= 39.32   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.51,3.93,4.91,0.00,0.00,0.00); trace/3= 4.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.153571                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.047607              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.847  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.049507              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.251   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1148      final r-factor (work) = 0.1105          |
| start r-factor (free) = 0.1559      final r-factor (free) = 0.1557          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3292 = 2.05 * 0.50 * 5.1515 + 1.00 * 0.0551                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3214 = 2.05 * 0.50 * 5.1361 + 1.00 * 0.0630                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1105      final r-factor (work) = 0.1103          |
| start r-factor (free) = 0.1557      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4064 = 1.05 * 1.00 * 5.1361 + 1.00 * 0.0161                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4130 = 1.05 * 1.00 * 5.1315 + 1.00 * 0.0275                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.60   10.93    None  None   None       |
|    all(noH): 2823   0      0.00    79.60   10.93    None  None   None       |
|    Sol.    : 438    0      0.14    74.26   33.14    None  None   None       |
|    Mac.    : 2385   0      0.00    79.60   6.85     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.960: 1772   |   5:    39.799 -  47.759:   96        |
|      1:     7.960 -  15.920:  489   |   6:    47.759 -  55.719:   64        |
|      2:    15.920 -  23.879:  139   |   7:    55.719 -  63.678:   25        |
|      3:    23.879 -  31.839:  118   |   8:    63.678 -  71.638:   11        |
|      4:    31.839 -  39.799:  104   |   9:    71.638 -  79.598:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1103 r_free = 0.1556             target_work(ml) = 5.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1101 r_free = 0.1557             target_work(ml) = 5.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1101   r_free= 0.1557   ksol= 0.32   Bsol= 39.32   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.51,3.93,4.91,0.00,0.00,0.00); trace/3= 4.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.131760                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1101   r_free= 0.1556   ksol= 0.32   Bsol= 42.82   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.60,3.98,4.99,0.00,0.00,0.00); trace/3= 4.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.131502                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.685193              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 164.678  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.792475              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.919   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1101      final r-factor (work) = 0.1110          |
| start r-factor (free) = 0.1556      final r-factor (free) = 0.1567          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3870 = 1.69 * 0.50 * 5.1317 + 1.00 * 0.0630                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3840 = 1.69 * 0.50 * 5.1356 + 1.00 * 0.0568                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1110      final r-factor (work) = 0.1110          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1565          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1006 = 0.79 * 1.00 * 5.1356 + 1.00 * 0.0308                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0869 = 0.79 * 1.00 * 5.1403 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.40   10.84    None  None   None       |
|    all(noH): 2823   0      0.00    84.40   10.84    None  None   None       |
|    Sol.    : 438    0      0.37    74.43   32.84    None  None   None       |
|    Mac.    : 2385   0      0.00    84.40   6.80     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 -   8.441: 1834   |   5:    42.202 -  50.643:   84        |
|      1:     8.441 -  16.881:  452   |   6:    50.643 -  59.083:   50        |
|      2:    16.881 -  25.321:  151   |   7:    59.083 -  67.524:   12        |
|      3:    25.321 -  33.762:  116   |   8:    67.524 -  75.964:    6        |
|      4:    33.762 -  42.202:  114   |   9:    75.964 -  84.405:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1110 r_free = 0.1565             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1110 r_free = 0.1565             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1110   r_free= 0.1565   ksol= 0.32   Bsol= 42.82   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.60,3.98,4.99,0.00,0.00,0.00); trace/3= 4.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.141025                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7717 0.99   1363  152 0.1001 0.1314      5.3925      5.5234|
|  2:  4.7717 -  3.8079 0.99   1299  144 0.0858 0.1128       5.443      5.6461|
|  3:  3.8079 -  3.3326 0.99   1272  141 0.1043 0.1433      5.4746      5.8138|
|  4:  3.3326 -  3.0306 0.99   1277  142 0.1186 0.1556      5.4469      5.6185|
|  5:  3.0306 -  2.8149 0.99   1255  140 0.1285 0.1742      5.3273      5.5465|
|  6:  2.8149 -  2.6499 0.99   1266  140 0.1179 0.1738      5.2077      5.4508|
|  7:  2.6499 -  2.5179 0.99   1246  139 0.1248 0.1673       5.163       5.382|
|  8:  2.5179 -  2.4087 0.98   1249  138 0.1158 0.1703      5.0828      5.3571|
|  9:  2.4087 -  2.3163 0.98   1233  137 0.1172 0.1708      5.0443      5.2522|
| 10:  2.3163 -  2.2367 1.00   1237  138 0.1117 0.1841      4.9785      5.3209|
| 11:  2.2367 -  2.1669 0.97   1250  139 0.1135 0.1554      4.9384      5.1916|
| 12:  2.1669 -  2.1052 0.97   1224  136 0.1122 0.1810      4.8847      5.2818|
| 13:  2.1052 -  2.0499 0.99   1229  136 0.1136 0.1660      4.8225       5.047|
| 14:  2.0499 -  2.0000 0.97   1230  137 0.1080 0.1800      4.6987      4.9865|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9944 -  4.7717  1363   152  0.94   9.22   0.98     0.95       7362.78|
|  2:  4.7717 -  3.8079  1299   144  0.95   7.99   1.01     1.00       9112.47|
|  3:  3.8079 -  3.3326  1272   141  0.94  10.82   1.03     1.02      10277.62|
|  4:  3.3326 -  3.0306  1277   142  0.93  13.00   1.01     0.99      10035.70|
|  5:  3.0306 -  2.8149  1255   140  0.90  15.46   1.00     0.97       8333.35|
|  6:  2.8149 -  2.6499  1266   140  0.90  15.67   0.99     0.96       7063.88|
|  7:  2.6499 -  2.5179  1246   139  0.91  15.36   0.99     0.96       6085.54|
|  8:  2.5179 -  2.4087  1249   138  0.91  14.64   0.99     0.97       5357.72|
|  9:  2.4087 -  2.3163  1233   137  0.91  15.55   1.01     0.98       5162.45|
| 10:  2.3163 -  2.2367  1237   138  0.91  15.22   1.00     0.96       4409.16|
| 11:  2.2367 -  2.1669  1250   139  0.90  15.97   1.00     0.96       4379.54|
| 12:  2.1669 -  2.1052  1224   136  0.91  14.99   1.01     0.99       3892.58|
| 13:  2.1052 -  2.0499  1229   136  0.91  15.73   1.01     0.99       3527.90|
| 14:  2.0499 -  2.0000  1230   137  0.91  15.17   0.98     0.94       2727.95|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2727.95 max =        10277.62 mean =      6306.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.86|
|phase err.(test): min =        0.00 max =           89.97 mean =        13.42|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1110   r_free= 0.1565   ksol= 0.32   Bsol= 47.02   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.59,-0.22,0.81,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.141019                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1110   r_free= 0.1565   ksol= 0.32   Bsol= 47.02   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.59,-0.22,0.81,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.141019                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7717 0.99   1363  152 0.1001 0.1314      5.3926      5.5235|
|  2:  4.7717 -  3.8079 0.99   1299  144 0.0858 0.1128      5.4431      5.6462|
|  3:  3.8079 -  3.3326 0.99   1272  141 0.1043 0.1433      5.4746      5.8138|
|  4:  3.3326 -  3.0306 0.99   1277  142 0.1186 0.1556      5.4469      5.6185|
|  5:  3.0306 -  2.8149 0.99   1255  140 0.1285 0.1742      5.3273      5.5464|
|  6:  2.8149 -  2.6499 0.99   1266  140 0.1179 0.1738      5.2076      5.4506|
|  7:  2.6499 -  2.5179 0.99   1246  139 0.1248 0.1673       5.163       5.382|
|  8:  2.5179 -  2.4087 0.98   1249  138 0.1158 0.1703      5.0828      5.3571|
|  9:  2.4087 -  2.3163 0.98   1233  137 0.1172 0.1707      5.0443      5.2521|
| 10:  2.3163 -  2.2367 1.00   1237  138 0.1116 0.1841      4.9785      5.3211|
| 11:  2.2367 -  2.1669 0.97   1250  139 0.1135 0.1554      4.9384      5.1917|
| 12:  2.1669 -  2.1052 0.97   1224  136 0.1121 0.1810      4.8847      5.2819|
| 13:  2.1052 -  2.0499 0.99   1229  136 0.1136 0.1660      4.8225       5.047|
| 14:  2.0499 -  2.0000 0.97   1230  137 0.1080 0.1799      4.6986      4.9864|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9944 -  4.7717  1363   152  0.94   9.22   0.98     0.95       7363.76|
|  2:  4.7717 -  3.8079  1299   144  0.95   7.99   1.01     1.00       9113.22|
|  3:  3.8079 -  3.3326  1272   141  0.94  10.82   1.03     1.02      10278.25|
|  4:  3.3326 -  3.0306  1277   142  0.93  13.00   1.01     0.99      10035.46|
|  5:  3.0306 -  2.8149  1255   140  0.90  15.46   1.00     0.97       8331.98|
|  6:  2.8149 -  2.6499  1266   140  0.90  15.67   0.99     0.96       7063.18|
|  7:  2.6499 -  2.5179  1246   139  0.91  15.36   0.99     0.96       6085.03|
|  8:  2.5179 -  2.4087  1249   138  0.91  14.64   0.99     0.97       5357.20|
|  9:  2.4087 -  2.3163  1233   137  0.91  15.55   1.01     0.98       5162.61|
| 10:  2.3163 -  2.2367  1237   138  0.91  15.22   1.00     0.96       4408.99|
| 11:  2.2367 -  2.1669  1250   139  0.90  15.97   1.00     0.96       4380.47|
| 12:  2.1669 -  2.1052  1224   136  0.91  14.99   1.01     0.99       3892.91|
| 13:  2.1052 -  2.0499  1229   136  0.91  15.73   1.01     0.99       3527.71|
| 14:  2.0499 -  2.0000  1230   137  0.91  15.17   0.98     0.95       2726.93|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2726.93 max =        10278.25 mean =      6306.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.86|
|phase err.(test): min =        0.00 max =           89.97 mean =        13.42|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      4.20    88.61   15.04    None  None   None       |
|    all(noH): 2823   0      4.20    88.61   15.04    None  None   None       |
|    Sol.    : 438    0      4.57    78.63   37.04    None  None   None       |
|    Mac.    : 2385   0      4.20    88.61   11.00    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:     4.202 -  12.642: 1834   |   5:    46.404 -  54.844:   84        |
|      1:    12.642 -  21.083:  452   |   6:    54.844 -  63.285:   50        |
|      2:    21.083 -  29.523:  151   |   7:    63.285 -  71.725:   12        |
|      3:    29.523 -  37.963:  116   |   8:    71.725 -  80.166:    6        |
|      4:    37.963 -  46.404:  114   |   9:    80.166 -  88.606:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 298         
Filter by distance & map next to the model:
   mapped sites are within: 0.287 - 4.783
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 288 from: 298
   mapped sites are within: 0.719 - 4.783

peak=   11.041 closest distance to " CG2 VAL A 230 " =    1.408
peak=    7.734 closest distance to " CG2 VAL A 296 " =    1.160
peak=    6.244 closest distance to " CG  LEU A   5 " =    1.218
peak=    5.719 closest distance to " CG  LEU A 228 " =    1.173
peak=    5.645 closest distance to " CD2 LEU A   5 " =    1.197
peak=    5.530 closest distance to " NH2 ARG A  56 " =    2.225
peak=    5.466 closest distance to " CB  GLN A 223 " =    1.440
peak=    4.976 closest distance to " CB  ARG A 275 " =    0.918
peak=    4.962 closest distance to " CB  VAL A 296 " =    1.085
peak=    4.960 closest distance to " O   HOH Z 232 " =    2.333
peak=    4.900 closest distance to " O   HOH Z 126 " =    1.902
peak=    4.865 closest distance to " NE2 GLN A  11 " =    1.132
peak=    4.842 closest distance to " CG  PRO A 213 " =    1.232
peak=    4.840 closest distance to " CB  GLN A 183 " =    1.282
peak=    4.821 closest distance to " CB  VAL A 230 " =    1.180
peak=    4.795 closest distance to " CB  SER A  63 " =    1.287
peak=    4.732 closest distance to " O   HOH Z 142 " =    1.736
peak=    4.685 closest distance to " CG  PRO A 198 " =    1.220
peak=    4.563 closest distance to " O   HOH Z 209 " =    2.245
peak=    4.562 closest distance to " CG  PRO A 243 " =    1.119
peak=    4.559 closest distance to " O   HOH Z 427 " =    3.021
peak=    4.378 closest distance to " ND2 ASN A 187 " =    1.516
peak=    4.366 closest distance to " O   HOH Z 272 " =    1.878
peak=    4.356 closest distance to " CZ  PHE A 218 " =    1.093
peak=    4.343 closest distance to " O   HOH Z 316 " =    3.087
peak=    4.308 closest distance to " CB  GLU A 152 " =    1.188
peak=    4.283 closest distance to " C   PRO A 198 " =    1.517
peak=    4.276 closest distance to " O   HOH Z  78 " =    1.698
peak=    4.260 closest distance to " CB  ASN A 148 " =    1.363
peak=    4.252 closest distance to " O   HOH Z 423 " =    1.761
peak=    4.241 closest distance to " O   HOH Z  43 " =    1.976
peak=    4.240 closest distance to " CB  GLU A 128 " =    1.027
peak=    4.235 closest distance to " O   HOH Z 298 " =    1.804
peak=    4.231 closest distance to " O   SER A  87 " =    2.272
peak=    4.231 closest distance to " O   HOH Z  61 " =    1.669
peak=    4.214 closest distance to " O   HOH Z 369 " =    2.168
peak=    4.211 closest distance to " CD2 LEU A 228 " =    1.167
peak=    4.185 closest distance to " O   HOH Z 236 " =    1.889
peak=    4.181 closest distance to " OD1 ASN A  69 " =    2.621
peak=    4.180 closest distance to " CB  SER A   3 " =    1.264
peak=    4.179 closest distance to " O   HOH Z 203 " =    1.743
peak=    4.167 closest distance to " O   HOH Z 346 " =    1.631
peak=    4.156 closest distance to " O   HOH Z 368 " =    2.115
peak=    4.123 closest distance to " CA  TYR A  30 " =    0.934
peak=    4.105 closest distance to " O   HOH Z 193 " =    1.761
peak=    4.075 closest distance to " O   HOH Z 402 " =    1.440
peak=    4.060 closest distance to " O   HOH Z 261 " =    2.015
peak=    4.057 closest distance to " CB  ASN A  39 " =    0.940
peak=    4.029 closest distance to " O   HOH Z 303 " =    2.078
peak=    4.022 closest distance to " O   HOH Z  54 " =    2.411
peak=    4.021 closest distance to " CB  ARG A  79 " =    1.406
peak=    4.019 closest distance to " CB  TRP A 266 " =    0.959
peak=    4.012 closest distance to " O   HOH Z 158 " =    3.178
peak=    3.996 closest distance to " CB  PRO A  54 " =    0.855
peak=    3.995 closest distance to " O   HOH Z 189 " =    2.749
peak=    3.982 closest distance to " CB  VAL A 265 " =    1.282
peak=    3.965 closest distance to " O   HOH Z 234 " =    3.587
peak=    3.915 closest distance to " CB  ALA A   9 " =    1.623
peak=    3.901 closest distance to " O   HOH Z 403 " =    1.675
peak=    3.891 closest distance to " CB  ARG A 190 " =    1.640
peak=    3.889 closest distance to " CB  ASP A 140 " =    0.973
peak=    3.878 closest distance to " N   ASN A  39 " =    1.204
peak=    3.861 closest distance to " CG1BVAL A  72 " =    1.644
peak=    3.831 closest distance to " CB  LEU A 143 " =    1.166
peak=    3.828 closest distance to " CB  TRP A 179 " =    1.384
peak=    3.824 closest distance to " CD BLYS A 290 " =    1.087
peak=    3.821 closest distance to " CB  GLU A 277 " =    3.599
peak=    3.818 closest distance to " O   HOH Z 248 " =    1.658
peak=    3.815 closest distance to " O   HOH Z 280 " =    2.998
peak=    3.799 closest distance to " CA  ALA A  21 " =    1.154
peak=    3.781 closest distance to " O   HOH Z  15 " =    2.148
peak=    3.779 closest distance to " O   HOH Z 389 " =    1.870
peak=    3.761 closest distance to " CG2 VAL A 257 " =    0.860
peak=    3.758 closest distance to " O   HOH Z 411 " =    3.732
peak=    3.755 closest distance to " O   HOH Z  59 " =    2.099
peak=    3.740 closest distance to " CB  ALA A 291 " =    1.394
peak=    3.738 closest distance to " CB  VAL A 202 " =    1.579
peak=    3.728 closest distance to " O   HOH Z  97 " =    2.010
peak=    3.723 closest distance to " O   HOH Z 371 " =    3.128
peak=    3.720 closest distance to " CB  ALA A 248 " =    1.434
peak=    3.720 closest distance to " O   HOH Z 250 " =    1.344
peak=    3.704 closest distance to " CB  ASN A 142 " =    1.096
peak=    3.684 closest distance to " CB  HIS A 108 " =    0.819
peak=    3.682 closest distance to " CG1 VAL A 153 " =    0.943
peak=    3.681 closest distance to " NH2 ARG A 156 " =    1.122
peak=    3.680 closest distance to " NH1AARG A 145 " =    1.149
peak=    3.664 closest distance to " O   HOH Z 197 " =    3.122
peak=    3.664 closest distance to " CD  ARG A 269 " =    0.982
peak=    3.655 closest distance to " CA  ALA A  51 " =    0.956
peak=    3.651 closest distance to " O   HOH Z 145 " =    2.144
peak=    3.649 closest distance to " O   HOH Z 435 " =    1.982
peak=    3.648 closest distance to " CA  PHE A 283 " =    1.226
peak=    3.647 closest distance to " O   HOH Z 214 " =    2.168
peak=    3.646 closest distance to " O   HOH Z 273 " =    2.715
peak=    3.645 closest distance to " OD2 ASP A 286 " =    2.803
peak=    3.642 closest distance to " CD1 LEU A 300 " =    1.254
peak=    3.640 closest distance to " O   HOH Z 126 " =    2.051
peak=    3.637 closest distance to " CA  VAL A  41 " =    0.773
peak=    3.632 closest distance to " CA  ALA A 158 " =    1.243
peak=    3.628 closest distance to " O   HOH Z 263 " =    1.620
peak=    3.625 closest distance to " CB  THR A  31 " =    1.629
peak=    3.625 closest distance to " CA  ASN A 215 " =    1.180
peak=    3.621 closest distance to " CB  ASP A 124 " =    0.787
peak=    3.604 closest distance to " O   HOH Z 245 " =    1.378
peak=    3.603 closest distance to " NZ  LYS A 117 " =    3.206
peak=    3.600 closest distance to " CB  ARG A 139 " =    0.865
peak=    3.599 closest distance to " OG BSER A 164 " =    2.220
peak=    3.591 closest distance to " O   HOH Z 290 " =    1.093
peak=    3.587 closest distance to " N   PHE A 130 " =    1.244
peak=    3.582 closest distance to " O   HOH Z  66 " =    2.184
peak=    3.577 closest distance to " O   HOH Z 172 " =    3.660
peak=    3.572 closest distance to " O   TRP A 274 " =    1.847
peak=    3.565 closest distance to " O   HOH Z 193 " =    1.937
peak=    3.559 closest distance to " O   ASP A 124 " =    1.025
peak=    3.555 closest distance to " CG  LEU A 167 " =    1.168
peak=    3.551 closest distance to " O   HOH Z 147 " =    1.749
peak=    3.546 closest distance to " N   ARG A 156 " =    1.385
peak=    3.545 closest distance to " O   HOH Z  88 " =    2.919
peak=    3.541 closest distance to " O   HOH Z 112 " =    1.686
peak=    3.540 closest distance to " CA  ARG A  36 " =    1.024
peak=    3.539 closest distance to " CD  LYS A 166 " =    1.331
peak=    3.529 closest distance to " CA  ALA A 291 " =    0.893
peak=    3.526 closest distance to " O   HOH Z 313 " =    1.806
peak=    3.523 closest distance to " CE  LYS A  76 " =    0.888
peak=    3.523 closest distance to " CA  THR A 221 " =    0.956
peak=    3.521 closest distance to " O   HOH Z  48 " =    1.627
peak=    3.521 closest distance to " CG1 ILE A  49 " =    1.465
peak=    3.520 closest distance to " O   HOH Z 425 " =    2.056
peak=    3.519 closest distance to " CA  THR A 264 " =    0.755
peak=    3.511 closest distance to " CG  ARG A  66 " =    2.713
peak=    3.509 closest distance to " O   HOH Z 305 " =    3.609
peak=    3.499 closest distance to " CB AVAL A  41 " =    1.136
peak=    3.497 closest distance to " O   HOH Z  97 " =    2.541
peak=    3.494 closest distance to " O   HOH Z 344 " =    2.980
peak=    3.493 closest distance to " CB  THR A 157 " =    1.132
peak=    3.490 closest distance to " CA  TYR A  30 " =    1.070
peak=    3.488 closest distance to " O   GLN A 278 " =    1.324
peak=    3.482 closest distance to " ND2 ASN A 110 " =    1.654
peak=    3.476 closest distance to " NE2 GLN A  77 " =    3.240
peak=    3.476 closest distance to " CG2 ILE A 120 " =    1.298
peak=    3.475 closest distance to " CB  ASN A 110 " =    1.117
peak=    3.468 closest distance to " O   MET A 105 " =    1.853
peak=    3.465 closest distance to " O   HOH Z 285 " =    2.959
peak=    3.464 closest distance to " O   HOH Z 403 " =    1.407
peak=    3.464 closest distance to " CG2 THR A 221 " =    1.245
peak=    3.455 closest distance to " CB  SER A 216 " =    0.809
peak=    3.449 closest distance to " CA  LYS A 117 " =    1.232
peak=    3.448 closest distance to " CB  SER A 212 " =    1.209
peak=    3.448 closest distance to " O   HOH Z 193 " =    1.621
peak=    3.447 closest distance to " O   HOH Z  19 " =    2.369
peak=    3.441 closest distance to " CG1 VAL A 296 " =    1.213
peak=    3.437 closest distance to " CB  ARG A  79 " =    0.880
peak=    3.433 closest distance to " O   HOH Z  21 " =    1.696
peak=    3.429 closest distance to " O   HOH Z 227 " =    1.651
peak=    3.428 closest distance to " CA  SER A  87 " =    1.000
peak=    3.428 closest distance to " O   HOH Z 128 " =    2.143
peak=    3.426 closest distance to " N   SER A 135 " =    1.342
peak=    3.426 closest distance to " O   HOH Z 261 " =    1.558
peak=    3.416 closest distance to " O   HOH Z 426 " =    1.594
peak=    3.416 closest distance to " O   HOH Z 247 " =    1.347
peak=    3.416 closest distance to " CA  ARG A 195 " =    1.199
peak=    3.415 closest distance to " CB  GLN A  89 " =    1.195
peak=    3.415 closest distance to " O   HOH Z 291 " =    1.581
peak=    3.411 closest distance to " O   HOH Z 132 " =    2.496
peak=    3.409 closest distance to " CB  GLU A  46 " =    0.972
peak=    3.408 closest distance to " O   HOH Z 422 " =    2.628
peak=    3.407 closest distance to " O   HOH Z 417 " =    3.136
peak=    3.404 closest distance to " CD2 LEU A 297 " =    0.930
peak=    3.403 closest distance to " CG  MET A 185 " =    1.228
peak=    3.401 closest distance to " CG  MET A 185 " =    1.083
peak=    3.397 closest distance to " O   HOH Z 425 " =    1.306
peak=    3.394 closest distance to " CE1 TYR A 186 " =    1.347
peak=    3.393 closest distance to " O   HOH Z 407 " =    2.526
peak=    3.393 closest distance to " O   HOH Z 145 " =    3.683
peak=    3.392 closest distance to " CD2 TRP A 179 " =    1.382
peak=    3.391 closest distance to " O   HOH Z 128 " =    2.140
peak=    3.391 closest distance to " CD1 ILE A  33 " =    1.664
peak=    3.374 closest distance to " CG1 ILE A  33 " =    1.323
peak=    3.370 closest distance to " O   HOH Z 250 " =    1.401
peak=    3.370 closest distance to " O   HOH Z 368 " =    3.551
peak=    3.362 closest distance to " CB  LEU A 228 " =    1.310
peak=    3.358 closest distance to " O   HOH Z  40 " =    1.449
peak=    3.354 closest distance to " CB  SER A  26 " =    1.764
peak=    3.347 closest distance to " CE1 HIS A 108 " =    1.123
peak=    3.340 closest distance to " CB  ALA A 295 " =    1.183
peak=    3.337 closest distance to " CA  SER A 146 " =    1.725
peak=    3.337 closest distance to " CB  ALA A 242 " =    0.815
peak=    3.331 closest distance to " CB  MET A  40 " =    0.809
peak=    3.330 closest distance to " O   HOH Z 329 " =    3.910
peak=    3.325 closest distance to " CB  GLN A 278 " =    0.864
peak=    3.322 closest distance to " ND1 HIS A  81 " =    1.659
peak=    3.318 closest distance to " CG2 VAL A 202 " =    1.114
peak=    3.315 closest distance to " CA  MET A  40 " =    1.084
peak=    3.314 closest distance to " CG2 ILE A  20 " =    1.442
peak=    3.310 closest distance to " CD1 ILE A 106 " =    0.985
peak=    3.302 closest distance to " CG  MET A 113 " =    1.108
peak=    3.301 closest distance to " O   HOH Z 234 " =    1.789
peak=    3.296 closest distance to " CA  ASP A 140 " =    1.226
peak=    3.291 closest distance to " CB  ILE A  20 " =    1.406
peak=    3.290 closest distance to " O   HOH Z 366 " =    3.030
peak=    3.289 closest distance to " CD1 LEU A 228 " =    2.003
peak=    3.287 closest distance to " CG1 ILE A 151 " =    1.029
peak=    3.283 closest distance to " O   HOH Z 437 " =    1.881
peak=    3.283 closest distance to " CA  ASN A 127 " =    1.046
peak=    3.281 closest distance to " CD2 LEU A   5 " =    0.760
peak=    3.280 closest distance to " O   HOH Z  10 " =    1.774
peak=    3.276 closest distance to " NZ  LYS A  48 " =    1.329
peak=    3.276 closest distance to " N   VAL A 126 " =    1.401
peak=    3.274 closest distance to " CA  ASN A 176 " =    1.123
peak=    3.272 closest distance to " NH1BARG A 190 " =    2.054
peak=    3.272 closest distance to " CB  SER A 273 " =    0.846
peak=    3.269 closest distance to " CB  LYS A 117 " =    1.221
peak=    3.265 closest distance to " CD  LYS A 119 " =    1.519
peak=    3.265 closest distance to " O   HOH Z 325 " =    2.187
peak=    3.264 closest distance to " CG  GLN A  88 " =    1.060
peak=    3.263 closest distance to " CB  LEU A 255 " =    0.785
peak=    3.262 closest distance to " CB  VAL A 268 " =    0.807
peak=    3.261 closest distance to " OG1 THR A 294 " =    2.359
peak=    3.257 closest distance to " N   GLN A 278 " =    1.124
peak=    3.256 closest distance to " O   HOH Z 251 " =    1.506
peak=    3.255 closest distance to " ND1 HIS A  86 " =    1.681
peak=    3.253 closest distance to " OG  SER A  22 " =    2.789
peak=    3.246 closest distance to " O   HOH Z 185 " =    1.803
peak=    3.245 closest distance to " O   HOH Z   1 " =    1.908
peak=    3.243 closest distance to " CB  MET A  47 " =    1.055
peak=    3.242 closest distance to " O   HOH Z  80 " =    1.599
peak=    3.241 closest distance to " O   HOH Z 282 " =    1.947
peak=    3.240 closest distance to " CG2 THR A 294 " =    1.702
peak=    3.239 closest distance to " O   HOH Z 180 " =    2.133
peak=    3.236 closest distance to " O   HOH Z 148 " =    3.333
peak=    3.235 closest distance to " O   HOH Z 383 " =    1.894
peak=    3.230 closest distance to " O   HOH Z 421 " =    1.698
peak=    3.230 closest distance to " O  BHOH Z 338 " =    2.464
peak=    3.229 closest distance to " O   HOH Z  66 " =    2.112
peak=    3.228 closest distance to " O   HOH Z 133 " =    1.521
peak=    3.227 closest distance to " CB  ILE A 120 " =    1.272
peak=    3.223 closest distance to " NZ  LYS A  76 " =    1.516
peak=    3.221 closest distance to " CA  GLN A 194 " =    1.232
peak=    3.219 closest distance to " O   HOH Z 345 " =    3.309
peak=    3.217 closest distance to " O   ARG A  56 " =    2.829
peak=    3.212 closest distance to " CB  ASN A 215 " =    1.182
peak=    3.210 closest distance to " O   HOH Z 126 " =    1.540
peak=    3.209 closest distance to " O   HOH Z 154 " =    2.028
peak=    3.208 closest distance to " O   ALA A 292 " =    1.736
peak=    3.205 closest distance to " CB  LYS A 290 " =    0.973
peak=    3.203 closest distance to " O   HOH Z   9 " =    1.920
peak=    3.203 closest distance to " O   HOH Z 353 " =    2.656
peak=    3.202 closest distance to " O   HOH Z 227 " =    2.151
peak=    3.198 closest distance to " CA  ASP A 162 " =    1.055
peak=    3.197 closest distance to " CB  ASN A 224 " =    1.035
peak=    3.194 closest distance to " O   HOH Z 173 " =    2.234
peak=    3.192 closest distance to " CA  LYS A 290 " =    1.245
peak=    3.192 closest distance to " CG  GLN A  77 " =    2.296
peak=    3.190 closest distance to " CB  GLN A 205 " =    1.114
peak=    3.188 closest distance to " CA  ILE A 106 " =    0.719
peak=    3.182 closest distance to " O   HOH Z 109 " =    2.594
peak=    3.182 closest distance to " O   HOH Z 359 " =    3.700
peak=    3.180 closest distance to " O   ALA A 158 " =    1.315
peak=    3.180 closest distance to " CB  ALA A 114 " =    1.235
peak=    3.177 closest distance to " CA  ALA A 154 " =    0.966
peak=    3.175 closest distance to " O   HOH Z 423 " =    2.975
peak=    3.175 closest distance to " OE2 GLU A  53 " =    1.973
peak=    3.173 closest distance to " CA  MET A 105 " =    0.968
peak=    3.170 closest distance to " NH2BARG A 145 " =    2.052
peak=    3.164 closest distance to " CB  TRP A 150 " =    1.406
peak=    3.162 closest distance to " CA  LEU A 282 " =    1.065
peak=    3.162 closest distance to " O   HOH Z 336 " =    1.802
peak=    3.155 closest distance to " CA  ASP A 191 " =    1.109
peak=    3.146 closest distance to " O   HOH Z 133 " =    2.495
peak=    3.143 closest distance to " CG2 VAL A 197 " =    1.006
peak=    3.141 closest distance to " CD1 LEU A 261 " =    1.188
peak=    3.139 closest distance to " O   HOH Z   3 " =    1.752
peak=    3.137 closest distance to " CB  SER A 141 " =    1.020
peak=    3.130 closest distance to " O   HOH Z 187 " =    2.304
peak=    3.126 closest distance to " O   HOH Z 294 " =    1.563
peak=    3.125 closest distance to " O   HOH Z 124 " =    1.241
peak=    3.122 closest distance to " N   ASN A 127 " =    1.212
peak=    3.097 closest distance to " O   HOH Z   1 " =    4.783
peak=    3.095 closest distance to " O   HOH Z 409 " =    3.270
peak=    3.089 closest distance to " N   ASP A 162 " =    1.278
peak=    3.087 closest distance to " O   HOH Z  61 " =    1.603
peak=    3.085 closest distance to " C   ALA A 299 " =    0.916
peak=    3.081 closest distance to " CA  ILE A 234 " =    0.822
peak=    3.076 closest distance to " CB  TYR A 116 " =    0.806
peak=    3.061 closest distance to " O   HOH Z  49 " =    2.506
peak=    3.053 closest distance to " O   HOH Z 293 " =    1.666
peak=    3.052 closest distance to " ND2 ASN A 249 " =    0.848
peak=    3.027 closest distance to " CZ3 TRP A  85 " =    0.908

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.516 - 5.465
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 199
   mapped sites are within: 0.785 - 5.465

peak=   -5.131 closest distance to " CG2 VAL A 230 " =    0.806
peak=   -4.457 closest distance to " CD  ARG A 156 " =    2.019
peak=   -4.446 closest distance to " SG  CYS A 254 " =    3.307
peak=   -4.349 closest distance to " OG BSER A 134 " =    1.182
peak=   -4.308 closest distance to " CB  PRO A 243 " =    2.648
peak=   -4.241 closest distance to " O   HOH Z 266 " =    5.143
peak=   -4.206 closest distance to " C   HIS A 108 " =    1.194
peak=   -4.163 closest distance to " CE2 TYR A  30 " =    2.766
peak=   -4.075 closest distance to " O   ILE A 109 " =    2.608
peak=   -4.072 closest distance to " CG2 VAL A 296 " =    1.451
peak=   -4.065 closest distance to " CG  GLN A 223 " =    2.094
peak=   -4.062 closest distance to " O   HOH Z 114 " =    3.051
peak=   -4.025 closest distance to " O   HOH Z 351 " =    1.488
peak=   -4.012 closest distance to " CD  GLN A  58 " =    1.119
peak=   -3.973 closest distance to " CB  PHE A 192 " =    1.882
peak=   -3.936 closest distance to " O   HOH Z 231 " =    2.066
peak=   -3.922 closest distance to " O   HOH Z 290 " =    1.156
peak=   -3.908 closest distance to " OXT GLY A 302 " =    2.859
peak=   -3.855 closest distance to " O   HOH Z 185 " =    2.365
peak=   -3.851 closest distance to " CE  MET A 105 " =    2.187
peak=   -3.827 closest distance to " N   ALA A 226 " =    2.072
peak=   -3.825 closest distance to " O   VAL A  67 " =    2.668
peak=   -3.821 closest distance to " O   PRO A 163 " =    2.137
peak=   -3.813 closest distance to " O   HOH Z 166 " =    1.947
peak=   -3.806 closest distance to " ND2 ASN A  45 " =    1.048
peak=   -3.805 closest distance to " CE2 PHE A 218 " =    2.598
peak=   -3.802 closest distance to " O   HOH Z 389 " =    1.925
peak=   -3.801 closest distance to " N   ALA A  43 " =    2.562
peak=   -3.794 closest distance to " O   HOH Z 196 " =    2.154
peak=   -3.769 closest distance to " CG  ASP A 231 " =    0.785
peak=   -3.766 closest distance to " CZ3 TRP A 179 " =    1.220
peak=   -3.734 closest distance to " OD1 ASN A 187 " =    1.600
peak=   -3.710 closest distance to " CG1 VAL A 112 " =    2.651
peak=   -3.707 closest distance to " ND2 ASN A 187 " =    1.505
peak=   -3.676 closest distance to " O   HOH Z  37 " =    1.887
peak=   -3.671 closest distance to " CB  ALA A  43 " =    2.491
peak=   -3.670 closest distance to " NE2 GLN A  88 " =    1.965
peak=   -3.669 closest distance to " CA  VAL A  67 " =    2.692
peak=   -3.665 closest distance to " O   HOH Z 394 " =    1.568
peak=   -3.653 closest distance to " O   HOH Z 435 " =    2.790
peak=   -3.633 closest distance to " CB  PRO A 280 " =    2.129
peak=   -3.630 closest distance to " CG2 ILE A 263 " =    2.331
peak=   -3.623 closest distance to " O   HOH Z  52 " =    1.486
peak=   -3.623 closest distance to " CB  ALA A 248 " =    2.100
peak=   -3.616 closest distance to " C   MET A 188 " =    1.434
peak=   -3.612 closest distance to " CB  ALA A 291 " =    2.180
peak=   -3.606 closest distance to " O   HOH Z  11 " =    1.884
peak=   -3.591 closest distance to " NH2AARG A 275 " =    5.160
peak=   -3.588 closest distance to " CG1 VAL A 296 " =    1.337
peak=   -3.571 closest distance to " O   PRO A 198 " =    1.217
peak=   -3.565 closest distance to " OG  SER A  97 " =    2.277
peak=   -3.551 closest distance to " CA  GLY A 241 " =    3.084
peak=   -3.549 closest distance to " CG1 VAL A 112 " =    2.869
peak=   -3.548 closest distance to " CB  ASP A 132 " =    2.323
peak=   -3.542 closest distance to " C   ALA A 158 " =    1.269
peak=   -3.534 closest distance to " O   HOH Z 211 " =    1.619
peak=   -3.533 closest distance to " CA  ASP A 298 " =    1.034
peak=   -3.532 closest distance to " O   HOH Z  44 " =    2.224
peak=   -3.527 closest distance to " CB  ALA A 248 " =    2.339
peak=   -3.527 closest distance to " O   HOH Z 407 " =    3.029
peak=   -3.515 closest distance to " CD2 LEU A 300 " =    2.796
peak=   -3.515 closest distance to " CG1 VAL A 250 " =    2.731
peak=   -3.510 closest distance to " ND2 ASN A  45 " =    1.585
peak=   -3.509 closest distance to " CD1 LEU A 101 " =    2.872
peak=   -3.505 closest distance to " N   THR A 157 " =    1.476
peak=   -3.501 closest distance to " CB  ALA A 291 " =    2.245
peak=   -3.484 closest distance to " CD1 LEU A 101 " =    2.392
peak=   -3.480 closest distance to " OD1 ASN A 148 " =    1.476
peak=   -3.477 closest distance to " O   HOH Z 166 " =    1.606
peak=   -3.466 closest distance to " CD  LYS A 289 " =    2.512
peak=   -3.465 closest distance to " O   HOH Z 102 " =    1.601
peak=   -3.464 closest distance to " N   GLN A  58 " =    1.879
peak=   -3.461 closest distance to " CE3 TRP A 150 " =    2.044
peak=   -3.461 closest distance to " CE BMET A  47 " =    1.678
peak=   -3.447 closest distance to " CG  TRP A 266 " =    1.856
peak=   -3.440 closest distance to " NH2 ARG A  79 " =    1.958
peak=   -3.431 closest distance to " N   THR A 235 " =    1.271
peak=   -3.430 closest distance to " O   HOH Z 262 " =    2.835
peak=   -3.424 closest distance to " CB  ASN A  39 " =    2.275
peak=   -3.419 closest distance to " C   LEU A 143 " =    1.033
peak=   -3.418 closest distance to " O   HOH Z 292 " =    4.593
peak=   -3.410 closest distance to " CG  ARG A 269 " =    2.363
peak=   -3.401 closest distance to " O   HOH Z 295 " =    1.573
peak=   -3.398 closest distance to " O   GLY A 196 " =    1.117
peak=   -3.397 closest distance to " CB  VAL A 296 " =    1.212
peak=   -3.397 closest distance to " CZ  PHE A  59 " =    1.532
peak=   -3.392 closest distance to " CG1 VAL A 197 " =    2.270
peak=   -3.392 closest distance to " O   VAL A 189 " =    2.592
peak=   -3.382 closest distance to " CB  ASN A  69 " =    1.168
peak=   -3.381 closest distance to " CB  ASP A 171 " =    2.275
peak=   -3.381 closest distance to " N   PHE A  59 " =    2.280
peak=   -3.378 closest distance to " O   MET A  40 " =    2.706
peak=   -3.377 closest distance to " O   HOH Z  13 " =    1.569
peak=   -3.370 closest distance to " CD  ARG A 139 " =    1.626
peak=   -3.369 closest distance to " O   SER A 271 " =    2.157
peak=   -3.369 closest distance to " O   HOH Z 198 " =    2.189
peak=   -3.362 closest distance to " O   SER A  95 " =    1.641
peak=   -3.359 closest distance to " CD1 LEU A 228 " =    2.215
peak=   -3.358 closest distance to " CG  PHE A 283 " =    2.671
peak=   -3.357 closest distance to " NZ  LYS A 119 " =    3.527
peak=   -3.353 closest distance to " O   HOH Z  10 " =    1.465
peak=   -3.347 closest distance to " O   HOH Z 417 " =    2.744
peak=   -3.347 closest distance to " N   ASP A 171 " =    2.318
peak=   -3.346 closest distance to " CG  GLU A 277 " =    1.124
peak=   -3.342 closest distance to " C   ASP A 231 " =    2.544
peak=   -3.341 closest distance to " ND2 ASN A  60 " =    1.402
peak=   -3.339 closest distance to " CB  ALA A  10 " =    2.271
peak=   -3.332 closest distance to " N   SER A 276 " =    1.331
peak=   -3.328 closest distance to " CB  ASP A 132 " =    2.384
peak=   -3.326 closest distance to " O   HOH Z  43 " =    1.682
peak=   -3.325 closest distance to " CB  PRO A 163 " =    2.548
peak=   -3.323 closest distance to " O   HOH Z 426 " =    1.683
peak=   -3.323 closest distance to " O   HOH Z  60 " =    1.954
peak=   -3.321 closest distance to " O   HOH Z  73 " =    2.196
peak=   -3.317 closest distance to " CZ  TYR A 169 " =    1.696
peak=   -3.313 closest distance to " N   THR A  52 " =    1.679
peak=   -3.311 closest distance to " NE2 GLN A 278 " =    1.985
peak=   -3.305 closest distance to " CG1 VAL A 230 " =    1.913
peak=   -3.299 closest distance to " N   ALA A 248 " =    1.596
peak=   -3.296 closest distance to " CB  TYR A  15 " =    2.210
peak=   -3.295 closest distance to " O   HOH Z 275 " =    1.837
peak=   -3.288 closest distance to " O   HOH Z  38 " =    1.622
peak=   -3.284 closest distance to " O   HOH Z 123 " =    2.438
peak=   -3.283 closest distance to " O   HOH Z 256 " =    1.340
peak=   -3.282 closest distance to " O   HOH Z 165 " =    1.889
peak=   -3.282 closest distance to " O   HOH Z  47 " =    1.586
peak=   -3.280 closest distance to " O   HOH Z 222 " =    1.426
peak=   -3.275 closest distance to " O   SER A  22 " =    2.299
peak=   -3.270 closest distance to " N   SER A 212 " =    1.966
peak=   -3.270 closest distance to " N   HIS A 115 " =    2.132
peak=   -3.268 closest distance to " CD1 ILE A 239 " =    2.158
peak=   -3.265 closest distance to " CA  GLY A 241 " =    2.295
peak=   -3.265 closest distance to " N   VAL A 230 " =    1.132
peak=   -3.262 closest distance to " C   PHE A  59 " =    1.323
peak=   -3.254 closest distance to " CG  LEU A 228 " =    1.009
peak=   -3.245 closest distance to " O   HOH Z 175 " =    4.292
peak=   -3.245 closest distance to " ND2 ASN A  69 " =    1.791
peak=   -3.244 closest distance to " O   HOH Z 313 " =    1.600
peak=   -3.242 closest distance to " O   HOH Z 136 " =    2.195
peak=   -3.241 closest distance to " O   HOH Z 139 " =    3.076
peak=   -3.239 closest distance to " O   HOH Z 191 " =    5.465
peak=   -3.237 closest distance to " O   ILE A 106 " =    1.981
peak=   -3.232 closest distance to " O   HOH Z 372 " =    2.373
peak=   -3.230 closest distance to " O   ALA A  10 " =    1.719
peak=   -3.227 closest distance to " O   HOH Z 423 " =    2.112
peak=   -3.227 closest distance to " O   HOH Z 309 " =    2.491
peak=   -3.227 closest distance to " CD1 TYR A 247 " =    2.763
peak=   -3.222 closest distance to " NE2 GLN A  58 " =    2.642
peak=   -3.220 closest distance to " O   HOH Z 149 " =    2.225
peak=   -3.218 closest distance to " OG  SER A 206 " =    1.683
peak=   -3.218 closest distance to " O   GLY A  80 " =    2.466
peak=   -3.217 closest distance to " OG  SER A  87 " =    1.435
peak=   -3.213 closest distance to " C   ASN A 187 " =    1.918
peak=   -3.211 closest distance to " CB  VAL A 230 " =    1.046
peak=   -3.210 closest distance to " CA  GLY A 133 " =    1.981
peak=   -3.208 closest distance to " CA  GLY A 203 " =    2.431
peak=   -3.201 closest distance to " O   ALA A  51 " =    1.382
peak=   -3.199 closest distance to " O   HOH Z 353 " =    2.059
peak=   -3.197 closest distance to " C   LEU A 222 " =    0.807
peak=   -3.195 closest distance to " N   THR A  18 " =    1.332
peak=   -3.192 closest distance to " CB  GLN A  11 " =    1.836
peak=   -3.191 closest distance to " ND2 ASN A 249 " =    2.392
peak=   -3.190 closest distance to " O   HOH Z  19 " =    2.427
peak=   -3.179 closest distance to " CD1 ILE A 199 " =    2.510
peak=   -3.178 closest distance to " NH2 ARG A  79 " =    1.537
peak=   -3.176 closest distance to " O   HOH Z 174 " =    2.492
peak=   -3.167 closest distance to " O   HOH Z 311 " =    3.748
peak=   -3.159 closest distance to " CD2 TYR A 293 " =    2.087
peak=   -3.157 closest distance to " O   HOH Z 281 " =    2.729
peak=   -3.155 closest distance to " O   HOH Z 359 " =    3.262
peak=   -3.154 closest distance to " N   GLN A  77 " =    1.524
peak=   -3.151 closest distance to " CD  ARG A 195 " =    5.172
peak=   -3.149 closest distance to " O   HOH Z 253 " =    3.875
peak=   -3.147 closest distance to " CD2 TYR A 247 " =    2.322
peak=   -3.147 closest distance to " CA  VAL A 296 " =    0.988
peak=   -3.147 closest distance to " O   HOH Z   6 " =    1.691
peak=   -3.142 closest distance to " NE2 GLN A 194 " =    1.793
peak=   -3.140 closest distance to " ND2 ASN A 252 " =    1.819
peak=   -3.137 closest distance to " CA  GLY A  98 " =    1.927
peak=   -3.134 closest distance to " CG1 VAL A  67 " =    3.045
peak=   -3.133 closest distance to " O   HOH Z 313 " =    1.127
peak=   -3.127 closest distance to " N   ALA A 248 " =    2.562
peak=   -3.111 closest distance to " NH1 ARG A  36 " =    2.005
peak=   -3.107 closest distance to " OE1 GLN A  88 " =    1.103
peak=   -3.103 closest distance to " O   HOH Z 265 " =    1.630
peak=   -3.098 closest distance to " O   PRO A 198 " =    1.322
peak=   -3.094 closest distance to " O   HOH Z 234 " =    4.111
peak=   -3.091 closest distance to " OG BSER A 134 " =    1.757
peak=   -3.089 closest distance to " OG  SER A  62 " =    1.707
peak=   -3.089 closest distance to " CD  PRO A 243 " =    2.069
peak=   -3.087 closest distance to " CA  SER A 135 " =    1.340
peak=   -3.068 closest distance to " CG  ASP A  50 " =    2.399
peak=   -3.061 closest distance to " O   HOH Z 210 " =    1.178
peak=   -3.057 closest distance to " O   HOH Z 128 " =    2.477
peak=   -3.052 closest distance to " O   HOH Z 193 " =    1.781
peak=   -3.044 closest distance to " CG1 VAL A 296 " =    1.309
peak=   -3.030 closest distance to " O   HOH Z 111 " =    1.345

================= 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    :  0.4012 0.3869   6.179790e+00   6.148767e+00
   1_bss:  0.3931 0.3765   6.177375e+00   6.130972e+00
   1_xyz:  0.2749 0.2961   5.895648e+00   5.949359e+00
   1_adp:  0.1908 0.2172   5.549329e+00   5.681438e+00
   1_occ:  0.1902 0.2171   5.547310e+00   5.681570e+00
   2_bss:  0.1836 0.2094   5.541718e+00   5.670975e+00
   2_xyz:  0.1317 0.1658   5.248308e+00   5.442199e+00
   2_adp:  0.1232 0.1594   5.193993e+00   5.400933e+00
   2_occ:  0.1231 0.1594   5.193284e+00   5.400496e+00
   3_bss:  0.1229 0.1594   5.193894e+00   5.401356e+00
   3_xyz:  0.1182 0.1562   5.166915e+00   5.385305e+00
   3_adp:  0.1148 0.1559   5.154047e+00   5.386721e+00
   3_occ:  0.1148 0.1559   5.153926e+00   5.386730e+00
   4_bss:  0.1148 0.1559   5.153571e+00   5.386399e+00
   4_xyz:  0.1105 0.1557   5.133179e+00   5.382302e+00
   4_adp:  0.1103 0.1556   5.132139e+00   5.382089e+00
   4_occ:  0.1101 0.1557   5.131760e+00   5.381887e+00
   5_bss:  0.1101 0.1556   5.131502e+00   5.381613e+00
   5_xyz:  0.1110 0.1567   5.140481e+00   5.390485e+00
   5_adp:  0.1110 0.1565   5.140908e+00   5.390525e+00
   5_occ:  0.1110 0.1565   5.141025e+00   5.390767e+00
   5_bss:  0.1110 0.1565   5.141019e+00   5.390769e+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:  0.350  20.002   7.355   8.269   8.282   0.000   0.000   0.000
   1_xyz:  0.350  20.002   7.355   8.269   8.282   0.000   0.000   0.000
   1_adp:  0.350  20.002   7.355   8.269   8.282   0.000   0.000   0.000
   1_occ:  0.350  20.002   7.355   8.269   8.282   0.000   0.000   0.000
   2_bss:  0.336  39.158   4.120   4.592   5.463   0.000   0.000   0.000
   2_xyz:  0.336  39.158   4.120   4.592   5.463   0.000   0.000   0.000
   2_adp:  0.336  39.158   4.120   4.592   5.463   0.000   0.000   0.000
   2_occ:  0.336  39.158   4.120   4.592   5.463   0.000   0.000   0.000
   3_bss:  0.326  39.315   3.510   3.927   4.908   0.000   0.000   0.000
   3_xyz:  0.326  39.315   3.510   3.927   4.908   0.000   0.000   0.000
   3_adp:  0.326  39.315   3.510   3.927   4.908   0.000   0.000   0.000
   3_occ:  0.326  39.315   3.510   3.927   4.908   0.000   0.000   0.000
   4_bss:  0.319  39.315   3.510   3.927   4.908   0.000   0.000   0.000
   4_xyz:  0.319  39.315   3.510   3.927   4.908   0.000   0.000   0.000
   4_adp:  0.319  39.315   3.510   3.927   4.908   0.000   0.000   0.000
   4_occ:  0.319  39.315   3.510   3.927   4.908   0.000   0.000   0.000
   5_bss:  0.323  42.817   3.604   3.984   4.990   0.000   0.000   0.000
   5_xyz:  0.323  42.817   3.604   3.984   4.990   0.000   0.000   0.000
   5_adp:  0.323  42.817   3.604   3.984   4.990   0.000   0.000   0.000
   5_occ:  0.323  42.817   3.604   3.984   4.990   0.000   0.000   0.000
   5_bss:  0.323  47.018  -0.586  -0.221   0.807   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  41.169 0.6314  0.6871    41736.563
   1_bss:  40.841 0.6330  0.8764    39157.496
   1_xyz:  30.840 0.7478  1.0045    23056.614
   1_adp:  20.364 0.8595  1.0880    11609.073
   1_occ:  20.357 0.8595  1.0879    11588.533
   2_bss:  20.031 0.8625  0.9677    11226.670
   2_xyz:  15.055 0.9062  0.9958     6991.999
   2_adp:  14.144 0.9139  1.0013     6494.853
   2_occ:  14.136 0.9140  1.0011     6483.154
   3_bss:  14.181 0.9136  0.9779     6521.677
   3_xyz:  13.701 0.9178  0.9778     6265.957
   3_adp:  13.735 0.9176  0.9754     6249.330
   3_occ:  13.735 0.9177  0.9753     6249.554
   4_bss:  13.727 0.9177  0.9753     6241.233
   4_xyz:  13.675 0.9180  0.9757     6214.587
   4_adp:  13.670 0.9180  0.9739     6199.473
   4_occ:  13.667 0.9180  0.9738     6198.648
   5_bss:  13.659 0.9181  0.9768     6197.128
   5_xyz:  13.800 0.9171  0.9760     6309.518
   5_adp:  13.811 0.9170  0.9745     6304.497
   5_occ:  13.813 0.9170  0.9744     6306.613
   5_bss:  13.813 0.9170  0.9747     6306.555
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.3787e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.3787e+01
   1_xyz:   1.382  0.010  0.097 17.830  0.005  4.123   1.0206e-01
   1_adp:   1.382  0.010  0.097 17.830  0.005  4.123   1.0206e-01
   1_occ:   1.382  0.010  0.097 17.830  0.005  4.123   1.0206e-01
   2_bss:   1.382  0.010  0.097 17.830  0.005  4.123   1.0206e-01
   2_xyz:   1.026  0.008  0.082 16.230  0.004  4.125   6.5966e-02
   2_adp:   1.026  0.008  0.082 16.230  0.004  4.125   6.5966e-02
   2_occ:   1.026  0.008  0.082 16.230  0.004  4.125   6.5966e-02
   3_bss:   1.026  0.008  0.082 16.230  0.004  4.125   6.5966e-02
   3_xyz:   0.914  0.006  0.076 15.750  0.003  4.113   5.5054e-02
   3_adp:   0.914  0.006  0.076 15.750  0.003  4.113   5.5054e-02
   3_occ:   0.914  0.006  0.076 15.750  0.003  4.113   5.5054e-02
   4_bss:   0.914  0.006  0.076 15.750  0.003  4.113   5.5054e-02
   4_xyz:   1.003  0.007  0.083 15.785  0.004  4.115   6.3047e-02
   4_adp:   1.003  0.007  0.083 15.785  0.004  4.115   6.3047e-02
   4_occ:   1.003  0.007  0.083 15.785  0.004  4.115   6.3047e-02
   5_bss:   1.003  0.007  0.083 15.785  0.004  4.115   6.3047e-02
   5_xyz:   0.933  0.006  0.077 15.587  0.003  4.115   5.6810e-02
   5_adp:   0.933  0.006  0.077 15.587  0.003  4.115   5.6810e-02
   5_occ:   0.933  0.006  0.077 15.587  0.003  4.115   5.6810e-02
   5_bss:   0.933  0.006  0.077 15.587  0.003  4.115   5.6810e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9743e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9743e+00
   1_xyz:  10.557  0.116  0.431 87.600  0.034  2.251   7.3496e-02
   1_adp:  10.557  0.116  0.431 87.600  0.034  2.251   7.3496e-02
   1_occ:  10.557  0.116  0.431 87.600  0.034  2.251   7.3496e-02
   2_bss:  10.557  0.116  0.431 87.600  0.034  2.251   7.3496e-02
   2_xyz:   6.678  0.045  0.537 84.453  0.036  2.252   5.4027e-02
   2_adp:   6.678  0.045  0.537 84.453  0.036  2.252   5.4027e-02
   2_occ:   6.678  0.045  0.537 84.453  0.036  2.252   5.4027e-02
   3_bss:   6.678  0.045  0.537 84.453  0.036  2.252   5.4027e-02
   3_xyz:   6.585  0.044  0.478 83.518  0.035  2.393   3.3172e-02
   3_adp:   6.585  0.044  0.478 83.518  0.035  2.393   3.3172e-02
   3_occ:   6.585  0.044  0.478 83.518  0.035  2.393   3.3172e-02
   4_bss:   6.585  0.044  0.478 83.518  0.035  2.393   3.3172e-02
   4_xyz:   6.676  0.043  0.581 83.389  0.037  2.354   4.1811e-02
   4_adp:   6.676  0.043  0.581 83.389  0.037  2.354   4.1811e-02
   4_occ:   6.676  0.043  0.581 83.389  0.037  2.354   4.1811e-02
   5_bss:   6.676  0.043  0.581 83.389  0.037  2.354   4.1811e-02
   5_xyz:   6.647  0.044  0.486 82.817  0.035  2.381   3.5393e-02
   5_adp:   6.647  0.044  0.486 82.817  0.035  2.381   3.5393e-02
   5_occ:   6.647  0.044  0.486 82.817  0.035  2.381   3.5393e-02
   5_bss:   6.647  0.044  0.486 82.817  0.035  2.381   3.5393e-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:  55.12   0.00   9.88  55.12   0.00   6.61  53.21   0.00  27.65
   1_occ:  55.12   0.00   9.88  55.12   0.00   6.61  53.21   0.00  27.65
   2_bss:  55.12   0.00   9.88  55.12   0.00   6.61  53.21   0.00  27.65
   2_xyz:  55.12   0.00   9.88  55.12   0.00   6.61  53.21   0.00  27.65
   2_adp:  57.91   0.00  10.18  57.91   0.00   6.59  53.84   0.67  29.78
   2_occ:  57.91   0.00  10.18  57.91   0.00   6.59  53.84   0.67  29.78
   3_bss:  57.91   0.00  10.18  57.91   0.00   6.59  53.84   0.67  29.78
   3_xyz:  57.91   0.00  10.18  57.91   0.00   6.59  53.84   0.67  29.78
   3_adp:  70.72   0.00  10.90  70.72   0.00   6.82  68.45   0.18  33.13
   3_occ:  70.72   0.00  10.90  70.72   0.00   6.82  68.45   0.18  33.13
   4_bss:  70.72   0.00  10.90  70.72   0.00   6.82  68.45   0.18  33.13
   4_xyz:  70.72   0.00  10.90  70.72   0.00   6.82  68.45   0.18  33.13
   4_adp:  79.60   0.00  10.93  79.60   0.00   6.85  74.26   0.14  33.14
   4_occ:  79.60   0.00  10.93  79.60   0.00   6.85  74.26   0.14  33.14
   5_bss:  79.60   0.00  10.93  79.60   0.00   6.85  74.26   0.14  33.14
   5_xyz:  79.60   0.00  10.93  79.60   0.00   6.85  74.26   0.14  33.14
   5_adp:  84.40   0.00  10.84  84.40   0.00   6.80  74.43   0.37  32.84
   5_occ:  84.40   0.00  10.84  84.40   0.00   6.80  74.43   0.37  32.84
   5_bss:  88.61   4.20  15.04  88.61   4.20  11.00  78.63   4.57  37.04
------------------------------------------------------------------------
 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:    1.142    0.014    0.394
   1_adp:    1.142    0.014    0.394
   1_occ:    1.142    0.014    0.394
   2_bss:    1.142    0.014    0.394
   2_xyz:    1.296    0.032    0.455
   2_adp:    1.296    0.032    0.455
   2_occ:    1.296    0.032    0.455
   3_bss:    1.296    0.032    0.455
   3_xyz:    1.360    0.048    0.469
   3_adp:    1.360    0.048    0.469
   3_occ:    1.360    0.048    0.469
   4_bss:    1.360    0.048    0.469
   4_xyz:    1.412    0.037    0.478
   4_adp:    1.412    0.037    0.478
   4_occ:    1.412    0.037    0.478
   5_bss:    1.412    0.037    0.478
   5_xyz:    1.472    0.041    0.482
   5_adp:    1.472    0.041    0.482
   5_occ:    1.472    0.041    0.482
   5_bss:    1.472    0.041    0.482
------------------------------------------------------------------------

CPU time actual refinement: 312.51


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_665/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_665/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_665/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_665/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_665/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 312.35 
  Macro-tasks:
    bulk solvent and scale       = 40.76  
    individual site refinement   = 125.29 
    weights calculation          = 31.89  
    collect and process          = 6.70   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 204.75 
  Micro-tasks:
    mask                            = 1.16   
    f_calc                          = 93.47  
    alpha_beta                      = 8.34   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 103.41 
    fmodel                         = 7.14   
    r_factors                      = 0.17   
    phase_errors                   = 11.17  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 226.28 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.468 micro seconds
Total CPU time: 5.43 minutes
from_scatterers_fft:    617 calls, 93.22 s
gradients_fft:          561 calls, 90.63 s

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

# Date 2008-01-16 Time 02:08:03 PST -0800 (1200478083.51 s)
Start R-work = 0.4012, R-free = 0.3869 (no bulk solvent and anisotropic scale)
Final R-work = 0.1287, R-free = 0.1722 (no bulk solvent and anisotropic scale)

Start R-work = 0.3931, R-free = 0.3765
Final R-work = 0.1110, R-free = 0.1565