# Date 2008-01-16 Time 02:41:15 PST -0800 (1200480075.29 s)
#phil __OFF__

Command line arguments: "../934.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11238
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 934

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 47.3993, 88.5498, 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: 3.33, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.3993, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 2.02025
Completeness in resolution range: 0.972014
Completeness with d_max=infinity: 0.968985

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2039
                             d_min =   2.0203

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.3993, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 2.02025
Completeness in resolution range: 0.972014
Completeness with d_max=infinity: 0.968985

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2043 -  4.3223 [2123/2147]  1908   215  10.1%
  bin  2:  4.3223 -  3.4438 [2031/2051]  1832   199   9.8%
  bin  3:  3.4438 -  3.0124 [2012/2031]  1811   201  10.0%
  bin  4:  3.0124 -  2.7387 [1967/1997]  1766   201  10.2%
  bin  5:  2.7387 -  2.5434 [1990/2009]  1791   199  10.0%
  bin  6:  2.5434 -  2.3940 [1967/1992]  1772   195   9.9%
  bin  7:  2.3940 -  2.2745 [1946/1974]  1751   195  10.0%
  bin  8:  2.2745 -  2.1758 [1959/1995]  1764   195  10.0%
  bin  9:  2.1758 -  2.0923 [1929/1971]  1734   195  10.1%
  bin 10:  2.0923 -  2.0203 [1665/1986]  1501   164   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_934/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.73 -     2.36: 11
        2.36 -     3.00: 1838
        3.00 -     3.63: 4473
        3.63 -     4.27: 8923
        4.27 -     4.90: 12437
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.725 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.827 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.827 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  2.028 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27677 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_934/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_934/model_refine_001.geo

CPU time processing inputs: 9.04


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 47.3993 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4868   r_free= 0.4785   ksol= 0.00   Bsol= 0.00   scale= 0.772    |
|                                                                             |
| 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:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.286346                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.8206 0.99   1382  152 0.3999 0.3731      6.6086       6.518|
|  2:  4.8206 -  3.8466 0.99   1312  151 0.4067 0.4558       6.806      6.9564|
|  3:  3.8466 -  3.3664 0.99   1298  141 0.4544 0.4253       6.705      6.6767|
|  4:  3.3664 -  3.0614 0.99   1295  141 0.4807 0.4100      6.5516      6.4389|
|  5:  3.0614 -  2.8435 0.99   1267  144 0.5064 0.4968      6.3851      6.4062|
|  6:  2.8435 -  2.6768 0.99   1290  143 0.5110 0.5713      6.2893      6.2209|
|  7:  2.6768 -  2.5434 0.99   1264  143 0.5289 0.4804       6.251      6.1879|
|  8:  2.5434 -  2.4331 0.98   1272  137 0.5267 0.4478      6.1992      6.1576|
|  9:  2.4331 -  2.3398 0.98   1248  142 0.5160 0.6007      6.1177      6.1839|
| 10:  2.3398 -  2.2593 1.00   1269  139 0.5411 0.4901      6.1325      6.1187|
| 11:  2.2593 -  2.1889 0.97   1253  138 0.5203 0.5508      6.0332      6.0871|
| 12:  2.1889 -  2.1265 0.98   1250  138 0.5421 0.5055      5.9887      6.0383|
| 13:  2.1265 -  2.0707 0.99   1253  139 0.5264 0.5152      5.9051      5.8491|
| 14:  2.0707 -  2.0203 0.77    977  111 0.5435 0.5271      5.8616      5.7803|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2043 -  4.8206  1382   152  0.71  33.71   0.78     0.73      68427.07|
|  2:  4.8206 -  3.8466  1312   151  0.70  35.05   0.86     0.75     107609.09|
|  3:  3.8466 -  3.3664  1298   141  0.60  43.80   0.81     0.70     113975.34|
|  4:  3.3664 -  3.0614  1295   141  0.50  51.54   0.78     0.58     101398.13|
|  5:  3.0614 -  2.8435  1267   144  0.42  58.52   0.73     0.48      82021.02|
|  6:  2.8435 -  2.6768  1290   143  0.37  61.78   0.70     0.42      74566.46|
|  7:  2.6768 -  2.5434  1264   143  0.37  62.54   0.71     0.41      66017.63|
|  8:  2.5434 -  2.4331  1272   137  0.37  62.29   0.73     0.42      58706.76|
|  9:  2.4331 -  2.3398  1248   142  0.35  63.70   0.70     0.40      55221.66|
| 10:  2.3398 -  2.2593  1269   139  0.32  66.28   0.71     0.36      51974.77|
| 11:  2.2593 -  2.1889  1253   138  0.29  68.07   0.73     0.35      49552.78|
| 12:  2.1889 -  2.1265  1250   138  0.30  67.97   0.72     0.36      44720.98|
| 13:  2.1265 -  2.0707  1253   139  0.28  68.81   0.71     0.33      38868.59|
| 14:  2.0707 -  2.0203   977   111  0.24  72.08   0.70     0.25      32863.45|
|alpha:            min =        0.25 max =            0.75 mean =         0.47|
|beta:             min =    32863.45 max =       113975.34 mean =     68457.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           89.98 mean =        57.79|
|phase err.(test): min =        0.00 max =           89.96 mean =        57.94|
|-----------------------------------------------------------------------------|

============================== 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 = 15.708584             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.592   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.579882              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.732   (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:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      162 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      668 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1479 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2558 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3815 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4965 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6454 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7559 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.691 |
| 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 |       1.716 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.401)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.401)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4912   r_free= 0.4796   ksol= 0.00   Bsol= 0.00   scale= 0.745    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.287851                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4789   r_free= 0.4669   ksol= 0.30   Bsol= 50.00   scale= 0.955   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.23,7.41,11.14,0.00,0.00,0.00); trace/3= 8.26                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.281464                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.746850             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.195   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.350244              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.621   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4789      final r-factor (work) = 0.3980          |
| start r-factor (free) = 0.4669      final r-factor (free) = 0.4275          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 97.8943 = 13.75 * 0.50 * 6.2856 + 1.00 * 54.6907                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.7523 = 13.75 * 0.50 * 6.1979 + 1.00 * 0.1516                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3980      final r-factor (work) = 0.3529          |
| start r-factor (free) = 0.4275      final r-factor (free) = 0.4083          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.3831 = 1.35 * 1.00 * 6.1979 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2819 = 1.35 * 1.00 * 6.1187 + 1.00 * 0.0201                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.401)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.06  14.30    None  None   None       |
|    all(noH): 2823   0      0.00    103.06  14.30    None  None   None       |
|    Sol.    : 438    0      0.00    103.06  29.12    None  None   None       |
|    Mac.    : 2385   0      0.00    79.51   11.58    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.306: 1397   |   5:    51.532 -  61.838:   40        |
|      1:    10.306 -  20.613:  757   |   6:    61.838 -  72.144:   24        |
|      2:    20.613 -  30.919:  354   |   7:    72.144 -  82.451:   13        |
|      3:    30.919 -  41.225:  172   |   8:    82.451 -  92.757:    2        |
|      4:    41.225 -  51.532:   63   |   9:    92.757 - 103.063:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3529 r_free = 0.4083             target_work(ml) = 6.098         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3524 r_free = 0.4086             target_work(ml) = 6.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3524   r_free= 0.4086   ksol= 0.30   Bsol= 50.00   scale= 1.067   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.23,7.41,11.14,0.00,0.00,0.00); trace/3= 8.26                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.097309                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3513   r_free= 0.4064   ksol= 0.31   Bsol= 50.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.62,4.87,7.97,0.00,0.00,0.00); trace/3= 5.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.099215                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.318761              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.884   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.540448              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.552  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3513      final r-factor (work) = 0.2756          |
| start r-factor (free) = 0.4064      final r-factor (free) = 0.3306          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.4618 = 6.32 * 0.50 * 6.1120 + 1.00 * 0.1516                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.0482 = 6.32 * 0.50 * 5.9976 + 1.00 * 0.0996                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2756      final r-factor (work) = 0.2527          |
| start r-factor (free) = 0.3306      final r-factor (free) = 0.3091          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3113 = 0.54 * 1.00 * 5.9976 + 1.00 * 0.0700                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3301 = 0.54 * 1.00 * 5.8623 + 1.00 * 0.1618                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.401)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.09  13.57    None  None   None       |
|    all(noH): 2823   0      0.00    104.09  13.57    None  None   None       |
|    Sol.    : 438    0      0.00    104.09  33.57    None  None   None       |
|    Mac.    : 2385   0      0.00    69.15   9.90     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.409: 1599   |   5:    52.044 -  62.453:   53        |
|      1:    10.409 -  20.818:  658   |   6:    62.453 -  72.862:   14        |
|      2:    20.818 -  31.227:  242   |   7:    72.862 -  83.271:    6        |
|      3:    31.227 -  41.635:  152   |   8:    83.271 -  93.680:    0        |
|      4:    41.635 -  52.044:   98   |   9:    93.680 - 104.089:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2527 r_free = 0.3091             target_work(ml) = 5.838         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2524 r_free = 0.3092             target_work(ml) = 5.837         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2524   r_free= 0.3092   ksol= 0.31   Bsol= 50.00   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.62,4.87,7.97,0.00,0.00,0.00); trace/3= 5.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.837463                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2512   r_free= 0.3087   ksol= 0.33   Bsol= 70.58   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.25,3.16,5.35,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.839595                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.099471              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.032   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 8.017246              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.782   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2512      final r-factor (work) = 0.1821          |
| start r-factor (free) = 0.3087      final r-factor (free) = 0.2361          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.9838 = 6.10 * 0.50 * 5.8642 + 1.00 * 0.0996                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.5157 = 6.10 * 0.50 * 5.7157 + 1.00 * 0.0844                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1821      final r-factor (work) = 0.1628          |
| start r-factor (free) = 0.2361      final r-factor (free) = 0.2217          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 45.8426 = 8.02 * 1.00 * 5.7157 + 1.00 * 0.0186                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 44.1497 = 8.02 * 1.00 * 5.5043 + 1.00 * 0.0205                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.401)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.39  14.87    None  None   None       |
|    all(noH): 2823   0      0.00    105.39  14.87    None  None   None       |
|    Sol.    : 438    0      0.35    105.39  43.24    None  None   None       |
|    Mac.    : 2385   0      0.00    93.10   9.66     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.539: 1680   |   5:    52.695 -  63.234:   95        |
|      1:    10.539 -  21.078:  585   |   6:    63.234 -  73.773:   59        |
|      2:    21.078 -  31.617:  161   |   7:    73.773 -  84.311:   26        |
|      3:    31.617 -  42.156:  106   |   8:    84.311 -  94.850:   12        |
|      4:    42.156 -  52.695:   97   |   9:    94.850 - 105.389:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1628 r_free = 0.2217             target_work(ml) = 5.475         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1626 r_free = 0.2217             target_work(ml) = 5.475         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1626   r_free= 0.2217   ksol= 0.33   Bsol= 70.58   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.25,3.16,5.35,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.475012                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1628   r_free= 0.2215   ksol= 0.34   Bsol= 87.79   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.87,2.46,4.24,0.00,0.00,0.00); trace/3= 2.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.474732                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.448845              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.250  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.382348              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.915  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1628      final r-factor (work) = 0.1440          |
| start r-factor (free) = 0.2215      final r-factor (free) = 0.1981          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8281 = 2.45 * 0.50 * 5.5077 + 1.00 * 0.0844                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7105 = 2.45 * 0.50 * 5.4265 + 1.00 * 0.0661                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1440      final r-factor (work) = 0.1401          |
| start r-factor (free) = 0.1981      final r-factor (free) = 0.1876          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0952 = 0.38 * 1.00 * 5.4265 + 1.00 * 0.0203                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0647 = 0.38 * 1.00 * 5.3577 + 1.00 * 0.0161                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.401)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.10  13.85    None  None   None       |
|    all(noH): 2823   0      0.00    103.10  13.85    None  None   None       |
|    Sol.    : 438    0      0.92    103.10  40.90    None  None   None       |
|    Mac.    : 2385   0      0.00    84.51   8.88     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.310: 1753   |   5:    51.551 -  61.861:   78        |
|      1:    10.310 -  20.620:  560   |   6:    61.861 -  72.171:   50        |
|      2:    20.620 -  30.930:  133   |   7:    72.171 -  82.481:   19        |
|      3:    30.930 -  41.241:  107   |   8:    82.481 -  92.791:   10        |
|      4:    41.241 -  51.551:  110   |   9:    92.791 - 103.101:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1401 r_free = 0.1876             target_work(ml) = 5.331         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1399 r_free = 0.1875             target_work(ml) = 5.330         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1399   r_free= 0.1875   ksol= 0.34   Bsol= 87.79   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.87,2.46,4.24,0.00,0.00,0.00); trace/3= 2.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.330467                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1399   r_free= 0.1878   ksol= 0.34   Bsol= 80.00   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.96,2.46,4.09,0.00,0.00,0.00); trace/3= 2.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.330283                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.783354              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.830  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.692464              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.499   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1399      final r-factor (work) = 0.1310          |
| start r-factor (free) = 0.1878      final r-factor (free) = 0.1763          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8429 = 1.78 * 0.50 * 5.3571 + 1.00 * 0.0661                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7915 = 1.78 * 0.50 * 5.3024 + 1.00 * 0.0634                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1310      final r-factor (work) = 0.1293          |
| start r-factor (free) = 0.1763      final r-factor (free) = 0.1759          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6939 = 0.69 * 1.00 * 5.3024 + 1.00 * 0.0222                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7204 = 0.69 * 1.00 * 5.2644 + 1.00 * 0.0749                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.401)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.55  13.62    None  None   None       |
|    all(noH): 2823   0      0.00    104.55  13.62    None  None   None       |
|    Sol.    : 438    0      0.75    104.55  40.34    None  None   None       |
|    Mac.    : 2385   0      0.00    86.69   8.71     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.455: 1824   |   5:    52.274 -  62.729:   79        |
|      1:    10.455 -  20.910:  498   |   6:    62.729 -  73.184:   37        |
|      2:    20.910 -  31.364:  132   |   7:    73.184 -  83.638:   21        |
|      3:    31.364 -  41.819:  120   |   8:    83.638 -  94.093:    9        |
|      4:    41.819 -  52.274:  101   |   9:    94.093 - 104.548:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1293 r_free = 0.1759             target_work(ml) = 5.263         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1291 r_free = 0.1760             target_work(ml) = 5.263         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1291   r_free= 0.1760   ksol= 0.34   Bsol= 80.00   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.96,2.46,4.09,0.00,0.00,0.00); trace/3= 2.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.263143                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.8206 0.99   1382  152 0.1055 0.1353       5.435      5.5503|
|  2:  4.8206 -  3.8466 0.99   1312  151 0.0906 0.1162      5.4883      5.7029|
|  3:  3.8466 -  3.3664 0.99   1298  141 0.1177 0.1560       5.573      5.8844|
|  4:  3.3664 -  3.0614 0.99   1295  141 0.1366 0.1860       5.557      5.7414|
|  5:  3.0614 -  2.8435 0.99   1267  144 0.1599 0.1914      5.4929      5.6352|
|  6:  2.8435 -  2.6768 0.99   1290  143 0.1437 0.2413      5.3558      5.6782|
|  7:  2.6768 -  2.5434 0.99   1264  143 0.1511 0.1739      5.3135      5.4479|
|  8:  2.5434 -  2.4331 0.98   1272  137 0.1437 0.1801      5.2376      5.4409|
|  9:  2.4331 -  2.3398 0.98   1248  142 0.1384 0.2132      5.1615      5.4205|
| 10:  2.3398 -  2.2593 1.00   1269  139 0.1379 0.1845      5.1117      5.3177|
| 11:  2.2593 -  2.1889 0.97   1253  138 0.1347 0.1978      5.0679      5.2877|
| 12:  2.1889 -  2.1265 0.98   1250  138 0.1348 0.1986       5.008       5.361|
| 13:  2.1265 -  2.0707 0.99   1253  139 0.1311 0.1995      4.9244      5.1461|
| 14:  2.0707 -  2.0203 0.77    977  111 0.1219 0.1884      4.8021      5.0628|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2043 -  4.8206  1382   152  0.94   9.69   0.96     0.93       7921.19|
|  2:  4.8206 -  3.8466  1312   151  0.95   8.62   1.00     0.98       9902.57|
|  3:  3.8466 -  3.3664  1298   141  0.93  12.27   1.02     1.01      12099.54|
|  4:  3.3664 -  3.0614  1295   141  0.91  15.07   1.00     0.98      12203.39|
|  5:  3.0614 -  2.8435  1267   144  0.88  18.56   1.00     0.97      11157.36|
|  6:  2.8435 -  2.6768  1290   143  0.88  18.51   0.98     0.94       9315.18|
|  7:  2.6768 -  2.5434  1264   143  0.88  18.37   0.98     0.95       8235.66|
|  8:  2.5434 -  2.4331  1272   137  0.89  17.66   0.98     0.94       6994.76|
|  9:  2.4331 -  2.3398  1248   142  0.89  17.60   1.00     0.95       6381.19|
| 10:  2.3398 -  2.2593  1269   139  0.88  17.89   0.98     0.93       5506.24|
| 11:  2.2593 -  2.1889  1253   138  0.88  18.12   0.98     0.93       5438.14|
| 12:  2.1889 -  2.1265  1250   138  0.88  18.23   0.99     0.97       5046.79|
| 13:  2.1265 -  2.0707  1253   139  0.88  18.14   0.97     0.94       4280.56|
| 14:  2.0707 -  2.0203   977   111  0.90  16.42   0.95     0.90       3199.56|
|alpha:            min =        0.90 max =            1.01 mean =         0.95|
|beta:             min =     3199.56 max =        12203.39 mean =      7797.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.93 mean =        16.01|
|phase err.(test): min =        0.00 max =           89.67 mean =        15.35|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1291   r_free= 0.1759   ksol= 0.33   Bsol= 76.52   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,-0.42,1.20,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.263023                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1291   r_free= 0.1759   ksol= 0.33   Bsol= 76.52   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,-0.42,1.20,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.263023                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.8206 0.99   1382  152 0.1052 0.1352      5.4321      5.5491|
|  2:  4.8206 -  3.8466 0.99   1312  151 0.0903 0.1157      5.4865      5.6995|
|  3:  3.8466 -  3.3664 0.99   1298  141 0.1177 0.1560      5.5725      5.8852|
|  4:  3.3664 -  3.0614 0.99   1295  141 0.1368 0.1861      5.5584      5.7423|
|  5:  3.0614 -  2.8435 0.99   1267  144 0.1601 0.1914      5.4942      5.6363|
|  6:  2.8435 -  2.6768 0.99   1290  143 0.1437 0.2415      5.3566       5.679|
|  7:  2.6768 -  2.5434 0.99   1264  143 0.1512 0.1744      5.3143      5.4491|
|  8:  2.5434 -  2.4331 0.98   1272  137 0.1438 0.1800      5.2382      5.4409|
|  9:  2.4331 -  2.3398 0.98   1248  142 0.1384 0.2133      5.1615      5.4206|
| 10:  2.3398 -  2.2593 1.00   1269  139 0.1379 0.1846      5.1116      5.3184|
| 11:  2.2593 -  2.1889 0.97   1253  138 0.1347 0.1976      5.0676      5.2867|
| 12:  2.1889 -  2.1265 0.98   1250  138 0.1348 0.1983      5.0077      5.3602|
| 13:  2.1265 -  2.0707 0.99   1253  139 0.1311 0.1996      4.9242      5.1466|
| 14:  2.0707 -  2.0203 0.77    977  111 0.1219 0.1882       4.802       5.062|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2043 -  4.8206  1382   152  0.94   9.67   0.96     0.93       7885.60|
|  2:  4.8206 -  3.8466  1312   151  0.95   8.59   1.00     0.98       9866.04|
|  3:  3.8466 -  3.3664  1298   141  0.93  12.26   1.02     1.02      12071.30|
|  4:  3.3664 -  3.0614  1295   141  0.91  15.09   1.00     0.98      12225.23|
|  5:  3.0614 -  2.8435  1267   144  0.88  18.58   1.00     0.98      11185.36|
|  6:  2.8435 -  2.6768  1290   143  0.88  18.54   0.98     0.95       9334.69|
|  7:  2.6768 -  2.5434  1264   143  0.88  18.39   0.99     0.95       8250.54|
|  8:  2.5434 -  2.4331  1272   137  0.89  17.67   0.98     0.95       7001.03|
|  9:  2.4331 -  2.3398  1248   142  0.89  17.62   1.01     0.96       6388.42|
| 10:  2.3398 -  2.2593  1269   139  0.88  17.88   0.99     0.94       5500.78|
| 11:  2.2593 -  2.1889  1253   138  0.88  18.11   0.99     0.93       5433.67|
| 12:  2.1889 -  2.1265  1250   138  0.88  18.21   1.00     0.98       5042.84|
| 13:  2.1265 -  2.0707  1253   139  0.88  18.14   0.98     0.95       4278.05|
| 14:  2.0707 -  2.0203   977   111  0.90  16.41   0.96     0.91       3195.59|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     3195.59 max =        12225.23 mean =      7795.67|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        16.00|
|phase err.(test): min =        0.00 max =           89.50 mean =        15.34|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.401)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.97    107.52  16.59    None  None   None       |
|    all(noH): 2823   0      2.97    107.52  16.59    None  None   None       |
|    Sol.    : 438    0      3.73    107.52  43.31    None  None   None       |
|    Mac.    : 2385   0      2.97    89.67   11.68    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:     2.973 -  13.428: 1824   |   5:    55.247 -  65.702:   79        |
|      1:    13.428 -  23.883:  498   |   6:    65.702 -  76.157:   37        |
|      2:    23.883 -  34.337:  132   |   7:    76.157 -  86.611:   21        |
|      3:    34.337 -  44.792:  120   |   8:    86.611 -  97.066:    9        |
|      4:    44.792 -  55.247:  101   |   9:    97.066 - 107.521:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 339         
Filter by distance & map next to the model:
   mapped sites are within: 0.371 - 5.787
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 333 from: 339
   mapped sites are within: 0.709 - 5.787

peak=    9.901 closest distance to " CB  VAL A 230 " =    1.465
peak=    5.626 closest distance to " CG1 VAL A 296 " =    1.250
peak=    5.566 closest distance to " CD2 LEU A   5 " =    1.191
peak=    5.390 closest distance to " CB  GLN A 223 " =    1.495
peak=    5.160 closest distance to " O   HOH Z 210 " =    1.200
peak=    5.022 closest distance to " CG  PRO A 280 " =    0.958
peak=    4.886 closest distance to " CG  LEU A 228 " =    1.329
peak=    4.862 closest distance to " CD1AILE A 234 " =    1.122
peak=    4.819 closest distance to " CG  LEU A   5 " =    1.233
peak=    4.808 closest distance to " CG  ARG A 138 " =    1.290
peak=    4.798 closest distance to " CG  PRO A 198 " =    1.329
peak=    4.725 closest distance to " CZ  PHE A 218 " =    1.110
peak=    4.669 closest distance to " O   HOH Z 232 " =    2.203
peak=    4.627 closest distance to " NH2 ARG A  56 " =    2.179
peak=    4.618 closest distance to " O   HOH Z 248 " =    1.438
peak=    4.608 closest distance to " CG2 VAL A 296 " =    1.064
peak=    4.605 closest distance to " O   HOH Z 127 " =    1.000
peak=    4.577 closest distance to " CD2 LEU A 228 " =    1.253
peak=    4.550 closest distance to " CB  VAL A 296 " =    1.153
peak=    4.546 closest distance to " O   HOH Z 425 " =    1.567
peak=    4.545 closest distance to " CA  TYR A  30 " =    1.015
peak=    4.538 closest distance to " O   HOH Z 411 " =    3.753
peak=    4.494 closest distance to " CZ3 TRP A 266 " =    1.208
peak=    4.471 closest distance to " NH2AARG A 145 " =    1.207
peak=    4.470 closest distance to " O   HOH Z 369 " =    2.080
peak=    4.420 closest distance to " CB  SER A  63 " =    1.221
peak=    4.367 closest distance to " CA  ALA A  51 " =    1.017
peak=    4.348 closest distance to " CB  GLN A 183 " =    1.248
peak=    4.275 closest distance to " NE2 GLN A  11 " =    1.057
peak=    4.240 closest distance to " O   PRO A 198 " =    1.556
peak=    4.239 closest distance to " CB  ASP A 124 " =    0.831
peak=    4.237 closest distance to " O   HOH Z 142 " =    1.843
peak=    4.234 closest distance to " O   HOH Z 247 " =    1.478
peak=    4.205 closest distance to " CG  PRO A 243 " =    1.165
peak=    4.170 closest distance to " O   SER A  87 " =    2.333
peak=    4.166 closest distance to " CB  ASN A 142 " =    1.130
peak=    4.163 closest distance to " CA  VAL A 230 " =    1.169
peak=    4.163 closest distance to " CG AARG A 275 " =    1.379
peak=    4.161 closest distance to " O   HOH Z 214 " =    1.453
peak=    4.153 closest distance to " O   HOH Z 128 " =    1.444
peak=    4.153 closest distance to " O   HOH Z 126 " =    1.649
peak=    4.150 closest distance to " CD2 TRP A 179 " =    1.334
peak=    4.147 closest distance to " CB  ARG A 190 " =    1.643
peak=    4.090 closest distance to " O   ASP A 124 " =    1.118
peak=    4.089 closest distance to " CB  TYR A 169 " =    0.770
peak=    4.081 closest distance to " O   HOH Z 265 " =    2.027
peak=    4.076 closest distance to " O   HOH Z 368 " =    2.561
peak=    4.071 closest distance to " O   HOH Z 207 " =    1.315
peak=    4.028 closest distance to " N   SER A 164 " =    0.958
peak=    4.011 closest distance to " CB  GLU A 277 " =    3.818
peak=    4.005 closest distance to " CA  ARG A 195 " =    1.222
peak=    3.996 closest distance to " CD1 LEU A  96 " =    0.836
peak=    3.988 closest distance to " O   ASP A 200 " =    1.748
peak=    3.987 closest distance to " O   HOH Z   4 " =    1.697
peak=    3.979 closest distance to " CD  LYS A 166 " =    1.413
peak=    3.972 closest distance to " CB  GLU A 128 " =    1.016
peak=    3.970 closest distance to " CG  MET A 185 " =    1.329
peak=    3.969 closest distance to " CA  ALA A 295 " =    1.046
peak=    3.967 closest distance to " CD  ARG A  66 " =    2.547
peak=    3.959 closest distance to " O   HOH Z 251 " =    1.722
peak=    3.944 closest distance to " CB  TRP A 266 " =    1.054
peak=    3.917 closest distance to " CB  LEU A  83 " =    0.720
peak=    3.891 closest distance to " O   HOH Z 130 " =    1.115
peak=    3.890 closest distance to " O   HOH Z 287 " =    1.841
peak=    3.883 closest distance to " CB  ASN A  39 " =    0.903
peak=    3.880 closest distance to " O   HOH Z  69 " =    0.838
peak=    3.877 closest distance to " CB  ARG A  79 " =    1.402
peak=    3.876 closest distance to " CB  ASN A 148 " =    1.398
peak=    3.869 closest distance to " O   HOH Z 188 " =    3.076
peak=    3.866 closest distance to " CE3 TRP A  85 " =    1.113
peak=    3.856 closest distance to " CA  GLY A 267 " =    0.880
peak=    3.848 closest distance to " OG  SER A 276 " =    1.473
peak=    3.844 closest distance to " O   HOH Z  76 " =    1.214
peak=    3.842 closest distance to " CG2 THR A 221 " =    1.074
peak=    3.830 closest distance to " CB  ARG A 275 " =    0.999
peak=    3.825 closest distance to " O   HOH Z  80 " =    1.989
peak=    3.819 closest distance to " CB BVAL A  41 " =    1.291
peak=    3.806 closest distance to " CA  GLU A 152 " =    0.926
peak=    3.806 closest distance to " O   HOH Z  49 " =    1.423
peak=    3.790 closest distance to " CG2 ILE A 234 " =    0.997
peak=    3.788 closest distance to " CA  MET A 105 " =    0.998
peak=    3.779 closest distance to " CB  VAL A 202 " =    1.572
peak=    3.776 closest distance to " CB  GLN A  89 " =    1.163
peak=    3.757 closest distance to " CG  GLU A  37 " =    0.980
peak=    3.753 closest distance to " CB  SER A 273 " =    1.089
peak=    3.753 closest distance to " CD  ARG A 159 " =    0.739
peak=    3.750 closest distance to " O   HOH Z 427 " =    3.059
peak=    3.744 closest distance to " CB  SER A  62 " =    0.995
peak=    3.744 closest distance to " O   HOH Z 261 " =    2.071
peak=    3.737 closest distance to " O   HOH Z 359 " =    1.808
peak=    3.735 closest distance to " CA  ALA A 291 " =    0.897
peak=    3.733 closest distance to " ND2 ASN A 187 " =    1.646
peak=    3.728 closest distance to " CD  ARG A 269 " =    0.944
peak=    3.716 closest distance to " CA  ALA A 160 " =    1.035
peak=    3.714 closest distance to " N   ASN A  39 " =    1.254
peak=    3.711 closest distance to " CB  TRP A 179 " =    1.390
peak=    3.709 closest distance to " CG  PRO A 213 " =    1.188
peak=    3.709 closest distance to " CZ3 TRP A  85 " =    0.876
peak=    3.705 closest distance to " CE  LYS A  76 " =    0.868
peak=    3.703 closest distance to " CA  ARG A  36 " =    1.099
peak=    3.700 closest distance to " O  BHOH Z  74 " =    1.202
peak=    3.697 closest distance to " O   HOH Z 154 " =    1.407
peak=    3.696 closest distance to " CA  SER A  87 " =    0.952
peak=    3.692 closest distance to " O   HOH Z 234 " =    3.727
peak=    3.690 closest distance to " NE2 GLN A  77 " =    3.315
peak=    3.682 closest distance to " O   HOH Z 313 " =    1.776
peak=    3.682 closest distance to " O   HOH Z 261 " =    1.433
peak=    3.680 closest distance to " O   HOH Z 280 " =    2.921
peak=    3.678 closest distance to " O   THR A 220 " =    1.238
peak=    3.678 closest distance to " O   HOH Z  78 " =    1.789
peak=    3.667 closest distance to " CG  LEU A 167 " =    1.076
peak=    3.665 closest distance to " CA  VAL A 125 " =    1.290
peak=    3.658 closest distance to " O   HOH Z 184 " =    1.487
peak=    3.656 closest distance to " O   HOH Z 422 " =    2.662
peak=    3.648 closest distance to " CZ3 TRP A 274 " =    4.586
peak=    3.646 closest distance to " O   HOH Z 303 " =    2.231
peak=    3.644 closest distance to " CA  ALA A  21 " =    1.185
peak=    3.640 closest distance to " NH2 ARG A  56 " =    1.128
peak=    3.637 closest distance to " O   HOH Z 107 " =    0.994
peak=    3.636 closest distance to " O   HOH Z 353 " =    2.566
peak=    3.629 closest distance to " O   HOH Z  19 " =    2.221
peak=    3.626 closest distance to " O   HOH Z 402 " =    1.426
peak=    3.624 closest distance to " N   ALA A 256 " =    1.216
peak=    3.618 closest distance to " O   HOH Z  63 " =    1.862
peak=    3.618 closest distance to " O   THR A 182 " =    1.417
peak=    3.617 closest distance to " CB  GLU A  46 " =    0.910
peak=    3.617 closest distance to " O   HOH Z 131 " =    2.262
peak=    3.614 closest distance to " CG  PHE A 204 " =    0.908
peak=    3.614 closest distance to " O   HOH Z 290 " =    1.225
peak=    3.614 closest distance to " CD  LYS A 119 " =    1.834
peak=    3.605 closest distance to " CG1 VAL A 153 " =    0.999
peak=    3.603 closest distance to " O   HOH Z 316 " =    3.203
peak=    3.595 closest distance to " O   HOH Z 146 " =    1.580
peak=    3.594 closest distance to " CB  ASN A 173 " =    1.076
peak=    3.593 closest distance to " O   HOH Z 193 " =    1.814
peak=    3.592 closest distance to " CZ  PHE A 192 " =    1.000
peak=    3.591 closest distance to " OE1 GLN A  55 " =    1.339
peak=    3.590 closest distance to " CA  ILE A 106 " =    0.799
peak=    3.580 closest distance to " CG1 ILE A  20 " =    1.313
peak=    3.579 closest distance to " O   HOH Z   9 " =    1.308
peak=    3.578 closest distance to " O   HOH Z 298 " =    1.976
peak=    3.576 closest distance to " CB  SER A 216 " =    0.932
peak=    3.575 closest distance to " ND2 ASN A 249 " =    1.882
peak=    3.572 closest distance to " CB  GLU A 152 " =    1.176
peak=    3.571 closest distance to " NE2 HIS A 207 " =    1.057
peak=    3.571 closest distance to " NH1AARG A 145 " =    1.274
peak=    3.560 closest distance to " CA  ASP A 140 " =    1.542
peak=    3.555 closest distance to " CB  LEU A 143 " =    1.286
peak=    3.548 closest distance to " CB  VAL A 265 " =    1.222
peak=    3.546 closest distance to " O   HOH Z 214 " =    3.077
peak=    3.546 closest distance to " CA  ALA A 154 " =    1.061
peak=    3.545 closest distance to " CG2 VAL A 197 " =    1.104
peak=    3.544 closest distance to " CZ  PHE A  38 " =    1.158
peak=    3.538 closest distance to " O   HOH Z 172 " =    3.889
peak=    3.530 closest distance to " CD1 ILE A 199 " =    0.969
peak=    3.527 closest distance to " OG  SER A 245 " =    1.661
peak=    3.523 closest distance to " CA  TYR A 116 " =    1.406
peak=    3.519 closest distance to " O   HOH Z 193 " =    1.985
peak=    3.519 closest distance to " CG1 ILE A 120 " =    1.105
peak=    3.508 closest distance to " O   HOH Z 438 " =    2.700
peak=    3.507 closest distance to " CD1 LEU A   5 " =    1.399
peak=    3.506 closest distance to " CG  GLN A  58 " =    0.982
peak=    3.503 closest distance to " O   HOH Z  43 " =    2.091
peak=    3.496 closest distance to " OG BSER A 164 " =    2.248
peak=    3.495 closest distance to " O   HOH Z 199 " =    1.608
peak=    3.493 closest distance to " CB  SER A 288 " =    1.464
peak=    3.490 closest distance to " CB  SER A  62 " =    1.178
peak=    3.490 closest distance to " O   HOH Z 346 " =    1.545
peak=    3.485 closest distance to " CG2AVAL A 121 " =    2.147
peak=    3.482 closest distance to " O  BHOH Z 338 " =    2.265
peak=    3.472 closest distance to " O   HOH Z 406 " =    1.557
peak=    3.470 closest distance to " N   PHE A 130 " =    1.349
peak=    3.461 closest distance to " CB  SER A   3 " =    1.398
peak=    3.461 closest distance to " CD ALYS A 290 " =    1.026
peak=    3.455 closest distance to " O   HOH Z 394 " =    1.352
peak=    3.449 closest distance to " CA  ASP A 162 " =    0.992
peak=    3.444 closest distance to " CB  ALA A 242 " =    0.807
peak=    3.442 closest distance to " CD1 LEU A 300 " =    1.082
peak=    3.439 closest distance to " CB  ASP A 140 " =    1.009
peak=    3.429 closest distance to " O   HOH Z 163 " =    1.530
peak=    3.414 closest distance to " ND2BASN A 224 " =    0.907
peak=    3.411 closest distance to " O   HOH Z 357 " =    2.491
peak=    3.411 closest distance to " O   THR A 294 " =    1.535
peak=    3.410 closest distance to " O   HOH Z  56 " =    1.651
peak=    3.402 closest distance to " NH1 ARG A  14 " =    1.040
peak=    3.399 closest distance to " O   HOH Z 213 " =    1.913
peak=    3.396 closest distance to " O   TYR A 116 " =    1.304
peak=    3.396 closest distance to " O   HOH Z 158 " =    3.042
peak=    3.394 closest distance to " O   HOH Z 368 " =    3.387
peak=    3.389 closest distance to " O   HOH Z 126 " =    1.958
peak=    3.389 closest distance to " O   HOH Z 343 " =    2.775
peak=    3.388 closest distance to " O   HOH Z 124 " =    1.946
peak=    3.388 closest distance to " O   HOH Z 227 " =    1.748
peak=    3.387 closest distance to " CG  ARG A 269 " =    1.831
peak=    3.384 closest distance to " O   HOH Z 327 " =    2.111
peak=    3.381 closest distance to " CB  MET A  40 " =    0.868
peak=    3.380 closest distance to " O   HOH Z 145 " =    1.227
peak=    3.379 closest distance to " O   ASN A  74 " =    1.435
peak=    3.378 closest distance to " O   HOH Z 423 " =    1.695
peak=    3.375 closest distance to " O   THR A 251 " =    1.118
peak=    3.367 closest distance to " CA  LEU A 282 " =    1.092
peak=    3.360 closest distance to " O   HOH Z 171 " =    3.936
peak=    3.355 closest distance to " CE1 HIS A 115 " =    1.013
peak=    3.351 closest distance to " CG1 ILE A  33 " =    1.281
peak=    3.349 closest distance to " CA  GLY A 211 " =    1.423
peak=    3.349 closest distance to " ND1 HIS A  81 " =    1.862
peak=    3.348 closest distance to " O   HOH Z 391 " =    2.914
peak=    3.345 closest distance to " O   PHE A  61 " =    1.430
peak=    3.345 closest distance to " CA  ALA A 184 " =    0.989
peak=    3.342 closest distance to " CE3 TRP A 150 " =    1.145
peak=    3.336 closest distance to " O   HOH Z 132 " =    2.964
peak=    3.331 closest distance to " CB  PRO A  90 " =    1.218
peak=    3.330 closest distance to " O   HOH Z 383 " =    1.961
peak=    3.329 closest distance to " CB  TRP A 150 " =    1.449
peak=    3.325 closest distance to " O   HOH Z 203 " =    1.677
peak=    3.325 closest distance to " CG2 VAL A 257 " =    0.851
peak=    3.321 closest distance to " N   ARG A 156 " =    1.656
peak=    3.319 closest distance to " CB  PRO A 243 " =    1.335
peak=    3.316 closest distance to " CA  ALA A 100 " =    0.936
peak=    3.314 closest distance to " CA  ASP A 191 " =    1.226
peak=    3.313 closest distance to " CG  GLN A  11 " =    1.425
peak=    3.310 closest distance to " CA  GLN A  94 " =    0.829
peak=    3.305 closest distance to " CB  ARG A 138 " =    0.980
peak=    3.303 closest distance to " O   HOH Z 144 " =    1.675
peak=    3.303 closest distance to " CA  ASN A 284 " =    0.944
peak=    3.303 closest distance to " O   HOH Z  88 " =    3.131
peak=    3.301 closest distance to " CB  ASN A 187 " =    1.148
peak=    3.299 closest distance to " CB  GLU A  37 " =    0.889
peak=    3.298 closest distance to " N   SER A 271 " =    1.107
peak=    3.297 closest distance to " O   ALA A 165 " =    1.447
peak=    3.295 closest distance to " O   GLN A  88 " =    1.653
peak=    3.295 closest distance to " CD1 ILE A  33 " =    1.890
peak=    3.292 closest distance to " CB  ALA A 291 " =    1.188
peak=    3.289 closest distance to " CB  SER A  26 " =    1.779
peak=    3.289 closest distance to " CD2 LEU A 255 " =    1.715
peak=    3.280 closest distance to " O   PRO A 213 " =    1.473
peak=    3.278 closest distance to " O   HOH Z 365 " =    2.859
peak=    3.277 closest distance to " O   HOH Z 152 " =    2.029
peak=    3.277 closest distance to " O   HOH Z 102 " =    1.260
peak=    3.277 closest distance to " O   HOH Z  54 " =    1.510
peak=    3.275 closest distance to " O   HOH Z 272 " =    1.856
peak=    3.274 closest distance to " O   HOH Z 222 " =    1.023
peak=    3.271 closest distance to " CB  ALA A   9 " =    1.669
peak=    3.270 closest distance to " N   CYS A 260 " =    0.776
peak=    3.268 closest distance to " CB  MET A  47 " =    0.989
peak=    3.267 closest distance to " O   HOH Z 258 " =    1.831
peak=    3.264 closest distance to " CA  VAL A  41 " =    0.709
peak=    3.262 closest distance to " CA  ARG A 139 " =    1.243
peak=    3.261 closest distance to " O   GLU A   2 " =    1.604
peak=    3.260 closest distance to " CA  ASN A 127 " =    1.106
peak=    3.259 closest distance to " CA  ILE A 263 " =    0.926
peak=    3.259 closest distance to " N   TYR A  15 " =    0.902
peak=    3.256 closest distance to " O   HOH Z 171 " =    3.965
peak=    3.255 closest distance to " CD2 LEU A 297 " =    0.856
peak=    3.253 closest distance to " O   PHE A 192 " =    1.386
peak=    3.250 closest distance to " CG2 ILE A 120 " =    1.147
peak=    3.247 closest distance to " O   HOH Z 176 " =    1.444
peak=    3.247 closest distance to " CD  LYS A  76 " =    2.093
peak=    3.247 closest distance to " OG1 THR A 279 " =    1.486
peak=    3.245 closest distance to " CB  SER A 210 " =    0.906
peak=    3.245 closest distance to " O   HOH Z 285 " =    2.159
peak=    3.242 closest distance to " CH2 TRP A  70 " =    1.065
peak=    3.240 closest distance to " CB  GLN A  88 " =    1.258
peak=    3.236 closest distance to " O   HOH Z  21 " =    1.775
peak=    3.232 closest distance to " CA  LYS A 117 " =    1.248
peak=    3.225 closest distance to " CB  ASN A 215 " =    1.271
peak=    3.224 closest distance to " O   HOH Z 417 " =    3.074
peak=    3.217 closest distance to " CB  ALA A 248 " =    1.400
peak=    3.216 closest distance to " CB  LYS A 117 " =    1.215
peak=    3.213 closest distance to " CB  ALA A   1 " =    4.966
peak=    3.210 closest distance to " O   HOH Z 437 " =    1.327
peak=    3.209 closest distance to " O   HOH Z 166 " =    3.699
peak=    3.208 closest distance to " O   HOH Z 403 " =    1.540
peak=    3.205 closest distance to " CB  PRO A  54 " =    0.795
peak=    3.203 closest distance to " O   HOH Z 313 " =    1.566
peak=    3.200 closest distance to " O   HOH Z 368 " =    4.175
peak=    3.196 closest distance to " CZ3 TRP A  92 " =    1.313
peak=    3.192 closest distance to " CG1 VAL A 257 " =    1.310
peak=    3.189 closest distance to " CA  VAL A 112 " =    1.146
peak=    3.186 closest distance to " CE1 TYR A 186 " =    1.203
peak=    3.184 closest distance to " O   HOH Z  47 " =    2.916
peak=    3.181 closest distance to " NE  ARG A 138 " =    1.117
peak=    3.171 closest distance to " OG  SER A  62 " =    2.956
peak=    3.169 closest distance to " N   TYR A 247 " =    1.237
peak=    3.166 closest distance to " CB  ASP A 107 " =    1.205
peak=    3.166 closest distance to " CG AARG A 102 " =    1.070
peak=    3.166 closest distance to " N   VAL A 126 " =    1.663
peak=    3.165 closest distance to " O   HOH Z 148 " =    2.041
peak=    3.163 closest distance to " CA  ARG A 156 " =    1.147
peak=    3.159 closest distance to " O   HOH Z 344 " =    3.033
peak=    3.158 closest distance to " O   HOH Z 116 " =    1.968
peak=    3.157 closest distance to " O   HOH Z 345 " =    3.878
peak=    3.157 closest distance to " O   HOH Z 420 " =    5.787
peak=    3.157 closest distance to " CB  ASN A 285 " =    0.950
peak=    3.150 closest distance to " OG  SER A 135 " =    1.356
peak=    3.150 closest distance to " OG1 THR A  82 " =    0.947
peak=    3.146 closest distance to " OD1 ASN A 217 " =    1.500
peak=    3.145 closest distance to " CA  THR A 264 " =    0.772
peak=    3.142 closest distance to " CA  SER A  12 " =    1.377
peak=    3.136 closest distance to " O   ASN A 209 " =    1.353
peak=    3.135 closest distance to " O   HOH Z 151 " =    1.564
peak=    3.134 closest distance to " O   HOH Z 109 " =    2.783
peak=    3.133 closest distance to " O   HOH Z 329 " =    4.219
peak=    3.132 closest distance to " OD2 ASP A  65 " =    2.949
peak=    3.127 closest distance to " CA  ASN A  74 " =    1.231
peak=    3.127 closest distance to " CG1 ILE A  49 " =    1.656
peak=    3.126 closest distance to " CB  VAL A 268 " =    0.831
peak=    3.126 closest distance to " CB  ALA A 114 " =    0.724
peak=    3.124 closest distance to " O   HOH Z 393 " =    3.068
peak=    3.122 closest distance to " CB  THR A  31 " =    1.437
peak=    3.117 closest distance to " CA  GLY A 133 " =    3.737
peak=    3.116 closest distance to " N   ASP A 162 " =    1.456
peak=    3.110 closest distance to " O   MET A 105 " =    1.687
peak=    3.105 closest distance to " O   PRO A  90 " =    1.542
peak=    3.098 closest distance to " OH  TYR A 214 " =    1.318
peak=    3.098 closest distance to " O   HOH Z 293 " =    1.936
peak=    3.096 closest distance to " O   HOH Z 430 " =    5.625
peak=    3.096 closest distance to " O   ALA A 158 " =    1.300
peak=    3.094 closest distance to " CD  ARG A  66 " =    2.393
peak=    3.093 closest distance to " O   HOH Z 366 " =    2.642
peak=    3.091 closest distance to " CB  LEU A 300 " =    0.871
peak=    3.087 closest distance to " O   HOH Z 117 " =    1.907
peak=    3.086 closest distance to " O   HOH Z 350 " =    1.548
peak=    3.083 closest distance to " O   HOH Z 211 " =    1.378
peak=    3.074 closest distance to " CB  ALA A 292 " =    0.839
peak=    3.068 closest distance to " CB  GLN A  58 " =    1.103
peak=    3.056 closest distance to " CB  VAL A 257 " =    0.791
peak=    3.053 closest distance to " O   HOH Z 299 " =    4.404
peak=    3.050 closest distance to " NE2 GLN A  58 " =    4.679
peak=    3.037 closest distance to " O   HOH Z 371 " =    2.376
peak=    3.030 closest distance to " CG2 ILE A  20 " =    1.290
peak=    3.027 closest distance to " CG  LEU A 281 " =    1.044
peak=    3.008 closest distance to " CG  GLN A  55 " =    2.581

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 219         
Filter by distance & map next to the model:
   mapped sites are within: 0.688 - 5.636
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 217 from: 219
   mapped sites are within: 0.745 - 5.636

peak=   -5.349 closest distance to " CG1 VAL A 296 " =    1.051
peak=   -4.847 closest distance to " CG2 VAL A 230 " =    0.788
peak=   -4.443 closest distance to " CG1 VAL A 250 " =    2.756
peak=   -4.356 closest distance to " CA  ASP A 298 " =    1.067
peak=   -4.314 closest distance to " CD  GLN A  58 " =    1.012
peak=   -4.244 closest distance to " O   HOH Z 166 " =    2.480
peak=   -4.238 closest distance to " CD  ARG A  14 " =    3.254
peak=   -4.231 closest distance to " O   PRO A 198 " =    1.295
peak=   -4.223 closest distance to " CD1 PHE A  59 " =    2.087
peak=   -4.216 closest distance to " CB  PRO A 243 " =    2.825
peak=   -4.171 closest distance to " O   HOH Z 166 " =    1.582
peak=   -4.133 closest distance to " CE3 TRP A  70 " =    1.937
peak=   -4.133 closest distance to " CE2 TYR A  30 " =    2.696
peak=   -3.971 closest distance to " O   HOH Z  73 " =    2.553
peak=   -3.922 closest distance to " CD  ARG A 156 " =    2.134
peak=   -3.921 closest distance to " O   HOH Z   5 " =    1.615
peak=   -3.917 closest distance to " CG  ARG A 269 " =    2.374
peak=   -3.872 closest distance to " CG1 VAL A 112 " =    2.684
peak=   -3.863 closest distance to " O   VAL A  67 " =    2.775
peak=   -3.863 closest distance to " O   HOH Z 193 " =    1.044
peak=   -3.835 closest distance to " O   HOH Z 411 " =    5.410
peak=   -3.820 closest distance to " O   HOH Z 295 " =    1.571
peak=   -3.819 closest distance to " O   HOH Z 119 " =    2.101
peak=   -3.804 closest distance to " CD2 TYR A 293 " =    1.935
peak=   -3.803 closest distance to " CB  VAL A 230 " =    1.125
peak=   -3.803 closest distance to " O   SER A 271 " =    2.091
peak=   -3.801 closest distance to " CE3 TRP A 150 " =    2.081
peak=   -3.795 closest distance to " O   HOH Z 394 " =    1.584
peak=   -3.769 closest distance to " CA  GLY A 241 " =    2.321
peak=   -3.765 closest distance to " CE2 TRP A  70 " =    2.269
peak=   -3.757 closest distance to " CZ2 TRP A  92 " =    2.898
peak=   -3.745 closest distance to " CZ  PHE A  38 " =    2.579
peak=   -3.735 closest distance to " O   HOH Z 149 " =    2.072
peak=   -3.730 closest distance to " CD  GLN A 223 " =    1.408
peak=   -3.715 closest distance to " CD  GLN A  55 " =    1.062
peak=   -3.710 closest distance to " CG  GLU A 277 " =    1.356
peak=   -3.703 closest distance to " O   HOH Z 231 " =    2.255
peak=   -3.689 closest distance to " O   GLY A  17 " =    1.332
peak=   -3.679 closest distance to " O   HOH Z 359 " =    2.990
peak=   -3.671 closest distance to " OD1 ASN A 148 " =    1.365
peak=   -3.661 closest distance to " O   HOH Z 351 " =    1.719
peak=   -3.653 closest distance to " O   HOH Z 127 " =    1.067
peak=   -3.653 closest distance to " O   TYR A 186 " =    1.912
peak=   -3.645 closest distance to " O   HOH Z 103 " =    1.968
peak=   -3.643 closest distance to " CG1 VAL A 112 " =    2.638
peak=   -3.641 closest distance to " O   HOH Z  68 " =    1.514
peak=   -3.620 closest distance to " OG1 THR A  82 " =    1.370
peak=   -3.620 closest distance to " CE2 PHE A  61 " =    2.671
peak=   -3.618 closest distance to " O   HOH Z 251 " =    4.816
peak=   -3.599 closest distance to " O   HOH Z 110 " =    1.322
peak=   -3.596 closest distance to " O   HOH Z  52 " =    1.590
peak=   -3.585 closest distance to " O   HOH Z 368 " =    1.967
peak=   -3.579 closest distance to " CD  GLN A  88 " =    0.956
peak=   -3.574 closest distance to " O   HOH Z 128 " =    2.547
peak=   -3.572 closest distance to " C   LEU A 143 " =    1.133
peak=   -3.572 closest distance to " NE  ARG A  79 " =    1.150
peak=   -3.562 closest distance to " CG2 VAL A 189 " =    2.058
peak=   -3.560 closest distance to " C   HIS A 108 " =    1.204
peak=   -3.559 closest distance to " O   HOH Z 377 " =    1.992
peak=   -3.557 closest distance to " O   HOH Z 183 " =    1.214
peak=   -3.550 closest distance to " N   ALA A  43 " =    2.725
peak=   -3.549 closest distance to " O   ILE A 109 " =    2.655
peak=   -3.542 closest distance to " CG1 VAL A 125 " =    1.890
peak=   -3.537 closest distance to " O   HOH Z 106 " =    1.906
peak=   -3.535 closest distance to " CH2 TRP A 179 " =    1.170
peak=   -3.529 closest distance to " O   HOH Z 238 " =    0.993
peak=   -3.524 closest distance to " O   HOH Z 100 " =    0.792
peak=   -3.523 closest distance to " CG  GLN A  11 " =    1.525
peak=   -3.519 closest distance to " CG  GLN A 103 " =    2.501
peak=   -3.518 closest distance to " O   PRO A 163 " =    2.145
peak=   -3.515 closest distance to " NE2 GLN A 194 " =    2.035
peak=   -3.509 closest distance to " C   ALA A 158 " =    1.361
peak=   -3.508 closest distance to " O   HOH Z 133 " =    0.887
peak=   -3.504 closest distance to " CG2 THR A 178 " =    2.391
peak=   -3.504 closest distance to " O   HOH Z 216 " =    1.059
peak=   -3.504 closest distance to " CB  HIS A  86 " =    1.154
peak=   -3.503 closest distance to " CD1 LEU A 101 " =    2.353
peak=   -3.492 closest distance to " NE2 GLN A  55 " =    2.349
peak=   -3.484 closest distance to " O   HOH Z 285 " =    2.036
peak=   -3.480 closest distance to " OG  SER A  62 " =    4.376
peak=   -3.477 closest distance to " O   HOH Z 111 " =    1.427
peak=   -3.476 closest distance to " O   VAL A  67 " =    2.683
peak=   -3.469 closest distance to " CG2 VAL A 202 " =    2.817
peak=   -3.468 closest distance to " O   HOH Z 340 " =    1.527
peak=   -3.463 closest distance to " OE1 GLN A 223 " =    2.329
peak=   -3.462 closest distance to " CG  PRO A 243 " =    1.672
peak=   -3.460 closest distance to " CD2 PHE A 225 " =    1.032
peak=   -3.460 closest distance to " CG  ASP A 231 " =    0.924
peak=   -3.458 closest distance to " CB  ALA A 248 " =    2.149
peak=   -3.458 closest distance to " O   HOH Z  30 " =    1.501
peak=   -3.455 closest distance to " O   HOH Z 438 " =    3.115
peak=   -3.455 closest distance to " O   HOH Z  11 " =    1.733
peak=   -3.450 closest distance to " OG BSER A 134 " =    1.480
peak=   -3.445 closest distance to " CE  LYS A  76 " =    2.614
peak=   -3.442 closest distance to " N   PHE A  59 " =    1.938
peak=   -3.439 closest distance to " O   HOH Z 252 " =    3.815
peak=   -3.434 closest distance to " O   HOH Z 431 " =    2.043
peak=   -3.433 closest distance to " O   HOH Z  19 " =    2.069
peak=   -3.431 closest distance to " O   HOH Z 231 " =    1.483
peak=   -3.431 closest distance to " O   HOH Z  43 " =    1.645
peak=   -3.431 closest distance to " O   HOH Z 201 " =    2.060
peak=   -3.430 closest distance to " CG  MET A 105 " =    1.053
peak=   -3.422 closest distance to " O   HOH Z  64 " =    1.735
peak=   -3.411 closest distance to " O   HOH Z 398 " =    1.706
peak=   -3.411 closest distance to " CD2 HIS A 207 " =    2.240
peak=   -3.407 closest distance to " O   HOH Z 407 " =    3.006
peak=   -3.399 closest distance to " CD  PRO A 243 " =    1.967
peak=   -3.392 closest distance to " O   HOH Z 434 " =    1.804
peak=   -3.386 closest distance to " ND2 ASN A  45 " =    2.234
peak=   -3.373 closest distance to " O   HOH Z 411 " =    1.678
peak=   -3.371 closest distance to " C   ARG A  79 " =    2.659
peak=   -3.367 closest distance to " CG  LEU A   5 " =    0.977
peak=   -3.367 closest distance to " N   ILE A 120 " =    1.031
peak=   -3.366 closest distance to " O   HOH Z 154 " =    1.358
peak=   -3.365 closest distance to " O   HOH Z 368 " =    1.477
peak=   -3.365 closest distance to " CA  GLY A 241 " =    3.189
peak=   -3.364 closest distance to " CB  ALA A 129 " =    2.495
peak=   -3.357 closest distance to " CD  LYS A 289 " =    2.347
peak=   -3.354 closest distance to " O   HOH Z 255 " =    0.972
peak=   -3.343 closest distance to " O   HOH Z 215 " =    1.191
peak=   -3.342 closest distance to " N   SER A 134 " =    1.223
peak=   -3.340 closest distance to " OG  SER A  97 " =    2.273
peak=   -3.338 closest distance to " OD2 ASP A 171 " =    1.932
peak=   -3.335 closest distance to " CA  GLY A  98 " =    2.177
peak=   -3.334 closest distance to " N   ALA A 226 " =    2.124
peak=   -3.331 closest distance to " C   MET A 188 " =    1.304
peak=   -3.327 closest distance to " CZ  ARG A 259 " =    0.938
peak=   -3.323 closest distance to " CD1 LEU A   5 " =    2.532
peak=   -3.323 closest distance to " O   HOH Z 128 " =    1.180
peak=   -3.321 closest distance to " C   ASP A 270 " =    1.186
peak=   -3.315 closest distance to " O   HOH Z 275 " =    1.627
peak=   -3.312 closest distance to " O   HOH Z  93 " =    2.082
peak=   -3.312 closest distance to " O   GLY A 211 " =    1.311
peak=   -3.304 closest distance to " O   HOH Z 275 " =    1.885
peak=   -3.304 closest distance to " O   HOH Z 236 " =    1.532
peak=   -3.303 closest distance to " NH2 ARG A 159 " =    2.413
peak=   -3.302 closest distance to " SG  CYS A 260 " =    2.346
peak=   -3.299 closest distance to " O   HOH Z 115 " =    1.627
peak=   -3.297 closest distance to " O   HOH Z 100 " =    0.745
peak=   -3.295 closest distance to " CG2AVAL A  41 " =    2.729
peak=   -3.293 closest distance to " CB  TRP A  85 " =    2.680
peak=   -3.291 closest distance to " CG  ARG A 259 " =    2.514
peak=   -3.290 closest distance to " O   ASP A  27 " =    1.976
peak=   -3.289 closest distance to " OD1 ASN A 173 " =    1.334
peak=   -3.286 closest distance to " O   SER A 276 " =    1.852
peak=   -3.282 closest distance to " O   HOH Z 134 " =    1.969
peak=   -3.277 closest distance to " O   HOH Z 290 " =    1.058
peak=   -3.275 closest distance to " OE1 GLN A  88 " =    1.066
peak=   -3.268 closest distance to " O   HOH Z 177 " =    1.922
peak=   -3.268 closest distance to " O   HOH Z  60 " =    1.839
peak=   -3.261 closest distance to " CG  PRO A 163 " =    2.187
peak=   -3.260 closest distance to " O   HOH Z 175 " =    3.860
peak=   -3.256 closest distance to " O   HOH Z 165 " =    1.819
peak=   -3.252 closest distance to " CG1BVAL A  72 " =    2.550
peak=   -3.249 closest distance to " O   HOH Z 139 " =    5.322
peak=   -3.247 closest distance to " N   THR A  52 " =    1.600
peak=   -3.243 closest distance to " CB  ALA A  43 " =    2.797
peak=   -3.237 closest distance to " CB  HIS A  81 " =    0.992
peak=   -3.235 closest distance to " O   HOH Z 329 " =    1.534
peak=   -3.234 closest distance to " ND2 ASN A  45 " =    1.265
peak=   -3.234 closest distance to " OE1 GLU A 236 " =    1.161
peak=   -3.230 closest distance to " O   HOH Z  51 " =    1.108
peak=   -3.230 closest distance to " CG  LEU A 281 " =    1.900
peak=   -3.225 closest distance to " OE1 GLU A  44 " =    1.017
peak=   -3.220 closest distance to " O   HOH Z 191 " =    5.636
peak=   -3.220 closest distance to " CA  ALA A   8 " =    1.454
peak=   -3.217 closest distance to " CA  VAL A 197 " =    1.052
peak=   -3.211 closest distance to " CG2BVAL A  41 " =    1.815
peak=   -3.211 closest distance to " O   HOH Z 198 " =    2.106
peak=   -3.211 closest distance to " OH  TYR A 247 " =    1.853
peak=   -3.210 closest distance to " CA  GLY A 203 " =    2.528
peak=   -3.204 closest distance to " CG  LEU A  83 " =    2.176
peak=   -3.201 closest distance to " O   HOH Z 357 " =    2.253
peak=   -3.197 closest distance to " O   GLN A 240 " =    2.592
peak=   -3.194 closest distance to " O   HOH Z 174 " =    2.319
peak=   -3.191 closest distance to " O   SER A 210 " =    1.657
peak=   -3.190 closest distance to " O   HOH Z 185 " =    2.428
peak=   -3.189 closest distance to " O   HOH Z   6 " =    1.642
peak=   -3.187 closest distance to " CH2 TRP A 123 " =    2.426
peak=   -3.184 closest distance to " CG  GLN A  55 " =    1.203
peak=   -3.180 closest distance to " CA  GLY A 133 " =    2.344
peak=   -3.177 closest distance to " OE2 GLU A 277 " =    2.899
peak=   -3.175 closest distance to " NH2 ARG A  79 " =    2.310
peak=   -3.174 closest distance to " NE  ARG A 138 " =    2.084
peak=   -3.172 closest distance to " O   ASP A 253 " =    1.840
peak=   -3.169 closest distance to " OE1 GLN A  88 " =    1.129
peak=   -3.167 closest distance to " NH1 ARG A 195 " =    0.953
peak=   -3.166 closest distance to " CZ  TYR A 169 " =    1.815
peak=   -3.165 closest distance to " O   GLN A  94 " =    2.297
peak=   -3.165 closest distance to " C   ALA A 165 " =    1.977
peak=   -3.164 closest distance to " O   HOH Z 131 " =    4.021
peak=   -3.163 closest distance to " CG  TRP A 266 " =    1.793
peak=   -3.158 closest distance to " CG  ARG A 219 " =    2.846
peak=   -3.156 closest distance to " O   VAL A 189 " =    2.634
peak=   -3.154 closest distance to " O   HOH Z 140 " =    1.658
peak=   -3.152 closest distance to " O   TYR A  15 " =    1.825
peak=   -3.151 closest distance to " O   HOH Z 107 " =    0.991
peak=   -3.144 closest distance to " O   HOH Z 426 " =    1.784
peak=   -3.135 closest distance to " O   HOH Z 292 " =    1.700
peak=   -3.128 closest distance to " O   HOH Z 423 " =    2.040
peak=   -3.124 closest distance to " CG  ARG A 259 " =    1.375
peak=   -3.118 closest distance to " C   GLU A 236 " =    1.001
peak=   -3.117 closest distance to " NH2 ARG A  36 " =    2.555
peak=   -3.116 closest distance to " O   HOH Z 148 " =    3.921
peak=   -3.116 closest distance to " O   HOH Z 244 " =    2.003
peak=   -3.113 closest distance to " CG2 VAL A 296 " =    1.064
peak=   -3.112 closest distance to " NH2 ARG A  79 " =    1.491
peak=   -3.100 closest distance to " OG  SER A 141 " =    1.706
peak=   -3.092 closest distance to " O   HOH Z 377 " =    1.107
peak=   -3.085 closest distance to " O   HOH Z 214 " =    1.120
peak=   -3.080 closest distance to " O   HOH Z 372 " =    0.994
peak=   -3.076 closest distance to " CB  ALA A  10 " =    2.188
peak=   -3.075 closest distance to " N   ASN A  60 " =    1.240
peak=   -3.068 closest distance to " CZ  PHE A 283 " =    2.219
peak=   -3.044 closest distance to " O   ARG A  56 " =    3.399
peak=   -3.038 closest distance to " O   HOH Z 171 " =    2.287
peak=   -3.038 closest distance to " N   SER A 276 " =    1.476

================= 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    :  0.4868 0.4785   6.286346e+00   6.272347e+00
   1_bss:  0.4789 0.4669   6.281464e+00   6.263790e+00
   1_xyz:  0.3980 0.4275   6.176616e+00   6.205049e+00
   1_adp:  0.3529 0.4083   6.097790e+00   6.174463e+00
   1_occ:  0.3524 0.4086   6.097309e+00   6.175986e+00
   2_bss:  0.3513 0.4064   6.099215e+00   6.176882e+00
   2_xyz:  0.2756 0.3306   5.898536e+00   6.028935e+00
   2_adp:  0.2527 0.3091   5.837682e+00   5.983860e+00
   2_occ:  0.2524 0.3092   5.837463e+00   5.984245e+00
   3_bss:  0.2512 0.3087   5.839595e+00   5.985178e+00
   3_xyz:  0.1821 0.2361   5.556094e+00   5.752739e+00
   3_adp:  0.1628 0.2217   5.474677e+00   5.697307e+00
   3_occ:  0.1626 0.2217   5.475012e+00   5.698315e+00
   4_bss:  0.1628 0.2215   5.474732e+00   5.696663e+00
   4_xyz:  0.1440 0.1981   5.369497e+00   5.597089e+00
   4_adp:  0.1401 0.1876   5.330846e+00   5.548523e+00
   4_occ:  0.1399 0.1875   5.330467e+00   5.548707e+00
   5_bss:  0.1399 0.1878   5.330283e+00   5.548353e+00
   5_xyz:  0.1310 0.1763   5.271564e+00   5.491323e+00
   5_adp:  0.1293 0.1759   5.263498e+00   5.486339e+00
   5_occ:  0.1291 0.1760   5.263143e+00   5.486265e+00
   5_bss:  0.1291 0.1759   5.263023e+00   5.486186e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  50.000   6.226   7.413  11.144   0.000   0.000   0.000
   1_xyz:  0.300  50.000   6.226   7.413  11.144   0.000   0.000   0.000
   1_adp:  0.300  50.000   6.226   7.413  11.144   0.000   0.000   0.000
   1_occ:  0.300  50.000   6.226   7.413  11.144   0.000   0.000   0.000
   2_bss:  0.312  50.000   3.616   4.866   7.967   0.000   0.000   0.000
   2_xyz:  0.312  50.000   3.616   4.866   7.967   0.000   0.000   0.000
   2_adp:  0.312  50.000   3.616   4.866   7.967   0.000   0.000   0.000
   2_occ:  0.312  50.000   3.616   4.866   7.967   0.000   0.000   0.000
   3_bss:  0.327  70.583   2.251   3.160   5.347   0.000   0.000   0.000
   3_xyz:  0.327  70.583   2.251   3.160   5.347   0.000   0.000   0.000
   3_adp:  0.327  70.583   2.251   3.160   5.347   0.000   0.000   0.000
   3_occ:  0.327  70.583   2.251   3.160   5.347   0.000   0.000   0.000
   4_bss:  0.338  87.787   1.865   2.463   4.238   0.000   0.000   0.000
   4_xyz:  0.338  87.787   1.865   2.463   4.238   0.000   0.000   0.000
   4_adp:  0.338  87.787   1.865   2.463   4.238   0.000   0.000   0.000
   4_occ:  0.338  87.787   1.865   2.463   4.238   0.000   0.000   0.000
   5_bss:  0.335  80.000   1.964   2.462   4.085   0.000   0.000   0.000
   5_xyz:  0.335  80.000   1.964   2.462   4.085   0.000   0.000   0.000
   5_adp:  0.335  80.000   1.964   2.462   4.085   0.000   0.000   0.000
   5_occ:  0.335  80.000   1.964   2.462   4.085   0.000   0.000   0.000
   5_bss:  0.329  76.518  -0.785  -0.416   1.200   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.804 0.4218  0.4734    68457.156
   1_bss:  55.920 0.4458  0.6387    66426.375
   1_xyz:  48.854 0.5337  0.7449    51579.420
   1_adp:  45.198 0.5796  0.8491    46438.541
   1_occ:  45.252 0.5789  0.8473    46618.233
   2_bss:  45.223 0.5792  0.7717    46641.577
   2_xyz:  35.034 0.7006  0.9222    29579.661
   2_adp:  32.207 0.7333  0.9502    25970.424
   2_occ:  32.262 0.7327  0.9488    25998.146
   3_bss:  32.219 0.7333  0.8883    26079.561
   3_xyz:  23.125 0.8305  0.9706    14208.656
   3_adp:  21.272 0.8493  0.9708    12465.661
   3_occ:  21.311 0.8489  0.9702    12480.784
   4_bss:  21.235 0.8496  0.9458    12409.911
   4_xyz:  18.678 0.8741  0.9574     9870.333
   4_adp:  17.380 0.8866  0.9533     8948.375
   4_occ:  17.383 0.8865  0.9532     8940.179
   5_bss:  17.388 0.8865  0.9528     8949.340
   5_xyz:  16.071 0.8981  0.9610     7854.863
   5_adp:  15.938 0.8994  0.9540     7799.530
   5_occ:  15.939 0.8994  0.9537     7797.255
   5_bss:  15.937 0.8994  0.9583     7795.356
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4691e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4691e+01
   1_xyz:   1.760  0.014  0.111 18.394  0.007  4.112   1.5163e-01
   1_adp:   1.760  0.014  0.111 18.394  0.007  4.112   1.5163e-01
   1_occ:   1.760  0.014  0.111 18.394  0.007  4.112   1.5163e-01
   2_bss:   1.760  0.014  0.111 18.394  0.007  4.112   1.5163e-01
   2_xyz:   1.299  0.010  0.082 16.703  0.005  4.115   9.9638e-02
   2_adp:   1.299  0.010  0.082 16.703  0.005  4.115   9.9638e-02
   2_occ:   1.299  0.010  0.082 16.703  0.005  4.115   9.9638e-02
   3_bss:   1.299  0.010  0.082 16.703  0.005  4.115   9.9638e-02
   3_xyz:   1.218  0.010  0.089 16.332  0.004  4.138   8.4402e-02
   3_adp:   1.218  0.010  0.089 16.332  0.004  4.138   8.4402e-02
   3_occ:   1.218  0.010  0.089 16.332  0.004  4.138   8.4402e-02
   4_bss:   1.218  0.010  0.089 16.332  0.004  4.138   8.4402e-02
   4_xyz:   1.010  0.008  0.077 15.902  0.003  4.117   6.6098e-02
   4_adp:   1.010  0.008  0.077 15.902  0.003  4.117   6.6098e-02
   4_occ:   1.010  0.008  0.077 15.902  0.003  4.117   6.6098e-02
   5_bss:   1.010  0.008  0.077 15.902  0.003  4.117   6.6098e-02
   5_xyz:   1.018  0.008  0.078 15.456  0.003  4.124   6.3429e-02
   5_adp:   1.018  0.008  0.078 15.456  0.003  4.124   6.3429e-02
   5_occ:   1.018  0.008  0.078 15.456  0.003  4.124   6.3429e-02
   5_bss:   1.018  0.008  0.078 15.456  0.003  4.124   6.3429e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0908e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0908e+00
   1_xyz:  14.796  0.177  0.455 88.029  0.037  2.258   1.1198e-01
   1_adp:  14.796  0.177  0.455 88.029  0.037  2.258   1.1198e-01
   1_occ:  14.796  0.177  0.455 88.029  0.037  2.258   1.1198e-01
   2_bss:  14.796  0.177  0.455 88.029  0.037  2.258   1.1198e-01
   2_xyz:   8.306  0.090  0.312 86.651  0.035  2.027   1.7253e-01
   2_adp:   8.306  0.090  0.312 86.651  0.035  2.027   1.7253e-01
   2_occ:   8.306  0.090  0.312 86.651  0.035  2.027   1.7253e-01
   3_bss:   8.306  0.090  0.312 86.651  0.035  2.027   1.7253e-01
   3_xyz:   9.584  0.107  0.343 87.631  0.041  2.321   6.7773e-02
   3_adp:   9.584  0.107  0.343 87.631  0.041  2.321   6.7773e-02
   3_occ:   9.584  0.107  0.343 87.631  0.041  2.321   6.7773e-02
   4_bss:   9.584  0.107  0.343 87.631  0.041  2.321   6.7773e-02
   4_xyz:   8.365  0.052  0.297 84.020  0.036  2.400   5.9565e-02
   4_adp:   8.365  0.052  0.297 84.020  0.036  2.400   5.9565e-02
   4_occ:   8.365  0.052  0.297 84.020  0.036  2.400   5.9565e-02
   5_bss:   8.365  0.052  0.297 84.020  0.036  2.400   5.9565e-02
   5_xyz:   7.676  0.048  0.321 82.117  0.034  2.428   3.3211e-02
   5_adp:   7.676  0.048  0.321 82.117  0.034  2.428   3.3211e-02
   5_occ:   7.676  0.048  0.321 82.117  0.034  2.428   3.3211e-02
   5_bss:   7.676  0.048  0.321 82.117  0.034  2.428   3.3211e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp: 103.06   0.00  14.30  79.51   0.00  11.58 103.06   0.00  29.12
   1_occ: 103.06   0.00  14.30  79.51   0.00  11.58 103.06   0.00  29.12
   2_bss: 103.06   0.00  14.30  79.51   0.00  11.58 103.06   0.00  29.12
   2_xyz: 103.06   0.00  14.30  79.51   0.00  11.58 103.06   0.00  29.12
   2_adp: 104.09   0.00  13.57  69.15   0.00   9.90 104.09   0.00  33.57
   2_occ: 104.09   0.00  13.57  69.15   0.00   9.90 104.09   0.00  33.57
   3_bss: 104.09   0.00  13.57  69.15   0.00   9.90 104.09   0.00  33.57
   3_xyz: 104.09   0.00  13.57  69.15   0.00   9.90 104.09   0.00  33.57
   3_adp: 105.39   0.00  14.87  93.10   0.00   9.66 105.39   0.35  43.24
   3_occ: 105.39   0.00  14.87  93.10   0.00   9.66 105.39   0.35  43.24
   4_bss: 105.39   0.00  14.87  93.10   0.00   9.66 105.39   0.35  43.24
   4_xyz: 105.39   0.00  14.87  93.10   0.00   9.66 105.39   0.35  43.24
   4_adp: 103.10   0.00  13.85  84.51   0.00   8.88 103.10   0.92  40.90
   4_occ: 103.10   0.00  13.85  84.51   0.00   8.88 103.10   0.92  40.90
   5_bss: 103.10   0.00  13.85  84.51   0.00   8.88 103.10   0.92  40.90
   5_xyz: 103.10   0.00  13.85  84.51   0.00   8.88 103.10   0.92  40.90
   5_adp: 104.55   0.00  13.62  86.69   0.00   8.71 104.55   0.75  40.34
   5_occ: 104.55   0.00  13.62  86.69   0.00   8.71 104.55   0.75  40.34
   5_bss: 107.52   2.97  16.59  89.67   2.97  11.68 107.52   3.73  43.31
------------------------------------------------------------------------
 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:    1.282    0.022    0.416
   1_adp:    1.282    0.022    0.416
   1_occ:    1.282    0.022    0.416
   2_bss:    1.282    0.022    0.416
   2_xyz:    1.961    0.032    0.590
   2_adp:    1.961    0.032    0.590
   2_occ:    1.961    0.032    0.590
   3_bss:    1.961    0.032    0.590
   3_xyz:    1.786    0.053    0.677
   3_adp:    1.786    0.053    0.677
   3_occ:    1.786    0.053    0.677
   4_bss:    1.786    0.053    0.677
   4_xyz:    2.063    0.063    0.728
   4_adp:    2.063    0.063    0.728
   4_occ:    2.063    0.063    0.728
   5_bss:    2.063    0.063    0.728
   5_xyz:    2.127    0.053    0.747
   5_adp:    2.127    0.053    0.747
   5_occ:    2.127    0.053    0.747
   5_bss:    2.127    0.053    0.747
------------------------------------------------------------------------

CPU time actual refinement: 328.59


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_934/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_934/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_934/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_934/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_934/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 328.45 
  Macro-tasks:
    bulk solvent and scale       = 47.70  
    individual site refinement   = 127.95 
    weights calculation          = 30.61  
    collect and process          = 6.53   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 212.89 
  Micro-tasks:
    mask                            = 2.16   
    f_calc                          = 99.92  
    alpha_beta                      = 8.41   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 104.90 
    fmodel                         = 7.97   
    r_factors                      = 0.29   
    phase_errors                   = 11.23  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 236.28 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.690 micro seconds
Total CPU time: 5.70 minutes
from_scatterers_fft:    628 calls, 99.42 s
gradients_fft:          573 calls, 93.93 s

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

# Date 2008-01-16 Time 02:46:57 PST -0800 (1200480417.90 s)
Start R-work = 0.4868, R-free = 0.4785 (no bulk solvent and anisotropic scale)
Final R-work = 0.1451, R-free = 0.1905 (no bulk solvent and anisotropic scale)

Start R-work = 0.4789, R-free = 0.4669
Final R-work = 0.1291, R-free = 0.1759