# Date 2008-01-16 Time 02:19:49 PST -0800 (1200478789.08 s)
#phil __OFF__

Command line arguments: "../782.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1447
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 782

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 46.93, 84.6622, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.93, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9645 1.96124
Completeness in resolution range: 0.945369
Completeness with d_max=infinity: 0.942504

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9645
                             d_min =   1.9612

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.93, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9645 1.96124
Completeness in resolution range: 0.945369
Completeness with d_max=infinity: 0.942504

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9649 -  4.1972 [2180/2209]  1965   215   9.9%
  bin  2:  4.1972 -  3.3437 [2086/2105]  1875   211  10.1%
  bin  3:  3.3437 -  2.9246 [2056/2076]  1850   206  10.0%
  bin  4:  2.9246 -  2.6588 [2050/2075]  1851   199   9.7%
  bin  5:  2.6588 -  2.4692 [2047/2066]  1835   212  10.4%
  bin  6:  2.4692 -  2.3241 [2021/2068]  1823   198   9.8%
  bin  7:  2.3241 -  2.2081 [2001/2033]  1797   204  10.2%
  bin  8:  2.2081 -  2.1123 [1999/2035]  1800   199  10.0%
  bin  9:  2.1123 -  2.0312 [2001/2030]  1802   199   9.9%
  bin 10:  2.0312 -  1.9612 [1148/2024]  1032   116  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_782/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:
        1.76 -     2.38: 24
        2.38 -     3.01: 2024
        3.01 -     3.64: 4662
        3.64 -     4.27: 9183
        4.27 -     4.90: 12621
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.756 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.756 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.959 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z  17 " - " O   HOH Z 333 "  2.072 3.040 -x,y+1/2,-z+1/2
  ... (remaining 28509 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_782/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_782/model_refine_001.geo

CPU time processing inputs: 9.12


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.93 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4486   r_free= 0.4482   ksol= 0.00   Bsol= 0.00   scale= 0.817    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.246945                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9649 -  4.6816 0.99   1410  157 0.3745 0.3647      6.5466      6.5544|
|  2:  4.6816 -  3.7350 0.99   1362  146 0.3575 0.3511      6.7037      6.6846|
|  3:  3.7350 -  3.2685 0.99   1329  156 0.4058 0.3774      6.6041      6.6654|
|  4:  3.2685 -  2.9722 0.99   1340  147 0.4176 0.4293      6.4648      6.4488|
|  5:  2.9722 -  2.7606 0.99   1315  146 0.4617 0.4774      6.3339      6.3578|
|  6:  2.7606 -  2.5987 0.98   1307  143 0.4695 0.4976      6.2357      6.1799|
|  7:  2.5987 -  2.4692 0.99   1313  148 0.4964 0.4615      6.2437      6.1669|
|  8:  2.4692 -  2.3621 0.98   1288  142 0.5026 0.5175      6.1362      6.1695|
|  9:  2.3621 -  2.2715 0.98   1305  150 0.4972 0.4814      6.1067      6.0876|
| 10:  2.2715 -  2.1934 0.98   1282  136 0.5073 0.5231      6.0833      6.1023|
| 11:  2.1934 -  2.1250 0.99   1290  145 0.5069 0.4741      6.0245      6.0033|
| 12:  2.1250 -  2.0644 0.98   1277  138 0.4931 0.5573      5.9449      5.9989|
| 13:  2.0644 -  2.0102 0.97   1275  143 0.5219 0.5245      5.8723       5.819|
| 14:  2.0102 -  1.9612 0.41    537   62 0.5281 0.5490      5.8357      5.7703|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9649 -  4.6816  1410   157  0.72  32.63   0.81     0.74      64077.85|
|  2:  4.6816 -  3.7350  1362   146  0.74  31.74   0.90     0.81      87386.32|
|  3:  3.7350 -  3.2685  1329   156  0.65  39.80   0.86     0.77      94425.95|
|  4:  3.2685 -  2.9722  1340   147  0.58  45.57   0.84     0.68      85985.43|
|  5:  2.9722 -  2.7606  1315   146  0.48  53.62   0.77     0.57      74475.92|
|  6:  2.7606 -  2.5987  1307   143  0.46  55.44   0.76     0.53      63903.03|
|  7:  2.5987 -  2.4692  1313   148  0.46  54.90   0.75     0.52      56318.75|
|  8:  2.4692 -  2.3621  1288   142  0.45  56.20   0.73     0.53      51493.51|
|  9:  2.3621 -  2.2715  1305   150  0.44  56.70   0.76     0.52      46899.60|
| 10:  2.2715 -  2.1934  1282   136  0.42  58.52   0.77     0.50      44860.36|
| 11:  2.1934 -  2.1250  1290   145  0.39  60.86   0.78     0.47      42395.97|
| 12:  2.1250 -  2.0644  1277   138  0.35  64.11   0.77     0.43      42258.83|
| 13:  2.0644 -  2.0102  1275   143  0.31  67.09   0.75     0.39      37225.59|
| 14:  2.0102 -  1.9612   537    62  0.32  66.42   0.72     0.36      30553.65|
|alpha:            min =        0.36 max =            0.81 mean =         0.57|
|beta:             min =    30553.65 max =        94425.95 mean =     60297.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           90.00 mean =        52.25|
|phase err.(test): min =        0.00 max =           90.00 mean =        52.57|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.492729             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.020   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.899077              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.456   (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:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       26 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      168 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      705 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1517 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2661 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3955 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5104 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6587 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7766 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.472 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.807 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.747)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.747)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4568   r_free= 0.4556   ksol= 0.00   Bsol= 0.00   scale= 0.785    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.251424                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4404   r_free= 0.4365   ksol= 0.37   Bsol= 20.00   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.15,7.75,9.55,0.00,0.00,0.00); trace/3= 8.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.244538                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.680305              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.184   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.822971              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.914   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4404      final r-factor (work) = 0.3483          |
| start r-factor (free) = 0.4365      final r-factor (free) = 0.3753          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 80.5995 = 8.68 * 0.50 * 6.2505 + 1.00 * 53.4715                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.7279 = 8.68 * 0.50 * 6.1294 + 1.00 * 0.1255                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3483      final r-factor (work) = 0.2928          |
| start r-factor (free) = 0.3753      final r-factor (free) = 0.3441          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0586 = 0.82 * 1.00 * 6.1294 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9525 = 0.82 * 1.00 * 6.0010 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.747)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.73   11.43    None  None   None       |
|    all(noH): 2823   0      0.00    62.73   11.43    None  None   None       |
|    Sol.    : 438    0      0.00    62.73   26.64    None  None   None       |
|    Mac.    : 2385   0      0.00    58.64   8.64     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.273: 1175   |   5:    31.364 -  37.636:  103        |
|      1:     6.273 -  12.546:  729   |   6:    37.636 -  43.909:   64        |
|      2:    12.546 -  18.818:  370   |   7:    43.909 -  50.182:   30        |
|      3:    18.818 -  25.091:  214   |   8:    50.182 -  56.455:   10        |
|      4:    25.091 -  31.364:  125   |   9:    56.455 -  62.727:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2928 r_free = 0.3441             target_work(ml) = 5.968         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2924 r_free = 0.3445             target_work(ml) = 5.968         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2924   r_free= 0.3445   ksol= 0.37   Bsol= 20.00   scale= 1.098   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.15,7.75,9.55,0.00,0.00,0.00); trace/3= 8.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.967846                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2881   r_free= 0.3398   ksol= 0.34   Bsol= 32.94   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.70,3.89,6.34,0.00,0.00,0.00); trace/3= 4.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.967339                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.369481              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.480   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.398680              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.418  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2881      final r-factor (work) = 0.2000          |
| start r-factor (free) = 0.3398      final r-factor (free) = 0.2569          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.2414 = 5.37 * 0.50 * 6.0028 + 1.00 * 0.1255                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.6877 = 5.37 * 0.50 * 5.8153 + 1.00 * 0.0751                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2000      final r-factor (work) = 0.1791          |
| start r-factor (free) = 0.2569      final r-factor (free) = 0.2319          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3627 = 0.40 * 1.00 * 5.8153 + 1.00 * 0.0443                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2426 = 0.40 * 1.00 * 5.6004 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.747)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.42   11.84    None  None   None       |
|    all(noH): 2823   0      0.00    66.42   11.84    None  None   None       |
|    Sol.    : 438    0      1.04    66.42   31.90    None  None   None       |
|    Mac.    : 2385   0      0.00    61.55   8.16     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.642: 1326   |   5:    33.211 -  39.853:  116        |
|      1:     6.642 -  13.284:  764   |   6:    39.853 -  46.495:   94        |
|      2:    13.284 -  19.927:  230   |   7:    46.495 -  53.137:   44        |
|      3:    19.927 -  26.569:  122   |   8:    53.137 -  59.779:   15        |
|      4:    26.569 -  33.211:  108   |   9:    59.779 -  66.422:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1791 r_free = 0.2319             target_work(ml) = 5.548         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1789 r_free = 0.2317             target_work(ml) = 5.547         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1789   r_free= 0.2317   ksol= 0.34   Bsol= 32.94   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.70,3.89,6.34,0.00,0.00,0.00); trace/3= 4.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.547165                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1773   r_free= 0.2294   ksol= 0.33   Bsol= 39.70   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.55,2.71,3.82,0.00,0.00,0.00); trace/3= 3.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.542831                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.526083              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.751   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.071626              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.734  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1773      final r-factor (work) = 0.1335          |
| start r-factor (free) = 0.2294      final r-factor (free) = 0.1790          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7711 = 4.53 * 0.50 * 5.6101 + 1.00 * 0.0751                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.3612 = 4.53 * 0.50 * 5.4312 + 1.00 * 0.0703                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1335      final r-factor (work) = 0.1237          |
| start r-factor (free) = 0.1790      final r-factor (free) = 0.1706          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8300 = 1.07 * 1.00 * 5.4312 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6436 = 1.07 * 1.00 * 5.2547 + 1.00 * 0.0125                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.747)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.54   12.59    None  None   None       |
|    all(noH): 2823   0      0.00    82.54   12.59    None  None   None       |
|    Sol.    : 438    0      2.08    76.54   36.34    None  None   None       |
|    Mac.    : 2385   0      0.00    82.54   8.23     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.254: 1633   |   5:    41.269 -  49.522:   99        |
|      1:     8.254 -  16.507:  595   |   6:    49.522 -  57.776:   71        |
|      2:    16.507 -  24.761:  169   |   7:    57.776 -  66.030:   31        |
|      3:    24.761 -  33.015:  100   |   8:    66.030 -  74.283:   13        |
|      4:    33.015 -  41.269:  107   |   9:    74.283 -  82.537:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1237 r_free = 0.1706             target_work(ml) = 5.228         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1236 r_free = 0.1705             target_work(ml) = 5.227         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1236   r_free= 0.1705   ksol= 0.33   Bsol= 39.70   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.55,2.71,3.82,0.00,0.00,0.00); trace/3= 3.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.227430                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1237   r_free= 0.1702   ksol= 0.32   Bsol= 39.70   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.43,2.56,3.21,0.00,0.00,0.00); trace/3= 2.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.227237                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.716692              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 127.096  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.245913              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.973  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1237      final r-factor (work) = 0.1143          |
| start r-factor (free) = 0.1702      final r-factor (free) = 0.1613          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2081 = 2.72 * 0.50 * 5.2548 + 1.00 * 0.0703                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1252 = 2.72 * 0.50 * 5.1978 + 1.00 * 0.0648                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1143      final r-factor (work) = 0.1139          |
| start r-factor (free) = 0.1613      final r-factor (free) = 0.1591          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2906 = 0.25 * 1.00 * 5.1978 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2816 = 0.25 * 1.00 * 5.1713 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.747)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.32   12.09    None  None   None       |
|    all(noH): 2823   0      0.00    83.32   12.09    None  None   None       |
|    Sol.    : 438    0      1.63    71.92   33.92    None  None   None       |
|    Mac.    : 2385   0      0.00    83.32   8.08     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.332: 1663   |   5:    41.662 -  49.994:   86        |
|      1:     8.332 -  16.665:  602   |   6:    49.994 -  58.326:   51        |
|      2:    16.665 -  24.997:  149   |   7:    58.326 -  66.659:   20        |
|      3:    24.997 -  33.329:  125   |   8:    66.659 -  74.991:    6        |
|      4:    33.329 -  41.662:  117   |   9:    74.991 -  83.323:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1139 r_free = 0.1591             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1138 r_free = 0.1589             target_work(ml) = 5.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1589   ksol= 0.32   Bsol= 39.70   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.43,2.56,3.21,0.00,0.00,0.00); trace/3= 2.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.161818                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1589   ksol= 0.32   Bsol= 38.78   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.43,2.56,3.21,0.00,0.00,0.00); trace/3= 2.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.161957                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.247055              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.834  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.225480              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 160.080  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1113          |
| start r-factor (free) = 0.1589      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8745 = 2.25 * 0.50 * 5.1710 + 1.00 * 0.0648                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8529 = 2.25 * 0.50 * 5.1535 + 1.00 * 0.0628                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1113      final r-factor (work) = 0.1114          |
| start r-factor (free) = 0.1571      final r-factor (free) = 0.1570          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1719 = 0.23 * 1.00 * 5.1535 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1775 = 0.23 * 1.00 * 5.1478 + 1.00 * 0.0168                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.747)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.35   12.01    None  None   None       |
|    all(noH): 2823   0      0.00    83.35   12.01    None  None   None       |
|    Sol.    : 438    0      1.55    71.53   33.68    None  None   None       |
|    Mac.    : 2385   0      0.00    83.35   8.04     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.336: 1671   |   5:    41.677 -  50.013:   88        |
|      1:     8.336 -  16.671:  595   |   6:    50.013 -  58.348:   51        |
|      2:    16.671 -  25.006:  152   |   7:    58.348 -  66.684:   18        |
|      3:    25.006 -  33.342:  127   |   8:    66.684 -  75.019:    6        |
|      4:    33.342 -  41.677:  111   |   9:    75.019 -  83.355:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1114 r_free = 0.1570             target_work(ml) = 5.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1113 r_free = 0.1571             target_work(ml) = 5.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1571   ksol= 0.32   Bsol= 38.78   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.43,2.56,3.21,0.00,0.00,0.00); trace/3= 2.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.147006                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9649 -  4.6816 0.99   1410  157 0.0991 0.1288      5.3838      5.5461|
|  2:  4.6816 -  3.7350 0.99   1362  146 0.0852 0.1133      5.4282      5.6323|
|  3:  3.7350 -  3.2685 0.99   1329  156 0.1046 0.1571      5.4626      5.8569|
|  4:  3.2685 -  2.9722 0.99   1340  147 0.1210 0.1510      5.4527      5.5918|
|  5:  2.9722 -  2.7606 0.99   1315  146 0.1292 0.1674      5.3145      5.4976|
|  6:  2.7606 -  2.5987 0.98   1307  143 0.1223 0.1847      5.2049      5.4605|
|  7:  2.5987 -  2.4692 0.99   1313  148 0.1243 0.1679      5.1695      5.4065|
|  8:  2.4692 -  2.3621 0.98   1288  142 0.1161 0.1709      5.0595      5.2924|
|  9:  2.3621 -  2.2715 0.98   1305  150 0.1172 0.1760      5.0287      5.2956|
| 10:  2.2715 -  2.1934 0.98   1282  136 0.1141 0.1734      4.9672      5.2272|
| 11:  2.1934 -  2.1250 0.99   1290  145 0.1129 0.1762      4.9311      5.2843|
| 12:  2.1250 -  2.0644 0.98   1277  138 0.1092 0.1620       4.865       5.059|
| 13:  2.0644 -  2.0102 0.97   1275  143 0.1176 0.1813      4.7843      5.0607|
| 14:  2.0102 -  1.9612 0.41    537   62 0.1018 0.1607      4.6392       4.874|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9649 -  4.6816  1410   157  0.94   8.83   0.99     0.96       7142.04|
|  2:  4.6816 -  3.7350  1362   146  0.95   7.98   1.02     1.01       8859.57|
|  3:  3.7350 -  3.2685  1329   156  0.93  11.50   1.03     1.02      10392.41|
|  4:  3.2685 -  2.9722  1340   147  0.92  13.73   1.01     0.99      10390.79|
|  5:  2.9722 -  2.7606  1315   146  0.90  16.08   0.99     0.96       8165.80|
|  6:  2.7606 -  2.5987  1307   143  0.90  16.10   0.99     0.96       7037.56|
|  7:  2.5987 -  2.4692  1313   148  0.91  15.31   0.99     0.96       6195.41|
|  8:  2.4692 -  2.3621  1288   142  0.90  15.82   0.99     0.97       5416.28|
|  9:  2.3621 -  2.2715  1305   150  0.90  15.71   1.01     0.99       5027.90|
| 10:  2.2715 -  2.1934  1282   136  0.90  15.62   1.01     0.98       4484.29|
| 11:  2.1934 -  2.1250  1290   145  0.90  16.08   1.01     0.97       4279.83|
| 12:  2.1250 -  2.0644  1277   138  0.91  15.25   1.01     1.00       3940.97|
| 13:  2.0644 -  2.0102  1275   143  0.90  16.24   1.01     1.00       3271.20|
| 14:  2.0102 -  1.9612   537    62  0.91  14.92   1.01     0.98       2456.23|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2456.23 max =        10392.41 mean =      6425.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.13|
|phase err.(test): min =        0.00 max =           89.56 mean =        13.66|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1571   ksol= 0.32   Bsol= 41.46   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.29,-0.12,0.41,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.146909                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1571   ksol= 0.32   Bsol= 41.46   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.29,-0.12,0.41,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.146909                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9649 -  4.6816 0.99   1410  157 0.0990 0.1288      5.3834      5.5457|
|  2:  4.6816 -  3.7350 0.99   1362  146 0.0852 0.1133       5.428      5.6323|
|  3:  3.7350 -  3.2685 0.99   1329  156 0.1046 0.1571      5.4626      5.8568|
|  4:  3.2685 -  2.9722 0.99   1340  147 0.1211 0.1510      5.4527       5.592|
|  5:  2.9722 -  2.7606 0.99   1315  146 0.1292 0.1674      5.3144      5.4973|
|  6:  2.7606 -  2.5987 0.98   1307  143 0.1223 0.1850      5.2051      5.4614|
|  7:  2.5987 -  2.4692 0.99   1313  148 0.1243 0.1679      5.1698      5.4067|
|  8:  2.4692 -  2.3621 0.98   1288  142 0.1161 0.1709      5.0595      5.2924|
|  9:  2.3621 -  2.2715 0.98   1305  150 0.1172 0.1760      5.0286      5.2958|
| 10:  2.2715 -  2.1934 0.98   1282  136 0.1140 0.1735       4.967      5.2261|
| 11:  2.1934 -  2.1250 0.99   1290  145 0.1129 0.1762      4.9309       5.284|
| 12:  2.1250 -  2.0644 0.98   1277  138 0.1092 0.1618      4.8644      5.0578|
| 13:  2.0644 -  2.0102 0.97   1275  143 0.1175 0.1811      4.7841      5.0598|
| 14:  2.0102 -  1.9612 0.41    537   62 0.1020 0.1614        4.64      4.8771|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9649 -  4.6816  1410   157  0.94   8.83   0.99     0.96       7137.13|
|  2:  4.6816 -  3.7350  1362   146  0.95   7.97   1.02     1.00       8856.28|
|  3:  3.7350 -  3.2685  1329   156  0.93  11.50   1.03     1.02      10392.07|
|  4:  3.2685 -  2.9722  1340   147  0.92  13.73   1.01     0.99      10391.25|
|  5:  2.9722 -  2.7606  1315   146  0.90  16.09   0.99     0.96       8171.23|
|  6:  2.7606 -  2.5987  1307   143  0.90  16.11   0.98     0.96       7041.07|
|  7:  2.5987 -  2.4692  1313   148  0.91  15.32   0.99     0.96       6200.86|
|  8:  2.4692 -  2.3621  1288   142  0.90  15.82   0.99     0.96       5417.01|
|  9:  2.3621 -  2.2715  1305   150  0.90  15.71   1.01     0.99       5026.77|
| 10:  2.2715 -  2.1934  1282   136  0.90  15.61   1.01     0.98       4480.34|
| 11:  2.1934 -  2.1250  1290   145  0.90  16.07   1.01     0.97       4276.65|
| 12:  2.1250 -  2.0644  1277   138  0.91  15.23   1.01     1.00       3933.97|
| 13:  2.0644 -  2.0102  1275   143  0.90  16.24   1.01     1.00       3271.00|
| 14:  2.0102 -  1.9612   537    62  0.91  14.91   1.00     0.97       2460.69|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2460.69 max =        10392.07 mean =      6424.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.13|
|phase err.(test): min =        0.00 max =           89.56 mean =        13.66|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.747)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.68    86.03   14.69    None  None   None       |
|    all(noH): 2823   0      2.68    86.03   14.69    None  None   None       |
|    Sol.    : 438    0      4.23    74.21   36.36    None  None   None       |
|    Mac.    : 2385   0      2.68    86.03   10.71    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:     2.679 -  11.015: 1671   |   5:    44.357 -  52.692:   88        |
|      1:    11.015 -  19.350:  595   |   6:    52.692 -  61.028:   51        |
|      2:    19.350 -  27.686:  152   |   7:    61.028 -  69.363:   18        |
|      3:    27.686 -  36.021:  127   |   8:    69.363 -  77.699:    6        |
|      4:    36.021 -  44.357:  111   |   9:    77.699 -  86.034:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 326         
Filter by distance & map next to the model:
   mapped sites are within: 0.441 - 5.717
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 323 from: 326
   mapped sites are within: 0.725 - 5.717

peak=   10.348 closest distance to " CG2 VAL A 230 " =    1.387
peak=    7.167 closest distance to " CG2 VAL A 296 " =    1.130
peak=    6.481 closest distance to " CG  LEU A   5 " =    1.275
peak=    5.894 closest distance to " NH2 ARG A  56 " =    2.187
peak=    5.623 closest distance to " CD2 LEU A   5 " =    1.183
peak=    5.387 closest distance to " CG  LEU A 228 " =    1.203
peak=    5.319 closest distance to " CG  PRO A  54 " =    1.253
peak=    5.249 closest distance to " NE2 GLN A  11 " =    1.138
peak=    5.237 closest distance to " CB  VAL A 296 " =    1.133
peak=    5.125 closest distance to " CB  GLN A 223 " =    1.426
peak=    5.115 closest distance to " CB  SER A  63 " =    1.301
peak=    5.109 closest distance to " CB  PRO A  54 " =    0.928
peak=    5.040 closest distance to " O   HOH Z 126 " =    1.827
peak=    5.013 closest distance to " O   HOH Z 278 " =    1.024
peak=    4.924 closest distance to " CB  VAL A 230 " =    1.206
peak=    4.816 closest distance to " O   HOH Z 193 " =    1.770
peak=    4.765 closest distance to " CB  GLN A 183 " =    1.267
peak=    4.761 closest distance to " C   PRO A 198 " =    1.519
peak=    4.752 closest distance to " OD1 ASN A  69 " =    2.636
peak=    4.688 closest distance to " CB  ARG A 275 " =    0.868
peak=    4.672 closest distance to " CG  PRO A 213 " =    1.228
peak=    4.666 closest distance to " CB  SER A   3 " =    1.385
peak=    4.648 closest distance to " CB  GLU A 152 " =    1.179
peak=    4.626 closest distance to " O   HOH Z 144 " =    1.665
peak=    4.598 closest distance to " O   HOH Z 232 " =    2.313
peak=    4.546 closest distance to " CD2 LEU A 228 " =    1.189
peak=    4.453 closest distance to " CB  ASN A 148 " =    1.363
peak=    4.444 closest distance to " O   HOH Z 236 " =    1.809
peak=    4.421 closest distance to " O   HOH Z 303 " =    1.991
peak=    4.416 closest distance to " O   HOH Z 427 " =    2.926
peak=    4.403 closest distance to " O   HOH Z 368 " =    2.083
peak=    4.370 closest distance to " CB  TYR A 169 " =    0.805
peak=    4.341 closest distance to " O   HOH Z 316 " =    2.898
peak=    4.280 closest distance to " O   HOH Z 272 " =    1.878
peak=    4.266 closest distance to " O   HOH Z 124 " =    1.407
peak=    4.262 closest distance to " O   HOH Z  78 " =    1.840
peak=    4.258 closest distance to " CB  GLU A 128 " =    1.044
peak=    4.255 closest distance to " O   SER A  87 " =    2.223
peak=    4.237 closest distance to " OD2 ASP A 286 " =    2.794
peak=    4.204 closest distance to " O   HOH Z 263 " =    1.617
peak=    4.202 closest distance to " CG  PRO A 243 " =    1.165
peak=    4.192 closest distance to " O   HOH Z 371 " =    3.186
peak=    4.182 closest distance to " O   HOH Z 298 " =    1.820
peak=    4.169 closest distance to " O   HOH Z 411 " =    3.785
peak=    4.152 closest distance to " O   HOH Z  48 " =    1.541
peak=    4.152 closest distance to " O   HOH Z 128 " =    2.004
peak=    4.116 closest distance to " O   HOH Z 108 " =    1.264
peak=    4.110 closest distance to " CG1BVAL A  72 " =    1.571
peak=    4.095 closest distance to " O   HOH Z 132 " =    0.758
peak=    4.087 closest distance to " O   HOH Z 203 " =    1.677
peak=    4.086 closest distance to " O   HOH Z 280 " =    2.970
peak=    4.077 closest distance to " CA  ALA A  21 " =    1.148
peak=    4.051 closest distance to " O   HOH Z 369 " =    1.962
peak=    4.034 closest distance to " O   HOH Z 234 " =    3.668
peak=    4.028 closest distance to " ND2 ASN A 187 " =    1.587
peak=    4.023 closest distance to " O   HOH Z  97 " =    1.924
peak=    4.021 closest distance to " CB  VAL A 265 " =    1.261
peak=    4.005 closest distance to " CG  PRO A 198 " =    1.304
peak=    3.990 closest distance to " CA  THR A 221 " =    0.899
peak=    3.963 closest distance to " CB  TRP A 179 " =    1.331
peak=    3.956 closest distance to " O   HOH Z  54 " =    1.601
peak=    3.954 closest distance to " O   TRP A 274 " =    1.899
peak=    3.940 closest distance to " CA  ALA A  51 " =    0.971
peak=    3.939 closest distance to " CB BVAL A  41 " =    0.774
peak=    3.937 closest distance to " O   HOH Z 344 " =    2.757
peak=    3.936 closest distance to " OG BSER A 164 " =    2.218
peak=    3.929 closest distance to " O   HOH Z 389 " =    1.886
peak=    3.925 closest distance to " O   HOH Z  93 " =    2.524
peak=    3.915 closest distance to " O   HOH Z  61 " =    1.629
peak=    3.885 closest distance to " CB  GLU A 277 " =    3.526
peak=    3.864 closest distance to " CB  ARG A  79 " =    1.380
peak=    3.862 closest distance to " CA  ASN A 215 " =    1.192
peak=    3.861 closest distance to " O   HOH Z 423 " =    1.859
peak=    3.861 closest distance to " CA  ALA A 248 " =    1.363
peak=    3.849 closest distance to " O   HOH Z 197 " =    3.018
peak=    3.843 closest distance to " O   HOH Z  15 " =    2.165
peak=    3.841 closest distance to " CB  ARG A 139 " =    0.937
peak=    3.835 closest distance to " O   HOH Z 346 " =    1.563
peak=    3.826 closest distance to " O   HOH Z 158 " =    3.045
peak=    3.802 closest distance to " NH2 ARG A 156 " =    1.118
peak=    3.801 closest distance to " CB  GLN A  88 " =    1.217
peak=    3.788 closest distance to " O   MET A 105 " =    1.761
peak=    3.785 closest distance to " CD1 LEU A 300 " =    1.223
peak=    3.785 closest distance to " O   HOH Z  88 " =    3.116
peak=    3.779 closest distance to " O   HOH Z 426 " =    1.508
peak=    3.773 closest distance to " CB  ASN A 148 " =    1.915
peak=    3.771 closest distance to " O   HOH Z  59 " =    2.125
peak=    3.770 closest distance to " O   HOH Z 145 " =    2.037
peak=    3.769 closest distance to " CG  ARG A  66 " =    2.609
peak=    3.769 closest distance to " O   HOH Z 193 " =    1.976
peak=    3.755 closest distance to " CB  LEU A 143 " =    1.156
peak=    3.727 closest distance to " O   HOH Z 134 " =    1.414
peak=    3.724 closest distance to " CA  TYR A  30 " =    0.954
peak=    3.724 closest distance to " CB  VAL A 202 " =    1.586
peak=    3.708 closest distance to " O   HOH Z  21 " =    1.735
peak=    3.704 closest distance to " CB  TRP A 266 " =    0.939
peak=    3.702 closest distance to " O   HOH Z   6 " =    2.198
peak=    3.694 closest distance to " O   HOH Z 403 " =    1.689
peak=    3.690 closest distance to " CA  THR A 264 " =    0.781
peak=    3.681 closest distance to " O   HOH Z  43 " =    1.948
peak=    3.679 closest distance to " CA  VAL A  41 " =    0.814
peak=    3.677 closest distance to " O   HOH Z 273 " =    2.615
peak=    3.668 closest distance to " CD BLYS A 290 " =    1.133
peak=    3.657 closest distance to " CG1 ILE A  33 " =    1.343
peak=    3.647 closest distance to " O   HOH Z 189 " =    2.612
peak=    3.634 closest distance to " O   HOH Z  10 " =    1.812
peak=    3.633 closest distance to " O   HOH Z 133 " =    1.590
peak=    3.631 closest distance to " CB  SER A 216 " =    0.743
peak=    3.606 closest distance to " OG  SER A  22 " =    2.792
peak=    3.589 closest distance to " O   HOH Z 207 " =    1.716
peak=    3.587 closest distance to " O   HOH Z 130 " =    2.312
peak=    3.582 closest distance to " CB  ASN A  39 " =    0.847
peak=    3.579 closest distance to " O   HOH Z 209 " =    2.345
peak=    3.574 closest distance to " O   HOH Z 411 " =    1.782
peak=    3.571 closest distance to " O   HOH Z 265 " =    2.321
peak=    3.571 closest distance to " N   ASN A  39 " =    1.170
peak=    3.562 closest distance to " O   HOH Z 329 " =    3.823
peak=    3.559 closest distance to " O   HOH Z 250 " =    1.332
peak=    3.551 closest distance to " NH1BARG A 190 " =    2.002
peak=    3.543 closest distance to " CB  PRO A 198 " =    0.949
peak=    3.540 closest distance to " O   HOH Z 209 " =    2.399
peak=    3.531 closest distance to " O   HOH Z 295 " =    1.495
peak=    3.530 closest distance to " O   HOH Z 345 " =    3.310
peak=    3.525 closest distance to " O   HOH Z 313 " =    1.743
peak=    3.524 closest distance to " CA  ASP A 191 " =    0.775
peak=    3.522 closest distance to " N   PHE A 130 " =    1.333
peak=    3.521 closest distance to " CE  LYS A  76 " =    0.916
peak=    3.519 closest distance to " CD2 LEU A 255 " =    1.466
peak=    3.517 closest distance to " O   HOH Z 128 " =    2.130
peak=    3.517 closest distance to " O   HOH Z 180 " =    2.149
peak=    3.512 closest distance to " CD  ARG A 269 " =    0.965
peak=    3.506 closest distance to " O   HOH Z 425 " =    2.036
peak=    3.502 closest distance to " O   HOH Z 248 " =    1.768
peak=    3.499 closest distance to " CG2 THR A 221 " =    1.191
peak=    3.487 closest distance to " O   HOH Z 171 " =    2.447
peak=    3.480 closest distance to " CA  LEU A 282 " =    1.092
peak=    3.479 closest distance to " CG2 ILE A 120 " =    1.298
peak=    3.477 closest distance to " NE2 GLN A  58 " =    5.717
peak=    3.476 closest distance to " O   HOH Z 402 " =    1.446
peak=    3.472 closest distance to " O   HOH Z  61 " =    1.590
peak=    3.472 closest distance to " O   HOH Z  20 " =    1.548
peak=    3.470 closest distance to " O   HOH Z 407 " =    2.488
peak=    3.464 closest distance to " CB  GLN A 278 " =    0.886
peak=    3.463 closest distance to " CB  ALA A 291 " =    1.364
peak=    3.461 closest distance to " NZ  LYS A 117 " =    3.209
peak=    3.460 closest distance to " O   HOH Z 227 " =    1.670
peak=    3.457 closest distance to " CE1 TYR A 186 " =    1.319
peak=    3.455 closest distance to " O   HOH Z 279 " =    2.144
peak=    3.450 closest distance to " O   HOH Z 132 " =    2.712
peak=    3.450 closest distance to " CG  MET A 185 " =    1.212
peak=    3.448 closest distance to " O   HOH Z  68 " =    1.590
peak=    3.446 closest distance to " O   HOH Z 135 " =    1.734
peak=    3.443 closest distance to " O   HOH Z 281 " =    4.465
peak=    3.443 closest distance to " CD  ARG A 159 " =    0.748
peak=    3.437 closest distance to " O   HOH Z  68 " =    1.938
peak=    3.435 closest distance to " CB  ALA A   9 " =    1.601
peak=    3.434 closest distance to " O   HOH Z 112 " =    1.561
peak=    3.433 closest distance to " O   ALA A 158 " =    1.337
peak=    3.433 closest distance to " O   HOH Z 116 " =    1.710
peak=    3.427 closest distance to " O   HOH Z 164 " =    2.039
peak=    3.426 closest distance to " O   ALA A   1 " =    1.537
peak=    3.422 closest distance to " O   HOH Z 247 " =    1.251
peak=    3.421 closest distance to " CB  ASP A 140 " =    0.817
peak=    3.420 closest distance to " CG2 VAL A 257 " =    0.901
peak=    3.419 closest distance to " O   HOH Z 374 " =    2.503
peak=    3.416 closest distance to " C   ALA A 299 " =    0.965
peak=    3.413 closest distance to " O   HOH Z 172 " =    3.743
peak=    3.413 closest distance to " O   HOH Z   9 " =    1.981
peak=    3.412 closest distance to " O   HOH Z 260 " =    1.194
peak=    3.406 closest distance to " O   HOH Z 286 " =    2.309
peak=    3.406 closest distance to " CA  ASP A 140 " =    1.189
peak=    3.404 closest distance to " O   HOH Z 214 " =    2.034
peak=    3.404 closest distance to " O   HOH Z 126 " =    1.582
peak=    3.403 closest distance to " CB  ALA A   1 " =    1.259
peak=    3.397 closest distance to " O   HOH Z 151 " =    1.728
peak=    3.395 closest distance to " CA  ALA A 158 " =    1.181
peak=    3.391 closest distance to " O   HOH Z 271 " =    1.924
peak=    3.389 closest distance to " O   HOH Z 222 " =    2.479
peak=    3.387 closest distance to " O   HOH Z 425 " =    1.286
peak=    3.385 closest distance to " CG  LEU A 167 " =    1.195
peak=    3.379 closest distance to " O   HOH Z 334 " =    1.404
peak=    3.378 closest distance to " CA  VAL A 126 " =    0.934
peak=    3.378 closest distance to " NE2 GLN A  58 " =    4.141
peak=    3.377 closest distance to " CB  LEU A 228 " =    1.292
peak=    3.372 closest distance to " O   HOH Z 419 " =    1.702
peak=    3.369 closest distance to " O   HOH Z 128 " =    1.806
peak=    3.366 closest distance to " NH2 ARG A 219 " =    1.821
peak=    3.356 closest distance to " O   HOH Z 227 " =    2.085
peak=    3.351 closest distance to " ND1 HIS A  86 " =    1.633
peak=    3.346 closest distance to " O   HOH Z 163 " =    1.869
peak=    3.341 closest distance to " CA  MET A  40 " =    1.122
peak=    3.336 closest distance to " O   HOH Z  80 " =    1.571
peak=    3.331 closest distance to " O   HOH Z 280 " =    1.663
peak=    3.331 closest distance to " CG1 ILE A  49 " =    1.403
peak=    3.331 closest distance to " CD  LYS A 166 " =    1.343
peak=    3.330 closest distance to " O   HOH Z  40 " =    2.364
peak=    3.330 closest distance to " O   HOH Z 368 " =    3.578
peak=    3.329 closest distance to " CG  MET A 185 " =    1.093
peak=    3.327 closest distance to " O   HOH Z 422 " =    2.747
peak=    3.325 closest distance to " N   SER A 135 " =    1.339
peak=    3.324 closest distance to " CA  SER A  87 " =    0.890
peak=    3.318 closest distance to " CZ2 TRP A 179 " =    1.691
peak=    3.317 closest distance to " OG1 THR A 294 " =    2.371
peak=    3.311 closest distance to " CB  SER A  62 " =    1.322
peak=    3.311 closest distance to " CA  GLN A 194 " =    1.278
peak=    3.310 closest distance to " CG2 THR A 220 " =    0.916
peak=    3.310 closest distance to " O   HOH Z 108 " =    2.470
peak=    3.308 closest distance to " N   ARG A 156 " =    1.294
peak=    3.306 closest distance to " CB  ALA A 248 " =    0.941
peak=    3.305 closest distance to " O   HOH Z 367 " =    3.443
peak=    3.303 closest distance to " CB  ASN A 142 " =    1.001
peak=    3.303 closest distance to " CA  ALA A 233 " =    1.367
peak=    3.299 closest distance to " CB  ALA A 295 " =    1.270
peak=    3.299 closest distance to " NZ  LYS A  76 " =    1.236
peak=    3.298 closest distance to " O   HOH Z 251 " =    1.587
peak=    3.298 closest distance to " O   HOH Z 357 " =    1.818
peak=    3.297 closest distance to " CZ2 TRP A 274 " =    1.599
peak=    3.293 closest distance to " O   HOH Z 276 " =    1.237
peak=    3.293 closest distance to " CZ  PHE A 218 " =    1.075
peak=    3.292 closest distance to " O   HOH Z 175 " =    2.137
peak=    3.291 closest distance to " CA  GLY A 267 " =    0.963
peak=    3.288 closest distance to " O   HOH Z 261 " =    2.095
peak=    3.285 closest distance to " O   HOH Z 406 " =    1.613
peak=    3.285 closest distance to " O   HOH Z 245 " =    1.382
peak=    3.285 closest distance to " CG  GLN A  88 " =    1.032
peak=    3.282 closest distance to " O   HOH Z 193 " =    1.594
peak=    3.278 closest distance to " CA  LYS A 117 " =    1.254
peak=    3.277 closest distance to " CD1 ILE A 106 " =    1.137
peak=    3.275 closest distance to " CA  ALA A 154 " =    1.131
peak=    3.275 closest distance to " NH1AARG A 145 " =    0.933
peak=    3.275 closest distance to " CB  ARG A 190 " =    1.722
peak=    3.274 closest distance to " O   HOH Z  49 " =    2.514
peak=    3.270 closest distance to " CB  SER A 212 " =    1.174
peak=    3.267 closest distance to " O   HOH Z 353 " =    2.751
peak=    3.266 closest distance to " O   GLN A  58 " =    1.551
peak=    3.263 closest distance to " O   HOH Z 189 " =    2.885
peak=    3.263 closest distance to " CG  MET A 188 " =    1.161
peak=    3.260 closest distance to " CA  ALA A 295 " =    1.018
peak=    3.259 closest distance to " CB  MET A  40 " =    0.914
peak=    3.259 closest distance to " N   ARG A 190 " =    1.020
peak=    3.255 closest distance to " CB  SER A  26 " =    1.610
peak=    3.255 closest distance to " O   HOH Z 383 " =    2.094
peak=    3.248 closest distance to " CG2 ILE A  20 " =    1.519
peak=    3.248 closest distance to " CB  SER A 141 " =    0.971
peak=    3.248 closest distance to " CB  LEU A 255 " =    0.810
peak=    3.247 closest distance to " O   HOH Z 147 " =    1.645
peak=    3.247 closest distance to " OD1 ASN A 217 " =    1.747
peak=    3.245 closest distance to " O   HOH Z 303 " =    1.741
peak=    3.244 closest distance to " O   HOH Z 291 " =    1.469
peak=    3.241 closest distance to " CG  GLN A  89 " =    1.523
peak=    3.241 closest distance to " CD1 ILE A  33 " =    1.594
peak=    3.239 closest distance to " NH2BARG A 145 " =    2.094
peak=    3.238 closest distance to " O   HOH Z  50 " =    1.452
peak=    3.236 closest distance to " CA  LYS A 290 " =    1.299
peak=    3.235 closest distance to " O   HOH Z 366 " =    2.966
peak=    3.230 closest distance to " O   HOH Z  40 " =    1.854
peak=    3.229 closest distance to " CB  THR A  31 " =    1.664
peak=    3.227 closest distance to " OG  SER A  97 " =    2.642
peak=    3.225 closest distance to " CA  ALA A 291 " =    1.001
peak=    3.221 closest distance to " O   HOH Z 359 " =    3.804
peak=    3.218 closest distance to " CB  LYS A 117 " =    1.153
peak=    3.216 closest distance to " CG BARG A 102 " =    1.879
peak=    3.215 closest distance to " CB  TRP A 150 " =    1.484
peak=    3.213 closest distance to " OD1 ASP A 231 " =    1.861
peak=    3.211 closest distance to " OD1 ASP A 286 " =    1.627
peak=    3.204 closest distance to " CA  ARG A  36 " =    1.061
peak=    3.201 closest distance to " CB  GLN A 205 " =    1.240
peak=    3.201 closest distance to " CB  ILE A  20 " =    1.427
peak=    3.195 closest distance to " O   HOH Z  80 " =    2.267
peak=    3.193 closest distance to " OD1BASN A 224 " =    2.172
peak=    3.193 closest distance to " CB  ASN A 215 " =    1.096
peak=    3.192 closest distance to " O   HOH Z 417 " =    2.055
peak=    3.187 closest distance to " O   HOH Z 128 " =    2.007
peak=    3.186 closest distance to " O   HOH Z   3 " =    1.535
peak=    3.183 closest distance to " ND1 HIS A  81 " =    1.600
peak=    3.182 closest distance to " O   HOH Z 280 " =    2.388
peak=    3.180 closest distance to " CB  THR A 157 " =    1.093
peak=    3.178 closest distance to " O   HOH Z 213 " =    2.290
peak=    3.176 closest distance to " CA  ASN A 176 " =    1.091
peak=    3.174 closest distance to " CB  GLU A  46 " =    1.082
peak=    3.172 closest distance to " O   HOH Z 374 " =    3.052
peak=    3.167 closest distance to " O   ALA A   1 " =    1.723
peak=    3.163 closest distance to " CD2 TYR A 186 " =    0.993
peak=    3.162 closest distance to " CA  ILE A 106 " =    0.791
peak=    3.158 closest distance to " N   VAL A 126 " =    1.328
peak=    3.157 closest distance to " CD2 HIS A  81 " =    1.132
peak=    3.153 closest distance to " CA  ARG A 195 " =    1.177
peak=    3.151 closest distance to " O   HOH Z 148 " =    3.207
peak=    3.149 closest distance to " O   HOH Z 163 " =    1.923
peak=    3.149 closest distance to " CD1 LEU A  96 " =    0.725
peak=    3.148 closest distance to " O   HOH Z 187 " =    2.228
peak=    3.148 closest distance to " O   HOH Z 435 " =    2.003
peak=    3.147 closest distance to " CB  ALA A 114 " =    1.219
peak=    3.145 closest distance to " O   HOH Z  48 " =    1.461
peak=    3.145 closest distance to " O   HOH Z  85 " =    1.416
peak=    3.144 closest distance to " O   HOH Z 427 " =    3.129
peak=    3.143 closest distance to " OE1 GLU A 277 " =    1.872
peak=    3.143 closest distance to " O   THR A  31 " =    1.491
peak=    3.138 closest distance to " O   HOH Z 423 " =    3.040
peak=    3.135 closest distance to " CA  ASN A  74 " =    1.132
peak=    3.135 closest distance to " O   HOH Z 409 " =    3.355
peak=    3.134 closest distance to " O   HOH Z 394 " =    1.746
peak=    3.124 closest distance to " O   GLN A 278 " =    1.514
peak=    3.122 closest distance to " CG1 ILE A 151 " =    1.069
peak=    3.121 closest distance to " O   HOH Z 329 " =    2.724
peak=    3.118 closest distance to " CB  VAL A 268 " =    0.801
peak=    3.112 closest distance to " O   HOH Z 291 " =    1.850
peak=    3.108 closest distance to " CZ  PHE A 192 " =    0.976
peak=    3.104 closest distance to " N   ASN A 127 " =    1.285
peak=    3.099 closest distance to " O   HOH Z 236 " =    1.576
peak=    3.098 closest distance to " O   HOH Z 154 " =    2.083
peak=    3.086 closest distance to " O   HOH Z 420 " =    4.309
peak=    3.083 closest distance to " O   HOH Z  71 " =    2.039
peak=    3.080 closest distance to " CB  GLU A 152 " =    1.303
peak=    3.075 closest distance to " O   HOH Z 255 " =    1.647
peak=    3.071 closest distance to " OE2 GLU A  53 " =    2.077
peak=    3.068 closest distance to " CD  LYS A 119 " =    1.413
peak=    3.061 closest distance to " OG  SER A 206 " =    1.226
peak=    3.044 closest distance to " O   HOH Z 211 " =    2.503
peak=    3.042 closest distance to " O   HOH Z 343 " =    2.685
peak=    3.037 closest distance to " NH2BARG A 190 " =    2.134
peak=    3.032 closest distance to " O   HOH Z 258 " =    1.841
peak=    3.000 closest distance to " O   HOH Z 427 " =    3.584

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.566 - 5.399
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 199
   mapped sites are within: 0.751 - 5.399

peak=   -5.617 closest distance to " CG2 VAL A 230 " =    0.822
peak=   -4.434 closest distance to " CB  ALA A 161 " =    2.563
peak=   -4.386 closest distance to " CD  ARG A 156 " =    2.003
peak=   -4.320 closest distance to " O   HOH Z 290 " =    1.085
peak=   -4.293 closest distance to " SG  CYS A 254 " =    3.131
peak=   -4.196 closest distance to " O   HOH Z 266 " =    4.477
peak=   -4.075 closest distance to " CG  ASP A 231 " =    0.795
peak=   -4.057 closest distance to " N   GLN A  58 " =    1.675
peak=   -3.983 closest distance to " OXT GLY A 302 " =    2.801
peak=   -3.940 closest distance to " CE2 TYR A  30 " =    2.834
peak=   -3.929 closest distance to " CD1 LEU A 101 " =    2.557
peak=   -3.925 closest distance to " CD2 LEU A 300 " =    2.841
peak=   -3.925 closest distance to " CG2 VAL A 296 " =    1.264
peak=   -3.925 closest distance to " CB  PRO A 243 " =    2.553
peak=   -3.880 closest distance to " C   ALA A 158 " =    1.277
peak=   -3.856 closest distance to " C   HIS A 108 " =    1.211
peak=   -3.854 closest distance to " O   VAL A  67 " =    2.641
peak=   -3.834 closest distance to " CG  GLN A 223 " =    1.963
peak=   -3.832 closest distance to " O   HOH Z  11 " =    1.913
peak=   -3.825 closest distance to " O   HOH Z  52 " =    1.509
peak=   -3.816 closest distance to " CD  ARG A 139 " =    1.600
peak=   -3.798 closest distance to " O   PRO A 163 " =    2.000
peak=   -3.788 closest distance to " CG  LEU A 228 " =    0.920
peak=   -3.768 closest distance to " N   ALA A 226 " =    2.078
peak=   -3.755 closest distance to " O   VAL A  67 " =    2.678
peak=   -3.750 closest distance to " CG  PHE A 283 " =    2.784
peak=   -3.723 closest distance to " CE  MET A 105 " =    2.017
peak=   -3.722 closest distance to " N   ALA A  43 " =    2.372
peak=   -3.721 closest distance to " CA  GLY A  98 " =    1.955
peak=   -3.720 closest distance to " CG  LEU A 101 " =    2.499
peak=   -3.717 closest distance to " NE2 GLN A  88 " =    2.108
peak=   -3.714 closest distance to " O   HOH Z  13 " =    1.443
peak=   -3.710 closest distance to " O   HOH Z 231 " =    1.752
peak=   -3.699 closest distance to " CB  ALA A 248 " =    1.962
peak=   -3.696 closest distance to " O   PRO A 198 " =    1.238
peak=   -3.696 closest distance to " O   HOH Z  43 " =    1.736
peak=   -3.691 closest distance to " O   HOH Z 407 " =    3.248
peak=   -3.690 closest distance to " OG BSER A 134 " =    1.713
peak=   -3.683 closest distance to " O   HOH Z 103 " =    1.860
peak=   -3.673 closest distance to " O   HOH Z 166 " =    1.852
peak=   -3.673 closest distance to " CG1 VAL A 250 " =    2.784
peak=   -3.659 closest distance to " CB  PRO A 163 " =    2.649
peak=   -3.659 closest distance to " CZ3 TRP A 179 " =    1.292
peak=   -3.651 closest distance to " OG  SER A  97 " =    2.241
peak=   -3.632 closest distance to " O   HOH Z 388 " =    2.071
peak=   -3.629 closest distance to " O   HOH Z 166 " =    1.485
peak=   -3.621 closest distance to " CB  PRO A 280 " =    2.095
peak=   -3.602 closest distance to " N   THR A 157 " =    1.473
peak=   -3.598 closest distance to " OG BSER A 134 " =    1.221
peak=   -3.598 closest distance to " CG  ASP A  50 " =    2.452
peak=   -3.593 closest distance to " CZ  PHE A  59 " =    1.535
peak=   -3.590 closest distance to " CB  TYR A  15 " =    2.221
peak=   -3.586 closest distance to " N   HIS A 115 " =    2.082
peak=   -3.579 closest distance to " CD  LYS A 289 " =    2.582
peak=   -3.575 closest distance to " ND2 ASN A  45 " =    0.973
peak=   -3.567 closest distance to " O   HOH Z 211 " =    1.597
peak=   -3.563 closest distance to " C   ASN A 187 " =    1.824
peak=   -3.560 closest distance to " CB  ASN A  39 " =    2.048
peak=   -3.560 closest distance to " CG1 VAL A 296 " =    1.318
peak=   -3.552 closest distance to " CG  LYS A 193 " =    2.272
peak=   -3.547 closest distance to " OG ASER A 134 " =    1.335
peak=   -3.541 closest distance to " O   GLY A 196 " =    1.125
peak=   -3.540 closest distance to " O   HOH Z 185 " =    2.347
peak=   -3.540 closest distance to " CZ  TYR A 169 " =    1.734
peak=   -3.539 closest distance to " NH2AARG A 275 " =    5.161
peak=   -3.536 closest distance to " O   HOH Z 426 " =    2.399
peak=   -3.527 closest distance to " O   HOH Z 311 " =    3.582
peak=   -3.526 closest distance to " O   HOH Z 389 " =    1.841
peak=   -3.519 closest distance to " O   HOH Z  92 " =    1.729
peak=   -3.512 closest distance to " C   ASN A 285 " =    2.465
peak=   -3.505 closest distance to " O   ALA A 161 " =    1.616
peak=   -3.504 closest distance to " O   HOH Z 118 " =    2.857
peak=   -3.500 closest distance to " C   ASP A 231 " =    2.561
peak=   -3.498 closest distance to " O   HOH Z 436 " =    1.501
peak=   -3.493 closest distance to " CG1 VAL A 112 " =    2.768
peak=   -3.479 closest distance to " O   GLY A 211 " =    1.377
peak=   -3.478 closest distance to " NH2 ARG A  79 " =    1.842
peak=   -3.465 closest distance to " CG  TRP A 266 " =    1.752
peak=   -3.463 closest distance to " O   HOH Z 394 " =    1.541
peak=   -3.462 closest distance to " CD  GLN A  88 " =    0.808
peak=   -3.458 closest distance to " CD1 PHE A  59 " =    1.971
peak=   -3.439 closest distance to " CB  ASP A 132 " =    2.295
peak=   -3.439 closest distance to " N   SER A 276 " =    1.255
peak=   -3.433 closest distance to " O   HOH Z 353 " =    2.137
peak=   -3.433 closest distance to " CG  MET A 105 " =    0.939
peak=   -3.431 closest distance to " O   MET A  40 " =    2.641
peak=   -3.429 closest distance to " C   MET A 188 " =    1.452
peak=   -3.413 closest distance to " N   ALA A 248 " =    1.595
peak=   -3.405 closest distance to " O   HOH Z 417 " =    2.771
peak=   -3.401 closest distance to " OG  SER A  62 " =    1.573
peak=   -3.400 closest distance to " CD1 LEU A 228 " =    2.278
peak=   -3.399 closest distance to " O   HOH Z 292 " =    4.450
peak=   -3.397 closest distance to " CE2 PHE A 218 " =    2.579
peak=   -3.392 closest distance to " CA  ASP A 298 " =    1.068
peak=   -3.391 closest distance to " C   GLN A 205 " =    2.011
peak=   -3.390 closest distance to " O   HOH Z 351 " =    1.442
peak=   -3.383 closest distance to " O   HOH Z 426 " =    1.594
peak=   -3.374 closest distance to " CG  GLU A   2 " =    1.819
peak=   -3.374 closest distance to " OG  SER A  26 " =    1.117
peak=   -3.372 closest distance to " O   HOH Z 222 " =    1.482
peak=   -3.370 closest distance to " O   HOH Z 148 " =    2.934
peak=   -3.369 closest distance to " ND2 ASN A 187 " =    1.571
peak=   -3.368 closest distance to " OG  SER A   3 " =    1.712
peak=   -3.362 closest distance to " CG  ARG A 269 " =    2.290
peak=   -3.361 closest distance to " CB  ALA A  43 " =    2.384
peak=   -3.358 closest distance to " OG  SER A 206 " =    1.693
peak=   -3.355 closest distance to " N   THR A 235 " =    1.273
peak=   -3.354 closest distance to " CB  PHE A 192 " =    1.766
peak=   -3.353 closest distance to " O   HOH Z 196 " =    2.188
peak=   -3.352 closest distance to " O   HOH Z  63 " =    1.058
peak=   -3.350 closest distance to " CG1 VAL A 112 " =    2.654
peak=   -3.348 closest distance to " CG  PRO A 163 " =    2.663
peak=   -3.344 closest distance to " OG  SER A  87 " =    1.377
peak=   -3.334 closest distance to " NH2 ARG A  66 " =    1.982
peak=   -3.333 closest distance to " O   HOH Z 241 " =    1.344
peak=   -3.326 closest distance to " O   VAL A 197 " =    1.303
peak=   -3.325 closest distance to " CB  ASP A 132 " =    2.181
peak=   -3.323 closest distance to " CE BMET A  47 " =    1.851
peak=   -3.321 closest distance to " O   HOH Z 191 " =    5.399
peak=   -3.310 closest distance to " CE3 TRP A 150 " =    2.059
peak=   -3.308 closest distance to " CB  GLN A  11 " =    1.846
peak=   -3.305 closest distance to " O   HOH Z  15 " =    1.572
peak=   -3.298 closest distance to " OD1 ASN A 148 " =    1.563
peak=   -3.297 closest distance to " NZ  LYS A 119 " =    3.397
peak=   -3.295 closest distance to " CA  GLY A 133 " =    1.947
peak=   -3.285 closest distance to " O   HOH Z 435 " =    2.714
peak=   -3.284 closest distance to " C   LEU A 222 " =    0.751
peak=   -3.280 closest distance to " CA  GLY A 133 " =    2.201
peak=   -3.277 closest distance to " O   PRO A 198 " =    1.282
peak=   -3.275 closest distance to " OXT GLY A 302 " =    3.483
peak=   -3.271 closest distance to " O   HOH Z  38 " =    1.772
peak=   -3.268 closest distance to " OG1 THR A 178 " =    1.217
peak=   -3.265 closest distance to " CB  VAL A 296 " =    1.187
peak=   -3.262 closest distance to " O   HOH Z  47 " =    1.520
peak=   -3.261 closest distance to " OE1 GLN A  73 " =    2.315
peak=   -3.260 closest distance to " ND2 ASN A  60 " =    1.525
peak=   -3.259 closest distance to " O   HOH Z  71 " =    1.089
peak=   -3.258 closest distance to " CD2 TYR A 293 " =    2.170
peak=   -3.256 closest distance to " OD1 ASP A 191 " =    1.567
peak=   -3.254 closest distance to " N   SER A 212 " =    1.960
peak=   -3.253 closest distance to " CB  ALA A  51 " =    1.874
peak=   -3.245 closest distance to " CA  GLY A 241 " =    2.998
peak=   -3.239 closest distance to " O   HOH Z 148 " =    3.688
peak=   -3.237 closest distance to " CG2 VAL A 112 " =    2.626
peak=   -3.237 closest distance to " O   HOH Z 148 " =    1.769
peak=   -3.236 closest distance to " O   VAL A 174 " =    2.013
peak=   -3.233 closest distance to " CD  ARG A 195 " =    5.176
peak=   -3.233 closest distance to " O   HOH Z 292 " =    2.865
peak=   -3.230 closest distance to " CG2 ILE A 263 " =    2.313
peak=   -3.228 closest distance to " O   HOH Z 275 " =    1.463
peak=   -3.228 closest distance to " CE3 TRP A 274 " =    2.459
peak=   -3.225 closest distance to " O   HOH Z  19 " =    2.263
peak=   -3.225 closest distance to " CG  GLU A 277 " =    1.108
peak=   -3.224 closest distance to " CG1 VAL A 197 " =    2.208
peak=   -3.221 closest distance to " O   ALA A  51 " =    1.432
peak=   -3.220 closest distance to " O   HOH Z 359 " =    3.017
peak=   -3.215 closest distance to " N   PHE A  59 " =    2.085
peak=   -3.215 closest distance to " O   HOH Z 244 " =    2.017
peak=   -3.213 closest distance to " O   HOH Z 283 " =    1.596
peak=   -3.213 closest distance to " O   HOH Z  97 " =    1.733
peak=   -3.210 closest distance to " N   VAL A 230 " =    1.183
peak=   -3.204 closest distance to " O   HOH Z 389 " =    4.545
peak=   -3.196 closest distance to " N   ASP A 171 " =    2.442
peak=   -3.195 closest distance to " CG  GLU A  53 " =    1.554
peak=   -3.189 closest distance to " O   ASP A 231 " =    2.480
peak=   -3.187 closest distance to " O   HOH Z 339 " =    1.833
peak=   -3.186 closest distance to " O   HOH Z  11 " =    1.869
peak=   -3.185 closest distance to " O   HOH Z 234 " =    4.248
peak=   -3.177 closest distance to " O   HOH Z 168 " =    1.757
peak=   -3.170 closest distance to " CE  MET A  93 " =    1.119
peak=   -3.164 closest distance to " CA  GLY A 203 " =    2.175
peak=   -3.160 closest distance to " O   HOH Z 174 " =    2.253
peak=   -3.153 closest distance to " CE  LYS A  76 " =    2.856
peak=   -3.151 closest distance to " O   HOH Z 423 " =    2.236
peak=   -3.149 closest distance to " O   HOH Z 313 " =    1.868
peak=   -3.135 closest distance to " O   HOH Z 344 " =    2.596
peak=   -3.135 closest distance to " CD  GLN A  58 " =    1.155
peak=   -3.129 closest distance to " SG ACYS A 201 " =    1.980
peak=   -3.126 closest distance to " O   HOH Z 210 " =    1.030
peak=   -3.126 closest distance to " NE  ARG A 259 " =    1.169
peak=   -3.125 closest distance to " O   HOH Z 252 " =    4.106
peak=   -3.123 closest distance to " O   LEU A 167 " =    1.508
peak=   -3.109 closest distance to " O   HOH Z 431 " =    1.671
peak=   -3.107 closest distance to " O   HOH Z 353 " =    2.083
peak=   -3.107 closest distance to " CG  GLU A 152 " =    2.306
peak=   -3.107 closest distance to " OG1 THR A  82 " =    1.433
peak=   -3.103 closest distance to " OD1 ASP A 191 " =    1.579
peak=   -3.100 closest distance to " O   HOH Z 175 " =    4.255
peak=   -3.097 closest distance to " O   HOH Z 369 " =    2.181
peak=   -3.097 closest distance to " O   HOH Z 193 " =    1.727
peak=   -3.096 closest distance to " O   HOH Z 205 " =    2.468
peak=   -3.095 closest distance to " O   HOH Z 281 " =    2.707
peak=   -3.089 closest distance to " NH2BARG A 145 " =    2.377
peak=   -3.086 closest distance to " O   SER A  22 " =    2.172
peak=   -3.077 closest distance to " N   MET A 105 " =    2.637
peak=   -3.062 closest distance to " CD1 TYR A 247 " =    2.383

================= 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    :  0.4486 0.4482   6.246945e+00   6.240302e+00
   1_bss:  0.4404 0.4365   6.244538e+00   6.229806e+00
   1_xyz:  0.3483 0.3753   6.089710e+00   6.134686e+00
   1_adp:  0.2928 0.3441   5.968453e+00   6.077430e+00
   1_occ:  0.2924 0.3445   5.967846e+00   6.078109e+00
   2_bss:  0.2881 0.3398   5.967339e+00   6.074845e+00
   2_xyz:  0.2000 0.2569   5.651608e+00   5.834805e+00
   2_adp:  0.1791 0.2319   5.548051e+00   5.747302e+00
   2_occ:  0.1789 0.2317   5.547165e+00   5.746672e+00
   3_bss:  0.1773 0.2294   5.542831e+00   5.741246e+00
   3_xyz:  0.1335 0.1790   5.287360e+00   5.512497e+00
   3_adp:  0.1237 0.1706   5.227943e+00   5.463030e+00
   3_occ:  0.1236 0.1705   5.227430e+00   5.462542e+00
   4_bss:  0.1237 0.1702   5.227237e+00   5.461750e+00
   4_xyz:  0.1143 0.1613   5.170841e+00   5.414356e+00
   4_adp:  0.1139 0.1591   5.162574e+00   5.400468e+00
   4_occ:  0.1138 0.1589   5.161818e+00   5.399768e+00
   5_bss:  0.1138 0.1589   5.161957e+00   5.399821e+00
   5_xyz:  0.1113 0.1571   5.147878e+00   5.391242e+00
   5_adp:  0.1114 0.1570   5.147355e+00   5.390489e+00
   5_occ:  0.1113 0.1571   5.147006e+00   5.390187e+00
   5_bss:  0.1113 0.1571   5.146909e+00   5.390094e+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:  0.368  20.001   7.148   7.750   9.552   0.000   0.000   0.000
   1_xyz:  0.368  20.001   7.148   7.750   9.552   0.000   0.000   0.000
   1_adp:  0.368  20.001   7.148   7.750   9.552   0.000   0.000   0.000
   1_occ:  0.368  20.001   7.148   7.750   9.552   0.000   0.000   0.000
   2_bss:  0.338  32.937   3.699   3.895   6.340   0.000   0.000   0.000
   2_xyz:  0.338  32.937   3.699   3.895   6.340   0.000   0.000   0.000
   2_adp:  0.338  32.937   3.699   3.895   6.340   0.000   0.000   0.000
   2_occ:  0.338  32.937   3.699   3.895   6.340   0.000   0.000   0.000
   3_bss:  0.329  39.701   2.551   2.711   3.818   0.000   0.000   0.000
   3_xyz:  0.329  39.701   2.551   2.711   3.818   0.000   0.000   0.000
   3_adp:  0.329  39.701   2.551   2.711   3.818   0.000   0.000   0.000
   3_occ:  0.329  39.701   2.551   2.711   3.818   0.000   0.000   0.000
   4_bss:  0.320  39.701   2.426   2.561   3.206   0.000   0.000   0.000
   4_xyz:  0.320  39.701   2.426   2.561   3.206   0.000   0.000   0.000
   4_adp:  0.320  39.701   2.426   2.561   3.206   0.000   0.000   0.000
   4_occ:  0.320  39.701   2.426   2.561   3.206   0.000   0.000   0.000
   5_bss:  0.323  38.776   2.426   2.561   3.206   0.000   0.000   0.000
   5_xyz:  0.323  38.776   2.426   2.561   3.206   0.000   0.000   0.000
   5_adp:  0.323  38.776   2.426   2.561   3.206   0.000   0.000   0.000
   5_occ:  0.323  38.776   2.426   2.561   3.206   0.000   0.000   0.000
   5_bss:  0.323  41.455  -0.290  -0.120   0.410   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.286 0.4924  0.5721    60300.701
   1_bss:  52.349 0.4887  0.7158    57080.349
   1_xyz:  41.888 0.6183  0.8928    39876.303
   1_adp:  37.126 0.6759  0.9870    33019.496
   1_occ:  37.200 0.6750  0.9858    33122.935
   2_bss:  36.916 0.6782  0.8735    32749.325
   2_xyz:  25.973 0.8006  0.9927    17227.487
   2_adp:  22.694 0.8354  1.0189    13920.357
   2_occ:  22.667 0.8356  1.0187    13881.930
   3_bss:  22.439 0.8377  0.9619    13643.407
   3_xyz:  16.816 0.8906  0.9894     8202.053
   3_adp:  15.683 0.9009  0.9913     7452.129
   3_occ:  15.665 0.9010  0.9913     7442.529
   4_bss:  15.667 0.9010  0.9803     7446.912
   4_xyz:  14.659 0.9095  0.9843     6733.265
   4_adp:  14.321 0.9125  0.9857     6562.152
   4_occ:  14.303 0.9127  0.9856     6553.829
   5_bss:  14.305 0.9126  0.9856     6554.593
   5_xyz:  14.120 0.9142  0.9845     6437.461
   5_adp:  14.087 0.9145  0.9827     6426.500
   5_occ:  14.084 0.9146  0.9826     6425.508
   5_bss:  14.082 0.9146  0.9808     6425.010
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3472e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3472e+01
   1_xyz:   1.580  0.012  0.103 18.010  0.006  4.110   1.2553e-01
   1_adp:   1.580  0.012  0.103 18.010  0.006  4.110   1.2553e-01
   1_occ:   1.580  0.012  0.103 18.010  0.006  4.110   1.2553e-01
   2_bss:   1.580  0.012  0.103 18.010  0.006  4.110   1.2553e-01
   2_xyz:   1.086  0.008  0.075 15.973  0.005  4.113   7.5120e-02
   2_adp:   1.086  0.008  0.075 15.973  0.005  4.113   7.5120e-02
   2_occ:   1.086  0.008  0.075 15.973  0.005  4.113   7.5120e-02
   3_bss:   1.086  0.008  0.075 15.973  0.005  4.113   7.5120e-02
   3_xyz:   1.110  0.007  0.084 15.964  0.004  4.121   7.0252e-02
   3_adp:   1.110  0.007  0.084 15.964  0.004  4.121   7.0252e-02
   3_occ:   1.110  0.007  0.084 15.964  0.004  4.121   7.0252e-02
   4_bss:   1.110  0.007  0.084 15.964  0.004  4.121   7.0252e-02
   4_xyz:   1.031  0.007  0.083 15.754  0.004  4.110   6.4761e-02
   4_adp:   1.031  0.007  0.083 15.754  0.004  4.110   6.4761e-02
   4_occ:   1.031  0.007  0.083 15.754  0.004  4.110   6.4761e-02
   5_bss:   1.031  0.007  0.083 15.754  0.004  4.110   6.4761e-02
   5_xyz:   1.023  0.007  0.081 15.496  0.004  4.110   6.2790e-02
   5_adp:   1.023  0.007  0.081 15.496  0.004  4.110   6.2790e-02
   5_occ:   1.023  0.007  0.081 15.496  0.004  4.110   6.2790e-02
   5_bss:   1.023  0.007  0.081 15.496  0.004  4.110   6.2790e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9321e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9321e+00
   1_xyz:  13.381  0.150  0.446 85.841  0.050  2.194   9.0222e-02
   1_adp:  13.381  0.150  0.446 85.841  0.050  2.194   9.0222e-02
   1_occ:  13.381  0.150  0.446 85.841  0.050  2.194   9.0222e-02
   2_bss:  13.381  0.150  0.446 85.841  0.050  2.194   9.0222e-02
   2_xyz:   7.132  0.075  0.232 88.547  0.037  2.283   1.2931e-01
   2_adp:   7.132  0.075  0.232 88.547  0.037  2.283   1.2931e-01
   2_occ:   7.132  0.075  0.232 88.547  0.037  2.283   1.2931e-01
   3_bss:   7.132  0.075  0.232 88.547  0.037  2.283   1.2931e-01
   3_xyz:   8.496  0.048  0.541 82.376  0.037  2.323   5.0143e-02
   3_adp:   8.496  0.048  0.541 82.376  0.037  2.323   5.0143e-02
   3_occ:   8.496  0.048  0.541 82.376  0.037  2.323   5.0143e-02
   4_bss:   8.496  0.048  0.541 82.376  0.037  2.323   5.0143e-02
   4_xyz:   6.753  0.041  0.592 83.171  0.039  2.323   4.7694e-02
   4_adp:   6.753  0.041  0.592 83.171  0.039  2.323   4.7694e-02
   4_occ:   6.753  0.041  0.592 83.171  0.039  2.323   4.7694e-02
   5_bss:   6.753  0.041  0.592 83.171  0.039  2.323   4.7694e-02
   5_xyz:   6.865  0.041  0.575 82.701  0.038  2.286   4.5906e-02
   5_adp:   6.865  0.041  0.575 82.701  0.038  2.286   4.5906e-02
   5_occ:   6.865  0.041  0.575 82.701  0.038  2.286   4.5906e-02
   5_bss:   6.865  0.041  0.575 82.701  0.038  2.286   4.5906e-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:  62.73   0.00  11.43  58.64   0.00   8.64  62.73   0.00  26.64
   1_occ:  62.73   0.00  11.43  58.64   0.00   8.64  62.73   0.00  26.64
   2_bss:  62.73   0.00  11.43  58.64   0.00   8.64  62.73   0.00  26.64
   2_xyz:  62.73   0.00  11.43  58.64   0.00   8.64  62.73   0.00  26.64
   2_adp:  66.42   0.00  11.84  61.55   0.00   8.16  66.42   1.04  31.90
   2_occ:  66.42   0.00  11.84  61.55   0.00   8.16  66.42   1.04  31.90
   3_bss:  66.42   0.00  11.84  61.55   0.00   8.16  66.42   1.04  31.90
   3_xyz:  66.42   0.00  11.84  61.55   0.00   8.16  66.42   1.04  31.90
   3_adp:  82.54   0.00  12.59  82.54   0.00   8.23  76.54   2.08  36.34
   3_occ:  82.54   0.00  12.59  82.54   0.00   8.23  76.54   2.08  36.34
   4_bss:  82.54   0.00  12.59  82.54   0.00   8.23  76.54   2.08  36.34
   4_xyz:  82.54   0.00  12.59  82.54   0.00   8.23  76.54   2.08  36.34
   4_adp:  83.32   0.00  12.09  83.32   0.00   8.08  71.92   1.63  33.92
   4_occ:  83.32   0.00  12.09  83.32   0.00   8.08  71.92   1.63  33.92
   5_bss:  83.32   0.00  12.09  83.32   0.00   8.08  71.92   1.63  33.92
   5_xyz:  83.32   0.00  12.09  83.32   0.00   8.08  71.92   1.63  33.92
   5_adp:  83.35   0.00  12.01  83.35   0.00   8.04  71.53   1.55  33.68
   5_occ:  83.35   0.00  12.01  83.35   0.00   8.04  71.53   1.55  33.68
   5_bss:  86.03   2.68  14.69  86.03   2.68  10.71  74.21   4.23  36.36
------------------------------------------------------------------------
 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:    1.195    0.004    0.404
   1_adp:    1.195    0.004    0.404
   1_occ:    1.195    0.004    0.404
   2_bss:    1.195    0.004    0.404
   2_xyz:    1.416    0.045    0.551
   2_adp:    1.416    0.045    0.551
   2_occ:    1.416    0.045    0.551
   3_bss:    1.416    0.045    0.551
   3_xyz:    1.478    0.056    0.596
   3_adp:    1.478    0.056    0.596
   3_occ:    1.478    0.056    0.596
   4_bss:    1.478    0.056    0.596
   4_xyz:    1.563    0.055    0.617
   4_adp:    1.563    0.055    0.617
   4_occ:    1.563    0.055    0.617
   5_bss:    1.563    0.055    0.617
   5_xyz:    1.667    0.048    0.628
   5_adp:    1.667    0.048    0.628
   5_occ:    1.667    0.048    0.628
   5_bss:    1.667    0.048    0.628
------------------------------------------------------------------------

CPU time actual refinement: 314.54


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_782/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_782/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_782/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_782/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_782/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 314.38 
  Macro-tasks:
    bulk solvent and scale       = 40.99  
    individual site refinement   = 125.24 
    weights calculation          = 31.08  
    collect and process          = 6.47   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 203.91 
  Micro-tasks:
    mask                            = 1.76   
    f_calc                          = 94.51  
    alpha_beta                      = 8.15   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 104.22 
    fmodel                         = 6.89   
    r_factors                      = 0.17   
    phase_errors                   = 10.72  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 227.85 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.513 micro seconds
Total CPU time: 5.47 minutes
from_scatterers_fft:    623 calls, 94.23 s
gradients_fft:          569 calls, 91.58 s

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

# Date 2008-01-16 Time 02:25:15 PST -0800 (1200479115.74 s)
Start R-work = 0.4486, R-free = 0.4482 (no bulk solvent and anisotropic scale)
Final R-work = 0.1283, R-free = 0.1733 (no bulk solvent and anisotropic scale)

Start R-work = 0.4404, R-free = 0.4365
Final R-work = 0.1113, R-free = 0.1571