# Date 2008-01-16 Time 01:40:47 PST -0800 (1200476447.58 s)
#phil __OFF__

Command line arguments: "../525.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31775
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 525

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 46.4607, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.31, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.4607, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9985 1.98218
Completeness in resolution range: 0.959587
Completeness with d_max=infinity: 0.956634

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9985
                             d_min =   1.9822

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.4607, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9985 1.98218
Completeness in resolution range: 0.959587
Completeness with d_max=infinity: 0.956634

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9990 -  4.2413 [2148/2172]  1929   219  10.2%
  bin  2:  4.2413 -  3.3791 [2053/2073]  1849   204   9.9%
  bin  3:  3.3791 -  2.9557 [2031/2050]  1833   198   9.7%
  bin  4:  2.9557 -  2.6871 [2015/2045]  1811   204  10.1%
  bin  5:  2.6871 -  2.4955 [1996/2015]  1795   201  10.1%
  bin  6:  2.4955 -  2.3489 [2007/2032]  1803   204  10.2%
  bin  7:  2.3489 -  2.2317 [1979/2007]  1780   199  10.1%
  bin  8:  2.2317 -  2.1348 [1962/1998]  1769   193   9.8%
  bin  9:  2.1348 -  2.0529 [1959/2001]  1767   192   9.8%
  bin 10:  2.0529 -  1.9822 [1439/2021]  1294   145  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_525/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.66 -     2.30: 14
        2.30 -     2.95: 1658
        2.95 -     3.60: 4549
        3.60 -     4.25: 9174
        4.25 -     4.90: 12917
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.656 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.855 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.934 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  53 " - " O   HOH Z 102 "  2.128 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28307 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_525/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_525/model_refine_001.geo

CPU time processing inputs: 9.42


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.4607 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4593   r_free= 0.4418   ksol= 0.00   Bsol= 0.00   scale= 0.808    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.258423                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9990 -  4.7305 0.99   1393  154 0.3811 0.3583      6.5651      6.5084|
|  2:  4.7305 -  3.7744 0.99   1339  152 0.3564 0.3567      6.6979      6.7283|
|  3:  3.7744 -  3.3031 0.99   1303  142 0.4008 0.3629      6.6161      6.5723|
|  4:  3.3031 -  3.0038 0.99   1313  145 0.4486 0.4305      6.5115      6.4615|
|  5:  3.0038 -  2.7899 0.99   1295  147 0.4853 0.4487      6.3487      6.3444|
|  6:  2.7899 -  2.6264 0.99   1301  143 0.4815 0.5258      6.2605      6.2211|
|  7:  2.6264 -  2.4955 0.99   1273  143 0.5014 0.4946      6.2222      6.1576|
|  8:  2.4955 -  2.3873 0.98   1278  138 0.5130 0.4543      6.1835      6.1911|
|  9:  2.3873 -  2.2957 0.98   1278  147 0.4981 0.5284      6.1006      6.1609|
| 10:  2.2957 -  2.2168 1.00   1297  138 0.5350 0.4577      6.1285      6.0433|
| 11:  2.2168 -  2.1476 0.97   1255  141 0.5100 0.4862      6.0262      6.0242|
| 12:  2.1476 -  2.0864 0.98   1253  143 0.5227 0.4852      5.9788      5.9966|
| 13:  2.0864 -  2.0316 0.99   1275  135 0.5038 0.4839      5.8729      5.8311|
| 14:  2.0316 -  1.9822 0.60    777   91 0.5385 0.5289      5.8874      5.7691|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9990 -  4.7305  1393   154  0.73  32.00   0.80     0.76      63118.53|
|  2:  4.7305 -  3.7744  1339   152  0.75  30.51   0.89     0.82      83848.25|
|  3:  3.7744 -  3.3031  1303   142  0.68  37.45   0.87     0.78      89399.90|
|  4:  3.3031 -  3.0038  1313   145  0.59  44.62   0.81     0.67      82274.23|
|  5:  3.0038 -  2.7899  1295   147  0.49  52.90   0.76     0.57      71991.32|
|  6:  2.7899 -  2.6264  1301   143  0.45  56.10   0.73     0.51      66099.76|
|  7:  2.6264 -  2.4955  1273   143  0.41  59.01   0.75     0.48      61870.22|
|  8:  2.4955 -  2.3873  1278   138  0.41  58.83   0.73     0.48      55270.38|
|  9:  2.3873 -  2.2957  1278   147  0.43  57.25   0.75     0.50      48929.47|
| 10:  2.2957 -  2.2168  1297   138  0.44  56.95   0.74     0.51      42832.31|
| 11:  2.2168 -  2.1476  1255   141  0.42  58.09   0.76     0.52      41336.99|
| 12:  2.1476 -  2.0864  1253   143  0.41  59.47   0.77     0.50      38147.70|
| 13:  2.0864 -  2.0316  1275   135  0.39  60.63   0.73     0.48      33881.09|
| 14:  2.0316 -  1.9822   777    91  0.42  58.93   0.74     0.45      27884.29|
|alpha:            min =        0.45 max =            0.82 mean =         0.58|
|beta:             min =    27884.29 max =        89399.90 mean =     58761.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.51|
|phase err.(work): min =        0.00 max =           89.98 mean =        51.17|
|phase err.(test): min =        0.00 max =           89.77 mean =        51.38|
|-----------------------------------------------------------------------------|

============================== 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 = 9.867545              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.604   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.854976              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.386   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      180 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      682 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1504 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2631 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3927 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5075 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6594 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7685 |
|-----------------------------------------------------------------------------|
|-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 |       53.755 |
| 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 |       1.813 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.854)------------------------------------------|
|    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 = 11.854)------------------------------------------|
|    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: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4678   r_free= 0.4452   ksol= 0.00   Bsol= 0.00   scale= 0.776    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.262746                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4509   r_free= 0.4303   ksol= 0.35   Bsol= 20.00   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.87,8.74,10.39,0.00,0.00,0.00); trace/3= 8.67                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.252125                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.195097              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.159   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.784659              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.071   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4509      final r-factor (work) = 0.3535          |
| start r-factor (free) = 0.4303      final r-factor (free) = 0.3723          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 79.4067 = 8.20 * 0.50 * 6.2603 + 1.00 * 53.7550                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.2551 = 8.20 * 0.50 * 6.1322 + 1.00 * 0.1281                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3535      final r-factor (work) = 0.3017          |
| start r-factor (free) = 0.3723      final r-factor (free) = 0.3474          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8264 = 0.78 * 1.00 * 6.1322 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7231 = 0.78 * 1.00 * 6.0018 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.854)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    55.55   11.48    None  None   None       |
|    all(noH): 2823   0      0.00    55.55   11.48    None  None   None       |
|    Sol.    : 438    0      0.00    55.55   24.82    None  None   None       |
|    Mac.    : 2385   0      0.00    43.12   9.03     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.555:  930   |   5:    27.776 -  33.331:  111        |
|      1:     5.555 -  11.110:  758   |   6:    33.331 -  38.886:   73        |
|      2:    11.110 -  16.666:  499   |   7:    38.886 -  44.442:   46        |
|      3:    16.666 -  22.221:  244   |   8:    44.442 -  49.997:   12        |
|      4:    22.221 -  27.776:  149   |   9:    49.997 -  55.552:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3017 r_free = 0.3474             target_work(ml) = 5.974         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3012 r_free = 0.3473             target_work(ml) = 5.973         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3012   r_free= 0.3473   ksol= 0.35   Bsol= 20.00   scale= 1.107   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.87,8.74,10.39,0.00,0.00,0.00); trace/3= 8.67                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.972595                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2965   r_free= 0.3422   ksol= 0.32   Bsol= 20.00   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.53,4.63,6.80,0.00,0.00,0.00); trace/3= 4.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.972893                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.821434              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.274   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.427615              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.317  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2965      final r-factor (work) = 0.2015          |
| start r-factor (free) = 0.3422      final r-factor (free) = 0.2504          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.5991 = 4.82 * 0.50 * 6.0030 + 1.00 * 0.1276                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.0657 = 4.82 * 0.50 * 5.8054 + 1.00 * 0.0705                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2015      final r-factor (work) = 0.1789          |
| start r-factor (free) = 0.2504      final r-factor (free) = 0.2292          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4959 = 0.43 * 1.00 * 5.8054 + 1.00 * 0.0134                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3938 = 0.43 * 1.00 * 5.5733 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.854)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    63.89   11.62    None  None   None       |
|    all(noH): 2823   0      0.00    63.89   11.62    None  None   None       |
|    Sol.    : 438    0      0.00    63.89   30.63    None  None   None       |
|    Mac.    : 2385   0      0.00    50.91   8.13     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 -   6.389: 1246   |   5:    31.946 -  38.335:  131        |
|      1:     6.389 -  12.778:  775   |   6:    38.335 -  44.725:   87        |
|      2:    12.778 -  19.168:  282   |   7:    44.725 -  51.114:   42        |
|      3:    19.168 -  25.557:  136   |   8:    51.114 -  57.503:    7        |
|      4:    25.557 -  31.946:  116   |   9:    57.503 -  63.892:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1789 r_free = 0.2292             target_work(ml) = 5.531         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1787 r_free = 0.2291             target_work(ml) = 5.530         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1787   r_free= 0.2291   ksol= 0.32   Bsol= 20.00   scale= 1.048   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.53,4.63,6.80,0.00,0.00,0.00); trace/3= 4.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.530488                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1765   r_free= 0.2275   ksol= 0.33   Bsol= 46.47   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.39,2.91,4.70,0.00,0.00,0.00); trace/3= 3.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.528654                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.910138              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.089  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.361738              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.826  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1765      final r-factor (work) = 0.1423          |
| start r-factor (free) = 0.2275      final r-factor (free) = 0.1879          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4043 = 1.91 * 0.50 * 5.5847 + 1.00 * 0.0705                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2444 = 1.91 * 0.50 * 5.4328 + 1.00 * 0.0556                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1423      final r-factor (work) = 0.1330          |
| start r-factor (free) = 0.1879      final r-factor (free) = 0.1832          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.2743 = 3.36 * 1.00 * 5.4328 + 1.00 * 0.0105                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.8405 = 3.36 * 1.00 * 5.3023 + 1.00 * 0.0155                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.854)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.78   12.97    None  None   None       |
|    all(noH): 2823   0      0.00    80.78   12.97    None  None   None       |
|    Sol.    : 438    0      0.56    80.35   38.12    None  None   None       |
|    Mac.    : 2385   0      0.00    80.78   8.35     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 -   8.078: 1554   |   5:    40.392 -  48.470:   88        |
|      1:     8.078 -  16.157:  626   |   6:    48.470 -  56.548:   80        |
|      2:    16.157 -  24.235:  191   |   7:    56.548 -  64.627:   43        |
|      3:    24.235 -  32.313:  108   |   8:    64.627 -  72.705:   31        |
|      4:    32.313 -  40.392:   93   |   9:    72.705 -  80.783:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1330 r_free = 0.1832             target_work(ml) = 5.291         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1329 r_free = 0.1832             target_work(ml) = 5.290         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1329   r_free= 0.1832   ksol= 0.33   Bsol= 46.47   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.39,2.91,4.70,0.00,0.00,0.00); trace/3= 3.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.290279                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1330   r_free= 0.1833   ksol= 0.32   Bsol= 46.47   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.27,2.62,4.44,0.00,0.00,0.00); trace/3= 3.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.290549                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.154304              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.410  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.648106              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.092  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1330      final r-factor (work) = 0.1203          |
| start r-factor (free) = 0.1833      final r-factor (free) = 0.1708          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7667 = 2.15 * 0.50 * 5.3020 + 1.00 * 0.0556                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7157 = 2.15 * 0.50 * 5.2501 + 1.00 * 0.0605                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1203      final r-factor (work) = 0.1183          |
| start r-factor (free) = 0.1708      final r-factor (free) = 0.1659          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4181 = 0.65 * 1.00 * 5.2501 + 1.00 * 0.0155                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3891 = 0.65 * 1.00 * 5.2079 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.854)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.15   12.59    None  None   None       |
|    all(noH): 2823   0      0.00    83.15   12.59    None  None   None       |
|    Sol.    : 438    0      1.13    79.40   37.20    None  None   None       |
|    Mac.    : 2385   0      0.00    83.15   8.07     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 -   8.315: 1651   |   5:    41.573 -  49.887:   83        |
|      1:     8.315 -  16.629:  585   |   6:    49.887 -  58.202:   75        |
|      2:    16.629 -  24.944:  160   |   7:    58.202 -  66.517:   38        |
|      3:    24.944 -  33.258:  114   |   8:    66.517 -  74.831:   24        |
|      4:    33.258 -  41.573:   88   |   9:    74.831 -  83.146:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1183 r_free = 0.1659             target_work(ml) = 5.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1182 r_free = 0.1658             target_work(ml) = 5.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1182   r_free= 0.1658   ksol= 0.32   Bsol= 46.47   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.27,2.62,4.44,0.00,0.00,0.00); trace/3= 3.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.193229                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1181   r_free= 0.1658   ksol= 0.32   Bsol= 46.47   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.43,2.67,4.45,0.00,0.00,0.00); trace/3= 3.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.193203                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.396562              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.414  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.620627              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.535  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1181      final r-factor (work) = 0.1139          |
| start r-factor (free) = 0.1658      final r-factor (free) = 0.1607          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3013 = 2.40 * 0.50 * 5.2080 + 1.00 * 0.0607                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2658 = 2.40 * 0.50 * 5.1774 + 1.00 * 0.0619                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1139      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1607      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2269 = 0.62 * 1.00 * 5.1774 + 1.00 * 0.0137                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2175 = 0.62 * 1.00 * 5.1631 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.854)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.36   12.30    None  None   None       |
|    all(noH): 2823   0      0.00    85.36   12.30    None  None   None       |
|    Sol.    : 438    0      1.41    78.90   36.17    None  None   None       |
|    Mac.    : 2385   0      0.00    85.36   7.92     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 -   8.536: 1707   |   5:    42.682 -  51.218:   91        |
|      1:     8.536 -  17.073:  546   |   6:    51.218 -  59.754:   53        |
|      2:    17.073 -  25.609:  164   |   7:    59.754 -  68.290:   37        |
|      3:    25.609 -  34.145:  114   |   8:    68.290 -  76.827:   13        |
|      4:    34.145 -  42.682:   94   |   9:    76.827 -  85.363:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1134 r_free = 0.1596             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1134 r_free = 0.1595             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1595   ksol= 0.32   Bsol= 46.47   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.43,2.67,4.45,0.00,0.00,0.00); trace/3= 3.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.159351                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9990 -  4.7305 0.99   1393  154 0.1002 0.1286      5.3956      5.5525|
|  2:  4.7305 -  3.7744 0.99   1339  152 0.0854 0.1119      5.4389      5.6336|
|  3:  3.7744 -  3.3031 0.99   1303  142 0.1062 0.1501      5.4851      5.8526|
|  4:  3.3031 -  3.0038 0.99   1313  145 0.1227 0.1779      5.4613      5.6461|
|  5:  3.0038 -  2.7899 0.99   1295  147 0.1329 0.1618        5.34       5.535|
|  6:  2.7899 -  2.6264 0.99   1301  143 0.1219 0.2112      5.2161      5.5437|
|  7:  2.6264 -  2.4955 0.99   1273  143 0.1318 0.1638      5.2013      5.3353|
|  8:  2.4955 -  2.3873 0.98   1278  138 0.1202 0.1675       5.102      5.3556|
|  9:  2.3873 -  2.2957 0.98   1278  147 0.1199 0.1911      5.0641      5.3409|
| 10:  2.2957 -  2.2168 1.00   1297  138 0.1154 0.1639      4.9796      5.1921|
| 11:  2.2168 -  2.1476 0.97   1255  141 0.1177 0.1796      4.9697      5.2731|
| 12:  2.1476 -  2.0864 0.98   1253  143 0.1170 0.1759      4.9007      5.2518|
| 13:  2.0864 -  2.0316 0.99   1275  135 0.1121 0.1636      4.7801      5.0084|
| 14:  2.0316 -  1.9822 0.60    777   91 0.0955 0.1572      4.6297      4.8377|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9990 -  4.7305  1393   154  0.94   9.51   0.98     0.95       7431.83|
|  2:  4.7305 -  3.7744  1339   152  0.95   7.96   1.02     1.00       9223.45|
|  3:  3.7744 -  3.3031  1303   142  0.93  11.38   1.03     1.03      10595.23|
|  4:  3.3031 -  3.0038  1313   145  0.92  13.60   1.01     0.99      10424.24|
|  5:  3.0038 -  2.7899  1295   147  0.90  15.87   1.01     0.98       8555.07|
|  6:  2.7899 -  2.6264  1301   143  0.90  16.38   0.98     0.96       7230.33|
|  7:  2.6264 -  2.4955  1273   143  0.90  16.01   0.99     0.95       6454.44|
|  8:  2.4955 -  2.3873  1278   138  0.90  15.71   0.99     0.97       5654.16|
|  9:  2.3873 -  2.2957  1278   147  0.91  15.49   1.01     0.97       5345.37|
| 10:  2.2957 -  2.2168  1297   138  0.89  16.69   1.00     0.96       4658.72|
| 11:  2.2168 -  2.1476  1255   141  0.90  16.74   1.00     0.96       4691.47|
| 12:  2.1476 -  2.0864  1253   143  0.90  16.25   1.01     1.00       4123.65|
| 13:  2.0864 -  2.0316  1275   135  0.91  15.81   1.00     0.98       3267.74|
| 14:  2.0316 -  1.9822   777    91  0.93  13.08   0.99     0.96       2384.76|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2384.76 max =        10595.23 mean =      6583.73|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.30|
|phase err.(test): min =        0.00 max =           89.40 mean =        13.75|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1595   ksol= 0.32   Bsol= 49.68   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.74,-0.53,1.27,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.159354                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1595   ksol= 0.32   Bsol= 49.68   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.74,-0.53,1.27,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.159354                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9990 -  4.7305 0.99   1393  154 0.1002 0.1286      5.3957      5.5527|
|  2:  4.7305 -  3.7744 0.99   1339  152 0.0854 0.1119       5.439      5.6336|
|  3:  3.7744 -  3.3031 0.99   1303  142 0.1062 0.1501      5.4851      5.8527|
|  4:  3.3031 -  3.0038 0.99   1313  145 0.1227 0.1778      5.4613      5.6461|
|  5:  3.0038 -  2.7899 0.99   1295  147 0.1329 0.1618      5.3399      5.5349|
|  6:  2.7899 -  2.6264 0.99   1301  143 0.1219 0.2112       5.216      5.5436|
|  7:  2.6264 -  2.4955 0.99   1273  143 0.1318 0.1639      5.2013      5.3354|
|  8:  2.4955 -  2.3873 0.98   1278  138 0.1202 0.1675       5.102      5.3556|
|  9:  2.3873 -  2.2957 0.98   1278  147 0.1199 0.1911      5.0641      5.3408|
| 10:  2.2957 -  2.2168 1.00   1297  138 0.1154 0.1640      4.9796      5.1923|
| 11:  2.2168 -  2.1476 0.97   1255  141 0.1177 0.1796      4.9697      5.2731|
| 12:  2.1476 -  2.0864 0.98   1253  143 0.1170 0.1759      4.9007      5.2518|
| 13:  2.0864 -  2.0316 0.99   1275  135 0.1121 0.1635        4.78      5.0082|
| 14:  2.0316 -  1.9822 0.60    777   91 0.0955 0.1572      4.6296      4.8375|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9990 -  4.7305  1393   154  0.94   9.51   0.98     0.95       7434.42|
|  2:  4.7305 -  3.7744  1339   152  0.95   7.96   1.02     1.00       9225.58|
|  3:  3.7744 -  3.3031  1303   142  0.93  11.38   1.03     1.03      10596.19|
|  4:  3.3031 -  3.0038  1313   145  0.92  13.60   1.01     1.00      10423.96|
|  5:  3.0038 -  2.7899  1295   147  0.90  15.87   1.01     0.98       8553.76|
|  6:  2.7899 -  2.6264  1301   143  0.90  16.38   0.98     0.96       7229.79|
|  7:  2.6264 -  2.4955  1273   143  0.90  16.01   0.99     0.96       6454.35|
|  8:  2.4955 -  2.3873  1278   138  0.90  15.71   0.99     0.97       5654.04|
|  9:  2.3873 -  2.2957  1278   147  0.91  15.49   1.01     0.98       5345.34|
| 10:  2.2957 -  2.2168  1297   138  0.89  16.69   1.00     0.96       4659.05|
| 11:  2.2168 -  2.1476  1255   141  0.90  16.74   1.00     0.96       4692.09|
| 12:  2.1476 -  2.0864  1253   143  0.90  16.26   1.01     1.01       4124.00|
| 13:  2.0864 -  2.0316  1275   135  0.91  15.81   1.00     0.98       3266.92|
| 14:  2.0316 -  1.9822   777    91  0.93  13.08   0.99     0.96       2383.31|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2383.31 max =        10596.19 mean =      6583.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.30|
|phase err.(test): min =        0.00 max =           89.40 mean =        13.75|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.854)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.21    88.57   15.51    None  None   None       |
|    all(noH): 2823   0      3.21    88.57   15.51    None  None   None       |
|    Sol.    : 438    0      4.62    82.11   39.38    None  None   None       |
|    Mac.    : 2385   0      3.21    88.57   11.13    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.209 -  11.745: 1707   |   5:    45.891 -  54.427:   91        |
|      1:    11.745 -  20.282:  546   |   6:    54.427 -  62.963:   53        |
|      2:    20.282 -  28.818:  164   |   7:    62.963 -  71.499:   37        |
|      3:    28.818 -  37.354:  114   |   8:    71.499 -  80.036:   13        |
|      4:    37.354 -  45.891:   94   |   9:    80.036 -  88.572:    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)= 316         
Filter by distance & map next to the model:
   mapped sites are within: 0.213 - 4.845
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 312 from: 316
   mapped sites are within: 0.703 - 4.845

peak=   11.184 closest distance to " CB  VAL A 230 " =    1.457
peak=    9.690 closest distance to " CG2 VAL A 296 " =    1.573
peak=    6.038 closest distance to " CG  LEU A   5 " =    1.180
peak=    5.971 closest distance to " CD2 LEU A   5 " =    1.195
peak=    5.924 closest distance to " NE2 GLN A  11 " =    1.149
peak=    5.827 closest distance to " NH2 ARG A  56 " =    2.089
peak=    5.564 closest distance to " CG  PRO A  54 " =    1.359
peak=    5.537 closest distance to " O   HOH Z   9 " =    1.896
peak=    5.485 closest distance to " O   HOH Z 142 " =    2.034
peak=    5.312 closest distance to " CG  LEU A 228 " =    1.189
peak=    5.188 closest distance to " O   HOH Z 232 " =    2.341
peak=    5.083 closest distance to " CB  GLN A 223 " =    1.500
peak=    4.897 closest distance to " CB  GLN A 183 " =    1.244
peak=    4.804 closest distance to " O   HOH Z 427 " =    2.807
peak=    4.742 closest distance to " CB  PRO A  54 " =    0.997
peak=    4.574 closest distance to " CB  ASN A 142 " =    1.077
peak=    4.474 closest distance to " CB  VAL A 265 " =    1.345
peak=    4.465 closest distance to " CB  ASN A 148 " =    1.366
peak=    4.461 closest distance to " O   HOH Z 209 " =    2.331
peak=    4.447 closest distance to " ND2 ASN A 187 " =    1.651
peak=    4.439 closest distance to " CB  ARG A 275 " =    0.954
peak=    4.430 closest distance to " O   HOH Z 346 " =    1.544
peak=    4.410 closest distance to " O   HOH Z 425 " =    1.470
peak=    4.380 closest distance to " O   HOH Z 130 " =    1.081
peak=    4.376 closest distance to " O   SER A  87 " =    2.308
peak=    4.329 closest distance to " NH2AARG A 190 " =    1.938
peak=    4.315 closest distance to " CG  PRO A 213 " =    1.199
peak=    4.311 closest distance to " CB  ARG A  79 " =    1.494
peak=    4.308 closest distance to " O   HOH Z 265 " =    2.127
peak=    4.253 closest distance to " CG  PRO A 198 " =    1.216
peak=    4.253 closest distance to " O   HOH Z 303 " =    2.120
peak=    4.243 closest distance to " O   HOH Z 287 " =    1.974
peak=    4.233 closest distance to " O   HOH Z 369 " =    2.233
peak=    4.227 closest distance to " O   HOH Z 248 " =    1.461
peak=    4.226 closest distance to " O   HOH Z  61 " =    1.693
peak=    4.190 closest distance to " CZ  PHE A 218 " =    1.126
peak=    4.177 closest distance to " CB  VAL A 230 " =    1.166
peak=    4.177 closest distance to " O   HOH Z 422 " =    2.576
peak=    4.175 closest distance to " CB  TRP A 266 " =    1.058
peak=    4.151 closest distance to " CB BVAL A  41 " =    1.177
peak=    4.144 closest distance to " CG  PRO A 243 " =    1.175
peak=    4.117 closest distance to " O   HOH Z  78 " =    1.603
peak=    4.113 closest distance to " O   HOH Z 126 " =    2.038
peak=    4.106 closest distance to " O   PRO A 198 " =    1.566
peak=    4.100 closest distance to " CB  ARG A 190 " =    1.433
peak=    4.097 closest distance to " CB  SER A  63 " =    1.274
peak=    4.075 closest distance to " CG  ARG A 138 " =    1.277
peak=    4.026 closest distance to " CG  LEU A 167 " =    1.249
peak=    3.987 closest distance to " O   HOH Z 272 " =    1.800
peak=    3.968 closest distance to " O   HOH Z  43 " =    1.906
peak=    3.943 closest distance to " CB  SER A   3 " =    1.337
peak=    3.932 closest distance to " CB  ASN A  39 " =    0.979
peak=    3.876 closest distance to " O   HOH Z 130 " =    2.679
peak=    3.876 closest distance to " O   HOH Z 234 " =    3.654
peak=    3.869 closest distance to " OG ASER A 258 " =    3.048
peak=    3.868 closest distance to " O   HOH Z 411 " =    3.745
peak=    3.866 closest distance to " CA  TYR A  30 " =    0.993
peak=    3.864 closest distance to " O   HOH Z 298 " =    1.680
peak=    3.856 closest distance to " N   PHE A 130 " =    1.276
peak=    3.854 closest distance to " CA  ALA A  51 " =    0.998
peak=    3.851 closest distance to " O   HOH Z 188 " =    2.926
peak=    3.842 closest distance to " CD2 TRP A 179 " =    1.291
peak=    3.842 closest distance to " CB  GLU A 277 " =    3.601
peak=    3.837 closest distance to " CG2 VAL A 257 " =    0.871
peak=    3.830 closest distance to " O   HOH Z 353 " =    2.544
peak=    3.823 closest distance to " OG BSER A 164 " =    2.133
peak=    3.822 closest distance to " O   HOH Z 214 " =    2.272
peak=    3.814 closest distance to " O   HOH Z 290 " =    1.052
peak=    3.813 closest distance to " O   HOH Z 359 " =    1.398
peak=    3.813 closest distance to " CB  LYS A 117 " =    1.225
peak=    3.796 closest distance to " O   HOH Z   3 " =    2.001
peak=    3.772 closest distance to " CE  LYS A  76 " =    0.881
peak=    3.766 closest distance to " O  BHOH Z 338 " =    2.429
peak=    3.764 closest distance to " CD1AILE A 234 " =    0.890
peak=    3.761 closest distance to " O   HOH Z 126 " =    1.516
peak=    3.761 closest distance to " CD2 LEU A 228 " =    1.183
peak=    3.748 closest distance to " O   HOH Z 368 " =    2.108
peak=    3.743 closest distance to " CB  VAL A 202 " =    1.641
peak=    3.742 closest distance to " CA  PHE A 283 " =    1.053
peak=    3.742 closest distance to " CB  ARG A  79 " =    0.903
peak=    3.742 closest distance to " O   HOH Z 380 " =    1.784
peak=    3.737 closest distance to " O   HOH Z 251 " =    1.556
peak=    3.735 closest distance to " O   HOH Z 403 " =    1.589
peak=    3.724 closest distance to " OD1 ASN A  69 " =    2.463
peak=    3.717 closest distance to " O   HOH Z  30 " =    1.518
peak=    3.714 closest distance to " O   HOH Z  10 " =    1.721
peak=    3.710 closest distance to " CB  GLU A 152 " =    1.252
peak=    3.704 closest distance to " CB  GLN A  88 " =    1.228
peak=    3.696 closest distance to " CH2 TRP A 266 " =    1.138
peak=    3.693 closest distance to " N   ASN A  39 " =    1.186
peak=    3.688 closest distance to " ND2 ASN A 249 " =    0.880
peak=    3.682 closest distance to " CB  ASP A 124 " =    0.775
peak=    3.667 closest distance to " CD  ARG A 269 " =    1.035
peak=    3.665 closest distance to " O   HOH Z  59 " =    1.738
peak=    3.663 closest distance to " CA  SER A  87 " =    0.994
peak=    3.652 closest distance to " N   ASP A 162 " =    1.178
peak=    3.645 closest distance to " O   HOH Z 222 " =    2.490
peak=    3.641 closest distance to " O   HOH Z   1 " =    1.758
peak=    3.637 closest distance to " NZ  LYS A  48 " =    1.180
peak=    3.637 closest distance to " CB  SER A 216 " =    0.808
peak=    3.636 closest distance to " CG BARG A 102 " =    1.872
peak=    3.635 closest distance to " O   HOH Z  40 " =    1.616
peak=    3.631 closest distance to " O   HOH Z 193 " =    1.670
peak=    3.630 closest distance to " CB  ASN A 110 " =    1.105
peak=    3.630 closest distance to " CA  LYS A 117 " =    1.196
peak=    3.621 closest distance to " O   HOH Z 406 " =    1.547
peak=    3.617 closest distance to " CG AARG A 275 " =    1.159
peak=    3.614 closest distance to " CB  GLU A 128 " =    1.005
peak=    3.612 closest distance to " O   HOH Z 371 " =    2.821
peak=    3.611 closest distance to " NZ  LYS A 117 " =    3.127
peak=    3.608 closest distance to " CG1BVAL A  72 " =    1.639
peak=    3.601 closest distance to " CB  TRP A 179 " =    1.433
peak=    3.595 closest distance to " CA  ASN A 215 " =    1.067
peak=    3.593 closest distance to " O   HOH Z 126 " =    1.750
peak=    3.587 closest distance to " CD1 ILE A  33 " =    1.755
peak=    3.584 closest distance to " OE2 GLU A   2 " =    1.883
peak=    3.584 closest distance to " O   HOH Z   2 " =    1.477
peak=    3.578 closest distance to " O   HOH Z 180 " =    2.097
peak=    3.577 closest distance to " CG  GLN A  88 " =    1.111
peak=    3.566 closest distance to " CB  ALA A   9 " =    1.576
peak=    3.565 closest distance to " CG1 ILE A  49 " =    1.504
peak=    3.562 closest distance to " CG  MET A 185 " =    1.146
peak=    3.559 closest distance to " CG2 ILE A 234 " =    0.937
peak=    3.544 closest distance to " NH1AARG A 145 " =    1.194
peak=    3.542 closest distance to " O   HOH Z 158 " =    3.198
peak=    3.535 closest distance to " O   HOH Z 368 " =    3.451
peak=    3.534 closest distance to " O   HOH Z  97 " =    2.066
peak=    3.530 closest distance to " O   HOH Z 261 " =    1.708
peak=    3.529 closest distance to " CG2 ILE A 120 " =    1.221
peak=    3.510 closest distance to " O   HOH Z 423 " =    1.442
peak=    3.509 closest distance to " O   HOH Z  21 " =    1.786
peak=    3.507 closest distance to " O   HOH Z  97 " =    2.419
peak=    3.507 closest distance to " O   HOH Z 419 " =    2.040
peak=    3.500 closest distance to " O   HOH Z 203 " =    1.718
peak=    3.495 closest distance to " O   HOH Z 261 " =    1.824
peak=    3.489 closest distance to " CB  SER A 212 " =    1.299
peak=    3.484 closest distance to " CB  PRO A  90 " =    1.135
peak=    3.481 closest distance to " CB  SER A  26 " =    1.702
peak=    3.480 closest distance to " CE3 TRP A 150 " =    0.984
peak=    3.480 closest distance to " O   HOH Z 273 " =    2.983
peak=    3.476 closest distance to " CA  ASP A 162 " =    1.011
peak=    3.475 closest distance to " O   HOH Z 299 " =    4.164
peak=    3.465 closest distance to " O   PHE A 192 " =    1.371
peak=    3.465 closest distance to " CB  HIS A 108 " =    0.835
peak=    3.459 closest distance to " CB  GLN A  89 " =    1.272
peak=    3.456 closest distance to " O   HOH Z  68 " =    2.218
peak=    3.454 closest distance to " O   HOH Z 128 " =    2.114
peak=    3.453 closest distance to " CB  LEU A  83 " =    0.721
peak=    3.451 closest distance to " CG2 ILE A  20 " =    1.528
peak=    3.450 closest distance to " O   HOH Z 193 " =    1.762
peak=    3.444 closest distance to " OE2 GLU A  53 " =    1.976
peak=    3.443 closest distance to " N   ASN A 127 " =    1.290
peak=    3.441 closest distance to " O   HOH Z 423 " =    1.769
peak=    3.432 closest distance to " O   HOH Z 437 " =    1.677
peak=    3.430 closest distance to " CD  LYS A 166 " =    1.319
peak=    3.427 closest distance to " O   HOH Z 303 " =    2.689
peak=    3.427 closest distance to " CB  ASN A 187 " =    1.088
peak=    3.422 closest distance to " CB  GLU A  46 " =    0.957
peak=    3.421 closest distance to " O   HOH Z  40 " =    2.411
peak=    3.418 closest distance to " O   HOH Z 402 " =    1.338
peak=    3.416 closest distance to " O   HOH Z 366 " =    2.969
peak=    3.405 closest distance to " O   HOH Z  90 " =    2.266
peak=    3.405 closest distance to " O   HOH Z 124 " =    1.220
peak=    3.402 closest distance to " CB  ASN A 215 " =    1.153
peak=    3.401 closest distance to " O   HOH Z  22 " =    2.071
peak=    3.401 closest distance to " O   HOH Z 280 " =    3.050
peak=    3.400 closest distance to " O   HOH Z  88 " =    2.950
peak=    3.398 closest distance to " CD1 LEU A  96 " =    0.727
peak=    3.393 closest distance to " CA  ARG A  36 " =    1.035
peak=    3.392 closest distance to " CG1 ILE A 151 " =    1.088
peak=    3.392 closest distance to " NE2 HIS A 207 " =    1.231
peak=    3.389 closest distance to " O   HOH Z 130 " =    1.964
peak=    3.388 closest distance to " N   SER A 135 " =    1.334
peak=    3.385 closest distance to " O   HOH Z  88 " =    2.770
peak=    3.384 closest distance to " CA  LYS A 290 " =    1.209
peak=    3.380 closest distance to " O   HOH Z 329 " =    4.114
peak=    3.378 closest distance to " CD  LYS A  76 " =    1.860
peak=    3.374 closest distance to " CA  ALA A 291 " =    0.877
peak=    3.373 closest distance to " O   HOH Z 133 " =    2.728
peak=    3.373 closest distance to " O   HOH Z 175 " =    2.050
peak=    3.371 closest distance to " O   HOH Z  44 " =    1.682
peak=    3.371 closest distance to " CE1 TYR A 186 " =    1.288
peak=    3.370 closest distance to " CB  ALA A 114 " =    1.433
peak=    3.370 closest distance to " O   HOH Z 258 " =    2.092
peak=    3.366 closest distance to " O   HOH Z 193 " =    1.648
peak=    3.365 closest distance to " CG2 THR A 221 " =    1.146
peak=    3.364 closest distance to " CG2 VAL A 197 " =    1.112
peak=    3.361 closest distance to " ND1 HIS A  86 " =    1.683
peak=    3.360 closest distance to " O   HOH Z 116 " =    2.995
peak=    3.356 closest distance to " O   ASN A  74 " =    1.526
peak=    3.355 closest distance to " CG  LEU A 281 " =    1.031
peak=    3.354 closest distance to " O   HOH Z 128 " =    2.111
peak=    3.354 closest distance to " C   ALA A 299 " =    0.948
peak=    3.348 closest distance to " NH2AARG A 145 " =    1.119
peak=    3.348 closest distance to " O   HOH Z  40 " =    1.848
peak=    3.346 closest distance to " CB  THR A  31 " =    1.648
peak=    3.343 closest distance to " O   HOH Z  61 " =    1.556
peak=    3.342 closest distance to " O   HOH Z 130 " =    2.388
peak=    3.341 closest distance to " CA  ARG A 195 " =    1.158
peak=    3.340 closest distance to " O   HOH Z 196 " =    1.393
peak=    3.339 closest distance to " CB  ARG A 138 " =    0.829
peak=    3.338 closest distance to " CG1 VAL A 153 " =    0.947
peak=    3.337 closest distance to " CB  ASP A 140 " =    0.970
peak=    3.334 closest distance to " O   HOH Z 322 " =    1.975
peak=    3.332 closest distance to " CB  GLN A 278 " =    0.949
peak=    3.330 closest distance to " CB  LEU A 228 " =    1.305
peak=    3.329 closest distance to " CA  ALA A 158 " =    1.322
peak=    3.326 closest distance to " CG  MET A 113 " =    1.119
peak=    3.325 closest distance to " CA  THR A 264 " =    0.822
peak=    3.324 closest distance to " CG  GLN A  58 " =    0.941
peak=    3.324 closest distance to " CA  GLY A 267 " =    0.862
peak=    3.323 closest distance to " O   HOH Z 421 " =    2.114
peak=    3.321 closest distance to " O   HOH Z 285 " =    2.322
peak=    3.319 closest distance to " CG  LYS A 119 " =    1.098
peak=    3.316 closest distance to " O   HOH Z 250 " =    1.377
peak=    3.315 closest distance to " O   HOH Z 145 " =    2.025
peak=    3.314 closest distance to " CB  THR A  52 " =    0.938
peak=    3.310 closest distance to " O   HOH Z 392 " =    3.163
peak=    3.309 closest distance to " O   HOH Z 172 " =    3.377
peak=    3.309 closest distance to " CB  LEU A 143 " =    1.176
peak=    3.305 closest distance to " CA  TYR A  30 " =    1.072
peak=    3.298 closest distance to " N   CYS A 260 " =    0.703
peak=    3.291 closest distance to " O   HOH Z   1 " =    1.714
peak=    3.290 closest distance to " O   HOH Z   7 " =    1.283
peak=    3.289 closest distance to " CA  TYR A 116 " =    1.427
peak=    3.288 closest distance to " CB  THR A 157 " =    1.191
peak=    3.285 closest distance to " CA  ASN A 127 " =    1.065
peak=    3.280 closest distance to " O   HOH Z  92 " =    2.422
peak=    3.279 closest distance to " O   HOH Z 405 " =    1.124
peak=    3.279 closest distance to " O   HOH Z 425 " =    2.038
peak=    3.278 closest distance to " CA  ALA A  21 " =    1.173
peak=    3.274 closest distance to " CB  SER A 210 " =    0.753
peak=    3.273 closest distance to " OG BSER A  99 " =    2.162
peak=    3.272 closest distance to " CB  THR A  82 " =    1.287
peak=    3.272 closest distance to " CB  ALA A 248 " =    1.348
peak=    3.271 closest distance to " CA  ILE A 234 " =    0.949
peak=    3.269 closest distance to " CB  SER A  62 " =    1.105
peak=    3.262 closest distance to " N   GLN A 278 " =    1.434
peak=    3.261 closest distance to " CD2 LEU A 297 " =    0.957
peak=    3.259 closest distance to " O   HOH Z 148 " =    3.534
peak=    3.256 closest distance to " CA  ALA A 129 " =    1.483
peak=    3.253 closest distance to " O   HOH Z 260 " =    1.559
peak=    3.252 closest distance to " O   HOH Z  88 " =    3.085
peak=    3.247 closest distance to " OG  SER A  62 " =    2.886
peak=    3.244 closest distance to " NE2 GLN A  77 " =    3.124
peak=    3.242 closest distance to " CB  ALA A 248 " =    1.096
peak=    3.240 closest distance to " CD2 TYR A 186 " =    1.058
peak=    3.239 closest distance to " O   HOH Z 234 " =    1.832
peak=    3.236 closest distance to " N   SER A 146 " =    1.706
peak=    3.230 closest distance to " O   HOH Z 305 " =    3.424
peak=    3.227 closest distance to " O   HOH Z 371 " =    3.328
peak=    3.226 closest distance to " O   HOH Z 153 " =    3.778
peak=    3.225 closest distance to " CA  ASN A 217 " =    1.244
peak=    3.223 closest distance to " CB  MET A  40 " =    0.818
peak=    3.223 closest distance to " CG  MET A 185 " =    1.007
peak=    3.216 closest distance to " CD1 ILE A 106 " =    0.977
peak=    3.214 closest distance to " CD2 LEU A 255 " =    1.632
peak=    3.214 closest distance to " N   ALA A 256 " =    1.024
peak=    3.212 closest distance to " CZ  PHE A  38 " =    1.132
peak=    3.212 closest distance to " CB  ARG A 139 " =    0.927
peak=    3.206 closest distance to " CG2 ILE A 239 " =    0.711
peak=    3.203 closest distance to " CB  VAL A 268 " =    0.844
peak=    3.202 closest distance to " O   HOH Z 154 " =    2.188
peak=    3.201 closest distance to " O   HOH Z 389 " =    1.704
peak=    3.188 closest distance to " O   PRO A 198 " =    1.252
peak=    3.183 closest distance to " O   HOH Z 227 " =    1.754
peak=    3.181 closest distance to " NH2AARG A 275 " =    3.543
peak=    3.175 closest distance to " O   LEU A 228 " =    1.944
peak=    3.173 closest distance to " CE  LYS A  48 " =    1.131
peak=    3.166 closest distance to " NE2 GLN A  73 " =    1.388
peak=    3.165 closest distance to " O   HOH Z  85 " =    1.500
peak=    3.161 closest distance to " CB  VAL A 250 " =    1.133
peak=    3.159 closest distance to " O   HOH Z 132 " =    2.462
peak=    3.159 closest distance to " O   HOH Z 389 " =    1.235
peak=    3.158 closest distance to " O   HOH Z 343 " =    3.317
peak=    3.158 closest distance to " CB  LEU A 300 " =    0.894
peak=    3.154 closest distance to " O   PRO A  90 " =    1.626
peak=    3.153 closest distance to " CB  PHE A 204 " =    0.981
peak=    3.153 closest distance to " CB  TRP A 150 " =    1.360
peak=    3.151 closest distance to " O   HOH Z 409 " =    2.977
peak=    3.150 closest distance to " CD1 LEU A 228 " =    2.002
peak=    3.146 closest distance to " CA  LEU A 282 " =    1.232
peak=    3.145 closest distance to " CA  MET A 105 " =    0.960
peak=    3.144 closest distance to " O   THR A 182 " =    1.433
peak=    3.144 closest distance to " O   HOH Z 327 " =    1.955
peak=    3.142 closest distance to " CD  ARG A 195 " =    3.527
peak=    3.142 closest distance to " O   HOH Z 213 " =    2.094
peak=    3.139 closest distance to " CA  ARG A 102 " =    1.140
peak=    3.138 closest distance to " O   HOH Z 227 " =    2.155
peak=    3.138 closest distance to " O   HOH Z 263 " =    1.644
peak=    3.137 closest distance to " CA  ALA A 154 " =    1.028
peak=    3.137 closest distance to " CB  VAL A 296 " =    1.052
peak=    3.136 closest distance to " CA  VAL A  41 " =    0.761
peak=    3.131 closest distance to " O   HOH Z 325 " =    2.196
peak=    3.128 closest distance to " O   HOH Z 423 " =    2.434
peak=    3.125 closest distance to " O   HOH Z  80 " =    1.492
peak=    3.120 closest distance to " CA  ILE A 106 " =    0.739
peak=    3.111 closest distance to " CD1 LEU A 300 " =    1.158
peak=    3.106 closest distance to " O   HOH Z 357 " =    2.005
peak=    3.105 closest distance to " O   HOH Z 394 " =    3.666
peak=    3.093 closest distance to " NH2BARG A 145 " =    2.021
peak=    3.092 closest distance to " CA  ALA A 233 " =    1.141
peak=    3.091 closest distance to " CB  ALA A 227 " =    1.099
peak=    3.081 closest distance to " O   HOH Z 171 " =    4.118
peak=    3.080 closest distance to " O   HOH Z 259 " =    2.209
peak=    3.073 closest distance to " CG  GLN A  55 " =    2.316
peak=    3.068 closest distance to " O   HOH Z  85 " =    2.079
peak=    3.066 closest distance to " CB  ALA A   1 " =    4.845
peak=    3.049 closest distance to " CB  ILE A  20 " =    1.428
peak=    3.048 closest distance to " CG  LYS A 289 " =    1.230
peak=    3.029 closest distance to " O   HOH Z 124 " =    2.129
peak=    3.026 closest distance to " O   HOH Z 148 " =    2.327

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.728 - 5.472
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 211
   mapped sites are within: 0.728 - 5.472

peak=   -4.790 closest distance to " CG2 VAL A 230 " =    0.728
peak=   -4.588 closest distance to " CD  ARG A 156 " =    2.064
peak=   -4.428 closest distance to " OG BSER A 134 " =    1.261
peak=   -4.411 closest distance to " CB  PRO A 243 " =    2.720
peak=   -4.341 closest distance to " O   VAL A  67 " =    2.524
peak=   -4.336 closest distance to " CD  ARG A  14 " =    3.191
peak=   -4.256 closest distance to " CZ2 TRP A  92 " =    2.846
peak=   -4.230 closest distance to " CG2 VAL A 202 " =    2.752
peak=   -4.168 closest distance to " CB  PHE A 192 " =    1.908
peak=   -4.164 closest distance to " CG  GLN A  58 " =    1.052
peak=   -4.116 closest distance to " O   HOH Z 266 " =    5.472
peak=   -4.105 closest distance to " O   HOH Z 231 " =    2.004
peak=   -4.088 closest distance to " CD  GLN A 223 " =    2.197
peak=   -4.001 closest distance to " C   HIS A 108 " =    1.208
peak=   -3.927 closest distance to " N   ALA A  43 " =    2.580
peak=   -3.923 closest distance to " O   HOH Z 211 " =    1.308
peak=   -3.904 closest distance to " O   HOH Z 185 " =    2.322
peak=   -3.897 closest distance to " CG1 VAL A 112 " =    2.876
peak=   -3.894 closest distance to " CD1 LEU A 255 " =    2.827
peak=   -3.879 closest distance to " O   PRO A 163 " =    2.044
peak=   -3.877 closest distance to " CE BMET A  47 " =    1.223
peak=   -3.868 closest distance to " O   HOH Z 394 " =    1.534
peak=   -3.858 closest distance to " CB  ALA A  43 " =    2.566
peak=   -3.841 closest distance to " O   HOH Z 290 " =    1.217
peak=   -3.834 closest distance to " CE2 TYR A  30 " =    2.661
peak=   -3.827 closest distance to " O   PRO A 198 " =    1.207
peak=   -3.810 closest distance to " CB  ALA A 161 " =    2.516
peak=   -3.797 closest distance to " O   HOH Z 351 " =    1.527
peak=   -3.795 closest distance to " N   THR A 157 " =    1.485
peak=   -3.717 closest distance to " O   HOH Z 166 " =    2.069
peak=   -3.702 closest distance to " CB  ALA A 248 " =    2.357
peak=   -3.689 closest distance to " CA  VAL A  67 " =    2.917
peak=   -3.680 closest distance to " CG2 VAL A 296 " =    1.821
peak=   -3.657 closest distance to " ND2 ASN A  45 " =    1.254
peak=   -3.654 closest distance to " CE  MET A 105 " =    2.395
peak=   -3.654 closest distance to " O   HOH Z 131 " =    4.095
peak=   -3.653 closest distance to " ND2 ASN A  45 " =    1.649
peak=   -3.647 closest distance to " ND2 ASN A 249 " =    2.410
peak=   -3.639 closest distance to " CB  ALA A 248 " =    2.078
peak=   -3.624 closest distance to " O   HOH Z 359 " =    3.097
peak=   -3.623 closest distance to " O   HOH Z 114 " =    2.995
peak=   -3.622 closest distance to " CA  GLY A 241 " =    2.289
peak=   -3.605 closest distance to " O   HOH Z  11 " =    1.807
peak=   -3.595 closest distance to " O   HOH Z 286 " =    1.722
peak=   -3.593 closest distance to " ND2 ASN A 187 " =    1.510
peak=   -3.592 closest distance to " CE2 PHE A 218 " =    2.466
peak=   -3.588 closest distance to " CG  TRP A 266 " =    1.946
peak=   -3.585 closest distance to " CG2 THR A 178 " =    2.338
peak=   -3.579 closest distance to " O   HOH Z 357 " =    2.014
peak=   -3.557 closest distance to " CD  PRO A 213 " =    2.059
peak=   -3.556 closest distance to " CD1 LEU A 101 " =    2.306
peak=   -3.553 closest distance to " O   HOH Z 100 " =    1.060
peak=   -3.545 closest distance to " N   ALA A 226 " =    2.036
peak=   -3.545 closest distance to " CD1 ILE A 199 " =    2.490
peak=   -3.541 closest distance to " C   MET A 188 " =    1.462
peak=   -3.540 closest distance to " CA  ASN A 127 " =    1.219
peak=   -3.537 closest distance to " OG  SER A  87 " =    1.373
peak=   -3.536 closest distance to " O   HOH Z 191 " =    5.447
peak=   -3.530 closest distance to " CD2 TYR A 293 " =    1.936
peak=   -3.527 closest distance to " O   HOH Z 140 " =    1.674
peak=   -3.525 closest distance to " O   HOH Z 389 " =    2.178
peak=   -3.523 closest distance to " OH  TYR A 172 " =    1.814
peak=   -3.520 closest distance to " OXT GLY A 302 " =    3.014
peak=   -3.515 closest distance to " N   THR A  52 " =    1.705
peak=   -3.512 closest distance to " OG  SER A  62 " =    4.437
peak=   -3.499 closest distance to " O   HOH Z 243 " =    1.947
peak=   -3.478 closest distance to " CA  ASP A 298 " =    1.073
peak=   -3.471 closest distance to " NH2 ARG A  79 " =    2.039
peak=   -3.467 closest distance to " CD2 LEU A 237 " =    2.824
peak=   -3.460 closest distance to " ND2 ASN A 252 " =    1.895
peak=   -3.459 closest distance to " O   HOH Z  52 " =    1.431
peak=   -3.456 closest distance to " N   ALA A 248 " =    1.573
peak=   -3.452 closest distance to " NE2 GLN A 278 " =    1.765
peak=   -3.451 closest distance to " O   HOH Z 377 " =    2.117
peak=   -3.441 closest distance to " O   HOH Z 198 " =    1.910
peak=   -3.434 closest distance to " O   HOH Z  73 " =    2.339
peak=   -3.429 closest distance to " O   HOH Z 103 " =    1.783
peak=   -3.427 closest distance to " OG  SER A  97 " =    2.258
peak=   -3.423 closest distance to " O   HOH Z 166 " =    2.112
peak=   -3.422 closest distance to " OE1 GLN A  88 " =    0.981
peak=   -3.422 closest distance to " O   HOH Z  43 " =    1.821
peak=   -3.420 closest distance to " CZ2 TRP A 274 " =    0.945
peak=   -3.420 closest distance to " CA  GLY A 203 " =    2.480
peak=   -3.419 closest distance to " O   HOH Z  65 " =    1.143
peak=   -3.418 closest distance to " O   VAL A 189 " =    2.537
peak=   -3.417 closest distance to " CG1 VAL A 125 " =    2.006
peak=   -3.412 closest distance to " CB  ALA A 114 " =    2.442
peak=   -3.410 closest distance to " O   HOH Z 102 " =    1.644
peak=   -3.409 closest distance to " O   HOH Z 313 " =    1.586
peak=   -3.402 closest distance to " O   SER A  22 " =    2.387
peak=   -3.402 closest distance to " CZ3 TRP A 179 " =    1.250
peak=   -3.399 closest distance to " O   HOH Z 193 " =    1.442
peak=   -3.395 closest distance to " CG  LEU A   5 " =    0.944
peak=   -3.394 closest distance to " CD2 HIS A 207 " =    2.308
peak=   -3.394 closest distance to " O   HOH Z 350 " =    1.803
peak=   -3.390 closest distance to " CE3 TRP A 150 " =    2.086
peak=   -3.385 closest distance to " CA  GLY A 133 " =    1.952
peak=   -3.380 closest distance to " CB  PRO A 163 " =    2.423
peak=   -3.379 closest distance to " O   HOH Z 295 " =    1.597
peak=   -3.377 closest distance to " CG1 VAL A 250 " =    2.729
peak=   -3.376 closest distance to " O   HOH Z 165 " =    2.125
peak=   -3.373 closest distance to " O   HOH Z 389 " =    1.403
peak=   -3.364 closest distance to " CG1 VAL A 112 " =    2.619
peak=   -3.358 closest distance to " N   HIS A 115 " =    2.219
peak=   -3.357 closest distance to " O   HOH Z 318 " =    2.115
peak=   -3.357 closest distance to " O   HOH Z 345 " =    2.107
peak=   -3.350 closest distance to " CG2 VAL A 296 " =    1.056
peak=   -3.348 closest distance to " O   HOH Z 285 " =    2.161
peak=   -3.347 closest distance to " O   ARG A 145 " =    1.517
peak=   -3.344 closest distance to " O   ALA A  10 " =    1.810
peak=   -3.328 closest distance to " O   SER A 135 " =    1.399
peak=   -3.326 closest distance to " O   PHE A 218 " =    1.533
peak=   -3.320 closest distance to " CB  ALA A  10 " =    2.336
peak=   -3.316 closest distance to " O   HOH Z 147 " =    2.069
peak=   -3.313 closest distance to " O   GLY A  80 " =    2.483
peak=   -3.308 closest distance to " CZ  TYR A 169 " =    1.728
peak=   -3.305 closest distance to " O   HOH Z  90 " =    2.638
peak=   -3.299 closest distance to " O   HOH Z 281 " =    2.742
peak=   -3.298 closest distance to " CG2 ILE A 151 " =    2.545
peak=   -3.291 closest distance to " O   HOH Z 359 " =    1.563
peak=   -3.289 closest distance to " O   SER A 210 " =    1.841
peak=   -3.282 closest distance to " CZ  PHE A 192 " =    2.830
peak=   -3.278 closest distance to " OE2 GLU A 152 " =    1.258
peak=   -3.276 closest distance to " NH2AARG A 275 " =    5.128
peak=   -3.270 closest distance to " O   HOH Z 253 " =    3.787
peak=   -3.269 closest distance to " CE2 TRP A  70 " =    2.166
peak=   -3.268 closest distance to " CB  ASN A  39 " =    2.252
peak=   -3.267 closest distance to " NE2 GLN A 278 " =    1.789
peak=   -3.264 closest distance to " O   HOH Z  38 " =    2.014
peak=   -3.259 closest distance to " CE1 PHE A  59 " =    1.967
peak=   -3.258 closest distance to " O   HOH Z 134 " =    3.973
peak=   -3.258 closest distance to " O   HOH Z 437 " =    1.756
peak=   -3.252 closest distance to " O   HOH Z  51 " =    1.038
peak=   -3.249 closest distance to " CD2 LEU A   5 " =    1.113
peak=   -3.248 closest distance to " CB  ASP A 132 " =    2.397
peak=   -3.248 closest distance to " N   ALA A 248 " =    1.863
peak=   -3.247 closest distance to " O   GLY A  17 " =    1.155
peak=   -3.243 closest distance to " O   HOH Z 231 " =    1.382
peak=   -3.240 closest distance to " CD  LYS A 289 " =    2.387
peak=   -3.236 closest distance to " CB  PRO A 213 " =    2.193
peak=   -3.235 closest distance to " OD1 ASN A 187 " =    1.614
peak=   -3.232 closest distance to " C   LEU A 143 " =    1.039
peak=   -3.230 closest distance to " CD2 TYR A 247 " =    2.498
peak=   -3.221 closest distance to " O   GLY A 203 " =    2.454
peak=   -3.220 closest distance to " O   ASN A 301 " =    1.662
peak=   -3.219 closest distance to " O   SER A 271 " =    2.151
peak=   -3.212 closest distance to " OD1 ASN A  39 " =    2.188
peak=   -3.206 closest distance to " CG2 ILE A 263 " =    2.281
peak=   -3.200 closest distance to " CB  ALA A 291 " =    2.224
peak=   -3.196 closest distance to " CA  GLY A  98 " =    1.854
peak=   -3.195 closest distance to " O   HOH Z 189 " =    2.208
peak=   -3.194 closest distance to " CB  GLN A  11 " =    1.884
peak=   -3.189 closest distance to " CD  GLU A 236 " =    1.100
peak=   -3.189 closest distance to " O   HOH Z 371 " =    2.222
peak=   -3.188 closest distance to " N   GLN A  58 " =    1.873
peak=   -3.185 closest distance to " CE  LYS A  76 " =    2.709
peak=   -3.183 closest distance to " O   HOH Z 111 " =    1.739
peak=   -3.183 closest distance to " O   HOH Z 407 " =    2.974
peak=   -3.182 closest distance to " C   LEU A 222 " =    0.849
peak=   -3.179 closest distance to " O   HOH Z 426 " =    1.677
peak=   -3.179 closest distance to " CG  ASP A 231 " =    0.803
peak=   -3.178 closest distance to " N   SER A 276 " =    1.378
peak=   -3.173 closest distance to " O   LEU A 101 " =    2.813
peak=   -3.170 closest distance to " O   HOH Z 138 " =    1.333
peak=   -3.170 closest distance to " CA  ASP A  27 " =    2.433
peak=   -3.167 closest distance to " CD  ARG A 139 " =    1.677
peak=   -3.165 closest distance to " OG  SER A  63 " =    1.180
peak=   -3.162 closest distance to " OE1 GLN A 183 " =    1.519
peak=   -3.161 closest distance to " CB  GLN A  55 " =    1.276
peak=   -3.152 closest distance to " NE2 GLN A 194 " =    1.800
peak=   -3.152 closest distance to " O   ASP A  27 " =    1.922
peak=   -3.151 closest distance to " CA  GLY A 241 " =    3.141
peak=   -3.151 closest distance to " O   HOH Z 377 " =    0.896
peak=   -3.148 closest distance to " N   ASP A 286 " =    2.311
peak=   -3.144 closest distance to " O   PRO A 198 " =    1.340
peak=   -3.144 closest distance to " O   HOH Z 421 " =    3.079
peak=   -3.143 closest distance to " OD2 ASP A 191 " =    1.285
peak=   -3.140 closest distance to " CB  ALA A 291 " =    2.232
peak=   -3.139 closest distance to " O   HOH Z 236 " =    1.401
peak=   -3.136 closest distance to " CD2 PHE A 225 " =    1.142
peak=   -3.136 closest distance to " CB  SER A 210 " =    1.128
peak=   -3.133 closest distance to " OD2 ASP A 171 " =    2.218
peak=   -3.133 closest distance to " O   HOH Z 390 " =    2.353
peak=   -3.131 closest distance to " CB  ASN A  69 " =    1.307
peak=   -3.131 closest distance to " O   HOH Z 238 " =    1.009
peak=   -3.128 closest distance to " NH2 ARG A 219 " =    1.698
peak=   -3.124 closest distance to " CG  PHE A 283 " =    2.586
peak=   -3.122 closest distance to " O   HOH Z 166 " =    1.572
peak=   -3.121 closest distance to " O   HOH Z 346 " =    1.786
peak=   -3.119 closest distance to " O   ALA A   1 " =    1.682
peak=   -3.114 closest distance to " CB  ALA A  64 " =    2.658
peak=   -3.104 closest distance to " O   HOH Z 134 " =    3.478
peak=   -3.104 closest distance to " O   HOH Z 111 " =    4.364
peak=   -3.102 closest distance to " O   GLN A 240 " =    2.493
peak=   -3.102 closest distance to " C   ASP A 231 " =    2.484
peak=   -3.095 closest distance to " O   HOH Z 412 " =    4.159
peak=   -3.094 closest distance to " O   HOH Z 353 " =    1.948
peak=   -3.092 closest distance to " CG  GLN A 103 " =    2.408
peak=   -3.084 closest distance to " O   SER A 276 " =    1.612
peak=   -3.083 closest distance to " C   ARG A 269 " =    1.367
peak=   -3.074 closest distance to " O   HOH Z 139 " =    3.061
peak=   -3.068 closest distance to " CG  ARG A 269 " =    2.324
peak=   -3.064 closest distance to " CG1 VAL A 197 " =    2.321
peak=   -3.057 closest distance to " O   HOH Z 368 " =    1.627
peak=   -3.054 closest distance to " CD2 PHE A  61 " =    2.003
peak=   -3.049 closest distance to " O   GLY A  80 " =    2.492
peak=   -3.047 closest distance to " CD  PRO A 243 " =    2.079
peak=   -3.027 closest distance to " O   ALA A 227 " =    1.597
peak=   -3.025 closest distance to " OG BSER A 134 " =    1.785
peak=   -3.008 closest distance to " OD1 ASN A 301 " =    2.017
peak=   -2.966 closest distance to " O   HOH Z 231 " =    1.654

================= 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    :  0.4593 0.4418   6.258423e+00   6.233309e+00
   1_bss:  0.4509 0.4303   6.252125e+00   6.220323e+00
   1_xyz:  0.3535 0.3723   6.093128e+00   6.116197e+00
   1_adp:  0.3017 0.3474   5.973648e+00   6.066568e+00
   1_occ:  0.3012 0.3473   5.972595e+00   6.067949e+00
   2_bss:  0.2965 0.3422   5.972893e+00   6.066232e+00
   2_xyz:  0.2015 0.2504   5.634881e+00   5.803180e+00
   2_adp:  0.1789 0.2292   5.530951e+00   5.717573e+00
   2_occ:  0.1787 0.2291   5.530488e+00   5.717568e+00
   3_bss:  0.1765 0.2275   5.528654e+00   5.715359e+00
   3_xyz:  0.1423 0.1879   5.335283e+00   5.543436e+00
   3_adp:  0.1330 0.1832   5.290562e+00   5.517986e+00
   3_occ:  0.1329 0.1832   5.290279e+00   5.517881e+00
   4_bss:  0.1330 0.1833   5.290549e+00   5.518240e+00
   4_xyz:  0.1203 0.1708   5.214001e+00   5.455858e+00
   4_adp:  0.1183 0.1659   5.193558e+00   5.430349e+00
   4_occ:  0.1182 0.1658   5.193229e+00   5.430181e+00
   5_bss:  0.1181 0.1658   5.193203e+00   5.430231e+00
   5_xyz:  0.1139 0.1607   5.165015e+00   5.408936e+00
   5_adp:  0.1134 0.1596   5.159527e+00   5.401853e+00
   5_occ:  0.1134 0.1595   5.159351e+00   5.401760e+00
   5_bss:  0.1134 0.1595   5.159354e+00   5.401758e+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:  0.352  20.000   6.865   8.740  10.390   0.000   0.000   0.000
   1_xyz:  0.352  20.000   6.865   8.740  10.390   0.000   0.000   0.000
   1_adp:  0.352  20.000   6.865   8.740  10.390   0.000   0.000   0.000
   1_occ:  0.352  20.000   6.865   8.740  10.390   0.000   0.000   0.000
   2_bss:  0.315  20.002   3.530   4.633   6.802   0.000   0.000   0.000
   2_xyz:  0.315  20.002   3.530   4.633   6.802   0.000   0.000   0.000
   2_adp:  0.315  20.002   3.530   4.633   6.802   0.000   0.000   0.000
   2_occ:  0.315  20.002   3.530   4.633   6.802   0.000   0.000   0.000
   3_bss:  0.331  46.467   2.385   2.911   4.695   0.000   0.000   0.000
   3_xyz:  0.331  46.467   2.385   2.911   4.695   0.000   0.000   0.000
   3_adp:  0.331  46.467   2.385   2.911   4.695   0.000   0.000   0.000
   3_occ:  0.331  46.467   2.385   2.911   4.695   0.000   0.000   0.000
   4_bss:  0.320  46.467   2.270   2.623   4.439   0.000   0.000   0.000
   4_xyz:  0.320  46.467   2.270   2.623   4.439   0.000   0.000   0.000
   4_adp:  0.320  46.467   2.270   2.623   4.439   0.000   0.000   0.000
   4_occ:  0.320  46.467   2.270   2.623   4.439   0.000   0.000   0.000
   5_bss:  0.320  46.467   2.431   2.667   4.448   0.000   0.000   0.000
   5_xyz:  0.320  46.467   2.431   2.667   4.448   0.000   0.000   0.000
   5_adp:  0.320  46.467   2.431   2.667   4.448   0.000   0.000   0.000
   5_occ:  0.320  46.467   2.431   2.667   4.448   0.000   0.000   0.000
   5_bss:  0.320  49.676  -0.745  -0.526   1.271   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.191 0.5065  0.5791    58760.366
   1_bss:  50.807 0.5097  0.7543    56115.240
   1_xyz:  40.539 0.6352  0.9086    37665.934
   1_adp:  36.389 0.6848  0.9978    31918.301
   1_occ:  36.495 0.6834  0.9941    31983.035
   2_bss:  36.229 0.6863  0.8739    31587.624
   2_xyz:  24.662 0.8145  1.0000    15679.881
   2_adp:  21.785 0.8444  1.0151    12948.656
   2_occ:  21.781 0.8445  1.0152    12939.995
   3_bss:  21.664 0.8458  0.9586    12892.162
   3_xyz:  17.394 0.8861  0.9828     8841.658
   3_adp:  16.752 0.8920  0.9792     8398.954
   3_occ:  16.748 0.8921  0.9793     8395.217
   4_bss:  16.757 0.8920  0.9712     8418.265
   4_xyz:  15.464 0.9028  0.9773     7335.398
   4_adp:  14.865 0.9081  0.9760     6980.359
   4_occ:  14.862 0.9081  0.9760     6974.643
   5_bss:  14.862 0.9081  0.9787     6976.576
   5_xyz:  14.406 0.9119  0.9803     6673.486
   5_adp:  14.240 0.9134  0.9773     6588.331
   5_occ:  14.241 0.9134  0.9772     6583.616
   5_bss:  14.241 0.9134  0.9782     6583.849
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3755e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3755e+01
   1_xyz:   1.611  0.012  0.104 18.007  0.006  4.120   1.2812e-01
   1_adp:   1.611  0.012  0.104 18.007  0.006  4.120   1.2812e-01
   1_occ:   1.611  0.012  0.104 18.007  0.006  4.120   1.2812e-01
   2_bss:   1.611  0.012  0.104 18.007  0.006  4.120   1.2812e-01
   2_xyz:   1.058  0.008  0.079 16.121  0.004  4.123   7.0476e-02
   2_adp:   1.058  0.008  0.079 16.121  0.004  4.123   7.0476e-02
   2_occ:   1.058  0.008  0.079 16.121  0.004  4.123   7.0476e-02
   3_bss:   1.058  0.008  0.079 16.121  0.004  4.123   7.0476e-02
   3_xyz:   0.931  0.006  0.071 15.698  0.003  4.122   5.5648e-02
   3_adp:   0.931  0.006  0.071 15.698  0.003  4.122   5.5648e-02
   3_occ:   0.931  0.006  0.071 15.698  0.003  4.122   5.5648e-02
   4_bss:   0.931  0.006  0.071 15.698  0.003  4.122   5.5648e-02
   4_xyz:   0.995  0.007  0.077 15.752  0.004  4.128   6.0540e-02
   4_adp:   0.995  0.007  0.077 15.752  0.004  4.128   6.0540e-02
   4_occ:   0.995  0.007  0.077 15.752  0.004  4.128   6.0540e-02
   5_bss:   0.995  0.007  0.077 15.752  0.004  4.128   6.0540e-02
   5_xyz:   1.001  0.008  0.078 15.447  0.004  4.118   6.1876e-02
   5_adp:   1.001  0.008  0.078 15.447  0.004  4.118   6.1876e-02
   5_occ:   1.001  0.008  0.078 15.447  0.004  4.118   6.1876e-02
   5_bss:   1.001  0.008  0.078 15.447  0.004  4.118   6.1876e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9688e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9688e+00
   1_xyz:  12.919  0.157  0.390 85.760  0.032  2.154   9.3547e-02
   1_adp:  12.919  0.157  0.390 85.760  0.032  2.154   9.3547e-02
   1_occ:  12.919  0.157  0.390 85.760  0.032  2.154   9.3547e-02
   2_bss:  12.919  0.157  0.390 85.760  0.032  2.154   9.3547e-02
   2_xyz:   6.256  0.086  0.259 85.525  0.038  2.291   6.2428e-02
   2_adp:   6.256  0.086  0.259 85.525  0.038  2.291   6.2428e-02
   2_occ:   6.256  0.086  0.259 85.525  0.038  2.291   6.2428e-02
   3_bss:   6.256  0.086  0.259 85.525  0.038  2.291   6.2428e-02
   3_xyz:   6.710  0.041  0.340 84.691  0.027  2.306   3.8099e-02
   3_adp:   6.710  0.041  0.340 84.691  0.027  2.306   3.8099e-02
   3_occ:   6.710  0.041  0.340 84.691  0.027  2.306   3.8099e-02
   4_bss:   6.710  0.041  0.340 84.691  0.027  2.306   3.8099e-02
   4_xyz:   8.390  0.052  0.346 82.347  0.038  2.356   3.4922e-02
   4_adp:   8.390  0.052  0.346 82.347  0.038  2.356   3.4922e-02
   4_occ:   8.390  0.052  0.346 82.347  0.038  2.356   3.4922e-02
   5_bss:   8.390  0.052  0.346 82.347  0.038  2.356   3.4922e-02
   5_xyz:   6.129  0.047  0.353 83.773  0.039  2.324   4.4628e-02
   5_adp:   6.129  0.047  0.353 83.773  0.039  2.324   4.4628e-02
   5_occ:   6.129  0.047  0.353 83.773  0.039  2.324   4.4628e-02
   5_bss:   6.129  0.047  0.353 83.773  0.039  2.324   4.4628e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  55.55   0.00  11.48  43.12   0.00   9.03  55.55   0.00  24.82
   1_occ:  55.55   0.00  11.48  43.12   0.00   9.03  55.55   0.00  24.82
   2_bss:  55.55   0.00  11.48  43.12   0.00   9.03  55.55   0.00  24.82
   2_xyz:  55.55   0.00  11.48  43.12   0.00   9.03  55.55   0.00  24.82
   2_adp:  63.89   0.00  11.62  50.91   0.00   8.13  63.89   0.00  30.63
   2_occ:  63.89   0.00  11.62  50.91   0.00   8.13  63.89   0.00  30.63
   3_bss:  63.89   0.00  11.62  50.91   0.00   8.13  63.89   0.00  30.63
   3_xyz:  63.89   0.00  11.62  50.91   0.00   8.13  63.89   0.00  30.63
   3_adp:  80.78   0.00  12.97  80.78   0.00   8.35  80.35   0.56  38.12
   3_occ:  80.78   0.00  12.97  80.78   0.00   8.35  80.35   0.56  38.12
   4_bss:  80.78   0.00  12.97  80.78   0.00   8.35  80.35   0.56  38.12
   4_xyz:  80.78   0.00  12.97  80.78   0.00   8.35  80.35   0.56  38.12
   4_adp:  83.15   0.00  12.59  83.15   0.00   8.07  79.40   1.13  37.20
   4_occ:  83.15   0.00  12.59  83.15   0.00   8.07  79.40   1.13  37.20
   5_bss:  83.15   0.00  12.59  83.15   0.00   8.07  79.40   1.13  37.20
   5_xyz:  83.15   0.00  12.59  83.15   0.00   8.07  79.40   1.13  37.20
   5_adp:  85.36   0.00  12.30  85.36   0.00   7.92  78.90   1.41  36.17
   5_occ:  85.36   0.00  12.30  85.36   0.00   7.92  78.90   1.41  36.17
   5_bss:  88.57   3.21  15.51  88.57   3.21  11.13  82.11   4.62  39.38
------------------------------------------------------------------------
 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:    1.248    0.027    0.405
   1_adp:    1.248    0.027    0.405
   1_occ:    1.248    0.027    0.405
   2_bss:    1.248    0.027    0.405
   2_xyz:    1.545    0.017    0.547
   2_adp:    1.545    0.017    0.547
   2_occ:    1.545    0.017    0.547
   3_bss:    1.545    0.017    0.547
   3_xyz:    1.606    0.039    0.587
   3_adp:    1.606    0.039    0.587
   3_occ:    1.606    0.039    0.587
   4_bss:    1.606    0.039    0.587
   4_xyz:    1.683    0.054    0.618
   4_adp:    1.683    0.054    0.618
   4_occ:    1.683    0.054    0.618
   5_bss:    1.683    0.054    0.618
   5_xyz:    1.713    0.058    0.626
   5_adp:    1.713    0.058    0.626
   5_occ:    1.713    0.058    0.626
   5_bss:    1.713    0.058    0.626
------------------------------------------------------------------------

CPU time actual refinement: 339.77


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_525/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_525/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_525/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_525/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_525/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 339.62 
  Macro-tasks:
    bulk solvent and scale       = 44.45  
    individual site refinement   = 139.27 
    weights calculation          = 33.22  
    collect and process          = 6.51   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 223.58 
  Micro-tasks:
    mask                            = 1.81   
    f_calc                          = 103.14 
    alpha_beta                      = 8.41   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 114.72 
    fmodel                         = 8.04   
    r_factors                      = 0.22   
    phase_errors                   = 10.50  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 248.32 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.698 micro seconds
Total CPU time: 5.89 minutes
from_scatterers_fft:    669 calls, 102.74 s
gradients_fft:          614 calls, 100.68 s

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

# Date 2008-01-16 Time 01:46:40 PST -0800 (1200476800.26 s)
Start R-work = 0.4593, R-free = 0.4418 (no bulk solvent and anisotropic scale)
Final R-work = 0.1309, R-free = 0.1767 (no bulk solvent and anisotropic scale)

Start R-work = 0.4509, R-free = 0.4303
Final R-work = 0.1134, R-free = 0.1595