# Date 2008-01-16 Time 01:58:45 PST -0800 (1200477525.39 s)
#phil __OFF__

Command line arguments: "../649.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 = 7984
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 649

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.6953, 84.2302, 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: 3.34, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.6953, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8895 1.95123
Completeness in resolution range: 0.945005
Completeness with d_max=infinity: 0.942141

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8895
                             d_min =   1.9512

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.6953, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8895 1.95123
Completeness in resolution range: 0.945005
Completeness with d_max=infinity: 0.942141

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8899 -  4.1758 [2180/2209]  1965   215   9.9%
  bin  2:  4.1758 -  3.3266 [2086/2105]  1875   211  10.1%
  bin  3:  3.3266 -  2.9097 [2059/2079]  1852   207  10.1%
  bin  4:  2.9097 -  2.6453 [2051/2076]  1852   199   9.7%
  bin  5:  2.6453 -  2.4566 [2045/2065]  1834   211  10.3%
  bin  6:  2.4566 -  2.3123 [2020/2066]  1822   198   9.8%
  bin  7:  2.3123 -  2.1969 [2001/2033]  1797   204  10.2%
  bin  8:  2.1969 -  2.1015 [2001/2037]  1802   199   9.9%
  bin  9:  2.1015 -  2.0208 [2001/2031]  1802   199   9.9%
  bin 10:  2.0208 -  1.9512 [1145/2028]  1029   116  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_649/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.63 -     2.29: 30
        2.29 -     2.94: 1651
        2.94 -     3.59: 4557
        3.59 -     4.25: 9332
        4.25 -     4.90: 13185
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.632 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.662 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.744 3.120 -x,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.845 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28750 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_649/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_649/model_refine_001.geo

CPU time processing inputs: 9.40


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.69535 84.23025 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: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4672   r_free= 0.4647   ksol= 0.00   Bsol= 0.00   scale= 0.810    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.269191                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6578 0.99   1410  157 0.3895 0.3884      6.5774      6.6171|
|  2:  4.6578 -  3.7159 0.99   1362  146 0.3859 0.3811      6.7619      6.7351|
|  3:  3.7159 -  3.2518 0.99   1330  156 0.4284 0.3994      6.6546      6.7391|
|  4:  3.2518 -  2.9570 0.99   1339  147 0.4399 0.4545      6.5012       6.485|
|  5:  2.9570 -  2.7465 0.99   1316  146 0.4895 0.4828      6.3604      6.3548|
|  6:  2.7465 -  2.5854 0.98   1309  144 0.4852 0.5287      6.2542      6.2026|
|  7:  2.5854 -  2.4566 0.99   1312  147 0.5082 0.4594       6.251       6.188|
|  8:  2.4566 -  2.3501 0.98   1289  142 0.5162 0.5483      6.1483      6.1811|
|  9:  2.3501 -  2.2599 0.98   1305  150 0.5100 0.4891      6.1207      6.0989|
| 10:  2.2599 -  2.1822 0.98   1283  137 0.5262 0.5234      6.0956      6.1064|
| 11:  2.1822 -  2.1141 0.99   1288  144 0.5252 0.4968      6.0389      6.0171|
| 12:  2.1141 -  2.0539 0.98   1281  138 0.5017 0.5379      5.9503      5.9926|
| 13:  2.0539 -  1.9999 0.97   1273  143 0.5320 0.5177       5.877      5.8249|
| 14:  1.9999 -  1.9512 0.41    533   62 0.5440 0.5574      5.8396      5.7693|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8899 -  4.6578  1410   157  0.68  35.57   0.81     0.72      74340.07|
|  2:  4.6578 -  3.7159  1362   146  0.70  35.11   0.89     0.79     105190.89|
|  3:  3.7159 -  3.2518  1330   156  0.60  43.54   0.85     0.74     112734.25|
|  4:  3.2518 -  2.9570  1339   147  0.53  49.44   0.83     0.64      99181.83|
|  5:  2.9570 -  2.7465  1316   146  0.43  57.21   0.76     0.53      82072.23|
|  6:  2.7465 -  2.5854  1309   144  0.41  58.75   0.74     0.49      69545.58|
|  7:  2.5854 -  2.4566  1312   147  0.41  59.24   0.75     0.46      61817.87|
|  8:  2.4566 -  2.3501  1289   142  0.39  60.81   0.72     0.47      56896.88|
|  9:  2.3501 -  2.2599  1305   150  0.39  60.82   0.76     0.46      51416.09|
| 10:  2.2599 -  2.1822  1283   137  0.37  61.91   0.77     0.46      48025.43|
| 11:  2.1822 -  2.1141  1288   144  0.36  62.87   0.78     0.45      44378.17|
| 12:  2.1141 -  2.0539  1281   138  0.34  64.98   0.77     0.43      43153.52|
| 13:  2.0539 -  1.9999  1273   143  0.29  68.40   0.75     0.38      37813.74|
| 14:  1.9999 -  1.9512   533    62  0.28  69.23   0.71     0.32      31589.62|
|alpha:            min =        0.32 max =            0.79 mean =         0.54|
|beta:             min =    31589.62 max =       112734.25 mean =     67523.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           89.99 mean =        55.44|
|phase err.(test): min =        0.00 max =           89.89 mean =        55.89|
|-----------------------------------------------------------------------------|

============================== 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 = 11.834521             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.840   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.140861              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.999   (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:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       25 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      178 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      719 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1530 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2687 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3974 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5151 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6640 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7840 |
|-----------------------------------------------------------------------------|
|-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 |       53.105 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       2.016 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.558)------------------------------------------|
|    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 = 11.558)------------------------------------------|
|    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: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4743   r_free= 0.4727   ksol= 0.00   Bsol= 0.00   scale= 0.777    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.272343                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4583   r_free= 0.4555   ksol= 0.36   Bsol= 6.65   scale= 1.007    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.85,7.88,10.09,0.00,0.00,0.00); trace/3= 8.28                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.265074                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.821945              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.532   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.016668              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.085   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4583      final r-factor (work) = 0.3822          |
| start r-factor (free) = 0.4555      final r-factor (free) = 0.4014          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 83.8897 = 9.82 * 0.50 * 6.2685 + 1.00 * 53.1054                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.4757 = 9.82 * 0.50 * 6.1795 + 1.00 * 0.1284                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3822      final r-factor (work) = 0.3335          |
| start r-factor (free) = 0.4014      final r-factor (free) = 0.3838          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2968 = 1.02 * 1.00 * 6.1795 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2016 = 1.02 * 1.00 * 6.0854 + 1.00 * 0.0148                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.558)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.92   12.75    None  None   None       |
|    all(noH): 2823   0      0.00    82.92   12.75    None  None   None       |
|    Sol.    : 438    0      0.00    79.30   26.15    None  None   None       |
|    Mac.    : 2385   0      0.00    82.92   10.29    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 -   8.292: 1268   |   5:    41.459 -  49.750:   53        |
|      1:     8.292 -  16.583:  781   |   6:    49.750 -  58.042:   16        |
|      2:    16.583 -  24.875:  377   |   7:    58.042 -  66.334:    7        |
|      3:    24.875 -  33.167:  212   |   8:    66.334 -  74.625:    5        |
|      4:    33.167 -  41.459:  100   |   9:    74.625 -  82.917:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3335 r_free = 0.3838             target_work(ml) = 6.071         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3328 r_free = 0.3839             target_work(ml) = 6.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3328   r_free= 0.3839   ksol= 0.36   Bsol= 6.65   scale= 1.107    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.85,7.88,10.09,0.00,0.00,0.00); trace/3= 8.28                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.070788                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3286   r_free= 0.3807   ksol= 0.34   Bsol= 26.21   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.21,3.70,6.57,0.00,0.00,0.00); trace/3= 4.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.069722                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.212764              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.705   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.476386              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.454  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3286      final r-factor (work) = 0.2525          |
| start r-factor (free) = 0.3807      final r-factor (free) = 0.3105          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.0249 = 6.21 * 0.50 * 6.0831 + 1.00 * 0.1284                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.5825 = 6.21 * 0.50 * 5.9578 + 1.00 * 0.0753                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2525      final r-factor (work) = 0.2342          |
| start r-factor (free) = 0.3105      final r-factor (free) = 0.2923          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8529 = 0.48 * 1.00 * 5.9578 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7834 = 0.48 * 1.00 * 5.8203 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.558)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.31   12.89    None  None   None       |
|    all(noH): 2823   0      0.00    83.31   12.89    None  None   None       |
|    Sol.    : 438    0      0.00    75.47   30.36    None  None   None       |
|    Mac.    : 2385   0      0.00    83.31   9.68     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.331: 1367   |   5:    41.656 -  49.987:   64        |
|      1:     8.331 -  16.662:  722   |   6:    49.987 -  58.318:   16        |
|      2:    16.662 -  24.993:  298   |   7:    58.318 -  66.649:    9        |
|      3:    24.993 -  33.325:  202   |   8:    66.649 -  74.980:    2        |
|      4:    33.325 -  41.656:  139   |   9:    74.980 -  83.311:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2342 r_free = 0.2923             target_work(ml) = 5.794         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2339 r_free = 0.2927             target_work(ml) = 5.794         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2339   r_free= 0.2927   ksol= 0.34   Bsol= 26.21   scale= 1.054   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.21,3.70,6.57,0.00,0.00,0.00); trace/3= 4.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.793800                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2335   r_free= 0.2915   ksol= 0.33   Bsol= 26.21   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.12,2.58,4.26,0.00,0.00,0.00); trace/3= 2.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.791447                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.801107              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.307  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.429948              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.096  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2335      final r-factor (work) = 0.1807          |
| start r-factor (free) = 0.2915      final r-factor (free) = 0.2353          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2280 = 2.80 * 0.50 * 5.8210 + 1.00 * 0.0753                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0271 = 2.80 * 0.50 * 5.6892 + 1.00 * 0.0591                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1807      final r-factor (work) = 0.1623          |
| start r-factor (free) = 0.2353      final r-factor (free) = 0.2213          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.8351 = 2.43 * 1.00 * 5.6892 + 1.00 * 0.0107                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.4263 = 2.43 * 1.00 * 5.5190 + 1.00 * 0.0154                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.558)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.32   14.15    None  None   None       |
|    all(noH): 2823   0      0.00    96.32   14.15    None  None   None       |
|    Sol.    : 438    0      1.83    85.04   39.47    None  None   None       |
|    Mac.    : 2385   0      0.00    96.32   9.50     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 -   9.632: 1657   |   5:    48.161 -  57.793:   89        |
|      1:     9.632 -  19.264:  568   |   6:    57.793 -  67.425:   48        |
|      2:    19.264 -  28.897:  174   |   7:    67.425 -  77.057:   26        |
|      3:    28.897 -  38.529:  123   |   8:    77.057 -  86.689:    7        |
|      4:    38.529 -  48.161:  128   |   9:    86.689 -  96.322:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1623 r_free = 0.2213             target_work(ml) = 5.485         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1621 r_free = 0.2212             target_work(ml) = 5.485         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1621   r_free= 0.2212   ksol= 0.33   Bsol= 26.21   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.12,2.58,4.26,0.00,0.00,0.00); trace/3= 2.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.484629                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1616   r_free= 0.2202   ksol= 0.32   Bsol= 33.87   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.75,2.00,2.85,0.00,0.00,0.00); trace/3= 2.20                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.478988                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.858865              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.944  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.770576              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.731  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1616      final r-factor (work) = 0.1315          |
| start r-factor (free) = 0.2202      final r-factor (free) = 0.1813          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7114 = 3.86 * 0.50 * 5.5209 + 1.00 * 0.0591                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4807 = 3.86 * 0.50 * 5.3983 + 1.00 * 0.0650                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1315      final r-factor (work) = 0.1245          |
| start r-factor (free) = 0.1813      final r-factor (free) = 0.1720          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1751 = 0.77 * 1.00 * 5.3983 + 1.00 * 0.0152                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0717 = 0.77 * 1.00 * 5.2675 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.558)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.75  13.72    None  None   None       |
|    all(noH): 2823   0      0.00    102.75  13.72    None  None   None       |
|    Sol.    : 438    0      2.72    87.05   38.91    None  None   None       |
|    Mac.    : 2385   0      0.00    102.75  9.10     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.275: 1781   |   5:    51.373 -  61.648:   70        |
|      1:    10.275 -  20.549:  516   |   6:    61.648 -  71.922:   44        |
|      2:    20.549 -  30.824:  147   |   7:    71.922 -  82.197:   12        |
|      3:    30.824 -  41.098:  134   |   8:    82.197 -  92.471:    4        |
|      4:    41.098 -  51.373:  112   |   9:    92.471 - 102.746:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1245 r_free = 0.1720             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1243 r_free = 0.1717             target_work(ml) = 5.233         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1243   r_free= 0.1717   ksol= 0.32   Bsol= 33.87   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.75,2.00,2.85,0.00,0.00,0.00); trace/3= 2.20                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.233057                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1246   r_free= 0.1722   ksol= 0.32   Bsol= 36.27   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.69,1.87,2.42,0.00,0.00,0.00); trace/3= 1.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.234742                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.599780              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 133.819  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.924533              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.970  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1246      final r-factor (work) = 0.1135          |
| start r-factor (free) = 0.1722      final r-factor (free) = 0.1632          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5470 = 3.60 * 0.50 * 5.2681 + 1.00 * 0.0650                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4285 = 3.60 * 0.50 * 5.1990 + 1.00 * 0.0709                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1135      final r-factor (work) = 0.1113          |
| start r-factor (free) = 0.1632      final r-factor (free) = 0.1615          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8193 = 0.92 * 1.00 * 5.1990 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7827 = 0.92 * 1.00 * 5.1597 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.558)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.63  13.44    None  None   None       |
|    all(noH): 2823   0      0.00    106.63  13.44    None  None   None       |
|    Sol.    : 438    0      2.42    90.35   38.02    None  None   None       |
|    Mac.    : 2385   0      0.00    106.63  8.93     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.663: 1846   |   5:    53.314 -  63.977:   58        |
|      1:    10.663 -  21.326:  482   |   6:    63.977 -  74.640:   30        |
|      2:    21.326 -  31.988:  146   |   7:    74.640 -  85.303:   13        |
|      3:    31.988 -  42.651:  135   |   8:    85.303 -  95.965:    3        |
|      4:    42.651 -  53.314:  108   |   9:    95.965 - 106.628:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1113 r_free = 0.1615             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1112 r_free = 0.1614             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1614   ksol= 0.32   Bsol= 36.27   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.69,1.87,2.42,0.00,0.00,0.00); trace/3= 1.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.153509                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6578 0.99   1410  157 0.0972 0.1254       5.369      5.5257|
|  2:  4.6578 -  3.7159 0.99   1362  146 0.0839 0.1173      5.4133      5.6498|
|  3:  3.7159 -  3.2518 0.99   1330  156 0.1058 0.1558      5.4693      5.8313|
|  4:  3.2518 -  2.9570 0.99   1339  147 0.1221 0.1623      5.4578      5.6298|
|  5:  2.9570 -  2.7465 0.99   1316  146 0.1276 0.1654      5.3141      5.4846|
|  6:  2.7465 -  2.5854 0.98   1309  144 0.1240 0.1998      5.2252      5.5114|
|  7:  2.5854 -  2.4566 0.99   1312  147 0.1247 0.1721      5.1793       5.421|
|  8:  2.4566 -  2.3501 0.98   1289  142 0.1138 0.1626      5.0587      5.2826|
|  9:  2.3501 -  2.2599 0.98   1305  150 0.1122 0.1862      5.0158      5.3171|
| 10:  2.2599 -  2.1822 0.98   1283  137 0.1130 0.1766      4.9818       5.234|
| 11:  2.1822 -  2.1141 0.99   1288  144 0.1138 0.1864      4.9523      5.3237|
| 12:  2.1141 -  2.0539 0.98   1281  138 0.1092 0.1691      4.8806      5.1035|
| 13:  2.0539 -  1.9999 0.97   1273  143 0.1196 0.1841      4.8061      5.0495|
| 14:  1.9999 -  1.9512 0.41    533   62 0.1027 0.1705      4.6829      4.9638|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8899 -  4.6578  1410   157  0.94   8.59   0.98     0.96       6843.59|
|  2:  4.6578 -  3.7159  1362   146  0.95   7.77   1.03     1.01       8648.02|
|  3:  3.7159 -  3.2518  1330   156  0.93  11.61   1.04     1.04      10519.18|
|  4:  3.2518 -  2.9570  1339   147  0.92  13.92   1.02     1.01      10553.44|
|  5:  2.9570 -  2.7465  1316   146  0.89  16.44   1.00     0.96       8395.39|
|  6:  2.7465 -  2.5854  1309   144  0.89  16.66   0.99     0.96       7530.83|
|  7:  2.5854 -  2.4566  1312   147  0.90  15.97   1.00     0.96       6525.40|
|  8:  2.4566 -  2.3501  1289   142  0.90  16.12   0.99     0.96       5517.58|
|  9:  2.3501 -  2.2599  1305   150  0.90  15.78   1.01     1.00       5077.42|
| 10:  2.2599 -  2.1822  1283   137  0.90  16.08   1.01     0.98       4734.23|
| 11:  2.1822 -  2.1141  1288   144  0.90  16.70   1.01     0.98       4600.81|
| 12:  2.1141 -  2.0539  1281   138  0.91  15.77   1.01     0.99       4133.12|
| 13:  2.0539 -  1.9999  1273   143  0.90  16.85   1.01     1.00       3486.18|
| 14:  1.9999 -  1.9512   533    62  0.90  16.28   1.01     0.98       2839.89|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2839.89 max =        10553.44 mean =      6579.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.87 mean =        14.46|
|phase err.(test): min =        0.00 max =           88.53 mean =        13.96|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1613   ksol= 0.32   Bsol= 38.28   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.26,-0.11,0.37,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.153525                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1613   ksol= 0.32   Bsol= 38.28   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.26,-0.11,0.37,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.153525                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6578 0.99   1410  157 0.0973 0.1254      5.3702      5.5265|
|  2:  4.6578 -  3.7159 0.99   1362  146 0.0838 0.1173      5.4131      5.6492|
|  3:  3.7159 -  3.2518 0.99   1330  156 0.1058 0.1558      5.4691      5.8314|
|  4:  3.2518 -  2.9570 0.99   1339  147 0.1221 0.1623      5.4578      5.6299|
|  5:  2.9570 -  2.7465 0.99   1316  146 0.1275 0.1654       5.314      5.4845|
|  6:  2.7465 -  2.5854 0.98   1309  144 0.1240 0.2001      5.2254      5.5123|
|  7:  2.5854 -  2.4566 0.99   1312  147 0.1247 0.1721      5.1797      5.4214|
|  8:  2.4566 -  2.3501 0.98   1289  142 0.1138 0.1625      5.0588      5.2824|
|  9:  2.3501 -  2.2599 0.98   1305  150 0.1122 0.1862      5.0158      5.3175|
| 10:  2.2599 -  2.1822 0.98   1283  137 0.1131 0.1767      4.9816      5.2332|
| 11:  2.1822 -  2.1141 0.99   1288  144 0.1138 0.1864      4.9521      5.3236|
| 12:  2.1141 -  2.0539 0.98   1281  138 0.1092 0.1690      4.8798      5.1024|
| 13:  2.0539 -  1.9999 0.97   1273  143 0.1195 0.1837      4.8059      5.0481|
| 14:  1.9999 -  1.9512 0.41    533   62 0.1028 0.1709      4.6832      4.9663|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8899 -  4.6578  1410   157  0.94   8.60   0.98     0.96       6861.78|
|  2:  4.6578 -  3.7159  1362   146  0.95   7.78   1.03     1.01       8652.17|
|  3:  3.7159 -  3.2518  1330   156  0.93  11.60   1.05     1.04      10515.18|
|  4:  3.2518 -  2.9570  1339   147  0.92  13.92   1.02     1.01      10550.75|
|  5:  2.9570 -  2.7465  1316   146  0.89  16.44   1.00     0.96       8400.26|
|  6:  2.7465 -  2.5854  1309   144  0.89  16.67   0.99     0.96       7534.09|
|  7:  2.5854 -  2.4566  1312   147  0.90  15.98   1.00     0.96       6532.70|
|  8:  2.4566 -  2.3501  1289   142  0.90  16.12   0.99     0.96       5518.87|
|  9:  2.3501 -  2.2599  1305   150  0.90  15.78   1.02     1.00       5077.39|
| 10:  2.2599 -  2.1822  1283   137  0.90  16.07   1.01     0.98       4730.87|
| 11:  2.1822 -  2.1141  1288   144  0.90  16.70   1.01     0.98       4598.83|
| 12:  2.1141 -  2.0539  1281   138  0.91  15.75   1.01     1.00       4124.88|
| 13:  2.0539 -  1.9999  1273   143  0.90  16.84   1.01     1.00       3484.00|
| 14:  1.9999 -  1.9512   533    62  0.90  16.29   1.01     0.99       2842.37|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2842.37 max =        10550.75 mean =      6581.21|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.88 mean =        14.46|
|phase err.(test): min =        0.00 max =           88.56 mean =        13.96|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.558)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.01    108.64  15.45    None  None   None       |
|    all(noH): 2823   0      2.01    108.64  15.45    None  None   None       |
|    Sol.    : 438    0      4.43    92.36   40.03    None  None   None       |
|    Mac.    : 2385   0      2.01    108.64  10.94    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.011 -  12.674: 1846   |   5:    55.325 -  65.988:   58        |
|      1:    12.674 -  23.336:  482   |   6:    65.988 -  76.650:   30        |
|      2:    23.336 -  33.999:  146   |   7:    76.650 -  87.313:   13        |
|      3:    33.999 -  44.662:  135   |   8:    87.313 -  97.976:    3        |
|      4:    44.662 -  55.325:  108   |   9:    97.976 - 108.639:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 321         
Filter by distance & map next to the model:
   mapped sites are within: 0.457 - 5.557
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 317 from: 321
   mapped sites are within: 0.700 - 5.557

peak=   10.773 closest distance to " CB  VAL A 230 " =    1.415
peak=    9.261 closest distance to " CG2 VAL A 296 " =    1.363
peak=    6.338 closest distance to " O   HOH Z 278 " =    1.550
peak=    6.307 closest distance to " CD1AILE A 234 " =    1.075
peak=    6.080 closest distance to " CG  LEU A   5 " =    1.216
peak=    5.767 closest distance to " NE2 GLN A  11 " =    1.171
peak=    5.535 closest distance to " CD2 LEU A   5 " =    1.216
peak=    5.485 closest distance to " O   HOH Z 132 " =    1.501
peak=    5.367 closest distance to " NH2 ARG A  56 " =    2.072
peak=    5.150 closest distance to " O   HOH Z 202 " =    1.402
peak=    4.949 closest distance to " O   HOH Z 124 " =    1.447
peak=    4.938 closest distance to " CB  SER A  63 " =    1.269
peak=    4.932 closest distance to " O   HOH Z 126 " =    1.987
peak=    4.922 closest distance to " CG  LEU A 228 " =    1.201
peak=    4.903 closest distance to " O   HOH Z 142 " =    1.801
peak=    4.867 closest distance to " O   HOH Z 193 " =    1.737
peak=    4.849 closest distance to " CB  GLN A 183 " =    1.329
peak=    4.818 closest distance to " O   HOH Z 427 " =    2.843
peak=    4.809 closest distance to " CG  PRO A  54 " =    1.141
peak=    4.762 closest distance to " CA  GLY A 241 " =    3.843
peak=    4.700 closest distance to " CB  GLN A 223 " =    1.454
peak=    4.644 closest distance to " O   HOH Z   3 " =    1.907
peak=    4.621 closest distance to " O   HOH Z 203 " =    1.626
peak=    4.608 closest distance to " O   HOH Z 260 " =    1.330
peak=    4.567 closest distance to " CB  ASN A 148 " =    1.394
peak=    4.566 closest distance to " O   HOH Z 263 " =    1.469
peak=    4.566 closest distance to " CB  ARG A 275 " =    0.881
peak=    4.492 closest distance to " CB  VAL A 230 " =    1.177
peak=    4.445 closest distance to " O   HOH Z 232 " =    2.172
peak=    4.426 closest distance to " O   HOH Z 371 " =    3.229
peak=    4.404 closest distance to " O   SER A  87 " =    2.349
peak=    4.351 closest distance to " O   HOH Z  97 " =    1.319
peak=    4.346 closest distance to " O   HOH Z  48 " =    1.551
peak=    4.340 closest distance to " CB  SER A   3 " =    1.387
peak=    4.334 closest distance to " O   HOH Z 236 " =    1.478
peak=    4.310 closest distance to " O   HOH Z 133 " =    1.512
peak=    4.302 closest distance to " O   PRO A 198 " =    1.523
peak=    4.294 closest distance to " O   HOH Z  15 " =    2.190
peak=    4.293 closest distance to " O   HOH Z 134 " =    1.413
peak=    4.263 closest distance to " O   HOH Z  97 " =    2.079
peak=    4.246 closest distance to " CB  GLN A  88 " =    1.278
peak=    4.244 closest distance to " CB  TYR A 169 " =    1.043
peak=    4.239 closest distance to " CD2 LEU A 228 " =    1.239
peak=    4.226 closest distance to " O   HOH Z  59 " =    1.770
peak=    4.224 closest distance to " CB  PRO A  54 " =    0.862
peak=    4.206 closest distance to " O   HOH Z 108 " =    1.450
peak=    4.144 closest distance to " O   HOH Z 303 " =    2.170
peak=    4.130 closest distance to " CB  GLU A 152 " =    1.143
peak=    4.130 closest distance to " O   HOH Z  78 " =    1.810
peak=    4.126 closest distance to " CA  ALA A  21 " =    1.077
peak=    4.115 closest distance to " O   HOH Z 368 " =    2.025
peak=    4.111 closest distance to " O   HOH Z  93 " =    2.428
peak=    4.106 closest distance to " CB  TRP A 179 " =    1.254
peak=    4.103 closest distance to " O   HOH Z 272 " =    1.848
peak=    4.097 closest distance to " O   HOH Z 205 " =    0.935
peak=    4.096 closest distance to " CB  VAL A 265 " =    1.232
peak=    4.083 closest distance to " O   HOH Z 192 " =    1.559
peak=    4.082 closest distance to " O   HOH Z 334 " =    2.928
peak=    4.078 closest distance to " CG1BVAL A  72 " =    1.437
peak=    4.057 closest distance to " OD1 ASN A  69 " =    2.589
peak=    4.050 closest distance to " O   HOH Z 227 " =    1.824
peak=    4.048 closest distance to " CB  ARG A  79 " =    1.396
peak=    4.033 closest distance to " CA  VAL A  41 " =    0.908
peak=    4.032 closest distance to " CG  PRO A 198 " =    1.299
peak=    4.031 closest distance to " O   HOH Z 214 " =    1.152
peak=    4.021 closest distance to " NZ  LYS A 117 " =    3.205
peak=    3.995 closest distance to " O   HOH Z 326 " =    1.420
peak=    3.981 closest distance to " O   HOH Z 143 " =    1.013
peak=    3.979 closest distance to " OE1 GLU A   2 " =    2.053
peak=    3.946 closest distance to " O   HOH Z 316 " =    2.819
peak=    3.943 closest distance to " O   HOH Z 128 " =    1.969
peak=    3.942 closest distance to " O   HOH Z 298 " =    1.828
peak=    3.919 closest distance to " O   HOH Z 346 " =    1.543
peak=    3.907 closest distance to " CG  PRO A 213 " =    1.159
peak=    3.901 closest distance to " CA  TYR A  30 " =    1.043
peak=    3.879 closest distance to " O   HOH Z 193 " =    1.976
peak=    3.859 closest distance to " CB  VAL A 296 " =    1.025
peak=    3.859 closest distance to " CB  VAL A 202 " =    1.693
peak=    3.855 closest distance to " O   HOH Z 276 " =    1.371
peak=    3.846 closest distance to " O   HOH Z 234 " =    3.683
peak=    3.835 closest distance to " CB  LEU A 228 " =    1.403
peak=    3.828 closest distance to " CB  GLU A 128 " =    1.224
peak=    3.812 closest distance to " O   HOH Z 426 " =    1.426
peak=    3.798 closest distance to " O   HOH Z  59 " =    2.168
peak=    3.793 closest distance to " O   HOH Z 116 " =    1.696
peak=    3.785 closest distance to " OD2 ASP A 286 " =    2.608
peak=    3.776 closest distance to " O   HOH Z 250 " =    1.346
peak=    3.776 closest distance to " O   HOH Z 369 " =    1.897
peak=    3.773 closest distance to " O   HOH Z 279 " =    1.139
peak=    3.766 closest distance to " O   HOH Z  37 " =    1.204
peak=    3.765 closest distance to " O   HOH Z 345 " =    3.201
peak=    3.764 closest distance to " CB  GLU A 277 " =    3.527
peak=    3.762 closest distance to " O   HOH Z 189 " =    2.566
peak=    3.762 closest distance to " O   MET A 105 " =    1.750
peak=    3.741 closest distance to " O   HOH Z 209 " =    2.354
peak=    3.727 closest distance to " O   HOH Z  88 " =    3.135
peak=    3.726 closest distance to " O   HOH Z 392 " =    2.776
peak=    3.710 closest distance to " O   HOH Z 180 " =    2.212
peak=    3.708 closest distance to " O   HOH Z 425 " =    1.344
peak=    3.705 closest distance to " O   HOH Z  68 " =    1.673
peak=    3.704 closest distance to " O   HOH Z 425 " =    2.118
peak=    3.695 closest distance to " O   HOH Z 214 " =    2.054
peak=    3.694 closest distance to " O   HOH Z 344 " =    1.285
peak=    3.693 closest distance to " O   HOH Z 199 " =    0.929
peak=    3.687 closest distance to " O   HOH Z 357 " =    1.831
peak=    3.686 closest distance to " O   HOH Z 403 " =    1.691
peak=    3.682 closest distance to " CG  GLN A  88 " =    1.100
peak=    3.680 closest distance to " CG  LEU A 167 " =    1.173
peak=    3.668 closest distance to " O   HOH Z  10 " =    1.816
peak=    3.668 closest distance to " CA  ASN A 215 " =    1.194
peak=    3.664 closest distance to " O   HOH Z  54 " =    1.603
peak=    3.662 closest distance to " O   HOH Z  61 " =    1.654
peak=    3.660 closest distance to " CG2 VAL A 257 " =    0.842
peak=    3.658 closest distance to " CG1 ILE A  33 " =    1.328
peak=    3.648 closest distance to " CA  VAL A 126 " =    1.117
peak=    3.648 closest distance to " O   HOH Z 280 " =    1.539
peak=    3.648 closest distance to " O   HOH Z 193 " =    1.511
peak=    3.647 closest distance to " O   HOH Z 284 " =    1.492
peak=    3.644 closest distance to " O   HOH Z 344 " =    2.636
peak=    3.642 closest distance to " CD BLYS A 290 " =    1.220
peak=    3.641 closest distance to " CG  ARG A  66 " =    2.772
peak=    3.641 closest distance to " O   ALA A 158 " =    1.295
peak=    3.629 closest distance to " CE1 TYR A 186 " =    1.214
peak=    3.623 closest distance to " O   HOH Z 261 " =    2.011
peak=    3.622 closest distance to " CA  THR A 221 " =    0.883
peak=    3.616 closest distance to " O   HOH Z  61 " =    1.602
peak=    3.615 closest distance to " O   HOH Z 118 " =    1.497
peak=    3.613 closest distance to " O   HOH Z 172 " =    3.747
peak=    3.612 closest distance to " CB  ARG A 139 " =    0.959
peak=    3.610 closest distance to " O   HOH Z  85 " =    1.145
peak=    3.610 closest distance to " OG BSER A 164 " =    2.224
peak=    3.607 closest distance to " O   HOH Z 303 " =    1.750
peak=    3.599 closest distance to " O   HOH Z 130 " =    2.277
peak=    3.592 closest distance to " O   HOH Z 287 " =    1.843
peak=    3.591 closest distance to " O   HOH Z 123 " =    1.011
peak=    3.591 closest distance to " CA  ALA A 295 " =    1.094
peak=    3.583 closest distance to " CB  LEU A 255 " =    0.758
peak=    3.576 closest distance to " SG ACYS A 201 " =    0.700
peak=    3.574 closest distance to " O   HOH Z 389 " =    1.649
peak=    3.567 closest distance to " O   HOH Z 281 " =    4.437
peak=    3.565 closest distance to " O   HOH Z 248 " =    1.808
peak=    3.564 closest distance to " NH1 ARG A  14 " =    1.058
peak=    3.558 closest distance to " O   HOH Z  63 " =    1.019
peak=    3.556 closest distance to " O   HOH Z 273 " =    2.762
peak=    3.551 closest distance to " C   ALA A 299 " =    0.942
peak=    3.549 closest distance to " O   HOH Z  30 " =    2.116
peak=    3.546 closest distance to " O   HOH Z 423 " =    1.824
peak=    3.546 closest distance to " O   HOH Z 158 " =    2.951
peak=    3.539 closest distance to " CD2 LEU A 255 " =    1.392
peak=    3.533 closest distance to " O   HOH Z 136 " =    1.042
peak=    3.530 closest distance to " OD1 ASN A 217 " =    1.687
peak=    3.527 closest distance to " O   HOH Z  80 " =    1.683
peak=    3.523 closest distance to " NE2 GLN A  58 " =    5.557
peak=    3.511 closest distance to " CZ AARG A 102 " =    1.869
peak=    3.509 closest distance to " O   HOH Z  20 " =    1.267
peak=    3.507 closest distance to " O   TRP A 274 " =    1.882
peak=    3.505 closest distance to " O   HOH Z 152 " =    2.965
peak=    3.502 closest distance to " O   HOH Z 422 " =    2.490
peak=    3.492 closest distance to " NH1 ARG A 138 " =    1.198
peak=    3.482 closest distance to " O   SER A  26 " =    1.570
peak=    3.476 closest distance to " O   HOH Z 247 " =    1.200
peak=    3.474 closest distance to " O   HOH Z 322 " =    2.010
peak=    3.474 closest distance to " CG2 THR A 221 " =    1.080
peak=    3.473 closest distance to " ND2 ASN A 187 " =    1.658
peak=    3.460 closest distance to " CB  SER A  26 " =    1.608
peak=    3.459 closest distance to " CA  PHE A 283 " =    1.406
peak=    3.458 closest distance to " O   HOH Z 112 " =    1.511
peak=    3.447 closest distance to " O   HOH Z 151 " =    1.745
peak=    3.441 closest distance to " O   HOH Z 411 " =    1.716
peak=    3.441 closest distance to " CB  SER A  62 " =    1.263
peak=    3.437 closest distance to " O   HOH Z 334 " =    1.482
peak=    3.433 closest distance to " CG  MET A 185 " =    1.075
peak=    3.428 closest distance to " CG  PRO A 243 " =    1.290
peak=    3.426 closest distance to " O   HOH Z 217 " =    1.222
peak=    3.423 closest distance to " CG AARG A 275 " =    1.059
peak=    3.422 closest distance to " CB  TYR A  30 " =    1.644
peak=    3.422 closest distance to " O   HOH Z 419 " =    1.697
peak=    3.413 closest distance to " CD1 ILE A  33 " =    1.510
peak=    3.410 closest distance to " CB  ALA A 295 " =    1.458
peak=    3.404 closest distance to " O   HOH Z  49 " =    2.229
peak=    3.403 closest distance to " O   HOH Z 108 " =    1.743
peak=    3.401 closest distance to " C   LYS A 290 " =    1.300
peak=    3.396 closest distance to " CB  ALA A 291 " =    1.451
peak=    3.395 closest distance to " O   HOH Z  53 " =    2.442
peak=    3.393 closest distance to " O   HOH Z 271 " =    1.900
peak=    3.391 closest distance to " NE2 GLN A  58 " =    4.022
peak=    3.388 closest distance to " CA  ASN A  74 " =    1.261
peak=    3.383 closest distance to " O   ALA A 165 " =    1.248
peak=    3.381 closest distance to " O   HOH Z  44 " =    1.823
peak=    3.366 closest distance to " CB  SER A 216 " =    0.835
peak=    3.363 closest distance to " OD1 ASP A 286 " =    1.569
peak=    3.361 closest distance to " CG2 ILE A  20 " =    1.616
peak=    3.361 closest distance to " CB BVAL A  41 " =    1.199
peak=    3.358 closest distance to " CA  ALA A  51 " =    0.970
peak=    3.357 closest distance to " O   HOH Z 189 " =    2.711
peak=    3.356 closest distance to " OG  SER A  22 " =    2.909
peak=    3.354 closest distance to " O   HOH Z 295 " =    1.563
peak=    3.353 closest distance to " O   HOH Z 374 " =    2.419
peak=    3.353 closest distance to " CA  ASN A 176 " =    1.112
peak=    3.352 closest distance to " O   HOH Z 280 " =    2.445
peak=    3.352 closest distance to " CA  MET A  40 " =    1.074
peak=    3.351 closest distance to " O   HOH Z 152 " =    1.676
peak=    3.344 closest distance to " O   HOH Z  89 " =    2.283
peak=    3.342 closest distance to " CD1 LEU A 300 " =    1.252
peak=    3.339 closest distance to " CD2 HIS A  81 " =    1.095
peak=    3.336 closest distance to " NZ  LYS A  76 " =    1.300
peak=    3.334 closest distance to " O   HOH Z  43 " =    2.144
peak=    3.332 closest distance to " CA  THR A 264 " =    0.800
peak=    3.331 closest distance to " CA  LEU A 282 " =    1.147
peak=    3.330 closest distance to " NH2BARG A 190 " =    1.768
peak=    3.327 closest distance to " CD2 TRP A 179 " =    1.429
peak=    3.325 closest distance to " CG  ASN A  60 " =    1.124
peak=    3.323 closest distance to " O   HOH Z 213 " =    1.751
peak=    3.320 closest distance to " O   HOH Z 331 " =    1.324
peak=    3.320 closest distance to " CA  GLN A 194 " =    1.274
peak=    3.317 closest distance to " ND1 HIS A  81 " =    1.537
peak=    3.311 closest distance to " CB  GLN A 205 " =    1.266
peak=    3.310 closest distance to " O   HOH Z 355 " =    1.797
peak=    3.308 closest distance to " CZ2 TRP A 179 " =    1.641
peak=    3.306 closest distance to " O   HOH Z 409 " =    3.410
peak=    3.303 closest distance to " O   HOH Z  89 " =    2.087
peak=    3.297 closest distance to " OD1 ASP A 231 " =    1.815
peak=    3.297 closest distance to " O   HOH Z 283 " =    1.680
peak=    3.297 closest distance to " CG  LYS A  76 " =    1.652
peak=    3.293 closest distance to " CA  LYS A 117 " =    1.184
peak=    3.293 closest distance to " O   HOH Z 380 " =    1.889
peak=    3.291 closest distance to " CA  ALA A 248 " =    1.230
peak=    3.279 closest distance to " CG2 ILE A 120 " =    1.304
peak=    3.270 closest distance to " CD  ARG A 269 " =    1.030
peak=    3.266 closest distance to " OE1 GLN A  11 " =    1.695
peak=    3.265 closest distance to " O   HOH Z 438 " =    2.221
peak=    3.262 closest distance to " CG1 VAL A 153 " =    0.918
peak=    3.261 closest distance to " O   GLN A 278 " =    1.270
peak=    3.261 closest distance to " CA  ALA A 154 " =    1.160
peak=    3.261 closest distance to " CA  ASP A 149 " =    1.365
peak=    3.259 closest distance to " CZ2 TRP A 274 " =    1.842
peak=    3.256 closest distance to " O   HOH Z 327 " =    1.560
peak=    3.255 closest distance to " CG  MET A 188 " =    1.455
peak=    3.248 closest distance to " O   HOH Z  21 " =    1.790
peak=    3.246 closest distance to " O   HOH Z 394 " =    1.658
peak=    3.245 closest distance to " O   HOH Z 409 " =    3.542
peak=    3.241 closest distance to " OE2 GLU A  53 " =    2.074
peak=    3.240 closest distance to " O   HOH Z 366 " =    2.870
peak=    3.240 closest distance to " CB  ALA A   9 " =    1.602
peak=    3.237 closest distance to " CB  ARG A 102 " =    0.728
peak=    3.232 closest distance to " CD  LYS A 119 " =    1.392
peak=    3.232 closest distance to " CB  LEU A 143 " =    1.229
peak=    3.231 closest distance to " O   HOH Z 279 " =    2.198
peak=    3.225 closest distance to " OG BSER A 258 " =    3.256
peak=    3.224 closest distance to " NH1AARG A 145 " =    0.916
peak=    3.224 closest distance to " O   HOH Z 417 " =    1.966
peak=    3.223 closest distance to " O   ASN A 217 " =    1.225
peak=    3.223 closest distance to " O   HOH Z 209 " =    2.437
peak=    3.219 closest distance to " O   HOH Z 194 " =    2.158
peak=    3.218 closest distance to " O   HOH Z 173 " =    2.029
peak=    3.217 closest distance to " CB  TRP A 266 " =    1.059
peak=    3.211 closest distance to " O   HOH Z 406 " =    1.728
peak=    3.208 closest distance to " O   HOH Z 244 " =    1.559
peak=    3.207 closest distance to " O   HOH Z 132 " =    2.829
peak=    3.205 closest distance to " NH2 ARG A 219 " =    1.774
peak=    3.204 closest distance to " CB  SER A 273 " =    0.824
peak=    3.201 closest distance to " O   HOH Z  30 " =    1.129
peak=    3.200 closest distance to " N   SER A 135 " =    1.410
peak=    3.196 closest distance to " O   HOH Z 153 " =    3.701
peak=    3.196 closest distance to " O   HOH Z 148 " =    3.165
peak=    3.195 closest distance to " O   HOH Z 106 " =    2.293
peak=    3.194 closest distance to " CD  LYS A 166 " =    1.405
peak=    3.193 closest distance to " O   HOH Z 261 " =    1.482
peak=    3.184 closest distance to " N   PHE A 130 " =    1.318
peak=    3.183 closest distance to " O   HOH Z 367 " =    3.577
peak=    3.179 closest distance to " O   GLY A  57 " =    2.452
peak=    3.177 closest distance to " CB  VAL A 268 " =    0.808
peak=    3.174 closest distance to " CB  THR A 157 " =    0.945
peak=    3.171 closest distance to " O   HOH Z  59 " =    1.791
peak=    3.170 closest distance to " CB  ASN A 142 " =    1.042
peak=    3.169 closest distance to " CB  LYS A 117 " =    1.221
peak=    3.168 closest distance to " O   HOH Z 291 " =    1.519
peak=    3.166 closest distance to " CE BMET A  47 " =    0.958
peak=    3.165 closest distance to " O   HOH Z 133 " =    2.273
peak=    3.164 closest distance to " O   HOH Z   1 " =    1.712
peak=    3.161 closest distance to " O   HOH Z 128 " =    2.135
peak=    3.160 closest distance to " CB  LEU A 237 " =    0.979
peak=    3.160 closest distance to " O   HOH Z 423 " =    2.840
peak=    3.160 closest distance to " CB  THR A  31 " =    1.638
peak=    3.157 closest distance to " CG2 VAL A 174 " =    1.359
peak=    3.157 closest distance to " CA  ALA A 158 " =    1.076
peak=    3.150 closest distance to " CA  ARG A 195 " =    1.169
peak=    3.150 closest distance to " O   HOH Z 164 " =    2.002
peak=    3.150 closest distance to " CG  LEU A 101 " =    1.367
peak=    3.149 closest distance to " CG  GLN A  77 " =    2.375
peak=    3.149 closest distance to " CA  LEU A 101 " =    1.571
peak=    3.147 closest distance to " O   HOH Z 265 " =    2.169
peak=    3.141 closest distance to " O   HOH Z 329 " =    3.257
peak=    3.137 closest distance to " CA  ASP A 140 " =    1.142
peak=    3.136 closest distance to " O   HOH Z 374 " =    3.029
peak=    3.136 closest distance to " CB  THR A 235 " =    0.853
peak=    3.132 closest distance to " OE1 GLU A 236 " =    1.584
peak=    3.113 closest distance to " O   HOH Z 280 " =    3.081
peak=    3.110 closest distance to " O   HOH Z  50 " =    1.573
peak=    3.105 closest distance to " OD1BASN A 224 " =    2.224
peak=    3.104 closest distance to " O   HOH Z 373 " =    1.562
peak=    3.104 closest distance to " O   HOH Z 383 " =    2.164
peak=    3.103 closest distance to " O   HOH Z 359 " =    3.643
peak=    3.097 closest distance to " ND1 HIS A  86 " =    1.747
peak=    3.095 closest distance to " CB  ASN A  39 " =    0.802
peak=    3.094 closest distance to " O   HOH Z  83 " =    1.595
peak=    3.081 closest distance to " N   ALA A 256 " =    1.059
peak=    3.080 closest distance to " O   THR A  31 " =    1.580
peak=    3.078 closest distance to " CB  ILE A  20 " =    1.446
peak=    3.073 closest distance to " O   HOH Z  59 " =    2.101
peak=    3.072 closest distance to " CG  ARG A 138 " =    1.000
peak=    3.060 closest distance to " O   GLY A  91 " =    1.816
peak=    3.050 closest distance to " O   HOH Z 175 " =    2.169
peak=    3.035 closest distance to " O   HOH Z 211 " =    2.170
peak=    3.006 closest distance to " O   HOH Z   9 " =    1.614
peak=    3.005 closest distance to " O   HOH Z 172 " =    3.421
peak=    3.003 closest distance to " O   HOH Z  20 " =    1.856

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.671 - 5.225
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 195 from: 197
   mapped sites are within: 0.755 - 5.225

peak=   -4.755 closest distance to " CG2 VAL A 230 " =    0.800
peak=   -4.622 closest distance to " CD  ARG A 156 " =    2.012
peak=   -4.460 closest distance to " SG  CYS A 254 " =    3.141
peak=   -4.376 closest distance to " O   HOH Z  92 " =    1.460
peak=   -4.286 closest distance to " CB  ALA A 161 " =    2.598
peak=   -4.186 closest distance to " CD1 LEU A 101 " =    2.394
peak=   -4.135 closest distance to " O   HOH Z 231 " =    1.668
peak=   -4.114 closest distance to " CB  PRO A 280 " =    2.117
peak=   -4.107 closest distance to " O   HOH Z  11 " =    1.938
peak=   -4.077 closest distance to " O   HOH Z 274 " =    2.767
peak=   -4.058 closest distance to " O   HOH Z 266 " =    4.305
peak=   -4.005 closest distance to " O   VAL A  67 " =    2.801
peak=   -3.994 closest distance to " O   HOH Z 198 " =    2.419
peak=   -3.989 closest distance to " O   PRO A 163 " =    2.005
peak=   -3.952 closest distance to " CG  GLN A 223 " =    2.264
peak=   -3.924 closest distance to " CB  ALA A 248 " =    1.899
peak=   -3.898 closest distance to " CE2 TYR A  30 " =    2.821
peak=   -3.898 closest distance to " N   GLN A  58 " =    1.731
peak=   -3.897 closest distance to " CB  TYR A  15 " =    2.147
peak=   -3.847 closest distance to " OG BSER A 134 " =    1.656
peak=   -3.845 closest distance to " O   HOH Z 166 " =    1.402
peak=   -3.839 closest distance to " O   HOH Z  43 " =    1.849
peak=   -3.836 closest distance to " N   SER A 276 " =    1.308
peak=   -3.835 closest distance to " CG2 VAL A 296 " =    1.673
peak=   -3.832 closest distance to " C   HIS A 108 " =    1.157
peak=   -3.830 closest distance to " CG  LYS A 193 " =    2.297
peak=   -3.830 closest distance to " N   HIS A 115 " =    1.875
peak=   -3.830 closest distance to " O   HOH Z  13 " =    1.421
peak=   -3.819 closest distance to " OG ASER A 134 " =    1.410
peak=   -3.789 closest distance to " O   ASN A 187 " =    1.471
peak=   -3.780 closest distance to " NH2 ARG A  79 " =    1.855
peak=   -3.766 closest distance to " O   HOH Z  98 " =    1.726
peak=   -3.761 closest distance to " N   ALA A 248 " =    1.644
peak=   -3.758 closest distance to " C   ASN A 187 " =    1.804
peak=   -3.741 closest distance to " CG  LEU A 228 " =    0.998
peak=   -3.733 closest distance to " CB  ALA A  51 " =    1.716
peak=   -3.730 closest distance to " CZ  TYR A 169 " =    1.720
peak=   -3.721 closest distance to " O   HOH Z 166 " =    1.906
peak=   -3.717 closest distance to " CZ  PHE A  59 " =    1.598
peak=   -3.713 closest distance to " O   ASP A 231 " =    2.573
peak=   -3.706 closest distance to " OG BSER A 134 " =    1.222
peak=   -3.702 closest distance to " CB  ASP A 132 " =    2.264
peak=   -3.702 closest distance to " CB  ASN A  39 " =    2.049
peak=   -3.689 closest distance to " O   ALA A  51 " =    1.393
peak=   -3.680 closest distance to " O   HOH Z  70 " =    1.394
peak=   -3.674 closest distance to " CD  ARG A 139 " =    1.740
peak=   -3.672 closest distance to " O   HOH Z 423 " =    1.075
peak=   -3.665 closest distance to " CG  PHE A 283 " =    2.665
peak=   -3.652 closest distance to " O   MET A  40 " =    2.731
peak=   -3.650 closest distance to " CB  PRO A 163 " =    2.617
peak=   -3.639 closest distance to " O   HOH Z  97 " =    2.023
peak=   -3.613 closest distance to " O   HOH Z 388 " =    1.887
peak=   -3.612 closest distance to " O   PRO A 198 " =    1.319
peak=   -3.611 closest distance to " CE  MET A 105 " =    2.013
peak=   -3.610 closest distance to " O   HOH Z 165 " =    2.119
peak=   -3.603 closest distance to " CG  ASP A 231 " =    0.755
peak=   -3.600 closest distance to " CD1 LEU A 255 " =    2.742
peak=   -3.591 closest distance to " O   HOH Z 436 " =    1.436
peak=   -3.588 closest distance to " NH2AARG A 275 " =    5.225
peak=   -3.583 closest distance to " CB  PRO A 243 " =    2.617
peak=   -3.577 closest distance to " O   ALA A 161 " =    1.714
peak=   -3.577 closest distance to " CD  LYS A 289 " =    2.516
peak=   -3.572 closest distance to " CB  ALA A  43 " =    2.330
peak=   -3.560 closest distance to " O   SER A 135 " =    1.571
peak=   -3.560 closest distance to " N   THR A 157 " =    1.518
peak=   -3.555 closest distance to " O   HOH Z 385 " =    1.923
peak=   -3.555 closest distance to " CD  GLN A  88 " =    0.985
peak=   -3.552 closest distance to " OD2 ASP A  50 " =    1.531
peak=   -3.548 closest distance to " O   PRO A 198 " =    1.335
peak=   -3.546 closest distance to " CA  GLY A  35 " =    2.013
peak=   -3.542 closest distance to " O   HOH Z 389 " =    1.695
peak=   -3.542 closest distance to " CD  GLN A  88 " =    2.342
peak=   -3.541 closest distance to " O   HOH Z  11 " =    1.854
peak=   -3.539 closest distance to " CG  GLU A   2 " =    2.052
peak=   -3.535 closest distance to " O   HOH Z 103 " =    1.767
peak=   -3.529 closest distance to " O   TRP A  70 " =    1.585
peak=   -3.528 closest distance to " CD2 LEU A 300 " =    2.833
peak=   -3.519 closest distance to " O   HOH Z 350 " =    2.094
peak=   -3.514 closest distance to " OD1 ASN A 249 " =    1.277
peak=   -3.514 closest distance to " OH  TYR A 214 " =    1.347
peak=   -3.513 closest distance to " O   VAL A  67 " =    2.719
peak=   -3.511 closest distance to " NH1 ARG A  56 " =    2.481
peak=   -3.503 closest distance to " O   HOH Z 426 " =    2.289
peak=   -3.497 closest distance to " CE2 PHE A 218 " =    2.517
peak=   -3.488 closest distance to " O   HOH Z 339 " =    1.753
peak=   -3.488 closest distance to " CG  TRP A 266 " =    1.585
peak=   -3.481 closest distance to " CA  ASP A  27 " =    2.461
peak=   -3.473 closest distance to " O   HOH Z  63 " =    0.883
peak=   -3.463 closest distance to " CA  ASN A 127 " =    1.083
peak=   -3.454 closest distance to " OG  SER A  26 " =    1.097
peak=   -3.453 closest distance to " CB  CYS A 254 " =    2.394
peak=   -3.451 closest distance to " O   HOH Z  93 " =    1.567
peak=   -3.450 closest distance to " O   HOH Z 290 " =    1.013
peak=   -3.450 closest distance to " O   HOH Z 148 " =    1.678
peak=   -3.420 closest distance to " CG  ASN A  45 " =    1.753
peak=   -3.420 closest distance to " CD1 LEU A 228 " =    2.149
peak=   -3.416 closest distance to " C   ALA A 158 " =    1.209
peak=   -3.414 closest distance to " CD1 PHE A  59 " =    1.890
peak=   -3.412 closest distance to " CA  ASP A 298 " =    1.041
peak=   -3.411 closest distance to " O   ALA A   8 " =    1.745
peak=   -3.395 closest distance to " OG  SER A 206 " =    1.724
peak=   -3.395 closest distance to " OD1 ASP A 200 " =    1.264
peak=   -3.391 closest distance to " O   HOH Z 137 " =    1.419
peak=   -3.391 closest distance to " CA  GLY A 133 " =    1.889
peak=   -3.390 closest distance to " O   HOH Z 407 " =    3.025
peak=   -3.389 closest distance to " O   HOH Z 189 " =    1.756
peak=   -3.384 closest distance to " O   HOH Z 292 " =    4.317
peak=   -3.382 closest distance to " CG2AVAL A  41 " =    2.907
peak=   -3.377 closest distance to " OG  SER A  87 " =    1.287
peak=   -3.375 closest distance to " CZ  TYR A 172 " =    1.711
peak=   -3.374 closest distance to " CG  PRO A 163 " =    2.705
peak=   -3.370 closest distance to " O   HOH Z 410 " =    2.006
peak=   -3.369 closest distance to " CG  MET A 105 " =    0.947
peak=   -3.369 closest distance to " CB  ALA A 291 " =    2.507
peak=   -3.368 closest distance to " ND2 ASN A  45 " =    1.048
peak=   -3.367 closest distance to " ND2 ASN A  60 " =    1.469
peak=   -3.366 closest distance to " CG1 VAL A 250 " =    2.702
peak=   -3.358 closest distance to " CD  GLU A 152 " =    2.516
peak=   -3.358 closest distance to " O   HOH Z 389 " =    4.524
peak=   -3.356 closest distance to " OD1 ASP A 191 " =    1.645
peak=   -3.349 closest distance to " O   HOH Z 396 " =    1.522
peak=   -3.344 closest distance to " C   ASN A 285 " =    2.326
peak=   -3.344 closest distance to " NH2 ARG A  66 " =    1.963
peak=   -3.341 closest distance to " CB  ALA A 227 " =    2.391
peak=   -3.339 closest distance to " O   GLU A  44 " =    1.752
peak=   -3.338 closest distance to " OXT GLY A 302 " =    3.629
peak=   -3.334 closest distance to " OD1 ASP A 191 " =    1.425
peak=   -3.330 closest distance to " O   HOH Z  52 " =    1.560
peak=   -3.324 closest distance to " C   LEU A 143 " =    1.156
peak=   -3.321 closest distance to " O   SER A  22 " =    2.257
peak=   -3.309 closest distance to " O   HOH Z 281 " =    2.931
peak=   -3.308 closest distance to " O   HOH Z 423 " =    2.153
peak=   -3.305 closest distance to " O   HOH Z 100 " =    1.205
peak=   -3.301 closest distance to " O   GLY A 211 " =    1.343
peak=   -3.299 closest distance to " O   HOH Z 143 " =    1.342
peak=   -3.294 closest distance to " N   GLN A  77 " =    1.629
peak=   -3.286 closest distance to " N   ALA A 248 " =    1.887
peak=   -3.282 closest distance to " O   HOH Z  97 " =    0.921
peak=   -3.277 closest distance to " O   HOH Z  15 " =    1.583
peak=   -3.265 closest distance to " O   HOH Z 365 " =    1.450
peak=   -3.260 closest distance to " O   HOH Z 292 " =    2.820
peak=   -3.253 closest distance to " O   HOH Z 313 " =    1.699
peak=   -3.230 closest distance to " CG2 VAL A 112 " =    2.556
peak=   -3.229 closest distance to " CD1 TYR A 247 " =    2.870
peak=   -3.228 closest distance to " O   HOH Z 266 " =    4.542
peak=   -3.224 closest distance to " CE3 TRP A 274 " =    2.428
peak=   -3.220 closest distance to " O   ASP A 191 " =    1.677
peak=   -3.217 closest distance to " O   HOH Z  10 " =    1.399
peak=   -3.216 closest distance to " O   HOH Z 211 " =    1.219
peak=   -3.213 closest distance to " CB  SER A 245 " =    2.382
peak=   -3.213 closest distance to " N   ALA A 226 " =    2.066
peak=   -3.209 closest distance to " OE1 GLN A  77 " =    1.657
peak=   -3.205 closest distance to " O   HOH Z  90 " =    2.696
peak=   -3.201 closest distance to " N   PHE A 283 " =    1.805
peak=   -3.200 closest distance to " CG  ASP A  50 " =    2.168
peak=   -3.199 closest distance to " O   VAL A 197 " =    1.287
peak=   -3.195 closest distance to " O   HOH Z 123 " =    1.121
peak=   -3.193 closest distance to " ND2 ASN A 249 " =    2.178
peak=   -3.189 closest distance to " O   PHE A 218 " =    1.434
peak=   -3.188 closest distance to " C   GLN A 240 " =    2.345
peak=   -3.185 closest distance to " OG  SER A  87 " =    1.640
peak=   -3.185 closest distance to " N   PHE A  59 " =    2.121
peak=   -3.184 closest distance to " O   HOH Z 346 " =    1.764
peak=   -3.183 closest distance to " N   ALA A   9 " =    1.435
peak=   -3.174 closest distance to " CE2 TRP A 179 " =    1.320
peak=   -3.172 closest distance to " CB  PHE A 192 " =    1.784
peak=   -3.171 closest distance to " O   HOH Z 427 " =    1.529
peak=   -3.169 closest distance to " OG1 THR A 178 " =    1.098
peak=   -3.161 closest distance to " ND2 ASN A 209 " =    1.866
peak=   -3.160 closest distance to " NH2 ARG A 269 " =    2.319
peak=   -3.159 closest distance to " O   HOH Z 278 " =    1.434
peak=   -3.156 closest distance to " OD1 ASN A 187 " =    1.675
peak=   -3.149 closest distance to " O   VAL A 174 " =    2.086
peak=   -3.139 closest distance to " O   HOH Z 385 " =    2.070
peak=   -3.136 closest distance to " OE1 GLN A  73 " =    2.279
peak=   -3.134 closest distance to " CD1 ILE A 239 " =    2.564
peak=   -3.131 closest distance to " O   HOH Z  98 " =    1.530
peak=   -3.125 closest distance to " O   HOH Z  78 " =    1.835
peak=   -3.124 closest distance to " CD2 TYR A 293 " =    2.082
peak=   -3.123 closest distance to " O   HOH Z 353 " =    2.313
peak=   -3.117 closest distance to " CG2 VAL A 189 " =    1.973
peak=   -3.112 closest distance to " O   HOH Z 234 " =    4.094
peak=   -3.111 closest distance to " OG  SER A  62 " =    1.663
peak=   -3.100 closest distance to " O   HOH Z  60 " =    2.270
peak=   -3.092 closest distance to " CZ2 TRP A  92 " =    2.717
peak=   -3.091 closest distance to " O   TRP A  92 " =    1.715
peak=   -3.089 closest distance to " O   HOH Z 210 " =    1.154
peak=   -3.089 closest distance to " O   HOH Z 407 " =    3.516
peak=   -3.087 closest distance to " O   GLY A 196 " =    1.100
peak=   -3.083 closest distance to " O   HOH Z 364 " =    2.712
peak=   -3.074 closest distance to " O   HOH Z 431 " =    1.620
peak=   -3.074 closest distance to " NH2 ARG A 156 " =    1.219
peak=   -3.074 closest distance to " O   HOH Z 198 " =    1.589
peak=   -3.069 closest distance to " ND2 ASN A  39 " =    1.424
peak=   -3.035 closest distance to " O   SER A 146 " =    0.880

================= 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    :  0.4672 0.4647   6.269191e+00   6.263730e+00
   1_bss:  0.4583 0.4555   6.265074e+00   6.253760e+00
   1_xyz:  0.3822 0.4014   6.153822e+00   6.186952e+00
   1_adp:  0.3335 0.3838   6.070965e+00   6.161497e+00
   1_occ:  0.3328 0.3839   6.070788e+00   6.162079e+00
   2_bss:  0.3286 0.3807   6.069722e+00   6.158828e+00
   2_xyz:  0.2525 0.3105   5.852603e+00   6.004567e+00
   2_adp:  0.2342 0.2923   5.794194e+00   5.960183e+00
   2_occ:  0.2339 0.2927   5.793800e+00   5.960493e+00
   3_bss:  0.2335 0.2915   5.791447e+00   5.957187e+00
   3_xyz:  0.1807 0.2353   5.568647e+00   5.765935e+00
   3_adp:  0.1623 0.2213   5.485242e+00   5.709574e+00
   3_occ:  0.1621 0.2212   5.484629e+00   5.708879e+00
   4_bss:  0.1616 0.2202   5.478988e+00   5.703200e+00
   4_xyz:  0.1315 0.1813   5.287798e+00   5.526765e+00
   4_adp:  0.1245 0.1720   5.233911e+00   5.468232e+00
   4_occ:  0.1243 0.1717   5.233057e+00   5.467294e+00
   5_bss:  0.1246 0.1722   5.234742e+00   5.468496e+00
   5_xyz:  0.1135 0.1632   5.166681e+00   5.414721e+00
   5_adp:  0.1113 0.1615   5.153893e+00   5.404241e+00
   5_occ:  0.1112 0.1614   5.153509e+00   5.404018e+00
   5_bss:  0.1112 0.1613   5.153525e+00   5.403979e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.362   6.651   6.854   7.881  10.092   0.000   0.000   0.000
   1_xyz:  0.362   6.651   6.854   7.881  10.092   0.000   0.000   0.000
   1_adp:  0.362   6.651   6.854   7.881  10.092   0.000   0.000   0.000
   1_occ:  0.362   6.651   6.854   7.881  10.092   0.000   0.000   0.000
   2_bss:  0.338  26.208   3.213   3.695   6.567   0.000   0.000   0.000
   2_xyz:  0.338  26.208   3.213   3.695   6.567   0.000   0.000   0.000
   2_adp:  0.338  26.208   3.213   3.695   6.567   0.000   0.000   0.000
   2_occ:  0.338  26.208   3.213   3.695   6.567   0.000   0.000   0.000
   3_bss:  0.327  26.208   2.125   2.583   4.263   0.000   0.000   0.000
   3_xyz:  0.327  26.208   2.125   2.583   4.263   0.000   0.000   0.000
   3_adp:  0.327  26.208   2.125   2.583   4.263   0.000   0.000   0.000
   3_occ:  0.327  26.208   2.125   2.583   4.263   0.000   0.000   0.000
   4_bss:  0.317  33.866   1.755   2.000   2.848   0.000   0.000   0.000
   4_xyz:  0.317  33.866   1.755   2.000   2.848   0.000   0.000   0.000
   4_adp:  0.317  33.866   1.755   2.000   2.848   0.000   0.000   0.000
   4_occ:  0.317  33.866   1.755   2.000   2.848   0.000   0.000   0.000
   5_bss:  0.316  36.272   1.685   1.867   2.422   0.000   0.000   0.000
   5_xyz:  0.316  36.272   1.685   1.867   2.422   0.000   0.000   0.000
   5_adp:  0.316  36.272   1.685   1.867   2.422   0.000   0.000   0.000
   5_occ:  0.316  36.272   1.685   1.867   2.422   0.000   0.000   0.000
   5_bss:  0.319  38.282  -0.264  -0.106   0.371  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.482 0.4522  0.5365    67528.105
   1_bss:  55.628 0.4476  0.6677    63812.324
   1_xyz:  45.914 0.5698  0.8380    47350.185
   1_adp:  43.271 0.6027  0.9228    43868.303
   1_occ:  43.403 0.6010  0.9199    44020.276
   2_bss:  43.046 0.6053  0.8129    43496.192
   2_xyz:  33.389 0.7187  0.9445    26795.771
   2_adp:  30.795 0.7487  0.9811    23741.706
   2_occ:  30.802 0.7486  0.9808    23748.309
   3_bss:  30.556 0.7511  0.9313    23418.438
   3_xyz:  23.424 0.8275  0.9912    14519.035
   3_adp:  21.603 0.8463  0.9981    12777.106
   3_occ:  21.590 0.8464  0.9979    12754.374
   4_bss:  21.363 0.8484  0.9710    12527.781
   4_xyz:  17.264 0.8863  0.9909     8467.269
   4_adp:  15.810 0.8998  0.9925     7535.374
   4_occ:  15.780 0.9000  0.9925     7516.903
   5_bss:  15.811 0.8998  0.9847     7578.816
   5_xyz:  14.691 0.9091  0.9893     6725.505
   5_adp:  14.423 0.9115  0.9864     6586.001
   5_occ:  14.414 0.9116  0.9863     6580.291
   5_bss:  14.414 0.9116  0.9870     6581.729
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3105e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3105e+01
   1_xyz:   1.585  0.012  0.103 18.211  0.006  4.108   1.2845e-01
   1_adp:   1.585  0.012  0.103 18.211  0.006  4.108   1.2845e-01
   1_occ:   1.585  0.012  0.103 18.211  0.006  4.108   1.2845e-01
   2_bss:   1.585  0.012  0.103 18.211  0.006  4.108   1.2845e-01
   2_xyz:   1.082  0.008  0.078 16.284  0.004  4.108   7.5336e-02
   2_adp:   1.082  0.008  0.078 16.284  0.004  4.108   7.5336e-02
   2_occ:   1.082  0.008  0.078 16.284  0.004  4.108   7.5336e-02
   3_bss:   1.082  0.008  0.078 16.284  0.004  4.108   7.5336e-02
   3_xyz:   0.975  0.006  0.071 15.691  0.004  4.120   5.9139e-02
   3_adp:   0.975  0.006  0.071 15.691  0.004  4.120   5.9139e-02
   3_occ:   0.975  0.006  0.071 15.691  0.004  4.120   5.9139e-02
   4_bss:   0.975  0.006  0.071 15.691  0.004  4.120   5.9139e-02
   4_xyz:   1.054  0.007  0.078 15.734  0.004  4.108   6.5008e-02
   4_adp:   1.054  0.007  0.078 15.734  0.004  4.108   6.5008e-02
   4_occ:   1.054  0.007  0.078 15.734  0.004  4.108   6.5008e-02
   5_bss:   1.054  0.007  0.078 15.734  0.004  4.108   6.5008e-02
   5_xyz:   1.111  0.008  0.083 15.824  0.004  4.108   7.0851e-02
   5_adp:   1.111  0.008  0.083 15.824  0.004  4.108   7.0851e-02
   5_occ:   1.111  0.008  0.083 15.824  0.004  4.108   7.0851e-02
   5_bss:   1.111  0.008  0.083 15.824  0.004  4.108   7.0851e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8830e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8830e+00
   1_xyz:  13.282  0.151  0.428 84.925  0.049  2.241   8.8515e-02
   1_adp:  13.282  0.151  0.428 84.925  0.049  2.241   8.8515e-02
   1_occ:  13.282  0.151  0.428 84.925  0.049  2.241   8.8515e-02
   2_bss:  13.282  0.151  0.428 84.925  0.049  2.241   8.8515e-02
   2_xyz:   6.170  0.063  0.283 83.404  0.029  2.289   5.7142e-02
   2_adp:   6.170  0.063  0.283 83.404  0.029  2.289   5.7142e-02
   2_occ:   6.170  0.063  0.283 83.404  0.029  2.289   5.7142e-02
   3_bss:   6.170  0.063  0.283 83.404  0.029  2.289   5.7142e-02
   3_xyz:   6.516  0.044  0.299 87.190  0.029  2.327   5.5048e-02
   3_adp:   6.516  0.044  0.299 87.190  0.029  2.327   5.5048e-02
   3_occ:   6.516  0.044  0.299 87.190  0.029  2.327   5.5048e-02
   4_bss:   6.516  0.044  0.299 87.190  0.029  2.327   5.5048e-02
   4_xyz:   6.830  0.049  0.422 81.417  0.037  2.349   4.6246e-02
   4_adp:   6.830  0.049  0.422 81.417  0.037  2.349   4.6246e-02
   4_occ:   6.830  0.049  0.422 81.417  0.037  2.349   4.6246e-02
   5_bss:   6.830  0.049  0.422 81.417  0.037  2.349   4.6246e-02
   5_xyz:   7.139  0.046  0.540 83.487  0.042  2.239   5.4067e-02
   5_adp:   7.139  0.046  0.540 83.487  0.042  2.239   5.4067e-02
   5_occ:   7.139  0.046  0.540 83.487  0.042  2.239   5.4067e-02
   5_bss:   7.139  0.046  0.540 83.487  0.042  2.239   5.4067e-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:  82.92   0.00  12.75  82.92   0.00  10.29  79.30   0.00  26.15
   1_occ:  82.92   0.00  12.75  82.92   0.00  10.29  79.30   0.00  26.15
   2_bss:  82.92   0.00  12.75  82.92   0.00  10.29  79.30   0.00  26.15
   2_xyz:  82.92   0.00  12.75  82.92   0.00  10.29  79.30   0.00  26.15
   2_adp:  83.31   0.00  12.89  83.31   0.00   9.68  75.47   0.00  30.36
   2_occ:  83.31   0.00  12.89  83.31   0.00   9.68  75.47   0.00  30.36
   3_bss:  83.31   0.00  12.89  83.31   0.00   9.68  75.47   0.00  30.36
   3_xyz:  83.31   0.00  12.89  83.31   0.00   9.68  75.47   0.00  30.36
   3_adp:  96.32   0.00  14.15  96.32   0.00   9.50  85.04   1.83  39.47
   3_occ:  96.32   0.00  14.15  96.32   0.00   9.50  85.04   1.83  39.47
   4_bss:  96.32   0.00  14.15  96.32   0.00   9.50  85.04   1.83  39.47
   4_xyz:  96.32   0.00  14.15  96.32   0.00   9.50  85.04   1.83  39.47
   4_adp: 102.75   0.00  13.72 102.75   0.00   9.10  87.05   2.72  38.91
   4_occ: 102.75   0.00  13.72 102.75   0.00   9.10  87.05   2.72  38.91
   5_bss: 102.75   0.00  13.72 102.75   0.00   9.10  87.05   2.72  38.91
   5_xyz: 102.75   0.00  13.72 102.75   0.00   9.10  87.05   2.72  38.91
   5_adp: 106.63   0.00  13.44 106.63   0.00   8.93  90.35   2.42  38.02
   5_occ: 106.63   0.00  13.44 106.63   0.00   8.93  90.35   2.42  38.02
   5_bss: 108.64   2.01  15.45 108.64   2.01  10.94  92.36   4.43  40.03
------------------------------------------------------------------------
 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:    1.214    0.019    0.402
   1_adp:    1.214    0.019    0.402
   1_occ:    1.214    0.019    0.402
   2_bss:    1.214    0.019    0.402
   2_xyz:    1.528    0.038    0.554
   2_adp:    1.528    0.038    0.554
   2_occ:    1.528    0.038    0.554
   3_bss:    1.528    0.038    0.554
   3_xyz:    1.506    0.020    0.619
   3_adp:    1.506    0.020    0.619
   3_occ:    1.506    0.020    0.619
   4_bss:    1.506    0.020    0.619
   4_xyz:    1.652    0.050    0.675
   4_adp:    1.652    0.050    0.675
   4_occ:    1.652    0.050    0.675
   5_bss:    1.652    0.050    0.675
   5_xyz:    1.726    0.018    0.694
   5_adp:    1.726    0.018    0.694
   5_occ:    1.726    0.018    0.694
   5_bss:    1.726    0.018    0.694
------------------------------------------------------------------------

CPU time actual refinement: 346.19


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_649/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_649/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_649/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_649/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_649/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 346.04 
  Macro-tasks:
    bulk solvent and scale       = 41.16  
    individual site refinement   = 146.57 
    weights calculation          = 32.75  
    collect and process          = 6.63   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 227.22 
  Micro-tasks:
    mask                            = 2.55   
    f_calc                          = 108.90 
    alpha_beta                      = 8.43   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 118.47 
    fmodel                         = 6.96   
    r_factors                      = 0.27   
    phase_errors                   = 10.36  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 257.39 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.878 micro seconds
Total CPU time: 6.00 minutes
from_scatterers_fft:    626 calls, 108.57 s
gradients_fft:          571 calls, 105.38 s

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

# Date 2008-01-16 Time 02:04:45 PST -0800 (1200477885.37 s)
Start R-work = 0.4672, R-free = 0.4647 (no bulk solvent and anisotropic scale)
Final R-work = 0.1283, R-free = 0.1784 (no bulk solvent and anisotropic scale)

Start R-work = 0.4583, R-free = 0.4555
Final R-work = 0.1112, R-free = 0.1613