# Date 2008-01-16 Time 01:47:16 PST -0800 (1200476836.73 s)
#phil __OFF__

Command line arguments: "../572.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 13123
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 572

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 47.6339, 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: 2.75, per 1000 atoms: 0.97


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8572 1.95149
Completeness in resolution range: 0.930903
Completeness with d_max=infinity: 0.928125

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8572
                             d_min =   1.9515

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8572 1.95149
Completeness in resolution range: 0.930903
Completeness with d_max=infinity: 0.928125

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8576 -  4.1762 [2213/2242]  1991   222  10.0%
  bin  2:  4.1762 -  3.3270 [2109/2132]  1900   209   9.9%
  bin  3:  3.3270 -  2.9100 [2087/2112]  1876   211  10.1%
  bin  4:  2.9100 -  2.6456 [2074/2091]  1869   205   9.9%
  bin  5:  2.6456 -  2.4569 [2075/2118]  1866   209  10.1%
  bin  6:  2.4569 -  2.3126 [2046/2074]  1849   197   9.6%
  bin  7:  2.3126 -  2.1971 [2025/2061]  1820   205  10.1%
  bin  8:  2.1971 -  2.1018 [2030/2072]  1822   208  10.2%
  bin  9:  2.1018 -  2.0211 [2010/2068]  1806   204  10.1%
  bin 10:  2.0211 -  1.9515 [ 920/2073]   831    89   9.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_572/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.48 -     2.17: 26
        2.17 -     2.85: 1131
        2.85 -     3.53: 4436
        3.53 -     4.22: 9337
        4.22 -     4.90: 13639
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.483 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.498 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.606 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.678 3.040 -x+1/2,-y+1,z+1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.728 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28564 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_572/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_572/model_refine_001.geo

CPU time processing inputs: 8.00


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 47.63395 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 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4930   r_free= 0.4957   ksol= 0.00   Bsol= 0.00   scale= 0.788    |
|                                                                             |
| 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:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.294589                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8576 -  4.6581 0.99   1435  163 0.4072 0.4086      6.6196      6.6415|
|  2:  4.6581 -  3.7163 0.99   1376  147 0.4181 0.4312      6.8184      6.8235|
|  3:  3.7163 -  3.2522 0.99   1350  153 0.4565 0.4366      6.6914      6.7399|
|  4:  3.2522 -  2.9574 0.99   1343  147 0.4675 0.4785      6.5223      6.5225|
|  5:  2.9574 -  2.7468 0.99   1341  149 0.5198 0.5534      6.3806       6.363|
|  6:  2.7468 -  2.5858 0.99   1324  150 0.5154 0.5319      6.2776      6.2185|
|  7:  2.5858 -  2.4569 0.98   1333  147 0.5301 0.4598      6.2649      6.1835|
|  8:  2.4569 -  2.3504 0.98   1310  143 0.5418 0.5372      6.1631      6.1738|
|  9:  2.3504 -  2.2602 0.99   1316  143 0.5554 0.5471       6.142      6.1399|
| 10:  2.2602 -  2.1825 0.98   1312  148 0.5370 0.5695      6.0986      6.1448|
| 11:  2.1825 -  2.1144 0.97   1288  143 0.5403 0.5216      6.0409      6.0133|
| 12:  2.1144 -  2.0541 0.98   1302  150 0.5434 0.6054      5.9496       5.996|
| 13:  2.0541 -  2.0002 0.91   1197  134 0.5506 0.5364      5.8867      5.8322|
| 14:  2.0002 -  1.9515 0.30    403   42 0.5700 0.5599      5.8296      5.7186|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8576 -  4.6581  1435   163  0.67  37.31   0.79     0.69      81011.96|
|  2:  4.6581 -  3.7163  1376   147  0.67  38.25   0.87     0.73     120178.93|
|  3:  3.7163 -  3.2522  1350   153  0.55  48.21   0.83     0.67     130617.46|
|  4:  3.2522 -  2.9574  1343   147  0.45  55.99   0.80     0.55     115224.34|
|  5:  2.9574 -  2.7468  1341   149  0.35  63.34   0.73     0.45      93105.58|
|  6:  2.7468 -  2.5858  1324   150  0.36  63.10   0.73     0.43      75773.09|
|  7:  2.5858 -  2.4569  1333   147  0.37  62.52   0.73     0.42      65405.57|
|  8:  2.4569 -  2.3504  1310   143  0.34  64.35   0.71     0.41      60289.22|
|  9:  2.3504 -  2.2602  1316   143  0.27  69.61   0.72     0.33      58523.52|
| 10:  2.2602 -  2.1825  1312   148  0.20  75.09   0.76     0.25      58216.79|
| 11:  2.1825 -  2.1144  1288   143  0.13  80.68   0.76     0.16      55914.73|
| 12:  2.1144 -  2.0541  1302   150  0.11  81.89   0.73     0.15      51908.98|
| 13:  2.0541 -  2.0002  1197   134  0.16  77.84   0.74     0.21      41841.33|
| 14:  2.0002 -  1.9515   403    42  0.31  66.76   0.68     0.38      31076.43|
|alpha:            min =        0.15 max =            0.73 mean =         0.42|
|beta:             min =    31076.43 max =       130617.46 mean =     77121.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.36|
|phase err.(work): min =        0.00 max =           89.99 mean =        62.58|
|phase err.(test): min =        0.00 max =           89.97 mean =        62.99|
|-----------------------------------------------------------------------------|

============================== 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 = 17.632302             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.521   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.688378              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.477   (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 |  0.997 -  1.387:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.387 -  1.777:       11 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.777 -  2.168:       93 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.168 -  2.558:      516 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.558 -  2.948:     1304 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.948 -  3.339:     2470 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.339 -  3.729:     3966 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.729 -  4.119:     5208 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.119 -  4.510:     6844 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.510 -  4.900:     8207 |
|-----------------------------------------------------------------------------|
|-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 |       53.308 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  0.997 |       2.271 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    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 = 11.686)------------------------------------------|
|    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 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4979   r_free= 0.5018   ksol= 0.00   Bsol= 0.00   scale= 0.758    |
|                                                                             |
| 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:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.295540                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4861   r_free= 0.4861   ksol= 0.35   Bsol= 20.00   scale= 0.962   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.58,9.09,7.97,0.00,0.00,0.00); trace/3= 7.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.292489                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.386769             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.482   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.410992              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.124   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4861      final r-factor (work) = 0.4241          |
| start r-factor (free) = 0.4861      final r-factor (free) = 0.4400          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 98.5648 = 14.39 * 0.50 * 6.2914 + 1.00 * 53.3084                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.9424 = 14.39 * 0.50 * 6.2268 + 1.00 * 0.1504                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4241      final r-factor (work) = 0.3831          |
| start r-factor (free) = 0.4400      final r-factor (free) = 0.4286          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.8003 = 1.41 * 1.00 * 6.2268 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7255 = 1.41 * 1.00 * 6.1712 + 1.00 * 0.0180                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.87   14.67    None  None   None       |
|    all(noH): 2823   0      0.00    85.87   14.67    None  None   None       |
|    Sol.    : 438    0      0.00    85.87   25.95    None  None   None       |
|    Mac.    : 2385   0      0.00    73.29   12.59    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.587: 1100   |   5:    42.936 -  51.523:   57        |
|      1:     8.587 -  17.175:  814   |   6:    51.523 -  60.111:   24        |
|      2:    17.175 -  25.762:  458   |   7:    60.111 -  68.698:   20        |
|      3:    25.762 -  34.349:  225   |   8:    68.698 -  77.285:    7        |
|      4:    34.349 -  42.936:  113   |   9:    77.285 -  85.872:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3831 r_free = 0.4286             target_work(ml) = 6.161         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3824 r_free = 0.4282             target_work(ml) = 6.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3824   r_free= 0.4282   ksol= 0.35   Bsol= 20.00   scale= 1.086   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.58,9.09,7.97,0.00,0.00,0.00); trace/3= 7.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.160226                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3813   r_free= 0.4259   ksol= 0.33   Bsol= 34.18   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.83,6.16,5.68,0.00,0.00,0.00); trace/3= 4.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.161166                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.580413             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.811  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.690954              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.716  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3813      final r-factor (work) = 0.2969          |
| start r-factor (free) = 0.4259      final r-factor (free) = 0.3584          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 45.1173 = 14.58 * 0.50 * 6.1681 + 1.00 * 0.1504                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.3538 = 14.58 * 0.50 * 6.0681 + 1.00 * 0.1164                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2969      final r-factor (work) = 0.2711          |
| start r-factor (free) = 0.3584      final r-factor (free) = 0.3347          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2112 = 0.69 * 1.00 * 6.0681 + 1.00 * 0.0184                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1135 = 0.69 * 1.00 * 5.9310 + 1.00 * 0.0155                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.34   14.81    None  None   None       |
|    all(noH): 2823   0      0.00    84.34   14.81    None  None   None       |
|    Sol.    : 438    0      0.00    84.34   32.32    None  None   None       |
|    Mac.    : 2385   0      0.00    77.45   11.59    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.434: 1126   |   5:    42.170 -  50.604:   82        |
|      1:     8.434 -  16.868:  851   |   6:    50.604 -  59.038:   39        |
|      2:    16.868 -  25.302:  355   |   7:    59.038 -  67.472:   20        |
|      3:    25.302 -  33.736:  215   |   8:    67.472 -  75.906:    5        |
|      4:    33.736 -  42.170:  125   |   9:    75.906 -  84.340:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2711 r_free = 0.3347             target_work(ml) = 5.900         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2707 r_free = 0.3347             target_work(ml) = 5.900         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2707   r_free= 0.3347   ksol= 0.33   Bsol= 34.18   scale= 1.079   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.83,6.16,5.68,0.00,0.00,0.00); trace/3= 4.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.899792                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2670   r_free= 0.3303   ksol= 0.31   Bsol= 34.18   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.12,2.91,2.70,0.00,0.00,0.00); trace/3= 2.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.896409                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.559967              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.366  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.621182              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.719  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2670      final r-factor (work) = 0.1913          |
| start r-factor (free) = 0.3303      final r-factor (free) = 0.2427          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.5832 = 6.56 * 0.50 * 5.9350 + 1.00 * 0.1164                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.0361 = 6.56 * 0.50 * 5.7783 + 1.00 * 0.0835                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1913      final r-factor (work) = 0.1677          |
| start r-factor (free) = 0.2427      final r-factor (free) = 0.2196          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6025 = 0.62 * 1.00 * 5.7783 + 1.00 * 0.0131                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4569 = 0.62 * 1.00 * 5.5468 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.12   14.86    None  None   None       |
|    all(noH): 2823   0      0.00    78.12   14.86    None  None   None       |
|    Sol.    : 438    0      3.76    76.71   38.19    None  None   None       |
|    Mac.    : 2385   0      0.00    78.12   10.57    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.812: 1156   |   5:    39.062 -  46.875:  121        |
|      1:     7.812 -  15.625:  889   |   6:    46.875 -  54.687:   80        |
|      2:    15.625 -  23.437:  261   |   7:    54.687 -  62.499:   49        |
|      3:    23.437 -  31.250:  133   |   8:    62.499 -  70.312:   20        |
|      4:    31.250 -  39.062:  102   |   9:    70.312 -  78.124:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1677 r_free = 0.2196             target_work(ml) = 5.492         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1674 r_free = 0.2194             target_work(ml) = 5.491         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1674   r_free= 0.2194   ksol= 0.31   Bsol= 34.18   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.12,2.91,2.70,0.00,0.00,0.00); trace/3= 2.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.491020                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1669   r_free= 0.2189   ksol= 0.32   Bsol= 39.16   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.22,1.64,1.35,0.00,0.00,0.00); trace/3= 1.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.489561                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.210330              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.263   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.587092              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.403  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1669      final r-factor (work) = 0.1421          |
| start r-factor (free) = 0.2189      final r-factor (free) = 0.1909          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2202 = 2.21 * 0.50 * 5.5528 + 1.00 * 0.0835                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0490 = 2.21 * 0.50 * 5.4228 + 1.00 * 0.0559                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1421      final r-factor (work) = 0.1357          |
| start r-factor (free) = 0.1909      final r-factor (free) = 0.1841          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1950 = 0.59 * 1.00 * 5.4228 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1393 = 0.59 * 1.00 * 5.3272 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.36   15.00    None  None   None       |
|    all(noH): 2823   0      0.00    92.36   15.00    None  None   None       |
|    Sol.    : 438    0      3.39    80.29   40.27    None  None   None       |
|    Mac.    : 2385   0      0.00    92.36   10.35    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.236: 1427   |   5:    46.182 -  55.418:   95        |
|      1:     9.236 -  18.473:  780   |   6:    55.418 -  64.655:   70        |
|      2:    18.473 -  27.709:  196   |   7:    64.655 -  73.891:   30        |
|      3:    27.709 -  36.946:   95   |   8:    73.891 -  83.128:    8        |
|      4:    36.946 -  46.182:  117   |   9:    83.128 -  92.364:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1357 r_free = 0.1841             target_work(ml) = 5.310         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1355 r_free = 0.1841             target_work(ml) = 5.309         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1355   r_free= 0.1841   ksol= 0.32   Bsol= 39.16   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.22,1.64,1.35,0.00,0.00,0.00); trace/3= 1.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.309444                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1357   r_free= 0.1847   ksol= 0.32   Bsol= 39.16   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.16,1.32,1.04,0.00,0.00,0.00); trace/3= 0.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.311695                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.899115              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.425  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.438552              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.936  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1357      final r-factor (work) = 0.1212          |
| start r-factor (free) = 0.1847      final r-factor (free) = 0.1686          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7788 = 2.90 * 0.50 * 5.3277 + 1.00 * 0.0560                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7007 = 2.90 * 0.50 * 5.2655 + 1.00 * 0.0680                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1212      final r-factor (work) = 0.1191          |
| start r-factor (free) = 0.1686      final r-factor (free) = 0.1667          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3209 = 0.44 * 1.00 * 5.2655 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2994 = 0.44 * 1.00 * 5.2137 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.45   14.62    None  None   None       |
|    all(noH): 2823   0      0.00    98.45   14.62    None  None   None       |
|    Sol.    : 438    0      2.41    81.35   39.18    None  None   None       |
|    Mac.    : 2385   0      0.00    98.45   10.11    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 -   9.845: 1597   |   5:    49.223 -  59.067:   80        |
|      1:     9.845 -  19.689:  678   |   6:    59.067 -  68.912:   47        |
|      2:    19.689 -  29.534:  164   |   7:    68.912 -  78.756:   20        |
|      3:    29.534 -  39.378:  116   |   8:    78.756 -  88.601:    3        |
|      4:    39.378 -  49.223:  114   |   9:    88.601 -  98.445:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1191 r_free = 0.1667             target_work(ml) = 5.209         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1190 r_free = 0.1666             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1666   ksol= 0.32   Bsol= 39.16   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.16,1.32,1.04,0.00,0.00,0.00); trace/3= 0.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.208250                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8576 -  4.6581 0.99   1435  163 0.0955 0.1216      5.3561      5.5247|
|  2:  4.6581 -  3.7163 0.99   1376  147 0.0868 0.1161      5.4497      5.6859|
|  3:  3.7163 -  3.2522 0.99   1350  153 0.1117 0.1681      5.5162      5.9108|
|  4:  3.2522 -  2.9574 0.99   1343  147 0.1355 0.1592      5.5159      5.6645|
|  5:  2.9574 -  2.7468 0.99   1341  149 0.1399 0.1716      5.3731      5.5109|
|  6:  2.7468 -  2.5858 0.99   1324  150 0.1365 0.2229      5.3005      5.6134|
|  7:  2.5858 -  2.4569 0.98   1333  147 0.1355 0.1727      5.2379      5.4193|
|  8:  2.4569 -  2.3504 0.98   1310  143 0.1267 0.1709      5.1342      5.3308|
|  9:  2.3504 -  2.2602 0.99   1316  143 0.1272 0.1914      5.0812      5.3275|
| 10:  2.2602 -  2.1825 0.98   1312  148 0.1204 0.1989       5.047      5.3938|
| 11:  2.1825 -  2.1144 0.97   1288  143 0.1255 0.1908      5.0034      5.2732|
| 12:  2.1144 -  2.0541 0.98   1302  150 0.1211 0.1795      4.9143      5.1342|
| 13:  2.0541 -  2.0002 0.91   1197  134 0.1218 0.1868      4.8356      5.0524|
| 14:  2.0002 -  1.9515 0.30    403   42 0.1197 0.1882      4.7424      5.0482|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8576 -  4.6581  1435   163  0.94   9.01   0.98     0.96       7166.77|
|  2:  4.6581 -  3.7163  1376   147  0.95   8.22   1.02     1.00       9294.26|
|  3:  3.7163 -  3.2522  1350   153  0.92  12.53   1.03     1.03      11692.58|
|  4:  3.2522 -  2.9574  1343   147  0.91  15.21   1.01     0.99      11489.61|
|  5:  2.9574 -  2.7468  1341   149  0.88  17.68   1.00     0.97       9379.51|
|  6:  2.7468 -  2.5858  1324   150  0.89  17.72   0.98     0.96       8536.66|
|  7:  2.5858 -  2.4569  1333   147  0.89  17.29   0.99     0.95       7261.80|
|  8:  2.4569 -  2.3504  1310   143  0.89  17.27   1.00     0.97       6356.61|
|  9:  2.3504 -  2.2602  1316   143  0.89  17.62   1.00     0.97       5699.33|
| 10:  2.2602 -  2.1825  1312   148  0.89  16.92   1.00     0.96       5387.04|
| 11:  2.1825 -  2.1144  1288   143  0.88  18.19   1.00     0.96       5110.84|
| 12:  2.1144 -  2.0541  1302   150  0.90  16.56   1.00     0.99       4301.56|
| 13:  2.0541 -  2.0002  1197   134  0.89  17.58   1.00     1.00       3695.43|
| 14:  2.0002 -  1.9515   403    42  0.88  17.70   0.98     0.95       3093.18|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     3093.18 max =        11692.58 mean =      7294.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.85 mean =        15.48|
|phase err.(test): min =        0.00 max =           89.63 mean =        14.93|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1666   ksol= 0.32   Bsol= 42.29   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.62,0.41,0.21,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.208314                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1666   ksol= 0.32   Bsol= 42.29   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.62,0.41,0.21,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.208314                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8576 -  4.6581 0.99   1435  163 0.0956 0.1218      5.3584      5.5275|
|  2:  4.6581 -  3.7163 0.99   1376  147 0.0870 0.1164      5.4517       5.688|
|  3:  3.7163 -  3.2522 0.99   1350  153 0.1118 0.1683      5.5175      5.9118|
|  4:  3.2522 -  2.9574 0.99   1343  147 0.1355 0.1593      5.5161      5.6649|
|  5:  2.9574 -  2.7468 0.99   1341  149 0.1398 0.1715      5.3725      5.5101|
|  6:  2.7468 -  2.5858 0.99   1324  150 0.1364 0.2227      5.2998      5.6128|
|  7:  2.5858 -  2.4569 0.98   1333  147 0.1355 0.1728      5.2373      5.4196|
|  8:  2.4569 -  2.3504 0.98   1310  143 0.1265 0.1705      5.1336      5.3293|
|  9:  2.3504 -  2.2602 0.99   1316  143 0.1271 0.1916      5.0807      5.3279|
| 10:  2.2602 -  2.1825 0.98   1312  148 0.1203 0.1988      5.0464      5.3933|
| 11:  2.1825 -  2.1144 0.97   1288  143 0.1254 0.1907      5.0029      5.2726|
| 12:  2.1144 -  2.0541 0.98   1302  150 0.1212 0.1794      4.9139      5.1341|
| 13:  2.0541 -  2.0002 0.91   1197  134 0.1218 0.1864      4.8351      5.0509|
| 14:  2.0002 -  1.9515 0.30    403   42 0.1197 0.1880      4.7415      5.0474|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8576 -  4.6581  1435   163  0.94   9.04   0.98     0.97       7217.38|
|  2:  4.6581 -  3.7163  1376   147  0.95   8.25   1.02     1.00       9342.15|
|  3:  3.7163 -  3.2522  1350   153  0.92  12.56   1.03     1.03      11734.88|
|  4:  3.2522 -  2.9574  1343   147  0.91  15.22   1.01     0.99      11498.93|
|  5:  2.9574 -  2.7468  1341   149  0.88  17.67   1.00     0.97       9370.24|
|  6:  2.7468 -  2.5858  1324   150  0.89  17.71   0.99     0.96       8525.21|
|  7:  2.5858 -  2.4569  1333   147  0.89  17.27   0.99     0.96       7253.00|
|  8:  2.4569 -  2.3504  1310   143  0.89  17.26   1.01     0.97       6350.93|
|  9:  2.3504 -  2.2602  1316   143  0.89  17.61   1.00     0.97       5696.77|
| 10:  2.2602 -  2.1825  1312   148  0.89  16.91   1.00     0.96       5380.55|
| 11:  2.1825 -  2.1144  1288   143  0.88  18.18   1.00     0.96       5103.90|
| 12:  2.1144 -  2.0541  1302   150  0.90  16.54   1.00     0.99       4296.13|
| 13:  2.0541 -  2.0002  1197   134  0.89  17.56   1.00     1.00       3688.76|
| 14:  2.0002 -  1.9515   403    42  0.88  17.68   0.98     0.95       3083.93|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     3083.93 max =        11734.88 mean =      7301.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.90 mean =        15.48|
|phase err.(test): min =        0.00 max =           89.65 mean =        14.94|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.86    99.30   15.48    None  None   None       |
|    all(noH): 2823   0      0.86    99.30   15.48    None  None   None       |
|    Sol.    : 438    0      3.27    82.21   40.04    None  None   None       |
|    Mac.    : 2385   0      0.86    99.30   10.96    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:     0.859 -  10.704: 1597   |   5:    50.082 -  59.926:   80        |
|      1:    10.704 -  20.548:  678   |   6:    59.926 -  69.771:   47        |
|      2:    20.548 -  30.393:  164   |   7:    69.771 -  79.615:   20        |
|      3:    30.393 -  40.237:  116   |   8:    79.615 -  89.460:    3        |
|      4:    40.237 -  50.082:  114   |   9:    89.460 -  99.304:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 342         
Filter by distance & map next to the model:
   mapped sites are within: 0.603 - 5.900
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 340 from: 342
   mapped sites are within: 0.748 - 5.900

peak=   10.314 closest distance to " O   HOH Z 138 " =    1.487
peak=    9.651 closest distance to " CB  VAL A 230 " =    1.421
peak=    8.965 closest distance to " O   HOH Z 120 " =    1.556
peak=    8.481 closest distance to " CG2 VAL A 296 " =    1.303
peak=    6.775 closest distance to " O   HOH Z 279 " =    1.386
peak=    5.974 closest distance to " CG  LEU A   5 " =    1.340
peak=    5.947 closest distance to " O   HOH Z 278 " =    1.456
peak=    5.856 closest distance to " O   HOH Z 124 " =    1.707
peak=    5.800 closest distance to " NH2 ARG A  56 " =    2.217
peak=    5.746 closest distance to " O   HOH Z 199 " =    1.242
peak=    5.642 closest distance to " CD1AILE A 234 " =    1.112
peak=    5.426 closest distance to " O   HOH Z  11 " =    1.399
peak=    5.309 closest distance to " O   HOH Z 316 " =    1.069
peak=    5.306 closest distance to " O   HOH Z 247 " =    1.425
peak=    5.226 closest distance to " CD2 LEU A   5 " =    1.211
peak=    4.946 closest distance to " O   HOH Z 316 " =    2.144
peak=    4.930 closest distance to " O   HOH Z 202 " =    1.389
peak=    4.906 closest distance to " O   HOH Z  48 " =    1.919
peak=    4.875 closest distance to " O   HOH Z 210 " =    1.140
peak=    4.859 closest distance to " O   HOH Z 132 " =    1.432
peak=    4.836 closest distance to " O   HOH Z  43 " =    1.718
peak=    4.827 closest distance to " O   HOH Z 411 " =    3.614
peak=    4.786 closest distance to " CG  PRO A  54 " =    1.171
peak=    4.777 closest distance to " CB  GLN A 223 " =    1.393
peak=    4.744 closest distance to " O   HOH Z  37 " =    1.199
peak=    4.740 closest distance to " O   SER A  87 " =    2.273
peak=    4.696 closest distance to " O   HOH Z 389 " =    1.839
peak=    4.694 closest distance to " CB  SER A  63 " =    1.288
peak=    4.658 closest distance to " O   HOH Z 156 " =    3.254
peak=    4.600 closest distance to " O   HOH Z 346 " =    1.524
peak=    4.593 closest distance to " O   HOH Z 192 " =    1.482
peak=    4.584 closest distance to " C   PRO A 198 " =    1.495
peak=    4.560 closest distance to " O   HOH Z 193 " =    1.831
peak=    4.558 closest distance to " CB  GLN A 183 " =    1.333
peak=    4.529 closest distance to " CB  VAL A 230 " =    1.271
peak=    4.497 closest distance to " O   HOH Z 136 " =    1.307
peak=    4.481 closest distance to " CA  ALA A  21 " =    1.289
peak=    4.455 closest distance to " O   HOH Z 326 " =    1.601
peak=    4.448 closest distance to " O   HOH Z 155 " =    1.789
peak=    4.429 closest distance to " CG  PRO A 198 " =    1.245
peak=    4.427 closest distance to " O   HOH Z 402 " =    1.525
peak=    4.426 closest distance to " O   HOH Z 134 " =    1.878
peak=    4.403 closest distance to " CG  LEU A 228 " =    1.280
peak=    4.398 closest distance to " O   HOH Z 403 " =    1.864
peak=    4.395 closest distance to " O   HOH Z 232 " =    2.238
peak=    4.392 closest distance to " O   HOH Z 126 " =    1.830
peak=    4.386 closest distance to " O   HOH Z 108 " =    1.423
peak=    4.371 closest distance to " CG  PRO A 213 " =    1.218
peak=    4.367 closest distance to " O   HOH Z  80 " =    1.853
peak=    4.365 closest distance to " O   HOH Z 154 " =    2.355
peak=    4.335 closest distance to " O   HOH Z  97 " =    1.770
peak=    4.330 closest distance to " O   HOH Z 394 " =    1.588
peak=    4.302 closest distance to " O   HOH Z 130 " =    1.089
peak=    4.267 closest distance to " O   HOH Z 133 " =    1.767
peak=    4.265 closest distance to " O   HOH Z  30 " =    1.455
peak=    4.228 closest distance to " O   HOH Z 263 " =    1.411
peak=    4.214 closest distance to " CB  TYR A 169 " =    0.932
peak=    4.211 closest distance to " O   HOH Z 154 " =    1.533
peak=    4.194 closest distance to " O   HOH Z  20 " =    1.730
peak=    4.184 closest distance to " O   ASP A 132 " =    3.878
peak=    4.168 closest distance to " O   HOH Z 331 " =    1.394
peak=    4.118 closest distance to " O   HOH Z  40 " =    1.646
peak=    4.080 closest distance to " CG1BVAL A  72 " =    1.642
peak=    4.066 closest distance to " CB  TRP A 179 " =    1.287
peak=    4.063 closest distance to " O   HOH Z 260 " =    1.293
peak=    4.056 closest distance to " O   HOH Z 284 " =    2.910
peak=    4.049 closest distance to " OE1 GLN A  11 " =    1.843
peak=    4.045 closest distance to " O   HOH Z  78 " =    1.774
peak=    4.044 closest distance to " CD2 LEU A 228 " =    1.167
peak=    4.043 closest distance to " CA  TYR A  30 " =    1.072
peak=    4.033 closest distance to " CG2 THR A 221 " =    1.111
peak=    4.014 closest distance to " O   HOH Z 227 " =    1.773
peak=    4.010 closest distance to " O   HOH Z 180 " =    2.165
peak=    4.010 closest distance to " CB  SER A   3 " =    1.351
peak=    4.004 closest distance to " CD  ARG A 269 " =    0.999
peak=    4.003 closest distance to " O   HOH Z 272 " =    1.966
peak=    4.000 closest distance to " CB  LEU A 228 " =    1.422
peak=    3.999 closest distance to " O   HOH Z 193 " =    2.234
peak=    3.996 closest distance to " O   HOH Z 423 " =    1.959
peak=    3.986 closest distance to " O   HOH Z 426 " =    1.446
peak=    3.976 closest distance to " CB  SER A 141 " =    1.054
peak=    3.966 closest distance to " CG AARG A 275 " =    1.081
peak=    3.929 closest distance to " CB  PRO A  54 " =    0.778
peak=    3.925 closest distance to " CB  GLU A 152 " =    1.056
peak=    3.922 closest distance to " O   HOH Z 217 " =    1.664
peak=    3.919 closest distance to " O   HOH Z 163 " =    1.483
peak=    3.916 closest distance to " O   HOH Z 128 " =    1.985
peak=    3.909 closest distance to " NE2 GLN A  11 " =    1.028
peak=    3.907 closest distance to " CB  GLU A 277 " =    3.607
peak=    3.894 closest distance to " O   HOH Z  67 " =    1.901
peak=    3.892 closest distance to " O   HOH Z 137 " =    1.816
peak=    3.880 closest distance to " O   HOH Z 203 " =    1.561
peak=    3.878 closest distance to " CB  ARG A 275 " =    0.859
peak=    3.862 closest distance to " O   HOH Z 327 " =    1.683
peak=    3.855 closest distance to " O   HOH Z  54 " =    1.574
peak=    3.855 closest distance to " O   HOH Z 406 " =    1.730
peak=    3.843 closest distance to " O   HOH Z  15 " =    2.203
peak=    3.840 closest distance to " NZ  LYS A 117 " =    3.105
peak=    3.832 closest distance to " O   HOH Z 295 " =    1.615
peak=    3.831 closest distance to " O   HOH Z 149 " =    2.255
peak=    3.828 closest distance to " O   HOH Z 227 " =    1.523
peak=    3.825 closest distance to " O   HOH Z  48 " =    2.664
peak=    3.812 closest distance to " O   HOH Z 345 " =    2.868
peak=    3.811 closest distance to " OD2 ASP A 286 " =    2.753
peak=    3.810 closest distance to " OE1 GLU A   2 " =    2.132
peak=    3.804 closest distance to " O   HOH Z 344 " =    2.599
peak=    3.800 closest distance to " O   HOH Z 280 " =    1.596
peak=    3.789 closest distance to " O   HOH Z 365 " =    2.314
peak=    3.781 closest distance to " O   HOH Z 369 " =    2.101
peak=    3.779 closest distance to " O   HOH Z  85 " =    1.554
peak=    3.768 closest distance to " O   HOH Z 133 " =    1.882
peak=    3.765 closest distance to " O   HOH Z 236 " =    1.642
peak=    3.765 closest distance to " CA  ASP A 191 " =    0.951
peak=    3.764 closest distance to " CB  ALA A 100 " =    1.312
peak=    3.760 closest distance to " O   MET A 105 " =    1.818
peak=    3.751 closest distance to " CB  ARG A 275 " =    1.219
peak=    3.741 closest distance to " CB  VAL A 265 " =    1.219
peak=    3.739 closest distance to " CB  ASN A 148 " =    1.185
peak=    3.736 closest distance to " O   HOH Z 118 " =    1.367
peak=    3.722 closest distance to " O   HOH Z 344 " =    1.921
peak=    3.722 closest distance to " CG1 ILE A  33 " =    1.255
peak=    3.717 closest distance to " O   HOH Z  47 " =    1.539
peak=    3.710 closest distance to " O   HOH Z  97 " =    2.385
peak=    3.701 closest distance to " O   HOH Z 194 " =    1.882
peak=    3.697 closest distance to " OE1 GLN A  58 " =    5.900
peak=    3.693 closest distance to " OD1 ASN A  69 " =    2.433
peak=    3.692 closest distance to " O   GLY A  91 " =    1.384
peak=    3.685 closest distance to " O   HOH Z 138 " =    1.515
peak=    3.685 closest distance to " O   HOH Z 102 " =    1.264
peak=    3.683 closest distance to " O   HOH Z 298 " =    1.981
peak=    3.681 closest distance to " O   HOH Z 112 " =    1.543
peak=    3.679 closest distance to " O   HOH Z  61 " =    1.574
peak=    3.679 closest distance to " CB  GLU A 128 " =    1.154
peak=    3.674 closest distance to " O   HOH Z 276 " =    1.451
peak=    3.670 closest distance to " O   HOH Z 114 " =    1.238
peak=    3.656 closest distance to " O   HOH Z 236 " =    1.738
peak=    3.656 closest distance to " O   HOH Z 261 " =    1.761
peak=    3.642 closest distance to " CB  ALA A 256 " =    1.062
peak=    3.641 closest distance to " O   HOH Z 284 " =    1.331
peak=    3.631 closest distance to " O   HOH Z  88 " =    3.300
peak=    3.628 closest distance to " OG BSER A 164 " =    2.225
peak=    3.618 closest distance to " CB  SER A  62 " =    1.251
peak=    3.605 closest distance to " NH2BARG A 145 " =    2.213
peak=    3.604 closest distance to " CA  LYS A 117 " =    1.290
peak=    3.603 closest distance to " O   ALA A 158 " =    1.236
peak=    3.596 closest distance to " OG1 THR A 294 " =    2.258
peak=    3.596 closest distance to " CB  ILE A 199 " =    1.080
peak=    3.589 closest distance to " CB AVAL A  41 " =    1.074
peak=    3.584 closest distance to " CB  VAL A 202 " =    1.597
peak=    3.582 closest distance to " O   HOH Z 214 " =    2.281
peak=    3.582 closest distance to " O   HOH Z 374 " =    2.482
peak=    3.581 closest distance to " O   HOH Z 414 " =    1.512
peak=    3.579 closest distance to " OD1 ASN A  60 " =    1.286
peak=    3.579 closest distance to " O   HOH Z 366 " =    2.948
peak=    3.578 closest distance to " CD2 LEU A 255 " =    1.153
peak=    3.573 closest distance to " O   HOH Z 408 " =    1.584
peak=    3.573 closest distance to " CA  ARG A 195 " =    1.123
peak=    3.563 closest distance to " O   HOH Z 427 " =    2.829
peak=    3.559 closest distance to " O   HOH Z 221 " =    1.277
peak=    3.559 closest distance to " O   HOH Z 301 " =    1.809
peak=    3.553 closest distance to " NH2 ARG A 156 " =    1.123
peak=    3.552 closest distance to " O   HOH Z 174 " =    2.344
peak=    3.550 closest distance to " CA  VAL A  41 " =    0.794
peak=    3.550 closest distance to " O   HOH Z 261 " =    1.798
peak=    3.548 closest distance to " CB  VAL A 296 " =    1.018
peak=    3.535 closest distance to " CG  GLN A  58 " =    2.480
peak=    3.535 closest distance to " NH1 ARG A  14 " =    1.067
peak=    3.531 closest distance to " O   HOH Z 126 " =    1.531
peak=    3.528 closest distance to " O   HOH Z 334 " =    1.546
peak=    3.523 closest distance to " CD  LYS A 119 " =    1.603
peak=    3.522 closest distance to " O   HOH Z  63 " =    1.592
peak=    3.520 closest distance to " CD2 HIS A  81 " =    1.243
peak=    3.519 closest distance to " CA  ALA A 160 " =    0.839
peak=    3.509 closest distance to " CE  LYS A 119 " =    1.080
peak=    3.507 closest distance to " O   HOH Z 248 " =    1.728
peak=    3.502 closest distance to " O   HOH Z 152 " =    1.810
peak=    3.502 closest distance to " O   HOH Z 291 " =    1.509
peak=    3.499 closest distance to " O   GLY A 211 " =    1.330
peak=    3.495 closest distance to " CG  ARG A  66 " =    0.985
peak=    3.490 closest distance to " O   HOH Z 151 " =    1.797
peak=    3.485 closest distance to " O   HOH Z 189 " =    2.694
peak=    3.485 closest distance to " C   SER A  32 " =    1.134
peak=    3.485 closest distance to " CA  VAL A 126 " =    1.037
peak=    3.478 closest distance to " CB  ALA A   9 " =    1.496
peak=    3.475 closest distance to " CD  LYS A 166 " =    1.412
peak=    3.465 closest distance to " O   HOH Z 145 " =    2.084
peak=    3.464 closest distance to " O   HOH Z 208 " =    1.236
peak=    3.464 closest distance to " CD  ARG A 195 " =    3.412
peak=    3.461 closest distance to " CA  THR A 221 " =    0.904
peak=    3.458 closest distance to " O   HOH Z   4 " =    1.587
peak=    3.457 closest distance to " CB  SER A  26 " =    1.697
peak=    3.457 closest distance to " CB  GLN A  88 " =    1.235
peak=    3.455 closest distance to " O   HOH Z 280 " =    2.158
peak=    3.453 closest distance to " O   HOH Z 435 " =    1.896
peak=    3.451 closest distance to " CD1 LEU A 300 " =    1.063
peak=    3.442 closest distance to " O   HOH Z 422 " =    2.495
peak=    3.440 closest distance to " O   HOH Z 313 " =    1.705
peak=    3.440 closest distance to " O   HOH Z 287 " =    1.733
peak=    3.430 closest distance to " O   HOH Z  48 " =    1.872
peak=    3.429 closest distance to " O   HOH Z 419 " =    1.555
peak=    3.429 closest distance to " O   HOH Z 120 " =    1.684
peak=    3.426 closest distance to " N   ASN A  39 " =    1.245
peak=    3.421 closest distance to " O   HOH Z  21 " =    1.905
peak=    3.414 closest distance to " O   HOH Z 273 " =    2.560
peak=    3.414 closest distance to " O   HOH Z 383 " =    1.799
peak=    3.413 closest distance to " CD  ARG A 159 " =    0.781
peak=    3.409 closest distance to " CD  PRO A  54 " =    1.042
peak=    3.408 closest distance to " CZ AARG A 102 " =    1.800
peak=    3.407 closest distance to " O   HOH Z 402 " =    2.785
peak=    3.406 closest distance to " CB  ARG A 190 " =    1.684
peak=    3.404 closest distance to " O   HOH Z  63 " =    2.456
peak=    3.393 closest distance to " O   HOH Z 425 " =    1.420
peak=    3.378 closest distance to " O   ARG A 102 " =    2.333
peak=    3.371 closest distance to " O   HOH Z 155 " =    2.450
peak=    3.363 closest distance to " ND1 HIS A  81 " =    1.408
peak=    3.357 closest distance to " O   HOH Z 279 " =    2.177
peak=    3.355 closest distance to " O   HOH Z 217 " =    2.170
peak=    3.355 closest distance to " O   HOH Z 214 " =    0.940
peak=    3.353 closest distance to " CB  ALA A  71 " =    1.213
peak=    3.353 closest distance to " CD2 TYR A 186 " =    1.044
peak=    3.348 closest distance to " CA  ALA A 295 " =    1.082
peak=    3.338 closest distance to " O   HOH Z  71 " =    1.781
peak=    3.335 closest distance to " O   HOH Z  13 " =    1.262
peak=    3.334 closest distance to " CG  PRO A 243 " =    1.243
peak=    3.330 closest distance to " O   HOH Z 175 " =    3.556
peak=    3.330 closest distance to " O   HOH Z 411 " =    1.726
peak=    3.330 closest distance to " CG1 VAL A 153 " =    1.028
peak=    3.329 closest distance to " O   HOH Z  63 " =    1.932
peak=    3.328 closest distance to " O   HOH Z 109 " =    2.421
peak=    3.324 closest distance to " O   HOH Z 345 " =    1.793
peak=    3.321 closest distance to " O   ASN A 217 " =    1.359
peak=    3.317 closest distance to " CD1 ILE A  33 " =    1.603
peak=    3.316 closest distance to " O   HOH Z 209 " =    2.556
peak=    3.316 closest distance to " O   SER A  26 " =    1.645
peak=    3.315 closest distance to " O   GLY A  57 " =    2.425
peak=    3.314 closest distance to " O   HOH Z 368 " =    3.069
peak=    3.310 closest distance to " CA  GLY A 211 " =    1.137
peak=    3.307 closest distance to " O   HOH Z  90 " =    3.281
peak=    3.307 closest distance to " O   HOH Z 219 " =    1.876
peak=    3.305 closest distance to " O   HOH Z 171 " =    2.849
peak=    3.300 closest distance to " O   HOH Z 303 " =    2.126
peak=    3.297 closest distance to " CA  ALA A 158 " =    1.093
peak=    3.292 closest distance to " O   PHE A 155 " =    1.855
peak=    3.292 closest distance to " O   HOH Z 352 " =    1.236
peak=    3.290 closest distance to " O   HOH Z 166 " =    1.597
peak=    3.290 closest distance to " O   HOH Z  54 " =    2.450
peak=    3.288 closest distance to " CG2 THR A  42 " =    0.833
peak=    3.280 closest distance to " O   HOH Z 128 " =    1.696
peak=    3.280 closest distance to " CD2 LEU A 297 " =    0.931
peak=    3.279 closest distance to " CA  LEU A 282 " =    1.213
peak=    3.275 closest distance to " OD1 ASP A 238 " =    0.895
peak=    3.275 closest distance to " CG2 ILE A 120 " =    1.318
peak=    3.273 closest distance to " CG  GLN A  55 " =    2.230
peak=    3.270 closest distance to " O   HOH Z 263 " =    1.899
peak=    3.269 closest distance to " CB  ARG A 102 " =    0.815
peak=    3.266 closest distance to " CA  GLY A  80 " =    1.126
peak=    3.263 closest distance to " NZ  LYS A 166 " =    2.962
peak=    3.262 closest distance to " O   HOH Z 329 " =    3.177
peak=    3.259 closest distance to " O   GLY A  23 " =    2.329
peak=    3.251 closest distance to " C   ALA A 299 " =    0.951
peak=    3.249 closest distance to " CB  ARG A 139 " =    0.981
peak=    3.249 closest distance to " O   HOH Z 277 " =    2.324
peak=    3.247 closest distance to " CB  PRO A 198 " =    1.013
peak=    3.246 closest distance to " CA  LEU A  83 " =    1.387
peak=    3.244 closest distance to " O   HOH Z 211 " =    2.325
peak=    3.244 closest distance to " O   HOH Z 292 " =    2.692
peak=    3.244 closest distance to " OD2 ASP A 298 " =    3.975
peak=    3.244 closest distance to " O   HOH Z 364 " =    2.206
peak=    3.243 closest distance to " O   HOH Z 332 " =    1.588
peak=    3.243 closest distance to " CH2 TRP A 274 " =    2.117
peak=    3.242 closest distance to " CB  SER A 273 " =    0.813
peak=    3.239 closest distance to " O   HOH Z 130 " =    2.294
peak=    3.237 closest distance to " CB  ASN A  39 " =    0.883
peak=    3.236 closest distance to " CB  THR A  31 " =    1.620
peak=    3.235 closest distance to " CG  MET A 188 " =    1.428
peak=    3.234 closest distance to " O   HOH Z 132 " =    3.015
peak=    3.228 closest distance to " CA  ASN A  74 " =    1.224
peak=    3.225 closest distance to " ND2 ASN A 187 " =    1.644
peak=    3.223 closest distance to " CZ3 TRP A  92 " =    0.977
peak=    3.222 closest distance to " NH1 ARG A 269 " =    0.851
peak=    3.216 closest distance to " O   HOH Z 266 " =    1.476
peak=    3.211 closest distance to " CB  ALA A 291 " =    1.248
peak=    3.211 closest distance to " C   ALA A   1 " =    1.648
peak=    3.207 closest distance to " O   HOH Z 126 " =    2.136
peak=    3.207 closest distance to " O   HOH Z  19 " =    2.058
peak=    3.206 closest distance to " CD2 TRP A 179 " =    1.335
peak=    3.206 closest distance to " O   HOH Z 395 " =    1.377
peak=    3.204 closest distance to " CA  LEU A 101 " =    1.568
peak=    3.204 closest distance to " CG  ARG A 219 " =    1.183
peak=    3.202 closest distance to " NH1BARG A 190 " =    2.145
peak=    3.202 closest distance to " O   HOH Z 421 " =    1.553
peak=    3.199 closest distance to " CG  GLN A  88 " =    1.044
peak=    3.193 closest distance to " O   HOH Z 156 " =    2.422
peak=    3.193 closest distance to " O   HOH Z  96 " =    2.033
peak=    3.184 closest distance to " O   HOH Z 250 " =    1.336
peak=    3.181 closest distance to " N   GLY A 241 " =    1.642
peak=    3.180 closest distance to " O   HOH Z  13 " =    2.091
peak=    3.176 closest distance to " O   HOH Z 284 " =    1.669
peak=    3.171 closest distance to " O   GLN A 278 " =    1.426
peak=    3.171 closest distance to " O   HOH Z 139 " =    5.230
peak=    3.168 closest distance to " CB  ALA A   1 " =    1.358
peak=    3.165 closest distance to " NE1 TRP A 274 " =    0.885
peak=    3.164 closest distance to " O   SER A 164 " =    1.128
peak=    3.163 closest distance to " O   HOH Z  50 " =    2.059
peak=    3.163 closest distance to " CG2 THR A 220 " =    0.748
peak=    3.154 closest distance to " CA  THR A 264 " =    0.874
peak=    3.152 closest distance to " CA  ASP A 140 " =    1.282
peak=    3.146 closest distance to " O   HOH Z 197 " =    2.216
peak=    3.144 closest distance to " NE AARG A 275 " =    1.262
peak=    3.141 closest distance to " O   HOH Z 336 " =    3.790
peak=    3.141 closest distance to " O   HOH Z  59 " =    2.062
peak=    3.140 closest distance to " CB  GLN A  89 " =    1.121
peak=    3.138 closest distance to " O   HOH Z   9 " =    2.340
peak=    3.135 closest distance to " CE1 TYR A 186 " =    1.177
peak=    3.132 closest distance to " CG1BVAL A 121 " =    1.237
peak=    3.132 closest distance to " OG  SER A  97 " =    2.490
peak=    3.122 closest distance to " CB  MET A  47 " =    1.552
peak=    3.120 closest distance to " CG2 THR A 251 " =    1.087
peak=    3.115 closest distance to " CD2 LEU A  83 " =    1.589
peak=    3.112 closest distance to " NZ  LYS A 117 " =    1.181
peak=    3.111 closest distance to " O   HOH Z 143 " =    1.101
peak=    3.105 closest distance to " CB  TRP A 266 " =    1.072
peak=    3.103 closest distance to " CD1 TRP A 266 " =    1.210
peak=    3.102 closest distance to " O   TRP A 274 " =    1.817
peak=    3.102 closest distance to " O   HOH Z  63 " =    1.805
peak=    3.095 closest distance to " O   HOH Z 197 " =    2.357
peak=    3.093 closest distance to " CB  TYR A  30 " =    1.529
peak=    3.089 closest distance to " CG  MET A  93 " =    1.101
peak=    3.086 closest distance to " O   HOH Z 147 " =    1.734
peak=    3.083 closest distance to " O   HOH Z 150 " =    3.223
peak=    3.082 closest distance to " CB  ARG A 259 " =    1.875
peak=    3.081 closest distance to " O   HOH Z 116 " =    1.631
peak=    3.081 closest distance to " O   THR A  31 " =    1.531
peak=    3.063 closest distance to " NH1BARG A 145 " =    1.141
peak=    3.047 closest distance to " CB  VAL A 296 " =    1.531
peak=    3.044 closest distance to " O   HOH Z  10 " =    1.800
peak=    3.044 closest distance to " CB  GLN A  58 " =    0.770
peak=    3.041 closest distance to " CA  ASN A 176 " =    1.008
peak=    3.038 closest distance to " CD1 LEU A 228 " =    1.389
peak=    3.007 closest distance to " CB  PRO A  54 " =    1.263

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.780 - 5.020
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 205
   mapped sites are within: 0.780 - 5.020

peak=   -5.108 closest distance to " CG2 VAL A 230 " =    0.857
peak=   -4.724 closest distance to " O   HOH Z  13 " =    1.246
peak=   -4.532 closest distance to " CA  SER A 164 " =    2.076
peak=   -4.259 closest distance to " O   VAL A  67 " =    2.725
peak=   -4.230 closest distance to " OG ASER A 134 " =    1.221
peak=   -4.188 closest distance to " CD1 PHE A  59 " =    1.862
peak=   -4.176 closest distance to " CG2 THR A   4 " =    1.792
peak=   -4.175 closest distance to " CD  ARG A 156 " =    2.000
peak=   -4.131 closest distance to " O   HOH Z 210 " =    0.780
peak=   -4.067 closest distance to " O   HOH Z 166 " =    1.770
peak=   -4.036 closest distance to " CH2 TRP A 179 " =    1.308
peak=   -4.018 closest distance to " O   HOH Z 266 " =    4.182
peak=   -4.012 closest distance to " OXT GLY A 302 " =    2.774
peak=   -3.995 closest distance to " O   HOH Z  92 " =    1.261
peak=   -3.967 closest distance to " CD1 LEU A 101 " =    2.586
peak=   -3.955 closest distance to " N   ALA A 226 " =    1.970
peak=   -3.955 closest distance to " CB  CYS A 254 " =    2.580
peak=   -3.953 closest distance to " O   HOH Z  97 " =    1.254
peak=   -3.949 closest distance to " SG  CYS A 254 " =    3.236
peak=   -3.926 closest distance to " O   HOH Z 266 " =    4.374
peak=   -3.907 closest distance to " O   HOH Z 407 " =    3.104
peak=   -3.883 closest distance to " CD  LYS A 289 " =    2.534
peak=   -3.844 closest distance to " O   HOH Z 126 " =    1.864
peak=   -3.836 closest distance to " C   ALA A 158 " =    1.209
peak=   -3.834 closest distance to " CD2 LEU A 300 " =    2.771
peak=   -3.830 closest distance to " CE2 TYR A  30 " =    2.754
peak=   -3.821 closest distance to " O   ASN A 187 " =    1.473
peak=   -3.815 closest distance to " OG BSER A 134 " =    1.724
peak=   -3.814 closest distance to " O   HOH Z 221 " =    1.157
peak=   -3.812 closest distance to " N   SER A 276 " =    1.426
peak=   -3.802 closest distance to " CD2 LEU A 237 " =    2.597
peak=   -3.794 closest distance to " CB  ALA A 161 " =    2.576
peak=   -3.790 closest distance to " O   HOH Z  11 " =    1.542
peak=   -3.785 closest distance to " O   LEU A 228 " =    2.346
peak=   -3.747 closest distance to " CZ  TYR A 169 " =    1.853
peak=   -3.747 closest distance to " O   HOH Z 292 " =    4.443
peak=   -3.736 closest distance to " O   HOH Z 208 " =    1.019
peak=   -3.703 closest distance to " NH2 ARG A  66 " =    1.396
peak=   -3.694 closest distance to " O   HOH Z 423 " =    2.309
peak=   -3.663 closest distance to " CG  ASP A 231 " =    0.857
peak=   -3.662 closest distance to " O   HOH Z 151 " =    1.471
peak=   -3.649 closest distance to " O   HOH Z 292 " =    2.630
peak=   -3.648 closest distance to " CD1 LEU A 101 " =    2.797
peak=   -3.642 closest distance to " O   VAL A  67 " =    2.559
peak=   -3.642 closest distance to " O   HOH Z  71 " =    1.151
peak=   -3.637 closest distance to " O   HOH Z 290 " =    0.922
peak=   -3.627 closest distance to " O   ALA A 161 " =    1.389
peak=   -3.625 closest distance to " N   GLN A  58 " =    1.742
peak=   -3.615 closest distance to " CG  LYS A 193 " =    2.283
peak=   -3.613 closest distance to " OG  SER A  97 " =    2.255
peak=   -3.610 closest distance to " O   HOH Z 103 " =    1.885
peak=   -3.577 closest distance to " O   HOH Z 377 " =    1.079
peak=   -3.576 closest distance to " CD1 LEU A 255 " =    2.574
peak=   -3.576 closest distance to " OG  SER A  62 " =    1.434
peak=   -3.562 closest distance to " CG2 VAL A 112 " =    2.507
peak=   -3.560 closest distance to " O   HOH Z 150 " =    1.236
peak=   -3.554 closest distance to " N   THR A 235 " =    1.310
peak=   -3.550 closest distance to " O   HOH Z 136 " =    2.001
peak=   -3.539 closest distance to " CG  ASP A  50 " =    2.270
peak=   -3.537 closest distance to " O   HOH Z 231 " =    1.993
peak=   -3.536 closest distance to " ND2 ASN A 187 " =    1.773
peak=   -3.533 closest distance to " OE2 GLU A   2 " =    1.764
peak=   -3.528 closest distance to " CB  TYR A  15 " =    2.220
peak=   -3.527 closest distance to " O   ALA A 161 " =    2.709
peak=   -3.524 closest distance to " O   HOH Z  52 " =    1.940
peak=   -3.522 closest distance to " C   HIS A 108 " =    1.221
peak=   -3.516 closest distance to " ND2 ASN A  45 " =    1.096
peak=   -3.513 closest distance to " ND2 ASN A  60 " =    1.437
peak=   -3.506 closest distance to " CG  MET A 105 " =    0.864
peak=   -3.503 closest distance to " O   HOH Z  10 " =    1.397
peak=   -3.502 closest distance to " O   HOH Z 426 " =    2.252
peak=   -3.493 closest distance to " O   HOH Z 166 " =    2.134
peak=   -3.489 closest distance to " NH2AARG A 275 " =    5.020
peak=   -3.477 closest distance to " OG BSER A 134 " =    1.334
peak=   -3.477 closest distance to " N   ALA A 248 " =    1.774
peak=   -3.476 closest distance to " C   ASN A 285 " =    2.249
peak=   -3.473 closest distance to " O   ASP A 191 " =    1.370
peak=   -3.472 closest distance to " O   HOH Z  48 " =    1.193
peak=   -3.469 closest distance to " OD1 ASP A 191 " =    1.643
peak=   -3.467 closest distance to " O   HOH Z  37 " =    1.277
peak=   -3.466 closest distance to " O   PRO A 198 " =    1.372
peak=   -3.462 closest distance to " CE3 TRP A 150 " =    2.170
peak=   -3.461 closest distance to " O   ALA A  51 " =    1.468
peak=   -3.457 closest distance to " O   HOH Z 426 " =    1.809
peak=   -3.449 closest distance to " O   ALA A   1 " =    1.877
peak=   -3.447 closest distance to " CB  ALA A 248 " =    1.912
peak=   -3.446 closest distance to " O   HOH Z 313 " =    1.248
peak=   -3.446 closest distance to " CB  ALA A 227 " =    2.273
peak=   -3.436 closest distance to " O   HOH Z 138 " =    0.941
peak=   -3.429 closest distance to " O   GLY A 196 " =    0.954
peak=   -3.426 closest distance to " O   TRP A  92 " =    1.938
peak=   -3.413 closest distance to " CB  ALA A 248 " =    2.315
peak=   -3.410 closest distance to " CD  GLN A  88 " =    0.841
peak=   -3.406 closest distance to " O   HOH Z 234 " =    4.308
peak=   -3.404 closest distance to " O   HOH Z 165 " =    2.214
peak=   -3.398 closest distance to " CA  GLY A 133 " =    1.866
peak=   -3.395 closest distance to " O   HOH Z 250 " =    1.344
peak=   -3.394 closest distance to " CG2 THR A 182 " =    2.284
peak=   -3.394 closest distance to " CB  SER A 245 " =    2.419
peak=   -3.390 closest distance to " O   HOH Z  17 " =    1.293
peak=   -3.387 closest distance to " O   HOH Z  98 " =    1.567
peak=   -3.382 closest distance to " O   SER A 273 " =    1.373
peak=   -3.381 closest distance to " CD  ARG A 139 " =    1.605
peak=   -3.380 closest distance to " CD  GLN A  88 " =    2.322
peak=   -3.377 closest distance to " O   HOH Z 310 " =    1.533
peak=   -3.376 closest distance to " O   HOH Z 345 " =    2.163
peak=   -3.371 closest distance to " C   GLY A  91 " =    1.388
peak=   -3.370 closest distance to " NH2 ARG A  79 " =    1.854
peak=   -3.366 closest distance to " CG  TRP A 266 " =    1.685
peak=   -3.363 closest distance to " O   HOH Z 427 " =    1.368
peak=   -3.358 closest distance to " O   HOH Z 138 " =    1.350
peak=   -3.357 closest distance to " O   HOH Z 275 " =    1.424
peak=   -3.356 closest distance to " OD1 ASP A 200 " =    1.139
peak=   -3.354 closest distance to " O   MET A  40 " =    2.698
peak=   -3.353 closest distance to " O   HOH Z 435 " =    2.503
peak=   -3.349 closest distance to " O   HOH Z 198 " =    2.157
peak=   -3.345 closest distance to " N   THR A 157 " =    1.595
peak=   -3.343 closest distance to " CB  ALA A  51 " =    1.813
peak=   -3.342 closest distance to " O   HOH Z 396 " =    1.629
peak=   -3.337 closest distance to " O   HOH Z 193 " =    1.583
peak=   -3.337 closest distance to " CG  GLU A  53 " =    1.555
peak=   -3.332 closest distance to " O   HOH Z  93 " =    1.200
peak=   -3.320 closest distance to " O   HOH Z 145 " =    1.689
peak=   -3.320 closest distance to " CD1 TRP A 179 " =    1.202
peak=   -3.317 closest distance to " CB  ALA A 100 " =    1.806
peak=   -3.315 closest distance to " CG2 VAL A 189 " =    1.952
peak=   -3.311 closest distance to " OD1 ASN A 148 " =    1.693
peak=   -3.309 closest distance to " OG BSER A 210 " =    1.355
peak=   -3.308 closest distance to " CG1 VAL A  78 " =    2.562
peak=   -3.307 closest distance to " OXT GLY A 302 " =    3.602
peak=   -3.300 closest distance to " CD2 LEU A 167 " =    1.750
peak=   -3.299 closest distance to " CG  GLN A  58 " =    1.235
peak=   -3.296 closest distance to " CA  ASP A  27 " =    2.435
peak=   -3.292 closest distance to " CA  GLY A 203 " =    2.102
peak=   -3.292 closest distance to " CG1 VAL A 112 " =    2.464
peak=   -3.283 closest distance to " OE1 GLN A 223 " =    2.410
peak=   -3.281 closest distance to " CE1 HIS A  81 " =    1.263
peak=   -3.274 closest distance to " O   PHE A 218 " =    1.529
peak=   -3.271 closest distance to " CA  LEU A 222 " =    2.522
peak=   -3.270 closest distance to " O   VAL A 197 " =    1.256
peak=   -3.266 closest distance to " O   HOH Z 311 " =    3.500
peak=   -3.263 closest distance to " O   HOH Z 377 " =    2.095
peak=   -3.260 closest distance to " C   GLY A 133 " =    1.301
peak=   -3.254 closest distance to " CE BMET A  47 " =    1.567
peak=   -3.251 closest distance to " O   HOH Z  60 " =    2.413
peak=   -3.249 closest distance to " OD1 ASP A 171 " =    1.723
peak=   -3.240 closest distance to " CA  ASP A 298 " =    1.088
peak=   -3.236 closest distance to " O  BHOH Z 338 " =    1.542
peak=   -3.235 closest distance to " CD1 LEU A 228 " =    2.363
peak=   -3.234 closest distance to " O   HOH Z 130 " =    2.317
peak=   -3.234 closest distance to " CD2 TYR A 293 " =    2.199
peak=   -3.219 closest distance to " O   HOH Z 120 " =    1.322
peak=   -3.218 closest distance to " OD2 ASP A 286 " =    2.474
peak=   -3.213 closest distance to " C   THR A 279 " =    1.129
peak=   -3.211 closest distance to " ND2 ASN A  39 " =    1.148
peak=   -3.210 closest distance to " O   HOH Z  70 " =    1.430
peak=   -3.208 closest distance to " O   HOH Z 265 " =    1.830
peak=   -3.208 closest distance to " O   SER A 146 " =    0.864
peak=   -3.205 closest distance to " O   HOH Z  78 " =    1.811
peak=   -3.203 closest distance to " O   ASP A 270 " =    1.862
peak=   -3.201 closest distance to " O   HOH Z 166 " =    1.392
peak=   -3.197 closest distance to " O   HOH Z 287 " =    2.088
peak=   -3.195 closest distance to " OD2 ASP A 171 " =    1.807
peak=   -3.187 closest distance to " O   HOH Z  43 " =    2.075
peak=   -3.182 closest distance to " CD2 PHE A  61 " =    1.828
peak=   -3.181 closest distance to " O   SER A 258 " =    1.947
peak=   -3.181 closest distance to " CE  MET A 105 " =    2.026
peak=   -3.175 closest distance to " CG  LYS A 119 " =    2.791
peak=   -3.173 closest distance to " CA  ARG A  66 " =    1.863
peak=   -3.172 closest distance to " O   HOH Z 163 " =    4.830
peak=   -3.171 closest distance to " OG1 THR A  82 " =    1.400
peak=   -3.170 closest distance to " O   HOH Z  38 " =    1.630
peak=   -3.166 closest distance to " CB  SER A 146 " =    2.159
peak=   -3.166 closest distance to " CB  PHE A 208 " =    2.243
peak=   -3.165 closest distance to " CD1 ILE A 151 " =    2.281
peak=   -3.158 closest distance to " O   ALA A   8 " =    1.831
peak=   -3.153 closest distance to " C   LEU A 143 " =    1.306
peak=   -3.149 closest distance to " OG1 THR A 178 " =    1.216
peak=   -3.145 closest distance to " CD1 LEU A  96 " =    2.498
peak=   -3.144 closest distance to " CG2 THR A 251 " =    1.844
peak=   -3.143 closest distance to " O   HOH Z 366 " =    1.407
peak=   -3.141 closest distance to " O   HOH Z  40 " =    3.642
peak=   -3.135 closest distance to " O   HOH Z 350 " =    1.779
peak=   -3.132 closest distance to " O   HOH Z 171 " =    2.195
peak=   -3.130 closest distance to " O   CYS A 260 " =    0.946
peak=   -3.129 closest distance to " C   LEU A 101 " =    0.918
peak=   -3.124 closest distance to " O   ARG A 275 " =    2.189
peak=   -3.120 closest distance to " CZ  TYR A  68 " =    1.201
peak=   -3.115 closest distance to " O   HOH Z 185 " =    2.134
peak=   -3.113 closest distance to " C   PRO A 163 " =    1.167
peak=   -3.105 closest distance to " O   HOH Z 297 " =    2.907
peak=   -3.097 closest distance to " CE2 PHE A  59 " =    1.874
peak=   -3.095 closest distance to " O   SER A 271 " =    2.173
peak=   -3.093 closest distance to " CG  ARG A 269 " =    2.235
peak=   -3.088 closest distance to " OG  SER A  32 " =    1.185
peak=   -3.086 closest distance to " O   HOH Z 313 " =    1.736
peak=   -3.083 closest distance to " CG  GLU A 152 " =    2.349
peak=   -3.081 closest distance to " CD2 LEU A 237 " =    2.959
peak=   -3.075 closest distance to " CB  PRO A 163 " =    2.446
peak=   -3.049 closest distance to " O   HOH Z 377 " =    1.724
peak=   -3.036 closest distance to " O   HOH Z 135 " =    1.566
peak=   -3.021 closest distance to " N   ALA A 248 " =    1.848
peak=   -3.017 closest distance to " O   HOH Z 166 " =    1.104
peak=   -3.010 closest distance to " C   LEU A 255 " =    1.621

================= 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    :  0.4930 0.4957   6.294589e+00   6.287271e+00
   1_bss:  0.4861 0.4861   6.292489e+00   6.278720e+00
   1_xyz:  0.4241 0.4400   6.213350e+00   6.240737e+00
   1_adp:  0.3831 0.4286   6.160959e+00   6.229848e+00
   1_occ:  0.3824 0.4282   6.160226e+00   6.229318e+00
   2_bss:  0.3813 0.4259   6.161166e+00   6.227411e+00
   2_xyz:  0.2969 0.3584   5.971408e+00   6.106006e+00
   2_adp:  0.2711 0.3347   5.900360e+00   6.053458e+00
   2_occ:  0.2707 0.3347   5.899792e+00   6.053257e+00
   3_bss:  0.2670 0.3303   5.896409e+00   6.049304e+00
   3_xyz:  0.1913 0.2427   5.604499e+00   5.802937e+00
   3_adp:  0.1677 0.2196   5.491625e+00   5.701578e+00
   3_occ:  0.1674 0.2194   5.491020e+00   5.701401e+00
   4_bss:  0.1669 0.2189   5.489561e+00   5.700256e+00
   4_xyz:  0.1421 0.1909   5.346696e+00   5.565569e+00
   4_adp:  0.1357 0.1841   5.309913e+00   5.530799e+00
   4_occ:  0.1355 0.1841   5.309444e+00   5.530495e+00
   5_bss:  0.1357 0.1847   5.311695e+00   5.533581e+00
   5_xyz:  0.1212 0.1686   5.220498e+00   5.456057e+00
   5_adp:  0.1191 0.1667   5.208522e+00   5.445799e+00
   5_occ:  0.1190 0.1666   5.208250e+00   5.446051e+00
   5_bss:  0.1190 0.1666   5.208314e+00   5.446185e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.350  20.001   5.576   9.093   7.970   0.000   0.000   0.000
   1_xyz:  0.350  20.001   5.576   9.093   7.970   0.000   0.000   0.000
   1_adp:  0.350  20.001   5.576   9.093   7.970   0.000   0.000   0.000
   1_occ:  0.350  20.001   5.576   9.093   7.970   0.000   0.000   0.000
   2_bss:  0.329  34.185   2.828   6.160   5.680   0.000   0.000   0.000
   2_xyz:  0.329  34.185   2.828   6.160   5.680   0.000   0.000   0.000
   2_adp:  0.329  34.185   2.828   6.160   5.680   0.000   0.000   0.000
   2_occ:  0.329  34.185   2.828   6.160   5.680   0.000   0.000   0.000
   3_bss:  0.314  34.185   1.122   2.913   2.699   0.000   0.000   0.000
   3_xyz:  0.314  34.185   1.122   2.913   2.699   0.000   0.000   0.000
   3_adp:  0.314  34.185   1.122   2.913   2.699   0.000   0.000   0.000
   3_occ:  0.314  34.185   1.122   2.913   2.699   0.000   0.000   0.000
   4_bss:  0.315  39.158   0.216   1.636   1.349   0.000   0.000   0.000
   4_xyz:  0.315  39.158   0.216   1.636   1.349   0.000   0.000   0.000
   4_adp:  0.315  39.158   0.216   1.636   1.349   0.000   0.000   0.000
   4_occ:  0.315  39.158   0.216   1.636   1.349   0.000   0.000   0.000
   5_bss:  0.315  39.158   0.156   1.316   1.035   0.000   0.000   0.000
   5_xyz:  0.315  39.158   0.156   1.316   1.035   0.000   0.000   0.000
   5_adp:  0.315  39.158   0.156   1.316   1.035   0.000   0.000   0.000
   5_occ:  0.315  39.158   0.156   1.316   1.035   0.000   0.000   0.000
   5_bss:  0.320  42.287  -0.624   0.415   0.209   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  62.620 0.3592  0.4249    77114.565
   1_bss:  62.176 0.3627  0.5244    73697.991
   1_xyz:  55.510 0.4476  0.6388    60577.790
   1_adp:  53.094 0.4787  0.7403    57399.571
   1_occ:  52.964 0.4804  0.7423    57258.289
   2_bss:  52.728 0.4833  0.6862    56912.233
   2_xyz:  39.180 0.6516  0.9290    36252.112
   2_adp:  35.675 0.6931  0.9840    30931.221
   2_occ:  35.669 0.6931  0.9833    30914.737
   3_bss:  35.349 0.6966  0.8986    30356.736
   3_xyz:  24.702 0.8137  0.9916    15709.606
   3_adp:  21.451 0.8475  1.0053    12655.197
   3_occ:  21.457 0.8474  1.0052    12659.342
   4_bss:  21.373 0.8482  0.9640    12582.858
   4_xyz:  18.121 0.8789  0.9825     9307.311
   4_adp:  17.225 0.8875  0.9842     8664.348
   4_occ:  17.216 0.8876  0.9842     8659.099
   5_bss:  17.285 0.8871  0.9755     8748.413
   5_xyz:  15.717 0.9005  0.9808     7433.367
   5_adp:  15.428 0.9032  0.9777     7289.446
   5_occ:  15.428 0.9032  0.9775     7293.797
   5_bss:  15.428 0.9032  0.9786     7300.704
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3308e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3308e+01
   1_xyz:   1.747  0.014  0.109 18.326  0.007  4.108   1.5043e-01
   1_adp:   1.747  0.014  0.109 18.326  0.007  4.108   1.5043e-01
   1_occ:   1.747  0.014  0.109 18.326  0.007  4.108   1.5043e-01
   2_bss:   1.747  0.014  0.109 18.326  0.007  4.108   1.5043e-01
   2_xyz:   1.390  0.011  0.091 17.201  0.006  4.114   1.1643e-01
   2_adp:   1.390  0.011  0.091 17.201  0.006  4.114   1.1643e-01
   2_occ:   1.390  0.011  0.091 17.201  0.006  4.114   1.1643e-01
   3_bss:   1.390  0.011  0.091 17.201  0.006  4.114   1.1643e-01
   3_xyz:   1.161  0.009  0.081 15.755  0.004  4.115   8.3461e-02
   3_adp:   1.161  0.009  0.081 15.755  0.004  4.115   8.3461e-02
   3_occ:   1.161  0.009  0.081 15.755  0.004  4.115   8.3461e-02
   4_bss:   1.161  0.009  0.081 15.755  0.004  4.115   8.3461e-02
   4_xyz:   0.940  0.006  0.070 15.201  0.003  4.120   5.5903e-02
   4_adp:   0.940  0.006  0.070 15.201  0.003  4.120   5.5903e-02
   4_occ:   0.940  0.006  0.070 15.201  0.003  4.120   5.5903e-02
   5_bss:   0.940  0.006  0.070 15.201  0.003  4.120   5.5903e-02
   5_xyz:   1.094  0.007  0.081 15.503  0.004  4.122   6.8039e-02
   5_adp:   1.094  0.007  0.081 15.503  0.004  4.122   6.8039e-02
   5_occ:   1.094  0.007  0.081 15.503  0.004  4.122   6.8039e-02
   5_bss:   1.094  0.007  0.081 15.503  0.004  4.122   6.8039e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.997   6.9073e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.997   6.9073e+00
   1_xyz:  15.267  0.172  0.499 87.223  0.057  2.185   1.0206e-01
   1_adp:  15.267  0.172  0.499 87.223  0.057  2.185   1.0206e-01
   1_occ:  15.267  0.172  0.499 87.223  0.057  2.185   1.0206e-01
   2_bss:  15.267  0.172  0.499 87.223  0.057  2.185   1.0206e-01
   2_xyz:  10.409  0.153  0.317 85.476  0.056  2.066   9.8518e-02
   2_adp:  10.409  0.153  0.317 85.476  0.056  2.066   9.8518e-02
   2_occ:  10.409  0.153  0.317 85.476  0.056  2.066   9.8518e-02
   3_bss:  10.409  0.153  0.317 85.476  0.056  2.066   9.8518e-02
   3_xyz:   7.071  0.065  0.418 88.256  0.024  2.203   1.6193e-01
   3_adp:   7.071  0.065  0.418 88.256  0.024  2.203   1.6193e-01
   3_occ:   7.071  0.065  0.418 88.256  0.024  2.203   1.6193e-01
   4_bss:   7.071  0.065  0.418 88.256  0.024  2.203   1.6193e-01
   4_xyz:   6.693  0.034  0.353 78.517  0.026  2.382   4.1406e-02
   4_adp:   6.693  0.034  0.353 78.517  0.026  2.382   4.1406e-02
   4_occ:   6.693  0.034  0.353 78.517  0.026  2.382   4.1406e-02
   5_bss:   6.693  0.034  0.353 78.517  0.026  2.382   4.1406e-02
   5_xyz:   7.164  0.043  0.528 82.561  0.025  2.294   4.8213e-02
   5_adp:   7.164  0.043  0.528 82.561  0.025  2.294   4.8213e-02
   5_occ:   7.164  0.043  0.528 82.561  0.025  2.294   4.8213e-02
   5_bss:   7.164  0.043  0.528 82.561  0.025  2.294   4.8213e-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:  85.87   0.00  14.67  73.29   0.00  12.59  85.87   0.00  25.95
   1_occ:  85.87   0.00  14.67  73.29   0.00  12.59  85.87   0.00  25.95
   2_bss:  85.87   0.00  14.67  73.29   0.00  12.59  85.87   0.00  25.95
   2_xyz:  85.87   0.00  14.67  73.29   0.00  12.59  85.87   0.00  25.95
   2_adp:  84.34   0.00  14.81  77.45   0.00  11.59  84.34   0.00  32.32
   2_occ:  84.34   0.00  14.81  77.45   0.00  11.59  84.34   0.00  32.32
   3_bss:  84.34   0.00  14.81  77.45   0.00  11.59  84.34   0.00  32.32
   3_xyz:  84.34   0.00  14.81  77.45   0.00  11.59  84.34   0.00  32.32
   3_adp:  78.12   0.00  14.86  78.12   0.00  10.57  76.71   3.76  38.19
   3_occ:  78.12   0.00  14.86  78.12   0.00  10.57  76.71   3.76  38.19
   4_bss:  78.12   0.00  14.86  78.12   0.00  10.57  76.71   3.76  38.19
   4_xyz:  78.12   0.00  14.86  78.12   0.00  10.57  76.71   3.76  38.19
   4_adp:  92.36   0.00  15.00  92.36   0.00  10.35  80.29   3.39  40.27
   4_occ:  92.36   0.00  15.00  92.36   0.00  10.35  80.29   3.39  40.27
   5_bss:  92.36   0.00  15.00  92.36   0.00  10.35  80.29   3.39  40.27
   5_xyz:  92.36   0.00  15.00  92.36   0.00  10.35  80.29   3.39  40.27
   5_adp:  98.45   0.00  14.62  98.45   0.00  10.11  81.35   2.41  39.18
   5_occ:  98.45   0.00  14.62  98.45   0.00  10.11  81.35   2.41  39.18
   5_bss:  99.30   0.86  15.48  99.30   0.86  10.96  82.21   3.27  40.04
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.186    0.019    0.413
   1_adp:    1.186    0.019    0.413
   1_occ:    1.186    0.019    0.413
   2_bss:    1.186    0.019    0.413
   2_xyz:    1.952    0.043    0.640
   2_adp:    1.952    0.043    0.640
   2_occ:    1.952    0.043    0.640
   3_bss:    1.952    0.043    0.640
   3_xyz:    1.686    0.035    0.751
   3_adp:    1.686    0.035    0.751
   3_occ:    1.686    0.035    0.751
   4_bss:    1.686    0.035    0.751
   4_xyz:    1.854    0.024    0.795
   4_adp:    1.854    0.024    0.795
   4_occ:    1.854    0.024    0.795
   5_bss:    1.854    0.024    0.795
   5_xyz:    1.863    0.054    0.826
   5_adp:    1.863    0.054    0.826
   5_occ:    1.863    0.054    0.826
   5_bss:    1.863    0.054    0.826
------------------------------------------------------------------------

CPU time actual refinement: 282.40


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_572/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_572/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_572/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_572/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_572/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 282.27 
  Macro-tasks:
    bulk solvent and scale       = 35.62  
    individual site refinement   = 114.85 
    weights calculation          = 26.92  
    collect and process          = 5.36   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 182.84 
  Micro-tasks:
    mask                            = 2.07   
    f_calc                          = 88.07  
    alpha_beta                      = 6.85   
    target                          = 0.96   
    gradients_wrt_atomic_parameters = 95.76  
    fmodel                         = 5.80   
    r_factors                      = 0.22   
    phase_errors                   = 8.46   
    foms                           = 0.28   
    TOTAL for micro-tasks          = 208.47 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.034 micro seconds
Total CPU time: 4.90 minutes
from_scatterers_fft:    626 calls, 87.81 s
gradients_fft:          570 calls, 84.97 s

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

# Date 2008-01-16 Time 01:52:10 PST -0800 (1200477130.79 s)
Start R-work = 0.4930, R-free = 0.4957 (no bulk solvent and anisotropic scale)
Final R-work = 0.1363, R-free = 0.1846 (no bulk solvent and anisotropic scale)

Start R-work = 0.4861, R-free = 0.4861
Final R-work = 0.1190, R-free = 0.1666