# Date 2008-01-16 Time 01:07:44 PST -0800 (1200474464.38 s)
#phil __OFF__

Command line arguments: "../288.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 = 591
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 288

-------------------------------------------------------------------------------
  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: (69.1963, 46.6953, 85.0941, 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: 2.78, per 1000 atoms: 0.98


================================== 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: (69.1963, 46.6953, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7691 1.97045
Completeness in resolution range: 0.976764
Completeness with d_max=infinity: 0.973657

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7691
                             d_min =   1.9705

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: (69.1963, 46.6953, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7691 1.97045
Completeness in resolution range: 0.976764
Completeness with d_max=infinity: 0.973657

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7695 -  4.2154 [2105/2132]  1895   210  10.0%
  bin  2:  4.2154 -  3.3588 [2025/2041]  1822   203  10.0%
  bin  3:  3.3588 -  2.9380 [1993/2012]  1792   201  10.1%
  bin  4:  2.9380 -  2.6711 [1976/2006]  1783   193   9.8%
  bin  5:  2.6711 -  2.4806 [1963/1982]  1763   200  10.2%
  bin  6:  2.4806 -  2.3350 [1957/1982]  1760   197  10.1%
  bin  7:  2.3350 -  2.2185 [1951/1985]  1763   188   9.6%
  bin  8:  2.2185 -  2.1222 [1937/1968]  1740   197  10.2%
  bin  9:  2.1222 -  2.0407 [1923/1964]  1728   195  10.1%
  bin 10:  2.0407 -  1.9705 [1759/1983]  1584   175   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_288/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: 0.11 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:
        1.38 -     2.09: 11
        2.09 -     2.79: 707
        2.79 -     3.49: 4564
        3.49 -     4.20: 9511
        4.20 -     4.90: 14003
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.385 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.657 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.734 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.795 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28791 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_288/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_288/model_refine_001.geo

CPU time processing inputs: 8.18


============================ 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 = 69.19625 46.69535 85.09415 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: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4594   r_free= 0.4487   ksol= 0.00   Bsol= 0.00   scale= 0.819    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.256192                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7695 -  4.7012 0.99   1373  153 0.3783 0.3736      6.5457      6.5599|
|  2:  4.7012 -  3.7516 0.99   1308  146 0.3752 0.3695      6.7188      6.7269|
|  3:  3.7516 -  3.2833 0.99   1294  143 0.4039 0.3826      6.6237      6.6821|
|  4:  3.2833 -  2.9858 0.99   1286  139 0.4303 0.4254      6.4928      6.4462|
|  5:  2.9858 -  2.7733 0.99   1263  142 0.4758 0.5025      6.3551      6.3371|
|  6:  2.7733 -  2.6108 0.99   1273  144 0.4898 0.5397      6.2768      6.2827|
|  7:  2.6108 -  2.4806 0.99   1258  140 0.4931 0.4681      6.2344       6.145|
|  8:  2.4806 -  2.3731 0.98   1261  141 0.5023 0.4900      6.1817      6.1881|
|  9:  2.3731 -  2.2821 0.98   1250  137 0.5161 0.4956      6.1139      6.1207|
| 10:  2.2821 -  2.2036 0.98   1248  137 0.5122 0.4989      6.1218      6.0672|
| 11:  2.2036 -  2.1349 0.99   1259  144 0.5195 0.4700      6.0476      6.0579|
| 12:  2.1349 -  2.0741 0.97   1244  132 0.5063 0.4770      5.9927      6.0013|
| 13:  2.0741 -  2.0196 0.99   1237  138 0.5343 0.5174      5.9049      5.8783|
| 14:  2.0196 -  1.9705 0.85   1076  123 0.5231 0.4970      5.8456      5.7667|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7695 -  4.7012  1373   153  0.68  35.71   0.81     0.72      74137.63|
|  2:  4.7012 -  3.7516  1308   146  0.72  33.83   0.90     0.79      97738.32|
|  3:  3.7516 -  3.2833  1294   143  0.64  40.45   0.88     0.76     101052.92|
|  4:  3.2833 -  2.9858  1286   139  0.57  45.99   0.84     0.67      88916.12|
|  5:  2.9858 -  2.7733  1263   142  0.48  53.35   0.76     0.57      75010.18|
|  6:  2.7733 -  2.6108  1273   144  0.45  55.89   0.74     0.52      66056.47|
|  7:  2.6108 -  2.4806  1258   140  0.43  57.23   0.75     0.50      60432.73|
|  8:  2.4806 -  2.3731  1261   141  0.44  56.89   0.76     0.51      53528.66|
|  9:  2.3731 -  2.2821  1250   137  0.44  56.79   0.74     0.52      47382.19|
| 10:  2.2821 -  2.2036  1248   137  0.48  54.06   0.78     0.55      40847.76|
| 11:  2.2036 -  2.1349  1259   144  0.45  56.19   0.76     0.55      39478.91|
| 12:  2.1349 -  2.0741  1244   132  0.42  58.72   0.77     0.51      38946.81|
| 13:  2.0741 -  2.0196  1237   138  0.34  64.74   0.76     0.42      36485.29|
| 14:  2.0196 -  1.9705  1076   123  0.30  67.48   0.75     0.34      30749.35|
|alpha:            min =        0.34 max =            0.79 mean =         0.57|
|beta:             min =    30749.35 max =       101052.92 mean =     61467.45|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           89.96 mean =        52.29|
|phase err.(test): min =        0.00 max =           89.93 mean =        52.54|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.398198             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.523   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.893138              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.647   (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 |  0.943 -  1.338:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.338 -  1.734:        8 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.734 -  2.130:       76 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.130 -  2.526:      475 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.526 -  2.921:     1259 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.921 -  3.317:     2431 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.317 -  3.713:     4001 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.713 -  4.108:     5344 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.108 -  4.504:     6929 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.504 -  4.900:     8295 |
|-----------------------------------------------------------------------------|
|-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 |       53.014 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.087    4.900  0.943 |       2.222 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.486)------------------------------------------|
|    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 = 11.486)------------------------------------------|
|    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: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4663   r_free= 0.4548   ksol= 0.00   Bsol= 0.00   scale= 0.786    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.259384                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4505   r_free= 0.4393   ksol= 0.36   Bsol= 7.80   scale= 1.022    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.86,8.25,8.93,0.00,0.00,0.00); trace/3= 8.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.248550                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.206700              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.764   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.858678              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.541   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4505      final r-factor (work) = 0.3574          |
| start r-factor (free) = 0.4393      final r-factor (free) = 0.3759          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 81.8406 = 9.21 * 0.50 * 6.2622 + 1.00 * 53.0136                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.3943 = 9.21 * 0.50 * 6.1393 + 1.00 * 0.1328                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3574      final r-factor (work) = 0.3030          |
| start r-factor (free) = 0.3759      final r-factor (free) = 0.3448          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2860 = 0.86 * 1.00 * 6.1393 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1729 = 0.86 * 1.00 * 6.0073 + 1.00 * 0.0146                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.486)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.56   11.85    None  None   None       |
|    all(noH): 2823   0      0.00    77.56   11.85    None  None   None       |
|    Sol.    : 438    0      0.00    67.81   27.44    None  None   None       |
|    Mac.    : 2385   0      0.00    77.56   8.99     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 -   7.756: 1341   |   5:    38.782 -  46.538:   70        |
|      1:     7.756 -  15.513:  751   |   6:    46.538 -  54.294:   27        |
|      2:    15.513 -  23.269:  324   |   7:    54.294 -  62.050:   13        |
|      3:    23.269 -  31.025:  184   |   8:    62.050 -  69.807:    4        |
|      4:    31.025 -  38.782:  108   |   9:    69.807 -  77.563:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3030 r_free = 0.3448             target_work(ml) = 5.971         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3023 r_free = 0.3447             target_work(ml) = 5.970         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3023   r_free= 0.3447   ksol= 0.36   Bsol= 7.80   scale= 1.109    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.86,8.25,8.93,0.00,0.00,0.00); trace/3= 8.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.969948                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2977   r_free= 0.3390   ksol= 0.33   Bsol= 20.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.20,4.22,5.62,0.00,0.00,0.00); trace/3= 4.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.967930                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.275200              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.990   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.392124              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.724  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2977      final r-factor (work) = 0.1984          |
| start r-factor (free) = 0.3390      final r-factor (free) = 0.2432          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.9754 = 5.28 * 0.50 * 6.0064 + 1.00 * 0.1328                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.3655 = 5.28 * 0.50 * 5.7980 + 1.00 * 0.0727                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1984      final r-factor (work) = 0.1736          |
| start r-factor (free) = 0.2432      final r-factor (free) = 0.2171          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2975 = 0.39 * 1.00 * 5.7980 + 1.00 * 0.0239                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2184 = 0.39 * 1.00 * 5.5564 + 1.00 * 0.0396                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.486)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.42   12.03    None  None   None       |
|    all(noH): 2823   0      0.00    80.42   12.03    None  None   None       |
|    Sol.    : 438    0      1.65    67.82   32.76    None  None   None       |
|    Mac.    : 2385   0      0.00    80.42   8.22     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 -   8.042: 1593   |   5:    40.210 -  48.252:   90        |
|      1:     8.042 -  16.084:  601   |   6:    48.252 -  56.294:   48        |
|      2:    16.084 -  24.126:  194   |   7:    56.294 -  64.337:   14        |
|      3:    24.126 -  32.168:  135   |   8:    64.337 -  72.379:    8        |
|      4:    32.168 -  40.210:  138   |   9:    72.379 -  80.421:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1736 r_free = 0.2171             target_work(ml) = 5.500         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1731 r_free = 0.2165             target_work(ml) = 5.498         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1731   r_free= 0.2165   ksol= 0.33   Bsol= 20.00   scale= 1.052   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.20,4.22,5.62,0.00,0.00,0.00); trace/3= 4.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.498422                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1714   r_free= 0.2149   ksol= 0.32   Bsol= 30.51   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.51,2.94,3.95,0.00,0.00,0.00); trace/3= 3.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.494678                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.971736              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.873  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.625009              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.561   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1714      final r-factor (work) = 0.1310          |
| start r-factor (free) = 0.2149      final r-factor (free) = 0.1705          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3412 = 2.97 * 0.50 * 5.5651 + 1.00 * 0.0722                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0549 = 2.97 * 0.50 * 5.3786 + 1.00 * 0.0630                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1310      final r-factor (work) = 0.1224          |
| start r-factor (free) = 0.1705      final r-factor (free) = 0.1650          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3953 = 0.63 * 1.00 * 5.3786 + 1.00 * 0.0336                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2763 = 0.63 * 1.00 * 5.2231 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.486)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.73   12.42    None  None   None       |
|    all(noH): 2823   0      0.00    87.73   12.42    None  None   None       |
|    Sol.    : 438    0      0.64    73.64   35.96    None  None   None       |
|    Mac.    : 2385   0      0.00    87.73   8.09     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 -   8.773: 1733   |   5:    43.866 -  52.639:   90        |
|      1:     8.773 -  17.546:  542   |   6:    52.639 -  61.412:   54        |
|      2:    17.546 -  26.320:  139   |   7:    61.412 -  70.186:   23        |
|      3:    26.320 -  35.093:  113   |   8:    70.186 -  78.959:    5        |
|      4:    35.093 -  43.866:  121   |   9:    78.959 -  87.732:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1224 r_free = 0.1650             target_work(ml) = 5.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1224 r_free = 0.1649             target_work(ml) = 5.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1224   r_free= 0.1649   ksol= 0.32   Bsol= 30.51   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.51,2.94,3.95,0.00,0.00,0.00); trace/3= 3.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.202629                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1225   r_free= 0.1650   ksol= 0.32   Bsol= 30.51   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.24,2.71,3.52,0.00,0.00,0.00); trace/3= 2.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.202412                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.836837              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.314  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.266032              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.402  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1225      final r-factor (work) = 0.1144          |
| start r-factor (free) = 0.1650      final r-factor (free) = 0.1586          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8605 = 1.84 * 0.50 * 5.2237 + 1.00 * 0.0629                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8098 = 1.84 * 0.50 * 5.1748 + 1.00 * 0.0571                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1144      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1586      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3885 = 0.27 * 1.00 * 5.1748 + 1.00 * 0.0118                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3810 = 0.27 * 1.00 * 5.1525 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.486)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.98   12.02    None  None   None       |
|    all(noH): 2823   0      0.00    88.98   12.02    None  None   None       |
|    Sol.    : 438    0      1.43    74.06   34.25    None  None   None       |
|    Mac.    : 2385   0      0.00    88.98   7.93     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.898: 1775   |   5:    44.489 -  53.387:   83        |
|      1:     8.898 -  17.796:  525   |   6:    53.387 -  62.285:   42        |
|      2:    17.796 -  26.694:  137   |   7:    62.285 -  71.183:   12        |
|      3:    26.694 -  35.592:  128   |   8:    71.183 -  80.081:    3        |
|      4:    35.592 -  44.489:  115   |   9:    80.081 -  88.979:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1140 r_free = 0.1576             target_work(ml) = 5.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1139 r_free = 0.1575             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1575   ksol= 0.32   Bsol= 30.51   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.24,2.71,3.52,0.00,0.00,0.00); trace/3= 2.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.146140                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1575   ksol= 0.32   Bsol= 33.19   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.24,2.71,3.52,0.00,0.00,0.00); trace/3= 2.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.145967                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.595105              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.561  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.305666              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.372  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1139      final r-factor (work) = 0.1085          |
| start r-factor (free) = 0.1575      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7423 = 2.60 * 0.50 * 5.1522 + 1.00 * 0.0571                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7157 = 2.60 * 0.50 * 5.1233 + 1.00 * 0.0680                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1085      final r-factor (work) = 0.1081          |
| start r-factor (free) = 0.1547      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5763 = 0.31 * 1.00 * 5.1233 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5725 = 0.31 * 1.00 * 5.1109 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.486)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.12   11.88    None  None   None       |
|    all(noH): 2823   0      0.00    89.12   11.88    None  None   None       |
|    Sol.    : 438    0      1.16    73.68   33.90    None  None   None       |
|    Mac.    : 2385   0      0.00    89.12   7.83     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 -   8.912: 1779   |   5:    44.561 -  53.473:   80        |
|      1:     8.912 -  17.825:  523   |   6:    53.473 -  62.386:   37        |
|      2:    17.825 -  26.737:  139   |   7:    62.386 -  71.298:   12        |
|      3:    26.737 -  35.649:  129   |   8:    71.298 -  80.210:    3        |
|      4:    35.649 -  44.561:  118   |   9:    80.210 -  89.122:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1081 r_free = 0.1549             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1081 r_free = 0.1548             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1548   ksol= 0.32   Bsol= 33.19   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.24,2.71,3.52,0.00,0.00,0.00); trace/3= 2.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.112006                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7695 -  4.7012 0.99   1373  153 0.1005 0.1278      5.3876       5.521|
|  2:  4.7012 -  3.7516 0.99   1308  146 0.0842 0.1140      5.4264      5.6313|
|  3:  3.7516 -  3.2833 0.99   1294  143 0.1025 0.1504      5.4535      5.8349|
|  4:  3.2833 -  2.9858 0.99   1286  139 0.1164 0.1548      5.4214      5.5957|
|  5:  2.9858 -  2.7733 0.99   1263  142 0.1215 0.1656      5.2802      5.4856|
|  6:  2.7733 -  2.6108 0.99   1273  144 0.1173 0.1714      5.1829      5.4054|
|  7:  2.6108 -  2.4806 0.99   1258  140 0.1202 0.1633      5.1381      5.3689|
|  8:  2.4806 -  2.3731 0.98   1261  141 0.1128 0.1757      5.0623      5.3553|
|  9:  2.3731 -  2.2821 0.98   1250  137 0.1132 0.1644      4.9998      5.2298|
| 10:  2.2821 -  2.2036 0.98   1248  137 0.1072 0.1756      4.9315      5.2007|
| 11:  2.2036 -  2.1349 0.99   1259  144 0.1090 0.1661      4.8961      5.2384|
| 12:  2.1349 -  2.0741 0.97   1244  132 0.1068 0.1646      4.8475      5.1805|
| 13:  2.0741 -  2.0196 0.99   1237  138 0.1072 0.1607      4.7669      5.0028|
| 14:  2.0196 -  1.9705 0.85   1076  123 0.1020 0.1713      4.6391      4.9413|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7695 -  4.7012  1373   153  0.94   9.08   0.99     0.97       7072.20|
|  2:  4.7012 -  3.7516  1308   146  0.95   7.78   1.03     1.02       8891.33|
|  3:  3.7516 -  3.2833  1294   143  0.94  11.02   1.04     1.03      10083.50|
|  4:  3.2833 -  2.9858  1286   139  0.93  12.64   1.02     1.01       9552.16|
|  5:  2.9858 -  2.7733  1263   142  0.91  14.83   1.00     0.97       7638.76|
|  6:  2.7733 -  2.6108  1273   144  0.91  15.33   0.98     0.95       6560.38|
|  7:  2.6108 -  2.4806  1258   140  0.91  15.38   0.99     0.96       5995.08|
|  8:  2.4806 -  2.3731  1261   141  0.91  14.44   1.00     0.98       5190.12|
|  9:  2.3731 -  2.2821  1250   137  0.91  14.84   1.02     0.99       4704.72|
| 10:  2.2821 -  2.2036  1248   137  0.91  14.75   1.01     0.98       4131.31|
| 11:  2.2036 -  2.1349  1259   144  0.91  15.31   1.01     0.98       4020.63|
| 12:  2.1349 -  2.0741  1244   132  0.92  14.53   1.02     1.01       3715.38|
| 13:  2.0741 -  2.0196  1237   138  0.91  14.87   1.02     1.01       3162.38|
| 14:  2.0196 -  1.9705  1076   123  0.92  14.06   1.01     0.98       2395.85|
|alpha:            min =        0.95 max =            1.03 mean =         0.99|
|beta:             min =     2395.85 max =        10083.50 mean =      6010.68|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.43|
|phase err.(test): min =        0.00 max =           87.17 mean =        12.98|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1548   ksol= 0.33   Bsol= 38.83   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.59,-0.11,0.70,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.111805                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1548   ksol= 0.33   Bsol= 38.83   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.59,-0.11,0.70,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.111805                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7695 -  4.7012 0.99   1373  153 0.1006 0.1279      5.3885      5.5223|
|  2:  4.7012 -  3.7516 0.99   1308  146 0.0844 0.1143      5.4286      5.6337|
|  3:  3.7516 -  3.2833 0.99   1294  143 0.1026 0.1504      5.4547      5.8358|
|  4:  3.2833 -  2.9858 0.99   1286  139 0.1164 0.1546      5.4213      5.5948|
|  5:  2.9858 -  2.7733 0.99   1263  142 0.1215 0.1655      5.2794      5.4847|
|  6:  2.7733 -  2.6108 0.99   1273  144 0.1171 0.1712      5.1819      5.4043|
|  7:  2.6108 -  2.4806 0.99   1258  140 0.1201 0.1632      5.1369      5.3681|
|  8:  2.4806 -  2.3731 0.98   1261  141 0.1127 0.1755      5.0616      5.3541|
|  9:  2.3731 -  2.2821 0.98   1250  137 0.1132 0.1646      4.9993      5.2304|
| 10:  2.2821 -  2.2036 0.98   1248  137 0.1071 0.1758      4.9313      5.2005|
| 11:  2.2036 -  2.1349 0.99   1259  144 0.1089 0.1658      4.8955      5.2377|
| 12:  2.1349 -  2.0741 0.97   1244  132 0.1067 0.1644       4.847      5.1803|
| 13:  2.0741 -  2.0196 0.99   1237  138 0.1072 0.1608      4.7662      5.0026|
| 14:  2.0196 -  1.9705 0.85   1076  123 0.1020 0.1710      4.6378      4.9395|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7695 -  4.7012  1373   153  0.94   9.09   0.99     0.97       7095.19|
|  2:  4.7012 -  3.7516  1308   146  0.95   7.79   1.03     1.02       8920.55|
|  3:  3.7516 -  3.2833  1294   143  0.94  11.03   1.04     1.03      10105.41|
|  4:  3.2833 -  2.9858  1286   139  0.93  12.63   1.02     1.01       9544.30|
|  5:  2.9858 -  2.7733  1263   142  0.91  14.82   1.00     0.97       7626.40|
|  6:  2.7733 -  2.6108  1273   144  0.91  15.31   0.98     0.95       6549.17|
|  7:  2.6108 -  2.4806  1258   140  0.91  15.35   0.99     0.96       5983.05|
|  8:  2.4806 -  2.3731  1261   141  0.91  14.43   1.00     0.98       5183.33|
|  9:  2.3731 -  2.2821  1250   137  0.91  14.84   1.02     1.00       4701.71|
| 10:  2.2821 -  2.2036  1248   137  0.91  14.75   1.01     0.98       4132.04|
| 11:  2.2036 -  2.1349  1259   144  0.91  15.31   1.01     0.98       4018.17|
| 12:  2.1349 -  2.0741  1244   132  0.92  14.52   1.02     1.01       3711.47|
| 13:  2.0741 -  2.0196  1237   138  0.91  14.83   1.02     1.01       3154.89|
| 14:  2.0196 -  1.9705  1076   123  0.92  14.03   1.01     0.98       2386.87|
|alpha:            min =        0.95 max =            1.03 mean =         0.99|
|beta:             min =     2386.87 max =        10105.41 mean =      6010.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.42|
|phase err.(test): min =        0.00 max =           87.08 mean =        12.97|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.486)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.82    91.94   14.70    None  None   None       |
|    all(noH): 2823   0      2.82    91.94   14.70    None  None   None       |
|    Sol.    : 438    0      3.98    76.50   36.72    None  None   None       |
|    Mac.    : 2385   0      2.82    91.94   10.65    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.821 -  11.734: 1779   |   5:    47.382 -  56.295:   80        |
|      1:    11.734 -  20.646:  523   |   6:    56.295 -  65.207:   37        |
|      2:    20.646 -  29.558:  139   |   7:    65.207 -  74.119:   12        |
|      3:    29.558 -  38.470:  129   |   8:    74.119 -  83.031:    3        |
|      4:    38.470 -  47.382:  118   |   9:    83.031 -  91.943:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 294         
Filter by distance & map next to the model:
   mapped sites are within: 0.347 - 5.621
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 290 from: 294
   mapped sites are within: 0.727 - 5.621

peak=   11.446 closest distance to " CB  VAL A 230 " =    1.445
peak=    8.679 closest distance to " CG2 VAL A 296 " =    1.240
peak=    6.367 closest distance to " CG  LEU A   5 " =    1.201
peak=    5.772 closest distance to " NE2 GLN A  11 " =    1.136
peak=    5.621 closest distance to " O   HOH Z 193 " =    1.754
peak=    5.590 closest distance to " O   HOH Z 142 " =    1.817
peak=    5.530 closest distance to " CD2 LEU A   5 " =    1.199
peak=    5.306 closest distance to " CG  LEU A 228 " =    1.205
peak=    5.155 closest distance to " O   HOH Z 126 " =    1.872
peak=    5.153 closest distance to " CB  GLN A 183 " =    1.255
peak=    5.104 closest distance to " O   HOH Z 209 " =    2.265
peak=    4.967 closest distance to " O   HOH Z 272 " =    1.891
peak=    4.966 closest distance to " NH2 ARG A  56 " =    2.056
peak=    4.948 closest distance to " CB  ARG A 275 " =    0.933
peak=    4.839 closest distance to " O   HOH Z 124 " =    1.452
peak=    4.790 closest distance to " C   PRO A 198 " =    1.480
peak=    4.722 closest distance to " CB  VAL A 296 " =    1.053
peak=    4.720 closest distance to " CB  GLN A 223 " =    1.457
peak=    4.705 closest distance to " O   HOH Z 232 " =    2.363
peak=    4.690 closest distance to " O   HOH Z 427 " =    2.743
peak=    4.613 closest distance to " CB  GLU A 152 " =    1.185
peak=    4.559 closest distance to " CB  VAL A 230 " =    1.160
peak=    4.515 closest distance to " O   HOH Z  85 " =    1.472
peak=    4.495 closest distance to " CB  SER A  63 " =    1.184
peak=    4.479 closest distance to " O   HOH Z 236 " =    1.901
peak=    4.466 closest distance to " O   SER A  87 " =    2.278
peak=    4.449 closest distance to " O   HOH Z 278 " =    0.951
peak=    4.427 closest distance to " CG  PRO A 213 " =    1.218
peak=    4.425 closest distance to " O   HOH Z  44 " =    1.901
peak=    4.351 closest distance to " CB  ARG A  79 " =    1.484
peak=    4.345 closest distance to " O   HOH Z 346 " =    1.596
peak=    4.341 closest distance to " O   HOH Z 316 " =    2.887
peak=    4.304 closest distance to " O   HOH Z  97 " =    2.491
peak=    4.291 closest distance to " O   HOH Z  54 " =    1.634
peak=    4.282 closest distance to " CB  SER A   3 " =    1.293
peak=    4.280 closest distance to " O   HOH Z  59 " =    1.942
peak=    4.258 closest distance to " O   HOH Z 298 " =    1.793
peak=    4.223 closest distance to " O   HOH Z 303 " =    2.072
peak=    4.210 closest distance to " O   HOH Z 203 " =    1.586
peak=    4.198 closest distance to " O   HOH Z 403 " =    1.815
peak=    4.176 closest distance to " O   HOH Z   9 " =    2.255
peak=    4.175 closest distance to " O   HOH Z 402 " =    1.401
peak=    4.165 closest distance to " O   HOH Z 368 " =    2.050
peak=    4.147 closest distance to " O   HOH Z  61 " =    1.608
peak=    4.136 closest distance to " ND2 ASN A 187 " =    1.504
peak=    4.136 closest distance to " CB  TYR A 169 " =    0.818
peak=    4.130 closest distance to " O   HOH Z 234 " =    3.433
peak=    4.117 closest distance to " O   HOH Z 322 " =    2.054
peak=    4.115 closest distance to " O   HOH Z 250 " =    1.340
peak=    4.080 closest distance to " OD1 ASN A  69 " =    2.598
peak=    4.068 closest distance to " O   HOH Z 371 " =    3.053
peak=    4.058 closest distance to " CB  VAL A 265 " =    1.268
peak=    4.055 closest distance to " O   HOH Z 248 " =    1.721
peak=    4.052 closest distance to " O   HOH Z 392 " =    2.922
peak=    4.050 closest distance to " O   HOH Z 227 " =    2.235
peak=    4.050 closest distance to " O   HOH Z  78 " =    1.738
peak=    4.041 closest distance to " CG1BVAL A  72 " =    1.502
peak=    4.032 closest distance to " OG BSER A 164 " =    2.131
peak=    4.031 closest distance to " O   HOH Z 411 " =    3.676
peak=    4.030 closest distance to " O   HOH Z 128 " =    1.986
peak=    4.009 closest distance to " CB  ARG A 139 " =    1.033
peak=    4.007 closest distance to " O   HOH Z 130 " =    2.336
peak=    3.996 closest distance to " CB  ASN A 148 " =    1.455
peak=    3.988 closest distance to " O   HOH Z  97 " =    1.921
peak=    3.986 closest distance to " O   HOH Z 369 " =    2.140
peak=    3.973 closest distance to " CB  SER A  26 " =    1.661
peak=    3.967 closest distance to " O   HOH Z 144 " =    2.148
peak=    3.942 closest distance to " CD2 TRP A 179 " =    1.422
peak=    3.927 closest distance to " O   HOH Z  66 " =    2.154
peak=    3.922 closest distance to " CB  TRP A 179 " =    1.283
peak=    3.906 closest distance to " O   HOH Z 118 " =    1.552
peak=    3.906 closest distance to " OD2 ASP A 286 " =    2.653
peak=    3.905 closest distance to " O   HOH Z  78 " =    2.109
peak=    3.902 closest distance to " N   ASN A  39 " =    1.163
peak=    3.864 closest distance to " O   HOH Z 366 " =    2.870
peak=    3.858 closest distance to " CD2 LEU A 228 " =    1.219
peak=    3.849 closest distance to " O   HOH Z 327 " =    1.607
peak=    3.833 closest distance to " O   HOH Z 425 " =    2.049
peak=    3.833 closest distance to " O   HOH Z 189 " =    2.607
peak=    3.832 closest distance to " CB  VAL A 202 " =    1.582
peak=    3.831 closest distance to " O   HOH Z 118 " =    1.374
peak=    3.826 closest distance to " OE1 GLU A   2 " =    2.223
peak=    3.825 closest distance to " O   HOH Z   9 " =    1.996
peak=    3.812 closest distance to " O   HOH Z 407 " =    2.426
peak=    3.812 closest distance to " O   HOH Z 286 " =    2.334
peak=    3.811 closest distance to " CB  TRP A 266 " =    1.039
peak=    3.805 closest distance to " CA  ASN A 215 " =    1.045
peak=    3.791 closest distance to " CG2 ILE A  20 " =    1.525
peak=    3.790 closest distance to " CB  GLN A  88 " =    1.210
peak=    3.785 closest distance to " O   HOH Z 128 " =    2.033
peak=    3.778 closest distance to " O   HOH Z 251 " =    1.640
peak=    3.775 closest distance to " O   HOH Z 284 " =    2.926
peak=    3.771 closest distance to " CA  ALA A  21 " =    1.136
peak=    3.761 closest distance to " O   HOH Z  10 " =    1.799
peak=    3.759 closest distance to " O   HOH Z 345 " =    3.080
peak=    3.756 closest distance to " O   HOH Z 423 " =    1.882
peak=    3.750 closest distance to " CB  THR A  31 " =    1.676
peak=    3.740 closest distance to " O   HOH Z 344 " =    2.748
peak=    3.740 closest distance to " O   HOH Z   3 " =    1.828
peak=    3.736 closest distance to " CG2 ILE A 120 " =    1.255
peak=    3.730 closest distance to " N   PHE A 130 " =    1.335
peak=    3.729 closest distance to " O   HOH Z  80 " =    2.275
peak=    3.728 closest distance to " CB  ASN A  39 " =    0.808
peak=    3.725 closest distance to " O   HOH Z  61 " =    1.552
peak=    3.717 closest distance to " CD  GLN A 194 " =    1.386
peak=    3.714 closest distance to " O   HOH Z  43 " =    2.073
peak=    3.712 closest distance to " O   HOH Z 263 " =    1.521
peak=    3.695 closest distance to " CD1 ILE A 106 " =    1.155
peak=    3.688 closest distance to " O   HOH Z 374 " =    2.451
peak=    3.684 closest distance to " O   HOH Z 425 " =    1.305
peak=    3.655 closest distance to " O   TRP A 274 " =    1.865
peak=    3.652 closest distance to " O   HOH Z 273 " =    2.739
peak=    3.636 closest distance to " O   HOH Z  55 " =    2.373
peak=    3.634 closest distance to " O   HOH Z  48 " =    1.530
peak=    3.627 closest distance to " CB  GLU A 128 " =    0.992
peak=    3.627 closest distance to " O   HOH Z 158 " =    3.015
peak=    3.624 closest distance to " CB  ALA A 248 " =    1.345
peak=    3.617 closest distance to " O   HOH Z 329 " =    3.736
peak=    3.614 closest distance to " O   HOH Z 435 " =    1.930
peak=    3.610 closest distance to " O   HOH Z 130 " =    2.841
peak=    3.607 closest distance to " NZ  LYS A 117 " =    2.954
peak=    3.601 closest distance to " CA  VAL A  41 " =    0.826
peak=    3.597 closest distance to " CA  TYR A  30 " =    0.971
peak=    3.596 closest distance to " O   HOH Z 299 " =    4.220
peak=    3.592 closest distance to " O   HOH Z 426 " =    1.467
peak=    3.575 closest distance to " O   HOH Z 164 " =    2.077
peak=    3.562 closest distance to " O   HOH Z 175 " =    2.339
peak=    3.557 closest distance to " CB BVAL A  41 " =    1.151
peak=    3.555 closest distance to " CA  PHE A 283 " =    1.248
peak=    3.554 closest distance to " O   HOH Z 389 " =    1.737
peak=    3.548 closest distance to " CA  ALA A  51 " =    0.966
peak=    3.543 closest distance to " CB  ALA A   9 " =    1.605
peak=    3.538 closest distance to " N   ARG A 156 " =    1.316
peak=    3.538 closest distance to " O   HOH Z 245 " =    1.388
peak=    3.531 closest distance to " CD BLYS A 290 " =    1.194
peak=    3.530 closest distance to " CG  PRO A 243 " =    1.210
peak=    3.529 closest distance to " O   HOH Z 145 " =    1.998
peak=    3.528 closest distance to " CG  GLN A  77 " =    2.218
peak=    3.526 closest distance to " O   ASP A 124 " =    1.234
peak=    3.509 closest distance to " CB  GLU A 277 " =    3.460
peak=    3.490 closest distance to " O   HOH Z 193 " =    1.848
peak=    3.479 closest distance to " O   HOH Z 180 " =    2.145
peak=    3.476 closest distance to " O   HOH Z 422 " =    2.548
peak=    3.470 closest distance to " O   HOH Z 147 " =    1.621
peak=    3.464 closest distance to " CD  ARG A 269 " =    1.051
peak=    3.462 closest distance to " O   HOH Z 132 " =    2.488
peak=    3.461 closest distance to " O   HOH Z 227 " =    1.576
peak=    3.457 closest distance to " CA  ASN A 176 " =    1.028
peak=    3.455 closest distance to " O   HOH Z 334 " =    1.322
peak=    3.453 closest distance to " O   HOH Z  43 " =    2.729
peak=    3.450 closest distance to " OD1 ASN A 148 " =    1.694
peak=    3.447 closest distance to " O   HOH Z 417 " =    3.195
peak=    3.446 closest distance to " CB  ASN A 110 " =    1.100
peak=    3.446 closest distance to " CG  MET A 185 " =    1.166
peak=    3.445 closest distance to " CA  ALA A 158 " =    1.239
peak=    3.436 closest distance to " O   HOH Z   1 " =    1.788
peak=    3.435 closest distance to " O   HOH Z 388 " =    1.905
peak=    3.433 closest distance to " O   HOH Z 207 " =    1.722
peak=    3.432 closest distance to " CB  GLN A 278 " =    0.789
peak=    3.424 closest distance to " O   HOH Z 108 " =    2.269
peak=    3.424 closest distance to " CA  ASP A 162 " =    1.006
peak=    3.423 closest distance to " CG1 ILE A  33 " =    1.331
peak=    3.423 closest distance to " CB  ALA A 295 " =    1.195
peak=    3.416 closest distance to " CD1 ILE A  33 " =    1.617
peak=    3.416 closest distance to " O   HOH Z 173 " =    2.203
peak=    3.402 closest distance to " O   HOH Z 303 " =    1.710
peak=    3.397 closest distance to " CG AARG A 275 " =    1.085
peak=    3.394 closest distance to " OE2 GLU A  53 " =    2.013
peak=    3.392 closest distance to " CB  SER A 216 " =    0.727
peak=    3.391 closest distance to " O   HOH Z  21 " =    1.714
peak=    3.389 closest distance to " O   HOH Z 112 " =    1.623
peak=    3.386 closest distance to " O   HOH Z 433 " =    1.860
peak=    3.385 closest distance to " CG2 VAL A 257 " =    0.813
peak=    3.376 closest distance to " O   LYS A 290 " =    2.363
peak=    3.376 closest distance to " N   SER A 135 " =    1.277
peak=    3.375 closest distance to " CA  LYS A 117 " =    1.248
peak=    3.373 closest distance to " O   HOH Z 233 " =    1.940
peak=    3.372 closest distance to " O   HOH Z 271 " =    1.576
peak=    3.370 closest distance to " O   HOH Z 380 " =    1.817
peak=    3.361 closest distance to " CB  ASP A 140 " =    0.879
peak=    3.356 closest distance to " CB  ALA A   1 " =    1.147
peak=    3.353 closest distance to " O   HOH Z  59 " =    2.179
peak=    3.350 closest distance to " O   HOH Z 227 " =    1.719
peak=    3.348 closest distance to " CB  GLN A 205 " =    1.274
peak=    3.347 closest distance to " CG  LYS A 119 " =    1.142
peak=    3.345 closest distance to " O   HOH Z 438 " =    2.053
peak=    3.344 closest distance to " O   HOH Z  88 " =    2.718
peak=    3.342 closest distance to " CB  ALA A  71 " =    1.357
peak=    3.339 closest distance to " O   HOH Z  59 " =    1.999
peak=    3.334 closest distance to " O   HOH Z 250 " =    1.446
peak=    3.330 closest distance to " O   HOH Z 134 " =    1.350
peak=    3.330 closest distance to " CG  PRO A 198 " =    1.245
peak=    3.327 closest distance to " O   HOH Z  40 " =    1.899
peak=    3.317 closest distance to " CG  MET A 185 " =    1.089
peak=    3.315 closest distance to " O  BHOH Z 338 " =    2.445
peak=    3.314 closest distance to " CA  VAL A 126 " =    0.956
peak=    3.312 closest distance to " O   HOH Z 214 " =    2.225
peak=    3.309 closest distance to " CG1 ILE A 120 " =    1.308
peak=    3.304 closest distance to " CG2 THR A 221 " =    1.284
peak=    3.299 closest distance to " O   HOH Z 261 " =    1.627
peak=    3.298 closest distance to " O   HOH Z 344 " =    1.319
peak=    3.298 closest distance to " CB  ILE A  20 " =    1.458
peak=    3.297 closest distance to " O   HOH Z 250 " =    1.802
peak=    3.297 closest distance to " O   HOH Z 383 " =    1.773
peak=    3.297 closest distance to " O   HOH Z 151 " =    1.750
peak=    3.290 closest distance to " O   HOH Z 406 " =    1.503
peak=    3.290 closest distance to " O   HOH Z 163 " =    1.818
peak=    3.287 closest distance to " CZ  PHE A 218 " =    1.084
peak=    3.282 closest distance to " CB  ALA A  10 " =    1.473
peak=    3.276 closest distance to " CZ2 TRP A 179 " =    1.741
peak=    3.272 closest distance to " CE1 TYR A 186 " =    1.296
peak=    3.271 closest distance to " CG  LEU A 167 " =    1.155
peak=    3.266 closest distance to " CA  LYS A 290 " =    1.291
peak=    3.266 closest distance to " CB  ALA A 291 " =    1.350
peak=    3.265 closest distance to " O   HOH Z 423 " =    2.847
peak=    3.257 closest distance to " CG  GLN A  88 " =    1.029
peak=    3.254 closest distance to " O   ALA A   1 " =    1.740
peak=    3.254 closest distance to " O   HOH Z 187 " =    2.204
peak=    3.248 closest distance to " CD2 TYR A  30 " =    0.938
peak=    3.247 closest distance to " CZ2 TRP A 274 " =    1.657
peak=    3.246 closest distance to " CA  ALA A 233 " =    1.101
peak=    3.245 closest distance to " O   HOH Z  71 " =    1.794
peak=    3.244 closest distance to " CZ AARG A 102 " =    1.764
peak=    3.241 closest distance to " CG2 THR A 294 " =    1.577
peak=    3.239 closest distance to " CA  ASP A 140 " =    1.170
peak=    3.237 closest distance to " CD2 HIS A  81 " =    1.125
peak=    3.237 closest distance to " O   HOH Z 148 " =    3.281
peak=    3.233 closest distance to " CD1 LEU A 228 " =    1.850
peak=    3.233 closest distance to " CB  ASN A 215 " =    1.072
peak=    3.231 closest distance to " CE  MET A  93 " =    1.525
peak=    3.229 closest distance to " NZ  LYS A  76 " =    1.418
peak=    3.229 closest distance to " CA  ALA A 291 " =    0.886
peak=    3.228 closest distance to " O   HOH Z 437 " =    2.055
peak=    3.225 closest distance to " N   ASP A 162 " =    1.262
peak=    3.224 closest distance to " CB  ARG A 190 " =    1.727
peak=    3.220 closest distance to " CD2 LEU A 255 " =    1.482
peak=    3.219 closest distance to " N   VAL A 126 " =    1.199
peak=    3.214 closest distance to " O   HOH Z 151 " =    1.667
peak=    3.214 closest distance to " O   HOH Z 189 " =    2.499
peak=    3.213 closest distance to " O   HOH Z 244 " =    1.536
peak=    3.208 closest distance to " O   HOH Z  88 " =    2.409
peak=    3.207 closest distance to " O   HOH Z 421 " =    1.507
peak=    3.205 closest distance to " CG  ARG A  66 " =    2.476
peak=    3.204 closest distance to " O   HOH Z 368 " =    3.602
peak=    3.204 closest distance to " O   HOH Z 409 " =    3.383
peak=    3.202 closest distance to " O   MET A 105 " =    1.866
peak=    3.200 closest distance to " O   HOH Z 430 " =    5.621
peak=    3.199 closest distance to " CA  ARG A  36 " =    1.007
peak=    3.196 closest distance to " CB  LEU A 255 " =    0.803
peak=    3.194 closest distance to " O   HOH Z 302 " =    1.849
peak=    3.194 closest distance to " O   HOH Z 172 " =    3.750
peak=    3.189 closest distance to " O   HOH Z 109 " =    2.444
peak=    3.187 closest distance to " CA  GLN A 194 " =    1.246
peak=    3.185 closest distance to " O   HOH Z  47 " =    1.720
peak=    3.184 closest distance to " O   HOH Z 280 " =    2.448
peak=    3.180 closest distance to " O   PHE A  38 " =    1.937
peak=    3.179 closest distance to " O   HOH Z  19 " =    2.213
peak=    3.177 closest distance to " OG BSER A 258 " =    2.905
peak=    3.176 closest distance to " CE BLYS A 290 " =    0.920
peak=    3.175 closest distance to " OG  SER A  62 " =    2.871
peak=    3.173 closest distance to " O   HOH Z 279 " =    2.199
peak=    3.172 closest distance to " CA  SER A 146 " =    1.855
peak=    3.168 closest distance to " CB  SER A  62 " =    1.288
peak=    3.164 closest distance to " CE  LYS A  48 " =    1.382
peak=    3.163 closest distance to " O   HOH Z  40 " =    1.286
peak=    3.160 closest distance to " OD1 ASP A 286 " =    1.572
peak=    3.160 closest distance to " O   GLN A  58 " =    1.422
peak=    3.159 closest distance to " NZ  LYS A  48 " =    2.232
peak=    3.159 closest distance to " NH2AARG A 190 " =    1.801
peak=    3.156 closest distance to " CA  THR A 264 " =    0.791
peak=    3.154 closest distance to " O   HOH Z 199 " =    2.116
peak=    3.128 closest distance to " CB  THR A 157 " =    1.036
peak=    3.125 closest distance to " CD  LYS A 166 " =    1.295
peak=    3.122 closest distance to " C   ALA A 299 " =    0.924
peak=    3.122 closest distance to " O   HOH Z  62 " =    2.211
peak=    3.118 closest distance to " O   HOH Z 305 " =    3.527
peak=    3.116 closest distance to " CD2 TYR A 186 " =    0.997
peak=    3.116 closest distance to " NE2 GLN A 223 " =    1.756
peak=    3.114 closest distance to " CD2 LEU A 297 " =    1.017
peak=    3.100 closest distance to " NE AARG A 275 " =    1.793
peak=    3.093 closest distance to " O   HOH Z 367 " =    3.443
peak=    3.082 closest distance to " O   HOH Z 143 " =    1.022
peak=    3.082 closest distance to " O   HOH Z  19 " =    2.161
peak=    3.078 closest distance to " O   HOH Z 195 " =    2.961
peak=    3.063 closest distance to " O   SER A 164 " =    1.180
peak=    3.060 closest distance to " O   HOH Z 291 " =    1.643
peak=    3.059 closest distance to " CD1 LEU A 261 " =    1.114
peak=    3.053 closest distance to " ND1 HIS A  81 " =    1.577
peak=    3.004 closest distance to " CB  ASP A 171 " =    1.127
peak=    3.001 closest distance to " CG AARG A 275 " =    1.025

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.530 - 5.942
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 201
   mapped sites are within: 0.740 - 5.942

peak=   -5.338 closest distance to " CG2 VAL A 230 " =    0.740
peak=   -4.863 closest distance to " CD  ARG A 156 " =    2.034
peak=   -4.603 closest distance to " SG  CYS A 254 " =    3.201
peak=   -4.401 closest distance to " O   HOH Z 266 " =    4.642
peak=   -4.400 closest distance to " O   HOH Z 290 " =    1.060
peak=   -4.260 closest distance to " OG BSER A 134 " =    1.200
peak=   -4.224 closest distance to " CG2 VAL A 296 " =    1.341
peak=   -4.141 closest distance to " C   HIS A 108 " =    1.213
peak=   -4.138 closest distance to " O   PRO A 163 " =    2.072
peak=   -4.129 closest distance to " CD1 LEU A 255 " =    2.771
peak=   -4.091 closest distance to " OXT GLY A 302 " =    2.739
peak=   -4.090 closest distance to " CA  VAL A  67 " =    2.718
peak=   -4.069 closest distance to " N   GLN A  58 " =    1.738
peak=   -4.046 closest distance to " O   HOH Z  11 " =    1.823
peak=   -4.039 closest distance to " CB  ALA A 161 " =    2.440
peak=   -3.979 closest distance to " O   HOH Z 166 " =    1.476
peak=   -3.973 closest distance to " CG  ASP A 231 " =    0.775
peak=   -3.961 closest distance to " CG  GLN A 223 " =    1.884
peak=   -3.944 closest distance to " CB  ALA A 248 " =    1.977
peak=   -3.942 closest distance to " CE2 TYR A  30 " =    2.799
peak=   -3.939 closest distance to " N   HIS A 115 " =    2.027
peak=   -3.929 closest distance to " CB  ASP A 132 " =    2.335
peak=   -3.921 closest distance to " O   HOH Z 429 " =    1.896
peak=   -3.894 closest distance to " O   VAL A  67 " =    2.684
peak=   -3.893 closest distance to " O   PRO A 198 " =    1.214
peak=   -3.784 closest distance to " CG  LEU A 228 " =    1.022
peak=   -3.775 closest distance to " CZ  TYR A 169 " =    1.767
peak=   -3.757 closest distance to " O   ALA A  51 " =    1.298
peak=   -3.752 closest distance to " N   ALA A 248 " =    1.601
peak=   -3.740 closest distance to " O   ALA A 161 " =    1.595
peak=   -3.737 closest distance to " C   GLN A 205 " =    1.907
peak=   -3.728 closest distance to " O   HOH Z 423 " =    2.188
peak=   -3.727 closest distance to " CB  ALA A  43 " =    2.263
peak=   -3.721 closest distance to " O   ALA A   8 " =    1.899
peak=   -3.715 closest distance to " CA  GLY A  23 " =    1.940
peak=   -3.714 closest distance to " O   HOH Z 114 " =    2.987
peak=   -3.712 closest distance to " OG  SER A   3 " =    1.394
peak=   -3.708 closest distance to " O   HOH Z 389 " =    1.809
peak=   -3.705 closest distance to " CA  GLY A  98 " =    1.884
peak=   -3.700 closest distance to " O   HOH Z 211 " =    1.555
peak=   -3.698 closest distance to " O   HOH Z 351 " =    1.500
peak=   -3.686 closest distance to " O   HOH Z 102 " =    1.638
peak=   -3.680 closest distance to " O   HOH Z 407 " =    2.951
peak=   -3.677 closest distance to " OD1 ASN A  39 " =    2.144
peak=   -3.674 closest distance to " CB  PRO A 163 " =    2.556
peak=   -3.671 closest distance to " CG1 VAL A 112 " =    2.715
peak=   -3.670 closest distance to " O   HOH Z 231 " =    2.049
peak=   -3.665 closest distance to " CB  PHE A 192 " =    1.889
peak=   -3.659 closest distance to " CD1 LEU A 101 " =    2.379
peak=   -3.652 closest distance to " CB  PRO A 243 " =    2.651
peak=   -3.649 closest distance to " CD  LYS A 289 " =    2.476
peak=   -3.640 closest distance to " CD1 PHE A  59 " =    1.926
peak=   -3.638 closest distance to " O   HOH Z 362 " =    5.942
peak=   -3.636 closest distance to " CG  PHE A 283 " =    2.632
peak=   -3.624 closest distance to " CE  MET A 105 " =    2.032
peak=   -3.618 closest distance to " N   ALA A 226 " =    1.907
peak=   -3.617 closest distance to " O   HOH Z 174 " =    4.335
peak=   -3.616 closest distance to " CB  ASP A 132 " =    2.225
peak=   -3.610 closest distance to " C   ASN A 187 " =    1.875
peak=   -3.595 closest distance to " NH2 ARG A  79 " =    1.905
peak=   -3.595 closest distance to " O   HOH Z 166 " =    2.008
peak=   -3.585 closest distance to " CB  ALA A 291 " =    2.381
peak=   -3.583 closest distance to " O   HOH Z 191 " =    5.296
peak=   -3.574 closest distance to " NE2 GLN A  88 " =    1.978
peak=   -3.573 closest distance to " CB  ASN A  39 " =    2.157
peak=   -3.568 closest distance to " CD2 LEU A 300 " =    2.882
peak=   -3.551 closest distance to " N   THR A 157 " =    1.422
peak=   -3.545 closest distance to " CE2 PHE A 218 " =    2.530
peak=   -3.538 closest distance to " ND2 ASN A 187 " =    1.500
peak=   -3.538 closest distance to " CZ  PHE A  59 " =    1.454
peak=   -3.533 closest distance to " ND2 ASN A  45 " =    1.036
peak=   -3.532 closest distance to " C   ASP A 231 " =    2.431
peak=   -3.528 closest distance to " O   PHE A 218 " =    1.654
peak=   -3.527 closest distance to " O   HOH Z 385 " =    2.054
peak=   -3.525 closest distance to " O   HOH Z 193 " =    1.571
peak=   -3.525 closest distance to " N   PHE A  59 " =    2.270
peak=   -3.522 closest distance to " CD  GLN A  58 " =    1.218
peak=   -3.511 closest distance to " O   HOH Z 185 " =    2.309
peak=   -3.501 closest distance to " N   SER A 276 " =    1.261
peak=   -3.485 closest distance to " O   HOH Z 394 " =    1.516
peak=   -3.484 closest distance to " O   SER A  22 " =    2.257
peak=   -3.479 closest distance to " OG BSER A 134 " =    1.642
peak=   -3.468 closest distance to " C   ILE A 239 " =    2.100
peak=   -3.463 closest distance to " OD2 ASP A 191 " =    1.345
peak=   -3.463 closest distance to " CD1 LEU A 228 " =    2.017
peak=   -3.455 closest distance to " CB  ALA A 248 " =    2.328
peak=   -3.451 closest distance to " O   HOH Z  13 " =    1.523
peak=   -3.450 closest distance to " O   MET A  40 " =    2.654
peak=   -3.437 closest distance to " O   HOH Z 165 " =    1.979
peak=   -3.437 closest distance to " O   HOH Z 389 " =    4.696
peak=   -3.426 closest distance to " C   ALA A 158 " =    1.244
peak=   -3.418 closest distance to " CA  GLY A 133 " =    1.919
peak=   -3.413 closest distance to " ND2 ASN A  60 " =    1.675
peak=   -3.412 closest distance to " OG  SER A  87 " =    1.249
peak=   -3.406 closest distance to " O   HOH Z 148 " =    1.810
peak=   -3.402 closest distance to " CG  GLU A   2 " =    1.995
peak=   -3.399 closest distance to " O   ASN A 187 " =    1.501
peak=   -3.398 closest distance to " O   HOH Z 295 " =    1.491
peak=   -3.396 closest distance to " CD  ARG A 139 " =    1.601
peak=   -3.390 closest distance to " CG  ASP A  50 " =    2.324
peak=   -3.384 closest distance to " O   HOH Z  47 " =    1.529
peak=   -3.384 closest distance to " O   HOH Z 427 " =    1.450
peak=   -3.383 closest distance to " CB  ALA A  51 " =    1.881
peak=   -3.381 closest distance to " O   SER A 146 " =    1.019
peak=   -3.375 closest distance to " OD1 ASN A 301 " =    2.002
peak=   -3.374 closest distance to " O   HOH Z 134 " =    2.801
peak=   -3.373 closest distance to " NZ  LYS A 119 " =    3.360
peak=   -3.371 closest distance to " O   HOH Z 198 " =    2.178
peak=   -3.364 closest distance to " OD1 ASN A 249 " =    1.447
peak=   -3.362 closest distance to " C   ASN A 285 " =    2.186
peak=   -3.361 closest distance to " O   HOH Z 281 " =    2.928
peak=   -3.360 closest distance to " OG  SER A  97 " =    2.127
peak=   -3.353 closest distance to " O   HOH Z 393 " =    3.661
peak=   -3.348 closest distance to " O   HOH Z 139 " =    3.118
peak=   -3.346 closest distance to " O   HOH Z 407 " =    3.355
peak=   -3.345 closest distance to " O   HOH Z  11 " =    1.966
peak=   -3.332 closest distance to " OG  SER A 206 " =    1.519
peak=   -3.331 closest distance to " CG  PRO A 163 " =    2.766
peak=   -3.327 closest distance to " O   HOH Z  56 " =    2.362
peak=   -3.327 closest distance to " O   HOH Z 140 " =    1.627
peak=   -3.321 closest distance to " O   PRO A 198 " =    1.236
peak=   -3.319 closest distance to " CB  ALA A 100 " =    2.549
peak=   -3.308 closest distance to " O   HOH Z 131 " =    4.019
peak=   -3.305 closest distance to " C   MET A 188 " =    1.478
peak=   -3.295 closest distance to " CG2 THR A 178 " =    2.118
peak=   -3.293 closest distance to " OD1 ASP A 191 " =    1.454
peak=   -3.293 closest distance to " O   HOH Z  15 " =    1.596
peak=   -3.289 closest distance to " O   HOH Z 313 " =    1.764
peak=   -3.288 closest distance to " CD  GLN A  88 " =    0.994
peak=   -3.286 closest distance to " CD2 TYR A 293 " =    2.096
peak=   -3.281 closest distance to " O   HOH Z 385 " =    1.919
peak=   -3.281 closest distance to " CD1 TYR A 247 " =    2.533
peak=   -3.280 closest distance to " OG  SER A  62 " =    1.327
peak=   -3.277 closest distance to " CG  TRP A 266 " =    1.945
peak=   -3.275 closest distance to " NH2AARG A 275 " =    4.954
peak=   -3.270 closest distance to " O   HOH Z 103 " =    1.796
peak=   -3.260 closest distance to " O   HOH Z 210 " =    1.139
peak=   -3.259 closest distance to " CB  SER A 210 " =    1.311
peak=   -3.258 closest distance to " O   SER A 210 " =    1.921
peak=   -3.254 closest distance to " O   HOH Z 250 " =    1.431
peak=   -3.250 closest distance to " O   HOH Z 193 " =    1.736
peak=   -3.248 closest distance to " O   HOH Z 166 " =    2.136
peak=   -3.248 closest distance to " CB  ASN A  69 " =    1.097
peak=   -3.247 closest distance to " OG ASER A 134 " =    1.191
peak=   -3.243 closest distance to " OD2 ASP A  50 " =    1.355
peak=   -3.238 closest distance to " C   LEU A 143 " =    1.025
peak=   -3.238 closest distance to " O   HOH Z 436 " =    1.460
peak=   -3.234 closest distance to " CE BMET A  47 " =    1.706
peak=   -3.231 closest distance to " CE1 HIS A  81 " =    1.402
peak=   -3.231 closest distance to " CG  GLU A 152 " =    1.169
peak=   -3.231 closest distance to " O   LYS A 117 " =    1.596
peak=   -3.228 closest distance to " CD1 ILE A 263 " =    2.722
peak=   -3.226 closest distance to " CG  LYS A 193 " =    2.091
peak=   -3.219 closest distance to " O   HOH Z  60 " =    1.967
peak=   -3.216 closest distance to " OD2 ASP A 171 " =    2.285
peak=   -3.213 closest distance to " O   HOH Z 123 " =    2.454
peak=   -3.209 closest distance to " O   HOH Z  63 " =    1.156
peak=   -3.209 closest distance to " ND2 ASN A 209 " =    1.893
peak=   -3.203 closest distance to " O   HOH Z 210 " =    0.996
peak=   -3.201 closest distance to " CZ  ARG A 259 " =    0.863
peak=   -3.200 closest distance to " O   TRP A  70 " =    1.515
peak=   -3.199 closest distance to " O   HOH Z 407 " =    3.096
peak=   -3.197 closest distance to " N   GLN A  77 " =    1.590
peak=   -3.196 closest distance to " O   HOH Z  90 " =    2.632
peak=   -3.195 closest distance to " O   HOH Z 353 " =    2.150
peak=   -3.191 closest distance to " CD2 LEU A 237 " =    2.726
peak=   -3.177 closest distance to " CG  MET A 105 " =    0.885
peak=   -3.176 closest distance to " O   HOH Z 311 " =    3.566
peak=   -3.175 closest distance to " CZ3 TRP A 179 " =    1.343
peak=   -3.174 closest distance to " OG1 THR A 178 " =    1.193
peak=   -3.169 closest distance to " O   HOH Z 426 " =    1.598
peak=   -3.166 closest distance to " O   HOH Z 421 " =    3.051
peak=   -3.164 closest distance to " O   VAL A 197 " =    1.209
peak=   -3.162 closest distance to " O   HOH Z 359 " =    3.160
peak=   -3.156 closest distance to " O   HOH Z 417 " =    2.658
peak=   -3.156 closest distance to " CA  GLY A 133 " =    2.164
peak=   -3.152 closest distance to " O   HOH Z  71 " =    1.185
peak=   -3.149 closest distance to " O   HOH Z 339 " =    1.814
peak=   -3.144 closest distance to " CG1 VAL A 197 " =    2.170
peak=   -3.143 closest distance to " NE2 GLN A 278 " =    1.915
peak=   -3.142 closest distance to " O   HOH Z 344 " =    2.492
peak=   -3.141 closest distance to " CA  ASP A 298 " =    1.078
peak=   -3.140 closest distance to " O   GLN A 240 " =    2.024
peak=   -3.136 closest distance to " O   HOH Z 200 " =    4.432
peak=   -3.134 closest distance to " O   VAL A 174 " =    2.019
peak=   -3.128 closest distance to " O   GLY A  80 " =    2.570
peak=   -3.128 closest distance to " O   HOH Z 234 " =    3.896
peak=   -3.128 closest distance to " CG1 VAL A 230 " =    1.816
peak=   -3.118 closest distance to " OD1 ASP A 200 " =    1.316
peak=   -3.115 closest distance to " CB  ALA A  64 " =    2.548
peak=   -3.113 closest distance to " O   VAL A 125 " =    2.270
peak=   -3.112 closest distance to " CB  ALA A  84 " =    2.543
peak=   -3.096 closest distance to " CD1 ILE A 199 " =    2.359
peak=   -3.075 closest distance to " NE2 GLN A 194 " =    1.730
peak=   -3.074 closest distance to " CG2 VAL A 189 " =    1.951
peak=   -3.069 closest distance to " O   HOH Z 152 " =    5.019
peak=   -3.038 closest distance to " O   HOH Z 417 " =    2.608
peak=   -3.031 closest distance to " CG1 VAL A 296 " =    1.378

================= 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    :  0.4594 0.4487   6.256192e+00   6.242735e+00
   1_bss:  0.4505 0.4393   6.248550e+00   6.228040e+00
   1_xyz:  0.3574 0.3759   6.098568e+00   6.128388e+00
   1_adp:  0.3030 0.3448   5.970850e+00   6.066460e+00
   1_occ:  0.3023 0.3447   5.969948e+00   6.067345e+00
   2_bss:  0.2977 0.3390   5.967930e+00   6.062983e+00
   2_xyz:  0.1984 0.2432   5.621273e+00   5.793281e+00
   2_adp:  0.1736 0.2171   5.499754e+00   5.686001e+00
   2_occ:  0.1731 0.2165   5.498422e+00   5.684558e+00
   3_bss:  0.1714 0.2149   5.494678e+00   5.679242e+00
   3_xyz:  0.1310 0.1705   5.253573e+00   5.464516e+00
   3_adp:  0.1224 0.1650   5.203281e+00   5.426056e+00
   3_occ:  0.1224 0.1649   5.202629e+00   5.425228e+00
   4_bss:  0.1225 0.1650   5.202412e+00   5.424878e+00
   4_xyz:  0.1144 0.1586   5.154220e+00   5.390789e+00
   4_adp:  0.1140 0.1576   5.146855e+00   5.380009e+00
   4_occ:  0.1139 0.1575   5.146140e+00   5.379158e+00
   5_bss:  0.1139 0.1575   5.145967e+00   5.379036e+00
   5_xyz:  0.1085 0.1547   5.112875e+00   5.363158e+00
   5_adp:  0.1081 0.1549   5.112251e+00   5.364444e+00
   5_occ:  0.1081 0.1548   5.112006e+00   5.364188e+00
   5_bss:  0.1081 0.1548   5.111805e+00   5.364019e+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:  0.364   7.797   7.855   8.255   8.928   0.000   0.000   0.000
   1_xyz:  0.364   7.797   7.855   8.255   8.928   0.000   0.000   0.000
   1_adp:  0.364   7.797   7.855   8.255   8.928   0.000   0.000   0.000
   1_occ:  0.364   7.797   7.855   8.255   8.928   0.000   0.000   0.000
   2_bss:  0.327  20.000   4.199   4.220   5.617   0.000   0.000   0.000
   2_xyz:  0.327  20.000   4.199   4.220   5.617   0.000   0.000   0.000
   2_adp:  0.327  20.000   4.199   4.220   5.617   0.000   0.000   0.000
   2_occ:  0.327  20.000   4.199   4.220   5.617   0.000   0.000   0.000
   3_bss:  0.324  30.509   2.511   2.944   3.953   0.000   0.000   0.000
   3_xyz:  0.324  30.509   2.511   2.944   3.953   0.000   0.000   0.000
   3_adp:  0.324  30.509   2.511   2.944   3.953   0.000   0.000   0.000
   3_occ:  0.324  30.509   2.511   2.944   3.953   0.000   0.000   0.000
   4_bss:  0.316  30.509   2.236   2.708   3.520   0.000   0.000   0.000
   4_xyz:  0.316  30.509   2.236   2.708   3.520   0.000   0.000   0.000
   4_adp:  0.316  30.509   2.236   2.708   3.520   0.000   0.000   0.000
   4_occ:  0.316  30.509   2.236   2.708   3.520   0.000   0.000   0.000
   5_bss:  0.322  33.195   2.236   2.708   3.520   0.000   0.000   0.000
   5_xyz:  0.322  33.195   2.236   2.708   3.520   0.000   0.000   0.000
   5_adp:  0.322  33.195   2.236   2.708   3.520   0.000   0.000   0.000
   5_occ:  0.322  33.195   2.236   2.708   3.520   0.000   0.000   0.000
   5_bss:  0.326  38.830  -0.585  -0.113   0.699   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.319 0.4929  0.5700    61462.874
   1_bss:  52.721 0.4852  0.7130    58229.760
   1_xyz:  41.574 0.6231  0.9009    39641.483
   1_adp:  35.961 0.6907  1.0072    31926.635
   1_occ:  35.974 0.6905  1.0060    31882.137
   2_bss:  35.635 0.6941  0.8853    31247.903
   2_xyz:  24.337 0.8176  1.0056    15151.381
   2_adp:  20.742 0.8550  1.0343    11982.719
   2_occ:  20.707 0.8553  1.0343    11936.797
   3_bss:  20.537 0.8568  0.9779    11761.169
   3_xyz:  15.680 0.9006  0.9989     7373.246
   3_adp:  14.784 0.9086  0.9984     6862.464
   3_occ:  14.766 0.9087  0.9984     6849.537
   4_bss:  14.756 0.9088  0.9864     6850.868
   4_xyz:  13.943 0.9156  0.9907     6304.168
   4_adp:  13.706 0.9176  0.9913     6198.826
   4_occ:  13.689 0.9177  0.9912     6186.664
   5_bss:  13.683 0.9178  0.9915     6189.161
   5_xyz:  13.383 0.9200  0.9911     5997.606
   5_adp:  13.389 0.9201  0.9880     6013.960
   5_occ:  13.385 0.9201  0.9879     6009.990
   5_bss:  13.377 0.9202  0.9881     6010.256
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.3014e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.3014e+01
   1_xyz:   1.632  0.013  0.105 18.149  0.006  4.107   1.3278e-01
   1_adp:   1.632  0.013  0.105 18.149  0.006  4.107   1.3278e-01
   1_occ:   1.632  0.013  0.105 18.149  0.006  4.107   1.3278e-01
   2_bss:   1.632  0.013  0.105 18.149  0.006  4.107   1.3278e-01
   2_xyz:   1.059  0.008  0.078 16.287  0.005  4.115   7.2711e-02
   2_adp:   1.059  0.008  0.078 16.287  0.005  4.115   7.2711e-02
   2_occ:   1.059  0.008  0.078 16.287  0.005  4.115   7.2711e-02
   3_bss:   1.059  0.008  0.078 16.287  0.005  4.115   7.2711e-02
   3_xyz:   1.030  0.006  0.077 16.113  0.004  4.115   6.2998e-02
   3_adp:   1.030  0.006  0.077 16.113  0.004  4.115   6.2998e-02
   3_occ:   1.030  0.006  0.077 16.113  0.004  4.115   6.2998e-02
   4_bss:   1.030  0.006  0.077 16.113  0.004  4.115   6.2998e-02
   4_xyz:   0.948  0.005  0.073 15.823  0.004  4.109   5.7126e-02
   4_adp:   0.948  0.005  0.073 15.823  0.004  4.109   5.7126e-02
   4_occ:   0.948  0.005  0.073 15.823  0.004  4.109   5.7126e-02
   5_bss:   0.948  0.005  0.073 15.823  0.004  4.109   5.7126e-02
   5_xyz:   1.072  0.007  0.084 15.930  0.004  4.113   6.7959e-02
   5_adp:   1.072  0.007  0.084 15.930  0.004  4.113   6.7959e-02
   5_occ:   1.072  0.007  0.084 15.930  0.004  4.113   6.7959e-02
   5_bss:   1.072  0.007  0.084 15.930  0.004  4.113   6.7959e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.943   6.8696e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.943   6.8696e+00
   1_xyz:  14.343  0.158  0.482 87.770  0.033  2.281   9.5607e-02
   1_adp:  14.343  0.158  0.482 87.770  0.033  2.281   9.5607e-02
   1_occ:  14.343  0.158  0.482 87.770  0.033  2.281   9.5607e-02
   2_bss:  14.343  0.158  0.482 87.770  0.033  2.281   9.5607e-02
   2_xyz:   6.808  0.110  0.305 86.957  0.043  2.333   6.7360e-02
   2_adp:   6.808  0.110  0.305 86.957  0.043  2.333   6.7360e-02
   2_occ:   6.808  0.110  0.305 86.957  0.043  2.333   6.7360e-02
   3_bss:   6.808  0.110  0.305 86.957  0.043  2.333   6.7360e-02
   3_xyz:   7.957  0.036  0.460 84.464  0.028  2.318   4.2770e-02
   3_adp:   7.957  0.036  0.460 84.464  0.028  2.318   4.2770e-02
   3_occ:   7.957  0.036  0.460 84.464  0.028  2.318   4.2770e-02
   4_bss:   7.957  0.036  0.460 84.464  0.028  2.318   4.2770e-02
   4_xyz:   6.166  0.033  0.445 83.287  0.031  2.351   3.5561e-02
   4_adp:   6.166  0.033  0.445 83.287  0.031  2.351   3.5561e-02
   4_occ:   6.166  0.033  0.445 83.287  0.031  2.351   3.5561e-02
   5_bss:   6.166  0.033  0.445 83.287  0.031  2.351   3.5561e-02
   5_xyz:   6.615  0.044  0.573 82.716  0.032  2.255   5.0436e-02
   5_adp:   6.615  0.044  0.573 82.716  0.032  2.255   5.0436e-02
   5_occ:   6.615  0.044  0.573 82.716  0.032  2.255   5.0436e-02
   5_bss:   6.615  0.044  0.573 82.716  0.032  2.255   5.0436e-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:  77.56   0.00  11.85  77.56   0.00   8.99  67.81   0.00  27.44
   1_occ:  77.56   0.00  11.85  77.56   0.00   8.99  67.81   0.00  27.44
   2_bss:  77.56   0.00  11.85  77.56   0.00   8.99  67.81   0.00  27.44
   2_xyz:  77.56   0.00  11.85  77.56   0.00   8.99  67.81   0.00  27.44
   2_adp:  80.42   0.00  12.03  80.42   0.00   8.22  67.82   1.65  32.76
   2_occ:  80.42   0.00  12.03  80.42   0.00   8.22  67.82   1.65  32.76
   3_bss:  80.42   0.00  12.03  80.42   0.00   8.22  67.82   1.65  32.76
   3_xyz:  80.42   0.00  12.03  80.42   0.00   8.22  67.82   1.65  32.76
   3_adp:  87.73   0.00  12.42  87.73   0.00   8.09  73.64   0.64  35.96
   3_occ:  87.73   0.00  12.42  87.73   0.00   8.09  73.64   0.64  35.96
   4_bss:  87.73   0.00  12.42  87.73   0.00   8.09  73.64   0.64  35.96
   4_xyz:  87.73   0.00  12.42  87.73   0.00   8.09  73.64   0.64  35.96
   4_adp:  88.98   0.00  12.02  88.98   0.00   7.93  74.06   1.43  34.25
   4_occ:  88.98   0.00  12.02  88.98   0.00   7.93  74.06   1.43  34.25
   5_bss:  88.98   0.00  12.02  88.98   0.00   7.93  74.06   1.43  34.25
   5_xyz:  88.98   0.00  12.02  88.98   0.00   7.93  74.06   1.43  34.25
   5_adp:  89.12   0.00  11.88  89.12   0.00   7.83  73.68   1.16  33.90
   5_occ:  89.12   0.00  11.88  89.12   0.00   7.83  73.68   1.16  33.90
   5_bss:  91.94   2.82  14.70  91.94   2.82  10.65  76.50   3.98  36.72
------------------------------------------------------------------------
 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:    1.220    0.016    0.409
   1_adp:    1.220    0.016    0.409
   1_occ:    1.220    0.016    0.409
   2_bss:    1.220    0.016    0.409
   2_xyz:    1.458    0.028    0.559
   2_adp:    1.458    0.028    0.559
   2_occ:    1.458    0.028    0.559
   3_bss:    1.458    0.028    0.559
   3_xyz:    1.426    0.054    0.603
   3_adp:    1.426    0.054    0.603
   3_occ:    1.426    0.054    0.603
   4_bss:    1.426    0.054    0.603
   4_xyz:    1.546    0.021    0.623
   4_adp:    1.546    0.021    0.623
   4_occ:    1.546    0.021    0.623
   5_bss:    1.546    0.021    0.623
   5_xyz:    1.485    0.045    0.637
   5_adp:    1.485    0.045    0.637
   5_occ:    1.485    0.045    0.637
   5_bss:    1.485    0.045    0.637
------------------------------------------------------------------------

CPU time actual refinement: 271.17


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_288/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_288/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_288/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_288/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_288/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 271.04 
  Macro-tasks:
    bulk solvent and scale       = 39.11  
    individual site refinement   = 104.35 
    weights calculation          = 27.48  
    collect and process          = 5.40   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 176.44 
  Micro-tasks:
    mask                            = 1.51   
    f_calc                          = 80.42  
    alpha_beta                      = 6.89   
    target                          = 1.00   
    gradients_wrt_atomic_parameters = 88.42  
    fmodel                         = 6.55   
    r_factors                      = 0.22   
    phase_errors                   = 8.81   
    foms                           = 0.25   
    TOTAL for micro-tasks          = 194.07 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 3.875 micro seconds
Total CPU time: 4.71 minutes
from_scatterers_fft:    627 calls, 80.23 s
gradients_fft:          571 calls, 77.48 s

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

# Date 2008-01-16 Time 01:12:25 PST -0800 (1200474745.95 s)
Start R-work = 0.4594, R-free = 0.4487 (no bulk solvent and anisotropic scale)
Final R-work = 0.1260, R-free = 0.1712 (no bulk solvent and anisotropic scale)

Start R-work = 0.4505, R-free = 0.4393
Final R-work = 0.1081, R-free = 0.1548