# Date 2008-01-16 Time 00:51:56 PST -0800 (1200473516.57 s)
#phil __OFF__

Command line arguments: "../189.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 12570
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 189

-------------------------------------------------------------------------------
  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: (68.845, 47.1647, 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: 3.33, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.1647, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.747 1.96059
Completeness in resolution range: 0.958085
Completeness with d_max=infinity: 0.955095

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7470
                             d_min =   1.9606

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: (68.845, 47.1647, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.747 1.96059
Completeness in resolution range: 0.958085
Completeness with d_max=infinity: 0.955095

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7474 -  4.1946 [2152/2180]  1936   216  10.0%
  bin  2:  4.1946 -  3.3421 [2045/2068]  1843   202   9.9%
  bin  3:  3.3421 -  2.9234 [2044/2066]  1838   206  10.1%
  bin  4:  2.9234 -  2.6578 [2015/2034]  1817   198   9.8%
  bin  5:  2.6578 -  2.4683 [2009/2038]  1800   209  10.4%
  bin  6:  2.4683 -  2.3233 [1977/2019]  1788   189   9.6%
  bin  7:  2.3233 -  2.2074 [1984/2020]  1786   198  10.0%
  bin  8:  2.2074 -  2.1116 [1979/2016]  1776   203  10.3%
  bin  9:  2.1116 -  2.0305 [1953/1985]  1757   196  10.0%
  bin 10:  2.0305 -  1.9606 [1431/2020]  1289   142   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_189/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.34 -     2.05: 15
        2.05 -     2.76: 487
        2.76 -     3.48: 4646
        3.48 -     4.19: 9512
        4.19 -     4.90: 14096
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.341 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.380 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.480 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.696 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28751 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_189/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_189/model_refine_001.geo

CPU time processing inputs: 9.05


============================ 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 = 68.845 47.16465 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: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4702   r_free= 0.4615   ksol= 0.00   Bsol= 0.00   scale= 0.810    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.268229                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7474 -  4.6781 0.99   1393  157 0.3860 0.3804      6.5655      6.6012|
|  2:  4.6781 -  3.7330 0.99   1343  148 0.3859 0.3672      6.7397      6.7611|
|  3:  3.7330 -  3.2670 0.99   1316  150 0.4186 0.4121      6.6477      6.7018|
|  4:  3.2670 -  2.9709 0.99   1309  133 0.4445 0.4290      6.4951      6.4474|
|  5:  2.9709 -  2.7595 0.98   1285  147 0.4893 0.5049      6.3717         6.4|
|  6:  2.7595 -  2.5977 0.98   1295  143 0.4953 0.5385      6.2643      6.2066|
|  7:  2.5977 -  2.4683 0.99   1293  153 0.5192 0.4752      6.2614      6.1565|
|  8:  2.4683 -  2.3613 0.99   1286  133 0.5172 0.5004      6.1737      6.1578|
|  9:  2.3613 -  2.2707 0.98   1284  147 0.5128 0.5210      6.1122      6.1536|
| 10:  2.2707 -  2.1926 0.97   1255  143 0.5231 0.5069      6.1143      6.0906|
| 11:  2.1926 -  2.1243 0.98   1270  141 0.5185 0.5460      6.0276      6.0726|
| 12:  2.1243 -  2.0637 0.99   1278  140 0.5293 0.5102      5.9804      6.0175|
| 13:  2.0637 -  2.0095 0.97   1261  134 0.5497 0.5170      5.9033      5.8673|
| 14:  2.0095 -  1.9606 0.60    762   90 0.5206 0.4745      5.8563      5.7393|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7474 -  4.6781  1393   157  0.68  35.85   0.81     0.70      73822.68|
|  2:  4.6781 -  3.7330  1343   148  0.70  35.43   0.90     0.76     103853.42|
|  3:  3.7330 -  3.2670  1316   150  0.62  42.59   0.87     0.73     108932.39|
|  4:  3.2670 -  2.9709  1309   133  0.55  48.21   0.82     0.65      93429.32|
|  5:  2.9709 -  2.7595  1285   147  0.46  55.12   0.75     0.55      78865.12|
|  6:  2.7595 -  2.5977  1295   143  0.43  57.59   0.74     0.50      66844.61|
|  7:  2.5977 -  2.4683  1293   153  0.42  58.08   0.74     0.48      61251.17|
|  8:  2.4683 -  2.3613  1286   133  0.42  58.16   0.75     0.49      53373.67|
|  9:  2.3613 -  2.2707  1284   147  0.39  60.45   0.74     0.48      51481.63|
| 10:  2.2707 -  2.1926  1255   143  0.38  61.75   0.78     0.45      48140.59|
| 11:  2.1926 -  2.1243  1270   141  0.32  65.79   0.75     0.40      47428.16|
| 12:  2.1243 -  2.0637  1278   140  0.31  67.17   0.76     0.39      45249.44|
| 13:  2.0637 -  2.0095  1261   134  0.31  66.92   0.75     0.39      37532.14|
| 14:  2.0095 -  1.9606   762    90  0.40  59.89   0.73     0.43      25899.00|
|alpha:            min =        0.39 max =            0.76 mean =         0.54|
|beta:             min =    25899.00 max =       108932.39 mean =     65533.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.46|
|phase err.(work): min =        0.00 max =           90.00 mean =        54.82|
|phase err.(test): min =        0.00 max =           89.95 mean =        55.00|
|-----------------------------------------------------------------------------|

============================== 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 = 12.570541             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.341   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.023153              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.000   (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 |  0.978 -  1.370:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.370 -  1.762:       12 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.762 -  2.155:       83 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.155 -  2.547:      512 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.547 -  2.939:     1305 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.939 -  3.331:     2460 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.331 -  3.723:     4006 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.723 -  4.116:     5280 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.116 -  4.508:     6879 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.508 -  4.900:     8247 |
|-----------------------------------------------------------------------------|
|-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 |       53.086 |
| 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  0.978 |       2.571 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.510)------------------------------------------|
|    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 = 11.510)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4764   r_free= 0.4689   ksol= 0.00   Bsol= 0.00   scale= 0.779    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.270515                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4613   r_free= 0.4521   ksol= 0.37   Bsol= 20.00   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.96,8.05,8.46,0.00,0.00,0.00); trace/3= 8.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.262117                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.378924             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.806   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.068815              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.347   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4613      final r-factor (work) = 0.3709          |
| start r-factor (free) = 0.4521      final r-factor (free) = 0.3946          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 88.7698 = 11.38 * 0.50 * 6.2720 + 1.00 * 53.0855                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.2122 = 11.38 * 0.50 * 6.1631 + 1.00 * 0.1477                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3709      final r-factor (work) = 0.3186          |
| start r-factor (free) = 0.3946      final r-factor (free) = 0.3659          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6015 = 1.07 * 1.00 * 6.1631 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4851 = 1.07 * 1.00 * 6.0527 + 1.00 * 0.0159                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.510)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.95   12.33    None  None   None       |
|    all(noH): 2823   0      0.00    87.95   12.33    None  None   None       |
|    Sol.    : 438    0      0.00    87.95   27.72    None  None   None       |
|    Mac.    : 2385   0      0.00    69.77   9.50     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.795: 1438   |   5:    43.973 -  52.768:   59        |
|      1:     8.795 -  17.589:  715   |   6:    52.768 -  61.562:   23        |
|      2:    17.589 -  26.384:  312   |   7:    61.562 -  70.357:    8        |
|      3:    26.384 -  35.178:  170   |   8:    70.357 -  79.151:    3        |
|      4:    35.178 -  43.973:   94   |   9:    79.151 -  87.946:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3186 r_free = 0.3659             target_work(ml) = 6.019         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3179 r_free = 0.3651             target_work(ml) = 6.017         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3179   r_free= 0.3651   ksol= 0.37   Bsol= 20.00   scale= 1.097   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.96,8.05,8.46,0.00,0.00,0.00); trace/3= 8.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 6.017342                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3148   r_free= 0.3593   ksol= 0.34   Bsol= 30.72   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.58,4.59,5.60,0.00,0.00,0.00); trace/3= 4.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.016538                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.728213              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.370   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.422988              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.308  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3148      final r-factor (work) = 0.2199          |
| start r-factor (free) = 0.3593      final r-factor (free) = 0.2638          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.4734 = 5.73 * 0.50 * 6.0492 + 1.00 * 0.1477                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.8893 = 5.73 * 0.50 * 5.8704 + 1.00 * 0.0757                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2199      final r-factor (work) = 0.1951          |
| start r-factor (free) = 0.2638      final r-factor (free) = 0.2396          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5004 = 0.42 * 1.00 * 5.8704 + 1.00 * 0.0172                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4009 = 0.42 * 1.00 * 5.6501 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.510)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.93   12.32    None  None   None       |
|    all(noH): 2823   0      0.00    88.93   12.32    None  None   None       |
|    Sol.    : 438    0      1.45    88.93   32.52    None  None   None       |
|    Mac.    : 2385   0      0.00    73.80   8.61     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 -   8.893: 1621   |   5:    44.467 -  53.360:   72        |
|      1:     8.893 -  17.787:  604   |   6:    53.360 -  62.254:   35        |
|      2:    17.787 -  26.680:  199   |   7:    62.254 -  71.147:    6        |
|      3:    26.680 -  35.574:  167   |   8:    71.147 -  80.040:    4        |
|      4:    35.574 -  44.467:  114   |   9:    80.040 -  88.934:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1951 r_free = 0.2396             target_work(ml) = 5.605         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1947 r_free = 0.2393             target_work(ml) = 5.604         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1947   r_free= 0.2393   ksol= 0.34   Bsol= 30.72   scale= 1.057   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.58,4.59,5.60,0.00,0.00,0.00); trace/3= 4.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.604368                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1923   r_free= 0.2373   ksol= 0.32   Bsol= 30.72   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.43,3.29,3.81,0.00,0.00,0.00); trace/3= 3.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.600106                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.711075              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.870  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.200824              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.286  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1923      final r-factor (work) = 0.1390          |
| start r-factor (free) = 0.2373      final r-factor (free) = 0.1826          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5736 = 3.71 * 0.50 * 5.6577 + 1.00 * 0.0755                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2097 = 3.71 * 0.50 * 5.4674 + 1.00 * 0.0647                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1390      final r-factor (work) = 0.1311          |
| start r-factor (free) = 0.1826      final r-factor (free) = 0.1708          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1088 = 0.20 * 1.00 * 5.4674 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0714 = 0.20 * 1.00 * 5.2911 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.510)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.16   12.17    None  None   None       |
|    all(noH): 2823   0      0.00    82.16   12.17    None  None   None       |
|    Sol.    : 438    0      2.31    82.16   33.39    None  None   None       |
|    Mac.    : 2385   0      0.00    77.48   8.28     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 -   8.216: 1621   |   5:    41.079 -  49.295:   89        |
|      1:     8.216 -  16.432:  621   |   6:    49.295 -  57.511:   54        |
|      2:    16.432 -  24.648:  162   |   7:    57.511 -  65.727:   14        |
|      3:    24.648 -  32.863:  123   |   8:    65.727 -  73.942:    5        |
|      4:    32.863 -  41.079:  132   |   9:    73.942 -  82.158:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1311 r_free = 0.1708             target_work(ml) = 5.256         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1309 r_free = 0.1708             target_work(ml) = 5.255         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1309   r_free= 0.1708   ksol= 0.32   Bsol= 30.72   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.43,3.29,3.81,0.00,0.00,0.00); trace/3= 3.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.255117                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1309   r_free= 0.1705   ksol= 0.32   Bsol= 32.68   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.70,2.69,3.13,0.00,0.00,0.00); trace/3= 2.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.255066                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.415905              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.383  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.207449              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.290  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1309      final r-factor (work) = 0.1218          |
| start r-factor (free) = 0.1705      final r-factor (free) = 0.1613          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8133 = 1.42 * 0.50 * 5.2953 + 1.00 * 0.0645                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7516 = 1.42 * 0.50 * 5.2254 + 1.00 * 0.0523                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1218      final r-factor (work) = 0.1198          |
| start r-factor (free) = 0.1613      final r-factor (free) = 0.1607          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0928 = 0.21 * 1.00 * 5.2254 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0859 = 0.21 * 1.00 * 5.1909 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.510)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.79   12.21    None  None   None       |
|    all(noH): 2823   0      0.00    78.79   12.21    None  None   None       |
|    Sol.    : 438    0      1.41    78.43   33.69    None  None   None       |
|    Mac.    : 2385   0      0.00    78.79   8.26     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 -   7.879: 1583   |   5:    39.395 -  47.273:   89        |
|      1:     7.879 -  15.758:  655   |   6:    47.273 -  55.152:   61        |
|      2:    15.758 -  23.637:  150   |   7:    55.152 -  63.031:   21        |
|      3:    23.637 -  31.516:  122   |   8:    63.031 -  70.910:    8        |
|      4:    31.516 -  39.395:  130   |   9:    70.910 -  78.789:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1198 r_free = 0.1607             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1197 r_free = 0.1607             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1197   r_free= 0.1607   ksol= 0.32   Bsol= 32.68   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.70,2.69,3.13,0.00,0.00,0.00); trace/3= 2.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.186779                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1197   r_free= 0.1607   ksol= 0.32   Bsol= 33.57   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.52,2.51,2.96,0.00,0.00,0.00); trace/3= 2.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.186599                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.890871              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.221  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.075910              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 160.897  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1197      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1607      final r-factor (free) = 0.1558          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5550 = 2.89 * 0.50 * 5.1907 + 1.00 * 0.0523                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5178 = 2.89 * 0.50 * 5.1504 + 1.00 * 0.0733                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1107      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1558      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5503 = 1.08 * 1.00 * 5.1504 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5230 = 1.08 * 1.00 * 5.1228 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.510)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.65   12.43    None  None   None       |
|    all(noH): 2823   0      0.00    82.65   12.43    None  None   None       |
|    Sol.    : 438    0      1.24    73.30   35.15    None  None   None       |
|    Mac.    : 2385   0      0.00    82.65   8.26     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 -   8.265: 1641   |   5:    41.324 -  49.589:   99        |
|      1:     8.265 -  16.530:  600   |   6:    49.589 -  57.854:   69        |
|      2:    16.530 -  24.795:  163   |   7:    57.854 -  66.119:   23        |
|      3:    24.795 -  33.059:  109   |   8:    66.119 -  74.383:    9        |
|      4:    33.059 -  41.324:  106   |   9:    74.383 -  82.648:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1088 r_free = 0.1571             target_work(ml) = 5.128         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1087 r_free = 0.1572             target_work(ml) = 5.128         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1572   ksol= 0.32   Bsol= 33.57   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.52,2.51,2.96,0.00,0.00,0.00); trace/3= 2.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.127610                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7474 -  4.6781 0.99   1393  157 0.1013 0.1312      5.4029      5.5543|
|  2:  4.6781 -  3.7330 0.99   1343  148 0.0845 0.1113        5.43      5.6353|
|  3:  3.7330 -  3.2670 0.99   1316  150 0.1016 0.1513      5.4445      5.8007|
|  4:  3.2670 -  2.9709 0.99   1309  133 0.1163 0.1584      5.4201      5.6156|
|  5:  2.9709 -  2.7595 0.98   1285  147 0.1239 0.1584      5.2919      5.4702|
|  6:  2.7595 -  2.5977 0.98   1295  143 0.1226 0.1934      5.2037      5.4725|
|  7:  2.5977 -  2.4683 0.99   1293  153 0.1137 0.1532      5.1261      5.3508|
|  8:  2.4683 -  2.3613 0.99   1286  133 0.1135 0.1838      5.0699      5.3664|
|  9:  2.3613 -  2.2707 0.98   1284  147 0.1165 0.1805      5.0161      5.3035|
| 10:  2.2707 -  2.1926 0.97   1255  143 0.1086 0.1650      4.9531      5.1517|
| 11:  2.1926 -  2.1243 0.98   1270  141 0.1084 0.1718      4.8996      5.2608|
| 12:  2.1243 -  2.0637 0.99   1278  140 0.1053 0.1747      4.8276      5.1354|
| 13:  2.0637 -  2.0095 0.97   1261  134 0.1065 0.1648      4.7645      4.9947|
| 14:  2.0095 -  1.9606 0.60    762   90 0.1073 0.1709      4.6944      4.9287|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7474 -  4.6781  1393   157  0.94   9.21   0.98     0.96       7373.42|
|  2:  4.6781 -  3.7330  1343   148  0.95   8.02   1.02     1.01       9068.84|
|  3:  3.7330 -  3.2670  1316   150  0.94  10.93   1.04     1.03      10008.28|
|  4:  3.2670 -  2.9709  1309   133  0.92  13.08   1.01     1.01       9751.42|
|  5:  2.9709 -  2.7595  1285   147  0.90  15.51   0.99     0.96       7976.22|
|  6:  2.7595 -  2.5977  1295   143  0.90  16.03   0.98     0.94       6890.90|
|  7:  2.5977 -  2.4683  1293   153  0.91  15.14   0.98     0.95       5928.82|
|  8:  2.4683 -  2.3613  1286   133  0.91  15.00   1.00     0.97       5440.23|
|  9:  2.3613 -  2.2707  1284   147  0.91  15.72   1.01     0.98       4933.64|
| 10:  2.2707 -  2.1926  1255   143  0.90  15.61   1.00     0.97       4463.43|
| 11:  2.1926 -  2.1243  1270   141  0.91  15.50   1.00     0.97       4133.52|
| 12:  2.1243 -  2.0637  1278   140  0.91  14.83   1.01     0.99       3626.21|
| 13:  2.0637 -  2.0095  1261   134  0.91  15.49   1.01     1.00       3254.66|
| 14:  2.0095 -  1.9606   762    90  0.91  15.25   0.99     0.95       2709.22|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2709.22 max =        10008.28 mean =      6251.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.85|
|phase err.(test): min =        0.00 max =           89.30 mean =        13.34|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1571   ksol= 0.32   Bsol= 38.57   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.80,0.17,0.63,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.127325                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1571   ksol= 0.32   Bsol= 38.57   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.80,0.17,0.63,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.127325                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7474 -  4.6781 0.99   1393  157 0.1013 0.1315      5.4022      5.5549|
|  2:  4.6781 -  3.7330 0.99   1343  148 0.0849 0.1114      5.4323      5.6379|
|  3:  3.7330 -  3.2670 0.99   1316  150 0.1017 0.1514      5.4459      5.8016|
|  4:  3.2670 -  2.9709 0.99   1309  133 0.1163 0.1580      5.4198      5.6147|
|  5:  2.9709 -  2.7595 0.98   1285  147 0.1238 0.1584      5.2909      5.4695|
|  6:  2.7595 -  2.5977 0.98   1295  143 0.1225 0.1932      5.2026      5.4711|
|  7:  2.5977 -  2.4683 0.99   1293  153 0.1137 0.1533       5.125      5.3509|
|  8:  2.4683 -  2.3613 0.99   1286  133 0.1135 0.1834       5.069      5.3644|
|  9:  2.3613 -  2.2707 0.98   1284  147 0.1165 0.1806      5.0156      5.3038|
| 10:  2.2707 -  2.1926 0.97   1255  143 0.1085 0.1650      4.9528      5.1511|
| 11:  2.1926 -  2.1243 0.98   1270  141 0.1083 0.1717      4.8993       5.261|
| 12:  2.1243 -  2.0637 0.99   1278  140 0.1053 0.1747      4.8275      5.1355|
| 13:  2.0637 -  2.0095 0.97   1261  134 0.1065 0.1646      4.7639      4.9938|
| 14:  2.0095 -  1.9606 0.60    762   90 0.1073 0.1706      4.6931      4.9269|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7474 -  4.6781  1393   157  0.94   9.20   0.99     0.96       7359.64|
|  2:  4.6781 -  3.7330  1343   148  0.95   8.05   1.03     1.01       9092.14|
|  3:  3.7330 -  3.2670  1316   150  0.94  10.95   1.04     1.03      10042.45|
|  4:  3.2670 -  2.9709  1309   133  0.92  13.08   1.02     1.01       9743.85|
|  5:  2.9709 -  2.7595  1285   147  0.90  15.50   1.00     0.97       7959.67|
|  6:  2.7595 -  2.5977  1295   143  0.90  16.01   0.98     0.95       6879.76|
|  7:  2.5977 -  2.4683  1293   153  0.91  15.12   0.99     0.96       5916.87|
|  8:  2.4683 -  2.3613  1286   133  0.91  14.99   1.00     0.98       5430.18|
|  9:  2.3613 -  2.2707  1284   147  0.91  15.70   1.02     0.99       4924.98|
| 10:  2.2707 -  2.1926  1255   143  0.90  15.60   1.01     0.98       4461.06|
| 11:  2.1926 -  2.1243  1270   141  0.91  15.50   1.01     0.98       4132.39|
| 12:  2.1243 -  2.0637  1278   140  0.91  14.82   1.02     1.00       3625.46|
| 13:  2.0637 -  2.0095  1261   134  0.91  15.48   1.02     1.01       3248.70|
| 14:  2.0095 -  1.9606   762    90  0.91  15.21   1.00     0.96       2698.05|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2698.05 max =        10042.45 mean =      6248.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.85|
|phase err.(test): min =        0.00 max =           89.21 mean =        13.33|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.510)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.47    85.12   14.91    None  None   None       |
|    all(noH): 2823   0      2.47    85.12   14.91    None  None   None       |
|    Sol.    : 438    0      3.71    75.77   37.62    None  None   None       |
|    Mac.    : 2385   0      2.47    85.12   10.74    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:     2.474 -  10.739: 1641   |   5:    43.798 -  52.063:   99        |
|      1:    10.739 -  19.004:  600   |   6:    52.063 -  60.328:   69        |
|      2:    19.004 -  27.268:  163   |   7:    60.328 -  68.593:   23        |
|      3:    27.268 -  35.533:  109   |   8:    68.593 -  76.857:    9        |
|      4:    35.533 -  43.798:  106   |   9:    76.857 -  85.122:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 300         
Filter by distance & map next to the model:
   mapped sites are within: 0.385 - 5.997
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 298 from: 300
   mapped sites are within: 0.730 - 5.997

peak=   11.115 closest distance to " CB  VAL A 230 " =    1.422
peak=    7.177 closest distance to " CG2 VAL A 296 " =    1.142
peak=    6.207 closest distance to " CG  LEU A   5 " =    1.134
peak=    5.898 closest distance to " CB  VAL A 296 " =    1.036
peak=    5.560 closest distance to " O   HOH Z 193 " =    1.799
peak=    5.310 closest distance to " CG  LEU A 228 " =    1.128
peak=    5.283 closest distance to " CB  GLN A 183 " =    1.323
peak=    5.271 closest distance to " NE2 GLN A  11 " =    1.076
peak=    5.257 closest distance to " O   HOH Z 126 " =    1.981
peak=    5.225 closest distance to " O   HOH Z 142 " =    1.773
peak=    5.135 closest distance to " O   HOH Z 278 " =    1.234
peak=    4.926 closest distance to " NH2 ARG A  56 " =    2.146
peak=    4.909 closest distance to " CB  ARG A 275 " =    0.968
peak=    4.880 closest distance to " CD2 LEU A   5 " =    1.117
peak=    4.877 closest distance to " CB  SER A  63 " =    1.164
peak=    4.790 closest distance to " O   SER A  87 " =    2.234
peak=    4.788 closest distance to " O   HOH Z  85 " =    1.541
peak=    4.781 closest distance to " O   HOH Z 232 " =    2.299
peak=    4.769 closest distance to " O   HOH Z 209 " =    2.360
peak=    4.695 closest distance to " CG  PRO A 213 " =    1.200
peak=    4.689 closest distance to " O   HOH Z 124 " =    1.479
peak=    4.662 closest distance to " C   PRO A 198 " =    1.459
peak=    4.631 closest distance to " CB  GLN A 223 " =    1.451
peak=    4.600 closest distance to " O   HOH Z 368 " =    2.115
peak=    4.581 closest distance to " O   HOH Z 403 " =    1.885
peak=    4.568 closest distance to " CG  PRO A  54 " =    1.157
peak=    4.558 closest distance to " O   HOH Z 128 " =    2.148
peak=    4.522 closest distance to " O   HOH Z 402 " =    1.451
peak=    4.519 closest distance to " O   HOH Z  59 " =    2.114
peak=    4.498 closest distance to " O   HOH Z 234 " =    3.552
peak=    4.496 closest distance to " CB  VAL A 230 " =    1.118
peak=    4.448 closest distance to " O   HOH Z 327 " =    1.785
peak=    4.418 closest distance to " CB  GLU A 152 " =    1.123
peak=    4.385 closest distance to " O   HOH Z 272 " =    1.866
peak=    4.353 closest distance to " O   HOH Z 369 " =    2.360
peak=    4.309 closest distance to " O   HOH Z  97 " =    2.441
peak=    4.300 closest distance to " O   HOH Z  54 " =    1.574
peak=    4.281 closest distance to " O   HOH Z 298 " =    1.864
peak=    4.260 closest distance to " O   HOH Z 316 " =    2.810
peak=    4.256 closest distance to " O   HOH Z 346 " =    1.540
peak=    4.211 closest distance to " CB  ARG A  79 " =    1.391
peak=    4.209 closest distance to " CD2 TRP A 179 " =    1.410
peak=    4.197 closest distance to " CB  SER A   3 " =    1.243
peak=    4.175 closest distance to " CA  ALA A  21 " =    1.153
peak=    4.165 closest distance to " CA  TYR A  30 " =    0.972
peak=    4.152 closest distance to " O   HOH Z 423 " =    1.866
peak=    4.149 closest distance to " O   HOH Z 203 " =    1.549
peak=    4.130 closest distance to " O   HOH Z 303 " =    2.053
peak=    4.117 closest distance to " O   HOH Z 411 " =    3.609
peak=    4.111 closest distance to " CB  TYR A 169 " =    0.882
peak=    4.108 closest distance to " CB  SER A  26 " =    1.684
peak=    4.106 closest distance to " O   HOH Z 345 " =    2.823
peak=    4.079 closest distance to " CB  ASN A 148 " =    1.440
peak=    4.066 closest distance to " O   HOH Z  97 " =    1.934
peak=    4.046 closest distance to " O   HOH Z  48 " =    1.788
peak=    4.014 closest distance to " O   HOH Z 250 " =    1.359
peak=    4.004 closest distance to " O   HOH Z 425 " =    2.033
peak=    3.997 closest distance to " O   HOH Z 322 " =    2.045
peak=    3.989 closest distance to " O   HOH Z  78 " =    1.582
peak=    3.981 closest distance to " NZ  LYS A 117 " =    2.913
peak=    3.968 closest distance to " CG2 ILE A  20 " =    1.457
peak=    3.964 closest distance to " O   HOH Z  43 " =    2.174
peak=    3.957 closest distance to " OE1 GLU A   2 " =    2.136
peak=    3.951 closest distance to " CD2 LEU A 228 " =    1.211
peak=    3.946 closest distance to " O   HOH Z 287 " =    1.819
peak=    3.945 closest distance to " CG  ARG A  66 " =    1.078
peak=    3.936 closest distance to " O   HOH Z 197 " =    3.002
peak=    3.925 closest distance to " O   HOH Z 134 " =    1.427
peak=    3.913 closest distance to " O   HOH Z 414 " =    1.474
peak=    3.908 closest distance to " O   HOH Z 426 " =    1.455
peak=    3.898 closest distance to " O   HOH Z 425 " =    1.367
peak=    3.898 closest distance to " ND2 ASN A 187 " =    1.445
peak=    3.897 closest distance to " O   HOH Z  80 " =    1.626
peak=    3.893 closest distance to " O   HOH Z 371 " =    3.171
peak=    3.882 closest distance to " O   HOH Z 427 " =    2.581
peak=    3.869 closest distance to " CB  TRP A 179 " =    1.204
peak=    3.862 closest distance to " O   HOH Z 280 " =    2.895
peak=    3.851 closest distance to " CD  ARG A 269 " =    1.066
peak=    3.850 closest distance to " CG  GLN A  77 " =    2.268
peak=    3.850 closest distance to " O   HOH Z 408 " =    1.626
peak=    3.846 closest distance to " N   ASN A  39 " =    1.224
peak=    3.845 closest distance to " O   HOH Z 357 " =    1.860
peak=    3.845 closest distance to " O   HOH Z  15 " =    2.059
peak=    3.838 closest distance to " O   HOH Z  61 " =    1.677
peak=    3.835 closest distance to " O   HOH Z 118 " =    1.684
peak=    3.828 closest distance to " O   HOH Z 265 " =    2.396
peak=    3.820 closest distance to " O   HOH Z  63 " =    2.204
peak=    3.812 closest distance to " CB  VAL A 265 " =    1.212
peak=    3.809 closest distance to " O   HOH Z 344 " =    2.666
peak=    3.801 closest distance to " CA  VAL A  41 " =    0.816
peak=    3.795 closest distance to " O   HOH Z  44 " =    1.961
peak=    3.790 closest distance to " CB  ARG A 139 " =    1.007
peak=    3.787 closest distance to " O   HOH Z 128 " =    1.866
peak=    3.787 closest distance to " CB  ALA A   9 " =    1.569
peak=    3.782 closest distance to " O   HOH Z 417 " =    3.306
peak=    3.782 closest distance to " O   HOH Z 137 " =    1.633
peak=    3.777 closest distance to " CB  GLU A 277 " =    3.460
peak=    3.777 closest distance to " CG1BVAL A  72 " =    1.530
peak=    3.775 closest distance to " O   HOH Z 102 " =    1.261
peak=    3.754 closest distance to " OD2 ASP A 298 " =    3.968
peak=    3.751 closest distance to " CG1 ILE A  33 " =    1.241
peak=    3.750 closest distance to " O   HOH Z 118 " =    1.384
peak=    3.749 closest distance to " OD1 ASN A  69 " =    2.651
peak=    3.749 closest distance to " O   HOH Z 406 " =    1.143
peak=    3.739 closest distance to " O   HOH Z 366 " =    2.867
peak=    3.735 closest distance to " O   HOH Z 416 " =    2.718
peak=    3.729 closest distance to " O   HOH Z  61 " =    1.521
peak=    3.716 closest distance to " O   HOH Z 245 " =    1.402
peak=    3.714 closest distance to " CB  PRO A  54 " =    0.837
peak=    3.712 closest distance to " O   HOH Z 108 " =    2.402
peak=    3.703 closest distance to " O   HOH Z 189 " =    2.395
peak=    3.700 closest distance to " O   ASP A 124 " =    1.236
peak=    3.700 closest distance to " O   HOH Z 236 " =    1.396
peak=    3.695 closest distance to " O   HOH Z 273 " =    2.765
peak=    3.686 closest distance to " O   TRP A 274 " =    1.918
peak=    3.672 closest distance to " OG1 THR A 294 " =    2.314
peak=    3.663 closest distance to " O   HOH Z 299 " =    4.265
peak=    3.661 closest distance to " CA  ALA A  51 " =    1.040
peak=    3.659 closest distance to " CG  ARG A  66 " =    2.853
peak=    3.652 closest distance to " OG BSER A 164 " =    2.155
peak=    3.651 closest distance to " O   HOH Z 213 " =    1.720
peak=    3.647 closest distance to " CB  ASN A 148 " =    1.940
peak=    3.646 closest distance to " O   HOH Z 303 " =    1.624
peak=    3.646 closest distance to " CA  ASN A 176 " =    1.031
peak=    3.643 closest distance to " O   HOH Z 419 " =    1.621
peak=    3.642 closest distance to " CG  GLN A  58 " =    2.702
peak=    3.639 closest distance to " O   HOH Z 422 " =    2.581
peak=    3.636 closest distance to " O   HOH Z 193 " =    2.060
peak=    3.630 closest distance to " O   HOH Z 406 " =    1.336
peak=    3.628 closest distance to " CB  GLU A 128 " =    1.151
peak=    3.626 closest distance to " CB  ALA A 295 " =    1.170
peak=    3.623 closest distance to " O   HOH Z 261 " =    1.999
peak=    3.616 closest distance to " O   HOH Z 227 " =    1.570
peak=    3.605 closest distance to " OD2 ASP A 286 " =    2.599
peak=    3.604 closest distance to " CG2AVAL A 121 " =    2.231
peak=    3.598 closest distance to " CG AARG A 275 " =    1.140
peak=    3.589 closest distance to " O   HOH Z 250 " =    1.474
peak=    3.580 closest distance to " CB  ASN A 110 " =    1.143
peak=    3.575 closest distance to " CA  LYS A 117 " =    1.287
peak=    3.569 closest distance to " O   HOH Z  66 " =    2.125
peak=    3.569 closest distance to " O   HOH Z 214 " =    2.487
peak=    3.563 closest distance to " CB  THR A  31 " =    1.651
peak=    3.563 closest distance to " CB  ALA A 248 " =    1.371
peak=    3.561 closest distance to " CB  TRP A 266 " =    1.059
peak=    3.558 closest distance to " CB  ASN A  39 " =    0.805
peak=    3.558 closest distance to " OD1 ASP A 286 " =    1.687
peak=    3.544 closest distance to " CB BVAL A  41 " =    1.106
peak=    3.540 closest distance to " CG2 ILE A 120 " =    1.211
peak=    3.533 closest distance to " O   HOH Z 109 " =    2.194
peak=    3.532 closest distance to " O   HOH Z 154 " =    1.397
peak=    3.512 closest distance to " CD1 ILE A 106 " =    1.220
peak=    3.511 closest distance to " O   HOH Z 389 " =    1.789
peak=    3.511 closest distance to " CG2 THR A 294 " =    1.550
peak=    3.510 closest distance to " O   HOH Z 367 " =    3.321
peak=    3.508 closest distance to " O   HOH Z 147 " =    1.671
peak=    3.503 closest distance to " O   HOH Z 263 " =    1.536
peak=    3.497 closest distance to " CA  ASP A 140 " =    1.136
peak=    3.496 closest distance to " CB  VAL A 202 " =    1.549
peak=    3.493 closest distance to " O   HOH Z 251 " =    1.622
peak=    3.488 closest distance to " O   HOH Z 209 " =    2.276
peak=    3.481 closest distance to " CD  GLN A 194 " =    1.484
peak=    3.480 closest distance to " O   HOH Z  40 " =    1.542
peak=    3.479 closest distance to " O   HOH Z 374 " =    2.389
peak=    3.475 closest distance to " O   HOH Z  59 " =    2.077
peak=    3.474 closest distance to " O   HOH Z 130 " =    2.471
peak=    3.468 closest distance to " O   HOH Z 249 " =    0.992
peak=    3.465 closest distance to " CD2 TYR A  30 " =    0.863
peak=    3.456 closest distance to " O   HOH Z 380 " =    1.913
peak=    3.445 closest distance to " O   HOH Z 148 " =    3.229
peak=    3.439 closest distance to " O   HOH Z 421 " =    1.612
peak=    3.438 closest distance to " CB  ALA A   1 " =    1.169
peak=    3.433 closest distance to " O   HOH Z 248 " =    1.619
peak=    3.432 closest distance to " O   HOH Z 404 " =    2.152
peak=    3.432 closest distance to " CZ AARG A 102 " =    1.707
peak=    3.425 closest distance to " O   HOH Z 344 " =    1.878
peak=    3.424 closest distance to " CG  PRO A 243 " =    1.235
peak=    3.421 closest distance to " C   ALA A   1 " =    1.717
peak=    3.421 closest distance to " O   HOH Z 261 " =    2.101
peak=    3.418 closest distance to " O   HOH Z  49 " =    2.207
peak=    3.418 closest distance to " CG2 THR A 221 " =    1.245
peak=    3.412 closest distance to " CE  LYS A 119 " =    1.049
peak=    3.409 closest distance to " CZ2 TRP A 179 " =    1.799
peak=    3.405 closest distance to " O   HOH Z 215 " =    1.394
peak=    3.400 closest distance to " NH2BARG A 145 " =    2.358
peak=    3.400 closest distance to " CG2 ILE A 234 " =    1.013
peak=    3.399 closest distance to " O   HOH Z 329 " =    3.705
peak=    3.395 closest distance to " CD BLYS A 290 " =    1.129
peak=    3.385 closest distance to " CA  ALA A 291 " =    0.870
peak=    3.380 closest distance to " O   HOH Z  35 " =    2.285
peak=    3.377 closest distance to " CA  SER A 146 " =    1.905
peak=    3.375 closest distance to " CE1 TYR A 186 " =    1.258
peak=    3.375 closest distance to " O   HOH Z 435 " =    1.955
peak=    3.371 closest distance to " CG  MET A 185 " =    1.149
peak=    3.366 closest distance to " CA  VAL A 126 " =    1.021
peak=    3.365 closest distance to " O   HOH Z 420 " =    2.039
peak=    3.357 closest distance to " O   HOH Z 227 " =    2.149
peak=    3.355 closest distance to " O   HOH Z 411 " =    1.757
peak=    3.352 closest distance to " CD  LYS A 166 " =    1.355
peak=    3.352 closest distance to " NH2 ARG A  79 " =    1.352
peak=    3.351 closest distance to " CB  THR A  52 " =    1.033
peak=    3.349 closest distance to " O   HOH Z   9 " =    2.276
peak=    3.346 closest distance to " O   HOH Z 158 " =    2.992
peak=    3.345 closest distance to " CA  ARG A  36 " =    1.032
peak=    3.345 closest distance to " O   HOH Z 423 " =    3.214
peak=    3.344 closest distance to " CD2 HIS A  81 " =    1.042
peak=    3.343 closest distance to " O   HOH Z  88 " =    2.996
peak=    3.340 closest distance to " NE2 GLN A  58 " =    5.997
peak=    3.338 closest distance to " CB  VAL A 268 " =    0.839
peak=    3.334 closest distance to " O   HOH Z 175 " =    2.179
peak=    3.323 closest distance to " O   HOH Z 326 " =    1.404
peak=    3.322 closest distance to " O   HOH Z 279 " =    2.093
peak=    3.319 closest distance to " CA  LYS A 290 " =    1.303
peak=    3.313 closest distance to " C   ILE A 106 " =    1.875
peak=    3.312 closest distance to " NH2 ARG A 156 " =    1.068
peak=    3.312 closest distance to " N   ASP A 162 " =    1.283
peak=    3.312 closest distance to " CD1 LEU A  96 " =    0.730
peak=    3.310 closest distance to " O   GLY A  91 " =    1.586
peak=    3.299 closest distance to " CA  ASP A 162 " =    1.073
peak=    3.299 closest distance to " O   HOH Z 189 " =    2.622
peak=    3.295 closest distance to " OH  TYR A 116 " =    1.109
peak=    3.294 closest distance to " O   HOH Z 261 " =    1.769
peak=    3.288 closest distance to " CB  TYR A 169 " =    0.793
peak=    3.288 closest distance to " O   HOH Z 132 " =    2.613
peak=    3.287 closest distance to " CB  ARG A 190 " =    1.714
peak=    3.287 closest distance to " NZ  LYS A  76 " =    1.750
peak=    3.287 closest distance to " O   HOH Z 337 " =    3.526
peak=    3.280 closest distance to " CA  ASN A 215 " =    1.174
peak=    3.280 closest distance to " O   HOH Z 145 " =    3.624
peak=    3.273 closest distance to " O   HOH Z 345 " =    1.559
peak=    3.266 closest distance to " O   HOH Z 292 " =    1.560
peak=    3.257 closest distance to " OG  SER A  62 " =    2.875
peak=    3.246 closest distance to " O   HOH Z 313 " =    1.819
peak=    3.244 closest distance to " CZ2 TRP A 150 " =    1.088
peak=    3.244 closest distance to " CD1 LEU A 228 " =    1.703
peak=    3.241 closest distance to " O   HOH Z 388 " =    1.874
peak=    3.240 closest distance to " O   HOH Z  21 " =    1.815
peak=    3.237 closest distance to " O   HOH Z 192 " =    1.840
peak=    3.232 closest distance to " CB  ALA A  71 " =    1.298
peak=    3.231 closest distance to " CB  GLN A  88 " =    1.204
peak=    3.225 closest distance to " CE  LYS A  48 " =    1.386
peak=    3.216 closest distance to " O   HOH Z 291 " =    1.627
peak=    3.209 closest distance to " O   HOH Z 271 " =    1.504
peak=    3.208 closest distance to " CZ2 TRP A 274 " =    1.674
peak=    3.205 closest distance to " CB  GLN A 278 " =    0.908
peak=    3.202 closest distance to " O   HOH Z 392 " =    1.749
peak=    3.202 closest distance to " CD2 LEU A 297 " =    0.984
peak=    3.200 closest distance to " OG BSER A 258 " =    3.100
peak=    3.197 closest distance to " CB  ILE A 120 " =    1.508
peak=    3.197 closest distance to " O   HOH Z 361 " =    3.135
peak=    3.195 closest distance to " O   HOH Z 180 " =    2.213
peak=    3.193 closest distance to " N   PHE A 130 " =    1.382
peak=    3.191 closest distance to " O   HOH Z 280 " =    2.562
peak=    3.187 closest distance to " O   HOH Z 250 " =    1.802
peak=    3.187 closest distance to " O   HOH Z 227 " =    1.689
peak=    3.187 closest distance to " CD  ARG A  79 " =    2.033
peak=    3.183 closest distance to " CG  MET A 188 " =    1.353
peak=    3.177 closest distance to " CB  GLN A 205 " =    1.261
peak=    3.176 closest distance to " O   HOH Z 244 " =    1.546
peak=    3.169 closest distance to " CA  ALA A  84 " =    1.391
peak=    3.169 closest distance to " CB  ASP A 140 " =    0.987
peak=    3.168 closest distance to " CA  SER A  32 " =    1.631
peak=    3.167 closest distance to " NH1 ARG A 138 " =    1.326
peak=    3.166 closest distance to " CA  GLY A  80 " =    0.953
peak=    3.162 closest distance to " CG1 ILE A  49 " =    1.373
peak=    3.157 closest distance to " N   ARG A 156 " =    1.313
peak=    3.154 closest distance to " CA  GLN A 194 " =    1.209
peak=    3.153 closest distance to " CB  PRO A 213 " =    1.949
peak=    3.151 closest distance to " CD  LYS A 119 " =    1.973
peak=    3.147 closest distance to " O   HOH Z 359 " =    1.340
peak=    3.146 closest distance to " O   HOH Z 299 " =    2.223
peak=    3.142 closest distance to " O   HOH Z  42 " =    2.170
peak=    3.142 closest distance to " O   HOH Z 128 " =    1.727
peak=    3.137 closest distance to " OE2 GLU A  53 " =    2.080
peak=    3.137 closest distance to " CG  GLN A  89 " =    1.595
peak=    3.132 closest distance to " NH2BARG A 190 " =    1.885
peak=    3.130 closest distance to " CB  ASN A 215 " =    1.049
peak=    3.123 closest distance to " CB  SER A 141 " =    1.109
peak=    3.118 closest distance to " O   HOH Z  39 " =    2.629
peak=    3.116 closest distance to " O   HOH Z  71 " =    1.696
peak=    3.109 closest distance to " O   HOH Z  68 " =    1.552
peak=    3.107 closest distance to " O   ASN A  69 " =    1.521
peak=    3.106 closest distance to " CB  ARG A 259 " =    1.921
peak=    3.096 closest distance to " CB  ALA A 291 " =    1.299
peak=    3.091 closest distance to " O   HOH Z 438 " =    1.979
peak=    3.085 closest distance to " O   HOH Z 197 " =    2.061
peak=    3.077 closest distance to " O   HOH Z 302 " =    1.582
peak=    3.075 closest distance to " O   HOH Z  83 " =    1.546
peak=    3.073 closest distance to " CB  TYR A  30 " =    0.990
peak=    3.072 closest distance to " O   HOH Z  88 " =    2.570
peak=    3.069 closest distance to " O   HOH Z 233 " =    1.504
peak=    3.065 closest distance to " O   HOH Z 266 " =    1.383
peak=    3.064 closest distance to " O   HOH Z   3 " =    1.590
peak=    3.064 closest distance to " CB  MET A  47 " =    1.290
peak=    3.055 closest distance to " O   HOH Z 362 " =    3.535
peak=    3.053 closest distance to " O   HOH Z 151 " =    1.658
peak=    3.047 closest distance to " CG  MET A 185 " =    1.030
peak=    3.027 closest distance to " N   SER A 135 " =    1.241
peak=    3.025 closest distance to " CG1 ILE A 120 " =    1.233

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.644 - 5.799
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 202
   mapped sites are within: 0.725 - 5.799

peak=   -4.746 closest distance to " CD  ARG A 156 " =    2.060
peak=   -4.742 closest distance to " SG  CYS A 254 " =    3.216
peak=   -4.700 closest distance to " CG2 VAL A 230 " =    0.814
peak=   -4.640 closest distance to " O   HOH Z 266 " =    4.581
peak=   -4.421 closest distance to " OXT GLY A 302 " =    2.770
peak=   -4.367 closest distance to " O   PRO A 163 " =    2.045
peak=   -4.355 closest distance to " C   HIS A 108 " =    1.212
peak=   -4.347 closest distance to " CD1 LEU A 101 " =    2.453
peak=   -4.172 closest distance to " CD2 TYR A  30 " =    2.765
peak=   -4.148 closest distance to " CB  ALA A 161 " =    2.494
peak=   -4.118 closest distance to " O   VAL A  67 " =    2.737
peak=   -4.114 closest distance to " N   ALA A 248 " =    1.718
peak=   -4.111 closest distance to " OG BSER A 134 " =    1.261
peak=   -4.110 closest distance to " CB  ALA A 291 " =    2.427
peak=   -4.052 closest distance to " OD1 ASN A  39 " =    2.168
peak=   -3.997 closest distance to " O   HOH Z 166 " =    1.571
peak=   -3.950 closest distance to " O   HOH Z 290 " =    1.024
peak=   -3.913 closest distance to " O   HOH Z  37 " =    1.832
peak=   -3.903 closest distance to " CG  GLN A 223 " =    2.109
peak=   -3.895 closest distance to " O   ASN A  45 " =    1.815
peak=   -3.870 closest distance to " O   HOH Z  13 " =    1.625
peak=   -3.867 closest distance to " O   HOH Z 114 " =    3.126
peak=   -3.824 closest distance to " OG  SER A  97 " =    2.199
peak=   -3.824 closest distance to " O   ALA A   8 " =    1.856
peak=   -3.785 closest distance to " O   HOH Z  11 " =    1.803
peak=   -3.782 closest distance to " CG2 VAL A 296 " =    1.433
peak=   -3.781 closest distance to " O   PHE A 218 " =    1.656
peak=   -3.776 closest distance to " O   GLY A  80 " =    2.429
peak=   -3.769 closest distance to " NH2 ARG A  79 " =    1.942
peak=   -3.766 closest distance to " O   HOH Z 166 " =    1.942
peak=   -3.761 closest distance to " O   HOH Z 351 " =    1.495
peak=   -3.744 closest distance to " ND2 ASN A  45 " =    1.070
peak=   -3.744 closest distance to " O   MET A  40 " =    2.711
peak=   -3.737 closest distance to " ND2 ASN A 187 " =    1.528
peak=   -3.733 closest distance to " O   HOH Z 102 " =    1.679
peak=   -3.715 closest distance to " CB  ALA A 248 " =    1.984
peak=   -3.702 closest distance to " CD  LYS A 289 " =    2.440
peak=   -3.701 closest distance to " CB  PRO A 163 " =    2.566
peak=   -3.679 closest distance to " N   GLN A  58 " =    1.812
peak=   -3.672 closest distance to " O   HOH Z 231 " =    2.237
peak=   -3.670 closest distance to " O   HOH Z 407 " =    2.867
peak=   -3.667 closest distance to " CG2BVAL A  41 " =    2.651
peak=   -3.662 closest distance to " OG  SER A   3 " =    1.410
peak=   -3.662 closest distance to " C   GLN A 205 " =    1.854
peak=   -3.659 closest distance to " CB  ASP A 132 " =    2.257
peak=   -3.658 closest distance to " CD  ARG A 139 " =    1.649
peak=   -3.654 closest distance to " O   HOH Z 426 " =    1.708
peak=   -3.650 closest distance to " O   HOH Z 362 " =    5.799
peak=   -3.647 closest distance to " O   HOH Z 165 " =    1.960
peak=   -3.646 closest distance to " CD2 LEU A 300 " =    2.799
peak=   -3.646 closest distance to " O   HOH Z 250 " =    1.355
peak=   -3.641 closest distance to " CD1 LEU A 255 " =    2.690
peak=   -3.641 closest distance to " O   HOH Z 196 " =    2.168
peak=   -3.639 closest distance to " O   ALA A 256 " =    1.486
peak=   -3.624 closest distance to " CD  GLN A  58 " =    1.330
peak=   -3.622 closest distance to " NE2 GLN A  88 " =    1.148
peak=   -3.618 closest distance to " O   HOH Z 423 " =    2.079
peak=   -3.614 closest distance to " O   ALA A 161 " =    1.656
peak=   -3.614 closest distance to " CB  ASP A 132 " =    2.283
peak=   -3.599 closest distance to " O   VAL A 197 " =    1.303
peak=   -3.590 closest distance to " N   SER A 276 " =    1.310
peak=   -3.588 closest distance to " O   ALA A  51 " =    1.242
peak=   -3.579 closest distance to " CB  ALA A  43 " =    2.258
peak=   -3.576 closest distance to " NE2 GLN A  88 " =    1.970
peak=   -3.576 closest distance to " CG2 THR A 178 " =    2.189
peak=   -3.570 closest distance to " O   HOH Z 191 " =    5.258
peak=   -3.556 closest distance to " OD2 ASP A 191 " =    1.489
peak=   -3.555 closest distance to " CB  PHE A 192 " =    1.910
peak=   -3.539 closest distance to " O   SER A 210 " =    1.869
peak=   -3.536 closest distance to " O   HOH Z 353 " =    2.120
peak=   -3.536 closest distance to " CB  ASN A  39 " =    2.132
peak=   -3.535 closest distance to " O   ALA A 160 " =    1.468
peak=   -3.534 closest distance to " CG1 VAL A  78 " =    2.591
peak=   -3.527 closest distance to " NE2 GLN A 194 " =    1.751
peak=   -3.526 closest distance to " N   ALA A 226 " =    1.947
peak=   -3.525 closest distance to " CZ  TYR A 169 " =    1.781
peak=   -3.521 closest distance to " CA  GLY A  23 " =    1.853
peak=   -3.516 closest distance to " CE  MET A 105 " =    2.140
peak=   -3.504 closest distance to " N   HIS A 115 " =    1.942
peak=   -3.497 closest distance to " CB  PRO A 280 " =    2.115
peak=   -3.494 closest distance to " CA  GLY A 133 " =    1.891
peak=   -3.491 closest distance to " O   HOH Z 174 " =    4.251
peak=   -3.490 closest distance to " CG  GLU A   2 " =    1.891
peak=   -3.485 closest distance to " NH2 ARG A  66 " =    1.661
peak=   -3.472 closest distance to " O   HOH Z 431 " =    1.770
peak=   -3.471 closest distance to " ND2 ASN A  39 " =    1.145
peak=   -3.470 closest distance to " CG1 VAL A 112 " =    2.722
peak=   -3.468 closest distance to " O   HOH Z 234 " =    3.976
peak=   -3.468 closest distance to " O   HOH Z  56 " =    2.255
peak=   -3.467 closest distance to " O   HOH Z 389 " =    1.753
peak=   -3.467 closest distance to " O   HOH Z  17 " =    1.379
peak=   -3.461 closest distance to " CG  LEU A 228 " =    1.107
peak=   -3.456 closest distance to " C   ASP A 231 " =    2.474
peak=   -3.455 closest distance to " O   HOH Z 193 " =    1.611
peak=   -3.455 closest distance to " OG ASER A 134 " =    1.178
peak=   -3.454 closest distance to " CG  LYS A 193 " =    2.147
peak=   -3.449 closest distance to " C   ASN A 187 " =    1.911
peak=   -3.442 closest distance to " N   PHE A  59 " =    2.120
peak=   -3.438 closest distance to " O   VAL A 125 " =    2.301
peak=   -3.436 closest distance to " N   THR A 157 " =    1.528
peak=   -3.433 closest distance to " OG BSER A 134 " =    1.586
peak=   -3.432 closest distance to " O   TRP A  92 " =    1.809
peak=   -3.429 closest distance to " N   ALA A 248 " =    2.226
peak=   -3.424 closest distance to " CD1 PHE A  59 " =    1.928
peak=   -3.418 closest distance to " CG  ASP A 231 " =    0.844
peak=   -3.405 closest distance to " N   ASP A 200 " =    1.611
peak=   -3.400 closest distance to " O   HOH Z 422 " =    1.602
peak=   -3.396 closest distance to " CA  ASP A 298 " =    1.029
peak=   -3.391 closest distance to " NH2AARG A 275 " =    4.837
peak=   -3.388 closest distance to " O   SER A 146 " =    1.027
peak=   -3.380 closest distance to " CG  ASP A  50 " =    2.460
peak=   -3.372 closest distance to " CE BMET A  47 " =    1.638
peak=   -3.367 closest distance to " CG  PHE A 283 " =    2.719
peak=   -3.364 closest distance to " O   HOH Z 427 " =    1.512
peak=   -3.361 closest distance to " O   HOH Z  11 " =    1.828
peak=   -3.356 closest distance to " C   MET A 188 " =    1.500
peak=   -3.356 closest distance to " CG  GLU A  53 " =    1.611
peak=   -3.355 closest distance to " O   PRO A 198 " =    1.268
peak=   -3.344 closest distance to " OG  SER A  26 " =    1.192
peak=   -3.342 closest distance to " C   ALA A 158 " =    1.256
peak=   -3.331 closest distance to " O   HOH Z  97 " =    1.191
peak=   -3.330 closest distance to " O   HOH Z 211 " =    1.481
peak=   -3.329 closest distance to " CD2 TYR A 293 " =    2.049
peak=   -3.316 closest distance to " CD1 TYR A 247 " =    2.375
peak=   -3.316 closest distance to " C   ILE A 234 " =    1.388
peak=   -3.315 closest distance to " O   VAL A 174 " =    1.918
peak=   -3.313 closest distance to " O   ALA A 184 " =    1.700
peak=   -3.310 closest distance to " OG  SER A  62 " =    1.286
peak=   -3.298 closest distance to " O   HOH Z  61 " =    1.584
peak=   -3.295 closest distance to " OG1 THR A  82 " =    1.319
peak=   -3.293 closest distance to " C   GLY A  91 " =    1.312
peak=   -3.291 closest distance to " CB  PRO A 243 " =    2.612
peak=   -3.289 closest distance to " O   HOH Z 311 " =    3.547
peak=   -3.284 closest distance to " OD1 ASN A 301 " =    1.934
peak=   -3.284 closest distance to " OD2 ASP A  50 " =    1.275
peak=   -3.284 closest distance to " O   SER A 273 " =    1.347
peak=   -3.283 closest distance to " O   HOH Z  88 " =    4.262
peak=   -3.279 closest distance to " OG BSER A 210 " =    1.420
peak=   -3.275 closest distance to " O   ASN A 187 " =    1.493
peak=   -3.272 closest distance to " C   THR A 279 " =    1.196
peak=   -3.271 closest distance to " O   ASN A  69 " =    1.403
peak=   -3.270 closest distance to " CG  TRP A 266 " =    2.141
peak=   -3.270 closest distance to " CB  PHE A 208 " =    2.250
peak=   -3.268 closest distance to " CD1AILE A 234 " =    2.724
peak=   -3.265 closest distance to " O   HOH Z  60 " =    2.037
peak=   -3.264 closest distance to " O   HOH Z 222 " =    3.064
peak=   -3.263 closest distance to " O   PRO A 198 " =    1.275
peak=   -3.262 closest distance to " OD1 ASP A 200 " =    1.289
peak=   -3.262 closest distance to " O   HOH Z 407 " =    3.400
peak=   -3.260 closest distance to " CG2 ILE A 263 " =    2.172
peak=   -3.258 closest distance to " OD1 ASP A 191 " =    1.480
peak=   -3.258 closest distance to " CG  GLU A 152 " =    1.196
peak=   -3.249 closest distance to " O   HOH Z 283 " =    1.753
peak=   -3.246 closest distance to " CD1 LEU A 228 " =    2.045
peak=   -3.242 closest distance to " CD1 ILE A 263 " =    2.702
peak=   -3.236 closest distance to " O   VAL A  67 " =    1.856
peak=   -3.229 closest distance to " CB  ALA A 291 " =    2.123
peak=   -3.226 closest distance to " O   HOH Z 139 " =    5.073
peak=   -3.226 closest distance to " O   HOH Z  15 " =    1.513
peak=   -3.225 closest distance to " O   HOH Z 131 " =    3.989
peak=   -3.223 closest distance to " CH2 TRP A 179 " =    1.383
peak=   -3.218 closest distance to " O   HOH Z 198 " =    2.094
peak=   -3.218 closest distance to " CA  GLY A 133 " =    2.218
peak=   -3.213 closest distance to " O   HOH Z 137 " =    1.529
peak=   -3.212 closest distance to " CB  ASP A 162 " =    2.580
peak=   -3.206 closest distance to " SG ACYS A 201 " =    2.369
peak=   -3.205 closest distance to " O   GLY A 196 " =    1.091
peak=   -3.203 closest distance to " CB  ALA A 248 " =    2.206
peak=   -3.200 closest distance to " O   LYS A 117 " =    1.588
peak=   -3.196 closest distance to " O   HOH Z 313 " =    1.781
peak=   -3.192 closest distance to " OXT GLY A 302 " =    3.412
peak=   -3.192 closest distance to " CD2 LEU A 167 " =    1.677
peak=   -3.189 closest distance to " O   HOH Z  71 " =    1.329
peak=   -3.188 closest distance to " O   ASP A 200 " =    1.253
peak=   -3.183 closest distance to " O   HOH Z 295 " =    1.369
peak=   -3.173 closest distance to " O   HOH Z 265 " =    2.043
peak=   -3.172 closest distance to " CG  GLU A 277 " =    1.133
peak=   -3.169 closest distance to " CG  GLU A 152 " =    2.119
peak=   -3.160 closest distance to " O   HOH Z  47 " =    1.591
peak=   -3.159 closest distance to " CE1 TYR A 169 " =    2.229
peak=   -3.151 closest distance to " O   GLY A  75 " =    1.717
peak=   -3.145 closest distance to " CD2 LEU A 237 " =    2.712
peak=   -3.143 closest distance to " O   SER A  22 " =    2.234
peak=   -3.142 closest distance to " O   HOH Z 111 " =    4.678
peak=   -3.140 closest distance to " CE1 HIS A  81 " =    1.363
peak=   -3.139 closest distance to " CB  SER A 210 " =    1.347
peak=   -3.130 closest distance to " CD  GLN A 223 " =    1.803
peak=   -3.125 closest distance to " OG  SER A  63 " =    1.141
peak=   -3.121 closest distance to " O   HOH Z 134 " =    2.657
peak=   -3.117 closest distance to " OD1 ASN A 249 " =    1.422
peak=   -3.111 closest distance to " CD  GLN A 223 " =    0.725
peak=   -3.108 closest distance to " O   HOH Z 139 " =    3.187
peak=   -3.107 closest distance to " O   HOH Z 310 " =    1.526
peak=   -3.100 closest distance to " OD1 ASP A 171 " =    1.642
peak=   -3.082 closest distance to " C   ASN A 148 " =    0.966
peak=   -3.077 closest distance to " CG2AVAL A  41 " =    2.909
peak=   -3.069 closest distance to " O   HOH Z  55 " =    2.464
peak=   -3.053 closest distance to " N   MET A 105 " =    2.625
peak=   -3.039 closest distance to " O   ASP A 171 " =    1.886
peak=   -3.007 closest distance to " CB  ASP A 132 " =    2.244

================= 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    :  0.4702 0.4615   6.268229e+00   6.261391e+00
   1_bss:  0.4613 0.4521   6.262117e+00   6.251660e+00
   1_xyz:  0.3709 0.3946   6.125737e+00   6.169239e+00
   1_adp:  0.3186 0.3659   6.018604e+00   6.115583e+00
   1_occ:  0.3179 0.3651   6.017342e+00   6.115141e+00
   2_bss:  0.3148 0.3593   6.016538e+00   6.113180e+00
   2_xyz:  0.2199 0.2638   5.709207e+00   5.864491e+00
   2_adp:  0.1951 0.2396   5.605157e+00   5.777527e+00
   2_occ:  0.1947 0.2393   5.604368e+00   5.776906e+00
   3_bss:  0.1923 0.2373   5.600106e+00   5.773125e+00
   3_xyz:  0.1390 0.1826   5.319110e+00   5.531009e+00
   3_adp:  0.1311 0.1708   5.256023e+00   5.462982e+00
   3_occ:  0.1309 0.1708   5.255117e+00   5.462438e+00
   4_bss:  0.1309 0.1705   5.255066e+00   5.460093e+00
   4_xyz:  0.1218 0.1613   5.199473e+00   5.407534e+00
   4_adp:  0.1198 0.1607   5.187144e+00   5.400105e+00
   4_occ:  0.1197 0.1607   5.186779e+00   5.400021e+00
   5_bss:  0.1197 0.1607   5.186599e+00   5.399864e+00
   5_xyz:  0.1107 0.1558   5.131729e+00   5.369844e+00
   5_adp:  0.1088 0.1571   5.127740e+00   5.376268e+00
   5_occ:  0.1087 0.1572   5.127610e+00   5.376229e+00
   5_bss:  0.1087 0.1571   5.127325e+00   5.376059e+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:  0.374  20.000   7.956   8.046   8.465   0.000   0.000   0.000
   1_xyz:  0.374  20.000   7.956   8.046   8.465   0.000   0.000   0.000
   1_adp:  0.374  20.000   7.956   8.046   8.465   0.000   0.000   0.000
   1_occ:  0.374  20.000   7.956   8.046   8.465   0.000   0.000   0.000
   2_bss:  0.339  30.722   4.578   4.586   5.604   0.000   0.000   0.000
   2_xyz:  0.339  30.722   4.578   4.586   5.604   0.000   0.000   0.000
   2_adp:  0.339  30.722   4.578   4.586   5.604   0.000   0.000   0.000
   2_occ:  0.339  30.722   4.578   4.586   5.604   0.000   0.000   0.000
   3_bss:  0.323  30.722   2.433   3.285   3.806   0.000   0.000   0.000
   3_xyz:  0.323  30.722   2.433   3.285   3.806   0.000   0.000   0.000
   3_adp:  0.323  30.722   2.433   3.285   3.806   0.000   0.000   0.000
   3_occ:  0.323  30.722   2.433   3.285   3.806   0.000   0.000   0.000
   4_bss:  0.322  32.678   1.698   2.685   3.133   0.000   0.000   0.000
   4_xyz:  0.322  32.678   1.698   2.685   3.133   0.000   0.000   0.000
   4_adp:  0.322  32.678   1.698   2.685   3.133   0.000   0.000   0.000
   4_occ:  0.322  32.678   1.698   2.685   3.133   0.000   0.000   0.000
   5_bss:  0.323  33.571   1.518   2.513   2.958   0.000   0.000   0.000
   5_xyz:  0.323  33.571   1.518   2.513   2.958   0.000   0.000   0.000
   5_adp:  0.323  33.571   1.518   2.513   2.958   0.000   0.000   0.000
   5_occ:  0.323  33.571   1.518   2.513   2.958   0.000   0.000   0.000
   5_bss:  0.322  38.569  -0.801   0.167   0.634   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.839 0.4607  0.5357    65523.166
   1_bss:  55.009 0.4561  0.6738    62769.927
   1_xyz:  45.433 0.5753  0.8360    45085.492
   1_adp:  39.541 0.6479  0.9594    37125.034
   1_occ:  39.463 0.6488  0.9596    36995.035
   2_bss:  39.175 0.6520  0.8583    36486.575
   2_xyz:  27.094 0.7883  0.9990    18315.082
   2_adp:  23.597 0.8261  1.0322    14846.946
   2_occ:  23.577 0.8264  1.0321    14823.875
   3_bss:  23.414 0.8277  0.9673    14605.969
   3_xyz:  17.233 0.8870  1.0033     8499.984
   3_adp:  15.636 0.9015  1.0111     7516.491
   3_occ:  15.614 0.9017  1.0111     7503.792
   4_bss:  15.579 0.9020  0.9862     7468.888
   4_xyz:  14.415 0.9120  0.9897     6669.473
   4_adp:  14.229 0.9137  0.9906     6594.867
   4_occ:  14.220 0.9138  0.9905     6592.179
   5_bss:  14.217 0.9138  0.9841     6591.000
   5_xyz:  13.678 0.9177  0.9847     6200.537
   5_adp:  13.802 0.9169  0.9795     6250.070
   5_occ:  13.800 0.9169  0.9794     6249.973
   5_bss:  13.794 0.9169  0.9848     6247.171
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.3086e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.3086e+01
   1_xyz:   1.735  0.014  0.110 18.126  0.007  4.107   1.4770e-01
   1_adp:   1.735  0.014  0.110 18.126  0.007  4.107   1.4770e-01
   1_occ:   1.735  0.014  0.110 18.126  0.007  4.107   1.4770e-01
   2_bss:   1.735  0.014  0.110 18.126  0.007  4.107   1.4770e-01
   2_xyz:   1.104  0.008  0.078 16.182  0.005  4.120   7.5737e-02
   2_adp:   1.104  0.008  0.078 16.182  0.005  4.120   7.5737e-02
   2_occ:   1.104  0.008  0.078 16.182  0.005  4.120   7.5737e-02
   3_bss:   1.104  0.008  0.078 16.182  0.005  4.120   7.5737e-02
   3_xyz:   1.057  0.007  0.078 15.576  0.004  4.115   6.4701e-02
   3_adp:   1.057  0.007  0.078 15.576  0.004  4.115   6.4701e-02
   3_occ:   1.057  0.007  0.078 15.576  0.004  4.115   6.4701e-02
   4_bss:   1.057  0.007  0.078 15.576  0.004  4.115   6.4701e-02
   4_xyz:   0.913  0.005  0.070 15.395  0.003  4.111   5.2275e-02
   4_adp:   0.913  0.005  0.070 15.395  0.003  4.111   5.2275e-02
   4_occ:   0.913  0.005  0.070 15.395  0.003  4.111   5.2275e-02
   5_bss:   0.913  0.005  0.070 15.395  0.003  4.111   5.2275e-02
   5_xyz:   1.141  0.008  0.089 15.683  0.004  4.112   7.3306e-02
   5_adp:   1.141  0.008  0.089 15.683  0.004  4.112   7.3306e-02
   5_occ:   1.141  0.008  0.089 15.683  0.004  4.112   7.3306e-02
   5_bss:   1.141  0.008  0.089 15.683  0.004  4.112   7.3306e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.978   6.8762e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.978   6.8762e+00
   1_xyz:  15.843  0.177  0.539 85.652  0.048  2.201   1.0502e-01
   1_adp:  15.843  0.177  0.539 85.652  0.048  2.201   1.0502e-01
   1_occ:  15.843  0.177  0.539 85.652  0.048  2.201   1.0502e-01
   2_bss:  15.843  0.177  0.539 85.652  0.048  2.201   1.0502e-01
   2_xyz:   7.124  0.113  0.362 82.288  0.044  2.283   6.5380e-02
   2_adp:   7.124  0.113  0.362 82.288  0.044  2.283   6.5380e-02
   2_occ:   7.124  0.113  0.362 82.288  0.044  2.283   6.5380e-02
   3_bss:   7.124  0.113  0.362 82.288  0.044  2.283   6.5380e-02
   3_xyz:   7.050  0.044  0.505 82.878  0.035  2.259   5.1443e-02
   3_adp:   7.050  0.044  0.505 82.878  0.035  2.259   5.1443e-02
   3_occ:   7.050  0.044  0.505 82.878  0.035  2.259   5.1443e-02
   4_bss:   7.050  0.044  0.505 82.878  0.035  2.259   5.1443e-02
   4_xyz:   5.986  0.032  0.407 81.532  0.029  2.353   2.7571e-02
   4_adp:   5.986  0.032  0.407 81.532  0.029  2.353   2.7571e-02
   4_occ:   5.986  0.032  0.407 81.532  0.029  2.353   2.7571e-02
   5_bss:   5.986  0.032  0.407 81.532  0.029  2.353   2.7571e-02
   5_xyz:   7.491  0.045  0.685 82.198  0.035  2.249   5.4227e-02
   5_adp:   7.491  0.045  0.685 82.198  0.035  2.249   5.4227e-02
   5_occ:   7.491  0.045  0.685 82.198  0.035  2.249   5.4227e-02
   5_bss:   7.491  0.045  0.685 82.198  0.035  2.249   5.4227e-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:  87.95   0.00  12.33  69.77   0.00   9.50  87.95   0.00  27.72
   1_occ:  87.95   0.00  12.33  69.77   0.00   9.50  87.95   0.00  27.72
   2_bss:  87.95   0.00  12.33  69.77   0.00   9.50  87.95   0.00  27.72
   2_xyz:  87.95   0.00  12.33  69.77   0.00   9.50  87.95   0.00  27.72
   2_adp:  88.93   0.00  12.32  73.80   0.00   8.61  88.93   1.45  32.52
   2_occ:  88.93   0.00  12.32  73.80   0.00   8.61  88.93   1.45  32.52
   3_bss:  88.93   0.00  12.32  73.80   0.00   8.61  88.93   1.45  32.52
   3_xyz:  88.93   0.00  12.32  73.80   0.00   8.61  88.93   1.45  32.52
   3_adp:  82.16   0.00  12.17  77.48   0.00   8.28  82.16   2.31  33.39
   3_occ:  82.16   0.00  12.17  77.48   0.00   8.28  82.16   2.31  33.39
   4_bss:  82.16   0.00  12.17  77.48   0.00   8.28  82.16   2.31  33.39
   4_xyz:  82.16   0.00  12.17  77.48   0.00   8.28  82.16   2.31  33.39
   4_adp:  78.79   0.00  12.21  78.79   0.00   8.26  78.43   1.41  33.69
   4_occ:  78.79   0.00  12.21  78.79   0.00   8.26  78.43   1.41  33.69
   5_bss:  78.79   0.00  12.21  78.79   0.00   8.26  78.43   1.41  33.69
   5_xyz:  78.79   0.00  12.21  78.79   0.00   8.26  78.43   1.41  33.69
   5_adp:  82.65   0.00  12.43  82.65   0.00   8.26  73.30   1.24  35.15
   5_occ:  82.65   0.00  12.43  82.65   0.00   8.26  73.30   1.24  35.15
   5_bss:  85.12   2.47  14.91  85.12   2.47  10.74  75.77   3.71  37.62
------------------------------------------------------------------------
 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:    1.235    0.022    0.419
   1_adp:    1.235    0.022    0.419
   1_occ:    1.235    0.022    0.419
   2_bss:    1.235    0.022    0.419
   2_xyz:    1.586    0.021    0.579
   2_adp:    1.586    0.021    0.579
   2_occ:    1.586    0.021    0.579
   3_bss:    1.586    0.021    0.579
   3_xyz:    1.630    0.021    0.635
   3_adp:    1.630    0.021    0.635
   3_occ:    1.630    0.021    0.635
   4_bss:    1.630    0.021    0.635
   4_xyz:    1.754    0.030    0.661
   4_adp:    1.754    0.030    0.661
   4_occ:    1.754    0.030    0.661
   5_bss:    1.754    0.030    0.661
   5_xyz:    1.650    0.040    0.676
   5_adp:    1.650    0.040    0.676
   5_occ:    1.650    0.040    0.676
   5_bss:    1.650    0.040    0.676
------------------------------------------------------------------------

CPU time actual refinement: 329.15


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_189/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_189/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_189/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_189/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_189/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 329.01 
  Macro-tasks:
    bulk solvent and scale       = 42.63  
    individual site refinement   = 129.20 
    weights calculation          = 32.96  
    collect and process          = 6.63   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 211.52 
  Micro-tasks:
    mask                            = 1.72   
    f_calc                          = 102.45 
    alpha_beta                      = 8.37   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 106.29 
    fmodel                         = 7.55   
    r_factors                      = 0.25   
    phase_errors                   = 11.48  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 239.56 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.723 micro seconds
Total CPU time: 5.71 minutes
from_scatterers_fft:    621 calls, 102.06 s
gradients_fft:          567 calls,  95.62 s

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

# Date 2008-01-16 Time 00:57:39 PST -0800 (1200473859.72 s)
Start R-work = 0.4702, R-free = 0.4615 (no bulk solvent and anisotropic scale)
Final R-work = 0.1268, R-free = 0.1725 (no bulk solvent and anisotropic scale)

Start R-work = 0.4613, R-free = 0.4521
Final R-work = 0.1087, R-free = 0.1571