# Date 2008-01-16 Time 03:33:52 PST -0800 (1200483232.11 s)
#phil __OFF__

Command line arguments: "../1292.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 23344
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1292

-------------------------------------------------------------------------------
  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: (72.0062, 47.3993, 86.39, 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: 3.30, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 47.3993, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2644 2.00112
Completeness in resolution range: 0.954676
Completeness with d_max=infinity: 0.9518

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2644
                             d_min =   2.0011

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: (72.0062, 47.3993, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2644 2.00112
Completeness in resolution range: 0.954676
Completeness with d_max=infinity: 0.9518

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2649 -  4.2825 [2152/2181]  1941   211   9.8%
  bin  2:  4.2825 -  3.4116 [2072/2088]  1862   210  10.1%
  bin  3:  3.4116 -  2.9840 [2032/2051]  1827   205  10.1%
  bin  4:  2.9840 -  2.7129 [2040/2070]  1839   201   9.9%
  bin  5:  2.7129 -  2.5194 [2020/2039]  1817   203  10.0%
  bin  6:  2.5194 -  2.3714 [1993/2018]  1788   205  10.3%
  bin  7:  2.3714 -  2.2530 [1986/2018]  1790   196   9.9%
  bin  8:  2.2530 -  2.1552 [1987/2019]  1792   195   9.8%
  bin  9:  2.1552 -  2.0725 [1988/2030]  1787   201  10.1%
  bin 10:  2.0725 -  2.0011 [1319/2005]  1187   132  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1292/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.37 -     2.07: 2
        2.07 -     2.78: 558
        2.78 -     3.49: 4420
        3.49 -     4.19: 9228
        4.19 -     4.90: 13669
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.368 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.126 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.155 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.216 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27872 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_1292/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1292/model_refine_001.geo

CPU time processing inputs: 9.79


============================ 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 = 72.00625 47.3993 86.39 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: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4706   r_free= 0.4568   ksol= 0.00   Bsol= 0.00   scale= 0.788    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.272392                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2649 -  4.7768 0.99   1395  155 0.3882 0.3624      6.5791      6.5078|
|  2:  4.7768 -  3.8109 0.99   1350  146 0.3820 0.4115      6.7689      6.7914|
|  3:  3.8109 -  3.3349 0.99   1322  149 0.4257 0.3955       6.645      6.6578|
|  4:  3.3349 -  3.0326 0.99   1321  152 0.4548 0.4094      6.5168      6.4303|
|  5:  3.0326 -  2.8167 0.99   1304  141 0.4925 0.5119      6.3623      6.4076|
|  6:  2.8167 -  2.6515 0.99   1291  145 0.5092 0.4983      6.2733      6.2408|
|  7:  2.6515 -  2.5194 0.99   1303  142 0.5161 0.4983      6.2537      6.2408|
|  8:  2.5194 -  2.4101 0.98   1268  146 0.5064 0.4938      6.1536       6.148|
|  9:  2.4101 -  2.3177 0.98   1291  146 0.5162 0.5340      6.1298      6.1741|
| 10:  2.3177 -  2.2380 0.99   1269  137 0.5180 0.4664      6.1016      6.0773|
| 11:  2.2380 -  2.1682 0.99   1290  141 0.5174 0.4972       6.041      6.0486|
| 12:  2.1682 -  2.1064 0.97   1261  136 0.5346 0.5190      5.9835      6.0099|
| 13:  2.1064 -  2.0510 0.99   1267  143 0.5219 0.5177      5.8851      5.8229|
| 14:  2.0510 -  2.0011 0.54    698   80 0.5344 0.4644      5.8388       5.757|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2649 -  4.7768  1395   155  0.72  32.71   0.79     0.75      65614.87|
|  2:  4.7768 -  3.8109  1350   146  0.73  32.90   0.89     0.77      94111.93|
|  3:  3.8109 -  3.3349  1322   149  0.63  41.39   0.82     0.72     102476.82|
|  4:  3.3349 -  3.0326  1321   152  0.54  48.55   0.80     0.63      94693.18|
|  5:  3.0326 -  2.8167  1304   141  0.44  56.45   0.73     0.52      79304.15|
|  6:  2.8167 -  2.6515  1291   145  0.40  59.81   0.73     0.46      70322.64|
|  7:  2.6515 -  2.5194  1303   142  0.39  60.94   0.73     0.43      64081.09|
|  8:  2.5194 -  2.4101  1268   146  0.35  63.72   0.70     0.42      60343.51|
|  9:  2.4101 -  2.3177  1291   146  0.37  62.26   0.72     0.42      53840.05|
| 10:  2.3177 -  2.2380  1269   137  0.37  62.55   0.74     0.43      49258.29|
| 11:  2.2380 -  2.1682  1290   141  0.37  62.46   0.75     0.43      43848.12|
| 12:  2.1682 -  2.1064  1261   136  0.35  63.59   0.73     0.43      41559.17|
| 13:  2.1064 -  2.0510  1267   143  0.37  62.53   0.71     0.43      34320.57|
| 14:  2.0510 -  2.0011   698    80  0.43  58.21   0.70     0.47      26289.80|
|alpha:            min =        0.42 max =            0.77 mean =         0.53|
|beta:             min =    26289.80 max =       102476.82 mean =     64445.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.46|
|phase err.(work): min =        0.00 max =           89.99 mean =        54.47|
|phase err.(test): min =        0.00 max =           89.97 mean =        54.24|
|-----------------------------------------------------------------------------|

============================== 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 = 13.528600             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.973   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.092551              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.666   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      160 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      674 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1483 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2589 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3846 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4993 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6489 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7596 |
|-----------------------------------------------------------------------------|
|-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 |       54.425 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.648 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.322)------------------------------------------|
|    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 = 12.322)------------------------------------------|
|    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: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4755   r_free= 0.4622   ksol= 0.00   Bsol= 0.00   scale= 0.760    |
|                                                                             |
| 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: 6.273382                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4633   r_free= 0.4466   ksol= 0.32   Bsol= 30.59   scale= 0.980   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.66,8.45,6.94,0.00,0.00,0.00); trace/3= 8.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.268263                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.852607             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.571   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.987347              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.887   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4633      final r-factor (work) = 0.3686          |
| start r-factor (free) = 0.4466      final r-factor (free) = 0.3993          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 91.5979 = 11.85 * 0.50 * 6.2725 + 1.00 * 54.4253                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.6647 = 11.85 * 0.50 * 6.1622 + 1.00 * 0.1458                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3686      final r-factor (work) = 0.3232          |
| start r-factor (free) = 0.3993      final r-factor (free) = 0.3694          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0986 = 0.99 * 1.00 * 6.1622 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0087 = 0.99 * 1.00 * 6.0710 + 1.00 * 0.0145                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.322)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.70   11.58    None  None   None       |
|    all(noH): 2823   0      0.00    95.70   11.58    None  None   None       |
|    Sol.    : 438    0      0.00    95.70   26.40    None  None   None       |
|    Mac.    : 2385   0      0.00    73.21   8.86     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.570: 1652   |   5:    47.851 -  57.421:   46        |
|      1:     9.570 -  19.140:  666   |   6:    57.421 -  66.991:   15        |
|      2:    19.140 -  28.711:  248   |   7:    66.991 -  76.562:    6        |
|      3:    28.711 -  38.281:  119   |   8:    76.562 -  86.132:    1        |
|      4:    38.281 -  47.851:   68   |   9:    86.132 -  95.702:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3232 r_free = 0.3694             target_work(ml) = 6.044         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3227 r_free = 0.3695             target_work(ml) = 6.043         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3227   r_free= 0.3695   ksol= 0.32   Bsol= 30.59   scale= 1.055   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.66,8.45,6.94,0.00,0.00,0.00); trace/3= 8.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.043008                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3217   r_free= 0.3666   ksol= 0.31   Bsol= 47.80   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.90,5.63,5.03,0.00,0.00,0.00); trace/3= 5.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.043874                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.352126              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.074   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.590373              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.671  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3217      final r-factor (work) = 0.2318          |
| start r-factor (free) = 0.3666      final r-factor (free) = 0.2913          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.4498 = 7.35 * 0.50 * 6.0674 + 1.00 * 0.1458                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.8258 = 7.35 * 0.50 * 5.9146 + 1.00 * 0.0833                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2318      final r-factor (work) = 0.2127          |
| start r-factor (free) = 0.2913      final r-factor (free) = 0.2702          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5126 = 0.59 * 1.00 * 5.9146 + 1.00 * 0.0208                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4610 = 0.59 * 1.00 * 5.7315 + 1.00 * 0.0773                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.322)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.19   11.97    None  None   None       |
|    all(noH): 2823   0      0.00    96.19   11.97    None  None   None       |
|    Sol.    : 438    0      0.00    95.55   30.41    None  None   None       |
|    Mac.    : 2385   0      0.00    96.19   8.58     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.619: 1647   |   5:    48.093 -  57.712:   44        |
|      1:     9.619 -  19.237:  640   |   6:    57.712 -  67.331:   16        |
|      2:    19.237 -  28.856:  251   |   7:    67.331 -  76.949:    6        |
|      3:    28.856 -  38.475:  138   |   8:    76.949 -  86.568:    1        |
|      4:    38.475 -  48.093:   77   |   9:    86.568 -  96.187:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2127 r_free = 0.2702             target_work(ml) = 5.696         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2123 r_free = 0.2705             target_work(ml) = 5.696         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2123   r_free= 0.2705   ksol= 0.31   Bsol= 47.80   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.90,5.63,5.03,0.00,0.00,0.00); trace/3= 5.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.695823                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2104   r_free= 0.2674   ksol= 0.32   Bsol= 47.80   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.11,3.71,3.99,0.00,0.00,0.00); trace/3= 3.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.695857                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.473479              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.104  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.673099              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.775   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2104      final r-factor (work) = 0.1570          |
| start r-factor (free) = 0.2674      final r-factor (free) = 0.2069          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.7766 = 5.47 * 0.50 * 5.7343 + 1.00 * 0.0833                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.3593 = 5.47 * 0.50 * 5.5807 + 1.00 * 0.0864                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1570      final r-factor (work) = 0.1381          |
| start r-factor (free) = 0.2069      final r-factor (free) = 0.1895          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.3565 = 1.67 * 1.00 * 5.5807 + 1.00 * 0.0195                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.0027 = 1.67 * 1.00 * 5.3714 + 1.00 * 0.0159                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.322)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.87   13.13    None  None   None       |
|    all(noH): 2823   0      0.00    91.87   13.13    None  None   None       |
|    Sol.    : 438    0      0.44    91.87   38.46    None  None   None       |
|    Mac.    : 2385   0      0.00    90.46   8.48     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.187: 1698   |   5:    45.934 -  55.121:   85        |
|      1:     9.187 -  18.374:  558   |   6:    55.121 -  64.307:   61        |
|      2:    18.374 -  27.560:  167   |   7:    64.307 -  73.494:   31        |
|      3:    27.560 -  36.747:  112   |   8:    73.494 -  82.681:   11        |
|      4:    36.747 -  45.934:   93   |   9:    82.681 -  91.868:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1381 r_free = 0.1895             target_work(ml) = 5.331         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1380 r_free = 0.1894             target_work(ml) = 5.330         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1380   r_free= 0.1894   ksol= 0.32   Bsol= 47.80   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.11,3.71,3.99,0.00,0.00,0.00); trace/3= 3.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.330055                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1378   r_free= 0.1894   ksol= 0.33   Bsol= 63.47   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.07,2.87,3.44,0.00,0.00,0.00); trace/3= 3.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.329915                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.645558              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.549  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.404747              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.634  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1378      final r-factor (work) = 0.1269          |
| start r-factor (free) = 0.1894      final r-factor (free) = 0.1793          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1974 = 2.65 * 0.50 * 5.3758 + 1.00 * 0.0864                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0824 = 2.65 * 0.50 * 5.2986 + 1.00 * 0.0735                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1269      final r-factor (work) = 0.1249          |
| start r-factor (free) = 0.1793      final r-factor (free) = 0.1748          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1604 = 0.40 * 1.00 * 5.2986 + 1.00 * 0.0158                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1421 = 0.40 * 1.00 * 5.2602 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.322)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.70   12.75    None  None   None       |
|    all(noH): 2823   0      0.00    90.70   12.75    None  None   None       |
|    Sol.    : 438    0      0.86    89.57   37.35    None  None   None       |
|    Mac.    : 2385   0      0.00    90.70   8.24     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.070: 1731   |   5:    45.348 -  54.418:   95        |
|      1:     9.070 -  18.139:  541   |   6:    54.418 -  63.487:   47        |
|      2:    18.139 -  27.209:  169   |   7:    63.487 -  72.557:   25        |
|      3:    27.209 -  36.279:  113   |   8:    72.557 -  81.627:   12        |
|      4:    36.279 -  45.348:   83   |   9:    81.627 -  90.696:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1249 r_free = 0.1748             target_work(ml) = 5.246         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1248 r_free = 0.1746             target_work(ml) = 5.245         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1248   r_free= 0.1746   ksol= 0.33   Bsol= 63.47   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.07,2.87,3.44,0.00,0.00,0.00); trace/3= 3.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.245417                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1248   r_free= 0.1746   ksol= 0.32   Bsol= 62.25   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.88,2.79,3.47,0.00,0.00,0.00); trace/3= 3.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.245340                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.975670              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 138.872  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.309986              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.480  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1248      final r-factor (work) = 0.1161          |
| start r-factor (free) = 0.1746      final r-factor (free) = 0.1666          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5289 = 3.98 * 0.50 * 5.2597 + 1.00 * 0.0735                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4607 = 3.98 * 0.50 * 5.2157 + 1.00 * 0.0927                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1161      final r-factor (work) = 0.1158          |
| start r-factor (free) = 0.1666      final r-factor (free) = 0.1653          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6298 = 0.31 * 1.00 * 5.2157 + 1.00 * 0.0130                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6221 = 0.31 * 1.00 * 5.1896 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.322)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.24   12.37    None  None   None       |
|    all(noH): 2823   0      0.00    89.24   12.37    None  None   None       |
|    Sol.    : 438    0      1.21    88.88   35.62    None  None   None       |
|    Mac.    : 2385   0      0.00    89.24   8.10     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.924: 1730   |   5:    44.619 -  53.543:   94        |
|      1:     8.924 -  17.848:  549   |   6:    53.543 -  62.466:   45        |
|      2:    17.848 -  26.771:  162   |   7:    62.466 -  71.390:   20        |
|      3:    26.771 -  35.695:  126   |   8:    71.390 -  80.314:    8        |
|      4:    35.695 -  44.619:   83   |   9:    80.314 -  89.238:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1158 r_free = 0.1653             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1157 r_free = 0.1652             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1652   ksol= 0.32   Bsol= 62.25   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.88,2.79,3.47,0.00,0.00,0.00); trace/3= 3.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.186325                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2649 -  4.7768 0.99   1395  155 0.1020 0.1423      5.4165      5.5978|
|  2:  4.7768 -  3.8109 0.99   1350  146 0.0868 0.1119      5.4614        5.66|
|  3:  3.8109 -  3.3349 0.99   1322  149 0.1086 0.1562       5.497      5.8747|
|  4:  3.3349 -  3.0326 0.99   1321  152 0.1234 0.1616      5.4838      5.6311|
|  5:  3.0326 -  2.8167 0.99   1304  141 0.1402 0.1886      5.3812       5.609|
|  6:  2.8167 -  2.6515 0.99   1291  145 0.1290 0.1924      5.2697      5.5186|
|  7:  2.6515 -  2.5194 0.99   1303  142 0.1300 0.1785      5.2179      5.4286|
|  8:  2.5194 -  2.4101 0.98   1268  146 0.1215 0.1838      5.0989      5.3818|
|  9:  2.4101 -  2.3177 0.98   1291  146 0.1208 0.1770      5.0776      5.3362|
| 10:  2.3177 -  2.2380 0.99   1269  137 0.1175 0.1874      5.0013      5.2671|
| 11:  2.2380 -  2.1682 0.99   1290  141 0.1220 0.1892      4.9985      5.3274|
| 12:  2.1682 -  2.1064 0.97   1261  136 0.1138 0.1654      4.9117      5.1143|
| 13:  2.1064 -  2.0510 0.99   1267  143 0.1247 0.1854      4.8276      5.1039|
| 14:  2.0510 -  2.0011 0.54    698   80 0.1075 0.1752      4.6567      4.9606|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2649 -  4.7768  1395   155  0.94   9.60   0.97     0.95       8067.86|
|  2:  4.7768 -  3.8109  1350   146  0.95   8.61   1.00     0.98       9850.09|
|  3:  3.8109 -  3.3349  1322   149  0.93  12.05   1.01     1.01      11149.54|
|  4:  3.3349 -  3.0326  1321   152  0.91  14.32   1.00     0.97      11197.12|
|  5:  3.0326 -  2.8167  1304   141  0.89  17.53   0.99     0.97       9481.88|
|  6:  2.8167 -  2.6515  1291   145  0.89  16.95   0.98     0.96       8067.52|
|  7:  2.6515 -  2.5194  1303   142  0.90  16.51   0.98     0.96       6949.29|
|  8:  2.5194 -  2.4101  1268   146  0.90  16.37   0.98     0.96       5811.85|
|  9:  2.4101 -  2.3177  1291   146  0.90  16.37   1.00     0.96       5577.40|
| 10:  2.3177 -  2.2380  1269   137  0.90  16.28   0.99     0.95       4729.45|
| 11:  2.2380 -  2.1682  1290   141  0.89  17.39   0.99     0.95       4904.85|
| 12:  2.1682 -  2.1064  1261   136  0.91  15.60   0.99     0.98       4292.64|
| 13:  2.1064 -  2.0510  1267   143  0.89  17.13   0.99     0.98       3570.93|
| 14:  2.0510 -  2.0011   698    80  0.91  14.91   0.97     0.94       2488.41|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2488.41 max =        11197.12 mean =      7061.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.91|
|phase err.(test): min =        0.00 max =           88.84 mean =        14.27|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1160   r_free= 0.1650   ksol= 0.32   Bsol= 65.30   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.17,-0.26,0.43,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.185917                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1160   r_free= 0.1650   ksol= 0.32   Bsol= 65.30   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.17,-0.26,0.43,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.185917                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2649 -  4.7768 0.99   1395  155 0.1033 0.1383      5.4104      5.5794|
|  2:  4.7768 -  3.8109 0.99   1350  146 0.0872 0.1128      5.4605      5.6604|
|  3:  3.8109 -  3.3349 0.99   1322  149 0.1091 0.1569      5.4985      5.8759|
|  4:  3.3349 -  3.0326 0.99   1321  152 0.1238 0.1621      5.4852      5.6358|
|  5:  3.0326 -  2.8167 0.99   1304  141 0.1403 0.1883      5.3812      5.6089|
|  6:  2.8167 -  2.6515 0.99   1291  145 0.1290 0.1920      5.2695      5.5187|
|  7:  2.6515 -  2.5194 0.99   1303  142 0.1300 0.1782      5.2179      5.4276|
|  8:  2.5194 -  2.4101 0.98   1268  146 0.1215 0.1843      5.0992      5.3823|
|  9:  2.4101 -  2.3177 0.98   1291  146 0.1208 0.1768      5.0773      5.3363|
| 10:  2.3177 -  2.2380 0.99   1269  137 0.1174 0.1875      5.0013      5.2675|
| 11:  2.2380 -  2.1682 0.99   1290  141 0.1219 0.1891       4.998      5.3264|
| 12:  2.1682 -  2.1064 0.97   1261  136 0.1138 0.1653      4.9114      5.1139|
| 13:  2.1064 -  2.0510 0.99   1267  143 0.1247 0.1854      4.8273      5.1042|
| 14:  2.0510 -  2.0011 0.54    698   80 0.1074 0.1753      4.6567      4.9607|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2649 -  4.7768  1395   155  0.94   9.69   0.97     0.95       7871.33|
|  2:  4.7768 -  3.8109  1350   146  0.95   8.59   1.00     0.98       9762.62|
|  3:  3.8109 -  3.3349  1322   149  0.93  12.04   1.01     1.01      11150.78|
|  4:  3.3349 -  3.0326  1321   152  0.91  14.34   1.00     0.97      11214.34|
|  5:  3.0326 -  2.8167  1304   141  0.89  17.52   0.99     0.97       9483.85|
|  6:  2.8167 -  2.6515  1291   145  0.89  16.97   0.98     0.95       8072.63|
|  7:  2.6515 -  2.5194  1303   142  0.90  16.50   0.98     0.96       6945.26|
|  8:  2.5194 -  2.4101  1268   146  0.90  16.37   0.98     0.96       5815.20|
|  9:  2.4101 -  2.3177  1291   146  0.90  16.37   1.00     0.96       5574.82|
| 10:  2.3177 -  2.2380  1269   137  0.90  16.27   0.99     0.95       4730.39|
| 11:  2.2380 -  2.1682  1290   141  0.89  17.38   0.99     0.95       4901.43|
| 12:  2.1682 -  2.1064  1261   136  0.91  15.59   0.99     0.98       4290.84|
| 13:  2.1064 -  2.0510  1267   143  0.89  17.13   0.99     0.98       3570.00|
| 14:  2.0510 -  2.0011   698    80  0.91  14.91   0.97     0.94       2489.05|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2489.05 max =        11214.34 mean =      7040.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.92|
|phase err.(test): min =        0.00 max =           89.95 mean =        14.31|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.322)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.05    92.28   15.41    None  None   None       |
|    all(noH): 2823   0      3.05    92.28   15.41    None  None   None       |
|    Sol.    : 438    0      4.25    91.92   38.67    None  None   None       |
|    Mac.    : 2385   0      3.05    92.28   11.14    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.046 -  11.970: 1730   |   5:    47.665 -  56.589:   94        |
|      1:    11.970 -  20.894:  549   |   6:    56.589 -  65.513:   45        |
|      2:    20.894 -  29.818:  162   |   7:    65.513 -  74.436:   20        |
|      3:    29.818 -  38.741:  126   |   8:    74.436 -  83.360:    8        |
|      4:    38.741 -  47.665:   83   |   9:    83.360 -  92.284:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 323         
Filter by distance & map next to the model:
   mapped sites are within: 0.377 - 4.812
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 315 from: 323
   mapped sites are within: 0.709 - 4.812

peak=    9.610 closest distance to " CG2 VAL A 230 " =    1.381
peak=    6.544 closest distance to " CG2 VAL A 296 " =    1.107
peak=    6.076 closest distance to " CG  LEU A   5 " =    1.203
peak=    5.713 closest distance to " O   HOH Z 111 " =    1.930
peak=    5.329 closest distance to " CB  GLN A 223 " =    1.421
peak=    5.323 closest distance to " CB  SER A  63 " =    1.336
peak=    5.227 closest distance to " CG  LEU A 228 " =    1.182
peak=    5.170 closest distance to " CB  VAL A 230 " =    1.278
peak=    4.729 closest distance to " O   HOH Z 265 " =    2.296
peak=    4.653 closest distance to " O   HOH Z 369 " =    2.015
peak=    4.599 closest distance to " CB  VAL A 296 " =    1.205
peak=    4.541 closest distance to " CB  GLN A 183 " =    1.255
peak=    4.511 closest distance to " O   HOH Z 368 " =    2.325
peak=    4.498 closest distance to " O   HOH Z 232 " =    2.256
peak=    4.428 closest distance to " CD2 LEU A   5 " =    1.144
peak=    4.419 closest distance to " O   HOH Z 303 " =    2.134
peak=    4.402 closest distance to " O   HOH Z 102 " =    1.449
peak=    4.390 closest distance to " O   HOH Z 403 " =    1.660
peak=    4.373 closest distance to " O   HOH Z  68 " =    1.821
peak=    4.351 closest distance to " CB  GLU A 152 " =    1.209
peak=    4.306 closest distance to " CB  GLU A 128 " =    1.101
peak=    4.298 closest distance to " NE2 GLN A  11 " =    1.148
peak=    4.289 closest distance to " O   HOH Z 112 " =    1.635
peak=    4.268 closest distance to " CG2 THR A 221 " =    1.019
peak=    4.262 closest distance to " O   HOH Z 184 " =    1.640
peak=    4.250 closest distance to " O   HOH Z 236 " =    1.901
peak=    4.227 closest distance to " O   HOH Z 410 " =    1.306
peak=    4.219 closest distance to " CG1 ILE A  33 " =    1.263
peak=    4.204 closest distance to " NH1AARG A 145 " =    1.184
peak=    4.185 closest distance to " CG  PRO A 213 " =    1.218
peak=    4.181 closest distance to " O   HOH Z 298 " =    1.834
peak=    4.168 closest distance to " O   HOH Z 272 " =    1.975
peak=    4.168 closest distance to " O   HOH Z 126 " =    1.556
peak=    4.165 closest distance to " CB  ARG A 190 " =    1.605
peak=    4.136 closest distance to " O   SER A  87 " =    2.338
peak=    4.134 closest distance to " CB  ASP A 140 " =    0.862
peak=    4.109 closest distance to " O   HOH Z  15 " =    1.986
peak=    4.095 closest distance to " O   HOH Z  78 " =    2.212
peak=    4.090 closest distance to " O   HOH Z 247 " =    1.444
peak=    4.084 closest distance to " O   HOH Z  63 " =    1.952
peak=    4.079 closest distance to " CB  TRP A 266 " =    0.929
peak=    4.060 closest distance to " CZ  PHE A 192 " =    1.011
peak=    4.057 closest distance to " CD1 LEU A 300 " =    1.185
peak=    4.048 closest distance to " O   PRO A 198 " =    1.561
peak=    4.048 closest distance to " CZ  PHE A 218 " =    1.107
peak=    4.046 closest distance to " O   HOH Z  88 " =    3.372
peak=    4.044 closest distance to " CB  GLU A 277 " =    3.729
peak=    4.043 closest distance to " CG  PRO A 243 " =    1.160
peak=    4.040 closest distance to " O   HOH Z  57 " =    1.457
peak=    4.006 closest distance to " O   HOH Z 425 " =    1.456
peak=    4.000 closest distance to " O   HOH Z 427 " =    3.136
peak=    3.999 closest distance to " O   HOH Z 193 " =    2.277
peak=    3.996 closest distance to " CD2 LEU A 228 " =    1.199
peak=    3.996 closest distance to " O   HOH Z 163 " =    1.761
peak=    3.991 closest distance to " O   HOH Z 234 " =    3.800
peak=    3.981 closest distance to " CB  ASN A 148 " =    1.381
peak=    3.978 closest distance to " CD1 LEU A   5 " =    1.297
peak=    3.965 closest distance to " CG BARG A 275 " =    1.495
peak=    3.959 closest distance to " CB  VAL A 265 " =    1.306
peak=    3.947 closest distance to " ND2 ASN A 187 " =    1.448
peak=    3.936 closest distance to " O   HOH Z 183 " =    1.371
peak=    3.923 closest distance to " CA  TYR A  30 " =    0.961
peak=    3.920 closest distance to " CB  ALA A   9 " =    1.629
peak=    3.919 closest distance to " O   HOH Z 316 " =    3.150
peak=    3.902 closest distance to " O   MET A 105 " =    1.859
peak=    3.898 closest distance to " OD1 ASN A  69 " =    2.644
peak=    3.894 closest distance to " O   HOH Z 214 " =    2.056
peak=    3.890 closest distance to " CD  ARG A  66 " =    2.446
peak=    3.887 closest distance to " O   HOH Z 437 " =    1.969
peak=    3.874 closest distance to " O   HOH Z  80 " =    1.790
peak=    3.865 closest distance to " O   HOH Z 261 " =    1.923
peak=    3.862 closest distance to " CB  VAL A 202 " =    1.504
peak=    3.858 closest distance to " CB  ARG A  79 " =    1.526
peak=    3.848 closest distance to " O   HOH Z 411 " =    3.649
peak=    3.847 closest distance to " CB  LEU A 228 " =    1.162
peak=    3.835 closest distance to " CA  MET A  40 " =    1.208
peak=    3.833 closest distance to " O   HOH Z  20 " =    2.062
peak=    3.831 closest distance to " O   ASP A 124 " =    1.189
peak=    3.825 closest distance to " O   HOH Z 126 " =    1.989
peak=    3.819 closest distance to " O   HOH Z  61 " =    1.612
peak=    3.811 closest distance to " O   HOH Z 433 " =    1.558
peak=    3.809 closest distance to " CB  LEU A 143 " =    1.165
peak=    3.806 closest distance to " O   HOH Z 135 " =    1.954
peak=    3.803 closest distance to " CG2 VAL A 296 " =    1.619
peak=    3.791 closest distance to " CG  MET A 185 " =    1.293
peak=    3.788 closest distance to " NH2 ARG A 156 " =    1.142
peak=    3.783 closest distance to " CB  TRP A 150 " =    1.378
peak=    3.783 closest distance to " O   HOH Z  97 " =    2.181
peak=    3.751 closest distance to " CB  SER A   3 " =    1.478
peak=    3.748 closest distance to " O   HOH Z 213 " =    1.940
peak=    3.736 closest distance to " O   HOH Z  21 " =    1.696
peak=    3.731 closest distance to " CB  TYR A 169 " =    0.738
peak=    3.726 closest distance to " CB  ARG A 275 " =    0.876
peak=    3.720 closest distance to " CD ALYS A 290 " =    1.028
peak=    3.719 closest distance to " O   HOH Z 133 " =    2.334
peak=    3.710 closest distance to " CD  ARG A 159 " =    0.799
peak=    3.710 closest distance to " ND2 ASN A 249 " =    1.931
peak=    3.710 closest distance to " O   HOH Z 295 " =    1.542
peak=    3.709 closest distance to " O   HOH Z  43 " =    1.895
peak=    3.687 closest distance to " NH2 ARG A  79 " =    1.455
peak=    3.675 closest distance to " OD2 ASP A 286 " =    2.913
peak=    3.675 closest distance to " O   HOH Z 423 " =    1.764
peak=    3.672 closest distance to " O   HOH Z 132 " =    2.609
peak=    3.668 closest distance to " O   HOH Z 197 " =    2.576
peak=    3.654 closest distance to " OD1 ASN A 217 " =    1.597
peak=    3.654 closest distance to " O   HOH Z 133 " =    1.773
peak=    3.646 closest distance to " O   HOH Z 128 " =    2.293
peak=    3.646 closest distance to " CA  ALA A 295 " =    1.118
peak=    3.636 closest distance to " CG  ARG A 138 " =    1.169
peak=    3.628 closest distance to " CD2 LEU A 255 " =    1.495
peak=    3.623 closest distance to " O   HOH Z 180 " =    2.084
peak=    3.613 closest distance to " O   HOH Z  19 " =    2.433
peak=    3.608 closest distance to " O   HOH Z 134 " =    1.450
peak=    3.605 closest distance to " OG1 THR A 294 " =    2.395
peak=    3.602 closest distance to " O   HOH Z 158 " =    3.044
peak=    3.595 closest distance to " CB  ASN A 187 " =    0.948
peak=    3.595 closest distance to " CB  SER A 212 " =    1.176
peak=    3.594 closest distance to " CB  ALA A 100 " =    1.374
peak=    3.590 closest distance to " O   HOH Z 280 " =    2.888
peak=    3.588 closest distance to " O   GLN A 278 " =    1.175
peak=    3.587 closest distance to " O   HOH Z 346 " =    1.528
peak=    3.585 closest distance to " CG AARG A 275 " =    1.277
peak=    3.576 closest distance to " CB  ASN A 142 " =    0.993
peak=    3.571 closest distance to " OE1 GLN A  11 " =    1.892
peak=    3.568 closest distance to " NH1 ARG A  56 " =    1.060
peak=    3.566 closest distance to " O   HOH Z   4 " =    1.790
peak=    3.561 closest distance to " NZ  LYS A 117 " =    3.175
peak=    3.554 closest distance to " O   HOH Z 263 " =    1.650
peak=    3.548 closest distance to " N   SER A 135 " =    1.487
peak=    3.547 closest distance to " CB  TRP A 179 " =    1.427
peak=    3.545 closest distance to " CB  ASN A  39 " =    0.877
peak=    3.544 closest distance to " CB  ILE A 120 " =    1.382
peak=    3.538 closest distance to " O   HOH Z 227 " =    1.764
peak=    3.535 closest distance to " OG BSER A 164 " =    2.156
peak=    3.534 closest distance to " O   HOH Z  48 " =    1.770
peak=    3.533 closest distance to " CA  ALA A  51 " =    0.968
peak=    3.532 closest distance to " CB  SER A 216 " =    0.838
peak=    3.532 closest distance to " CA  ALA A  21 " =    1.260
peak=    3.531 closest distance to " CA  ASP A 191 " =    0.774
peak=    3.529 closest distance to " CB  ALA A 248 " =    1.066
peak=    3.526 closest distance to " CG1 VAL A 153 " =    0.988
peak=    3.522 closest distance to " O   HOH Z 281 " =    4.582
peak=    3.521 closest distance to " CG2BVAL A  41 " =    1.187
peak=    3.514 closest distance to " N   ASN A  39 " =    1.281
peak=    3.511 closest distance to " O   HOH Z 422 " =    2.632
peak=    3.508 closest distance to " O   HOH Z  44 " =    2.043
peak=    3.506 closest distance to " CA  THR A 221 " =    0.900
peak=    3.506 closest distance to " N   VAL A 126 " =    1.428
peak=    3.501 closest distance to " O   HOH Z 387 " =    3.095
peak=    3.498 closest distance to " O   HOH Z 394 " =    1.412
peak=    3.494 closest distance to " ND1 HIS A  81 " =    1.702
peak=    3.493 closest distance to " CD  LYS A 166 " =    1.235
peak=    3.491 closest distance to " O   HOH Z 134 " =    2.461
peak=    3.490 closest distance to " CB  GLU A  46 " =    0.987
peak=    3.489 closest distance to " O   HOH Z 141 " =    1.685
peak=    3.488 closest distance to " O   HOH Z 171 " =    3.960
peak=    3.485 closest distance to " O   THR A  31 " =    1.541
peak=    3.481 closest distance to " O   ALA A 158 " =    1.365
peak=    3.480 closest distance to " CB  ALA A 104 " =    0.825
peak=    3.476 closest distance to " O   HOH Z 188 " =    3.092
peak=    3.469 closest distance to " CG1 ILE A  49 " =    1.564
peak=    3.465 closest distance to " CA  LEU A 282 " =    1.024
peak=    3.459 closest distance to " CA  LYS A 117 " =    1.232
peak=    3.459 closest distance to " O   HOH Z 128 " =    2.217
peak=    3.454 closest distance to " O   HOH Z  47 " =    1.512
peak=    3.454 closest distance to " CA  THR A 264 " =    0.709
peak=    3.452 closest distance to " O   HOH Z 271 " =    2.815
peak=    3.449 closest distance to " O   HOH Z 193 " =    2.044
peak=    3.448 closest distance to " O   HOH Z 419 " =    1.769
peak=    3.440 closest distance to " CB  GLN A  88 " =    1.266
peak=    3.438 closest distance to " O   HOH Z 420 " =    2.239
peak=    3.435 closest distance to " OD1 ASP A 231 " =    1.904
peak=    3.432 closest distance to " CB  SER A 141 " =    1.000
peak=    3.430 closest distance to " O   HOH Z 250 " =    1.372
peak=    3.430 closest distance to " O   HOH Z 355 " =    1.850
peak=    3.427 closest distance to " O   HOH Z 290 " =    1.299
peak=    3.421 closest distance to " O   HOH Z  58 " =    1.511
peak=    3.417 closest distance to " O   HOH Z  85 " =    2.091
peak=    3.415 closest distance to " O   HOH Z 126 " =    1.723
peak=    3.410 closest distance to " O   HOH Z 258 " =    2.222
peak=    3.409 closest distance to " ND2 ASN A 110 " =    1.638
peak=    3.405 closest distance to " CB  THR A  31 " =    1.592
peak=    3.405 closest distance to " O   HOH Z 345 " =    3.533
peak=    3.404 closest distance to " O   HOH Z 383 " =    2.163
peak=    3.404 closest distance to " O   HOH Z 350 " =    1.738
peak=    3.392 closest distance to " O   TRP A 274 " =    1.885
peak=    3.385 closest distance to " CA  ILE A  33 " =    1.690
peak=    3.385 closest distance to " O   HOH Z  30 " =    1.240
peak=    3.384 closest distance to " O   HOH Z 197 " =    1.911
peak=    3.383 closest distance to " CB  THR A  82 " =    1.402
peak=    3.382 closest distance to " CD  ARG A 269 " =    0.931
peak=    3.380 closest distance to " CA  ARG A 195 " =    1.237
peak=    3.377 closest distance to " CA  LYS A 181 " =    1.090
peak=    3.377 closest distance to " N   ASN A 127 " =    1.256
peak=    3.371 closest distance to " O  BHOH Z 338 " =    2.404
peak=    3.371 closest distance to " O   HOH Z 172 " =    3.841
peak=    3.365 closest distance to " O   HOH Z  61 " =    1.641
peak=    3.362 closest distance to " CG  LEU A 167 " =    1.174
peak=    3.358 closest distance to " OG  SER A  22 " =    2.932
peak=    3.358 closest distance to " O   HOH Z 174 " =    1.156
peak=    3.356 closest distance to " O   HOH Z 365 " =    2.815
peak=    3.354 closest distance to " O   HOH Z 371 " =    3.243
peak=    3.353 closest distance to " O   HOH Z 313 " =    1.871
peak=    3.353 closest distance to " O   HOH Z 248 " =    1.849
peak=    3.347 closest distance to " O   HOH Z  66 " =    2.352
peak=    3.346 closest distance to " CA  SER A  87 " =    0.895
peak=    3.342 closest distance to " CB  SER A  62 " =    1.297
peak=    3.342 closest distance to " CG  GLN A  88 " =    1.093
peak=    3.341 closest distance to " N   ARG A 190 " =    1.117
peak=    3.340 closest distance to " CA  ASN A 215 " =    1.165
peak=    3.338 closest distance to " CB  ALA A 242 " =    0.828
peak=    3.333 closest distance to " O   HOH Z 299 " =    4.436
peak=    3.332 closest distance to " CD1 TRP A 266 " =    1.076
peak=    3.332 closest distance to " O   ALA A 165 " =    1.366
peak=    3.323 closest distance to " CG  ARG A 269 " =    1.653
peak=    3.323 closest distance to " CG  PRO A 198 " =    1.334
peak=    3.316 closest distance to " O   HOH Z 203 " =    1.833
peak=    3.314 closest distance to " CA  ASP A 140 " =    1.276
peak=    3.314 closest distance to " NE2 HIS A 207 " =    1.342
peak=    3.314 closest distance to " CD1 LEU A 101 " =    1.092
peak=    3.313 closest distance to " O   HOH Z 326 " =    2.301
peak=    3.311 closest distance to " O   HOH Z  89 " =    1.898
peak=    3.310 closest distance to " O   HOH Z 406 " =    1.509
peak=    3.309 closest distance to " CA  ALA A 158 " =    1.146
peak=    3.306 closest distance to " CG  GLN A  58 " =    2.841
peak=    3.305 closest distance to " CA  TYR A 116 " =    1.477
peak=    3.305 closest distance to " O   HOH Z 116 " =    1.846
peak=    3.303 closest distance to " O   HOH Z  48 " =    1.491
peak=    3.298 closest distance to " O   HOH Z 216 " =    2.858
peak=    3.296 closest distance to " N   TYR A  15 " =    0.792
peak=    3.296 closest distance to " O   HOH Z 146 " =    2.271
peak=    3.294 closest distance to " O   HOH Z 244 " =    1.741
peak=    3.294 closest distance to " CG1BVAL A  72 " =    1.643
peak=    3.293 closest distance to " O   HOH Z 199 " =    1.715
peak=    3.291 closest distance to " CA  LYS A 290 " =    1.348
peak=    3.291 closest distance to " CA  GLY A 241 " =    0.775
peak=    3.288 closest distance to " NE  ARG A  79 " =    1.225
peak=    3.287 closest distance to " CB  ALA A 291 " =    1.317
peak=    3.275 closest distance to " O   HOH Z 340 " =    2.304
peak=    3.273 closest distance to " O   HOH Z 329 " =    3.870
peak=    3.271 closest distance to " O   HOH Z 175 " =    3.647
peak=    3.270 closest distance to " O   HOH Z 193 " =    1.680
peak=    3.270 closest distance to " O   HOH Z 353 " =    2.869
peak=    3.270 closest distance to " CA  ILE A 106 " =    0.819
peak=    3.266 closest distance to " O   HOH Z 125 " =    3.826
peak=    3.266 closest distance to " O   GLU A   2 " =    1.737
peak=    3.265 closest distance to " CB  TYR A 116 " =    0.999
peak=    3.264 closest distance to " NZ  LYS A 166 " =    3.124
peak=    3.264 closest distance to " O   HOH Z 145 " =    1.635
peak=    3.261 closest distance to " CG  MET A 188 " =    0.816
peak=    3.260 closest distance to " O   HOH Z 271 " =    2.101
peak=    3.258 closest distance to " O   HOH Z 359 " =    1.445
peak=    3.257 closest distance to " O   HOH Z 245 " =    1.442
peak=    3.256 closest distance to " CB  TYR A  30 " =    1.122
peak=    3.255 closest distance to " C   TYR A 214 " =    1.554
peak=    3.250 closest distance to " CD1 ILE A 106 " =    0.966
peak=    3.248 closest distance to " O   HOH Z 187 " =    2.311
peak=    3.248 closest distance to " O   HOH Z 114 " =    1.359
peak=    3.244 closest distance to " O   HOH Z  68 " =    1.898
peak=    3.244 closest distance to " CB  THR A 157 " =    1.180
peak=    3.241 closest distance to " O   HOH Z 313 " =    1.835
peak=    3.238 closest distance to " O   HOH Z 327 " =    1.856
peak=    3.231 closest distance to " O   HOH Z  49 " =    0.803
peak=    3.230 closest distance to " CD1 LEU A  96 " =    0.725
peak=    3.227 closest distance to " CB  LEU A  83 " =    0.836
peak=    3.217 closest distance to " O   HOH Z 368 " =    3.627
peak=    3.217 closest distance to " CD  ARG A 219 " =    1.063
peak=    3.212 closest distance to " CA  PHE A  59 " =    1.139
peak=    3.210 closest distance to " CA  ASP A 162 " =    1.145
peak=    3.207 closest distance to " N   PHE A 130 " =    1.230
peak=    3.207 closest distance to " O   HOH Z  49 " =    3.274
peak=    3.206 closest distance to " CG2 THR A  42 " =    0.846
peak=    3.205 closest distance to " CA  ALA A 154 " =    1.055
peak=    3.204 closest distance to " CD1 ILE A  33 " =    1.616
peak=    3.203 closest distance to " O   HOH Z  63 " =    1.219
peak=    3.198 closest distance to " CB  LYS A 117 " =    1.159
peak=    3.192 closest distance to " NH1 ARG A  14 " =    0.967
peak=    3.191 closest distance to " CB  ALA A 248 " =    1.365
peak=    3.186 closest distance to " CG2 ILE A 234 " =    0.901
peak=    3.185 closest distance to " CZ3 TRP A 274 " =    4.812
peak=    3.184 closest distance to " CZ3 TRP A  92 " =    1.430
peak=    3.184 closest distance to " NZ  LYS A  48 " =    1.382
peak=    3.180 closest distance to " NH2BARG A 190 " =    1.710
peak=    3.165 closest distance to " CD2 TRP A 179 " =    1.319
peak=    3.162 closest distance to " CB  ALA A  34 " =    0.762
peak=    3.157 closest distance to " CB  MET A  40 " =    0.778
peak=    3.156 closest distance to " O   HOH Z 256 " =    1.526
peak=    3.152 closest distance to " CG BARG A 102 " =    1.830
peak=    3.150 closest distance to " O   HOH Z 344 " =    3.036
peak=    3.149 closest distance to " O   HOH Z 128 " =    1.788
peak=    3.144 closest distance to " OG  SER A  62 " =    3.124
peak=    3.134 closest distance to " O   HOH Z  10 " =    1.797
peak=    3.129 closest distance to " CA  ALA A 160 " =    0.979
peak=    3.128 closest distance to " O   HOH Z 391 " =    2.979
peak=    3.126 closest distance to " O   HOH Z 139 " =    3.235
peak=    3.125 closest distance to " O   HOH Z 374 " =    2.969
peak=    3.125 closest distance to " OG BSER A 212 " =    2.447
peak=    3.124 closest distance to " O   HOH Z 419 " =    3.005
peak=    3.123 closest distance to " CB  ALA A  43 " =    0.923
peak=    3.120 closest distance to " O   HOH Z 162 " =    1.990
peak=    3.119 closest distance to " CG  GLU A  37 " =    0.865
peak=    3.112 closest distance to " O   HOH Z 384 " =    3.058
peak=    3.097 closest distance to " CB  VAL A 268 " =    0.813
peak=    3.094 closest distance to " CB  LYS A 193 " =    1.099
peak=    3.094 closest distance to " CB  GLN A 103 " =    1.008
peak=    3.093 closest distance to " O   HOH Z 305 " =    3.682
peak=    3.092 closest distance to " CE2 TYR A 186 " =    0.913
peak=    3.090 closest distance to " O   HOH Z 423 " =    2.893
peak=    3.083 closest distance to " O   HOH Z 302 " =    1.910
peak=    3.076 closest distance to " O   HOH Z 417 " =    3.302
peak=    3.068 closest distance to " CA  ARG A  36 " =    1.204
peak=    3.064 closest distance to " O   GLU A   2 " =    1.749
peak=    3.063 closest distance to " CB  GLN A  89 " =    1.107
peak=    3.061 closest distance to " O   HOH Z  90 " =    3.135
peak=    3.043 closest distance to " O   HOH Z 258 " =    1.851

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.790 - 5.392
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 197
   mapped sites are within: 0.790 - 5.392

peak=   -5.406 closest distance to " CG2 VAL A 230 " =    0.880
peak=   -4.276 closest distance to " O   HOH Z 231 " =    1.119
peak=   -4.242 closest distance to " CG1 VAL A 250 " =    2.765
peak=   -4.236 closest distance to " O   HOH Z 266 " =    5.058
peak=   -4.216 closest distance to " O   HOH Z 231 " =    1.728
peak=   -4.138 closest distance to " CB  ALA A 161 " =    2.626
peak=   -4.073 closest distance to " CD  ARG A 156 " =    1.988
peak=   -4.047 closest distance to " OE1 GLN A 223 " =    2.147
peak=   -3.993 closest distance to " CG2BVAL A  41 " =    2.700
peak=   -3.986 closest distance to " OG  SER A  97 " =    2.220
peak=   -3.962 closest distance to " O   PRO A 163 " =    2.126
peak=   -3.954 closest distance to " CD2 LEU A 167 " =    1.766
peak=   -3.948 closest distance to " CD2 LEU A 300 " =    2.810
peak=   -3.889 closest distance to " OG  SER A  87 " =    1.626
peak=   -3.866 closest distance to " O   HOH Z  10 " =    1.562
peak=   -3.861 closest distance to " C   ALA A 158 " =    1.286
peak=   -3.826 closest distance to " O   HOH Z  73 " =    2.107
peak=   -3.812 closest distance to " CG1 VAL A 296 " =    1.449
peak=   -3.777 closest distance to " CG  LEU A 101 " =    2.564
peak=   -3.768 closest distance to " CA  GLY A 241 " =    3.085
peak=   -3.766 closest distance to " CE2 TYR A  30 " =    2.760
peak=   -3.762 closest distance to " O   HOH Z  38 " =    1.229
peak=   -3.751 closest distance to " O   HOH Z 166 " =    1.935
peak=   -3.739 closest distance to " CD1 PHE A  59 " =    1.879
peak=   -3.733 closest distance to " NH2 ARG A  66 " =    1.822
peak=   -3.723 closest distance to " O   GLY A  80 " =    2.587
peak=   -3.721 closest distance to " CG  ASP A 231 " =    0.790
peak=   -3.711 closest distance to " O   HOH Z 113 " =    1.763
peak=   -3.707 closest distance to " OD1 ASN A 148 " =    1.529
peak=   -3.704 closest distance to " NH2AARG A 275 " =    5.392
peak=   -3.692 closest distance to " O   HOH Z 290 " =    1.373
peak=   -3.681 closest distance to " OG ASER A 134 " =    1.367
peak=   -3.675 closest distance to " CG2 VAL A 112 " =    2.615
peak=   -3.673 closest distance to " CD1 ILE A 151 " =    2.364
peak=   -3.671 closest distance to " O   HOH Z 426 " =    1.715
peak=   -3.670 closest distance to " OE1 GLN A  88 " =    0.950
peak=   -3.670 closest distance to " O   SER A 271 " =    2.271
peak=   -3.666 closest distance to " O   HOH Z  13 " =    1.483
peak=   -3.665 closest distance to " CH2 TRP A 177 " =    2.220
peak=   -3.657 closest distance to " CZ3 TRP A 179 " =    1.130
peak=   -3.656 closest distance to " O   HOH Z 196 " =    2.434
peak=   -3.640 closest distance to " CB  PRO A 243 " =    2.680
peak=   -3.637 closest distance to " O   HOH Z 389 " =    1.887
peak=   -3.631 closest distance to " N   ALA A  43 " =    2.735
peak=   -3.621 closest distance to " OG  SER A  26 " =    1.303
peak=   -3.602 closest distance to " O   HOH Z 184 " =    1.389
peak=   -3.596 closest distance to " CG  MET A 105 " =    0.941
peak=   -3.589 closest distance to " O   HOH Z 241 " =    1.149
peak=   -3.574 closest distance to " ND2 ASN A  60 " =    1.349
peak=   -3.573 closest distance to " O   HOH Z  52 " =    1.717
peak=   -3.566 closest distance to " CB  PRO A 163 " =    2.538
peak=   -3.565 closest distance to " CA  ASP A 298 " =    1.076
peak=   -3.562 closest distance to " CD  GLN A  58 " =    1.037
peak=   -3.559 closest distance to " CA  GLY A 241 " =    2.364
peak=   -3.557 closest distance to " O   HOH Z  94 " =    2.232
peak=   -3.547 closest distance to " CG  TRP A 266 " =    1.768
peak=   -3.543 closest distance to " O   HOH Z  11 " =    1.948
peak=   -3.542 closest distance to " O   GLY A 211 " =    1.515
peak=   -3.538 closest distance to " O   HOH Z 377 " =    1.240
peak=   -3.536 closest distance to " O   HOH Z 111 " =    2.105
peak=   -3.535 closest distance to " CZ2 TRP A  92 " =    2.859
peak=   -3.531 closest distance to " O   HOH Z 407 " =    3.470
peak=   -3.530 closest distance to " CG2 VAL A 296 " =    1.298
peak=   -3.528 closest distance to " O   HOH Z 351 " =    1.568
peak=   -3.527 closest distance to " CD1 LEU A 228 " =    2.484
peak=   -3.526 closest distance to " O   HOH Z 377 " =    1.497
peak=   -3.524 closest distance to " O   HOH Z  17 " =    1.391
peak=   -3.522 closest distance to " CD2 TYR A 293 " =    2.066
peak=   -3.513 closest distance to " CD1 LEU A   5 " =    2.546
peak=   -3.511 closest distance to " OG BSER A 134 " =    1.924
peak=   -3.494 closest distance to " O   HOH Z 353 " =    2.266
peak=   -3.493 closest distance to " OG1 THR A  82 " =    1.877
peak=   -3.491 closest distance to " O   HOH Z 396 " =    2.009
peak=   -3.491 closest distance to " OXT GLY A 302 " =    3.013
peak=   -3.487 closest distance to " C   ASN A 187 " =    1.734
peak=   -3.483 closest distance to " O   HOH Z 211 " =    1.522
peak=   -3.483 closest distance to " CD  GLN A  88 " =    0.825
peak=   -3.475 closest distance to " N   ALA A 226 " =    2.229
peak=   -3.466 closest distance to " O   HOH Z 103 " =    1.905
peak=   -3.465 closest distance to " C   ASN A 285 " =    2.542
peak=   -3.465 closest distance to " O   VAL A  67 " =    2.655
peak=   -3.464 closest distance to " O   HOH Z  19 " =    2.211
peak=   -3.463 closest distance to " O   PRO A 198 " =    1.276
peak=   -3.459 closest distance to " O   HOH Z 394 " =    1.606
peak=   -3.455 closest distance to " O   HOH Z 234 " =    4.488
peak=   -3.450 closest distance to " SG ACYS A 201 " =    1.131
peak=   -3.450 closest distance to " ND2 ASN A  45 " =    2.157
peak=   -3.449 closest distance to " CA  GLY A 133 " =    2.287
peak=   -3.448 closest distance to " O   HOH Z 109 " =    0.949
peak=   -3.446 closest distance to " CE3 TRP A  70 " =    1.812
peak=   -3.445 closest distance to " NH2 ARG A  79 " =    2.021
peak=   -3.444 closest distance to " CG  LYS A 193 " =    2.623
peak=   -3.433 closest distance to " SG  CYS A 254 " =    3.211
peak=   -3.429 closest distance to " O   HOH Z  43 " =    1.657
peak=   -3.424 closest distance to " O   HOH Z 275 " =    1.545
peak=   -3.417 closest distance to " O   HOH Z 177 " =    1.684
peak=   -3.416 closest distance to " NE2 GLN A 103 " =    1.783
peak=   -3.416 closest distance to " CG1 VAL A 112 " =    2.718
peak=   -3.413 closest distance to " CD1 TYR A 247 " =    2.335
peak=   -3.412 closest distance to " C   HIS A 108 " =    1.192
peak=   -3.395 closest distance to " CG2 ILE A 263 " =    2.424
peak=   -3.393 closest distance to " O   HOH Z 185 " =    2.481
peak=   -3.392 closest distance to " NE2 GLN A  88 " =    0.879
peak=   -3.385 closest distance to " CD1 LEU A 101 " =    2.810
peak=   -3.377 closest distance to " CG1 VAL A 112 " =    2.576
peak=   -3.357 closest distance to " CB  TRP A  85 " =    2.538
peak=   -3.354 closest distance to " CE BMET A  47 " =    2.207
peak=   -3.353 closest distance to " O   VAL A 125 " =    2.339
peak=   -3.352 closest distance to " CD  GLN A 223 " =    0.866
peak=   -3.348 closest distance to " O   HOH Z 186 " =    0.901
peak=   -3.342 closest distance to " OE2 GLU A   2 " =    1.802
peak=   -3.336 closest distance to " CD  LYS A 289 " =    2.489
peak=   -3.331 closest distance to " O   HOH Z 357 " =    2.106
peak=   -3.330 closest distance to " O   HOH Z  49 " =    1.279
peak=   -3.326 closest distance to " CD2 PHE A  61 " =    1.926
peak=   -3.325 closest distance to " O   HOH Z 292 " =    4.650
peak=   -3.323 closest distance to " CG  HIS A  86 " =    1.057
peak=   -3.309 closest distance to " OD2 ASP A  50 " =    2.262
peak=   -3.307 closest distance to " CG  ARG A 269 " =    2.348
peak=   -3.296 closest distance to " N   THR A 157 " =    1.547
peak=   -3.293 closest distance to " O   HOH Z 117 " =    4.612
peak=   -3.293 closest distance to " N   TYR A  68 " =    2.941
peak=   -3.291 closest distance to " CG1 VAL A 197 " =    2.344
peak=   -3.286 closest distance to " CG  GLU A  53 " =    1.755
peak=   -3.286 closest distance to " CB  ALA A 291 " =    2.251
peak=   -3.281 closest distance to " NE2 GLN A 194 " =    1.945
peak=   -3.280 closest distance to " O   HOH Z 118 " =    3.099
peak=   -3.278 closest distance to " O   HOH Z 313 " =    1.049
peak=   -3.277 closest distance to " O   ASN A 301 " =    1.374
peak=   -3.276 closest distance to " CD1 TRP A 179 " =    0.991
peak=   -3.270 closest distance to " O   HOH Z 183 " =    1.355
peak=   -3.270 closest distance to " O   HOH Z 252 " =    3.879
peak=   -3.269 closest distance to " ND2 ASN A  60 " =    1.900
peak=   -3.268 closest distance to " N   SER A   3 " =    2.220
peak=   -3.258 closest distance to " CG  PRO A 163 " =    2.409
peak=   -3.257 closest distance to " NE  ARG A 259 " =    1.103
peak=   -3.254 closest distance to " CB  VAL A 230 " =    1.027
peak=   -3.253 closest distance to " CZ  PHE A  38 " =    2.290
peak=   -3.253 closest distance to " N   THR A 235 " =    1.241
peak=   -3.251 closest distance to " CG  GLU A 277 " =    1.327
peak=   -3.248 closest distance to " O   SER A 276 " =    1.608
peak=   -3.243 closest distance to " CB  ALA A 291 " =    2.325
peak=   -3.242 closest distance to " O   HOH Z 184 " =    1.566
peak=   -3.241 closest distance to " N   THR A  18 " =    1.294
peak=   -3.238 closest distance to " CB  ASP A 286 " =    2.240
peak=   -3.235 closest distance to " NH2 ARG A  66 " =    1.309
peak=   -3.229 closest distance to " O   HOH Z 166 " =    1.688
peak=   -3.226 closest distance to " OG BSER A 134 " =    1.365
peak=   -3.221 closest distance to " OD1 ASN A 173 " =    1.282
peak=   -3.216 closest distance to " O   PHE A 218 " =    1.572
peak=   -3.198 closest distance to " O   HOH Z 435 " =    2.730
peak=   -3.197 closest distance to " O   HOH Z 222 " =    1.461
peak=   -3.197 closest distance to " OG BSER A 212 " =    1.592
peak=   -3.189 closest distance to " CE  LYS A  76 " =    2.607
peak=   -3.189 closest distance to " O   HOH Z 136 " =    2.448
peak=   -3.186 closest distance to " CD  ARG A 139 " =    1.718
peak=   -3.186 closest distance to " CG2 THR A 221 " =    2.250
peak=   -3.186 closest distance to " O   HOH Z 434 " =    1.728
peak=   -3.185 closest distance to " CA  GLY A 203 " =    2.359
peak=   -3.185 closest distance to " CD2 LEU A 237 " =    2.857
peak=   -3.183 closest distance to " O   HOH Z 114 " =    1.801
peak=   -3.181 closest distance to " O   HOH Z 128 " =    4.250
peak=   -3.178 closest distance to " O   HOH Z  60 " =    1.797
peak=   -3.178 closest distance to " O   HOH Z 106 " =    2.038
peak=   -3.178 closest distance to " O   HOH Z 390 " =    2.242
peak=   -3.176 closest distance to " N   ALA A 248 " =    2.470
peak=   -3.176 closest distance to " O   HOH Z 368 " =    1.726
peak=   -3.173 closest distance to " C   LEU A 143 " =    1.122
peak=   -3.172 closest distance to " CD  PRO A 213 " =    2.222
peak=   -3.165 closest distance to " O   HOH Z 348 " =    2.279
peak=   -3.164 closest distance to " N   SER A 212 " =    2.011
peak=   -3.159 closest distance to " O   HOH Z  71 " =    1.359
peak=   -3.152 closest distance to " O   HOH Z  60 " =    1.850
peak=   -3.151 closest distance to " OH  TYR A 214 " =    1.383
peak=   -3.141 closest distance to " N   PHE A  59 " =    2.127
peak=   -3.141 closest distance to " SG ACYS A 201 " =    2.010
peak=   -3.137 closest distance to " CE  MET A 105 " =    2.121
peak=   -3.132 closest distance to " O   GLY A 203 " =    2.407
peak=   -3.132 closest distance to " N   THR A  52 " =    1.748
peak=   -3.131 closest distance to " OG1 THR A 178 " =    1.332
peak=   -3.126 closest distance to " O   HOH Z 308 " =    1.775
peak=   -3.120 closest distance to " CA  ASN A 127 " =    1.108
peak=   -3.119 closest distance to " O   HOH Z 216 " =    2.020
peak=   -3.115 closest distance to " O   HOH Z 410 " =    1.661
peak=   -3.101 closest distance to " CD1 ILE A 199 " =    2.598
peak=   -3.100 closest distance to " CG2 VAL A 189 " =    2.091
peak=   -3.093 closest distance to " CB  ALA A 248 " =    2.457
peak=   -3.091 closest distance to " O   HOH Z 150 " =    2.059
peak=   -3.086 closest distance to " N   LYS A 166 " =    2.036
peak=   -3.084 closest distance to " OG  SER A  62 " =    1.741
peak=   -3.076 closest distance to " OD1 ASP A 191 " =    1.643
peak=   -3.067 closest distance to " O   HOH Z 236 " =    1.281
peak=   -3.045 closest distance to " CG  ARG A 269 " =    3.037
peak=   -3.043 closest distance to " O   THR A  18 " =    1.508
peak=   -3.031 closest distance to " O   ASP A  27 " =    2.020
peak=   -3.022 closest distance to " CB  TYR A  15 " =    2.228

================= 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    :  0.4706 0.4568   6.272392e+00   6.257939e+00
   1_bss:  0.4633 0.4466   6.268263e+00   6.249652e+00
   1_xyz:  0.3686 0.3993   6.132624e+00   6.179900e+00
   1_adp:  0.3232 0.3694   6.043854e+00   6.139789e+00
   1_occ:  0.3227 0.3695   6.043008e+00   6.140487e+00
   2_bss:  0.3217 0.3666   6.043874e+00   6.139889e+00
   2_xyz:  0.2318 0.2913   5.770985e+00   5.941516e+00
   2_adp:  0.2127 0.2702   5.696255e+00   5.877237e+00
   2_occ:  0.2123 0.2705   5.695823e+00   5.876909e+00
   3_bss:  0.2104 0.2674   5.695857e+00   5.874897e+00
   3_xyz:  0.1570 0.2069   5.427393e+00   5.641093e+00
   3_adp:  0.1381 0.1895   5.330537e+00   5.566719e+00
   3_occ:  0.1380 0.1894   5.330055e+00   5.566458e+00
   4_bss:  0.1378 0.1894   5.329915e+00   5.566472e+00
   4_xyz:  0.1269 0.1793   5.264193e+00   5.507084e+00
   4_adp:  0.1249 0.1748   5.245847e+00   5.482629e+00
   4_occ:  0.1248 0.1746   5.245417e+00   5.482128e+00
   5_bss:  0.1248 0.1746   5.245340e+00   5.482126e+00
   5_xyz:  0.1161 0.1666   5.190013e+00   5.440178e+00
   5_adp:  0.1158 0.1653   5.186522e+00   5.435055e+00
   5_occ:  0.1157 0.1652   5.186325e+00   5.434933e+00
   5_bss:  0.1160 0.1650   5.185917e+00   5.433894e+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:  0.316  30.586   9.665   8.446   6.942   0.000   0.000   0.000
   1_xyz:  0.316  30.586   9.665   8.446   6.942   0.000   0.000   0.000
   1_adp:  0.316  30.586   9.665   8.446   6.942   0.000   0.000   0.000
   1_occ:  0.316  30.586   9.665   8.446   6.942   0.000   0.000   0.000
   2_bss:  0.308  47.805   6.901   5.628   5.026   0.000   0.000   0.000
   2_xyz:  0.308  47.805   6.901   5.628   5.026   0.000   0.000   0.000
   2_adp:  0.308  47.805   6.901   5.628   5.026   0.000   0.000   0.000
   2_occ:  0.308  47.805   6.901   5.628   5.026   0.000   0.000   0.000
   3_bss:  0.319  47.805   4.108   3.706   3.988   0.000   0.000   0.000
   3_xyz:  0.319  47.805   4.108   3.706   3.988   0.000   0.000   0.000
   3_adp:  0.319  47.805   4.108   3.706   3.988   0.000   0.000   0.000
   3_occ:  0.319  47.805   4.108   3.706   3.988   0.000   0.000   0.000
   4_bss:  0.330  63.468   3.068   2.870   3.444   0.000   0.000   0.000
   4_xyz:  0.330  63.468   3.068   2.870   3.444   0.000   0.000   0.000
   4_adp:  0.330  63.468   3.068   2.870   3.444   0.000   0.000   0.000
   4_occ:  0.330  63.468   3.068   2.870   3.444   0.000   0.000   0.000
   5_bss:  0.325  62.251   2.876   2.790   3.473   0.000   0.000   0.000
   5_xyz:  0.325  62.251   2.876   2.790   3.473   0.000   0.000   0.000
   5_adp:  0.325  62.251   2.876   2.790   3.473   0.000   0.000   0.000
   5_occ:  0.325  62.251   2.876   2.790   3.473   0.000   0.000   0.000
   5_bss:  0.325  65.297  -0.171  -0.256   0.427   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.447 0.4652  0.5266    64449.296
   1_bss:  54.257 0.4660  0.6734    62318.041
   1_xyz:  46.776 0.5585  0.7851    47253.438
   1_adp:  42.059 0.6169  0.8721    40468.193
   1_occ:  42.113 0.6162  0.8706    40553.526
   2_bss:  41.969 0.6179  0.8013    40355.994
   2_xyz:  30.244 0.7540  0.9565    22669.680
   2_adp:  27.147 0.7887  0.9982    19245.957
   2_occ:  27.159 0.7886  0.9975    19243.557
   3_bss:  27.058 0.7898  0.9330    19155.415
   3_xyz:  19.856 0.8627  0.9826    10961.834
   3_adp:  18.029 0.8798  0.9874     9244.555
   3_occ:  18.020 0.8799  0.9872     9237.468
   4_bss:  17.993 0.8802  0.9596     9239.239
   4_xyz:  16.486 0.8942  0.9656     8097.259
   4_adp:  15.871 0.8998  0.9660     7745.126
   4_occ:  15.859 0.9000  0.9660     7737.982
   5_bss:  15.860 0.8999  0.9632     7736.520
   5_xyz:  14.984 0.9072  0.9674     7112.885
   5_adp:  14.846 0.9085  0.9664     7063.027
   5_occ:  14.846 0.9085  0.9663     7061.728
   5_bss:  14.856 0.9083  0.9659     7040.808
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4425e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4425e+01
   1_xyz:   1.719  0.014  0.110 18.169  0.007  4.111   1.4580e-01
   1_adp:   1.719  0.014  0.110 18.169  0.007  4.111   1.4580e-01
   1_occ:   1.719  0.014  0.110 18.169  0.007  4.111   1.4580e-01
   2_bss:   1.719  0.014  0.110 18.169  0.007  4.111   1.4580e-01
   2_xyz:   1.155  0.009  0.081 16.641  0.005  4.111   8.3303e-02
   2_adp:   1.155  0.009  0.081 16.641  0.005  4.111   8.3303e-02
   2_occ:   1.155  0.009  0.081 16.641  0.005  4.111   8.3303e-02
   3_bss:   1.155  0.009  0.081 16.641  0.005  4.111   8.3303e-02
   3_xyz:   1.195  0.010  0.089 16.483  0.004  4.136   8.6438e-02
   3_adp:   1.195  0.010  0.089 16.483  0.004  4.136   8.6438e-02
   3_occ:   1.195  0.010  0.089 16.483  0.004  4.136   8.6438e-02
   4_bss:   1.195  0.010  0.089 16.483  0.004  4.136   8.6438e-02
   4_xyz:   1.087  0.009  0.083 16.118  0.004  4.116   7.3547e-02
   4_adp:   1.087  0.009  0.083 16.118  0.004  4.116   7.3547e-02
   4_occ:   1.087  0.009  0.083 16.118  0.004  4.116   7.3547e-02
   5_bss:   1.087  0.009  0.083 16.118  0.004  4.116   7.3547e-02
   5_xyz:   1.227  0.012  0.097 16.059  0.005  4.121   9.2717e-02
   5_adp:   1.227  0.012  0.097 16.059  0.005  4.121   9.2717e-02
   5_occ:   1.227  0.012  0.097 16.059  0.005  4.121   9.2717e-02
   5_bss:   1.227  0.012  0.097 16.059  0.005  4.121   9.2717e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0570e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0570e+00
   1_xyz:  14.667  0.171  0.477 86.020  0.038  2.180   1.0809e-01
   1_adp:  14.667  0.171  0.477 86.020  0.038  2.180   1.0809e-01
   1_occ:  14.667  0.171  0.477 86.020  0.038  2.180   1.0809e-01
   2_bss:  14.667  0.171  0.477 86.020  0.038  2.180   1.0809e-01
   2_xyz:   7.515  0.071  0.294 83.213  0.031  2.187   6.8149e-02
   2_adp:   7.515  0.071  0.294 83.213  0.031  2.187   6.8149e-02
   2_occ:   7.515  0.071  0.294 83.213  0.031  2.187   6.8149e-02
   3_bss:   7.515  0.071  0.294 83.213  0.031  2.187   6.8149e-02
   3_xyz:   9.846  0.075  0.483 84.448  0.047  2.282   7.1832e-02
   3_adp:   9.846  0.075  0.483 84.448  0.047  2.282   7.1832e-02
   3_occ:   9.846  0.075  0.483 84.448  0.047  2.282   7.1832e-02
   4_bss:   9.846  0.075  0.483 84.448  0.047  2.282   7.1832e-02
   4_xyz:   8.571  0.053  0.460 82.724  0.043  2.395   4.6621e-02
   4_adp:   8.571  0.053  0.460 82.724  0.043  2.395   4.6621e-02
   4_occ:   8.571  0.053  0.460 82.724  0.043  2.395   4.6621e-02
   5_bss:   8.571  0.053  0.460 82.724  0.043  2.395   4.6621e-02
   5_xyz:   8.204  0.055  0.652 83.180  0.044  2.297   6.5943e-02
   5_adp:   8.204  0.055  0.652 83.180  0.044  2.297   6.5943e-02
   5_occ:   8.204  0.055  0.652 83.180  0.044  2.297   6.5943e-02
   5_bss:   8.204  0.055  0.652 83.180  0.044  2.297   6.5943e-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:  95.70   0.00  11.58  73.21   0.00   8.86  95.70   0.00  26.40
   1_occ:  95.70   0.00  11.58  73.21   0.00   8.86  95.70   0.00  26.40
   2_bss:  95.70   0.00  11.58  73.21   0.00   8.86  95.70   0.00  26.40
   2_xyz:  95.70   0.00  11.58  73.21   0.00   8.86  95.70   0.00  26.40
   2_adp:  96.19   0.00  11.97  96.19   0.00   8.58  95.55   0.00  30.41
   2_occ:  96.19   0.00  11.97  96.19   0.00   8.58  95.55   0.00  30.41
   3_bss:  96.19   0.00  11.97  96.19   0.00   8.58  95.55   0.00  30.41
   3_xyz:  96.19   0.00  11.97  96.19   0.00   8.58  95.55   0.00  30.41
   3_adp:  91.87   0.00  13.13  90.46   0.00   8.48  91.87   0.44  38.46
   3_occ:  91.87   0.00  13.13  90.46   0.00   8.48  91.87   0.44  38.46
   4_bss:  91.87   0.00  13.13  90.46   0.00   8.48  91.87   0.44  38.46
   4_xyz:  91.87   0.00  13.13  90.46   0.00   8.48  91.87   0.44  38.46
   4_adp:  90.70   0.00  12.75  90.70   0.00   8.24  89.57   0.86  37.35
   4_occ:  90.70   0.00  12.75  90.70   0.00   8.24  89.57   0.86  37.35
   5_bss:  90.70   0.00  12.75  90.70   0.00   8.24  89.57   0.86  37.35
   5_xyz:  90.70   0.00  12.75  90.70   0.00   8.24  89.57   0.86  37.35
   5_adp:  89.24   0.00  12.37  89.24   0.00   8.10  88.88   1.21  35.62
   5_occ:  89.24   0.00  12.37  89.24   0.00   8.10  88.88   1.21  35.62
   5_bss:  92.28   3.05  15.41  92.28   3.05  11.14  91.92   4.25  38.67
------------------------------------------------------------------------
 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:    1.213    0.006    0.416
   1_adp:    1.213    0.006    0.416
   1_occ:    1.213    0.006    0.416
   2_bss:    1.213    0.006    0.416
   2_xyz:    1.542    0.053    0.579
   2_adp:    1.542    0.053    0.579
   2_occ:    1.542    0.053    0.579
   3_bss:    1.542    0.053    0.579
   3_xyz:    1.518    0.037    0.673
   3_adp:    1.518    0.037    0.673
   3_occ:    1.518    0.037    0.673
   4_bss:    1.518    0.037    0.673
   4_xyz:    1.631    0.087    0.694
   4_adp:    1.631    0.087    0.694
   4_occ:    1.631    0.087    0.694
   5_bss:    1.631    0.087    0.694
   5_xyz:    1.681    0.070    0.712
   5_adp:    1.681    0.070    0.712
   5_occ:    1.681    0.070    0.712
   5_bss:    1.681    0.070    0.712
------------------------------------------------------------------------

CPU time actual refinement: 318.22


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1292/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_1292/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1292/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1292/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1292/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 318.06 
  Macro-tasks:
    bulk solvent and scale       = 37.98  
    individual site refinement   = 125.94 
    weights calculation          = 31.70  
    collect and process          = 6.45   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 202.18 
  Micro-tasks:
    mask                            = 2.36   
    f_calc                          = 96.54  
    alpha_beta                      = 8.24   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 107.04 
    fmodel                         = 6.37   
    r_factors                      = 0.19   
    phase_errors                   = 10.39  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 232.56 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.572 micro seconds
Total CPU time: 5.54 minutes
from_scatterers_fft:    637 calls, 96.24 s
gradients_fft:          583 calls, 94.28 s

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

# Date 2008-01-16 Time 03:39:22 PST -0800 (1200483562.75 s)
Start R-work = 0.4706, R-free = 0.4568 (no bulk solvent and anisotropic scale)
Final R-work = 0.1318, R-free = 0.1804 (no bulk solvent and anisotropic scale)

Start R-work = 0.4633, R-free = 0.4466
Final R-work = 0.1160, R-free = 0.1650