# Date 2008-01-16 Time 01:32:14 PST -0800 (1200475934.25 s)
#phil __OFF__

Command line arguments: "../451.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8281
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 451

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 47.6339, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.76, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8572 1.95148
Completeness in resolution range: 0.935572
Completeness with d_max=infinity: 0.932765

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8572 1.95148
Completeness in resolution range: 0.935572
Completeness with d_max=infinity: 0.932765

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8576 -  4.1761 [2201/2230]  1979   222  10.1%
  bin  2:  4.1761 -  3.3270 [2102/2125]  1893   209   9.9%
  bin  3:  3.3270 -  2.9100 [2074/2099]  1867   207  10.0%
  bin  4:  2.9100 -  2.6456 [2067/2084]  1867   200   9.7%
  bin  5:  2.6456 -  2.4569 [2047/2090]  1834   213  10.4%
  bin  6:  2.4569 -  2.3126 [2055/2083]  1858   197   9.6%
  bin  7:  2.3126 -  2.1971 [2014/2050]  1810   204  10.1%
  bin  8:  2.1971 -  2.1018 [2015/2057]  1812   203  10.1%
  bin  9:  2.1018 -  2.0211 [2007/2065]  1805   202  10.1%
  bin 10:  2.0211 -  1.9515 [1007/2055]   905   102  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_451/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.42 -     2.12: 28
        2.12 -     2.81: 858
        2.81 -     3.51: 4504
        3.51 -     4.20: 9400
        4.20 -     4.90: 13874
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.422 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.453 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.550 3.040 -x+1/2,-y+1,z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.674 3.040 -x+1/2,-y+1,z+1/2
  " OG  SER A  95 " - " O   SER A 271 "  1.680 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28659 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_451/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_451/model_refine_001.geo

CPU time processing inputs: 7.99


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 47.63395 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4984   r_free= 0.4964   ksol= 0.00   Bsol= 0.00   scale= 0.787    |
|                                                                             |
| 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:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.297248                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8576 -  4.6581 0.99   1429  160 0.4122 0.4126      6.6252      6.6433|
|  2:  4.6581 -  3.7163 0.99   1371  149 0.4263 0.4269      6.8263      6.8371|
|  3:  3.7163 -  3.2521 0.99   1341  152 0.4625 0.4417      6.7019      6.7503|
|  4:  3.2521 -  2.9573 0.99   1336  147 0.4718 0.4778      6.5253      6.5234|
|  5:  2.9573 -  2.7468 0.99   1336  147 0.5260 0.5568      6.3862        6.37|
|  6:  2.7468 -  2.5858 0.99   1319  148 0.5230 0.5459       6.281      6.2182|
|  7:  2.5858 -  2.4569 0.98   1308  148 0.5374 0.4534      6.2668      6.1769|
|  8:  2.4569 -  2.3503 0.98   1312  142 0.5440 0.5457      6.1738      6.2003|
|  9:  2.3503 -  2.2602 0.99   1319  147 0.5571 0.5590       6.141      6.1366|
| 10:  2.2602 -  2.1824 0.98   1309  141 0.5424 0.5684      6.1052      6.1467|
| 11:  2.1824 -  2.1144 0.97   1284  146 0.5472 0.5259      6.0456       6.011|
| 12:  2.1144 -  2.0541 0.98   1286  145 0.5444 0.5848      5.9551      6.0099|
| 13:  2.0541 -  2.0002 0.92   1208  138 0.5534 0.5429      5.8789      5.8385|
| 14:  2.0002 -  1.9515 0.35    472   49 0.5649 0.5004      5.8503      5.6773|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8576 -  4.6581  1429   160  0.65  38.45   0.79     0.68      84961.94|
|  2:  4.6581 -  3.7163  1371   149  0.65  39.22   0.87     0.72     125010.37|
|  3:  3.7163 -  3.2521  1341   152  0.54  48.96   0.83     0.66     134676.61|
|  4:  3.2521 -  2.9573  1336   147  0.44  56.57   0.80     0.55     117284.77|
|  5:  2.9573 -  2.7468  1336   147  0.34  64.32   0.72     0.43      95407.45|
|  6:  2.7468 -  2.5858  1319   148  0.34  64.56   0.73     0.40      77181.78|
|  7:  2.5858 -  2.4569  1308   148  0.34  64.08   0.73     0.40      67031.87|
|  8:  2.4569 -  2.3503  1312   142  0.33  65.10   0.71     0.40      61376.15|
|  9:  2.3503 -  2.2602  1319   147  0.27  69.70   0.72     0.34      59538.39|
| 10:  2.2602 -  2.1824  1309   141  0.21  74.64   0.75     0.25      58016.98|
| 11:  2.1824 -  2.1144  1284   146  0.13  80.33   0.77     0.17      54961.70|
| 12:  2.1144 -  2.0541  1286   145  0.13  80.52   0.73     0.17      51454.89|
| 13:  2.0541 -  2.0002  1208   138  0.19  75.69   0.73     0.25      40716.22|
| 14:  2.0002 -  1.9515   472    49  0.38  61.66   0.69     0.43      27726.26|
|alpha:            min =        0.17 max =            0.72 mean =         0.42|
|beta:             min =    27726.26 max =       134676.61 mean =     78335.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.36|
|phase err.(work): min =        0.00 max =           89.99 mean =        62.80|
|phase err.(test): min =        0.00 max =           90.00 mean =        63.14|
|-----------------------------------------------------------------------------|

============================== 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 = 19.071846             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.917   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.723248              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.237   (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 |  1.001 -  1.391:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.391 -  1.781:       13 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.781 -  2.171:      100 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.171 -  2.560:      517 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.560 -  2.950:     1329 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.950 -  3.340:     2484 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.340 -  3.730:     3970 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.730 -  4.120:     5199 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.120 -  4.510:     6869 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.510 -  4.900:     8218 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.199 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.001 |       2.401 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.616)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.616)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5030   r_free= 0.5033   ksol= 0.00   Bsol= 0.00   scale= 0.757    |
|                                                                             |
| 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:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.297918                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4915   r_free= 0.4884   ksol= 0.40   Bsol= 50.00   scale= 0.956   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.58,8.84,7.75,0.00,0.00,0.00); trace/3= 7.39                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.295285                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.941733             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.708   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.517976              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.090   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4915      final r-factor (work) = 0.4291          |
| start r-factor (free) = 0.4884      final r-factor (free) = 0.4441          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 103.3698 = 15.94 * 0.50 * 6.2943 + 1.00 * 53.1991                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 49.8410 = 15.94 * 0.50 * 6.2331 + 1.00 * 0.1576                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4291      final r-factor (work) = 0.3884          |
| start r-factor (free) = 0.4441      final r-factor (free) = 0.4308          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.4761 = 1.52 * 1.00 * 6.2331 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.4002 = 1.52 * 1.00 * 6.1796 + 1.00 * 0.0197                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.616)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.27   15.36    None  None   None       |
|    all(noH): 2823   0      0.00    98.27   15.36    None  None   None       |
|    Sol.    : 438    0      0.00    98.27   27.33    None  None   None       |
|    Mac.    : 2385   0      0.00    78.62   13.16    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 -   9.827: 1204   |   5:    49.135 -  58.962:   49        |
|      1:     9.827 -  19.654:  822   |   6:    58.962 -  68.789:   22        |
|      2:    19.654 -  29.481:  424   |   7:    68.789 -  78.615:   14        |
|      3:    29.481 -  39.308:  198   |   8:    78.615 -  88.442:    3        |
|      4:    39.308 -  49.135:   83   |   9:    88.442 -  98.269:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3884 r_free = 0.4308             target_work(ml) = 6.167         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3875 r_free = 0.4301             target_work(ml) = 6.166         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3875   r_free= 0.4301   ksol= 0.40   Bsol= 50.00   scale= 1.089   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.58,8.84,7.75,0.00,0.00,0.00); trace/3= 7.39                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.166484                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3860   r_free= 0.4276   ksol= 0.34   Bsol= 48.84   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.71,5.78,5.38,0.00,0.00,0.00); trace/3= 4.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.167097                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.929559              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.668  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.672017              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.901  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3860      final r-factor (work) = 0.3140          |
| start r-factor (free) = 0.4276      final r-factor (free) = 0.3733          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.8185 = 9.93 * 0.50 * 6.1757 + 1.00 * 0.1576                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.3221 = 9.93 * 0.50 * 6.0879 + 1.00 * 0.0971                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3140      final r-factor (work) = 0.2937          |
| start r-factor (free) = 0.3733      final r-factor (free) = 0.3569          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1109 = 0.67 * 1.00 * 6.0879 + 1.00 * 0.0197                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0366 = 0.67 * 1.00 * 5.9885 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.616)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.31   15.24    None  None   None       |
|    all(noH): 2823   0      0.00    99.31   15.24    None  None   None       |
|    Sol.    : 438    0      0.00    99.31   31.74    None  None   None       |
|    Mac.    : 2385   0      0.00    83.17   12.21    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 -   9.931: 1277   |   5:    49.656 -  59.587:   47        |
|      1:     9.931 -  19.862:  803   |   6:    59.587 -  69.518:   15        |
|      2:    19.862 -  29.794:  380   |   7:    69.518 -  79.449:    9        |
|      3:    29.794 -  39.725:  178   |   8:    79.449 -  89.380:    5        |
|      4:    39.725 -  49.656:  108   |   9:    89.380 -  99.312:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2937 r_free = 0.3569             target_work(ml) = 5.966         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2935 r_free = 0.3570             target_work(ml) = 5.965         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2935   r_free= 0.3570   ksol= 0.34   Bsol= 48.84   scale= 1.072   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.71,5.78,5.38,0.00,0.00,0.00); trace/3= 4.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.965492                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2913   r_free= 0.3541   ksol= 0.33   Bsol= 48.84   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.04,3.11,2.99,0.00,0.00,0.00); trace/3= 2.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.963930                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.923349              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.224  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.427222              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.369  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2913      final r-factor (work) = 0.2088          |
| start r-factor (free) = 0.3541      final r-factor (free) = 0.2665          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.8261 = 7.92 * 0.50 * 5.9896 + 1.00 * 0.0971                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.2437 = 7.92 * 0.50 * 5.8467 + 1.00 * 0.0811                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2088      final r-factor (work) = 0.1844          |
| start r-factor (free) = 0.2665      final r-factor (free) = 0.2381          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5100 = 0.43 * 1.00 * 5.8467 + 1.00 * 0.0122                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4149 = 0.43 * 1.00 * 5.6288 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.616)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.75   14.88    None  None   None       |
|    all(noH): 2823   0      0.00    87.75   14.88    None  None   None       |
|    Sol.    : 438    0      3.87    87.75   37.14    None  None   None       |
|    Mac.    : 2385   0      0.00    84.49   10.79    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 -   8.775: 1284   |   5:    43.875 -  52.650:   95        |
|      1:     8.775 -  17.550:  830   |   6:    52.650 -  61.425:   56        |
|      2:    17.550 -  26.325:  244   |   7:    61.425 -  70.200:   24        |
|      3:    26.325 -  35.100:  156   |   8:    70.200 -  78.975:   11        |
|      4:    35.100 -  43.875:  120   |   9:    78.975 -  87.750:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1844 r_free = 0.2381             target_work(ml) = 5.572         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1840 r_free = 0.2381             target_work(ml) = 5.571         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1840   r_free= 0.2381   ksol= 0.33   Bsol= 48.84   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.04,3.11,2.99,0.00,0.00,0.00); trace/3= 2.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.571486                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1830   r_free= 0.2365   ksol= 0.32   Bsol= 42.08   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.07,1.68,1.45,0.00,0.00,0.00); trace/3= 1.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.568318                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.081208              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.781  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.467683              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.965  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1830      final r-factor (work) = 0.1534          |
| start r-factor (free) = 0.2365      final r-factor (free) = 0.2033          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9442 = 2.08 * 0.50 * 5.6343 + 1.00 * 0.0811                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7710 = 2.08 * 0.50 * 5.4953 + 1.00 * 0.0526                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1534      final r-factor (work) = 0.1469          |
| start r-factor (free) = 0.2033      final r-factor (free) = 0.1977          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5803 = 0.47 * 1.00 * 5.4953 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5400 = 0.47 * 1.00 * 5.3954 + 1.00 * 0.0167                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.616)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.28   14.87    None  None   None       |
|    all(noH): 2823   0      0.00    86.28   14.87    None  None   None       |
|    Sol.    : 438    0      3.67    83.55   38.40    None  None   None       |
|    Mac.    : 2385   0      0.00    86.28   10.55    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 -   8.628: 1283   |   5:    43.140 -  51.768:  101        |
|      1:     8.628 -  17.256:  867   |   6:    51.768 -  60.396:   64        |
|      2:    17.256 -  25.884:  206   |   7:    60.396 -  69.024:   32        |
|      3:    25.884 -  34.512:  125   |   8:    69.024 -  77.652:   11        |
|      4:    34.512 -  43.140:  129   |   9:    77.652 -  86.279:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1469 r_free = 0.1977             target_work(ml) = 5.380         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1468 r_free = 0.1976             target_work(ml) = 5.379         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1468   r_free= 0.1976   ksol= 0.32   Bsol= 42.08   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.07,1.68,1.45,0.00,0.00,0.00); trace/3= 1.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.379004                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1470   r_free= 0.1976   ksol= 0.32   Bsol= 42.08   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.09,1.30,1.05,0.00,0.00,0.00); trace/3= 0.76                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.380228                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.300559              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.698  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.249746              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.837   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1470      final r-factor (work) = 0.1253          |
| start r-factor (free) = 0.1976      final r-factor (free) = 0.1723          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9580 = 3.30 * 0.50 * 5.3964 + 1.00 * 0.0525                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8382 = 3.30 * 0.50 * 5.3144 + 1.00 * 0.0679                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1253      final r-factor (work) = 0.1224          |
| start r-factor (free) = 0.1723      final r-factor (free) = 0.1679          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3443 = 0.25 * 1.00 * 5.3144 + 1.00 * 0.0171                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3161 = 0.25 * 1.00 * 5.2321 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.616)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.39    87.42   14.51    None  None   None       |
|    all(noH): 2823   0      0.39    87.42   14.51    None  None   None       |
|    Sol.    : 438    0      2.94    79.80   37.83    None  None   None       |
|    Mac.    : 2385   0      0.39    87.42   10.23    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:     0.387 -   9.091: 1427   |   5:    43.904 -  52.607:   96        |
|      1:     9.091 -  17.794:  781   |   6:    52.607 -  61.311:   60        |
|      2:    17.794 -  26.497:  191   |   7:    61.311 -  70.014:   27        |
|      3:    26.497 -  35.201:  109   |   8:    70.014 -  78.717:   11        |
|      4:    35.201 -  43.904:  116   |   9:    78.717 -  87.421:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1224 r_free = 0.1679             target_work(ml) = 5.218         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1223 r_free = 0.1679             target_work(ml) = 5.218         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1223   r_free= 0.1679   ksol= 0.32   Bsol= 42.08   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.09,1.30,1.05,0.00,0.00,0.00); trace/3= 0.76                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.218040                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8576 -  4.6581 0.99   1429  160 0.0957 0.1249      5.3659      5.5277|
|  2:  4.6581 -  3.7163 0.99   1371  149 0.0903 0.1179      5.4772      5.7106|
|  3:  3.7163 -  3.2521 0.99   1341  152 0.1162 0.1683      5.5446      5.9036|
|  4:  3.2521 -  2.9573 0.99   1336  147 0.1386 0.1657      5.5297      5.6964|
|  5:  2.9573 -  2.7468 0.99   1336  147 0.1460 0.1708      5.3933      5.5035|
|  6:  2.7468 -  2.5858 0.99   1319  148 0.1404 0.2261      5.3163      5.6151|
|  7:  2.5858 -  2.4569 0.98   1308  148 0.1377 0.1709      5.2445      5.4198|
|  8:  2.4569 -  2.3503 0.98   1312  142 0.1294 0.1715      5.1322       5.335|
|  9:  2.3503 -  2.2602 0.99   1319  147 0.1303 0.1876      5.0817      5.3004|
| 10:  2.2602 -  2.1824 0.98   1309  141 0.1253 0.1981      5.0509       5.388|
| 11:  2.1824 -  2.1144 0.97   1284  146 0.1266 0.1872      5.0105      5.2693|
| 12:  2.1144 -  2.0541 0.98   1286  145 0.1275 0.1815      4.9297      5.1551|
| 13:  2.0541 -  2.0002 0.92   1208  138 0.1255 0.1932      4.8439      5.0698|
| 14:  2.0002 -  1.9515 0.35    472   49 0.1213 0.1909      4.7543      5.0255|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8576 -  4.6581  1429   160  0.94   9.31   0.98     0.96       7412.40|
|  2:  4.6581 -  3.7163  1371   149  0.95   8.44   1.02     1.00       9691.02|
|  3:  3.7163 -  3.2521  1341   152  0.92  12.81   1.03     1.03      12056.92|
|  4:  3.2521 -  2.9573  1336   147  0.91  15.23   1.02     0.99      11587.05|
|  5:  2.9573 -  2.7468  1336   147  0.88  17.95   1.00     0.96       9487.24|
|  6:  2.7468 -  2.5858  1319   148  0.89  17.78   0.99     0.96       8651.93|
|  7:  2.5858 -  2.4569  1308   148  0.89  17.13   1.00     0.96       7199.08|
|  8:  2.4569 -  2.3503  1312   142  0.89  16.89   1.01     0.98       6121.26|
|  9:  2.3503 -  2.2602  1319   147  0.89  17.02   1.02     0.99       5524.49|
| 10:  2.2602 -  2.1824  1309   141  0.89  17.05   1.01     0.97       5316.90|
| 11:  2.1824 -  2.1144  1284   146  0.88  18.16   1.01     0.97       5104.58|
| 12:  2.1144 -  2.0541  1286   145  0.90  16.84   1.01     0.99       4300.53|
| 13:  2.0541 -  2.0002  1208   138  0.89  17.48   1.01     1.01       3678.53|
| 14:  2.0002 -  1.9515   472    49  0.88  17.49   1.00     0.97       3036.51|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     3036.51 max =        12056.92 mean =      7332.38|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.51|
|phase err.(test): min =        0.00 max =           88.42 mean =        14.95|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1227   r_free= 0.1686   ksol= 0.32   Bsol= 42.69   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.75,0.46,0.28,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.221349                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1227   r_free= 0.1686   ksol= 0.32   Bsol= 42.69   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.75,0.46,0.28,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.221349                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8576 -  4.6581 0.99   1429  160 0.0966 0.1282      5.3792      5.5503|
|  2:  4.6581 -  3.7163 0.99   1371  149 0.0918 0.1204      5.4948      5.7359|
|  3:  3.7163 -  3.2521 0.99   1341  152 0.1167 0.1686      5.5577      5.9024|
|  4:  3.2521 -  2.9573 0.99   1336  147 0.1389 0.1653      5.5317      5.6984|
|  5:  2.9573 -  2.7468 0.99   1336  147 0.1465 0.1703      5.3953      5.5036|
|  6:  2.7468 -  2.5858 0.99   1319  148 0.1401 0.2266      5.3166      5.6173|
|  7:  2.5858 -  2.4569 0.98   1308  148 0.1374 0.1716      5.2446      5.4242|
|  8:  2.4569 -  2.3503 0.98   1312  142 0.1289 0.1714      5.1313      5.3332|
|  9:  2.3503 -  2.2602 0.99   1319  147 0.1297 0.1868      5.0793      5.2985|
| 10:  2.2602 -  2.1824 0.98   1309  141 0.1252 0.1980      5.0489      5.3875|
| 11:  2.1824 -  2.1144 0.97   1284  146 0.1263 0.1869      5.0094       5.269|
| 12:  2.1144 -  2.0541 0.98   1286  145 0.1275 0.1819      4.9296       5.157|
| 13:  2.0541 -  2.0002 0.92   1208  138 0.1255 0.1926      4.8442      5.0685|
| 14:  2.0002 -  1.9515 0.35    472   49 0.1215 0.1904      4.7541      5.0246|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8576 -  4.6581  1429   160  0.94   9.45   0.98     0.96       7681.63|
|  2:  4.6581 -  3.7163  1371   149  0.95   8.75   1.02     1.00      10106.54|
|  3:  3.7163 -  3.2521  1341   152  0.92  13.15   1.03     1.03      12545.22|
|  4:  3.2521 -  2.9573  1336   147  0.91  15.28   1.01     0.99      11631.85|
|  5:  2.9573 -  2.7468  1336   147  0.88  17.97   1.00     0.96       9519.13|
|  6:  2.7468 -  2.5858  1319   148  0.89  17.83   0.98     0.96       8694.97|
|  7:  2.5858 -  2.4569  1308   148  0.89  17.15   0.99     0.95       7216.33|
|  8:  2.4569 -  2.3503  1312   142  0.89  16.89   1.01     0.98       6125.09|
|  9:  2.3503 -  2.2602  1319   147  0.89  17.01   1.01     0.99       5512.79|
| 10:  2.2602 -  2.1824  1309   141  0.89  17.02   1.00     0.97       5293.79|
| 11:  2.1824 -  2.1144  1284   146  0.88  18.14   1.00     0.97       5098.58|
| 12:  2.1144 -  2.0541  1286   145  0.90  16.82   1.00     0.98       4302.36|
| 13:  2.0541 -  2.0002  1208   138  0.89  17.49   1.00     1.00       3679.54|
| 14:  2.0002 -  1.9515   472    49  0.88  17.49   0.99     0.96       3030.79|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     3030.79 max =        12545.22 mean =      7431.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.58|
|phase err.(test): min =        0.00 max =           89.59 mean =        15.02|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.616)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.00    88.03   15.12    None  None   None       |
|    all(noH): 2823   0      1.00    88.03   15.12    None  None   None       |
|    Sol.    : 438    0      3.55    80.41   38.45    None  None   None       |
|    Mac.    : 2385   0      1.00    88.03   10.84    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:     1.000 -   9.703: 1427   |   5:    44.516 -  53.220:   96        |
|      1:     9.703 -  18.406:  781   |   6:    53.220 -  61.923:   60        |
|      2:    18.406 -  27.110:  191   |   7:    61.923 -  70.626:   27        |
|      3:    27.110 -  35.813:  109   |   8:    70.626 -  79.330:   11        |
|      4:    35.813 -  44.516:  116   |   9:    79.330 -  88.033:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 335         
Filter by distance & map next to the model:
   mapped sites are within: 0.614 - 5.912
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 334 from: 335
   mapped sites are within: 0.757 - 5.912

peak=   10.310 closest distance to " O   HOH Z 138 " =    1.476
peak=    9.585 closest distance to " CB  VAL A 230 " =    1.423
peak=    8.970 closest distance to " O   HOH Z 120 " =    1.849
peak=    7.600 closest distance to " CG2 VAL A 296 " =    1.214
peak=    6.321 closest distance to " O   HOH Z 279 " =    1.378
peak=    6.310 closest distance to " O   HOH Z 199 " =    1.375
peak=    6.293 closest distance to " O   HOH Z 316 " =    1.179
peak=    5.987 closest distance to " O   HOH Z 124 " =    1.811
peak=    5.793 closest distance to " CG  LEU A   5 " =    1.331
peak=    5.753 closest distance to " CD1AILE A 234 " =    1.137
peak=    5.678 closest distance to " NH2 ARG A  56 " =    2.206
peak=    5.598 closest distance to " O   HOH Z 247 " =    1.481
peak=    5.341 closest distance to " O   HOH Z 278 " =    1.623
peak=    5.079 closest distance to " O   HOH Z 411 " =    3.596
peak=    4.947 closest distance to " CD2 LEU A   5 " =    1.259
peak=    4.786 closest distance to " O   SER A  87 " =    2.227
peak=    4.779 closest distance to " O   HOH Z 132 " =    1.569
peak=    4.769 closest distance to " O   HOH Z 272 " =    1.949
peak=    4.742 closest distance to " O   HOH Z 402 " =    1.536
peak=    4.730 closest distance to " CB  GLN A 223 " =    1.473
peak=    4.715 closest distance to " O   HOH Z 403 " =    1.954
peak=    4.651 closest distance to " O   HOH Z 193 " =    1.819
peak=    4.630 closest distance to " O   HOH Z 389 " =    1.754
peak=    4.620 closest distance to " O   HOH Z  48 " =    1.781
peak=    4.611 closest distance to " O   HOH Z  37 " =    1.004
peak=    4.604 closest distance to " O   HOH Z  11 " =    1.328
peak=    4.602 closest distance to " O   HOH Z  43 " =    1.619
peak=    4.571 closest distance to " O   HOH Z  40 " =    1.729
peak=    4.546 closest distance to " O   HOH Z 155 " =    1.823
peak=    4.537 closest distance to " CG  PRO A  54 " =    1.138
peak=    4.516 closest distance to " C   PRO A 198 " =    1.517
peak=    4.512 closest distance to " O   HOH Z  97 " =    1.555
peak=    4.503 closest distance to " O   HOH Z 326 " =    1.569
peak=    4.458 closest distance to " O   HOH Z  80 " =    1.850
peak=    4.449 closest distance to " O   HOH Z 316 " =    2.021
peak=    4.446 closest distance to " O   HOH Z 156 " =    3.194
peak=    4.434 closest distance to " O   HOH Z 234 " =    3.849
peak=    4.416 closest distance to " CB  ASN A 187 " =    1.802
peak=    4.413 closest distance to " CB  VAL A 230 " =    1.242
peak=    4.393 closest distance to " O   HOH Z 134 " =    2.000
peak=    4.388 closest distance to " CB  SER A  63 " =    1.219
peak=    4.376 closest distance to " O   HOH Z 394 " =    1.541
peak=    4.374 closest distance to " O   HOH Z 108 " =    1.459
peak=    4.344 closest distance to " CG  PRO A 198 " =    1.257
peak=    4.318 closest distance to " O   HOH Z 154 " =    1.637
peak=    4.293 closest distance to " O   HOH Z 236 " =    1.505
peak=    4.289 closest distance to " CD2 LEU A 228 " =    1.225
peak=    4.288 closest distance to " O   HOH Z 263 " =    1.441
peak=    4.280 closest distance to " CA  ALA A  21 " =    1.260
peak=    4.279 closest distance to " O   HOH Z 346 " =    1.481
peak=    4.276 closest distance to " CB  VAL A 296 " =    1.076
peak=    4.270 closest distance to " O   HOH Z 284 " =    1.396
peak=    4.255 closest distance to " O   HOH Z 130 " =    1.133
peak=    4.215 closest distance to " CB  ARG A 275 " =    0.942
peak=    4.177 closest distance to " O   HOH Z 154 " =    2.309
peak=    4.173 closest distance to " CB  ARG A 275 " =    1.208
peak=    4.169 closest distance to " O   HOH Z 232 " =    2.192
peak=    4.160 closest distance to " O   HOH Z 202 " =    1.348
peak=    4.139 closest distance to " CA  VAL A  41 " =    0.851
peak=    4.096 closest distance to " O   HOH Z 423 " =    2.024
peak=    4.085 closest distance to " CG AARG A 275 " =    1.066
peak=    4.084 closest distance to " OE1 GLN A  11 " =    1.846
peak=    4.068 closest distance to " O   GLY A  91 " =    1.306
peak=    4.044 closest distance to " CB  TYR A 169 " =    0.805
peak=    4.042 closest distance to " O   HOH Z 192 " =    1.466
peak=    4.027 closest distance to " O   HOH Z 210 " =    1.099
peak=    4.023 closest distance to " CD  ARG A 269 " =    1.065
peak=    4.023 closest distance to " O   HOH Z 209 " =    2.502
peak=    4.022 closest distance to " NE2 GLN A  11 " =    1.059
peak=    4.018 closest distance to " O   HOH Z 118 " =    1.477
peak=    4.017 closest distance to " CG  LEU A 228 " =    1.281
peak=    4.006 closest distance to " O   HOH Z 276 " =    1.445
peak=    3.999 closest distance to " O   HOH Z 192 " =    1.413
peak=    3.981 closest distance to " O   HOH Z 331 " =    1.391
peak=    3.972 closest distance to " CG  GLN A  77 " =    0.863
peak=    3.966 closest distance to " CA  TYR A  30 " =    1.040
peak=    3.957 closest distance to " CB  ALA A 100 " =    1.223
peak=    3.954 closest distance to " O   HOH Z  47 " =    1.712
peak=    3.950 closest distance to " CB  GLU A 277 " =    3.591
peak=    3.930 closest distance to " O   HOH Z 217 " =    1.680
peak=    3.921 closest distance to " O   HOH Z 214 " =    1.101
peak=    3.919 closest distance to " O   HOH Z 406 " =    1.673
peak=    3.917 closest distance to " CG2 THR A 221 " =    1.162
peak=    3.915 closest distance to " O   HOH Z 136 " =    1.358
peak=    3.909 closest distance to " O   HOH Z 128 " =    1.911
peak=    3.909 closest distance to " CG1 ILE A  33 " =    1.301
peak=    3.898 closest distance to " OE1 GLU A   2 " =    2.173
peak=    3.896 closest distance to " O   HOH Z 327 " =    1.768
peak=    3.886 closest distance to " O   HOH Z 117 " =    1.049
peak=    3.875 closest distance to " O   HOH Z 102 " =    1.313
peak=    3.872 closest distance to " CE  LYS A 119 " =    1.261
peak=    3.870 closest distance to " CG  ARG A  66 " =    1.099
peak=    3.863 closest distance to " CB  SER A 141 " =    1.004
peak=    3.863 closest distance to " O   HOH Z  54 " =    1.516
peak=    3.860 closest distance to " O   HOH Z 395 " =    1.410
peak=    3.855 closest distance to " O   HOH Z 189 " =    2.505
peak=    3.850 closest distance to " O   HOH Z 137 " =    1.795
peak=    3.845 closest distance to " CB  GLU A 152 " =    1.010
peak=    3.845 closest distance to " O   HOH Z  97 " =    2.196
peak=    3.844 closest distance to " O   HOH Z  67 " =    1.908
peak=    3.843 closest distance to " CB  GLN A 183 " =    1.268
peak=    3.838 closest distance to " O   HOH Z 163 " =    1.525
peak=    3.836 closest distance to " O   HOH Z  30 " =    1.311
peak=    3.829 closest distance to " CB  VAL A 202 " =    1.593
peak=    3.828 closest distance to " O   HOH Z  78 " =    1.732
peak=    3.828 closest distance to " CG  PRO A 213 " =    1.245
peak=    3.826 closest distance to " O   HOH Z 124 " =    1.795
peak=    3.825 closest distance to " CB  PRO A  54 " =    0.811
peak=    3.820 closest distance to " O   HOH Z 364 " =    2.164
peak=    3.816 closest distance to " CB  VAL A 265 " =    1.137
peak=    3.811 closest distance to " O   HOH Z 248 " =    1.715
peak=    3.809 closest distance to " CG1BVAL A  72 " =    1.604
peak=    3.809 closest distance to " O   HOH Z 352 " =    1.254
peak=    3.808 closest distance to " O   HOH Z 345 " =    2.703
peak=    3.800 closest distance to " O   HOH Z  85 " =    1.581
peak=    3.792 closest distance to " CB  TRP A 179 " =    1.226
peak=    3.789 closest distance to " O   HOH Z  69 " =    1.138
peak=    3.787 closest distance to " CA  ASP A 191 " =    0.931
peak=    3.783 closest distance to " OG1 THR A 294 " =    2.268
peak=    3.770 closest distance to " O   HOH Z 112 " =    1.572
peak=    3.765 closest distance to " O   HOH Z 138 " =    1.550
peak=    3.761 closest distance to " O   HOH Z 203 " =    1.563
peak=    3.760 closest distance to " O   HOH Z 357 " =    2.255
peak=    3.759 closest distance to " O   HOH Z 130 " =    2.560
peak=    3.758 closest distance to " CB  ASN A 148 " =    1.172
peak=    3.753 closest distance to " O   HOH Z 344 " =    1.682
peak=    3.749 closest distance to " O   HOH Z 291 " =    1.517
peak=    3.746 closest distance to " OE1 GLN A  58 " =    5.912
peak=    3.734 closest distance to " O   HOH Z 414 " =    1.649
peak=    3.733 closest distance to " O   HOH Z 214 " =    2.205
peak=    3.729 closest distance to " OD2 ASP A 286 " =    2.643
peak=    3.727 closest distance to " O   HOH Z 191 " =    1.389
peak=    3.721 closest distance to " O   HOH Z 374 " =    2.471
peak=    3.720 closest distance to " O   HOH Z 280 " =    1.624
peak=    3.720 closest distance to " CB  ARG A 102 " =    0.776
peak=    3.719 closest distance to " CE BMET A  47 " =    1.180
peak=    3.712 closest distance to " CB  SER A   3 " =    1.381
peak=    3.705 closest distance to " O   HOH Z 227 " =    1.562
peak=    3.702 closest distance to " O   HOH Z   4 " =    1.501
peak=    3.689 closest distance to " O   HOH Z 166 " =    1.434
peak=    3.679 closest distance to " O   HOH Z 366 " =    2.984
peak=    3.678 closest distance to " O   HOH Z 261 " =    1.929
peak=    3.664 closest distance to " O   HOH Z 260 " =    1.478
peak=    3.664 closest distance to " NZ  LYS A 117 " =    3.122
peak=    3.659 closest distance to " O   HOH Z  15 " =    2.327
peak=    3.656 closest distance to " CD  ARG A 159 " =    0.786
peak=    3.642 closest distance to " NZ  LYS A 117 " =    0.879
peak=    3.638 closest distance to " CB AVAL A  41 " =    1.233
peak=    3.636 closest distance to " O   HOH Z 421 " =    1.721
peak=    3.634 closest distance to " O   HOH Z 180 " =    2.147
peak=    3.631 closest distance to " O   HOH Z  63 " =    1.801
peak=    3.624 closest distance to " NH2BARG A 145 " =    2.125
peak=    3.619 closest distance to " O   HOH Z 303 " =    2.161
peak=    3.619 closest distance to " O   HOH Z 284 " =    2.809
peak=    3.617 closest distance to " CB  LEU A 228 " =    1.446
peak=    3.615 closest distance to " O   HOH Z 369 " =    1.968
peak=    3.614 closest distance to " O   HOH Z 273 " =    2.582
peak=    3.608 closest distance to " ND2 ASN A 187 " =    1.683
peak=    3.605 closest distance to " O   HOH Z 408 " =    1.612
peak=    3.598 closest distance to " O   HOH Z 219 " =    1.955
peak=    3.596 closest distance to " CB  GLN A  58 " =    0.846
peak=    3.588 closest distance to " O   HOH Z 426 " =    1.428
peak=    3.583 closest distance to " CD  LYS A 119 " =    1.651
peak=    3.578 closest distance to " O   HOH Z  66 " =    2.315
peak=    3.577 closest distance to " O   HOH Z 133 " =    2.046
peak=    3.576 closest distance to " ND1 HIS A  81 " =    1.319
peak=    3.570 closest distance to " O   HOH Z 344 " =    2.542
peak=    3.565 closest distance to " CG  PRO A 243 " =    1.238
peak=    3.558 closest distance to " CB  ALA A 256 " =    1.021
peak=    3.556 closest distance to " CD  LYS A 166 " =    1.471
peak=    3.552 closest distance to " CA  VAL A 126 " =    0.921
peak=    3.551 closest distance to " OH  TYR A  30 " =    1.172
peak=    3.548 closest distance to " O   HOH Z 114 " =    1.243
peak=    3.543 closest distance to " CA  ARG A 195 " =    1.091
peak=    3.542 closest distance to " O   SER A 164 " =    1.046
peak=    3.542 closest distance to " O   HOH Z 194 " =    2.014
peak=    3.518 closest distance to " O   GLY A 211 " =    1.337
peak=    3.512 closest distance to " O   HOH Z 386 " =    2.222
peak=    3.511 closest distance to " CB  GLU A 128 " =    1.096
peak=    3.510 closest distance to " O   HOH Z 334 " =    1.556
peak=    3.509 closest distance to " O   HOH Z 227 " =    1.888
peak=    3.506 closest distance to " O   HOH Z 433 " =    1.411
peak=    3.488 closest distance to " O   HOH Z  63 " =    2.341
peak=    3.488 closest distance to " O   HOH Z  88 " =    3.306
peak=    3.488 closest distance to " O   HOH Z  61 " =    1.484
peak=    3.488 closest distance to " O   HOH Z  78 " =    1.964
peak=    3.483 closest distance to " CG1 VAL A 153 " =    1.055
peak=    3.483 closest distance to " O   HOH Z 315 " =    1.935
peak=    3.479 closest distance to " O   HOH Z 133 " =    1.523
peak=    3.479 closest distance to " CB  SER A  26 " =    1.671
peak=    3.478 closest distance to " O   HOH Z 221 " =    1.292
peak=    3.477 closest distance to " CA  LYS A 117 " =    1.331
peak=    3.473 closest distance to " N   HIS A 108 " =    1.919
peak=    3.467 closest distance to " O   HOH Z 155 " =    2.450
peak=    3.466 closest distance to " CD2 LEU A 255 " =    1.223
peak=    3.463 closest distance to " O   HOH Z 427 " =    2.818
peak=    3.459 closest distance to " NH2 ARG A 156 " =    1.132
peak=    3.459 closest distance to " CD  LYS A  76 " =    1.929
peak=    3.454 closest distance to " O   HOH Z 345 " =    1.791
peak=    3.450 closest distance to " O   HOH Z 126 " =    1.499
peak=    3.448 closest distance to " CD2 TRP A 179 " =    1.357
peak=    3.447 closest distance to " CB  ALA A  71 " =    1.121
peak=    3.447 closest distance to " OD1 ASN A  60 " =    1.263
peak=    3.442 closest distance to " O   ARG A 102 " =    2.312
peak=    3.441 closest distance to " O   HOH Z  48 " =    1.926
peak=    3.439 closest distance to " O   SER A  26 " =    1.690
peak=    3.439 closest distance to " CB  ARG A 139 " =    1.068
peak=    3.434 closest distance to " O   HOH Z 368 " =    2.308
peak=    3.433 closest distance to " CB  GLN A  88 " =    1.236
peak=    3.429 closest distance to " CB  PRO A 198 " =    1.033
peak=    3.422 closest distance to " O   HOH Z  44 " =    2.123
peak=    3.409 closest distance to " CH2 TRP A 274 " =    2.167
peak=    3.405 closest distance to " O   THR A  31 " =    1.568
peak=    3.401 closest distance to " O   HOH Z  20 " =    1.433
peak=    3.401 closest distance to " O   HOH Z 128 " =    1.717
peak=    3.398 closest distance to " O   ASN A 217 " =    1.363
peak=    3.392 closest distance to " CB  ARG A 190 " =    1.548
peak=    3.384 closest distance to " CA  LEU A 282 " =    1.102
peak=    3.378 closest distance to " CD2 HIS A  81 " =    1.333
peak=    3.375 closest distance to " O   HOH Z 152 " =    1.800
peak=    3.372 closest distance to " OG BSER A 210 " =    1.333
peak=    3.366 closest distance to " O   HOH Z 422 " =    2.529
peak=    3.363 closest distance to " O   HOH Z 174 " =    2.328
peak=    3.361 closest distance to " NH1 ARG A  14 " =    1.068
peak=    3.360 closest distance to " O   ALA A 158 " =    1.253
peak=    3.358 closest distance to " O   HOH Z 402 " =    2.661
peak=    3.346 closest distance to " O   HOH Z 359 " =    2.083
peak=    3.339 closest distance to " CD  ARG A 139 " =    1.258
peak=    3.338 closest distance to " CB  THR A  31 " =    1.569
peak=    3.338 closest distance to " CG  LYS A 166 " =    1.628
peak=    3.336 closest distance to " CB  SER A  62 " =    0.940
peak=    3.329 closest distance to " CA  ALA A 295 " =    1.055
peak=    3.328 closest distance to " OG  SER A 276 " =    1.541
peak=    3.326 closest distance to " CD1 ILE A 199 " =    1.015
peak=    3.321 closest distance to " O   HOH Z 336 " =    3.688
peak=    3.321 closest distance to " CE1 HIS A 108 " =    1.170
peak=    3.316 closest distance to " CB  ASN A  39 " =    0.835
peak=    3.314 closest distance to " OD1 ASN A  69 " =    2.532
peak=    3.306 closest distance to " O   HOH Z 301 " =    1.787
peak=    3.302 closest distance to " O   HOH Z 214 " =    2.259
peak=    3.299 closest distance to " O   HOH Z  88 " =    3.786
peak=    3.298 closest distance to " OG BSER A 258 " =    3.304
peak=    3.297 closest distance to " O   HOH Z  32 " =    1.732
peak=    3.289 closest distance to " O   HOH Z  85 " =    1.925
peak=    3.288 closest distance to " CD1 ILE A  33 " =    1.536
peak=    3.286 closest distance to " OD1 ASP A 238 " =    0.875
peak=    3.279 closest distance to " N   ASN A  39 " =    1.290
peak=    3.279 closest distance to " CB  GLN A 194 " =    0.838
peak=    3.275 closest distance to " O   HOH Z 298 " =    1.931
peak=    3.266 closest distance to " CA  ALA A 160 " =    0.838
peak=    3.265 closest distance to " O   HOH Z 267 " =    2.158
peak=    3.260 closest distance to " O   HOH Z 170 " =    2.044
peak=    3.259 closest distance to " O   HOH Z 108 " =    2.007
peak=    3.259 closest distance to " NE BARG A 190 " =    1.451
peak=    3.255 closest distance to " O   HOH Z 277 " =    2.391
peak=    3.253 closest distance to " CB  GLN A  89 " =    1.120
peak=    3.252 closest distance to " O   HOH Z 313 " =    1.774
peak=    3.250 closest distance to " O   HOH Z 412 " =    3.883
peak=    3.243 closest distance to " O   HOH Z  71 " =    1.661
peak=    3.242 closest distance to " O   HOH Z 236 " =    1.557
peak=    3.239 closest distance to " O   HOH Z 156 " =    2.470
peak=    3.238 closest distance to " O   HOH Z 261 " =    1.973
peak=    3.236 closest distance to " NZ  LYS A 166 " =    3.008
peak=    3.235 closest distance to " OG  SER A  62 " =    3.069
peak=    3.233 closest distance to " CG  GLN A  88 " =    1.019
peak=    3.230 closest distance to " O   TRP A 274 " =    1.829
peak=    3.226 closest distance to " CA  THR A 221 " =    0.918
peak=    3.226 closest distance to " CB  TRP A 266 " =    1.107
peak=    3.223 closest distance to " O   HOH Z 141 " =    1.553
peak=    3.222 closest distance to " O   ALA A   1 " =    1.615
peak=    3.221 closest distance to " CG2 ILE A 120 " =    1.250
peak=    3.220 closest distance to " O   HOH Z 217 " =    2.205
peak=    3.219 closest distance to " O   HOH Z 322 " =    2.022
peak=    3.217 closest distance to " CA  GLY A 211 " =    1.166
peak=    3.214 closest distance to " O   HOH Z 417 " =    3.230
peak=    3.210 closest distance to " O   HOH Z  71 " =    1.442
peak=    3.210 closest distance to " O   HOH Z 411 " =    1.760
peak=    3.204 closest distance to " C   PRO A 163 " =    1.614
peak=    3.193 closest distance to " O   HOH Z 197 " =    2.276
peak=    3.192 closest distance to " O   HOH Z 280 " =    2.369
peak=    3.191 closest distance to " O   HOH Z 132 " =    3.056
peak=    3.189 closest distance to " O   HOH Z  29 " =    1.416
peak=    3.185 closest distance to " O   HOH Z 143 " =    1.205
peak=    3.183 closest distance to " O   HOH Z 368 " =    2.985
peak=    3.182 closest distance to " NH1 ARG A 138 " =    1.366
peak=    3.174 closest distance to " O   GLY A  23 " =    2.270
peak=    3.173 closest distance to " CG2 THR A 220 " =    0.757
peak=    3.172 closest distance to " O   HOH Z 162 " =    1.392
peak=    3.172 closest distance to " O   HOH Z  20 " =    1.740
peak=    3.171 closest distance to " O   HOH Z 279 " =    2.141
peak=    3.169 closest distance to " NH2BARG A 190 " =    2.004
peak=    3.168 closest distance to " O   HOH Z 299 " =    4.107
peak=    3.168 closest distance to " C   SER A  32 " =    1.140
peak=    3.167 closest distance to " O   HOH Z 261 " =    1.891
peak=    3.165 closest distance to " O   HOH Z 383 " =    1.806
peak=    3.163 closest distance to " O   HOH Z 106 " =    1.672
peak=    3.161 closest distance to " O   HOH Z 171 " =    2.990
peak=    3.159 closest distance to " CB  ALA A 248 " =    1.290
peak=    3.157 closest distance to " O   HOH Z 419 " =    1.557
peak=    3.155 closest distance to " O   HOH Z  54 " =    2.528
peak=    3.154 closest distance to " O   HOH Z  59 " =    2.105
peak=    3.154 closest distance to " CB  ARG A 259 " =    1.872
peak=    3.150 closest distance to " O   HOH Z 145 " =    2.132
peak=    3.142 closest distance to " O  BHOH Z 338 " =    1.326
peak=    3.141 closest distance to " N   ASP A 162 " =    1.390
peak=    3.141 closest distance to " NE2 HIS A 115 " =    0.850
peak=    3.138 closest distance to " O   HOH Z 423 " =    3.142
peak=    3.136 closest distance to " O   HOH Z  66 " =    1.572
peak=    3.132 closest distance to " O   HOH Z 245 " =    1.441
peak=    3.129 closest distance to " O   HOH Z 152 " =    2.196
peak=    3.125 closest distance to " O   HOH Z 251 " =    1.840
peak=    3.119 closest distance to " O   HOH Z 350 " =    1.881
peak=    3.115 closest distance to " O   HOH Z 173 " =    2.242
peak=    3.112 closest distance to " CB  PHE A  59 " =    1.139
peak=    3.111 closest distance to " O   HOH Z 215 " =    1.423
peak=    3.109 closest distance to " NZ  LYS A 119 " =    1.311
peak=    3.106 closest distance to " CB  ALA A   9 " =    1.423
peak=    3.103 closest distance to " C   ALA A 299 " =    0.974
peak=    3.100 closest distance to " CB  LEU A   5 " =    1.115
peak=    3.093 closest distance to " CA  ALA A 158 " =    1.128
peak=    3.085 closest distance to " CG2 THR A 251 " =    1.110
peak=    3.084 closest distance to " O   HOH Z 197 " =    2.141
peak=    3.083 closest distance to " CE BLYS A 290 " =    1.009
peak=    3.083 closest distance to " CD2 TYR A 186 " =    1.014
peak=    3.073 closest distance to " CA  THR A 264 " =    0.821
peak=    3.050 closest distance to " CB  PRO A  90 " =    1.297
peak=    3.049 closest distance to " O   HOH Z 115 " =    1.902
peak=    3.047 closest distance to " O   HOH Z 329 " =    3.065
peak=    3.033 closest distance to " O   HOH Z 425 " =    1.350
peak=    3.033 closest distance to " O   HOH Z 109 " =    2.338
peak=    3.025 closest distance to " CA  ASN A 176 " =    1.040
peak=    3.024 closest distance to " O   ALA A 165 " =    1.185
peak=    3.015 closest distance to " O   GLN A 278 " =    1.511
peak=    3.011 closest distance to " CG  MET A  93 " =    1.105

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.445 - 5.009
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 199
   mapped sites are within: 0.707 - 5.009

peak=   -5.134 closest distance to " CG2 VAL A 230 " =    0.824
peak=   -4.840 closest distance to " CA  SER A 164 " =    1.985
peak=   -4.776 closest distance to " O   HOH Z  13 " =    1.086
peak=   -4.364 closest distance to " O   HOH Z 166 " =    1.797
peak=   -4.181 closest distance to " O   VAL A  67 " =    2.632
peak=   -4.169 closest distance to " O   HOH Z 210 " =    0.750
peak=   -4.001 closest distance to " CZ2 TRP A 179 " =    1.275
peak=   -3.996 closest distance to " O   HOH Z 151 " =    1.326
peak=   -3.987 closest distance to " O   HOH Z 423 " =    2.327
peak=   -3.984 closest distance to " O   HOH Z 155 " =    1.398
peak=   -3.978 closest distance to " CD1 LEU A 101 " =    2.510
peak=   -3.975 closest distance to " CD2 LEU A 300 " =    2.716
peak=   -3.959 closest distance to " SG  CYS A 254 " =    3.135
peak=   -3.940 closest distance to " O   HOH Z  71 " =    1.135
peak=   -3.933 closest distance to " C   ALA A 158 " =    1.194
peak=   -3.929 closest distance to " O   HOH Z  48 " =    1.168
peak=   -3.920 closest distance to " O   HOH Z 266 " =    4.187
peak=   -3.902 closest distance to " CD  ARG A 156 " =    2.027
peak=   -3.895 closest distance to " CD1 PHE A  59 " =    1.851
peak=   -3.892 closest distance to " O   HOH Z 407 " =    2.984
peak=   -3.890 closest distance to " OG ASER A 134 " =    1.336
peak=   -3.890 closest distance to " O   HOH Z 312 " =    1.510
peak=   -3.867 closest distance to " O   HOH Z  11 " =    1.500
peak=   -3.862 closest distance to " O   HOH Z 208 " =    1.018
peak=   -3.838 closest distance to " CE2 TYR A  30 " =    2.784
peak=   -3.837 closest distance to " OXT GLY A 302 " =    2.775
peak=   -3.824 closest distance to " O   HOH Z 266 " =    4.407
peak=   -3.802 closest distance to " OG1 THR A   4 " =    1.832
peak=   -3.787 closest distance to " CB  ALA A 161 " =    2.491
peak=   -3.778 closest distance to " CB  CYS A 254 " =    2.575
peak=   -3.777 closest distance to " OG BSER A 134 " =    1.675
peak=   -3.775 closest distance to " N   ALA A 226 " =    1.964
peak=   -3.769 closest distance to " NH2 ARG A  66 " =    1.374
peak=   -3.756 closest distance to " CG  ASP A  50 " =    2.172
peak=   -3.749 closest distance to " O   VAL A  67 " =    2.541
peak=   -3.736 closest distance to " O   HOH Z  92 " =    1.344
peak=   -3.720 closest distance to " O   HOH Z 126 " =    1.783
peak=   -3.714 closest distance to " O   HOH Z 221 " =    1.259
peak=   -3.708 closest distance to " O   HOH Z 290 " =    0.809
peak=   -3.706 closest distance to " CZ  TYR A 169 " =    1.790
peak=   -3.706 closest distance to " O   HOH Z 426 " =    1.754
peak=   -3.695 closest distance to " CG  ASP A 231 " =    0.846
peak=   -3.686 closest distance to " O   HOH Z  52 " =    2.000
peak=   -3.664 closest distance to " CA  SER A 276 " =    1.438
peak=   -3.659 closest distance to " O   SER A 273 " =    1.364
peak=   -3.654 closest distance to " O   HOH Z 292 " =    4.459
peak=   -3.649 closest distance to " CD  LYS A 289 " =    2.493
peak=   -3.641 closest distance to " O   LEU A 228 " =    2.346
peak=   -3.633 closest distance to " O   ALA A 161 " =    1.336
peak=   -3.609 closest distance to " CE3 TRP A 150 " =    2.363
peak=   -3.594 closest distance to " CB  LYS A 193 " =    2.272
peak=   -3.590 closest distance to " N   GLN A  58 " =    1.801
peak=   -3.588 closest distance to " C   HIS A 108 " =    1.235
peak=   -3.575 closest distance to " O   HOH Z 150 " =    1.305
peak=   -3.574 closest distance to " O   HOH Z 103 " =    1.826
peak=   -3.573 closest distance to " N   THR A 235 " =    1.246
peak=   -3.572 closest distance to " O   HOH Z 250 " =    1.362
peak=   -3.570 closest distance to " O   HOH Z  56 " =    2.210
peak=   -3.568 closest distance to " CG2 THR A 182 " =    2.325
peak=   -3.554 closest distance to " OD1 ASP A 200 " =    1.134
peak=   -3.551 closest distance to " O   HOH Z 435 " =    2.345
peak=   -3.543 closest distance to " C   THR A 279 " =    1.178
peak=   -3.533 closest distance to " O  BHOH Z 338 " =    1.563
peak=   -3.528 closest distance to " OG  SER A  62 " =    1.339
peak=   -3.527 closest distance to " O   HOH Z 313 " =    1.338
peak=   -3.511 closest distance to " OG  SER A  97 " =    2.207
peak=   -3.506 closest distance to " CD2 LEU A 237 " =    2.604
peak=   -3.505 closest distance to " CG  MET A 105 " =    0.868
peak=   -3.499 closest distance to " CE BMET A  47 " =    1.436
peak=   -3.498 closest distance to " C   ASN A 285 " =    2.311
peak=   -3.498 closest distance to " O   LEU A 143 " =    1.454
peak=   -3.498 closest distance to " C   GLY A  91 " =    1.345
peak=   -3.493 closest distance to " O   ALA A  51 " =    1.509
peak=   -3.491 closest distance to " O   HOH Z 138 " =    0.887
peak=   -3.488 closest distance to " CB  PRO A 163 " =    2.382
peak=   -3.477 closest distance to " O   HOH Z 292 " =    2.616
peak=   -3.470 closest distance to " NH2 ARG A  79 " =    1.844
peak=   -3.460 closest distance to " N   ALA A 248 " =    1.796
peak=   -3.459 closest distance to " O   SER A 146 " =    0.846
peak=   -3.451 closest distance to " CD2 PHE A  59 " =    2.485
peak=   -3.437 closest distance to " NE2 GLN A  58 " =    0.953
peak=   -3.433 closest distance to " O   HOH Z  17 " =    1.215
peak=   -3.431 closest distance to " O   HOH Z 231 " =    1.881
peak=   -3.425 closest distance to " O   HOH Z 126 " =    1.200
peak=   -3.424 closest distance to " O   HOH Z 426 " =    2.192
peak=   -3.423 closest distance to " O   HOH Z 166 " =    2.256
peak=   -3.409 closest distance to " CB  ALA A 248 " =    1.943
peak=   -3.402 closest distance to " O   HOH Z 395 " =    5.009
peak=   -3.397 closest distance to " CG  ARG A 269 " =    2.271
peak=   -3.394 closest distance to " OG BSER A 134 " =    1.296
peak=   -3.393 closest distance to " ND2 ASN A 187 " =    1.607
peak=   -3.390 closest distance to " O   HOH Z 145 " =    1.684
peak=   -3.388 closest distance to " C   GLY A  80 " =    2.222
peak=   -3.384 closest distance to " CE  LYS A 166 " =    2.900
peak=   -3.383 closest distance to " O   ALA A 161 " =    2.653
peak=   -3.376 closest distance to " CB  ALA A 248 " =    2.258
peak=   -3.376 closest distance to " CE  MET A 105 " =    2.006
peak=   -3.373 closest distance to " N   ALA A  43 " =    2.707
peak=   -3.351 closest distance to " CE  MET A 105 " =    2.154
peak=   -3.351 closest distance to " O   HOH Z 193 " =    1.715
peak=   -3.337 closest distance to " O   VAL A 197 " =    1.168
peak=   -3.335 closest distance to " CD2 TYR A 293 " =    2.160
peak=   -3.328 closest distance to " O   GLY A 211 " =    1.377
peak=   -3.324 closest distance to " O   HOH Z 297 " =    2.829
peak=   -3.321 closest distance to " CD1 PHE A  59 " =    1.665
peak=   -3.319 closest distance to " CB  SER A 245 " =    2.377
peak=   -3.318 closest distance to " O   ALA A   8 " =    1.937
peak=   -3.315 closest distance to " OG  SER A 206 " =    1.843
peak=   -3.313 closest distance to " O   HOH Z 165 " =    2.176
peak=   -3.311 closest distance to " O   ASP A 191 " =    1.363
peak=   -3.310 closest distance to " CD1 TRP A 179 " =    1.154
peak=   -3.307 closest distance to " CB  PHE A 208 " =    2.253
peak=   -3.303 closest distance to " CB  ALA A 100 " =    1.828
peak=   -3.302 closest distance to " CG2 VAL A 296 " =    0.866
peak=   -3.302 closest distance to " O   HOH Z  60 " =    1.946
peak=   -3.295 closest distance to " O   ALA A   1 " =    1.909
peak=   -3.294 closest distance to " CD  ARG A 139 " =    1.682
peak=   -3.294 closest distance to " OD1 ASN A 148 " =    1.656
peak=   -3.294 closest distance to " O   HOH Z 345 " =    2.150
peak=   -3.288 closest distance to " O   HOH Z 166 " =    1.524
peak=   -3.286 closest distance to " NH1BARG A 190 " =    2.042
peak=   -3.284 closest distance to " O   HOH Z 130 " =    2.231
peak=   -3.270 closest distance to " O   MET A  40 " =    2.632
peak=   -3.265 closest distance to " ND2 ASN A 252 " =    1.664
peak=   -3.265 closest distance to " CB  ASP A 124 " =    2.032
peak=   -3.262 closest distance to " O   GLY A 196 " =    0.944
peak=   -3.256 closest distance to " N   GLN A  77 " =    1.333
peak=   -3.255 closest distance to " N   HIS A 115 " =    2.020
peak=   -3.251 closest distance to " N   GLN A 122 " =    1.573
peak=   -3.250 closest distance to " N   THR A 235 " =    1.797
peak=   -3.249 closest distance to " O   HOH Z 138 " =    1.453
peak=   -3.242 closest distance to " OE2 GLU A   2 " =    1.618
peak=   -3.238 closest distance to " NH2AARG A 275 " =    4.901
peak=   -3.234 closest distance to " C   GLY A 133 " =    1.202
peak=   -3.226 closest distance to " OXT GLY A 302 " =    3.438
peak=   -3.222 closest distance to " O   HOH Z 265 " =    1.900
peak=   -3.222 closest distance to " O   ASN A  45 " =    1.874
peak=   -3.221 closest distance to " O   HOH Z  38 " =    1.764
peak=   -3.220 closest distance to " CD1 LEU A 228 " =    2.298
peak=   -3.216 closest distance to " O   HOH Z 136 " =    1.903
peak=   -3.216 closest distance to " O   HOH Z 132 " =    0.760
peak=   -3.215 closest distance to " CD1 LEU A  96 " =    2.509
peak=   -3.208 closest distance to " CA  GLY A 203 " =    1.943
peak=   -3.208 closest distance to " NH2 ARG A  66 " =    4.597
peak=   -3.207 closest distance to " O   HOH Z 377 " =    2.009
peak=   -3.203 closest distance to " O   HOH Z 424 " =    2.974
peak=   -3.201 closest distance to " O   HOH Z 280 " =    1.187
peak=   -3.198 closest distance to " O   HOH Z 281 " =    2.887
peak=   -3.197 closest distance to " O   HOH Z 366 " =    1.281
peak=   -3.195 closest distance to " O   ALA A 184 " =    1.569
peak=   -3.194 closest distance to " CD1 TRP A  85 " =    1.015
peak=   -3.190 closest distance to " O   PHE A 218 " =    1.494
peak=   -3.184 closest distance to " CB  GLN A  58 " =    1.612
peak=   -3.175 closest distance to " CB  SER A 273 " =    1.864
peak=   -3.174 closest distance to " CB  ALA A 291 " =    2.155
peak=   -3.174 closest distance to " CD2 LEU A 237 " =    2.908
peak=   -3.171 closest distance to " CA  VAL A 197 " =    0.936
peak=   -3.166 closest distance to " OG1 THR A  82 " =    1.422
peak=   -3.166 closest distance to " O   HOH Z 311 " =    3.468
peak=   -3.165 closest distance to " O   ARG A 275 " =    2.110
peak=   -3.163 closest distance to " OG1 THR A 178 " =    1.234
peak=   -3.156 closest distance to " O   HOH Z  78 " =    1.671
peak=   -3.155 closest distance to " CG1 VAL A 112 " =    2.369
peak=   -3.153 closest distance to " O   HOH Z 427 " =    1.376
peak=   -3.152 closest distance to " O   HOH Z 234 " =    4.245
peak=   -3.149 closest distance to " OD1 ASP A 171 " =    1.771
peak=   -3.144 closest distance to " CD2 TYR A  15 " =    2.248
peak=   -3.143 closest distance to " CD2 PHE A  61 " =    1.938
peak=   -3.138 closest distance to " OG  SER A  26 " =    1.535
peak=   -3.136 closest distance to " CG  TYR A 169 " =    1.909
peak=   -3.134 closest distance to " O   HOH Z   1 " =    0.707
peak=   -3.131 closest distance to " ND2 ASN A  45 " =    1.095
peak=   -3.128 closest distance to " O   HOH Z 360 " =    2.466
peak=   -3.125 closest distance to " O   TRP A  92 " =    1.932
peak=   -3.121 closest distance to " O   HOH Z 396 " =    1.589
peak=   -3.121 closest distance to " CD  GLN A  88 " =    0.865
peak=   -3.120 closest distance to " O   HOH Z  93 " =    1.202
peak=   -3.120 closest distance to " CA  ALA A 299 " =    2.348
peak=   -3.119 closest distance to " CG  TRP A 266 " =    1.580
peak=   -3.118 closest distance to " O   HOH Z 139 " =    3.046
peak=   -3.118 closest distance to " OG  SER A  26 " =    1.173
peak=   -3.115 closest distance to " O   HOH Z 133 " =    3.270
peak=   -3.113 closest distance to " OD1 ASP A 191 " =    1.720
peak=   -3.106 closest distance to " C   PRO A 163 " =    1.080
peak=   -3.096 closest distance to " O   HOH Z  39 " =    1.798
peak=   -3.096 closest distance to " CD1 TYR A 247 " =    2.188
peak=   -3.096 closest distance to " O   HOH Z 208 " =    1.538
peak=   -3.093 closest distance to " CZ  ARG A 156 " =    1.249
peak=   -3.092 closest distance to " CG2 VAL A 296 " =    1.413
peak=   -3.092 closest distance to " O   HOH Z  97 " =    1.564
peak=   -3.075 closest distance to " O   HOH Z 135 " =    1.421
peak=   -3.072 closest distance to " O   PRO A 198 " =    1.299
peak=   -3.065 closest distance to " N   ARG A  66 " =    1.789
peak=   -3.064 closest distance to " O   HOH Z 171 " =    2.207
peak=   -3.064 closest distance to " CD1 LEU A 255 " =    2.508
peak=   -3.062 closest distance to " CD1 LEU A 222 " =    2.540

================= 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    :  0.4984 0.4964   6.297248e+00   6.288759e+00
   1_bss:  0.4915 0.4884   6.295285e+00   6.281788e+00
   1_xyz:  0.4291 0.4441   6.219932e+00   6.246660e+00
   1_adp:  0.3884 0.4308   6.167243e+00   6.234059e+00
   1_occ:  0.3875 0.4301   6.166484e+00   6.233634e+00
   2_bss:  0.3860 0.4276   6.167097e+00   6.232508e+00
   2_xyz:  0.3140 0.3733   6.014964e+00   6.139846e+00
   2_adp:  0.2937 0.3569   5.965808e+00   6.104087e+00
   2_occ:  0.2935 0.3570   5.965492e+00   6.103878e+00
   3_bss:  0.2913 0.3541   5.963930e+00   6.101942e+00
   3_xyz:  0.2088 0.2665   5.683574e+00   5.872747e+00
   3_adp:  0.1844 0.2381   5.572196e+00   5.771355e+00
   3_occ:  0.1840 0.2381   5.571486e+00   5.771173e+00
   4_bss:  0.1830 0.2365   5.568318e+00   5.766297e+00
   4_xyz:  0.1534 0.2033   5.413724e+00   5.626000e+00
   4_adp:  0.1469 0.1977   5.379584e+00   5.594654e+00
   4_occ:  0.1468 0.1976   5.379004e+00   5.594223e+00
   5_bss:  0.1470 0.1976   5.380228e+00   5.595115e+00
   5_xyz:  0.1253 0.1723   5.242138e+00   5.473056e+00
   5_adp:  0.1224 0.1679   5.218095e+00   5.446801e+00
   5_occ:  0.1223 0.1679   5.218040e+00   5.447335e+00
   5_bss:  0.1227 0.1686   5.221349e+00   5.451359e+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:  0.401  50.000   5.577   8.841   7.754   0.000   0.000   0.000
   1_xyz:  0.401  50.000   5.577   8.841   7.754   0.000   0.000   0.000
   1_adp:  0.401  50.000   5.577   8.841   7.754   0.000   0.000   0.000
   1_occ:  0.401  50.000   5.577   8.841   7.754   0.000   0.000   0.000
   2_bss:  0.345  48.839   2.708   5.784   5.381   0.000   0.000   0.000
   2_xyz:  0.345  48.839   2.708   5.784   5.381   0.000   0.000   0.000
   2_adp:  0.345  48.839   2.708   5.784   5.381   0.000   0.000   0.000
   2_occ:  0.345  48.839   2.708   5.784   5.381   0.000   0.000   0.000
   3_bss:  0.334  48.839   1.044   3.113   2.993   0.000   0.000   0.000
   3_xyz:  0.334  48.839   1.044   3.113   2.993   0.000   0.000   0.000
   3_adp:  0.334  48.839   1.044   3.113   2.993   0.000   0.000   0.000
   3_occ:  0.334  48.839   1.044   3.113   2.993   0.000   0.000   0.000
   4_bss:  0.323  42.078   0.075   1.680   1.446   0.000   0.000   0.000
   4_xyz:  0.323  42.078   0.075   1.680   1.446   0.000   0.000   0.000
   4_adp:  0.323  42.078   0.075   1.680   1.446   0.000   0.000   0.000
   4_occ:  0.323  42.078   0.075   1.680   1.446   0.000   0.000   0.000
   5_bss:  0.323  42.078  -0.087   1.305   1.049   0.000   0.000   0.000
   5_xyz:  0.323  42.078  -0.087   1.305   1.049   0.000   0.000   0.000
   5_adp:  0.323  42.078  -0.087   1.305   1.049   0.000   0.000   0.000
   5_occ:  0.323  42.078  -0.087   1.305   1.049   0.000   0.000   0.000
   5_bss:  0.323  42.690  -0.749   0.464   0.285   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  62.832 0.3568  0.4230    78332.969
   1_bss:  62.442 0.3599  0.5225    75315.770
   1_xyz:  56.436 0.4361  0.6228    62363.045
   1_adp:  53.077 0.4797  0.7555    58572.571
   1_occ:  52.988 0.4808  0.7560    58415.059
   2_bss:  52.753 0.4837  0.6934    58063.223
   2_xyz:  41.821 0.6199  0.8894    40624.989
   2_adp:  38.800 0.6564  0.9402    35893.226
   2_occ:  38.804 0.6563  0.9400    35880.235
   3_bss:  38.560 0.6590  0.8709    35466.208
   3_xyz:  27.368 0.7855  0.9843    18863.983
   3_adp:  23.579 0.8263  1.0026    14992.776
   3_occ:  23.583 0.8263  1.0024    14985.337
   4_bss:  23.397 0.8279  0.9566    14715.661
   4_xyz:  19.521 0.8660  0.9815    10625.935
   4_adp:  18.629 0.8750  0.9839     9993.406
   4_occ:  18.614 0.8751  0.9839     9977.984
   5_bss:  18.639 0.8749  0.9728    10004.650
   5_xyz:  16.082 0.8972  0.9838     7715.447
   5_adp:  15.451 0.9029  0.9843     7323.540
   5_occ:  15.457 0.9028  0.9841     7332.313
   5_bss:  15.525 0.9024  0.9789     7431.234
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3199e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3199e+01
   1_xyz:   1.792  0.014  0.111 18.360  0.008  4.106   1.5756e-01
   1_adp:   1.792  0.014  0.111 18.360  0.008  4.106   1.5756e-01
   1_occ:   1.792  0.014  0.111 18.360  0.008  4.106   1.5756e-01
   2_bss:   1.792  0.014  0.111 18.360  0.008  4.106   1.5756e-01
   2_xyz:   1.268  0.009  0.084 16.799  0.006  4.109   9.7060e-02
   2_adp:   1.268  0.009  0.084 16.799  0.006  4.109   9.7060e-02
   2_occ:   1.268  0.009  0.084 16.799  0.006  4.109   9.7060e-02
   3_bss:   1.268  0.009  0.084 16.799  0.006  4.109   9.7060e-02
   3_xyz:   1.206  0.008  0.085 15.846  0.005  4.109   8.1122e-02
   3_adp:   1.206  0.008  0.085 15.846  0.005  4.109   8.1122e-02
   3_occ:   1.206  0.008  0.085 15.846  0.005  4.109   8.1122e-02
   4_bss:   1.206  0.008  0.085 15.846  0.005  4.109   8.1122e-02
   4_xyz:   0.907  0.005  0.066 15.078  0.003  4.114   5.2573e-02
   4_adp:   0.907  0.005  0.066 15.078  0.003  4.114   5.2573e-02
   4_occ:   0.907  0.005  0.066 15.078  0.003  4.114   5.2573e-02
   5_bss:   0.907  0.005  0.066 15.078  0.003  4.114   5.2573e-02
   5_xyz:   1.094  0.007  0.083 15.490  0.004  4.120   6.7891e-02
   5_adp:   1.094  0.007  0.083 15.490  0.004  4.120   6.7891e-02
   5_occ:   1.094  0.007  0.083 15.490  0.004  4.120   6.7891e-02
   5_bss:   1.094  0.007  0.083 15.490  0.004  4.120   6.7891e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.001   6.8921e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.001   6.8921e+00
   1_xyz:  15.757  0.179  0.524 87.174  0.057  2.179   1.0612e-01
   1_adp:  15.757  0.179  0.524 87.174  0.057  2.179   1.0612e-01
   1_occ:  15.757  0.179  0.524 87.174  0.057  2.179   1.0612e-01
   2_bss:  15.757  0.179  0.524 87.174  0.057  2.179   1.0612e-01
   2_xyz:  10.688  0.107  0.315 84.749  0.059  2.108   7.6597e-02
   2_adp:  10.688  0.107  0.315 84.749  0.059  2.108   7.6597e-02
   2_occ:  10.688  0.107  0.315 84.749  0.059  2.108   7.6597e-02
   3_bss:  10.688  0.107  0.315 84.749  0.059  2.108   7.6597e-02
   3_xyz:   6.653  0.049  0.419 87.301  0.037  2.232   5.7105e-02
   3_adp:   6.653  0.049  0.419 87.301  0.037  2.232   5.7105e-02
   3_occ:   6.653  0.049  0.419 87.301  0.037  2.232   5.7105e-02
   4_bss:   6.653  0.049  0.419 87.301  0.037  2.232   5.7105e-02
   4_xyz:   6.793  0.031  0.298 78.845  0.025  2.345   3.0237e-02
   4_adp:   6.793  0.031  0.298 78.845  0.025  2.345   3.0237e-02
   4_occ:   6.793  0.031  0.298 78.845  0.025  2.345   3.0237e-02
   5_bss:   6.793  0.031  0.298 78.845  0.025  2.345   3.0237e-02
   5_xyz:   7.319  0.049  0.574 80.928  0.025  2.285   4.8490e-02
   5_adp:   7.319  0.049  0.574 80.928  0.025  2.285   4.8490e-02
   5_occ:   7.319  0.049  0.574 80.928  0.025  2.285   4.8490e-02
   5_bss:   7.319  0.049  0.574 80.928  0.025  2.285   4.8490e-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:  98.27   0.00  15.36  78.62   0.00  13.16  98.27   0.00  27.33
   1_occ:  98.27   0.00  15.36  78.62   0.00  13.16  98.27   0.00  27.33
   2_bss:  98.27   0.00  15.36  78.62   0.00  13.16  98.27   0.00  27.33
   2_xyz:  98.27   0.00  15.36  78.62   0.00  13.16  98.27   0.00  27.33
   2_adp:  99.31   0.00  15.24  83.17   0.00  12.21  99.31   0.00  31.74
   2_occ:  99.31   0.00  15.24  83.17   0.00  12.21  99.31   0.00  31.74
   3_bss:  99.31   0.00  15.24  83.17   0.00  12.21  99.31   0.00  31.74
   3_xyz:  99.31   0.00  15.24  83.17   0.00  12.21  99.31   0.00  31.74
   3_adp:  87.75   0.00  14.88  84.49   0.00  10.79  87.75   3.87  37.14
   3_occ:  87.75   0.00  14.88  84.49   0.00  10.79  87.75   3.87  37.14
   4_bss:  87.75   0.00  14.88  84.49   0.00  10.79  87.75   3.87  37.14
   4_xyz:  87.75   0.00  14.88  84.49   0.00  10.79  87.75   3.87  37.14
   4_adp:  86.28   0.00  14.87  86.28   0.00  10.55  83.55   3.67  38.40
   4_occ:  86.28   0.00  14.87  86.28   0.00  10.55  83.55   3.67  38.40
   5_bss:  86.28   0.00  14.87  86.28   0.00  10.55  83.55   3.67  38.40
   5_xyz:  86.28   0.00  14.87  86.28   0.00  10.55  83.55   3.67  38.40
   5_adp:  87.42   0.39  14.51  87.42   0.39  10.23  79.80   2.94  37.83
   5_occ:  87.42   0.39  14.51  87.42   0.39  10.23  79.80   2.94  37.83
   5_bss:  88.03   1.00  15.12  88.03   1.00  10.84  80.41   3.55  38.45
------------------------------------------------------------------------
 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:    1.192    0.019    0.418
   1_adp:    1.192    0.019    0.418
   1_occ:    1.192    0.019    0.418
   2_bss:    1.192    0.019    0.418
   2_xyz:    1.894    0.019    0.599
   2_adp:    1.894    0.019    0.599
   2_occ:    1.894    0.019    0.599
   3_bss:    1.894    0.019    0.599
   3_xyz:    1.695    0.044    0.742
   3_adp:    1.695    0.044    0.742
   3_occ:    1.695    0.044    0.742
   4_bss:    1.695    0.044    0.742
   4_xyz:    1.805    0.064    0.788
   4_adp:    1.805    0.064    0.788
   4_occ:    1.805    0.064    0.788
   5_bss:    1.805    0.064    0.788
   5_xyz:    1.858    0.048    0.835
   5_adp:    1.858    0.048    0.835
   5_occ:    1.858    0.048    0.835
   5_bss:    1.858    0.048    0.835
------------------------------------------------------------------------

CPU time actual refinement: 272.72


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_451/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_451/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_451/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_451/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_451/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 272.59 
  Macro-tasks:
    bulk solvent and scale       = 29.67  
    individual site refinement   = 113.11 
    weights calculation          = 26.71  
    collect and process          = 5.24   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 174.82 
  Micro-tasks:
    mask                            = 2.52   
    f_calc                          = 85.81  
    alpha_beta                      = 6.92   
    target                          = 0.97   
    gradients_wrt_atomic_parameters = 93.90  
    fmodel                         = 5.21   
    r_factors                      = 0.12   
    phase_errors                   = 8.32   
    foms                           = 0.15   
    TOTAL for micro-tasks          = 203.92 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 3.914 micro seconds
Total CPU time: 4.74 minutes
from_scatterers_fft:    620 calls, 85.57 s
gradients_fft:          566 calls, 83.08 s

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

# Date 2008-01-16 Time 01:36:57 PST -0800 (1200476217.20 s)
Start R-work = 0.4984, R-free = 0.4964 (no bulk solvent and anisotropic scale)
Final R-work = 0.1396, R-free = 0.1864 (no bulk solvent and anisotropic scale)

Start R-work = 0.4915, R-free = 0.4884
Final R-work = 0.1227, R-free = 0.1686