# Date 2008-01-16 Time 02:22:51 PST -0800 (1200478971.35 s)
#phil __OFF__

Command line arguments: "../813.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 6138
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 813

-------------------------------------------------------------------------------
  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: (70.6012, 47.3993, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.30, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.3993, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1485 2.01067
Completeness in resolution range: 0.963362
Completeness with d_max=infinity: 0.960339

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1485
                             d_min =   2.0107

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: (70.6012, 47.3993, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1485 2.01067
Completeness in resolution range: 0.963362
Completeness with d_max=infinity: 0.960339

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1489 -  4.3019 [2144/2168]  1926   218  10.2%
  bin  2:  4.3019 -  3.4275 [2045/2064]  1845   200   9.8%
  bin  3:  3.4275 -  2.9981 [2028/2047]  1824   204  10.1%
  bin  4:  2.9981 -  2.7257 [1999/2029]  1794   205  10.3%
  bin  5:  2.7257 -  2.5313 [2006/2025]  1809   197   9.8%
  bin  6:  2.5313 -  2.3827 [1979/2004]  1781   198  10.0%
  bin  7:  2.3827 -  2.2638 [1976/2004]  1781   195   9.9%
  bin  8:  2.2638 -  2.1655 [1976/2012]  1777   199  10.1%
  bin  9:  2.1655 -  2.0824 [1942/1984]  1748   194  10.0%
  bin 10:  2.0824 -  2.0107 [1494/1997]  1345   149  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_813/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:
        1.54 -     2.21: 8
        2.21 -     2.88: 1241
        2.88 -     3.55: 4337
        3.55 -     4.23: 9023
        4.23 -     4.90: 13135
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.536 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.713 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.713 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.845 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27739 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_813/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_813/model_refine_001.geo

CPU time processing inputs: 8.89


============================ 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 = 70.60125 47.3993 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4824   r_free= 0.4734   ksol= 0.00   Bsol= 0.00   scale= 0.777    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.283473                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7979 0.99   1394  153 0.3949 0.3639      6.6052      6.5119|
|  2:  4.7979 -  3.8285 0.99   1326  152 0.4027 0.4564      6.7963      6.9502|
|  3:  3.8285 -  3.3505 0.99   1309  145 0.4449 0.4277      6.6871      6.6668|
|  4:  3.3505 -  3.0469 0.99   1302  139 0.4760 0.4111      6.5437      6.4514|
|  5:  3.0469 -  2.8300 0.99   1291  144 0.5082 0.4828      6.3796      6.3961|
|  6:  2.8300 -  2.6641 0.99   1293  149 0.5029 0.5554      6.2836      6.2133|
|  7:  2.6641 -  2.5313 0.99   1283  142 0.5187 0.4698      6.2423      6.1666|
|  8:  2.5313 -  2.4216 0.98   1280  137 0.5254 0.4487      6.1939       6.141|
|  9:  2.4216 -  2.3287 0.98   1260  145 0.5155 0.5741       6.114      6.1751|
| 10:  2.3287 -  2.2486 0.99   1281  142 0.5400 0.4974      6.1296      6.0973|
| 11:  2.2486 -  2.1785 0.98   1259  136 0.5199 0.5437      6.0318      6.0805|
| 12:  2.1785 -  2.1164 0.97   1247  139 0.5335 0.5110      5.9754      6.0532|
| 13:  2.1164 -  2.0608 1.00   1267  139 0.5299 0.5374       5.895      5.8237|
| 14:  2.0608 -  2.0107 0.65    838   97 0.5427 0.4979      5.8674      5.7697|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1489 -  4.7979  1394   153  0.71  33.39   0.79     0.73      66843.12|
|  2:  4.7979 -  3.8285  1326   152  0.71  34.75   0.86     0.75     105598.51|
|  3:  3.8285 -  3.3505  1309   145  0.61  43.34   0.81     0.70     112218.82|
|  4:  3.3505 -  3.0469  1302   139  0.51  51.07   0.78     0.58      99515.90|
|  5:  3.0469 -  2.8300  1291   144  0.42  57.92   0.73     0.49      80816.16|
|  6:  2.8300 -  2.6641  1293   149  0.39  60.53   0.71     0.44      72652.38|
|  7:  2.6641 -  2.5313  1283   142  0.39  60.53   0.72     0.44      63285.27|
|  8:  2.5313 -  2.4216  1280   137  0.41  59.18   0.72     0.47      54920.13|
|  9:  2.4216 -  2.3287  1260   145  0.39  60.47   0.71     0.45      51866.24|
| 10:  2.3287 -  2.2486  1281   142  0.36  63.38   0.72     0.41      49603.67|
| 11:  2.2486 -  2.1785  1259   136  0.31  66.90   0.73     0.37      48759.92|
| 12:  2.1785 -  2.1164  1247   139  0.31  67.18   0.73     0.37      44134.57|
| 13:  2.1164 -  2.0608  1267   139  0.29  68.04   0.71     0.35      38243.17|
| 14:  2.0608 -  2.0107   838    97  0.30  67.91   0.71     0.31      31173.85|
|alpha:            min =        0.31 max =            0.75 mean =         0.50|
|beta:             min =    31173.85 max =       112218.82 mean =     66893.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           90.00 mean =        56.20|
|phase err.(test): min =        0.00 max =           89.79 mean =        56.38|
|-----------------------------------------------------------------------------|

============================== 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 = 14.664523             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.858   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.393277              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.677   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       22 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      163 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      670 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1480 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2563 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3822 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4978 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6470 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7575 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.601 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.770 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.329)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.329)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4870   r_free= 0.4734   ksol= 0.00   Bsol= 0.00   scale= 0.750    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.285768                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4739   r_free= 0.4613   ksol= 0.30   Bsol= 20.00   scale= 0.976   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.31,8.11,11.82,0.00,0.00,0.00); trace/3= 8.74                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.277072                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.913478             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.625   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.227616              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.333   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4739      final r-factor (work) = 0.3904          |
| start r-factor (free) = 0.4613      final r-factor (free) = 0.4174          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 95.1712 = 12.91 * 0.50 * 6.2834 + 1.00 * 54.6011                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.1051 = 12.91 * 0.50 * 6.1885 + 1.00 * 0.1478                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3904      final r-factor (work) = 0.3462          |
| start r-factor (free) = 0.4174      final r-factor (free) = 0.4005          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6115 = 1.23 * 1.00 * 6.1885 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5125 = 1.23 * 1.00 * 6.1050 + 1.00 * 0.0180                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.329)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.49   13.41    None  None   None       |
|    all(noH): 2823   0      0.00    72.49   13.41    None  None   None       |
|    Sol.    : 438    0      0.00    72.49   26.08    None  None   None       |
|    Mac.    : 2385   0      0.00    65.04   11.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.249: 1049   |   5:    36.247 -  43.496:   74        |
|      1:     7.249 -  14.499:  770   |   6:    43.496 -  50.746:   44        |
|      2:    14.499 -  21.748:  430   |   7:    50.746 -  57.995:   23        |
|      3:    21.748 -  28.998:  282   |   8:    57.995 -  65.245:   11        |
|      4:    28.998 -  36.247:  136   |   9:    65.245 -  72.494:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3462 r_free = 0.4005             target_work(ml) = 6.083         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3458 r_free = 0.4010             target_work(ml) = 6.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3458   r_free= 0.4010   ksol= 0.30   Bsol= 20.00   scale= 1.085   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.31,8.11,11.82,0.00,0.00,0.00); trace/3= 8.74                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.083021                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3436   r_free= 0.3981   ksol= 0.33   Bsol= 54.31   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.10,4.77,7.94,0.00,0.00,0.00); trace/3= 5.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.084675                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.655086              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.001  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.536176              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.797  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3436      final r-factor (work) = 0.2682          |
| start r-factor (free) = 0.3981      final r-factor (free) = 0.3244          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.3939 = 5.66 * 0.50 * 6.0993 + 1.00 * 0.1478                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.9835 = 5.66 * 0.50 * 5.9765 + 1.00 * 0.0846                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2682      final r-factor (work) = 0.2452          |
| start r-factor (free) = 0.3244      final r-factor (free) = 0.3009          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2454 = 0.54 * 1.00 * 5.9765 + 1.00 * 0.0409                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2101 = 0.54 * 1.00 * 5.8424 + 1.00 * 0.0775                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.329)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.83   13.10    None  None   None       |
|    all(noH): 2823   0      0.00    76.83   13.10    None  None   None       |
|    Sol.    : 438    0      0.00    76.83   32.19    None  None   None       |
|    Mac.    : 2385   0      0.00    59.86   9.60     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.683: 1260   |   5:    38.417 -  46.100:   94        |
|      1:     7.683 -  15.367:  769   |   6:    46.100 -  53.783:   54        |
|      2:    15.367 -  23.050:  321   |   7:    53.783 -  61.466:   31        |
|      3:    23.050 -  30.733:  159   |   8:    61.466 -  69.150:   10        |
|      4:    30.733 -  38.417:  124   |   9:    69.150 -  76.833:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2452 r_free = 0.3009             target_work(ml) = 5.817         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2450 r_free = 0.3011             target_work(ml) = 5.816         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2450   r_free= 0.3011   ksol= 0.33   Bsol= 54.31   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.10,4.77,7.94,0.00,0.00,0.00); trace/3= 5.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.816193                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2442   r_free= 0.3014   ksol= 0.31   Bsol= 54.31   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.04,3.21,5.43,0.00,0.00,0.00); trace/3= 3.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.818276                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.116478              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.613   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.378695              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.763   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2442      final r-factor (work) = 0.1842          |
| start r-factor (free) = 0.3014      final r-factor (free) = 0.2341          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1137 = 4.12 * 0.50 * 5.8444 + 1.00 * 0.0846                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.8174 = 4.12 * 0.50 * 5.7048 + 1.00 * 0.0755                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1842      final r-factor (work) = 0.1653          |
| start r-factor (free) = 0.2341      final r-factor (free) = 0.2205          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 19.2977 = 3.38 * 1.00 * 5.7048 + 1.00 * 0.0228                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.6403 = 3.38 * 1.00 * 5.5113 + 1.00 * 0.0193                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.329)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.40  14.48    None  None   None       |
|    all(noH): 2823   0      0.00    101.40  14.48    None  None   None       |
|    Sol.    : 438    0      0.97    101.40  41.77    None  None   None       |
|    Mac.    : 2385   0      0.00    89.23   9.47     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 -  10.140: 1653   |   5:    50.700 -  60.840:   96        |
|      1:    10.140 -  20.280:  595   |   6:    60.840 -  70.981:   58        |
|      2:    20.280 -  30.420:  173   |   7:    70.981 -  81.121:   31        |
|      3:    30.420 -  40.560:  106   |   8:    81.121 -  91.261:    9        |
|      4:    40.560 -  50.700:  101   |   9:    91.261 - 101.401:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1653 r_free = 0.2205             target_work(ml) = 5.483         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1652 r_free = 0.2207             target_work(ml) = 5.484         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1652   r_free= 0.2207   ksol= 0.31   Bsol= 54.31   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.04,3.21,5.43,0.00,0.00,0.00); trace/3= 3.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.483991                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1652   r_free= 0.2200   ksol= 0.34   Bsol= 80.07   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.80,2.60,4.46,0.00,0.00,0.00); trace/3= 2.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.482200                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.779159              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.580  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.367005              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.489  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1652      final r-factor (work) = 0.1369          |
| start r-factor (free) = 0.2200      final r-factor (free) = 0.1884          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4925 = 3.78 * 0.50 * 5.5129 + 1.00 * 0.0755                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2926 = 3.78 * 0.50 * 5.4062 + 1.00 * 0.0771                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1369      final r-factor (work) = 0.1319          |
| start r-factor (free) = 0.1884      final r-factor (free) = 0.1792          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0032 = 0.37 * 1.00 * 5.4062 + 1.00 * 0.0191                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9647 = 0.37 * 1.00 * 5.3103 + 1.00 * 0.0158                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.329)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.21   13.48    None  None   None       |
|    all(noH): 2823   0      0.00    98.21   13.48    None  None   None       |
|    Sol.    : 438    0      1.38    98.21   39.30    None  None   None       |
|    Mac.    : 2385   0      0.00    82.10   8.73     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 -   9.821: 1721   |   5:    49.105 -  58.926:   89        |
|      1:     9.821 -  19.642:  573   |   6:    58.926 -  68.747:   43        |
|      2:    19.642 -  29.463:  145   |   7:    68.747 -  78.568:   21        |
|      3:    29.463 -  39.284:  110   |   8:    78.568 -  88.389:    9        |
|      4:    39.284 -  49.105:  110   |   9:    88.389 -  98.210:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1319 r_free = 0.1792             target_work(ml) = 5.282         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1317 r_free = 0.1790             target_work(ml) = 5.282         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1317   r_free= 0.1790   ksol= 0.34   Bsol= 80.07   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.80,2.60,4.46,0.00,0.00,0.00); trace/3= 2.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.281887                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1317   r_free= 0.1790   ksol= 0.33   Bsol= 73.83   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.95,2.52,4.20,0.00,0.00,0.00); trace/3= 2.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.280353                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.629274              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.105  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.348485              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.050  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1317      final r-factor (work) = 0.1236          |
| start r-factor (free) = 0.1790      final r-factor (free) = 0.1692          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0570 = 2.63 * 0.50 * 5.3093 + 1.00 * 0.0771                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9828 = 2.63 * 0.50 * 5.2552 + 1.00 * 0.0740                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1236      final r-factor (work) = 0.1224          |
| start r-factor (free) = 0.1692      final r-factor (free) = 0.1678          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8460 = 0.35 * 1.00 * 5.2552 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8488 = 0.35 * 1.00 * 5.2234 + 1.00 * 0.0285                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.329)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.36   13.03    None  None   None       |
|    all(noH): 2823   0      0.00    96.36   13.03    None  None   None       |
|    Sol.    : 438    0      1.30    96.36   37.68    None  None   None       |
|    Mac.    : 2385   0      0.00    82.10   8.51     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 -   9.636: 1763   |   5:    48.178 -  57.814:   87        |
|      1:     9.636 -  19.271:  534   |   6:    57.814 -  67.449:   45        |
|      2:    19.271 -  28.907:  152   |   7:    67.449 -  77.085:   15        |
|      3:    28.907 -  38.543:  128   |   8:    77.085 -  86.721:   11        |
|      4:    38.543 -  48.178:   87   |   9:    86.721 -  96.356:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1224 r_free = 0.1678             target_work(ml) = 5.220         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1222 r_free = 0.1677             target_work(ml) = 5.219         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1222   r_free= 0.1677   ksol= 0.33   Bsol= 73.83   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.95,2.52,4.20,0.00,0.00,0.00); trace/3= 2.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.219010                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7979 0.99   1394  153 0.1020 0.1336      5.4151      5.5475|
|  2:  4.7979 -  3.8285 0.99   1326  152 0.0881 0.1147      5.4672      5.6923|
|  3:  3.8285 -  3.3505 0.99   1309  145 0.1119 0.1566      5.5259      5.8748|
|  4:  3.3505 -  3.0469 0.99   1302  139 0.1308 0.1709      5.5121      5.6668|
|  5:  3.0469 -  2.8300 0.99   1291  144 0.1516 0.1734       5.434      5.5786|
|  6:  2.8300 -  2.6641 0.99   1293  149 0.1382 0.2267      5.3132      5.6223|
|  7:  2.6641 -  2.5313 0.99   1283  142 0.1426 0.1707      5.2748      5.3954|
|  8:  2.5313 -  2.4216 0.98   1280  137 0.1322 0.1762      5.1742      5.4217|
|  9:  2.4216 -  2.3287 0.98   1260  145 0.1310 0.2016      5.1177       5.388|
| 10:  2.3287 -  2.2486 0.99   1281  142 0.1263 0.1713      5.0399       5.218|
| 11:  2.2486 -  2.1785 0.98   1259  136 0.1288 0.1935      5.0295      5.2846|
| 12:  2.1785 -  2.1164 0.97   1247  139 0.1256 0.1851      4.9606      5.3446|
| 13:  2.1164 -  2.0608 1.00   1267  139 0.1215 0.1787      4.8564      5.0553|
| 14:  2.0608 -  2.0107 0.65    838   97 0.1107 0.1845      4.7153      5.0138|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1489 -  4.7979  1394   153  0.94   9.60   0.96     0.94       7855.66|
|  2:  4.7979 -  3.8285  1326   152  0.95   8.43   1.00     0.98       9645.82|
|  3:  3.8285 -  3.3505  1309   145  0.93  11.66   1.02     1.01      11208.09|
|  4:  3.3505 -  3.0469  1302   139  0.91  14.27   1.00     0.99      11194.88|
|  5:  3.0469 -  2.8300  1291   144  0.89  17.42   1.00     0.97       9733.00|
|  6:  2.8300 -  2.6641  1293   149  0.89  17.80   0.97     0.95       8569.19|
|  7:  2.6641 -  2.5313  1283   142  0.89  17.59   0.99     0.95       7569.85|
|  8:  2.5313 -  2.4216  1280   137  0.90  16.48   0.99     0.96       6291.77|
|  9:  2.4216 -  2.3287  1260   145  0.90  16.65   1.01     0.97       5824.67|
| 10:  2.3287 -  2.2486  1281   142  0.89  17.05   0.99     0.95       4944.36|
| 11:  2.2486 -  2.1785  1259   136  0.89  17.52   0.99     0.94       5106.92|
| 12:  2.1785 -  2.1164  1247   139  0.89  17.21   1.00     0.98       4620.73|
| 13:  2.1164 -  2.0608  1267   139  0.89  17.12   0.98     0.96       3813.74|
| 14:  2.0608 -  2.0107   838    97  0.91  15.12   0.96     0.92       2716.61|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2716.61 max =        11208.09 mean =      7224.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.22|
|phase err.(test): min =        0.00 max =           89.07 mean =        14.54|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1222   r_free= 0.1677   ksol= 0.32   Bsol= 67.71   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.84,-0.39,1.23,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.218658                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1222   r_free= 0.1677   ksol= 0.32   Bsol= 67.71   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.84,-0.39,1.23,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.218658                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7979 0.99   1394  153 0.1015 0.1333      5.4091      5.5432|
|  2:  4.7979 -  3.8285 0.99   1326  152 0.0876 0.1141      5.4635      5.6872|
|  3:  3.8285 -  3.3505 0.99   1309  145 0.1117 0.1567      5.5245      5.8758|
|  4:  3.3505 -  3.0469 0.99   1302  139 0.1310 0.1714       5.514      5.6687|
|  5:  3.0469 -  2.8300 0.99   1291  144 0.1518 0.1737       5.436      5.5806|
|  6:  2.8300 -  2.6641 0.99   1293  149 0.1383 0.2271      5.3146      5.6241|
|  7:  2.6641 -  2.5313 0.99   1283  142 0.1428 0.1713      5.2763      5.3974|
|  8:  2.5313 -  2.4216 0.98   1280  137 0.1323 0.1762      5.1753      5.4224|
|  9:  2.4216 -  2.3287 0.98   1260  145 0.1309 0.2017      5.1179      5.3885|
| 10:  2.3287 -  2.2486 0.99   1281  142 0.1264 0.1717      5.0398      5.2186|
| 11:  2.2486 -  2.1785 0.98   1259  136 0.1287 0.1929      5.0289      5.2832|
| 12:  2.1785 -  2.1164 0.97   1247  139 0.1256 0.1848      4.9605      5.3431|
| 13:  2.1164 -  2.0608 1.00   1267  139 0.1215 0.1793      4.8561      5.0574|
| 14:  2.0608 -  2.0107 0.65    838   97 0.1109 0.1844      4.7155      5.0123|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1489 -  4.7979  1394   153  0.94   9.52   0.96     0.94       7767.95|
|  2:  4.7979 -  3.8285  1326   152  0.95   8.38   1.00     0.98       9567.11|
|  3:  3.8285 -  3.3505  1309   145  0.93  11.63   1.01     1.01      11168.76|
|  4:  3.3505 -  3.0469  1302   139  0.91  14.30   1.00     0.98      11226.98|
|  5:  3.0469 -  2.8300  1291   144  0.89  17.45   0.99     0.96       9780.68|
|  6:  2.8300 -  2.6641  1293   149  0.89  17.83   0.97     0.94       8599.07|
|  7:  2.6641 -  2.5313  1283   142  0.89  17.62   0.98     0.94       7600.27|
|  8:  2.5313 -  2.4216  1280   137  0.90  16.50   0.98     0.95       6304.84|
|  9:  2.4216 -  2.3287  1260   145  0.90  16.67   1.00     0.96       5837.08|
| 10:  2.3287 -  2.2486  1281   142  0.89  17.04   0.99     0.94       4938.36|
| 11:  2.2486 -  2.1785  1259   136  0.89  17.50   0.99     0.94       5099.03|
| 12:  2.1785 -  2.1164  1247   139  0.89  17.20   0.99     0.98       4616.98|
| 13:  2.1164 -  2.0608  1267   139  0.89  17.11   0.97     0.95       3811.91|
| 14:  2.0608 -  2.0107   838    97  0.91  15.10   0.95     0.92       2712.70|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2712.70 max =        11226.98 mean =      7219.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.21|
|phase err.(test): min =        0.00 max =           89.06 mean =        14.54|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.329)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.78    99.13   15.81    None  None   None       |
|    all(noH): 2823   0      2.78    99.13   15.81    None  None   None       |
|    Sol.    : 438    0      4.07    99.13   40.46    None  None   None       |
|    Mac.    : 2385   0      2.78    84.87   11.28    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.776 -  12.411: 1763   |   5:    50.954 -  60.589:   87        |
|      1:    12.411 -  22.047:  534   |   6:    60.589 -  70.225:   45        |
|      2:    22.047 -  31.682:  152   |   7:    70.225 -  79.861:   15        |
|      3:    31.682 -  41.318:  128   |   8:    79.861 -  89.496:   11        |
|      4:    41.318 -  50.954:   87   |   9:    89.496 -  99.132:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 333         
Filter by distance & map next to the model:
   mapped sites are within: 0.246 - 5.670
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 326 from: 333
   mapped sites are within: 0.712 - 5.670

peak=   10.506 closest distance to " CB  VAL A 230 " =    1.475
peak=    5.576 closest distance to " CB  GLN A 223 " =    1.519
peak=    5.431 closest distance to " CG  LEU A   5 " =    1.285
peak=    5.322 closest distance to " NH2 ARG A  56 " =    2.155
peak=    5.084 closest distance to " CD2 LEU A   5 " =    1.151
peak=    5.042 closest distance to " CG  LEU A 228 " =    1.261
peak=    4.995 closest distance to " CB  VAL A 296 " =    1.113
peak=    4.948 closest distance to " CG  PRO A 280 " =    0.897
peak=    4.826 closest distance to " CG2 VAL A 296 " =    1.052
peak=    4.822 closest distance to " NE2 GLN A  11 " =    1.080
peak=    4.757 closest distance to " O   HOH Z 210 " =    1.120
peak=    4.757 closest distance to " CG1 VAL A 296 " =    1.211
peak=    4.719 closest distance to " CB  SER A  63 " =    1.181
peak=    4.716 closest distance to " CZ  PHE A 218 " =    1.126
peak=    4.690 closest distance to " O   HOH Z 142 " =    1.829
peak=    4.661 closest distance to " O   HOH Z 248 " =    1.479
peak=    4.644 closest distance to " CB  ARG A 190 " =    1.483
peak=    4.625 closest distance to " CG  PRO A  54 " =    1.373
peak=    4.591 closest distance to " CZ3 TRP A 266 " =    1.139
peak=    4.528 closest distance to " CB  GLN A 183 " =    1.238
peak=    4.494 closest distance to " CA  ALA A  51 " =    0.988
peak=    4.476 closest distance to " CD2 LEU A 228 " =    1.226
peak=    4.460 closest distance to " CG  PRO A 198 " =    1.324
peak=    4.450 closest distance to " CD1AILE A 234 " =    1.017
peak=    4.425 closest distance to " CB  PRO A  54 " =    0.988
peak=    4.420 closest distance to " O   PRO A 198 " =    1.541
peak=    4.407 closest distance to " O   HOH Z 425 " =    1.536
peak=    4.319 closest distance to " O   HOH Z 369 " =    2.146
peak=    4.302 closest distance to " O   HOH Z 411 " =    3.878
peak=    4.301 closest distance to " CG  PRO A 243 " =    1.198
peak=    4.299 closest distance to " O   HOH Z 126 " =    1.616
peak=    4.288 closest distance to " CB  ASP A 124 " =    0.803
peak=    4.285 closest distance to " O   HOH Z 232 " =    2.197
peak=    4.254 closest distance to " CB  ARG A 275 " =    0.946
peak=    4.247 closest distance to " CB  ASN A 142 " =    1.162
peak=    4.220 closest distance to " CG  MET A 185 " =    1.257
peak=    4.194 closest distance to " CB  GLU A 277 " =    3.774
peak=    4.122 closest distance to " O   HOH Z 251 " =    1.684
peak=    4.119 closest distance to " CA  TYR A  30 " =    1.015
peak=    4.117 closest distance to " CD2 TRP A 179 " =    1.265
peak=    4.107 closest distance to " O   SER A  87 " =    2.376
peak=    4.094 closest distance to " CB  TYR A 169 " =    0.770
peak=    4.087 closest distance to " CD1 LEU A  96 " =    0.842
peak=    4.077 closest distance to " O   HOH Z 368 " =    2.513
peak=    4.075 closest distance to " O   HOH Z  76 " =    1.271
peak=    4.060 closest distance to " O   HOH Z 214 " =    1.466
peak=    4.057 closest distance to " CD  LYS A 166 " =    1.373
peak=    4.048 closest distance to " ND2 ASN A 187 " =    1.689
peak=    4.044 closest distance to " CG AARG A 275 " =    1.246
peak=    4.027 closest distance to " O   HOH Z 265 " =    2.005
peak=    4.024 closest distance to " CB  ARG A  79 " =    1.458
peak=    4.021 closest distance to " O   HOH Z 128 " =    1.400
peak=    4.003 closest distance to " CB  TRP A 266 " =    1.006
peak=    3.995 closest distance to " O   HOH Z  49 " =    1.310
peak=    3.993 closest distance to " CE  LYS A  76 " =    0.892
peak=    3.984 closest distance to " CG  ARG A 138 " =    1.376
peak=    3.976 closest distance to " CB  LEU A  83 " =    0.715
peak=    3.962 closest distance to " O   HOH Z 154 " =    1.552
peak=    3.945 closest distance to " O   HOH Z 261 " =    2.234
peak=    3.938 closest distance to " O   ASP A 124 " =    1.193
peak=    3.930 closest distance to " NH2AARG A 145 " =    1.161
peak=    3.912 closest distance to " O   HOH Z 313 " =    1.821
peak=    3.907 closest distance to " O   HOH Z 303 " =    2.285
peak=    3.902 closest distance to " CG1 VAL A 153 " =    0.998
peak=    3.887 closest distance to " CD  ARG A 269 " =    0.956
peak=    3.883 closest distance to " CA  ALA A 295 " =    1.070
peak=    3.877 closest distance to " CB  GLU A 152 " =    1.165
peak=    3.877 closest distance to " O   HOH Z 188 " =    3.030
peak=    3.877 closest distance to " CA  TYR A 116 " =    1.437
peak=    3.866 closest distance to " CA  SER A  87 " =    0.967
peak=    3.852 closest distance to " O   HOH Z 359 " =    1.838
peak=    3.851 closest distance to " CB  ASN A 148 " =    1.408
peak=    3.849 closest distance to " CB  ASN A  39 " =    0.877
peak=    3.845 closest distance to " O   HOH Z   9 " =    1.358
peak=    3.843 closest distance to " CA  VAL A 230 " =    1.212
peak=    3.832 closest distance to " O   HOH Z 280 " =    2.908
peak=    3.831 closest distance to " CB  GLU A 128 " =    1.070
peak=    3.828 closest distance to " CA  ARG A  36 " =    1.084
peak=    3.827 closest distance to " CD  ARG A  66 " =    2.611
peak=    3.825 closest distance to " O   HOH Z 423 " =    1.821
peak=    3.820 closest distance to " O   HOH Z  78 " =    1.646
peak=    3.800 closest distance to " O   HOH Z 214 " =    2.153
peak=    3.798 closest distance to " OG  SER A 276 " =    1.373
peak=    3.795 closest distance to " O   HOH Z 422 " =    2.664
peak=    3.786 closest distance to " O   HOH Z 234 " =    3.731
peak=    3.769 closest distance to " O   HOH Z   4 " =    1.653
peak=    3.766 closest distance to " CB  TRP A 179 " =    1.397
peak=    3.753 closest distance to " CA  ARG A 195 " =    1.274
peak=    3.752 closest distance to " O   HOH Z  63 " =    1.786
peak=    3.746 closest distance to " CB  GLU A  46 " =    0.906
peak=    3.745 closest distance to " CB  ASP A 140 " =    1.064
peak=    3.734 closest distance to " N   ASN A  39 " =    1.230
peak=    3.728 closest distance to " CD  ARG A 159 " =    0.748
peak=    3.724 closest distance to " O   HOH Z 346 " =    1.507
peak=    3.718 closest distance to " O  BHOH Z 338 " =    2.246
peak=    3.714 closest distance to " CB  SER A 273 " =    1.021
peak=    3.705 closest distance to " CB  VAL A 202 " =    1.526
peak=    3.699 closest distance to " CG  LEU A 167 " =    1.110
peak=    3.698 closest distance to " O  BHOH Z  74 " =    1.216
peak=    3.696 closest distance to " CA  ILE A 106 " =    0.768
peak=    3.694 closest distance to " O   HOH Z 126 " =    1.980
peak=    3.689 closest distance to " O   ASP A 200 " =    1.650
peak=    3.685 closest distance to " O   HOH Z 406 " =    1.562
peak=    3.680 closest distance to " ND2 ASN A 249 " =    1.871
peak=    3.679 closest distance to " CG  GLU A  37 " =    0.957
peak=    3.662 closest distance to " CA  THR A 264 " =    0.776
peak=    3.662 closest distance to " CB  VAL A 265 " =    1.247
peak=    3.659 closest distance to " CB BVAL A  41 " =    1.169
peak=    3.641 closest distance to " O   HOH Z 402 " =    1.452
peak=    3.634 closest distance to " O   HOH Z 131 " =    2.346
peak=    3.633 closest distance to " O   HOH Z 273 " =    2.833
peak=    3.633 closest distance to " CA  ALA A 160 " =    1.062
peak=    3.628 closest distance to " O   HOH Z  21 " =    1.789
peak=    3.626 closest distance to " O   HOH Z 298 " =    1.910
peak=    3.622 closest distance to " O   HOH Z  43 " =    2.088
peak=    3.622 closest distance to " O   HOH Z 353 " =    2.579
peak=    3.621 closest distance to " O   HOH Z 287 " =    1.921
peak=    3.618 closest distance to " O   HOH Z  80 " =    1.867
peak=    3.613 closest distance to " CB  ALA A   9 " =    1.661
peak=    3.611 closest distance to " O   HOH Z 383 " =    1.904
peak=    3.610 closest distance to " NE2 HIS A 207 " =    1.070
peak=    3.606 closest distance to " NH1AARG A 145 " =    1.280
peak=    3.605 closest distance to " CG1 ILE A  20 " =    1.349
peak=    3.604 closest distance to " OG  SER A 245 " =    1.587
peak=    3.596 closest distance to " CB  ALA A 291 " =    1.170
peak=    3.593 closest distance to " CA  GLY A 267 " =    0.901
peak=    3.583 closest distance to " CD1 ILE A  33 " =    1.786
peak=    3.577 closest distance to " CG2 THR A 221 " =    1.034
peak=    3.576 closest distance to " CZ3 TRP A  85 " =    0.957
peak=    3.575 closest distance to " O   HOH Z 247 " =    1.383
peak=    3.574 closest distance to " CA  VAL A 125 " =    1.196
peak=    3.574 closest distance to " O   HOH Z  19 " =    2.183
peak=    3.568 closest distance to " O   HOH Z 427 " =    2.988
peak=    3.566 closest distance to " O   HOH Z 148 " =    3.251
peak=    3.564 closest distance to " O   HOH Z 130 " =    1.128
peak=    3.563 closest distance to " CG2AVAL A 121 " =    2.200
peak=    3.563 closest distance to " O   THR A 182 " =    1.385
peak=    3.546 closest distance to " CD  LYS A 119 " =    2.007
peak=    3.544 closest distance to " NE2 GLN A  77 " =    3.270
peak=    3.536 closest distance to " CZ3 TRP A 274 " =    4.524
peak=    3.529 closest distance to " NH2 ARG A 156 " =    1.078
peak=    3.528 closest distance to " O   HOH Z 158 " =    3.075
peak=    3.527 closest distance to " OD1 ASN A  69 " =    2.443
peak=    3.527 closest distance to " CA  ASP A 162 " =    0.914
peak=    3.521 closest distance to " OG BSER A 164 " =    2.339
peak=    3.518 closest distance to " O   HOH Z 193 " =    1.770
peak=    3.518 closest distance to " CB  LEU A 143 " =    1.228
peak=    3.514 closest distance to " O   HOH Z  61 " =    1.731
peak=    3.510 closest distance to " O   HOH Z 391 " =    2.892
peak=    3.508 closest distance to " CB  GLN A  89 " =    1.085
peak=    3.507 closest distance to " O   HOH Z 199 " =    1.674
peak=    3.506 closest distance to " CG2 VAL A 197 " =    1.043
peak=    3.506 closest distance to " CA  ALA A 291 " =    0.867
peak=    3.505 closest distance to " CA  PRO A  54 " =    1.389
peak=    3.502 closest distance to " CA  MET A 105 " =    0.993
peak=    3.501 closest distance to " CZ  PHE A  38 " =    1.120
peak=    3.498 closest distance to " O   HOH Z 227 " =    1.715
peak=    3.487 closest distance to " CA  VAL A  41 " =    0.712
peak=    3.486 closest distance to " O   PRO A 213 " =    1.409
peak=    3.486 closest distance to " CG2 ILE A 234 " =    1.094
peak=    3.482 closest distance to " CB  ASP A 298 " =    1.208
peak=    3.482 closest distance to " CB  SER A  62 " =    0.955
peak=    3.481 closest distance to " O   HOH Z 368 " =    3.382
peak=    3.474 closest distance to " CA  ASP A 140 " =    1.460
peak=    3.474 closest distance to " O   HOH Z 327 " =    2.180
peak=    3.466 closest distance to " CB  SER A   3 " =    1.360
peak=    3.465 closest distance to " O   ASN A 284 " =    1.767
peak=    3.464 closest distance to " CG  PRO A 213 " =    1.154
peak=    3.461 closest distance to " CB  GLN A  88 " =    1.197
peak=    3.456 closest distance to " O   HOH Z  69 " =    0.727
peak=    3.452 closest distance to " OE1 GLN A  55 " =    1.414
peak=    3.448 closest distance to " CA  GLU A 152 " =    0.912
peak=    3.447 closest distance to " O   HOH Z 172 " =    3.892
peak=    3.445 closest distance to " CB  ASN A 215 " =    1.250
peak=    3.441 closest distance to " O   HOH Z 290 " =    1.162
peak=    3.441 closest distance to " O   HOH Z  48 " =    1.652
peak=    3.437 closest distance to " CD1 ILE A 199 " =    1.014
peak=    3.436 closest distance to " CE3 TRP A  85 " =    1.113
peak=    3.429 closest distance to " O   HOH Z 250 " =    1.310
peak=    3.429 closest distance to " CB  THR A  31 " =    1.482
peak=    3.422 closest distance to " CB  ALA A 242 " =    0.867
peak=    3.417 closest distance to " O   HOH Z  44 " =    2.065
peak=    3.412 closest distance to " N   PHE A 130 " =    1.303
peak=    3.410 closest distance to " O   HOH Z 171 " =    4.067
peak=    3.404 closest distance to " CG  PHE A 204 " =    1.038
peak=    3.404 closest distance to " O   HOH Z 193 " =    1.920
peak=    3.401 closest distance to " CB  SER A  26 " =    1.795
peak=    3.399 closest distance to " CG1 ILE A  49 " =    1.605
peak=    3.395 closest distance to " O   HOH Z 407 " =    2.373
peak=    3.393 closest distance to " CA  ALA A 154 " =    1.108
peak=    3.389 closest distance to " CB  ASN A 173 " =    1.053
peak=    3.389 closest distance to " NH1 ARG A  14 " =    0.957
peak=    3.387 closest distance to " O   HOH Z 272 " =    1.849
peak=    3.384 closest distance to " CA  LEU A 282 " =    1.154
peak=    3.384 closest distance to " CE3 TRP A 150 " =    1.114
peak=    3.381 closest distance to " CA  GLY A 211 " =    1.424
peak=    3.378 closest distance to " O   GLN A  88 " =    1.671
peak=    3.378 closest distance to " O   ASN A  74 " =    1.350
peak=    3.374 closest distance to " O   HOH Z 163 " =    1.510
peak=    3.374 closest distance to " CA  LYS A 117 " =    1.218
peak=    3.369 closest distance to " CB  SER A 216 " =    0.844
peak=    3.367 closest distance to " O   THR A 220 " =    1.296
peak=    3.367 closest distance to " O   PHE A  61 " =    1.410
peak=    3.364 closest distance to " CE1 TYR A 186 " =    1.265
peak=    3.363 closest distance to " O   HOH Z 313 " =    1.516
peak=    3.360 closest distance to " ND1 HIS A  81 " =    1.826
peak=    3.359 closest distance to " CA  GLN A  94 " =    0.776
peak=    3.356 closest distance to " CG BARG A 275 " =    1.395
peak=    3.356 closest distance to " O   HOH Z 213 " =    1.884
peak=    3.355 closest distance to " CG AARG A 102 " =    1.109
peak=    3.355 closest distance to " CG2 VAL A 257 " =    0.781
peak=    3.355 closest distance to " O   HOH Z 258 " =    2.030
peak=    3.353 closest distance to " ND2 ASN A 249 " =    0.885
peak=    3.345 closest distance to " CB  PRO A 198 " =    1.056
peak=    3.337 closest distance to " O   LEU A 228 " =    1.935
peak=    3.332 closest distance to " CD1 LEU A 300 " =    1.111
peak=    3.331 closest distance to " O   HOH Z 403 " =    1.640
peak=    3.331 closest distance to " CA  ARG A 139 " =    1.151
peak=    3.330 closest distance to " CA  ALA A 100 " =    0.915
peak=    3.330 closest distance to " CB  SER A 288 " =    1.453
peak=    3.329 closest distance to " O   HOH Z 203 " =    1.695
peak=    3.327 closest distance to " O   HOH Z  83 " =    1.535
peak=    3.323 closest distance to " CB  PRO A  90 " =    1.254
peak=    3.323 closest distance to " O   ALA A 165 " =    1.440
peak=    3.323 closest distance to " O   HOH Z  88 " =    3.046
peak=    3.322 closest distance to " CG  MET A 185 " =    0.988
peak=    3.321 closest distance to " CD1 LEU A   5 " =    1.401
peak=    3.319 closest distance to " CB  LYS A 117 " =    1.207
peak=    3.318 closest distance to " CB  ALA A 299 " =    0.830
peak=    3.316 closest distance to " O   PHE A 192 " =    1.366
peak=    3.310 closest distance to " CA  ALA A  21 " =    1.136
peak=    3.308 closest distance to " CD  LYS A  76 " =    2.108
peak=    3.307 closest distance to " OG BSER A 134 " =    2.833
peak=    3.305 closest distance to " NZ  LYS A  48 " =    1.251
peak=    3.303 closest distance to " CB  ASN A 187 " =    1.112
peak=    3.303 closest distance to " O   HOH Z 299 " =    4.310
peak=    3.302 closest distance to " CB  MET A  40 " =    0.791
peak=    3.302 closest distance to " CB  TRP A 150 " =    1.409
peak=    3.298 closest distance to " O   HOH Z 393 " =    3.078
peak=    3.297 closest distance to " O   HOH Z 316 " =    3.153
peak=    3.295 closest distance to " CA  ASN A 127 " =    1.142
peak=    3.289 closest distance to " CA  ASP A 191 " =    1.186
peak=    3.283 closest distance to " O   HOH Z 417 " =    3.186
peak=    3.283 closest distance to " O   HOH Z  54 " =    1.487
peak=    3.281 closest distance to " O   HOH Z 298 " =    2.338
peak=    3.278 closest distance to " CB  PRO A 243 " =    1.453
peak=    3.276 closest distance to " N   CYS A 260 " =    0.811
peak=    3.274 closest distance to " CB  ARG A 138 " =    1.015
peak=    3.274 closest distance to " CD  PRO A  54 " =    0.840
peak=    3.273 closest distance to " CA  ASN A 217 " =    1.202
peak=    3.269 closest distance to " O   HOH Z 174 " =    2.365
peak=    3.262 closest distance to " O   MET A 105 " =    1.676
peak=    3.257 closest distance to " O   HOH Z 117 " =    1.922
peak=    3.257 closest distance to " O   HOH Z 361 " =    3.683
peak=    3.256 closest distance to " CD  ARG A 219 " =    1.062
peak=    3.256 closest distance to " OH  TYR A 116 " =    1.092
peak=    3.251 closest distance to " O   HOH Z 285 " =    2.140
peak=    3.250 closest distance to " O   HOH Z 145 " =    2.197
peak=    3.249 closest distance to " O   GLU A   2 " =    1.499
peak=    3.239 closest distance to " C   ALA A 299 " =    0.877
peak=    3.239 closest distance to " N   ALA A 256 " =    1.082
peak=    3.235 closest distance to " O   HOH Z 207 " =    1.196
peak=    3.234 closest distance to " O   HOH Z  44 " =    2.761
peak=    3.232 closest distance to " CG  GLN A  58 " =    0.990
peak=    3.226 closest distance to " O   HOH Z 343 " =    2.647
peak=    3.221 closest distance to " CB  ASN A 285 " =    0.970
peak=    3.220 closest distance to " CG  MET A 188 " =    0.815
peak=    3.217 closest distance to " CG2 ILE A  20 " =    1.316
peak=    3.215 closest distance to " CA  ALA A 158 " =    1.353
peak=    3.212 closest distance to " CB  PHE A 204 " =    1.016
peak=    3.209 closest distance to " NZ  LYS A  76 " =    1.398
peak=    3.207 closest distance to " CB  ASN A 110 " =    1.173
peak=    3.206 closest distance to " O   HOH Z 365 " =    2.832
peak=    3.206 closest distance to " O   HOH Z 146 " =    1.539
peak=    3.202 closest distance to " CB  ALA A 248 " =    1.298
peak=    3.198 closest distance to " O   HOH Z 238 " =    3.679
peak=    3.194 closest distance to " OH  TYR A 214 " =    1.249
peak=    3.188 closest distance to " O   HOH Z 368 " =    4.226
peak=    3.182 closest distance to " CZ  PHE A 192 " =    1.050
peak=    3.180 closest distance to " O   HOH Z 371 " =    2.784
peak=    3.179 closest distance to " CB  VAL A 268 " =    0.835
peak=    3.179 closest distance to " CD1 LEU A 101 " =    1.146
peak=    3.178 closest distance to " O   HOH Z 116 " =    1.831
peak=    3.177 closest distance to " OG  SER A 135 " =    1.322
peak=    3.177 closest distance to " O   HOH Z  40 " =    1.933
peak=    3.176 closest distance to " CG BARG A 102 " =    1.832
peak=    3.174 closest distance to " CZ3 TRP A  92 " =    1.417
peak=    3.173 closest distance to " CB  TYR A  30 " =    1.092
peak=    3.172 closest distance to " N   ASP A 162 " =    1.371
peak=    3.168 closest distance to " CB  LEU A 228 " =    1.289
peak=    3.168 closest distance to " O   ARG A  56 " =    3.121
peak=    3.167 closest distance to " O   HOH Z  47 " =    1.763
peak=    3.157 closest distance to " O   GLU A   2 " =    1.584
peak=    3.150 closest distance to " O   HOH Z 148 " =    2.038
peak=    3.147 closest distance to " O   HOH Z 344 " =    3.051
peak=    3.145 closest distance to " O   TYR A 116 " =    1.297
peak=    3.145 closest distance to " O   HOH Z 420 " =    5.670
peak=    3.138 closest distance to " CD  ARG A  66 " =    2.185
peak=    3.135 closest distance to " OG  SER A  62 " =    2.870
peak=    3.132 closest distance to " ND2AASN A 224 " =    0.863
peak=    3.129 closest distance to " O   HOH Z 437 " =    1.333
peak=    3.128 closest distance to " CB  ALA A 248 " =    1.110
peak=    3.128 closest distance to " NZ  LYS A 117 " =    1.332
peak=    3.124 closest distance to " O   HOH Z 261 " =    1.511
peak=    3.123 closest distance to " N   VAL A 126 " =    1.613
peak=    3.119 closest distance to " CG  GLN A  55 " =    2.609
peak=    3.117 closest distance to " O   HOH Z 394 " =    1.737
peak=    3.109 closest distance to " OG1 THR A 294 " =    2.456
peak=    3.107 closest distance to " O   HOH Z 366 " =    2.580
peak=    3.107 closest distance to " CG2 ILE A 120 " =    1.162
peak=    3.107 closest distance to " O   HOH Z 305 " =    3.591
peak=    3.098 closest distance to " CB  PHE A 283 " =    0.777
peak=    3.098 closest distance to " O   HOH Z 337 " =    1.862
peak=    3.094 closest distance to " CD ALYS A 290 " =    1.025
peak=    3.087 closest distance to " CB  ARG A  79 " =    0.863
peak=    3.076 closest distance to " CB  ALA A  43 " =    0.903
peak=    3.074 closest distance to " O   HOH Z 166 " =    3.674
peak=    3.070 closest distance to " CB  LEU A 300 " =    0.898
peak=    3.070 closest distance to " O   CYS A 168 " =    1.128
peak=    3.069 closest distance to " OD1 ASN A 217 " =    1.561
peak=    3.065 closest distance to " CD  ARG A 195 " =    0.984
peak=    3.053 closest distance to " CE1 HIS A 115 " =    0.943
peak=    3.053 closest distance to " O   HOH Z 329 " =    4.205
peak=    3.048 closest distance to " O   HOH Z 109 " =    2.773
peak=    3.047 closest distance to " OE2 GLU A   2 " =    1.981
peak=    3.036 closest distance to " O   HOH Z 124 " =    1.863

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.729 - 5.687
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 218 from: 218
   mapped sites are within: 0.729 - 5.687

peak=   -5.431 closest distance to " CG2 VAL A 230 " =    0.729
peak=   -4.619 closest distance to " CD  ARG A  14 " =    3.262
peak=   -4.499 closest distance to " CB  PRO A 243 " =    2.738
peak=   -4.436 closest distance to " O   HOH Z 211 " =    0.919
peak=   -4.408 closest distance to " CD  GLN A  58 " =    0.974
peak=   -4.382 closest distance to " O   HOH Z 193 " =    1.031
peak=   -4.351 closest distance to " CG1 VAL A 296 " =    1.122
peak=   -4.312 closest distance to " CA  ASP A 298 " =    1.117
peak=   -4.182 closest distance to " CD2 LEU A 237 " =    2.737
peak=   -4.153 closest distance to " O   HOH Z 394 " =    1.564
peak=   -4.143 closest distance to " CE2 TYR A  30 " =    2.684
peak=   -4.111 closest distance to " O   HOH Z 196 " =    2.383
peak=   -4.064 closest distance to " O   HOH Z 166 " =    1.719
peak=   -4.053 closest distance to " O   PRO A 198 " =    1.285
peak=   -3.997 closest distance to " CD  ARG A 156 " =    2.059
peak=   -3.984 closest distance to " O   SER A 271 " =    1.986
peak=   -3.975 closest distance to " C   HIS A 108 " =    1.201
peak=   -3.972 closest distance to " O   HOH Z 295 " =    1.612
peak=   -3.964 closest distance to " CG  GLU A 277 " =    1.272
peak=   -3.901 closest distance to " CD2 TYR A 293 " =    2.112
peak=   -3.901 closest distance to " O   HOH Z 351 " =    1.656
peak=   -3.899 closest distance to " CG1 VAL A 112 " =    2.655
peak=   -3.896 closest distance to " O   HOH Z 133 " =    0.958
peak=   -3.890 closest distance to " CE3 TRP A  70 " =    1.842
peak=   -3.857 closest distance to " O   HOH Z 411 " =    5.556
peak=   -3.838 closest distance to " O   VAL A  67 " =    2.715
peak=   -3.832 closest distance to " CD1 PHE A  59 " =    2.081
peak=   -3.814 closest distance to " CZ2 TRP A  92 " =    2.843
peak=   -3.809 closest distance to " O   HOH Z 290 " =    1.143
peak=   -3.796 closest distance to " CE3 TRP A 150 " =    2.256
peak=   -3.787 closest distance to " C   LEU A 143 " =    1.104
peak=   -3.777 closest distance to " O   HOH Z  37 " =    1.920
peak=   -3.776 closest distance to " O   VAL A  67 " =    2.823
peak=   -3.775 closest distance to " CD1 LEU A 101 " =    2.417
peak=   -3.755 closest distance to " CE2 PHE A  61 " =    2.628
peak=   -3.753 closest distance to " OE1 GLN A  88 " =    0.880
peak=   -3.747 closest distance to " CB  VAL A 230 " =    1.122
peak=   -3.729 closest distance to " O   HOH Z 110 " =    1.372
peak=   -3.719 closest distance to " CB  ALA A 248 " =    2.192
peak=   -3.717 closest distance to " O   HOH Z  10 " =    1.620
peak=   -3.717 closest distance to " O   HOH Z 238 " =    0.940
peak=   -3.715 closest distance to " CG  ARG A 269 " =    2.338
peak=   -3.694 closest distance to " OE1 GLN A 223 " =    2.225
peak=   -3.691 closest distance to " CG  GLN A 103 " =    2.517
peak=   -3.685 closest distance to " OXT GLY A 302 " =    3.046
peak=   -3.676 closest distance to " O   PRO A 163 " =    2.186
peak=   -3.676 closest distance to " CB  ALA A 248 " =    2.319
peak=   -3.675 closest distance to " O   HOH Z  73 " =    2.525
peak=   -3.669 closest distance to " O   HOH Z 210 " =    0.894
peak=   -3.661 closest distance to " CE2 TRP A  70 " =    2.182
peak=   -3.652 closest distance to " CD  PRO A 243 " =    1.941
peak=   -3.652 closest distance to " CB  ALA A 161 " =    2.611
peak=   -3.638 closest distance to " O   HOH Z  93 " =    2.269
peak=   -3.613 closest distance to " O   HOH Z 359 " =    2.848
peak=   -3.613 closest distance to " O   HOH Z 377 " =    2.038
peak=   -3.603 closest distance to " CA  GLY A 241 " =    2.407
peak=   -3.596 closest distance to " O   HOH Z 128 " =    2.579
peak=   -3.595 closest distance to " CH2 TRP A 179 " =    1.202
peak=   -3.595 closest distance to " O   HOH Z  52 " =    1.752
peak=   -3.586 closest distance to " N   THR A  52 " =    1.595
peak=   -3.584 closest distance to " O   ALA A  34 " =    2.647
peak=   -3.579 closest distance to " OD1 ASN A 148 " =    1.407
peak=   -3.567 closest distance to " O   HOH Z 231 " =    2.254
peak=   -3.554 closest distance to " CG2 VAL A 189 " =    2.060
peak=   -3.553 closest distance to " O   HOH Z 177 " =    1.856
peak=   -3.543 closest distance to " CB  ALA A 129 " =    2.488
peak=   -3.542 closest distance to " O   GLY A  17 " =    1.240
peak=   -3.539 closest distance to " NE2 GLN A 194 " =    1.951
peak=   -3.538 closest distance to " CD2 PHE A 225 " =    1.040
peak=   -3.534 closest distance to " O   HOH Z 285 " =    2.042
peak=   -3.533 closest distance to " CG2 THR A 178 " =    2.394
peak=   -3.531 closest distance to " O   HOH Z 136 " =    2.687
peak=   -3.517 closest distance to " NE  ARG A  79 " =    1.216
peak=   -3.515 closest distance to " O   HOH Z 149 " =    2.047
peak=   -3.513 closest distance to " N   ALA A  43 " =    2.650
peak=   -3.512 closest distance to " CB  TRP A  85 " =    2.636
peak=   -3.504 closest distance to " O   HOH Z 236 " =    1.399
peak=   -3.498 closest distance to " O   HOH Z 154 " =    1.323
peak=   -3.498 closest distance to " CG1 VAL A 112 " =    2.683
peak=   -3.498 closest distance to " O   ALA A 227 " =    1.345
peak=   -3.498 closest distance to " CB  HIS A  86 " =    1.204
peak=   -3.497 closest distance to " OG  SER A  97 " =    2.428
peak=   -3.481 closest distance to " O   HOH Z 216 " =    1.069
peak=   -3.479 closest distance to " CA  GLY A 241 " =    3.246
peak=   -3.477 closest distance to " O   TYR A 186 " =    1.848
peak=   -3.469 closest distance to " CE1 PHE A  59 " =    2.037
peak=   -3.461 closest distance to " CD2 PHE A  61 " =    2.094
peak=   -3.455 closest distance to " CG  ASP A 231 " =    0.863
peak=   -3.448 closest distance to " N   ALA A 226 " =    2.041
peak=   -3.447 closest distance to " OG BSER A 134 " =    1.431
peak=   -3.444 closest distance to " C   ALA A 158 " =    1.332
peak=   -3.444 closest distance to " O   HOH Z 131 " =    4.009
peak=   -3.437 closest distance to " CZ  PHE A  38 " =    2.541
peak=   -3.422 closest distance to " O   HOH Z  11 " =    1.821
peak=   -3.421 closest distance to " O   HOH Z 102 " =    1.669
peak=   -3.421 closest distance to " CG2 VAL A 296 " =    1.109
peak=   -3.419 closest distance to " CG  LEU A   5 " =    0.910
peak=   -3.417 closest distance to " CG  MET A 105 " =    1.026
peak=   -3.417 closest distance to " CE BMET A  47 " =    1.850
peak=   -3.411 closest distance to " CD1 ILE A 199 " =    2.505
peak=   -3.410 closest distance to " CG1 VAL A 125 " =    1.844
peak=   -3.408 closest distance to " C   MET A 188 " =    1.355
peak=   -3.401 closest distance to " NH2AARG A 275 " =    5.162
peak=   -3.400 closest distance to " CG  GLN A  11 " =    1.627
peak=   -3.392 closest distance to " NE2 GLN A  88 " =    1.016
peak=   -3.388 closest distance to " NE2 GLN A 103 " =    1.623
peak=   -3.387 closest distance to " NE  ARG A  66 " =    4.131
peak=   -3.386 closest distance to " CG  PRO A 243 " =    1.671
peak=   -3.385 closest distance to " O   SER A 210 " =    1.810
peak=   -3.383 closest distance to " CD  GLN A 223 " =    1.324
peak=   -3.383 closest distance to " CG  GLU A  53 " =    1.617
peak=   -3.383 closest distance to " O   HOH Z  68 " =    1.475
peak=   -3.381 closest distance to " O   HOH Z 368 " =    1.459
peak=   -3.376 closest distance to " CB  PHE A 192 " =    2.004
peak=   -3.373 closest distance to " O   HOH Z 106 " =    2.035
peak=   -3.360 closest distance to " CG  LYS A 166 " =    2.110
peak=   -3.357 closest distance to " O   HOH Z 115 " =    1.503
peak=   -3.355 closest distance to " O   HOH Z 340 " =    1.607
peak=   -3.351 closest distance to " CA  GLY A  98 " =    2.070
peak=   -3.349 closest distance to " CB  TYR A  15 " =    2.177
peak=   -3.348 closest distance to " CG  ARG A 219 " =    2.798
peak=   -3.347 closest distance to " O   GLY A 203 " =    2.420
peak=   -3.347 closest distance to " O   VAL A 189 " =    2.684
peak=   -3.343 closest distance to " O   HOH Z 111 " =    1.534
peak=   -3.343 closest distance to " O   HOH Z 251 " =    4.943
peak=   -3.341 closest distance to " CG1BVAL A  72 " =    2.524
peak=   -3.341 closest distance to " O   HOH Z 423 " =    2.148
peak=   -3.341 closest distance to " CB  ALA A  43 " =    2.655
peak=   -3.336 closest distance to " O   HOH Z 139 " =    5.411
peak=   -3.330 closest distance to " CB  ALA A  10 " =    2.249
peak=   -3.329 closest distance to " CZ  TYR A 169 " =    1.806
peak=   -3.327 closest distance to " NH2 ARG A 159 " =    2.356
peak=   -3.324 closest distance to " O   HOH Z 198 " =    1.898
peak=   -3.322 closest distance to " O   HOH Z 191 " =    5.687
peak=   -3.321 closest distance to " O   GLN A  94 " =    2.303
peak=   -3.318 closest distance to " O   HOH Z  17 " =    1.376
peak=   -3.317 closest distance to " CA  GLY A 203 " =    2.465
peak=   -3.316 closest distance to " O   HOH Z 357 " =    2.207
peak=   -3.314 closest distance to " O   HOH Z 128 " =    1.131
peak=   -3.314 closest distance to " CG2 VAL A 202 " =    2.784
peak=   -3.309 closest distance to " CG  TRP A 266 " =    1.776
peak=   -3.308 closest distance to " O   HOH Z  44 " =    0.771
peak=   -3.307 closest distance to " CB  ALA A 114 " =    2.502
peak=   -3.306 closest distance to " NH2 ARG A  36 " =    2.532
peak=   -3.305 closest distance to " O   GLY A  80 " =    2.658
peak=   -3.303 closest distance to " O   HOH Z 407 " =    3.084
peak=   -3.303 closest distance to " NH2 ARG A  79 " =    1.590
peak=   -3.301 closest distance to " O   ASP A  27 " =    2.016
peak=   -3.300 closest distance to " O   HOH Z  19 " =    2.202
peak=   -3.291 closest distance to " CD2 LEU A 167 " =    1.889
peak=   -3.288 closest distance to " O   HOH Z 411 " =    1.737
peak=   -3.287 closest distance to " CG2BVAL A  41 " =    1.802
peak=   -3.286 closest distance to " ND2 ASN A  45 " =    2.022
peak=   -3.286 closest distance to " CD  LYS A 289 " =    2.415
peak=   -3.280 closest distance to " O   HOH Z 176 " =    0.751
peak=   -3.279 closest distance to " OD1 ASP A 171 " =    1.692
peak=   -3.279 closest distance to " O   HOH Z 252 " =    3.676
peak=   -3.278 closest distance to " O   HOH Z 185 " =    2.465
peak=   -3.275 closest distance to " OE2 GLU A 277 " =    2.954
peak=   -3.274 closest distance to " ND2BASN A 224 " =    1.888
peak=   -3.270 closest distance to " O   HOH Z 431 " =    1.995
peak=   -3.269 closest distance to " O   HOH Z   9 " =    1.866
peak=   -3.267 closest distance to " O   HOH Z 434 " =    1.699
peak=   -3.263 closest distance to " O   SER A 276 " =    1.761
peak=   -3.248 closest distance to " CG  LEU A   5 " =    1.361
peak=   -3.244 closest distance to " CG1 VAL A 112 " =    2.792
peak=   -3.243 closest distance to " N   GLN A  77 " =    1.545
peak=   -3.240 closest distance to " O   HOH Z 435 " =    2.791
peak=   -3.239 closest distance to " CG2AVAL A  41 " =    2.779
peak=   -3.239 closest distance to " O   HOH Z 166 " =    1.665
peak=   -3.237 closest distance to " OD1 ASN A 173 " =    1.402
peak=   -3.234 closest distance to " N   PHE A  59 " =    2.035
peak=   -3.221 closest distance to " OD2 ASP A 171 " =    1.943
peak=   -3.216 closest distance to " O   HOH Z 265 " =    1.695
peak=   -3.214 closest distance to " O   HOH Z 175 " =    3.900
peak=   -3.211 closest distance to " ND2 ASN A  69 " =    2.070
peak=   -3.201 closest distance to " CD  GLU A 236 " =    1.112
peak=   -3.193 closest distance to " N   SER A 276 " =    1.440
peak=   -3.193 closest distance to " O   HOH Z  64 " =    1.609
peak=   -3.191 closest distance to " CD2 LEU A 237 " =    2.822
peak=   -3.190 closest distance to " O   HOH Z  60 " =    1.772
peak=   -3.185 closest distance to " O   HOH Z 174 " =    2.209
peak=   -3.183 closest distance to " CG  PRO A 163 " =    2.136
peak=   -3.182 closest distance to " O   HOH Z 234 " =    4.384
peak=   -3.173 closest distance to " O   HOH Z 140 " =    1.115
peak=   -3.167 closest distance to " CA  GLY A 133 " =    2.344
peak=   -3.165 closest distance to " O   HOH Z 100 " =    1.059
peak=   -3.165 closest distance to " OG  SER A 141 " =    1.683
peak=   -3.162 closest distance to " ND2 ASN A 249 " =    2.448
peak=   -3.160 closest distance to " CD  GLN A  88 " =    0.823
peak=   -3.159 closest distance to " CB  PRO A 163 " =    2.536
peak=   -3.159 closest distance to " SG BCYS A 201 " =    2.397
peak=   -3.158 closest distance to " CZ  ARG A 259 " =    0.919
peak=   -3.155 closest distance to " CD1 ILE A 239 " =    2.136
peak=   -3.148 closest distance to " O   HOH Z 426 " =    1.778
peak=   -3.148 closest distance to " C   VAL A 265 " =    0.864
peak=   -3.143 closest distance to " O   GLN A 240 " =    2.520
peak=   -3.136 closest distance to " O   HOH Z 145 " =    1.200
peak=   -3.135 closest distance to " O   ARG A  56 " =    3.330
peak=   -3.133 closest distance to " O   HOH Z 165 " =    1.860
peak=   -3.127 closest distance to " O   HOH Z 275 " =    1.592
peak=   -3.125 closest distance to " O   HOH Z  43 " =    1.582
peak=   -3.119 closest distance to " O   HOH Z 377 " =    1.267
peak=   -3.117 closest distance to " O   HOH Z 141 " =    1.978
peak=   -3.109 closest distance to " CA  SER A  62 " =    2.572
peak=   -3.104 closest distance to " CD2 HIS A 207 " =    2.215
peak=   -3.097 closest distance to " OH  TYR A 247 " =    1.903
peak=   -3.094 closest distance to " O   HOH Z  78 " =    1.983
peak=   -3.092 closest distance to " O   HOH Z 215 " =    1.303
peak=   -3.086 closest distance to " O   HOH Z   9 " =    3.126
peak=   -3.083 closest distance to " O   HOH Z 231 " =    1.799
peak=   -3.082 closest distance to " CH2 TRP A 150 " =    1.144
peak=   -3.082 closest distance to " CB  ASN A  69 " =    1.363
peak=   -3.067 closest distance to " CG1 VAL A  67 " =    2.999
peak=   -3.058 closest distance to " ND2 ASN A  45 " =    1.350
peak=   -3.048 closest distance to " O   HOH Z 171 " =    2.312
peak=   -3.032 closest distance to " CG2BVAL A  41 " =    1.276
peak=   -3.027 closest distance to " C   ASP A 270 " =    1.243

================= 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    :  0.4824 0.4734   6.283473e+00   6.267836e+00
   1_bss:  0.4739 0.4613   6.277072e+00   6.258369e+00
   1_xyz:  0.3904 0.4174   6.164808e+00   6.195747e+00
   1_adp:  0.3462 0.4005   6.083397e+00   6.163147e+00
   1_occ:  0.3458 0.4010   6.083021e+00   6.164679e+00
   2_bss:  0.3436 0.3981   6.084675e+00   6.164525e+00
   2_xyz:  0.2682 0.3244   5.879622e+00   6.014079e+00
   2_adp:  0.2452 0.3009   5.816543e+00   5.968387e+00
   2_occ:  0.2450 0.3011   5.816193e+00   5.968511e+00
   3_bss:  0.2442 0.3014   5.818276e+00   5.969895e+00
   3_xyz:  0.1842 0.2341   5.561998e+00   5.749634e+00
   3_adp:  0.1653 0.2205   5.483489e+00   5.696457e+00
   3_occ:  0.1652 0.2207   5.483991e+00   5.698066e+00
   4_bss:  0.1652 0.2200   5.482200e+00   5.695030e+00
   4_xyz:  0.1369 0.1884   5.323666e+00   5.556453e+00
   4_adp:  0.1319 0.1792   5.282377e+00   5.507003e+00
   4_occ:  0.1317 0.1790   5.281887e+00   5.506875e+00
   5_bss:  0.1317 0.1790   5.280353e+00   5.505246e+00
   5_xyz:  0.1236 0.1692   5.227760e+00   5.457396e+00
   5_adp:  0.1224 0.1678   5.219757e+00   5.450587e+00
   5_occ:  0.1222 0.1677   5.219010e+00   5.449899e+00
   5_bss:  0.1222 0.1677   5.218658e+00   5.449795e+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:  0.300  20.000   6.308   8.106  11.815   0.000   0.000   0.000
   1_xyz:  0.300  20.000   6.308   8.106  11.815   0.000   0.000   0.000
   1_adp:  0.300  20.000   6.308   8.106  11.815   0.000   0.000   0.000
   1_occ:  0.300  20.000   6.308   8.106  11.815   0.000   0.000   0.000
   2_bss:  0.325  54.305   3.104   4.768   7.945   0.000   0.000   0.000
   2_xyz:  0.325  54.305   3.104   4.768   7.945   0.000   0.000   0.000
   2_adp:  0.325  54.305   3.104   4.768   7.945   0.000   0.000   0.000
   2_occ:  0.325  54.305   3.104   4.768   7.945   0.000   0.000   0.000
   3_bss:  0.315  54.305   2.044   3.213   5.429   0.000   0.000   0.000
   3_xyz:  0.315  54.305   2.044   3.213   5.429   0.000   0.000   0.000
   3_adp:  0.315  54.305   2.044   3.213   5.429   0.000   0.000   0.000
   3_occ:  0.315  54.305   2.044   3.213   5.429   0.000   0.000   0.000
   4_bss:  0.337  80.072   1.802   2.600   4.455   0.000   0.000   0.000
   4_xyz:  0.337  80.072   1.802   2.600   4.455   0.000   0.000   0.000
   4_adp:  0.337  80.072   1.802   2.600   4.455   0.000   0.000   0.000
   4_occ:  0.337  80.072   1.802   2.600   4.455   0.000   0.000   0.000
   5_bss:  0.335  73.830   1.946   2.525   4.201   0.000   0.000   0.000
   5_xyz:  0.335  73.830   1.946   2.525   4.201   0.000   0.000   0.000
   5_adp:  0.335  73.830   1.946   2.525   4.201   0.000   0.000   0.000
   5_occ:  0.335  73.830   1.946   2.525   4.201   0.000   0.000   0.000
   5_bss:  0.324  67.714  -0.839  -0.388   1.227  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.218 0.4425  0.4988    66892.383
   1_bss:  54.766 0.4606  0.6737    65045.397
   1_xyz:  47.595 0.5493  0.7820    49660.421
   1_adp:  43.888 0.5955  0.8878    44412.863
   1_occ:  43.987 0.5943  0.8857    44629.026
   2_bss:  43.799 0.5967  0.7904    44484.015
   2_xyz:  34.231 0.7098  0.9266    28395.508
   2_adp:  31.367 0.7428  0.9508    24835.175
   2_occ:  31.390 0.7425  0.9501    24841.860
   3_bss:  31.345 0.7431  0.8953    24928.184
   3_xyz:  23.047 0.8313  0.9683    14137.663
   3_adp:  21.210 0.8501  0.9691    12400.246
   3_occ:  21.258 0.8496  0.9686    12425.957
   4_bss:  21.153 0.8505  0.9488    12292.761
   4_xyz:  17.850 0.8813  0.9664     9036.651
   4_adp:  16.573 0.8934  0.9631     8237.515
   4_occ:  16.565 0.8934  0.9631     8223.569
   5_bss:  16.542 0.8936  0.9614     8192.065
   5_xyz:  15.370 0.9040  0.9682     7319.914
   5_adp:  15.162 0.9060  0.9623     7234.822
   5_occ:  15.148 0.9061  0.9622     7224.147
   5_bss:  15.144 0.9061  0.9584     7218.883
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4601e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4601e+01
   1_xyz:   1.740  0.014  0.109 18.212  0.007  4.113   1.4775e-01
   1_adp:   1.740  0.014  0.109 18.212  0.007  4.113   1.4775e-01
   1_occ:   1.740  0.014  0.109 18.212  0.007  4.113   1.4775e-01
   2_bss:   1.740  0.014  0.109 18.212  0.007  4.113   1.4775e-01
   2_xyz:   1.225  0.009  0.079 16.217  0.004  4.114   8.4621e-02
   2_adp:   1.225  0.009  0.079 16.217  0.004  4.114   8.4621e-02
   2_occ:   1.225  0.009  0.079 16.217  0.004  4.114   8.4621e-02
   3_bss:   1.225  0.009  0.079 16.217  0.004  4.114   8.4621e-02
   3_xyz:   1.172  0.009  0.085 15.944  0.004  4.137   7.5488e-02
   3_adp:   1.172  0.009  0.085 15.944  0.004  4.137   7.5488e-02
   3_occ:   1.172  0.009  0.085 15.944  0.004  4.137   7.5488e-02
   4_bss:   1.172  0.009  0.085 15.944  0.004  4.137   7.5488e-02
   4_xyz:   1.127  0.010  0.085 15.620  0.004  4.117   7.7146e-02
   4_adp:   1.127  0.010  0.085 15.620  0.004  4.117   7.7146e-02
   4_occ:   1.127  0.010  0.085 15.620  0.004  4.117   7.7146e-02
   5_bss:   1.127  0.010  0.085 15.620  0.004  4.117   7.7146e-02
   5_xyz:   1.111  0.010  0.087 15.369  0.004  4.125   7.4018e-02
   5_adp:   1.111  0.010  0.087 15.369  0.004  4.125   7.4018e-02
   5_occ:   1.111  0.010  0.087 15.369  0.004  4.125   7.4018e-02
   5_bss:   1.111  0.010  0.087 15.369  0.004  4.125   7.4018e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0787e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0787e+00
   1_xyz:  14.679  0.173  0.450 87.235  0.044  2.217   1.0988e-01
   1_adp:  14.679  0.173  0.450 87.235  0.044  2.217   1.0988e-01
   1_occ:  14.679  0.173  0.450 87.235  0.044  2.217   1.0988e-01
   2_bss:  14.679  0.173  0.450 87.235  0.044  2.217   1.0988e-01
   2_xyz:   8.493  0.082  0.266 86.739  0.028  2.070   1.0103e-01
   2_adp:   8.493  0.082  0.266 86.739  0.028  2.070   1.0103e-01
   2_occ:   8.493  0.082  0.266 86.739  0.028  2.070   1.0103e-01
   3_bss:   8.493  0.082  0.266 86.739  0.028  2.070   1.0103e-01
   3_xyz:   8.078  0.081  0.308 89.313  0.050  2.243   5.5733e-02
   3_adp:   8.078  0.081  0.308 89.313  0.050  2.243   5.5733e-02
   3_occ:   8.078  0.081  0.308 89.313  0.050  2.243   5.5733e-02
   4_bss:   8.078  0.081  0.308 89.313  0.050  2.243   5.5733e-02
   4_xyz:   7.691  0.049  0.438 85.997  0.037  2.358   5.1814e-02
   4_adp:   7.691  0.049  0.438 85.997  0.037  2.358   5.1814e-02
   4_occ:   7.691  0.049  0.438 85.997  0.037  2.358   5.1814e-02
   5_bss:   7.691  0.049  0.438 85.997  0.037  2.358   5.1814e-02
   5_xyz:   7.344  0.054  0.454 81.290  0.035  2.293   4.6690e-02
   5_adp:   7.344  0.054  0.454 81.290  0.035  2.293   4.6690e-02
   5_occ:   7.344  0.054  0.454 81.290  0.035  2.293   4.6690e-02
   5_bss:   7.344  0.054  0.454 81.290  0.035  2.293   4.6690e-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:  72.49   0.00  13.41  65.04   0.00  11.09  72.49   0.00  26.08
   1_occ:  72.49   0.00  13.41  65.04   0.00  11.09  72.49   0.00  26.08
   2_bss:  72.49   0.00  13.41  65.04   0.00  11.09  72.49   0.00  26.08
   2_xyz:  72.49   0.00  13.41  65.04   0.00  11.09  72.49   0.00  26.08
   2_adp:  76.83   0.00  13.10  59.86   0.00   9.60  76.83   0.00  32.19
   2_occ:  76.83   0.00  13.10  59.86   0.00   9.60  76.83   0.00  32.19
   3_bss:  76.83   0.00  13.10  59.86   0.00   9.60  76.83   0.00  32.19
   3_xyz:  76.83   0.00  13.10  59.86   0.00   9.60  76.83   0.00  32.19
   3_adp: 101.40   0.00  14.48  89.23   0.00   9.47 101.40   0.97  41.77
   3_occ: 101.40   0.00  14.48  89.23   0.00   9.47 101.40   0.97  41.77
   4_bss: 101.40   0.00  14.48  89.23   0.00   9.47 101.40   0.97  41.77
   4_xyz: 101.40   0.00  14.48  89.23   0.00   9.47 101.40   0.97  41.77
   4_adp:  98.21   0.00  13.48  82.10   0.00   8.73  98.21   1.38  39.30
   4_occ:  98.21   0.00  13.48  82.10   0.00   8.73  98.21   1.38  39.30
   5_bss:  98.21   0.00  13.48  82.10   0.00   8.73  98.21   1.38  39.30
   5_xyz:  98.21   0.00  13.48  82.10   0.00   8.73  98.21   1.38  39.30
   5_adp:  96.36   0.00  13.03  82.10   0.00   8.51  96.36   1.30  37.68
   5_occ:  96.36   0.00  13.03  82.10   0.00   8.51  96.36   1.30  37.68
   5_bss:  99.13   2.78  15.81  84.87   2.78  11.28  99.13   4.07  40.46
------------------------------------------------------------------------
 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:    1.281    0.017    0.415
   1_adp:    1.281    0.017    0.415
   1_occ:    1.281    0.017    0.415
   2_bss:    1.281    0.017    0.415
   2_xyz:    1.972    0.043    0.581
   2_adp:    1.972    0.043    0.581
   2_occ:    1.972    0.043    0.581
   3_bss:    1.972    0.043    0.581
   3_xyz:    1.803    0.064    0.662
   3_adp:    1.803    0.064    0.662
   3_occ:    1.803    0.064    0.662
   4_bss:    1.803    0.064    0.662
   4_xyz:    2.087    0.057    0.721
   4_adp:    2.087    0.057    0.721
   4_occ:    2.087    0.057    0.721
   5_bss:    2.087    0.057    0.721
   5_xyz:    2.143    0.027    0.741
   5_adp:    2.143    0.027    0.741
   5_occ:    2.143    0.027    0.741
   5_bss:    2.143    0.027    0.741
------------------------------------------------------------------------

CPU time actual refinement: 354.96


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_813/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_813/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_813/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_813/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_813/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 354.82 
  Macro-tasks:
    bulk solvent and scale       = 51.26  
    individual site refinement   = 145.38 
    weights calculation          = 31.64  
    collect and process          = 6.60   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 234.97 
  Micro-tasks:
    mask                            = 2.21   
    f_calc                          = 108.90 
    alpha_beta                      = 8.65   
    target                          = 1.23   
    gradients_wrt_atomic_parameters = 115.39 
    fmodel                         = 8.77   
    r_factors                      = 0.23   
    phase_errors                   = 11.24  
    foms                           = 0.20   
    TOTAL for micro-tasks          = 256.82 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.883 micro seconds
Total CPU time: 6.13 minutes
from_scatterers_fft:    679 calls, 108.41 s
gradients_fft:          624 calls, 103.37 s

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

# Date 2008-01-16 Time 02:28:59 PST -0800 (1200479339.60 s)
Start R-work = 0.4824, R-free = 0.4734 (no bulk solvent and anisotropic scale)
Final R-work = 0.1390, R-free = 0.1828 (no bulk solvent and anisotropic scale)

Start R-work = 0.4739, R-free = 0.4613
Final R-work = 0.1222, R-free = 0.1677