# Date 2008-01-16 Time 02:02:40 PST -0800 (1200477760.58 s)
#phil __OFF__

Command line arguments: "../668.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14110
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 668

-------------------------------------------------------------------------------
  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: (70.25, 46.93, 87.6859, 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: 3.24, per 1000 atoms: 1.15


================================== 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: (70.25, 46.93, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 2.00025
Completeness in resolution range: 0.971966
Completeness with d_max=infinity: 0.968937

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0540
                             d_min =   2.0003

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: (70.25, 46.93, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 2.00025
Completeness in resolution range: 0.971966
Completeness with d_max=infinity: 0.968937

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0544 -  4.2795 [2124/2148]  1909   215  10.1%
  bin  2:  4.2795 -  3.4098 [2032/2052]  1833   199   9.8%
  bin  3:  3.4098 -  2.9825 [2010/2029]  1809   201  10.0%
  bin  4:  2.9825 -  2.7116 [1967/1997]  1766   201  10.2%
  bin  5:  2.7116 -  2.5182 [1992/2011]  1793   199  10.0%
  bin  6:  2.5182 -  2.3703 [1966/1991]  1771   195   9.9%
  bin  7:  2.3703 -  2.2520 [1947/1975]  1752   195  10.0%
  bin  8:  2.2520 -  2.1543 [1959/1995]  1764   195  10.0%
  bin  9:  2.1543 -  2.0716 [1930/1972]  1735   195  10.1%
  bin 10:  2.0716 -  2.0003 [1662/1984]  1498   164   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_668/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 15
        2.42 -     3.04: 2181
        3.04 -     3.66: 4603
        3.66 -     4.28: 8963
        4.28 -     4.90: 12312
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.845 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.956 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  2.032 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.104 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28069 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_668/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_668/model_refine_001.geo

CPU time processing inputs: 9.18


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.93 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4332   r_free= 0.4163   ksol= 0.00   Bsol= 0.00   scale= 0.817    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.227368                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7729 0.99   1382  152 0.3611 0.3300      6.5339       6.421|
|  2:  4.7729 -  3.8086 0.99   1312  151 0.3200 0.3443      6.6251      6.7329|
|  3:  3.8086 -  3.3331 0.99   1299  141 0.3802 0.3444      6.5752      6.5327|
|  4:  3.3331 -  3.0311 0.99   1295  141 0.4164 0.3858      6.4629      6.3596|
|  5:  3.0311 -  2.8153 0.99   1268  144 0.4456 0.4569      6.3135      6.3217|
|  6:  2.8153 -  2.6503 0.99   1288  144 0.4524 0.4974      6.2289      6.1908|
|  7:  2.6503 -  2.5182 0.99   1266  142 0.4765 0.4830       6.207      6.1726|
|  8:  2.5182 -  2.4090 0.98   1271  137 0.4878 0.4380      6.1584      6.1183|
|  9:  2.4090 -  2.3166 0.98   1249  142 0.4737 0.4709      6.0838      6.1063|
| 10:  2.3166 -  2.2370 1.00   1273  139 0.5054 0.4180      6.1178      6.0023|
| 11:  2.2370 -  2.1672 0.97   1249  138 0.4831 0.4822      6.0142       6.032|
| 12:  2.1672 -  2.1054 0.98   1251  139 0.5102 0.4572      5.9688      5.9814|
| 13:  2.1054 -  2.0502 0.99   1251  139 0.4903 0.4844      5.8853        5.84|
| 14:  2.0502 -  2.0003 0.77    976  110 0.4995 0.4380      5.8546      5.7063|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0544 -  4.7729  1382   152  0.75  29.49   0.81     0.77      53884.82|
|  2:  4.7729 -  3.8086  1312   151  0.78  27.88   0.91     0.83      71524.31|
|  3:  3.8086 -  3.3331  1299   141  0.71  34.24   0.87     0.79      75476.65|
|  4:  3.3331 -  3.0311  1295   141  0.65  39.88   0.82     0.70      68823.54|
|  5:  3.0311 -  2.8153  1268   144  0.56  47.54   0.78     0.62      61867.67|
|  6:  2.8153 -  2.6503  1288   144  0.52  50.81   0.75     0.57      57723.24|
|  7:  2.6503 -  2.5182  1266   142  0.49  52.58   0.75     0.56      53361.63|
|  8:  2.5182 -  2.4090  1271   137  0.50  52.04   0.75     0.57      46813.01|
|  9:  2.4090 -  2.3166  1249   142  0.54  49.26   0.75     0.60      40561.87|
| 10:  2.3166 -  2.2370  1273   139  0.53  49.91   0.76     0.61      35992.75|
| 11:  2.2370 -  2.1672  1249   138  0.52  50.48   0.76     0.60      34090.59|
| 12:  2.1672 -  2.1054  1251   139  0.48  53.49   0.77     0.58      32830.07|
| 13:  2.1054 -  2.0502  1251   139  0.49  53.48   0.75     0.56      28810.24|
| 14:  2.0502 -  2.0003   976   110  0.52  50.61   0.74     0.54      22591.10|
|alpha:            min =        0.54 max =            0.83 mean =         0.64|
|beta:             min =    22591.10 max =        75476.65 mean =     49549.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.58|
|phase err.(work): min =        0.00 max =           89.97 mean =        45.56|
|phase err.(test): min =        0.00 max =           89.86 mean =        45.71|
|-----------------------------------------------------------------------------|

============================== 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 = 7.366047              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.460   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.593614              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.522   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      164 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      682 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1479 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2590 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3903 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5039 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6512 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7685 |
|-----------------------------------------------------------------------------|
|-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 |       54.084 |
| 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 |       1.685 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.057)------------------------------------------|
|    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 = 12.057)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4418   r_free= 0.4188   ksol= 0.00   Bsol= 0.00   scale= 0.786    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.235278                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4244   r_free= 0.4050   ksol= 0.34   Bsol= 20.00   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.02,7.72,10.85,0.00,0.00,0.00); trace/3= 8.53                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.221265                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.842135              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.092   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.580009              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.084   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4244      final r-factor (work) = 0.3140          |
| start r-factor (free) = 0.4050      final r-factor (free) = 0.3310          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 75.4337 = 6.84 * 0.50 * 6.2406 + 1.00 * 54.0842                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.8441 = 6.84 * 0.50 * 6.0581 + 1.00 * 0.1191                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3140      final r-factor (work) = 0.2490          |
| start r-factor (free) = 0.3310      final r-factor (free) = 0.2823          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5285 = 0.58 * 1.00 * 6.0581 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4164 = 0.58 * 1.00 * 5.8706 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.057)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    61.26   10.78    None  None   None       |
|    all(noH): 2823   0      0.00    61.26   10.78    None  None   None       |
|    Sol.    : 438    0      0.00    61.26   27.76    None  None   None       |
|    Mac.    : 2385   0      0.00    53.77   7.66     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 -   6.126: 1268   |   5:    30.630 -  36.756:   85        |
|      1:     6.126 -  12.252:  750   |   6:    36.756 -  42.882:   64        |
|      2:    12.252 -  18.378:  309   |   7:    42.882 -  49.008:   39        |
|      3:    18.378 -  24.504:  127   |   8:    49.008 -  55.134:   20        |
|      4:    24.504 -  30.630:  153   |   9:    55.134 -  61.260:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2490 r_free = 0.2823             target_work(ml) = 5.808         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2483 r_free = 0.2830             target_work(ml) = 5.806         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2483   r_free= 0.2830   ksol= 0.34   Bsol= 20.00   scale= 1.093   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.02,7.72,10.85,0.00,0.00,0.00); trace/3= 8.53                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.806117                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2428   r_free= 0.2776   ksol= 0.33   Bsol= 50.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.68,4.07,7.10,0.00,0.00,0.00); trace/3= 4.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.804015                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.519956              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.431   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.326402              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.551  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2428      final r-factor (work) = 0.1655          |
| start r-factor (free) = 0.2776      final r-factor (free) = 0.2059          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4699 = 3.52 * 0.50 * 5.8814 + 1.00 * 0.1188                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9634 = 3.52 * 0.50 * 5.6239 + 1.00 * 0.0654                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1655      final r-factor (work) = 0.1501          |
| start r-factor (free) = 0.2059      final r-factor (free) = 0.1919          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8471 = 0.33 * 1.00 * 5.6239 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7751 = 0.33 * 1.00 * 5.4062 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.057)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    61.55   11.05    None  None   None       |
|    all(noH): 2823   0      0.00    61.55   11.05    None  None   None       |
|    Sol.    : 438    0      0.58    61.55   31.18    None  None   None       |
|    Mac.    : 2385   0      0.00    55.75   7.35     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 -   6.155: 1370   |   5:    30.774 -  36.929:  109        |
|      1:     6.155 -  12.310:  708   |   6:    36.929 -  43.084:  103        |
|      2:    12.310 -  18.464:  228   |   7:    43.084 -  49.238:   48        |
|      3:    18.464 -  24.619:  123   |   8:    49.238 -  55.393:   26        |
|      4:    24.619 -  30.774:   99   |   9:    55.393 -  61.548:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1501 r_free = 0.1919             target_work(ml) = 5.375         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1500 r_free = 0.1918             target_work(ml) = 5.374         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1500   r_free= 0.1918   ksol= 0.33   Bsol= 50.00   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.68,4.07,7.10,0.00,0.00,0.00); trace/3= 4.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.374310                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1493   r_free= 0.1917   ksol= 0.33   Bsol= 50.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.92,3.42,5.19,0.00,0.00,0.00); trace/3= 3.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.373878                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.691493              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.353  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.047912              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.638  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1493      final r-factor (work) = 0.1289          |
| start r-factor (free) = 0.1917      final r-factor (free) = 0.1702          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6434 = 1.69 * 0.50 * 5.4129 + 1.00 * 0.0654                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5471 = 1.69 * 0.50 * 5.3057 + 1.00 * 0.0598                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1289      final r-factor (work) = 0.1235          |
| start r-factor (free) = 0.1702      final r-factor (free) = 0.1673          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5704 = 1.05 * 1.00 * 5.3057 + 1.00 * 0.0104                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4914 = 1.05 * 1.00 * 5.2271 + 1.00 * 0.0139                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.057)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.69   11.72    None  None   None       |
|    all(noH): 2823   0      0.00    69.69   11.72    None  None   None       |
|    Sol.    : 438    0      0.20    68.91   34.82    None  None   None       |
|    Mac.    : 2385   0      0.00    69.69   7.48     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.969: 1522   |   5:    34.843 -  41.811:   86        |
|      1:     6.969 -  13.937:  633   |   6:    41.811 -  48.780:   80        |
|      2:    13.937 -  20.906:  191   |   7:    48.780 -  55.749:   78        |
|      3:    20.906 -  27.874:   99   |   8:    55.749 -  62.717:   27        |
|      4:    27.874 -  34.843:   96   |   9:    62.717 -  69.686:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1235 r_free = 0.1673             target_work(ml) = 5.223         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1234 r_free = 0.1673             target_work(ml) = 5.223         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1234   r_free= 0.1673   ksol= 0.33   Bsol= 50.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.92,3.42,5.19,0.00,0.00,0.00); trace/3= 3.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.222824                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1234   r_free= 0.1674   ksol= 0.32   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.89,3.31,4.87,0.00,0.00,0.00); trace/3= 3.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.222469                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.659745              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.067  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.842347              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.686  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1234      final r-factor (work) = 0.1181          |
| start r-factor (free) = 0.1674      final r-factor (free) = 0.1631          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3970 = 1.66 * 0.50 * 5.2263 + 1.00 * 0.0598                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3751 = 1.66 * 0.50 * 5.2029 + 1.00 * 0.0574                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1181      final r-factor (work) = 0.1173          |
| start r-factor (free) = 0.1631      final r-factor (free) = 0.1623          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3965 = 0.84 * 1.00 * 5.2029 + 1.00 * 0.0139                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4092 = 0.84 * 1.00 * 5.1874 + 1.00 * 0.0396                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.057)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.84   11.68    None  None   None       |
|    all(noH): 2823   0      0.00    72.84   11.68    None  None   None       |
|    Sol.    : 438    0      0.00    70.24   34.76    None  None   None       |
|    Mac.    : 2385   0      0.00    72.84   7.44     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 -   7.284: 1598   |   5:    36.422 -  43.706:   80        |
|      1:     7.284 -  14.569:  593   |   6:    43.706 -  50.990:   83        |
|      2:    14.569 -  21.853:  174   |   7:    50.990 -  58.274:   62        |
|      3:    21.853 -  29.137:  104   |   8:    58.274 -  65.559:   19        |
|      4:    29.137 -  36.422:  101   |   9:    65.559 -  72.843:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1173 r_free = 0.1623             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1171 r_free = 0.1623             target_work(ml) = 5.184         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1171   r_free= 0.1623   ksol= 0.32   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.89,3.31,4.87,0.00,0.00,0.00); trace/3= 3.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.184329                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1172   r_free= 0.1617   ksol= 0.33   Bsol= 54.01   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.95,3.33,4.85,0.00,0.00,0.00); trace/3= 3.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.183572                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.525688              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.529  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.931556              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.390   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1172      final r-factor (work) = 0.1126          |
| start r-factor (free) = 0.1617      final r-factor (free) = 0.1597          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6078 = 2.53 * 0.50 * 5.1870 + 1.00 * 0.0574                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5936 = 2.53 * 0.50 * 5.1651 + 1.00 * 0.0708                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1597      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.9936 = 1.93 * 1.00 * 5.1651 + 1.00 * 0.0169                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.9721 = 1.93 * 1.00 * 5.1550 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.057)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.72   11.72    None  None   None       |
|    all(noH): 2823   0      0.00    83.72   11.72    None  None   None       |
|    Sol.    : 438    0      0.00    77.52   35.24    None  None   None       |
|    Mac.    : 2385   0      0.00    83.72   7.40     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.373: 1753   |   5:    41.862 -  50.235:   93        |
|      1:     8.373 -  16.745:  506   |   6:    50.235 -  58.607:   60        |
|      2:    16.745 -  25.117:  151   |   7:    58.607 -  66.980:   30        |
|      3:    25.117 -  33.490:  107   |   8:    66.980 -  75.352:   15        |
|      4:    33.490 -  41.862:  104   |   9:    75.352 -  83.725:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1121 r_free = 0.1596             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1121 r_free = 0.1596             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1596   ksol= 0.33   Bsol= 54.01   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.95,3.33,4.85,0.00,0.00,0.00); trace/3= 3.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.155404                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7729 0.99   1382  152 0.1003 0.1307      5.3948       5.526|
|  2:  4.7729 -  3.8086 0.99   1312  151 0.0840 0.1083       5.429      5.6271|
|  3:  3.8086 -  3.3331 0.99   1299  141 0.1045 0.1451      5.4734      5.8204|
|  4:  3.3331 -  3.0311 0.99   1295  141 0.1185 0.1655      5.4437        5.62|
|  5:  3.0311 -  2.8153 0.99   1268  144 0.1306 0.1699      5.3321      5.5483|
|  6:  2.8153 -  2.6503 0.99   1288  144 0.1207 0.2082      5.2192      5.5565|
|  7:  2.6503 -  2.5182 0.99   1266  142 0.1284 0.1603      5.1907      5.3419|
|  8:  2.5182 -  2.4090 0.98   1271  137 0.1189 0.1723      5.1103      5.3717|
|  9:  2.4090 -  2.3166 0.98   1249  142 0.1187 0.1873      5.0602      5.3317|
| 10:  2.3166 -  2.2370 1.00   1273  139 0.1149 0.1698      4.9918      5.2514|
| 11:  2.2370 -  2.1672 0.97   1249  138 0.1149 0.1755      4.9711      5.2314|
| 12:  2.1672 -  2.1054 0.98   1251  139 0.1171 0.1820      4.9086       5.295|
| 13:  2.1054 -  2.0502 0.99   1251  139 0.1129 0.1751      4.8135      5.0623|
| 14:  2.0502 -  2.0003 0.77    976  110 0.1025 0.1665      4.6677      4.9375|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0544 -  4.7729  1382   152  0.94   9.47   0.97     0.95       7549.75|
|  2:  4.7729 -  3.8086  1312   151  0.95   7.90   1.01     0.99       8991.92|
|  3:  3.8086 -  3.3331  1299   141  0.94  11.00   1.03     1.02      10264.48|
|  4:  3.3331 -  3.0311  1295   141  0.92  13.16   1.00     0.98      10115.78|
|  5:  3.0311 -  2.8153  1268   144  0.90  15.64   1.00     0.97       8413.89|
|  6:  2.8153 -  2.6503  1288   144  0.90  16.29   0.98     0.95       7340.66|
|  7:  2.6503 -  2.5182  1266   142  0.90  16.01   0.98     0.94       6482.07|
|  8:  2.5182 -  2.4090  1271   137  0.91  15.53   0.99     0.96       5729.98|
|  9:  2.4090 -  2.3166  1249   142  0.90  16.04   1.00     0.97       5462.31|
| 10:  2.3166 -  2.2370  1273   139  0.90  16.34   0.99     0.94       4682.54|
| 11:  2.2370 -  2.1672  1249   138  0.90  16.78   0.99     0.96       4809.17|
| 12:  2.1672 -  2.1054  1251   139  0.90  16.30   1.00     0.98       4218.89|
| 13:  2.1054 -  2.0502  1251   139  0.90  15.99   0.98     0.96       3477.36|
| 14:  2.0502 -  2.0003   976   110  0.92  14.25   0.97     0.94       2560.45|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2560.45 max =        10264.48 mean =      6533.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.28|
|phase err.(test): min =        0.00 max =           89.85 mean =        13.78|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1595   ksol= 0.33   Bsol= 57.87   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.74,-0.39,1.13,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.155471                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1595   ksol= 0.33   Bsol= 57.87   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.74,-0.39,1.13,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.155471                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7729 0.99   1382  152 0.1003 0.1309      5.3953      5.5268|
|  2:  4.7729 -  3.8086 0.99   1312  151 0.0840 0.1084      5.4294      5.6271|
|  3:  3.8086 -  3.3331 0.99   1299  141 0.1046 0.1451      5.4735      5.8208|
|  4:  3.3331 -  3.0311 0.99   1295  141 0.1185 0.1655      5.4437      5.6201|
|  5:  3.0311 -  2.8153 0.99   1268  144 0.1305 0.1699       5.332      5.5481|
|  6:  2.8153 -  2.6503 0.99   1288  144 0.1207 0.2082      5.2191      5.5565|
|  7:  2.6503 -  2.5182 0.99   1266  142 0.1284 0.1604      5.1908      5.3421|
|  8:  2.5182 -  2.4090 0.98   1271  137 0.1190 0.1723      5.1104      5.3716|
|  9:  2.4090 -  2.3166 0.98   1249  142 0.1186 0.1873      5.0602      5.3317|
| 10:  2.3166 -  2.2370 1.00   1273  139 0.1149 0.1697      4.9918      5.2515|
| 11:  2.2370 -  2.1672 0.97   1249  138 0.1149 0.1754       4.971      5.2311|
| 12:  2.1672 -  2.1054 0.98   1251  139 0.1171 0.1819      4.9084      5.2947|
| 13:  2.1054 -  2.0502 0.99   1251  139 0.1129 0.1751      4.8135      5.0625|
| 14:  2.0502 -  2.0003 0.77    976  110 0.1025 0.1664      4.6677      4.9372|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0544 -  4.7729  1382   152  0.94   9.48   0.97     0.95       7561.00|
|  2:  4.7729 -  3.8086  1312   151  0.95   7.90   1.01     1.00       8999.95|
|  3:  3.8086 -  3.3331  1299   141  0.94  11.00   1.03     1.02      10268.05|
|  4:  3.3331 -  3.0311  1295   141  0.92  13.16   1.01     0.99      10115.31|
|  5:  3.0311 -  2.8153  1268   144  0.90  15.63   1.00     0.97       8412.27|
|  6:  2.8153 -  2.6503  1288   144  0.90  16.29   0.99     0.96       7339.27|
|  7:  2.6503 -  2.5182  1266   142  0.90  16.01   0.98     0.95       6483.10|
|  8:  2.5182 -  2.4090  1271   137  0.91  15.53   0.99     0.97       5731.18|
|  9:  2.4090 -  2.3166  1249   142  0.90  16.05   1.01     0.98       5464.31|
| 10:  2.3166 -  2.2370  1273   139  0.90  16.34   1.00     0.95       4681.64|
| 11:  2.2370 -  2.1672  1249   138  0.90  16.78   1.00     0.96       4808.13|
| 12:  2.1672 -  2.1054  1251   139  0.90  16.29   1.01     0.99       4217.40|
| 13:  2.1054 -  2.0502  1251   139  0.90  15.99   0.99     0.97       3476.46|
| 14:  2.0502 -  2.0003   976   110  0.92  14.26   0.98     0.94       2559.99|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2559.99 max =        10268.05 mean =      6535.45|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.28|
|phase err.(test): min =        0.00 max =           89.85 mean =        13.78|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.057)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.85    87.58   15.57    None  None   None       |
|    all(noH): 2823   0      3.85    87.58   15.57    None  None   None       |
|    Sol.    : 438    0      3.85    81.37   39.09    None  None   None       |
|    Mac.    : 2385   0      3.85    87.58   11.25    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.854 -  12.227: 1753   |   5:    45.717 -  54.089:   93        |
|      1:    12.227 -  20.599:  506   |   6:    54.089 -  62.461:   60        |
|      2:    20.599 -  28.972:  151   |   7:    62.461 -  70.834:   30        |
|      3:    28.972 -  37.344:  107   |   8:    70.834 -  79.206:   15        |
|      4:    37.344 -  45.717:  104   |   9:    79.206 -  87.579:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 313         
Filter by distance & map next to the model:
   mapped sites are within: 0.201 - 4.584
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 304 from: 313
   mapped sites are within: 0.706 - 4.584

peak=   11.080 closest distance to " CB  VAL A 230 " =    1.453
peak=    7.772 closest distance to " CG2 VAL A 296 " =    1.208
peak=    6.416 closest distance to " CG  LEU A   5 " =    1.192
peak=    6.136 closest distance to " NH2 ARG A  56 " =    2.195
peak=    5.730 closest distance to " CG  LEU A 228 " =    1.187
peak=    5.583 closest distance to " CG  PRO A  54 " =    1.325
peak=    5.365 closest distance to " NE2 GLN A  11 " =    1.136
peak=    5.309 closest distance to " CB  GLN A 223 " =    1.450
peak=    5.278 closest distance to " O   HOH Z 142 " =    1.883
peak=    5.213 closest distance to " CB  GLN A 183 " =    1.290
peak=    5.149 closest distance to " CD2 LEU A   5 " =    1.099
peak=    4.990 closest distance to " O   HOH Z 232 " =    2.325
peak=    4.859 closest distance to " O   HOH Z 265 " =    2.259
peak=    4.811 closest distance to " CB  PRO A  54 " =    0.963
peak=    4.565 closest distance to " O   SER A  87 " =    2.334
peak=    4.546 closest distance to " CB  ARG A 275 " =    0.934
peak=    4.521 closest distance to " CB  SER A  63 " =    1.206
peak=    4.514 closest distance to " O   HOH Z 369 " =    2.249
peak=    4.477 closest distance to " CG  PRO A 213 " =    1.197
peak=    4.455 closest distance to " O   HOH Z 126 " =    1.974
peak=    4.412 closest distance to " O   HOH Z 427 " =    3.063
peak=    4.397 closest distance to " ND2 ASN A 187 " =    1.527
peak=    4.394 closest distance to " CB  VAL A 296 " =    1.006
peak=    4.388 closest distance to " CB  ARG A  79 " =    1.501
peak=    4.380 closest distance to " O   HOH Z 248 " =    1.459
peak=    4.366 closest distance to " CB  VAL A 230 " =    1.187
peak=    4.343 closest distance to " CZ  PHE A 218 " =    1.162
peak=    4.330 closest distance to " O   HOH Z 346 " =    1.587
peak=    4.304 closest distance to " O   HOH Z  61 " =    1.820
peak=    4.297 closest distance to " CG  PRO A 243 " =    1.101
peak=    4.295 closest distance to " CG  PRO A 198 " =    1.247
peak=    4.293 closest distance to " CB  ARG A 190 " =    1.624
peak=    4.255 closest distance to " O   HOH Z  78 " =    1.652
peak=    4.192 closest distance to " C   PRO A 198 " =    1.576
peak=    4.156 closest distance to " O   HOH Z  43 " =    2.032
peak=    4.154 closest distance to " O   HOH Z 298 " =    1.832
peak=    4.154 closest distance to " O   HOH Z 188 " =    2.958
peak=    4.139 closest distance to " O   HOH Z 303 " =    2.091
peak=    4.135 closest distance to " CB  ASN A 142 " =    1.145
peak=    4.134 closest distance to " O   HOH Z 368 " =    2.212
peak=    4.112 closest distance to " CB  GLU A 277 " =    3.648
peak=    4.106 closest distance to " CB  TRP A 266 " =    1.060
peak=    4.090 closest distance to " CB  VAL A 202 " =    1.666
peak=    4.087 closest distance to " O   HOH Z 411 " =    3.865
peak=    4.067 closest distance to " CB  ALA A   9 " =    1.604
peak=    4.034 closest distance to " O   HOH Z 313 " =    1.833
peak=    4.033 closest distance to " O   HOH Z 353 " =    2.589
peak=    4.020 closest distance to " O   HOH Z 214 " =    2.226
peak=    4.014 closest distance to " OG ASER A 258 " =    3.129
peak=    4.010 closest distance to " CG  MET A 185 " =    1.269
peak=    4.005 closest distance to " NH1AARG A 145 " =    1.184
peak=    3.996 closest distance to " CA  TYR A  30 " =    1.006
peak=    3.988 closest distance to " O   HOH Z  59 " =    2.093
peak=    3.985 closest distance to " O   HOH Z 402 " =    1.394
peak=    3.978 closest distance to " O   HOH Z 251 " =    1.532
peak=    3.974 closest distance to " CB  GLU A 128 " =    1.020
peak=    3.958 closest distance to " CB  VAL A 265 " =    1.320
peak=    3.939 closest distance to " O   HOH Z  92 " =    2.343
peak=    3.934 closest distance to " O   HOH Z   9 " =    1.243
peak=    3.929 closest distance to " O   HOH Z 425 " =    1.352
peak=    3.916 closest distance to " OD1 ASN A  69 " =    2.597
peak=    3.915 closest distance to " CB  ASN A 148 " =    1.368
peak=    3.903 closest distance to " O   HOH Z 209 " =    2.331
peak=    3.902 closest distance to " N   ASN A  39 " =    1.217
peak=    3.865 closest distance to " O   HOH Z  63 " =    1.935
peak=    3.853 closest distance to " O   HOH Z  40 " =    1.600
peak=    3.843 closest distance to " CZ3 TRP A 266 " =    1.151
peak=    3.837 closest distance to " CB  LYS A 117 " =    1.258
peak=    3.837 closest distance to " O   HOH Z 158 " =    3.209
peak=    3.825 closest distance to " O   HOH Z 234 " =    3.663
peak=    3.821 closest distance to " O   HOH Z 287 " =    2.067
peak=    3.813 closest distance to " OG BSER A 164 " =    2.245
peak=    3.807 closest distance to " CB  ASP A 140 " =    1.086
peak=    3.803 closest distance to " CE  LYS A  76 " =    0.859
peak=    3.799 closest distance to " O   HOH Z 422 " =    2.656
peak=    3.791 closest distance to " CA  ALA A  51 " =    0.951
peak=    3.773 closest distance to " O   HOH Z 261 " =    1.691
peak=    3.773 closest distance to " CB BVAL A  41 " =    1.211
peak=    3.771 closest distance to " CA  ARG A 195 " =    1.221
peak=    3.769 closest distance to " O  BHOH Z 338 " =    2.397
peak=    3.764 closest distance to " O   HOH Z 261 " =    1.821
peak=    3.758 closest distance to " CB  TRP A 179 " =    1.474
peak=    3.747 closest distance to " CD2 LEU A 228 " =    1.121
peak=    3.738 closest distance to " O   HOH Z 290 " =    1.053
peak=    3.738 closest distance to " O   HOH Z 272 " =    1.822
peak=    3.735 closest distance to " CB  ASN A  39 " =    0.945
peak=    3.715 closest distance to " O   HOH Z 166 " =    3.881
peak=    3.714 closest distance to " O   HOH Z 365 " =    2.926
peak=    3.714 closest distance to " CB  SER A   3 " =    1.242
peak=    3.712 closest distance to " CG1BVAL A  72 " =    1.739
peak=    3.711 closest distance to " CB  GLU A 152 " =    1.202
peak=    3.699 closest distance to " CD  LYS A 166 " =    1.330
peak=    3.679 closest distance to " O   HOH Z 203 " =    1.663
peak=    3.673 closest distance to " O   HOH Z 423 " =    1.785
peak=    3.662 closest distance to " CB  GLN A  89 " =    1.274
peak=    3.661 closest distance to " CG  ARG A  66 " =    2.735
peak=    3.660 closest distance to " CA  VAL A 125 " =    1.262
peak=    3.658 closest distance to " O   HOH Z 371 " =    2.885
peak=    3.655 closest distance to " CA  ALA A 291 " =    0.857
peak=    3.646 closest distance to " O   HOH Z 285 " =    2.517
peak=    3.643 closest distance to " O   HOH Z 126 " =    1.559
peak=    3.631 closest distance to " CG2 VAL A 257 " =    0.852
peak=    3.630 closest distance to " O   HOH Z 128 " =    2.142
peak=    3.630 closest distance to " O   HOH Z 193 " =    1.712
peak=    3.620 closest distance to " CD BLYS A 290 " =    1.064
peak=    3.611 closest distance to " CZ  PHE A  38 " =    1.162
peak=    3.602 closest distance to " CD  ARG A 269 " =    0.989
peak=    3.599 closest distance to " CG  LEU A 167 " =    1.226
peak=    3.592 closest distance to " CG1 ILE A  49 " =    1.526
peak=    3.584 closest distance to " CG1 VAL A 153 " =    0.970
peak=    3.576 closest distance to " CB  SER A 212 " =    1.225
peak=    3.574 closest distance to " CB  ASN A 187 " =    1.298
peak=    3.563 closest distance to " O   HOH Z 273 " =    2.893
peak=    3.561 closest distance to " O   HOH Z 147 " =    1.769
peak=    3.558 closest distance to " O   HOH Z 299 " =    4.265
peak=    3.546 closest distance to " O   HOH Z   1 " =    1.688
peak=    3.542 closest distance to " ND2 ASN A 249 " =    0.884
peak=    3.540 closest distance to " NZ  LYS A 117 " =    3.235
peak=    3.538 closest distance to " CD  ARG A 159 " =    0.724
peak=    3.536 closest distance to " O   HOH Z 193 " =    1.890
peak=    3.532 closest distance to " N   GLY A 133 " =    3.743
peak=    3.532 closest distance to " O   HOH Z  66 " =    2.291
peak=    3.530 closest distance to " CD2 TRP A 179 " =    1.310
peak=    3.527 closest distance to " CA  PHE A 283 " =    1.086
peak=    3.527 closest distance to " O   ASP A 124 " =    1.041
peak=    3.524 closest distance to " NE2 GLN A  77 " =    3.274
peak=    3.521 closest distance to " CA  ARG A  36 " =    1.058
peak=    3.519 closest distance to " O   HOH Z 359 " =    1.410
peak=    3.515 closest distance to " O   HOH Z  97 " =    2.428
peak=    3.515 closest distance to " CA  ALA A  21 " =    1.081
peak=    3.511 closest distance to " O   HOH Z 389 " =    1.810
peak=    3.508 closest distance to " O   HOH Z   9 " =    1.915
peak=    3.507 closest distance to " O   HOH Z  80 " =    1.666
peak=    3.506 closest distance to " O   HOH Z 329 " =    4.163
peak=    3.496 closest distance to " O   HOH Z 172 " =    3.783
peak=    3.493 closest distance to " O   HOH Z   3 " =    1.819
peak=    3.489 closest distance to " O   HOH Z 280 " =    3.039
peak=    3.486 closest distance to " CD1 ILE A  33 " =    1.754
peak=    3.480 closest distance to " CA  GLY A 267 " =    0.706
peak=    3.476 closest distance to " O   HOH Z 403 " =    1.566
peak=    3.474 closest distance to " CG2 ILE A 234 " =    0.933
peak=    3.466 closest distance to " NZ  LYS A  48 " =    1.271
peak=    3.463 closest distance to " CB  GLU A  46 " =    0.949
peak=    3.461 closest distance to " O   HOH Z 368 " =    3.560
peak=    3.458 closest distance to " CD1 LEU A  96 " =    0.734
peak=    3.455 closest distance to " CE1 TYR A 186 " =    1.278
peak=    3.454 closest distance to " CA  ASN A 215 " =    1.105
peak=    3.453 closest distance to " N   PHE A 130 " =    1.278
peak=    3.449 closest distance to " O   HOH Z 406 " =    1.490
peak=    3.446 closest distance to " CB  SER A  26 " =    1.783
peak=    3.444 closest distance to " CB  THR A  31 " =    1.581
peak=    3.443 closest distance to " CA  TYR A 116 " =    1.431
peak=    3.436 closest distance to " CA  LYS A 117 " =    1.225
peak=    3.434 closest distance to " CA  SER A  87 " =    1.021
peak=    3.433 closest distance to " CB  THR A  82 " =    1.393
peak=    3.430 closest distance to " CB  GLN A  88 " =    1.197
peak=    3.418 closest distance to " O   HOH Z  10 " =    1.812
peak=    3.418 closest distance to " CA  ASP A 191 " =    1.103
peak=    3.417 closest distance to " O   HOH Z 227 " =    1.716
peak=    3.417 closest distance to " CB  LEU A  83 " =    0.717
peak=    3.403 closest distance to " CG BARG A 102 " =    1.809
peak=    3.394 closest distance to " O   HOH Z 145 " =    2.184
peak=    3.394 closest distance to " CB  PRO A  90 " =    1.182
peak=    3.392 closest distance to " CB  GLN A 205 " =    1.090
peak=    3.390 closest distance to " O   HOH Z 409 " =    3.318
peak=    3.386 closest distance to " CA  LEU A 282 " =    1.179
peak=    3.382 closest distance to " CD2 LEU A 297 " =    0.974
peak=    3.376 closest distance to " O   HOH Z 263 " =    1.703
peak=    3.376 closest distance to " N   ASP A 162 " =    1.214
peak=    3.370 closest distance to " CD1 LEU A 300 " =    1.215
peak=    3.370 closest distance to " CB  THR A  52 " =    0.847
peak=    3.370 closest distance to " O   HOH Z 180 " =    2.129
peak=    3.366 closest distance to " O   HOH Z 187 " =    2.328
peak=    3.361 closest distance to " CB  ARG A 139 " =    0.855
peak=    3.355 closest distance to " CB  SER A 273 " =    0.881
peak=    3.354 closest distance to " CB  ASN A 215 " =    1.143
peak=    3.354 closest distance to " O   HOH Z 193 " =    1.674
peak=    3.352 closest distance to " CG2 ILE A  20 " =    1.517
peak=    3.349 closest distance to " O   HOH Z 128 " =    2.173
peak=    3.346 closest distance to " O   HOH Z 148 " =    3.416
peak=    3.346 closest distance to " CG  MET A 185 " =    1.035
peak=    3.342 closest distance to " O   HOH Z 258 " =    2.118
peak=    3.341 closest distance to " CA  ASP A 162 " =    1.024
peak=    3.339 closest distance to " NH2AARG A 275 " =    3.512
peak=    3.334 closest distance to " CB  TRP A 150 " =    1.347
peak=    3.333 closest distance to " CA  ALA A 154 " =    1.039
peak=    3.329 closest distance to " O   MET A 105 " =    1.862
peak=    3.326 closest distance to " O   HOH Z  21 " =    1.746
peak=    3.318 closest distance to " CG  GLN A  88 " =    1.063
peak=    3.313 closest distance to " CB  ALA A 291 " =    1.402
peak=    3.312 closest distance to " NH2AARG A 145 " =    1.210
peak=    3.307 closest distance to " CB  ASN A 110 " =    1.096
peak=    3.306 closest distance to " O   HOH Z 392 " =    3.122
peak=    3.303 closest distance to " NE2 HIS A 207 " =    1.283
peak=    3.301 closest distance to " O   HOH Z 133 " =    2.455
peak=    3.301 closest distance to " OE1 GLN A  55 " =    1.495
peak=    3.296 closest distance to " O   HOH Z 213 " =    1.750
peak=    3.295 closest distance to " CA  THR A 264 " =    0.763
peak=    3.295 closest distance to " O   HOH Z 325 " =    2.210
peak=    3.294 closest distance to " O   HOH Z 417 " =    3.098
peak=    3.294 closest distance to " O   HOH Z  88 " =    3.003
peak=    3.293 closest distance to " O   HOH Z 350 " =    1.617
peak=    3.291 closest distance to " CA  VAL A  41 " =    0.740
peak=    3.283 closest distance to " CB  VAL A 268 " =    0.827
peak=    3.278 closest distance to " CA  MET A 105 " =    0.977
peak=    3.276 closest distance to " CB  ALA A  43 " =    0.835
peak=    3.275 closest distance to " O   HOH Z  97 " =    2.064
peak=    3.275 closest distance to " OG  SER A  22 " =    2.804
peak=    3.274 closest distance to " O   HOH Z 359 " =    3.943
peak=    3.274 closest distance to " O   ASN A  74 " =    1.516
peak=    3.266 closest distance to " O   HOH Z 305 " =    3.527
peak=    3.260 closest distance to " O   HOH Z   1 " =    1.893
peak=    3.260 closest distance to " CB  GLN A 103 " =    1.067
peak=    3.251 closest distance to " CE3 TRP A 150 " =    1.031
peak=    3.243 closest distance to " CD  ARG A  66 " =    2.574
peak=    3.243 closest distance to " O   HOH Z   4 " =    1.520
peak=    3.242 closest distance to " CB  PHE A 204 " =    0.981
peak=    3.240 closest distance to " O   HOH Z 425 " =    1.977
peak=    3.239 closest distance to " O   ASN A 284 " =    1.713
peak=    3.237 closest distance to " CA  GLY A 211 " =    1.391
peak=    3.237 closest distance to " O   HOH Z 109 " =    2.601
peak=    3.232 closest distance to " O   HOH Z 291 " =    1.563
peak=    3.223 closest distance to " NH2 ARG A 156 " =    1.102
peak=    3.220 closest distance to " CB  VAL A 257 " =    0.724
peak=    3.216 closest distance to " O   HOH Z 407 " =    2.460
peak=    3.215 closest distance to " O   HOH Z 380 " =    1.909
peak=    3.215 closest distance to " CB  SER A 216 " =    0.808
peak=    3.215 closest distance to " O   HOH Z 148 " =    2.165
peak=    3.214 closest distance to " O   ARG A  56 " =    2.890
peak=    3.213 closest distance to " CG1 ILE A 151 " =    1.029
peak=    3.212 closest distance to " O   HOH Z 327 " =    1.973
peak=    3.205 closest distance to " CB  ALA A 242 " =    0.833
peak=    3.204 closest distance to " CZ3 TRP A 274 " =    4.584
peak=    3.203 closest distance to " CB  MET A  40 " =    0.790
peak=    3.202 closest distance to " O   HOH Z 141 " =    1.647
peak=    3.200 closest distance to " CB  PRO A 243 " =    1.538
peak=    3.200 closest distance to " CA  ALA A 160 " =    0.929
peak=    3.199 closest distance to " CA  ALA A 233 " =    1.297
peak=    3.196 closest distance to " O   HOH Z 250 " =    1.270
peak=    3.194 closest distance to " O   HOH Z 171 " =    2.218
peak=    3.194 closest distance to " CA  ARG A 159 " =    1.170
peak=    3.193 closest distance to " CB  ASN A 148 " =    1.952
peak=    3.192 closest distance to " CA  ALA A 129 " =    1.458
peak=    3.190 closest distance to " N   ALA A 256 " =    1.146
peak=    3.189 closest distance to " CB  LEU A 228 " =    1.265
peak=    3.185 closest distance to " N   SER A 146 " =    1.742
peak=    3.184 closest distance to " CA  ASN A 127 " =    1.041
peak=    3.182 closest distance to " N   SER A 135 " =    1.420
peak=    3.180 closest distance to " NH1 ARG A 138 " =    1.048
peak=    3.178 closest distance to " O   HOH Z  48 " =    1.574
peak=    3.177 closest distance to " O   HOH Z 116 " =    1.774
peak=    3.177 closest distance to " CZ3 TRP A  85 " =    0.930
peak=    3.175 closest distance to " CG AARG A 275 " =    1.170
peak=    3.173 closest distance to " OE2 GLU A  53 " =    2.025
peak=    3.173 closest distance to " CB  HIS A 108 " =    0.828
peak=    3.171 closest distance to " CA  ILE A 234 " =    0.871
peak=    3.170 closest distance to " C   ALA A 299 " =    0.897
peak=    3.167 closest distance to " O   HOH Z 294 " =    1.501
peak=    3.158 closest distance to " O   HOH Z 102 " =    1.244
peak=    3.158 closest distance to " CZ3 TRP A  92 " =    1.384
peak=    3.157 closest distance to " CD1 ILE A 199 " =    0.963
peak=    3.149 closest distance to " CG  GLU A  37 " =    0.831
peak=    3.142 closest distance to " O   LYS A 290 " =    2.437
peak=    3.140 closest distance to " CB  ALA A  34 " =    1.022
peak=    3.139 closest distance to " CB  LYS A 290 " =    0.833
peak=    3.139 closest distance to " CB  THR A 157 " =    1.193
peak=    3.137 closest distance to " O   ALA A 158 " =    1.327
peak=    3.130 closest distance to " O   HOH Z 329 " =    2.940
peak=    3.130 closest distance to " O   HOH Z 361 " =    3.576
peak=    3.127 closest distance to " O   HOH Z 345 " =    3.345
peak=    3.126 closest distance to " O   PRO A  90 " =    1.405
peak=    3.125 closest distance to " O   HOH Z 421 " =    3.047
peak=    3.124 closest distance to " OE2 GLU A   2 " =    1.809
peak=    3.123 closest distance to " O   HOH Z 279 " =    2.198
peak=    3.123 closest distance to " CB  LEU A 300 " =    0.859
peak=    3.122 closest distance to " CB  ASN A 173 " =    1.043
peak=    3.122 closest distance to " CG2 THR A 220 " =    0.822
peak=    3.121 closest distance to " O   HOH Z 303 " =    3.062
peak=    3.121 closest distance to " CB  SER A  97 " =    1.092
peak=    3.118 closest distance to " CG  LYS A  76 " =    1.790
peak=    3.115 closest distance to " CA  ARG A 139 " =    1.023
peak=    3.115 closest distance to " O   GLN A 278 " =    1.514
peak=    3.115 closest distance to " CD  LYS A 119 " =    1.906
peak=    3.112 closest distance to " CB  ARG A 145 " =    0.785
peak=    3.111 closest distance to " CB  ALA A 295 " =    1.371
peak=    3.111 closest distance to " CD1 ILE A 263 " =    1.139
peak=    3.109 closest distance to " ND1 HIS A  81 " =    1.702
peak=    3.103 closest distance to " CB  TYR A 116 " =    0.805
peak=    3.102 closest distance to " O   HOH Z 417 " =    2.304
peak=    3.101 closest distance to " O   THR A 182 " =    1.415
peak=    3.098 closest distance to " CB  SER A  62 " =    1.151
peak=    3.098 closest distance to " CA  LYS A 290 " =    1.151
peak=    3.095 closest distance to " N   GLN A 278 " =    1.364
peak=    3.093 closest distance to " CG  LYS A  76 " =    0.960
peak=    3.084 closest distance to " O   HOH Z 344 " =    2.931
peak=    3.081 closest distance to " CD1 ILE A 106 " =    0.944
peak=    3.077 closest distance to " CA  ARG A 102 " =    1.155
peak=    3.072 closest distance to " O   SER A 164 " =    1.260
peak=    3.067 closest distance to " O   TRP A 274 " =    1.828
peak=    3.052 closest distance to " CG1 ILE A  33 " =    1.271
peak=    3.051 closest distance to " O   HOH Z  47 " =    1.787
peak=    3.049 closest distance to " CB  ALA A 248 " =    1.583
peak=    3.033 closest distance to " CG  LEU A 281 " =    0.995
peak=    3.017 closest distance to " O   HOH Z 128 " =    2.084

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.790 - 5.538
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 202
   mapped sites are within: 0.790 - 5.538

peak=   -4.717 closest distance to " CD  ARG A  14 " =    3.387
peak=   -4.676 closest distance to " CG2 VAL A 230 " =    0.790
peak=   -4.511 closest distance to " CD  GLN A  58 " =    1.055
peak=   -4.465 closest distance to " CD  ARG A 156 " =    2.050
peak=   -4.434 closest distance to " OG BSER A 134 " =    1.257
peak=   -4.430 closest distance to " CB  PRO A 243 " =    2.724
peak=   -4.411 closest distance to " O   HOH Z 266 " =    5.522
peak=   -4.345 closest distance to " O   VAL A  67 " =    2.676
peak=   -4.340 closest distance to " O   HOH Z 231 " =    2.097
peak=   -4.193 closest distance to " CB  PHE A 192 " =    1.975
peak=   -4.123 closest distance to " C   HIS A 108 " =    1.186
peak=   -4.110 closest distance to " OE1 GLN A 223 " =    2.254
peak=   -4.088 closest distance to " CZ2 TRP A  92 " =    2.873
peak=   -4.073 closest distance to " O   HOH Z 196 " =    2.269
peak=   -4.064 closest distance to " O   HOH Z 211 " =    1.319
peak=   -4.034 closest distance to " CG1 VAL A 112 " =    2.632
peak=   -3.966 closest distance to " CA  VAL A  67 " =    2.829
peak=   -3.931 closest distance to " CG1 VAL A 112 " =    2.786
peak=   -3.928 closest distance to " CA  ASP A 298 " =    1.055
peak=   -3.900 closest distance to " CB  ALA A 161 " =    2.628
peak=   -3.888 closest distance to " OG  SER A  97 " =    2.303
peak=   -3.849 closest distance to " O   PRO A 163 " =    2.123
peak=   -3.845 closest distance to " CE2 TYR A  30 " =    2.647
peak=   -3.813 closest distance to " CE3 TRP A 150 " =    2.203
peak=   -3.771 closest distance to " CG1 VAL A 250 " =    2.742
peak=   -3.768 closest distance to " O   HOH Z 114 " =    3.039
peak=   -3.748 closest distance to " O   HOH Z 198 " =    2.157
peak=   -3.731 closest distance to " CG2 VAL A 296 " =    1.425
peak=   -3.724 closest distance to " O   HOH Z 394 " =    1.581
peak=   -3.720 closest distance to " O   HOH Z  44 " =    2.278
peak=   -3.718 closest distance to " O   HOH Z 166 " =    1.981
peak=   -3.711 closest distance to " CE BMET A  47 " =    1.532
peak=   -3.701 closest distance to " ND2 ASN A  45 " =    1.748
peak=   -3.695 closest distance to " O   HOH Z 185 " =    2.371
peak=   -3.693 closest distance to " O   HOH Z 216 " =    1.332
peak=   -3.663 closest distance to " OXT GLY A 302 " =    2.973
peak=   -3.658 closest distance to " O   HOH Z  73 " =    2.262
peak=   -3.650 closest distance to " N   ALA A 248 " =    1.720
peak=   -3.643 closest distance to " CD1 LEU A 101 " =    2.409
peak=   -3.627 closest distance to " C   MET A 188 " =    1.428
peak=   -3.626 closest distance to " CB  ALA A 248 " =    2.325
peak=   -3.622 closest distance to " CB  ALA A  43 " =    2.568
peak=   -3.620 closest distance to " O   HOH Z 435 " =    2.809
peak=   -3.594 closest distance to " O   SER A 271 " =    2.140
peak=   -3.584 closest distance to " CE  MET A 105 " =    2.334
peak=   -3.581 closest distance to " O   HOH Z 290 " =    1.268
peak=   -3.578 closest distance to " CG2 VAL A 296 " =    0.880
peak=   -3.571 closest distance to " O   HOH Z 377 " =    2.120
peak=   -3.567 closest distance to " CA  GLY A 241 " =    2.341
peak=   -3.566 closest distance to " CZ3 TRP A 179 " =    1.218
peak=   -3.565 closest distance to " CB  ALA A 248 " =    2.110
peak=   -3.562 closest distance to " O   HOH Z 351 " =    1.583
peak=   -3.558 closest distance to " NE2 GLN A  88 " =    2.051
peak=   -3.553 closest distance to " ND2 ASN A  45 " =    1.252
peak=   -3.550 closest distance to " CA  GLY A 241 " =    3.127
peak=   -3.544 closest distance to " NE2 GLN A  11 " =    1.834
peak=   -3.542 closest distance to " CG  TRP A 266 " =    1.861
peak=   -3.538 closest distance to " OG  SER A  87 " =    1.407
peak=   -3.530 closest distance to " O   PRO A 198 " =    1.239
peak=   -3.523 closest distance to " O   HOH Z 193 " =    1.471
peak=   -3.521 closest distance to " O   HOH Z  13 " =    1.884
peak=   -3.518 closest distance to " O   HOH Z 102 " =    1.656
peak=   -3.518 closest distance to " CE2 PHE A  61 " =    2.632
peak=   -3.517 closest distance to " ND2 ASN A 249 " =    2.451
peak=   -3.514 closest distance to " C   ALA A 158 " =    1.288
peak=   -3.511 closest distance to " N   ALA A  43 " =    2.686
peak=   -3.505 closest distance to " O   HOH Z  11 " =    1.872
peak=   -3.483 closest distance to " C   LEU A 143 " =    1.063
peak=   -3.480 closest distance to " N   ALA A 226 " =    2.071
peak=   -3.471 closest distance to " O   HOH Z 133 " =    1.307
peak=   -3.469 closest distance to " O   SER A 210 " =    1.864
peak=   -3.464 closest distance to " CB  HIS A  86 " =    1.136
peak=   -3.462 closest distance to " N   THR A  52 " =    1.640
peak=   -3.454 closest distance to " O   VAL A 189 " =    2.620
peak=   -3.435 closest distance to " O   HOH Z 359 " =    3.073
peak=   -3.429 closest distance to " CB  ALA A 291 " =    2.198
peak=   -3.421 closest distance to " C   GLY A  17 " =    1.223
peak=   -3.415 closest distance to " O   HOH Z 103 " =    1.829
peak=   -3.414 closest distance to " CD2 TYR A 293 " =    2.051
peak=   -3.414 closest distance to " O   HOH Z 407 " =    3.032
peak=   -3.413 closest distance to " CB  ASP A 132 " =    2.332
peak=   -3.407 closest distance to " CD2 PHE A 225 " =    1.129
peak=   -3.406 closest distance to " N   THR A 157 " =    1.474
peak=   -3.395 closest distance to " CB  ARG A  79 " =    2.660
peak=   -3.395 closest distance to " O   HOH Z 431 " =    1.881
peak=   -3.390 closest distance to " CG2BVAL A  41 " =    1.773
peak=   -3.388 closest distance to " CG2 VAL A 202 " =    2.713
peak=   -3.382 closest distance to " N   ALA A 248 " =    2.301
peak=   -3.377 closest distance to " CG2 ILE A 263 " =    2.399
peak=   -3.377 closest distance to " C   LEU A 222 " =    0.879
peak=   -3.375 closest distance to " O   HOH Z  10 " =    1.437
peak=   -3.368 closest distance to " O   MET A  40 " =    2.823
peak=   -3.368 closest distance to " O   HOH Z  60 " =    1.826
peak=   -3.361 closest distance to " O   HOH Z 243 " =    1.850
peak=   -3.353 closest distance to " O   HOH Z 252 " =    3.952
peak=   -3.349 closest distance to " CB  ALA A 291 " =    2.312
peak=   -3.347 closest distance to " CD1 TYR A 247 " =    2.357
peak=   -3.343 closest distance to " CA  GLY A 203 " =    2.513
peak=   -3.339 closest distance to " OH  TYR A 214 " =    1.257
peak=   -3.338 closest distance to " N   ASP A 171 " =    2.310
peak=   -3.330 closest distance to " OD1 ASN A 148 " =    1.476
peak=   -3.325 closest distance to " CG1 VAL A 125 " =    1.908
peak=   -3.322 closest distance to " CB  VAL A 230 " =    1.125
peak=   -3.318 closest distance to " OG BSER A 210 " =    1.442
peak=   -3.313 closest distance to " CB  ASP A 171 " =    2.251
peak=   -3.310 closest distance to " O   PRO A 198 " =    1.391
peak=   -3.307 closest distance to " O   HOH Z 191 " =    5.538
peak=   -3.301 closest distance to " OD1 ASN A 187 " =    1.672
peak=   -3.300 closest distance to " O   HOH Z 275 " =    1.853
peak=   -3.295 closest distance to " O   HOH Z 389 " =    2.087
peak=   -3.291 closest distance to " OH  TYR A 247 " =    1.889
peak=   -3.289 closest distance to " NH2AARG A 275 " =    5.206
peak=   -3.287 closest distance to " O   HOH Z 350 " =    1.978
peak=   -3.282 closest distance to " O   HOH Z 345 " =    2.007
peak=   -3.280 closest distance to " O   HOH Z 106 " =    1.720
peak=   -3.279 closest distance to " CD1 PHE A  59 " =    1.959
peak=   -3.275 closest distance to " O   HOH Z 265 " =    1.789
peak=   -3.273 closest distance to " NH2 ARG A  79 " =    1.579
peak=   -3.272 closest distance to " O   HOH Z  43 " =    1.745
peak=   -3.271 closest distance to " O   PHE A 218 " =    1.629
peak=   -3.269 closest distance to " ND2 ASN A 187 " =    1.560
peak=   -3.268 closest distance to " O   HOH Z 295 " =    1.533
peak=   -3.266 closest distance to " O   HOH Z 313 " =    1.622
peak=   -3.263 closest distance to " CB  PRO A 163 " =    2.495
peak=   -3.261 closest distance to " O   HOH Z 149 " =    2.158
peak=   -3.257 closest distance to " CA  GLY A 133 " =    2.295
peak=   -3.253 closest distance to " O   HOH Z  11 " =    2.252
peak=   -3.251 closest distance to " O   SER A 276 " =    1.631
peak=   -3.240 closest distance to " CG1 VAL A 296 " =    1.450
peak=   -3.236 closest distance to " CG  ARG A 269 " =    2.341
peak=   -3.236 closest distance to " CG  PHE A 283 " =    2.672
peak=   -3.232 closest distance to " CG  LYS A 166 " =    2.137
peak=   -3.230 closest distance to " O   HOH Z 140 " =    1.485
peak=   -3.229 closest distance to " O   HOH Z 353 " =    2.098
peak=   -3.227 closest distance to " CB  ASN A  39 " =    2.277
peak=   -3.226 closest distance to " N   SER A 276 " =    1.396
peak=   -3.224 closest distance to " C   ASN A 187 " =    1.862
peak=   -3.222 closest distance to " CG1 VAL A  67 " =    2.895
peak=   -3.222 closest distance to " NE2 GLN A 278 " =    1.852
peak=   -3.217 closest distance to " O   HOH Z 285 " =    1.933
peak=   -3.211 closest distance to " OD1 ASN A  39 " =    2.226
peak=   -3.208 closest distance to " CG  GLU A 277 " =    1.207
peak=   -3.205 closest distance to " O   HOH Z 100 " =    1.086
peak=   -3.205 closest distance to " O   HOH Z 421 " =    3.138
peak=   -3.201 closest distance to " CG  ASP A 231 " =    0.807
peak=   -3.199 closest distance to " O   ASN A 252 " =    1.373
peak=   -3.196 closest distance to " O   LYS A  76 " =    1.477
peak=   -3.196 closest distance to " CA  ASP A  27 " =    2.465
peak=   -3.195 closest distance to " O   HOH Z  38 " =    1.713
peak=   -3.194 closest distance to " O   HOH Z 136 " =    2.497
peak=   -3.193 closest distance to " CZ  TYR A 169 " =    1.742
peak=   -3.192 closest distance to " CD1 ILE A 199 " =    2.431
peak=   -3.191 closest distance to " OD2 ASP A  50 " =    2.274
peak=   -3.189 closest distance to " CZ  PHE A 192 " =    2.830
peak=   -3.189 closest distance to " CD  PRO A 213 " =    2.070
peak=   -3.187 closest distance to " O   ASP A  27 " =    2.074
peak=   -3.183 closest distance to " CG1BVAL A  72 " =    2.359
peak=   -3.183 closest distance to " NE2 GLN A 194 " =    1.860
peak=   -3.181 closest distance to " O   HOH Z 139 " =    3.101
peak=   -3.179 closest distance to " O   HOH Z 389 " =    1.387
peak=   -3.178 closest distance to " O   HOH Z 232 " =    2.256
peak=   -3.178 closest distance to " CG1 VAL A 197 " =    2.290
peak=   -3.175 closest distance to " O   ALA A  51 " =    1.372
peak=   -3.174 closest distance to " CD2 LEU A 237 " =    2.877
peak=   -3.170 closest distance to " O   HOH Z 371 " =    2.198
peak=   -3.168 closest distance to " O   ALA A 227 " =    1.611
peak=   -3.167 closest distance to " CB  ALA A  10 " =    2.293
peak=   -3.164 closest distance to " ND2 ASN A 252 " =    1.949
peak=   -3.163 closest distance to " CD1 LEU A 228 " =    2.265
peak=   -3.162 closest distance to " CG2 VAL A 189 " =    1.988
peak=   -3.161 closest distance to " O   SER A 135 " =    1.422
peak=   -3.159 closest distance to " O   HOH Z 131 " =    4.039
peak=   -3.158 closest distance to " O   HOH Z 165 " =    1.946
peak=   -3.156 closest distance to " O   HOH Z 411 " =    1.597
peak=   -3.155 closest distance to " CD1 LEU A 101 " =    2.837
peak=   -3.149 closest distance to " O   HOH Z 426 " =    1.715
peak=   -3.148 closest distance to " O   HOH Z  52 " =    1.583
peak=   -3.142 closest distance to " O   HOH Z 281 " =    2.596
peak=   -3.141 closest distance to " O   ARG A 145 " =    1.647
peak=   -3.140 closest distance to " CD2 HIS A 207 " =    2.377
peak=   -3.136 closest distance to " CD  GLN A 223 " =    1.682
peak=   -3.128 closest distance to " O   ILE A 106 " =    1.928
peak=   -3.128 closest distance to " C   PHE A  59 " =    1.312
peak=   -3.126 closest distance to " O   HOH Z 236 " =    1.398
peak=   -3.123 closest distance to " O   HOH Z 292 " =    1.789
peak=   -3.122 closest distance to " O   HOH Z 313 " =    1.233
peak=   -3.117 closest distance to " O   HOH Z  96 " =    1.545
peak=   -3.114 closest distance to " O   SER A  95 " =    1.748
peak=   -3.112 closest distance to " O   HOH Z 128 " =    2.658
peak=   -3.107 closest distance to " OG BSER A 134 " =    1.767
peak=   -3.094 closest distance to " OXT GLY A 302 " =    3.436
peak=   -3.081 closest distance to " O   HOH Z  89 " =    2.842
peak=   -3.080 closest distance to " O   SER A  22 " =    2.385
peak=   -3.079 closest distance to " OD1 ASP A 171 " =    1.599
peak=   -3.076 closest distance to " OD1 ASN A 301 " =    2.014
peak=   -3.069 closest distance to " CD2 TYR A 247 " =    2.314
peak=   -3.051 closest distance to " O   ALA A 180 " =    1.447
peak=   -3.039 closest distance to " O   HOH Z 166 " =    1.719
peak=   -3.039 closest distance to " O   HOH Z 357 " =    2.040
peak=   -3.024 closest distance to " CD1 ILE A 151 " =    2.470
peak=   -3.017 closest distance to " C   GLN A  58 " =    1.997

================= 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    :  0.4332 0.4163   6.227368e+00   6.192815e+00
   1_bss:  0.4244 0.4050   6.221265e+00   6.179533e+00
   1_xyz:  0.3140 0.3310   6.004808e+00   6.036857e+00
   1_adp:  0.2490 0.2823   5.807521e+00   5.914960e+00
   1_occ:  0.2483 0.2830   5.806117e+00   5.917098e+00
   2_bss:  0.2428 0.2776   5.804015e+00   5.912034e+00
   2_xyz:  0.1655 0.2059   5.456958e+00   5.631050e+00
   2_adp:  0.1501 0.1919   5.374878e+00   5.566168e+00
   2_occ:  0.1500 0.1918   5.374310e+00   5.566002e+00
   3_bss:  0.1493 0.1917   5.373878e+00   5.566298e+00
   3_xyz:  0.1289 0.1702   5.248356e+00   5.461771e+00
   3_adp:  0.1235 0.1673   5.223103e+00   5.449828e+00
   3_occ:  0.1234 0.1673   5.222824e+00   5.449588e+00
   4_bss:  0.1234 0.1674   5.222469e+00   5.449574e+00
   4_xyz:  0.1181 0.1631   5.189712e+00   5.424975e+00
   4_adp:  0.1173 0.1623   5.184859e+00   5.420523e+00
   4_occ:  0.1171 0.1623   5.184329e+00   5.420292e+00
   5_bss:  0.1172 0.1617   5.183572e+00   5.417668e+00
   5_xyz:  0.1126 0.1597   5.157726e+00   5.406290e+00
   5_adp:  0.1121 0.1596   5.155490e+00   5.404864e+00
   5_occ:  0.1121 0.1596   5.155404e+00   5.404837e+00
   5_bss:  0.1121 0.1595   5.155471e+00   5.404891e+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:  0.338  20.001   7.016   7.720  10.846   0.000   0.000   0.000
   1_xyz:  0.338  20.001   7.016   7.720  10.846   0.000   0.000   0.000
   1_adp:  0.338  20.001   7.016   7.720  10.846   0.000   0.000   0.000
   1_occ:  0.338  20.001   7.016   7.720  10.846   0.000   0.000   0.000
   2_bss:  0.330  50.000   3.678   4.071   7.096   0.000   0.000   0.000
   2_xyz:  0.330  50.000   3.678   4.071   7.096   0.000   0.000   0.000
   2_adp:  0.330  50.000   3.678   4.071   7.096   0.000   0.000   0.000
   2_occ:  0.330  50.000   3.678   4.071   7.096   0.000   0.000   0.000
   3_bss:  0.332  50.000   2.916   3.422   5.187   0.000   0.000   0.000
   3_xyz:  0.332  50.000   2.916   3.422   5.187   0.000   0.000   0.000
   3_adp:  0.332  50.000   2.916   3.422   5.187   0.000   0.000   0.000
   3_occ:  0.332  50.000   2.916   3.422   5.187   0.000   0.000   0.000
   4_bss:  0.324  50.000   2.893   3.310   4.873   0.000   0.000   0.000
   4_xyz:  0.324  50.000   2.893   3.310   4.873   0.000   0.000   0.000
   4_adp:  0.324  50.000   2.893   3.310   4.873   0.000   0.000   0.000
   4_occ:  0.324  50.000   2.893   3.310   4.873   0.000   0.000   0.000
   5_bss:  0.327  54.014   2.951   3.330   4.849   0.000   0.000   0.000
   5_xyz:  0.327  54.014   2.951   3.330   4.849   0.000   0.000   0.000
   5_adp:  0.327  54.014   2.951   3.330   4.849   0.000   0.000   0.000
   5_occ:  0.327  54.014   2.951   3.330   4.849   0.000   0.000   0.000
   5_bss:  0.327  57.868  -0.736  -0.389   1.125   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  45.574 0.5773  0.6390    49549.238
   1_bss:  44.937 0.5838  0.8374    47193.020
   1_xyz:  35.175 0.6990  0.9649    29376.930
   1_adp:  28.461 0.7754  1.0430    20774.937
   1_occ:  28.521 0.7747  1.0415    20849.075
   2_bss:  28.208 0.7780  0.9193    20464.736
   2_xyz:  19.627 0.8651  0.9963    10528.809
   2_adp:  17.860 0.8820  1.0093     9247.855
   2_occ:  17.852 0.8821  1.0094     9235.582
   3_bss:  17.825 0.8824  0.9699     9265.659
   3_xyz:  15.456 0.9031  0.9767     7393.404
   3_adp:  15.181 0.9057  0.9737     7213.766
   3_occ:  15.174 0.9057  0.9736     7208.963
   4_bss:  15.169 0.9057  0.9685     7209.050
   4_xyz:  14.627 0.9103  0.9717     6830.544
   4_adp:  14.500 0.9115  0.9699     6759.683
   4_occ:  14.502 0.9115  0.9698     6761.249
   5_bss:  14.477 0.9116  0.9702     6719.647
   5_xyz:  14.261 0.9132  0.9707     6567.670
   5_adp:  14.228 0.9136  0.9665     6535.877
   5_occ:  14.226 0.9136  0.9664     6533.717
   5_bss:  14.228 0.9136  0.9715     6535.177
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4084e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4084e+01
   1_xyz:   1.532  0.012  0.102 17.840  0.006  4.124   1.1908e-01
   1_adp:   1.532  0.012  0.102 17.840  0.006  4.124   1.1908e-01
   1_occ:   1.532  0.012  0.102 17.840  0.006  4.124   1.1908e-01
   2_bss:   1.532  0.012  0.102 17.840  0.006  4.124   1.1908e-01
   2_xyz:   1.034  0.008  0.077 16.267  0.004  4.126   6.5446e-02
   2_adp:   1.034  0.008  0.077 16.267  0.004  4.126   6.5446e-02
   2_occ:   1.034  0.008  0.077 16.267  0.004  4.126   6.5446e-02
   3_bss:   1.034  0.008  0.077 16.267  0.004  4.126   6.5446e-02
   3_xyz:   0.976  0.007  0.077 15.751  0.003  4.134   5.9764e-02
   3_adp:   0.976  0.007  0.077 15.751  0.003  4.134   5.9764e-02
   3_occ:   0.976  0.007  0.077 15.751  0.003  4.134   5.9764e-02
   4_bss:   0.976  0.007  0.077 15.751  0.003  4.134   5.9764e-02
   4_xyz:   0.960  0.007  0.078 15.444  0.003  4.139   5.7397e-02
   4_adp:   0.960  0.007  0.078 15.444  0.003  4.139   5.7397e-02
   4_occ:   0.960  0.007  0.078 15.444  0.003  4.139   5.7397e-02
   5_bss:   0.960  0.007  0.078 15.444  0.003  4.139   5.7397e-02
   5_xyz:   1.085  0.009  0.087 15.471  0.004  4.114   7.0844e-02
   5_adp:   1.085  0.009  0.087 15.471  0.004  4.114   7.0844e-02
   5_occ:   1.085  0.009  0.087 15.471  0.004  4.114   7.0844e-02
   5_bss:   1.085  0.009  0.087 15.471  0.004  4.114   7.0844e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0124e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0124e+00
   1_xyz:  12.894  0.137  0.394 87.770  0.034  2.182   8.9433e-02
   1_adp:  12.894  0.137  0.394 87.770  0.034  2.182   8.9433e-02
   1_occ:  12.894  0.137  0.394 87.770  0.034  2.182   8.9433e-02
   2_bss:  12.894  0.137  0.394 87.770  0.034  2.182   8.9433e-02
   2_xyz:   7.210  0.062  0.360 89.733  0.034  2.321   4.2410e-02
   2_adp:   7.210  0.062  0.360 89.733  0.034  2.321   4.2410e-02
   2_occ:   7.210  0.062  0.360 89.733  0.034  2.321   4.2410e-02
   3_bss:   7.210  0.062  0.360 89.733  0.034  2.321   4.2410e-02
   3_xyz:   7.260  0.048  0.444 81.905  0.037  2.365   6.8706e-02
   3_adp:   7.260  0.048  0.444 81.905  0.037  2.365   6.8706e-02
   3_occ:   7.260  0.048  0.444 81.905  0.037  2.365   6.8706e-02
   4_bss:   7.260  0.048  0.444 81.905  0.037  2.365   6.8706e-02
   4_xyz:   6.583  0.038  0.464 82.665  0.038  2.398   3.3042e-02
   4_adp:   6.583  0.038  0.464 82.665  0.038  2.398   3.3042e-02
   4_occ:   6.583  0.038  0.464 82.665  0.038  2.398   3.3042e-02
   5_bss:   6.583  0.038  0.464 82.665  0.038  2.398   3.3042e-02
   5_xyz:   7.076  0.053  0.522 82.645  0.039  2.353   4.7607e-02
   5_adp:   7.076  0.053  0.522 82.645  0.039  2.353   4.7607e-02
   5_occ:   7.076  0.053  0.522 82.645  0.039  2.353   4.7607e-02
   5_bss:   7.076  0.053  0.522 82.645  0.039  2.353   4.7607e-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:  61.26   0.00  10.78  53.77   0.00   7.66  61.26   0.00  27.76
   1_occ:  61.26   0.00  10.78  53.77   0.00   7.66  61.26   0.00  27.76
   2_bss:  61.26   0.00  10.78  53.77   0.00   7.66  61.26   0.00  27.76
   2_xyz:  61.26   0.00  10.78  53.77   0.00   7.66  61.26   0.00  27.76
   2_adp:  61.55   0.00  11.05  55.75   0.00   7.35  61.55   0.58  31.18
   2_occ:  61.55   0.00  11.05  55.75   0.00   7.35  61.55   0.58  31.18
   3_bss:  61.55   0.00  11.05  55.75   0.00   7.35  61.55   0.58  31.18
   3_xyz:  61.55   0.00  11.05  55.75   0.00   7.35  61.55   0.58  31.18
   3_adp:  69.69   0.00  11.72  69.69   0.00   7.48  68.91   0.20  34.82
   3_occ:  69.69   0.00  11.72  69.69   0.00   7.48  68.91   0.20  34.82
   4_bss:  69.69   0.00  11.72  69.69   0.00   7.48  68.91   0.20  34.82
   4_xyz:  69.69   0.00  11.72  69.69   0.00   7.48  68.91   0.20  34.82
   4_adp:  72.84   0.00  11.68  72.84   0.00   7.44  70.24   0.00  34.76
   4_occ:  72.84   0.00  11.68  72.84   0.00   7.44  70.24   0.00  34.76
   5_bss:  72.84   0.00  11.68  72.84   0.00   7.44  70.24   0.00  34.76
   5_xyz:  72.84   0.00  11.68  72.84   0.00   7.44  70.24   0.00  34.76
   5_adp:  83.72   0.00  11.72  83.72   0.00   7.40  77.52   0.00  35.24
   5_occ:  83.72   0.00  11.72  83.72   0.00   7.40  77.52   0.00  35.24
   5_bss:  87.58   3.85  15.57  87.58   3.85  11.25  81.37   3.85  39.09
------------------------------------------------------------------------
 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:    1.223    0.021    0.403
   1_adp:    1.223    0.021    0.403
   1_occ:    1.223    0.021    0.403
   2_bss:    1.223    0.021    0.403
   2_xyz:    1.598    0.011    0.506
   2_adp:    1.598    0.011    0.506
   2_occ:    1.598    0.011    0.506
   3_bss:    1.598    0.011    0.506
   3_xyz:    1.658    0.040    0.531
   3_adp:    1.658    0.040    0.531
   3_occ:    1.658    0.040    0.531
   4_bss:    1.658    0.040    0.531
   4_xyz:    1.759    0.046    0.545
   4_adp:    1.759    0.046    0.545
   4_occ:    1.759    0.046    0.545
   5_bss:    1.759    0.046    0.545
   5_xyz:    1.770    0.031    0.551
   5_adp:    1.770    0.031    0.551
   5_occ:    1.770    0.031    0.551
   5_bss:    1.770    0.031    0.551
------------------------------------------------------------------------

CPU time actual refinement: 323.35


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_668/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_668/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_668/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_668/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_668/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 323.20 
  Macro-tasks:
    bulk solvent and scale       = 41.61  
    individual site refinement   = 129.43 
    weights calculation          = 30.98  
    collect and process          = 6.48   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 208.62 
  Micro-tasks:
    mask                            = 1.70   
    f_calc                          = 98.27  
    alpha_beta                      = 8.07   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 108.78 
    fmodel                         = 6.97   
    r_factors                      = 0.31   
    phase_errors                   = 10.98  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 236.48 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.568 micro seconds
Total CPU time: 5.61 minutes
from_scatterers_fft:    653 calls, 98.00 s
gradients_fft:          598 calls, 95.61 s

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

# Date 2008-01-16 Time 02:08:16 PST -0800 (1200478096.62 s)
Start R-work = 0.4332, R-free = 0.4163 (no bulk solvent and anisotropic scale)
Final R-work = 0.1296, R-free = 0.1763 (no bulk solvent and anisotropic scale)

Start R-work = 0.4244, R-free = 0.4050
Final R-work = 0.1121, R-free = 0.1595