# Date 2008-01-16 Time 00:39:39 PST -0800 (1200472779.81 s)
#phil __OFF__

Command line arguments: "../107.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 16674
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 107

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.4938, 47.8686, 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: 3.34, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 47.8686, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9941 1.95097
Completeness in resolution range: 0.907781
Completeness with d_max=infinity: 0.905096

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9941
                             d_min =   1.9510

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 47.8686, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9941 1.95097
Completeness in resolution range: 0.907781
Completeness with d_max=infinity: 0.905096

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9945 -  4.1758 [2261/2289]  2030   231  10.2%
  bin  2:  4.1758 -  3.3264 [2181/2204]  1962   219  10.0%
  bin  3:  3.3264 -  2.9094 [2153/2178]  1947   206   9.6%
  bin  4:  2.9094 -  2.6450 [2114/2141]  1897   217  10.3%
  bin  5:  2.6450 -  2.4563 [2097/2130]  1884   213  10.2%
  bin  6:  2.4563 -  2.3120 [2116/2144]  1908   208   9.8%
  bin  7:  2.3120 -  2.1966 [2079/2115]  1877   202   9.7%
  bin  8:  2.1966 -  2.1012 [2102/2144]  1889   213  10.1%
  bin  9:  2.1012 -  2.0205 [1947/2113]  1757   190   9.8%
  bin 10:  2.0205 -  1.9510 [ 539/2121]   479    60  11.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_107/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: 0.15 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:
        0.92 -     1.72: 9
        1.72 -     2.51: 55
        2.51 -     3.31: 3767
        3.31 -     4.10: 9398
        4.10 -     4.90: 15108
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  0.919 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.174 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.325 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.326 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.442 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28332 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_107/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_107/model_refine_001.geo

CPU time processing inputs: 9.33


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.49375 47.8686 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: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5212   r_free= 0.5172   ksol= 0.00   Bsol= 0.00   scale= 0.761    |
|                                                                             |
| 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:   0.95 A                  |
| x-ray target function (ml) for work reflections: 6.312964                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9945 -  4.6581 0.99   1472  161 0.4251 0.4316      6.6585        6.71|
|  2:  4.6581 -  3.7158 0.99   1416  156 0.4607 0.4919      6.8643      6.9092|
|  3:  3.7158 -  3.2515 0.99   1376  158 0.5064 0.4842      6.7187      6.7295|
|  4:  3.2515 -  2.9567 0.98   1384  145 0.5180 0.5113      6.5426      6.5222|
|  5:  2.9567 -  2.7462 0.99   1372  157 0.5628 0.5567      6.3818      6.4072|
|  6:  2.7462 -  2.5851 0.99   1370  151 0.5459 0.5391      6.2885      6.2061|
|  7:  2.5851 -  2.4563 0.98   1330  158 0.5431 0.4723      6.2375      6.1611|
|  8:  2.4563 -  2.3498 0.98   1376  145 0.5543 0.5442      6.1769      6.1934|
|  9:  2.3498 -  2.2596 0.99   1339  145 0.5645 0.5568      6.1245      6.1908|
| 10:  2.2596 -  2.1819 0.99   1354  146 0.5568 0.5773      6.0904      6.1091|
| 11:  2.1819 -  2.1139 0.97   1334  157 0.5639 0.5606      6.0097      6.0293|
| 12:  2.1139 -  2.0536 0.98   1333  149 0.5672 0.5591      5.9592      5.9336|
| 13:  2.0536 -  1.9997 0.71    954  104 0.5564 0.5672      5.8661      5.8226|
| 14:  1.9997 -  1.9510 0.16    220   27 0.5886 0.4899      5.9369      5.7081|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9945 -  4.6581  1472   161  0.62  41.14   0.78     0.63      95636.57|
|  2:  4.6581 -  3.7158  1416   156  0.59  44.28   0.85     0.65     148650.89|
|  3:  3.7158 -  3.2515  1376   158  0.46  55.23   0.78     0.58     156101.63|
|  4:  3.2515 -  2.9567  1384   145  0.36  62.97   0.75     0.46     130644.73|
|  5:  2.9567 -  2.7462  1372   157  0.27  69.85   0.69     0.35     101460.70|
|  6:  2.7462 -  2.5851  1370   151  0.25  71.56   0.69     0.31      85725.91|
|  7:  2.5851 -  2.4563  1330   158  0.23  72.64   0.71     0.28      76941.33|
|  8:  2.4563 -  2.3498  1376   145  0.26  70.58   0.70     0.32      65848.55|
|  9:  2.3498 -  2.2596  1339   145  0.25  71.75   0.69     0.31      62865.62|
| 10:  2.2596 -  2.1819  1354   146  0.22  73.30   0.72     0.28      55658.48|
| 11:  2.1819 -  2.1139  1334   157  0.16  77.88   0.71     0.22      55605.77|
| 12:  2.1139 -  2.0536  1333   149  0.16  77.88   0.72     0.23      50433.41|
| 13:  2.0536 -  1.9997   954   104  0.16  78.34   0.72     0.22      43804.56|
| 14:  1.9997 -  1.9510   220    27  0.22  73.62   0.74     0.23      31328.13|
|alpha:            min =        0.22 max =            0.65 mean =         0.38|
|beta:             min =    31328.13 max =       156101.63 mean =     87696.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.31|
|phase err.(work): min =        0.00 max =           89.99 mean =        66.25|
|phase err.(test): min =        0.00 max =           89.99 mean =        66.64|
|-----------------------------------------------------------------------------|

============================== 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 = 26.452919             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.712   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.649956              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.354   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  0.631 -  1.058:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.058 -  1.485:        3 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.485 -  1.912:       35 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  1.912 -  2.339:      219 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.339 -  2.765:      937 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.765 -  3.192:     2154 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.192 -  3.619:     3695 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.619 -  4.046:     5391 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.046 -  4.473:     7140 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.473 -  4.900:     8756 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.809 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.087    4.900  0.631 |       3.244 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.821)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.821)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5251   r_free= 0.5180   ksol= 0.00   Bsol= 0.00   scale= 0.733    |
|                                                                             |
| 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:   1.01 A                  |
| x-ray target function (ml) for work reflections: 6.313049                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5143   r_free= 0.5136   ksol= 0.31   Bsol= 0.00   scale= 0.963    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.22,10.77,9.27,0.00,0.00,0.00); trace/3= 9.08                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.01 A                  |
| x-ray target function (ml) for work reflections: 6.307937                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 23.492628             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.215   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.330131              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.195   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5143      final r-factor (work) = 0.4569          |
| start r-factor (free) = 0.5136      final r-factor (free) = 0.4802          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 127.9385 = 23.49 * 0.50 * 6.3109 + 1.00 * 53.8091                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 73.8025 = 23.49 * 0.50 * 6.2692 + 1.00 * 0.1625                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4569      final r-factor (work) = 0.4155          |
| start r-factor (free) = 0.4802      final r-factor (free) = 0.4800          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.6225 = 2.33 * 1.00 * 6.2692 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.5293 = 2.33 * 1.00 * 6.2245 + 1.00 * 0.0254                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 34     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.821)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.28  18.20    None  None   None       |
|    all(noH): 2823   0      0.00    102.28  18.20    None  None   None       |
|    Sol.    : 438    0      0.00    102.28  27.23    None  None   None       |
|    Mac.    : 2385   0      0.00    82.98   16.54    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.228: 1025   |   5:    51.139 -  61.366:   63        |
|      1:    10.228 -  20.455:  806   |   6:    61.366 -  71.594:   29        |
|      2:    20.455 -  30.683:  480   |   7:    71.594 -  81.822:   12        |
|      3:    30.683 -  40.911:  276   |   8:    81.822 -  92.049:    6        |
|      4:    40.911 -  51.139:  123   |   9:    92.049 - 102.277:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4155 r_free = 0.4800             target_work(ml) = 6.216         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4151 r_free = 0.4802             target_work(ml) = 6.216         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4151   r_free= 0.4802   ksol= 0.31   Bsol= 0.00   scale= 1.130    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.22,10.77,9.27,0.00,0.00,0.00); trace/3= 9.08                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.216187                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4132   r_free= 0.4746   ksol= 0.30   Bsol= 20.00   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.31,6.31,5.59,0.00,0.00,0.00); trace/3= 5.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.216010                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.003776             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.694  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.782943              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.151  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4132      final r-factor (work) = 0.3419          |
| start r-factor (free) = 0.4746      final r-factor (free) = 0.4088          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 56.1658 = 18.00 * 0.50 * 6.2213 + 1.00 * 0.1625                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 55.4773 = 18.00 * 0.50 * 6.1491 + 1.00 * 0.1243                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3419      final r-factor (work) = 0.3193          |
| start r-factor (free) = 0.4088      final r-factor (free) = 0.3885          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8410 = 0.78 * 1.00 * 6.1491 + 1.00 * 0.0267                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7569 = 0.78 * 1.00 * 6.0546 + 1.00 * 0.0166                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.821)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.62   16.26    None  None   None       |
|    all(noH): 2823   0      0.00    86.62   16.26    None  None   None       |
|    Sol.    : 438    0      0.00    86.62   30.02    None  None   None       |
|    Mac.    : 2385   0      0.00    83.17   13.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.662:  942   |   5:    43.309 -  51.971:   71        |
|      1:     8.662 -  17.324:  872   |   6:    51.971 -  60.633:   25        |
|      2:    17.324 -  25.985:  476   |   7:    60.633 -  69.295:   15        |
|      3:    25.985 -  34.647:  275   |   8:    69.295 -  77.956:    9        |
|      4:    34.647 -  43.309:  135   |   9:    77.956 -  86.618:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3193 r_free = 0.3885             target_work(ml) = 6.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3190 r_free = 0.3879             target_work(ml) = 6.029         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3190   r_free= 0.3879   ksol= 0.30   Bsol= 20.00   scale= 1.079   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.31,6.31,5.59,0.00,0.00,0.00); trace/3= 5.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.029008                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3158   r_free= 0.3825   ksol= 0.32   Bsol= 48.04   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.74,3.13,2.83,0.00,0.00,0.00); trace/3= 2.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.026205                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.857791              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.220  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.311115              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 100.612  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3158      final r-factor (work) = 0.2391          |
| start r-factor (free) = 0.3825      final r-factor (free) = 0.2949          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.9454 = 8.86 * 0.50 * 6.0559 + 1.00 * 0.1243                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.3855 = 8.86 * 0.50 * 5.9356 + 1.00 * 0.0973                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2391      final r-factor (work) = 0.2186          |
| start r-factor (free) = 0.2949      final r-factor (free) = 0.2713          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8599 = 0.31 * 1.00 * 5.9356 + 1.00 * 0.0132                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8038 = 0.31 * 1.00 * 5.7549 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.821)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.05   15.53    None  None   None       |
|    all(noH): 2823   0      0.00    81.05   15.53    None  None   None       |
|    Sol.    : 438    0      3.53    77.21   34.63    None  None   None       |
|    Mac.    : 2385   0      0.00    81.05   12.02    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 -   8.106:  965   |   5:    40.527 -  48.633:  112        |
|      1:     8.106 -  16.211:  972   |   6:    48.633 -  56.738:   52        |
|      2:    16.211 -  24.316:  359   |   7:    56.738 -  64.844:   22        |
|      3:    24.316 -  32.422:  183   |   8:    64.844 -  72.949:    8        |
|      4:    32.422 -  40.527:  143   |   9:    72.949 -  81.054:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2186 r_free = 0.2713             target_work(ml) = 5.715         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2181 r_free = 0.2710             target_work(ml) = 5.714         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2181   r_free= 0.2710   ksol= 0.32   Bsol= 48.04   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.74,3.13,2.83,0.00,0.00,0.00); trace/3= 2.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.713730                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2168   r_free= 0.2705   ksol= 0.32   Bsol= 48.04   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,1.37,1.53,0.00,0.00,0.00); trace/3= 0.69                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.714364                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.862425              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.642  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.655482              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.590   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2168      final r-factor (work) = 0.1639          |
| start r-factor (free) = 0.2705      final r-factor (free) = 0.2106          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.0998 = 4.86 * 0.50 * 5.7595 + 1.00 * 0.0973                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.7212 = 4.86 * 0.50 * 5.6106 + 1.00 * 0.0807                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1639      final r-factor (work) = 0.1484          |
| start r-factor (free) = 0.2106      final r-factor (free) = 0.1993          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6870 = 0.66 * 1.00 * 5.6106 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5651 = 0.66 * 1.00 * 5.4203 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.821)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.75   16.29    None  None   None       |
|    all(noH): 2823   0      0.00    91.75   16.29    None  None   None       |
|    Sol.    : 438    0      4.16    84.85   41.96    None  None   None       |
|    Mac.    : 2385   0      0.00    91.75   11.58    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.175: 1213   |   5:    45.875 -  55.049:  101        |
|      1:     9.175 -  18.350:  927   |   6:    55.049 -  64.224:   80        |
|      2:    18.350 -  27.525:  220   |   7:    64.224 -  73.399:   41        |
|      3:    27.525 -  36.700:  117   |   8:    73.399 -  82.574:   13        |
|      4:    36.700 -  45.875:  106   |   9:    82.574 -  91.749:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1484 r_free = 0.1993             target_work(ml) = 5.392         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1482 r_free = 0.1993             target_work(ml) = 5.391         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1482   r_free= 0.1993   ksol= 0.32   Bsol= 48.04   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,1.37,1.53,0.00,0.00,0.00); trace/3= 0.69                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.391080                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1482   r_free= 0.1995   ksol= 0.33   Bsol= 59.17   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.36,0.59,1.18,0.00,0.00,0.00); trace/3= 0.14                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.390639                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.588424              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.611  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.161925              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.164  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1482      final r-factor (work) = 0.1330          |
| start r-factor (free) = 0.1995      final r-factor (free) = 0.1837          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0989 = 2.59 * 0.50 * 5.4228 + 1.00 * 0.0807                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9858 = 2.59 * 0.50 * 5.3456 + 1.00 * 0.0675                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1330      final r-factor (work) = 0.1319          |
| start r-factor (free) = 0.1837      final r-factor (free) = 0.1796          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8776 = 0.16 * 1.00 * 5.3456 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9169 = 0.16 * 1.00 * 5.3032 + 1.00 * 0.0582                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.821)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.50   16.25    None  None   None       |
|    all(noH): 2823   0      0.00    91.50   16.25    None  None   None       |
|    Sol.    : 438    0      4.13    84.43   41.42    None  None   None       |
|    Mac.    : 2385   0      0.00    91.50   11.63    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.150: 1217   |   5:    45.750 -  54.899:   96        |
|      1:     9.150 -  18.300:  946   |   6:    54.899 -  64.049:   80        |
|      2:    18.300 -  27.450:  205   |   7:    64.049 -  73.199:   38        |
|      3:    27.450 -  36.600:  112   |   8:    73.199 -  82.349:   13        |
|      4:    36.600 -  45.750:  111   |   9:    82.349 -  91.499:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1319 r_free = 0.1796             target_work(ml) = 5.290         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1317 r_free = 0.1793             target_work(ml) = 5.288         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1317   r_free= 0.1793   ksol= 0.33   Bsol= 59.17   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.36,0.59,1.18,0.00,0.00,0.00); trace/3= 0.14                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.288248                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9945 -  4.6581 0.99   1472  161 0.1010 0.1463      5.4387      5.6588|
|  2:  4.6581 -  3.7158 0.99   1416  156 0.0934 0.1113      5.5215      5.7195|
|  3:  3.7158 -  3.2515 0.99   1376  158 0.1266 0.1726       5.608      5.9056|
|  4:  3.2515 -  2.9567 0.98   1384  145 0.1484 0.1927      5.5791      5.7657|
|  5:  2.9567 -  2.7462 0.99   1372  157 0.1625 0.1905      5.4894      5.6427|
|  6:  2.7462 -  2.5851 0.99   1370  151 0.1494 0.2339      5.3555      5.5813|
|  7:  2.5851 -  2.4563 0.98   1330  158 0.1482 0.1821      5.2913      5.4283|
|  8:  2.4563 -  2.3498 0.98   1376  145 0.1441 0.2103      5.2174      5.4599|
|  9:  2.3498 -  2.2596 0.99   1339  145 0.1380 0.1966      5.1447      5.3815|
| 10:  2.2596 -  2.1819 0.99   1354  146 0.1383 0.2052      5.0987      5.3098|
| 11:  2.1819 -  2.1139 0.97   1334  157 0.1377 0.2029      5.0384      5.3445|
| 12:  2.1139 -  2.0536 0.98   1333  149 0.1347 0.1758      4.9788      5.1712|
| 13:  2.0536 -  1.9997 0.71    954  104 0.1344 0.2052      4.8945      5.1069|
| 14:  1.9997 -  1.9510 0.16    220   27 0.1198 0.1805      4.8408      4.9765|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9945 -  4.6581  1472   161  0.93  10.40   0.97     0.95       8709.09|
|  2:  4.6581 -  3.7158  1416   156  0.94   9.53   1.02     1.01      11009.09|
|  3:  3.7158 -  3.2515  1376   158  0.92  13.67   1.03     1.02      13230.21|
|  4:  3.2515 -  2.9567  1384   145  0.89  16.99   1.02     1.01      13113.08|
|  5:  2.9567 -  2.7462  1372   157  0.88  18.99   1.01     0.99      11553.72|
|  6:  2.7462 -  2.5851  1370   151  0.87  19.78   0.98     0.95       9526.05|
|  7:  2.5851 -  2.4563  1330   158  0.88  18.61   1.00     0.96       8053.88|
|  8:  2.4563 -  2.3498  1376   145  0.88  18.99   1.01     0.97       7218.60|
|  9:  2.3498 -  2.2596  1339   145  0.88  18.31   1.01     0.97       6297.73|
| 10:  2.2596 -  2.1819  1354   146  0.87  19.08   1.01     0.99       5958.29|
| 11:  2.1819 -  2.1139  1334   157  0.88  19.13   1.01     0.96       5396.94|
| 12:  2.1139 -  2.0536  1333   149  0.88  18.37   1.01     1.00       4748.50|
| 13:  2.0536 -  1.9997   954   104  0.88  18.72   0.99     0.99       4092.63|
| 14:  1.9997 -  1.9510   220    27  0.90  15.79   0.98     0.92       3295.88|
|alpha:            min =        0.92 max =            1.02 mean =         0.98|
|beta:             min =     3295.88 max =        13230.21 mean =      8449.67|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.89 mean =        16.84|
|phase err.(test): min =        0.00 max =           89.70 mean =        16.34|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1316   r_free= 0.1794   ksol= 0.33   Bsol= 55.96   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.53,0.16,0.99,0.00,0.00,0.00); trace/3= -0.13                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.288142                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1316   r_free= 0.1794   ksol= 0.33   Bsol= 55.96   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.53,0.16,0.99,0.00,0.00,0.00); trace/3= -0.13                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.288142                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9945 -  4.6581 0.99   1472  161 0.1008 0.1460      5.4372      5.6557|
|  2:  4.6581 -  3.7158 0.99   1416  156 0.0932 0.1110      5.5195      5.7171|
|  3:  3.7158 -  3.2515 0.99   1376  158 0.1266 0.1725      5.6079      5.9067|
|  4:  3.2515 -  2.9567 0.98   1384  145 0.1484 0.1931      5.5797      5.7665|
|  5:  2.9567 -  2.7462 0.99   1372  157 0.1625 0.1903      5.4898      5.6423|
|  6:  2.7462 -  2.5851 0.99   1370  151 0.1493 0.2340      5.3555      5.5817|
|  7:  2.5851 -  2.4563 0.98   1330  158 0.1483 0.1822      5.2914      5.4284|
|  8:  2.4563 -  2.3498 0.98   1376  145 0.1440 0.2102      5.2174      5.4609|
|  9:  2.3498 -  2.2596 0.99   1339  145 0.1381 0.1967      5.1448      5.3821|
| 10:  2.2596 -  2.1819 0.99   1354  146 0.1381 0.2053      5.0987      5.3106|
| 11:  2.1819 -  2.1139 0.97   1334  157 0.1377 0.2031      5.0385      5.3443|
| 12:  2.1139 -  2.0536 0.98   1333  149 0.1348 0.1756      4.9794      5.1719|
| 13:  2.0536 -  1.9997 0.71    954  104 0.1346 0.2047      4.8947      5.1047|
| 14:  1.9997 -  1.9510 0.16    220   27 0.1197 0.1806      4.8421      4.9795|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9945 -  4.6581  1472   161  0.93  10.36   0.97     0.95       8678.70|
|  2:  4.6581 -  3.7158  1416   156  0.94   9.49   1.02     1.01      10965.43|
|  3:  3.7158 -  3.2515  1376   158  0.92  13.64   1.02     1.02      13203.77|
|  4:  3.2515 -  2.9567  1384   145  0.89  16.99   1.01     1.00      13129.61|
|  5:  2.9567 -  2.7462  1372   157  0.88  18.98   1.00     0.98      11556.01|
|  6:  2.7462 -  2.5851  1370   151  0.87  19.76   0.97     0.94       9529.41|
|  7:  2.5851 -  2.4563  1330   158  0.88  18.61   0.99     0.95       8053.45|
|  8:  2.4563 -  2.3498  1376   145  0.88  19.00   1.00     0.96       7228.56|
|  9:  2.3498 -  2.2596  1339   145  0.88  18.33   1.00     0.96       6310.35|
| 10:  2.2596 -  2.1819  1354   146  0.87  19.08   1.00     0.97       5965.95|
| 11:  2.1819 -  2.1139  1334   157  0.88  19.13   1.00     0.95       5402.40|
| 12:  2.1139 -  2.0536  1333   149  0.88  18.35   0.99     0.99       4747.57|
| 13:  2.0536 -  1.9997   954   104  0.88  18.71   0.98     0.97       4087.45|
| 14:  1.9997 -  1.9510   220    27  0.90  15.80   0.97     0.91       3293.76|
|alpha:            min =        0.91 max =            1.02 mean =         0.97|
|beta:             min =     3293.76 max =        13203.77 mean =      8445.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.91 mean =        16.83|
|phase err.(test): min =        0.00 max =           89.71 mean =        16.33|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.821)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.50   16.26    None  None   None       |
|    all(noH): 2823   0      0.00    91.50   16.26    None  None   None       |
|    Sol.    : 438    0      4.14    84.43   41.42    None  None   None       |
|    Mac.    : 2385   0      0.00    91.50   11.63    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:     0.003 -   9.153: 1217   |   5:    45.752 -  54.902:   96        |
|      1:     9.153 -  18.303:  946   |   6:    54.902 -  64.052:   80        |
|      2:    18.303 -  27.453:  205   |   7:    64.052 -  73.202:   38        |
|      3:    27.453 -  36.603:  112   |   8:    73.202 -  82.352:   13        |
|      4:    36.603 -  45.752:  111   |   9:    82.352 -  91.502:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 352         
Filter by distance & map next to the model:
   mapped sites are within: 0.384 - 4.597
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 342 from: 352
   mapped sites are within: 0.721 - 4.597

peak=    9.663 closest distance to " CB  VAL A 230 " =    1.411
peak=    6.530 closest distance to " CD1AILE A 234 " =    1.335
peak=    6.332 closest distance to " O   HOH Z 404 " =    1.634
peak=    6.137 closest distance to " O   HOH Z 255 " =    1.069
peak=    6.053 closest distance to " O   HOH Z 169 " =    0.969
peak=    5.807 closest distance to " O   HOH Z 117 " =    1.351
peak=    5.788 closest distance to " O   HOH Z 124 " =    1.614
peak=    5.700 closest distance to " O   HOH Z 403 " =    2.144
peak=    5.608 closest distance to " CG1 VAL A 296 " =    1.187
peak=    5.607 closest distance to " O   HOH Z 248 " =    1.587
peak=    5.550 closest distance to " O   HOH Z 210 " =    1.431
peak=    5.179 closest distance to " O   HOH Z  45 " =    1.029
peak=    5.159 closest distance to " O   HOH Z 277 " =    1.639
peak=    5.123 closest distance to " CD2 LEU A   5 " =    1.077
peak=    5.119 closest distance to " CD2 LEU A 228 " =    1.282
peak=    4.977 closest distance to " CB  ARG A 275 " =    0.864
peak=    4.963 closest distance to " O   HOH Z 128 " =    1.884
peak=    4.897 closest distance to " CG  LEU A   5 " =    1.394
peak=    4.844 closest distance to " O   HOH Z 425 " =    1.531
peak=    4.839 closest distance to " CG  PRO A  54 " =    1.407
peak=    4.744 closest distance to " O   HOH Z  76 " =    1.327
peak=    4.741 closest distance to " O   HOH Z  43 " =    2.404
peak=    4.693 closest distance to " O   HOH Z 102 " =    1.449
peak=    4.670 closest distance to " O   HOH Z 193 " =    2.125
peak=    4.572 closest distance to " CD2 TRP A 179 " =    1.355
peak=    4.547 closest distance to " CA  TYR A  30 " =    1.013
peak=    4.523 closest distance to " O   HOH Z 154 " =    1.855
peak=    4.477 closest distance to " O   HOH Z 394 " =    1.758
peak=    4.470 closest distance to " O   HOH Z  97 " =    1.409
peak=    4.465 closest distance to " O   GLN A  11 " =    0.812
peak=    4.450 closest distance to " NH2 ARG A  56 " =    2.096
peak=    4.422 closest distance to " O   HOH Z 402 " =    1.567
peak=    4.408 closest distance to " O   HOH Z  49 " =    1.562
peak=    4.396 closest distance to " CB  VAL A 296 " =    1.553
peak=    4.352 closest distance to " O   HOH Z 411 " =    3.569
peak=    4.344 closest distance to " CG2 VAL A 296 " =    1.041
peak=    4.343 closest distance to " O   HOH Z 130 " =    2.558
peak=    4.320 closest distance to " NH2 ARG A 156 " =    1.066
peak=    4.309 closest distance to " O   HOH Z 142 " =    2.520
peak=    4.291 closest distance to " O   HOH Z 238 " =    2.023
peak=    4.289 closest distance to " O   HOH Z 406 " =    1.616
peak=    4.258 closest distance to " CB  GLN A 223 " =    1.494
peak=    4.248 closest distance to " CD  ARG A 159 " =    0.801
peak=    4.220 closest distance to " CA  ALA A  51 " =    1.085
peak=    4.217 closest distance to " NE2 GLN A  11 " =    1.033
peak=    4.213 closest distance to " O   HOH Z 126 " =    1.557
peak=    4.203 closest distance to " O   PRO A 198 " =    1.608
peak=    4.187 closest distance to " O   HOH Z 146 " =    1.647
peak=    4.179 closest distance to " O   HOH Z 403 " =    1.583
peak=    4.174 closest distance to " CB  VAL A 230 " =    1.220
peak=    4.166 closest distance to " O   HOH Z 431 " =    1.360
peak=    4.155 closest distance to " CB  VAL A 296 " =    1.121
peak=    4.144 closest distance to " CB  SER A  26 " =    1.770
peak=    4.140 closest distance to " CZ3 TRP A 266 " =    1.046
peak=    4.140 closest distance to " O   HOH Z 359 " =    1.822
peak=    4.133 closest distance to " CB  SER A  63 " =    1.222
peak=    4.131 closest distance to " CB  GLN A 183 " =    1.269
peak=    4.127 closest distance to " NH1AARG A 275 " =    1.108
peak=    4.110 closest distance to " CG  ARG A  66 " =    0.958
peak=    4.107 closest distance to " CB  GLN A  55 " =    0.851
peak=    4.098 closest distance to " O   HOH Z  85 " =    1.778
peak=    4.081 closest distance to " O   HOH Z 234 " =    3.565
peak=    4.078 closest distance to " CD  PRO A  54 " =    0.972
peak=    4.077 closest distance to " O   HOH Z  80 " =    2.249
peak=    4.075 closest distance to " O   HOH Z 236 " =    1.695
peak=    4.071 closest distance to " O   HOH Z 433 " =    1.553
peak=    4.052 closest distance to " CB  PRO A  54 " =    1.027
peak=    4.028 closest distance to " CG AARG A 275 " =    1.293
peak=    4.021 closest distance to " O   HOH Z 272 " =    1.912
peak=    4.019 closest distance to " O   HOH Z 132 " =    2.769
peak=    4.015 closest distance to " O   HOH Z 193 " =    1.714
peak=    4.010 closest distance to " CG1 ILE A  20 " =    1.365
peak=    4.002 closest distance to " O   HOH Z 357 " =    2.048
peak=    3.999 closest distance to " O   HOH Z 120 " =    0.733
peak=    3.989 closest distance to " CZ  PHE A 218 " =    1.111
peak=    3.975 closest distance to " CB BVAL A  41 " =    0.964
peak=    3.975 closest distance to " CB  ASN A 148 " =    1.210
peak=    3.971 closest distance to " O   HOH Z 246 " =    1.247
peak=    3.969 closest distance to " CD  LYS A 166 " =    1.563
peak=    3.960 closest distance to " CE1 TYR A 186 " =    1.270
peak=    3.947 closest distance to " O   HOH Z 144 " =    1.642
peak=    3.928 closest distance to " CB  ASN A 187 " =    1.579
peak=    3.919 closest distance to " O   HOH Z 158 " =    1.060
peak=    3.911 closest distance to " O   HOH Z 414 " =    2.387
peak=    3.880 closest distance to " CA  ASP A 162 " =    1.025
peak=    3.856 closest distance to " CA  ASP A 191 " =    1.177
peak=    3.855 closest distance to " NZ  LYS A 117 " =    2.620
peak=    3.843 closest distance to " O   HOH Z 389 " =    2.057
peak=    3.839 closest distance to " O   HOH Z  63 " =    1.688
peak=    3.835 closest distance to " CB  GLU A 277 " =    0.932
peak=    3.828 closest distance to " O   HOH Z 409 " =    3.507
peak=    3.819 closest distance to " O   HOH Z 380 " =    1.921
peak=    3.819 closest distance to " CA  ALA A 295 " =    0.857
peak=    3.809 closest distance to " CB  ASN A 285 " =    0.939
peak=    3.808 closest distance to " CG  PRO A 243 " =    1.186
peak=    3.805 closest distance to " O   HOH Z  44 " =    1.366
peak=    3.805 closest distance to " CD  LYS A  76 " =    1.738
peak=    3.794 closest distance to " O   ASP A 200 " =    1.573
peak=    3.793 closest distance to " CG  PRO A 198 " =    1.297
peak=    3.790 closest distance to " CD2 LEU A 297 " =    0.870
peak=    3.790 closest distance to " OE1 GLN A  11 " =    1.961
peak=    3.785 closest distance to " O   HOH Z 126 " =    1.762
peak=    3.780 closest distance to " O   ASP A 124 " =    1.657
peak=    3.772 closest distance to " O   HOH Z 316 " =    3.123
peak=    3.770 closest distance to " O   HOH Z 368 " =    2.321
peak=    3.761 closest distance to " O   HOH Z 346 " =    1.654
peak=    3.757 closest distance to " O   HOH Z 423 " =    1.704
peak=    3.757 closest distance to " O   HOH Z 146 " =    1.366
peak=    3.748 closest distance to " O   HOH Z  40 " =    2.264
peak=    3.735 closest distance to " O   GLU A   2 " =    1.722
peak=    3.732 closest distance to " CB  SER A  62 " =    1.114
peak=    3.717 closest distance to " CB  ARG A  79 " =    1.199
peak=    3.717 closest distance to " CG2 VAL A 197 " =    1.098
peak=    3.717 closest distance to " NH2AARG A 145 " =    0.949
peak=    3.711 closest distance to " O   HOH Z 287 " =    1.757
peak=    3.709 closest distance to " O   HOH Z 134 " =    1.806
peak=    3.706 closest distance to " O   ALA A 165 " =    1.313
peak=    3.696 closest distance to " OD1 ASN A 301 " =    0.992
peak=    3.692 closest distance to " CZ  PHE A  38 " =    1.142
peak=    3.690 closest distance to " CA  ALA A 100 " =    1.096
peak=    3.686 closest distance to " O   HOH Z 371 " =    2.887
peak=    3.683 closest distance to " O   HOH Z 209 " =    2.334
peak=    3.667 closest distance to " CB  TYR A  30 " =    1.063
peak=    3.665 closest distance to " O   HOH Z 372 " =    0.948
peak=    3.659 closest distance to " CA  VAL A  41 " =    0.792
peak=    3.654 closest distance to " O   HOH Z 423 " =    2.023
peak=    3.652 closest distance to " O   HOH Z 327 " =    1.685
peak=    3.648 closest distance to " O   HOH Z   4 " =    1.702
peak=    3.639 closest distance to " CB  SER A 146 " =    1.046
peak=    3.637 closest distance to " CB  GLU A 152 " =    1.128
peak=    3.637 closest distance to " CB  VAL A 202 " =    1.354
peak=    3.633 closest distance to " OE1 GLU A   2 " =    1.499
peak=    3.623 closest distance to " CB  ASN A 142 " =    1.121
peak=    3.622 closest distance to " O   HOH Z 419 " =    2.004
peak=    3.621 closest distance to " CG2AVAL A 121 " =    1.988
peak=    3.617 closest distance to " O   HOH Z 298 " =    4.118
peak=    3.616 closest distance to " CB  SER A 141 " =    1.128
peak=    3.615 closest distance to " O   HOH Z  68 " =    1.911
peak=    3.611 closest distance to " O   SER A  87 " =    2.228
peak=    3.609 closest distance to " O   HOH Z 111 " =    1.648
peak=    3.594 closest distance to " O   HOH Z 369 " =    2.154
peak=    3.588 closest distance to " NE1 TRP A  92 " =    1.519
peak=    3.584 closest distance to " CB  TRP A 179 " =    1.294
peak=    3.584 closest distance to " CG2 THR A 220 " =    0.797
peak=    3.574 closest distance to " O   HOH Z 258 " =    1.285
peak=    3.573 closest distance to " O   HOH Z 339 " =    1.370
peak=    3.573 closest distance to " CE1 HIS A 108 " =    1.184
peak=    3.565 closest distance to " O   HOH Z 279 " =    0.973
peak=    3.562 closest distance to " O   HOH Z 299 " =    2.376
peak=    3.557 closest distance to " CB  ALA A 248 " =    1.443
peak=    3.552 closest distance to " O   HOH Z  61 " =    1.655
peak=    3.551 closest distance to " CD1 LEU A   5 " =    1.655
peak=    3.549 closest distance to " CA  SER A  12 " =    1.359
peak=    3.535 closest distance to " CG1BVAL A  72 " =    1.704
peak=    3.535 closest distance to " O   HOH Z 383 " =    1.972
peak=    3.533 closest distance to " CA  ARG A  36 " =    1.020
peak=    3.530 closest distance to " CB  PRO A 243 " =    1.139
peak=    3.528 closest distance to " CZ3 TRP A  85 " =    0.992
peak=    3.515 closest distance to " O   HOH Z 344 " =    1.717
peak=    3.513 closest distance to " O   HOH Z 188 " =    2.862
peak=    3.511 closest distance to " O   GLY A  91 " =    1.316
peak=    3.502 closest distance to " O   HOH Z 214 " =    3.141
peak=    3.500 closest distance to " O   HOH Z  30 " =    1.245
peak=    3.497 closest distance to " CD  LYS A 119 " =    1.745
peak=    3.493 closest distance to " OG  SER A 245 " =    1.488
peak=    3.490 closest distance to " O   HOH Z 232 " =    2.417
peak=    3.481 closest distance to " O   HOH Z 132 " =    2.461
peak=    3.477 closest distance to " O   HOH Z  88 " =    3.244
peak=    3.477 closest distance to " O   HOH Z  99 " =    1.913
peak=    3.471 closest distance to " CB  PRO A 198 " =    1.265
peak=    3.471 closest distance to " O  BHOH Z 338 " =    1.065
peak=    3.467 closest distance to " O   HOH Z 375 " =    1.024
peak=    3.466 closest distance to " CA  TRP A  85 " =    1.173
peak=    3.465 closest distance to " O   HOH Z  65 " =    0.869
peak=    3.464 closest distance to " CG  PHE A 204 " =    0.995
peak=    3.464 closest distance to " CD1 ILE A 199 " =    1.357
peak=    3.459 closest distance to " CG AARG A 102 " =    1.109
peak=    3.457 closest distance to " O   HOH Z 426 " =    1.250
peak=    3.453 closest distance to " OG  SER A  62 " =    2.647
peak=    3.453 closest distance to " OG BSER A 212 " =    2.472
peak=    3.451 closest distance to " O  BHOH Z  74 " =    1.319
peak=    3.448 closest distance to " NE2 GLN A  77 " =    3.255
peak=    3.445 closest distance to " CG2 ILE A 234 " =    1.267
peak=    3.444 closest distance to " CB  ASP A 140 " =    0.898
peak=    3.442 closest distance to " CD1 LEU A  96 " =    1.126
peak=    3.439 closest distance to " O   HOH Z 422 " =    2.802
peak=    3.438 closest distance to " N   SER A 164 " =    0.951
peak=    3.436 closest distance to " O   HOH Z 234 " =    1.902
peak=    3.434 closest distance to " CE1 TYR A  30 " =    1.127
peak=    3.434 closest distance to " CB  THR A 235 " =    1.301
peak=    3.433 closest distance to " O   HOH Z 315 " =    1.851
peak=    3.432 closest distance to " O  BHOH Z 338 " =    2.128
peak=    3.427 closest distance to " O   ALA A 292 " =    1.268
peak=    3.422 closest distance to " O   HOH Z 188 " =    1.300
peak=    3.421 closest distance to " CG  LEU A 167 " =    1.073
peak=    3.414 closest distance to " O   HOH Z 213 " =    1.446
peak=    3.413 closest distance to " O   HOH Z 142 " =    1.749
peak=    3.411 closest distance to " O   HOH Z  56 " =    1.608
peak=    3.411 closest distance to " CB  PHE A 204 " =    0.927
peak=    3.407 closest distance to " CB  SER A   3 " =    1.199
peak=    3.406 closest distance to " CG  LEU A 228 " =    1.274
peak=    3.401 closest distance to " O   THR A 182 " =    1.589
peak=    3.387 closest distance to " CG  PRO A 280 " =    0.904
peak=    3.384 closest distance to " O   HOH Z 345 " =    1.844
peak=    3.379 closest distance to " CB  MET A  47 " =    1.024
peak=    3.376 closest distance to " O   HOH Z 166 " =    1.707
peak=    3.372 closest distance to " CB  GLU A 175 " =    1.261
peak=    3.370 closest distance to " O   HOH Z 285 " =    1.816
peak=    3.369 closest distance to " O   HOH Z  39 " =    1.116
peak=    3.366 closest distance to " NZ  LYS A  76 " =    0.875
peak=    3.365 closest distance to " CA  THR A 246 " =    1.047
peak=    3.364 closest distance to " CB  GLN A  89 " =    1.318
peak=    3.357 closest distance to " CA  ARG A 195 " =    1.152
peak=    3.356 closest distance to " N   VAL A 126 " =    1.865
peak=    3.356 closest distance to " OD1 ASN A 217 " =    1.703
peak=    3.353 closest distance to " OE1 GLN A 223 " =    2.213
peak=    3.352 closest distance to " CD  ARG A 195 " =    1.020
peak=    3.351 closest distance to " O   HOH Z 361 " =    3.249
peak=    3.348 closest distance to " O   HOH Z  42 " =    2.388
peak=    3.342 closest distance to " CB  ASN A  45 " =    1.136
peak=    3.335 closest distance to " O   HOH Z 299 " =    3.921
peak=    3.331 closest distance to " O   HOH Z 214 " =    1.443
peak=    3.329 closest distance to " CG2 ILE A  20 " =    1.383
peak=    3.326 closest distance to " CA  THR A  82 " =    1.492
peak=    3.320 closest distance to " CA  ASN A 217 " =    1.244
peak=    3.320 closest distance to " NH2 ARG A  56 " =    1.082
peak=    3.310 closest distance to " CG  MET A 185 " =    1.372
peak=    3.303 closest distance to " N   THR A  42 " =    1.518
peak=    3.302 closest distance to " O   HOH Z   4 " =    1.931
peak=    3.299 closest distance to " O   HOH Z 417 " =    3.592
peak=    3.294 closest distance to " NH1 ARG A  14 " =    1.008
peak=    3.294 closest distance to " O   HOH Z 303 " =    2.343
peak=    3.289 closest distance to " CB  TRP A 179 " =    1.886
peak=    3.289 closest distance to " O   PRO A 213 " =    1.284
peak=    3.289 closest distance to " CB  ALA A 114 " =    0.721
peak=    3.288 closest distance to " CB  SER A 271 " =    1.226
peak=    3.285 closest distance to " O   HOH Z 313 " =    1.818
peak=    3.282 closest distance to " O   HOH Z 130 " =    1.102
peak=    3.272 closest distance to " CB  ARG A 190 " =    1.906
peak=    3.271 closest distance to " CB  SER A  62 " =    3.776
peak=    3.267 closest distance to " CB  GLN A  58 " =    0.950
peak=    3.266 closest distance to " O   HOH Z 375 " =    1.463
peak=    3.263 closest distance to " NH2 ARG A  79 " =    1.290
peak=    3.261 closest distance to " CB  PHE A  16 " =    1.262
peak=    3.261 closest distance to " CA  ALA A  21 " =    0.991
peak=    3.259 closest distance to " N   GLU A  44 " =    1.475
peak=    3.258 closest distance to " CZ2 TRP A 274 " =    1.074
peak=    3.257 closest distance to " CB  TYR A 169 " =    0.895
peak=    3.255 closest distance to " O   HOH Z 427 " =    2.843
peak=    3.252 closest distance to " CB  VAL A 265 " =    1.315
peak=    3.251 closest distance to " CD2 TYR A 186 " =    1.073
peak=    3.248 closest distance to " O   HOH Z 147 " =    1.629
peak=    3.248 closest distance to " O   HOH Z  95 " =    1.595
peak=    3.245 closest distance to " CA  ALA A 160 " =    0.943
peak=    3.245 closest distance to " O   HOH Z 214 " =    2.671
peak=    3.245 closest distance to " CA  GLY A 196 " =    0.742
peak=    3.245 closest distance to " SD  MET A 185 " =    1.382
peak=    3.244 closest distance to " O   GLN A  88 " =    1.475
peak=    3.243 closest distance to " O   HOH Z 337 " =    2.189
peak=    3.241 closest distance to " O   HOH Z 183 " =    1.886
peak=    3.237 closest distance to " O   HOH Z   1 " =    2.420
peak=    3.236 closest distance to " NH2 ARG A  36 " =    1.841
peak=    3.235 closest distance to " O   HOH Z 340 " =    1.483
peak=    3.234 closest distance to " O   HOH Z 251 " =    1.426
peak=    3.233 closest distance to " O   HOH Z 245 " =    1.476
peak=    3.233 closest distance to " O   HOH Z 257 " =    2.383
peak=    3.232 closest distance to " O   HOH Z  78 " =    1.587
peak=    3.232 closest distance to " CB  THR A  31 " =    1.469
peak=    3.230 closest distance to " O   HOH Z 109 " =    1.952
peak=    3.230 closest distance to " O   HOH Z 435 " =    1.808
peak=    3.228 closest distance to " O   CYS A 168 " =    1.471
peak=    3.227 closest distance to " CA  ASN A  39 " =    1.199
peak=    3.226 closest distance to " CA  ALA A 129 " =    0.811
peak=    3.226 closest distance to " O   HOH Z 265 " =    2.005
peak=    3.225 closest distance to " O   HOH Z 412 " =    3.516
peak=    3.225 closest distance to " O   ASP A 191 " =    1.686
peak=    3.223 closest distance to " O   HOH Z  46 " =    1.233
peak=    3.222 closest distance to " O   HOH Z 327 " =    3.060
peak=    3.215 closest distance to " O   HOH Z 156 " =    2.249
peak=    3.214 closest distance to " OG BSER A 258 " =    2.716
peak=    3.214 closest distance to " O   HOH Z 313 " =    1.842
peak=    3.212 closest distance to " CB  SER A  28 " =    0.926
peak=    3.211 closest distance to " CA  SER A  32 " =    1.729
peak=    3.206 closest distance to " CB  GLU A  46 " =    1.046
peak=    3.206 closest distance to " O   HOH Z  59 " =    2.051
peak=    3.205 closest distance to " N   TYR A  15 " =    0.825
peak=    3.203 closest distance to " O   HOH Z  83 " =    1.561
peak=    3.203 closest distance to " N   ASN A  39 " =    1.273
peak=    3.195 closest distance to " O   HOH Z  15 " =    2.375
peak=    3.193 closest distance to " N   ASN A 148 " =    0.892
peak=    3.191 closest distance to " CB  ALA A  71 " =    1.316
peak=    3.190 closest distance to " O   HOH Z 366 " =    2.155
peak=    3.185 closest distance to " O   HOH Z 244 " =    1.627
peak=    3.182 closest distance to " CB  ALA A   1 " =    1.285
peak=    3.182 closest distance to " CG1 ILE A  33 " =    1.204
peak=    3.182 closest distance to " CB  ASN A 209 " =    0.956
peak=    3.176 closest distance to " OH  TYR A 116 " =    1.182
peak=    3.167 closest distance to " O   HOH Z 423 " =    3.019
peak=    3.166 closest distance to " CA  ASP A 149 " =    1.295
peak=    3.162 closest distance to " O   HOH Z 129 " =    2.510
peak=    3.162 closest distance to " CB  ASP A 124 " =    0.771
peak=    3.161 closest distance to " N   GLN A 205 " =    1.078
peak=    3.158 closest distance to " O   HOH Z 301 " =    1.550
peak=    3.144 closest distance to " CG  ARG A 269 " =    1.835
peak=    3.142 closest distance to " O   HOH Z 298 " =    1.796
peak=    3.140 closest distance to " ND2AASN A 224 " =    0.877
peak=    3.136 closest distance to " O   HOH Z 259 " =    2.121
peak=    3.135 closest distance to " O   HOH Z 420 " =    4.597
peak=    3.130 closest distance to " CA  ILE A 120 " =    1.070
peak=    3.130 closest distance to " CB  ARG A 259 " =    1.999
peak=    3.126 closest distance to " O   HOH Z 199 " =    1.477
peak=    3.123 closest distance to " CB  PRO A  90 " =    1.138
peak=    3.123 closest distance to " O   HOH Z 428 " =    3.904
peak=    3.121 closest distance to " O   HOH Z 437 " =    2.213
peak=    3.121 closest distance to " NH2 ARG A 269 " =    1.077
peak=    3.120 closest distance to " CB  ARG A 156 " =    1.073
peak=    3.119 closest distance to " CA  LYS A 117 " =    1.187
peak=    3.113 closest distance to " O   HOH Z 151 " =    1.808
peak=    3.112 closest distance to " CG2 VAL A 268 " =    1.139
peak=    3.111 closest distance to " O   HOH Z 148 " =    3.246
peak=    3.109 closest distance to " O   HOH Z 193 " =    1.767
peak=    3.108 closest distance to " O   HOH Z 244 " =    1.724
peak=    3.106 closest distance to " O   HOH Z 423 " =    2.897
peak=    3.106 closest distance to " CA  ARG A 139 " =    1.418
peak=    3.106 closest distance to " O   HOH Z  94 " =    1.537
peak=    3.102 closest distance to " CB  ARG A 219 " =    1.141
peak=    3.102 closest distance to " CD1 LEU A 300 " =    0.756
peak=    3.093 closest distance to " CZ  ARG A  14 " =    1.404
peak=    3.092 closest distance to " CA  ASP A 140 " =    1.545
peak=    3.085 closest distance to " O   HOH Z 141 " =    1.603
peak=    3.082 closest distance to " CG  ARG A  56 " =    0.826
peak=    3.073 closest distance to " CA  GLU A 152 " =    0.896
peak=    3.068 closest distance to " O   HOH Z  35 " =    1.832
peak=    3.066 closest distance to " NH2AARG A 275 " =    3.490
peak=    3.064 closest distance to " O   HOH Z 343 " =    1.468
peak=    3.059 closest distance to " CG1 VAL A 153 " =    1.029
peak=    3.041 closest distance to " O   HOH Z  88 " =    2.753
peak=    3.041 closest distance to " CZ2 TRP A 150 " =    1.060
peak=    3.036 closest distance to " O   HOH Z 292 " =    2.316
peak=    3.036 closest distance to " O   HOH Z   9 " =    2.374
peak=    3.034 closest distance to " O   HOH Z 366 " =    1.609
peak=    3.034 closest distance to " ND1 HIS A  81 " =    1.464

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 196         
Filter by distance & map next to the model:
   mapped sites are within: 0.557 - 5.804
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 196
   mapped sites are within: 0.706 - 5.804

peak=   -5.382 closest distance to " CG2 VAL A 230 " =    0.799
peak=   -4.325 closest distance to " CD2 LEU A 237 " =    2.487
peak=   -4.253 closest distance to " CG  GLN A  58 " =    0.942
peak=   -4.222 closest distance to " CD1 PHE A  59 " =    1.988
peak=   -4.213 closest distance to " CD2 TYR A  30 " =    2.691
peak=   -4.057 closest distance to " OG BSER A 134 " =    1.440
peak=   -4.056 closest distance to " CD  ARG A 156 " =    1.969
peak=   -4.055 closest distance to " O   GLY A 241 " =    2.278
peak=   -4.046 closest distance to " CD  ARG A  14 " =    3.151
peak=   -4.042 closest distance to " O   HOH Z  13 " =    1.887
peak=   -4.028 closest distance to " CG  PRO A 243 " =    1.624
peak=   -4.019 closest distance to " O   HOH Z 422 " =    1.347
peak=   -4.016 closest distance to " CB  ALA A 248 " =    2.136
peak=   -4.014 closest distance to " CG1 VAL A 296 " =    1.053
peak=   -3.992 closest distance to " CD2 TYR A 293 " =    1.888
peak=   -3.969 closest distance to " O  BHOH Z 338 " =    1.121
peak=   -3.959 closest distance to " CG2BVAL A  41 " =    2.669
peak=   -3.952 closest distance to " CZ2 TRP A  92 " =    2.838
peak=   -3.942 closest distance to " O   HOH Z 166 " =    1.158
peak=   -3.910 closest distance to " CA  ASP A 298 " =    1.070
peak=   -3.905 closest distance to " CB  PHE A 208 " =    2.288
peak=   -3.885 closest distance to " O   PRO A 198 " =    1.275
peak=   -3.880 closest distance to " O   HOH Z 411 " =    5.502
peak=   -3.873 closest distance to " CG1 VAL A 112 " =    2.465
peak=   -3.842 closest distance to " O   HOH Z 423 " =    2.629
peak=   -3.824 closest distance to " CD1 LEU A 101 " =    2.477
peak=   -3.821 closest distance to " SD  MET A 105 " =    0.974
peak=   -3.800 closest distance to " O   HOH Z 166 " =    1.636
peak=   -3.796 closest distance to " O   SER A 271 " =    2.245
peak=   -3.785 closest distance to " C   HIS A 108 " =    1.130
peak=   -3.758 closest distance to " O   HOH Z 193 " =    1.127
peak=   -3.715 closest distance to " C   THR A 279 " =    1.106
peak=   -3.707 closest distance to " O   HOH Z 351 " =    1.737
peak=   -3.707 closest distance to " CG  GLN A 103 " =    2.394
peak=   -3.688 closest distance to " O   HOH Z 164 " =    5.804
peak=   -3.681 closest distance to " O   HOH Z 290 " =    0.817
peak=   -3.680 closest distance to " O   HOH Z 388 " =    2.165
peak=   -3.674 closest distance to " O   HOH Z 171 " =    2.416
peak=   -3.666 closest distance to " CB  ALA A 161 " =    2.363
peak=   -3.665 closest distance to " O   GLY A 196 " =    0.967
peak=   -3.664 closest distance to " O   HOH Z 285 " =    1.560
peak=   -3.660 closest distance to " O   HOH Z 221 " =    1.004
peak=   -3.651 closest distance to " O   GLN A  11 " =    1.250
peak=   -3.646 closest distance to " O   HOH Z 183 " =    1.696
peak=   -3.645 closest distance to " O   HOH Z 109 " =    2.726
peak=   -3.634 closest distance to " O   HOH Z 433 " =    0.984
peak=   -3.613 closest distance to " O   HOH Z 165 " =    1.945
peak=   -3.604 closest distance to " C   VAL A 265 " =    0.980
peak=   -3.603 closest distance to " O   HOH Z 250 " =    1.909
peak=   -3.603 closest distance to " O   HOH Z 124 " =    1.477
peak=   -3.576 closest distance to " OG  SER A  97 " =    2.383
peak=   -3.571 closest distance to " O   HOH Z 179 " =    2.184
peak=   -3.568 closest distance to " OD1 ASN A 301 " =    0.884
peak=   -3.566 closest distance to " O   PRO A 163 " =    2.181
peak=   -3.563 closest distance to " OH  TYR A 169 " =    0.836
peak=   -3.560 closest distance to " O   HOH Z  35 " =    2.023
peak=   -3.552 closest distance to " O   HOH Z 216 " =    1.332
peak=   -3.545 closest distance to " O   HOH Z 101 " =    1.423
peak=   -3.542 closest distance to " O   HOH Z 150 " =    1.749
peak=   -3.541 closest distance to " O   HOH Z   6 " =    1.978
peak=   -3.528 closest distance to " O   HOH Z 423 " =    3.854
peak=   -3.512 closest distance to " NE2 GLN A  11 " =    1.476
peak=   -3.509 closest distance to " CZ2 TRP A 179 " =    1.264
peak=   -3.506 closest distance to " CD2 TYR A 172 " =    2.138
peak=   -3.503 closest distance to " ND2BASN A 224 " =    1.901
peak=   -3.502 closest distance to " OXT GLY A 302 " =    2.850
peak=   -3.498 closest distance to " O   ASN A 187 " =    1.671
peak=   -3.497 closest distance to " OD1 ASP A 298 " =    2.164
peak=   -3.488 closest distance to " O   SER A 273 " =    1.096
peak=   -3.479 closest distance to " O   HOH Z 111 " =    1.445
peak=   -3.477 closest distance to " CE1 TYR A 247 " =    2.543
peak=   -3.471 closest distance to " O   HOH Z 136 " =    2.492
peak=   -3.471 closest distance to " O   HOH Z 345 " =    2.791
peak=   -3.459 closest distance to " CB  ALA A  43 " =    2.662
peak=   -3.446 closest distance to " O   HOH Z 425 " =    1.238
peak=   -3.442 closest distance to " O   HOH Z 151 " =    1.282
peak=   -3.441 closest distance to " N   THR A 235 " =    1.151
peak=   -3.437 closest distance to " OG1 THR A  82 " =    1.335
peak=   -3.437 closest distance to " CB  ALA A  10 " =    2.219
peak=   -3.429 closest distance to " CG2 VAL A 189 " =    1.977
peak=   -3.421 closest distance to " N   ASP A 272 " =    1.183
peak=   -3.421 closest distance to " CA  GLY A 133 " =    2.014
peak=   -3.415 closest distance to " C   ILE A 239 " =    2.210
peak=   -3.404 closest distance to " O   HOH Z 119 " =    1.960
peak=   -3.404 closest distance to " NE2 GLN A  88 " =    1.000
peak=   -3.400 closest distance to " O   HOH Z  56 " =    1.280
peak=   -3.398 closest distance to " O   HOH Z 126 " =    1.755
peak=   -3.398 closest distance to " O   HOH Z 107 " =    1.284
peak=   -3.393 closest distance to " O   HOH Z 219 " =    2.482
peak=   -3.392 closest distance to " CG2 ILE A  20 " =    2.861
peak=   -3.379 closest distance to " O   HOH Z 120 " =    1.242
peak=   -3.378 closest distance to " ND2 ASN A 249 " =    0.969
peak=   -3.377 closest distance to " O   HOH Z 269 " =    1.329
peak=   -3.376 closest distance to " O   HOH Z 340 " =    1.945
peak=   -3.375 closest distance to " O   HOH Z 131 " =    4.262
peak=   -3.375 closest distance to " O   HOH Z  52 " =    2.290
peak=   -3.364 closest distance to " NH2 ARG A  79 " =    1.658
peak=   -3.364 closest distance to " O   HOH Z  17 " =    1.483
peak=   -3.362 closest distance to " O   HOH Z  92 " =    1.376
peak=   -3.361 closest distance to " CA  SER A 276 " =    1.523
peak=   -3.352 closest distance to " CZ  TYR A 172 " =    1.887
peak=   -3.337 closest distance to " CA  ALA A 114 " =    1.035
peak=   -3.335 closest distance to " O   HOH Z 174 " =    3.654
peak=   -3.334 closest distance to " O   HOH Z 109 " =    3.879
peak=   -3.324 closest distance to " N   ALA A 295 " =    0.869
peak=   -3.320 closest distance to " CG2 VAL A 296 " =    1.094
peak=   -3.315 closest distance to " O   HOH Z 137 " =    1.642
peak=   -3.311 closest distance to " O   HOH Z 231 " =    2.103
peak=   -3.310 closest distance to " NE2 GLN A  88 " =    1.758
peak=   -3.308 closest distance to " CG  ARG A 219 " =    2.368
peak=   -3.305 closest distance to " O   HOH Z 424 " =    2.408
peak=   -3.303 closest distance to " O   HOH Z 340 " =    0.934
peak=   -3.301 closest distance to " O   HOH Z  44 " =    1.728
peak=   -3.297 closest distance to " CB  ASP A 132 " =    2.395
peak=   -3.296 closest distance to " SG  CYS A 260 " =    1.982
peak=   -3.293 closest distance to " O   ASP A 298 " =    1.764
peak=   -3.289 closest distance to " CH2 TRP A 150 " =    1.067
peak=   -3.287 closest distance to " CG  ARG A 259 " =    2.272
peak=   -3.287 closest distance to " CD  GLN A 223 " =    1.780
peak=   -3.282 closest distance to " O   HOH Z 313 " =    2.312
peak=   -3.281 closest distance to " O   PHE A 218 " =    1.481
peak=   -3.274 closest distance to " C   LYS A  76 " =    1.598
peak=   -3.266 closest distance to " CB  ALA A   9 " =    2.625
peak=   -3.255 closest distance to " CG2 THR A 182 " =    2.333
peak=   -3.253 closest distance to " O   GLY A  80 " =    2.725
peak=   -3.253 closest distance to " NZ  LYS A 119 " =    1.120
peak=   -3.251 closest distance to " CG  TRP A 266 " =    2.090
peak=   -3.243 closest distance to " O   HOH Z 273 " =    0.914
peak=   -3.241 closest distance to " CD  GLN A 223 " =    0.874
peak=   -3.240 closest distance to " O   ASN A  45 " =    1.908
peak=   -3.239 closest distance to " CE3 TRP A 150 " =    2.311
peak=   -3.235 closest distance to " O   HOH Z 145 " =    2.605
peak=   -3.233 closest distance to " O   SER A  95 " =    1.635
peak=   -3.228 closest distance to " N   ALA A 226 " =    2.009
peak=   -3.226 closest distance to " O   HOH Z 432 " =    1.099
peak=   -3.223 closest distance to " CZ  TYR A 169 " =    1.700
peak=   -3.220 closest distance to " CB  ASP A 286 " =    1.562
peak=   -3.219 closest distance to " O   HOH Z 198 " =    1.398
peak=   -3.217 closest distance to " O   SER A 210 " =    1.776
peak=   -3.214 closest distance to " OG1 THR A 294 " =    2.401
peak=   -3.213 closest distance to " CD  LYS A 289 " =    2.383
peak=   -3.211 closest distance to " O   HOH Z 116 " =    2.101
peak=   -3.211 closest distance to " O   HOH Z 384 " =    1.887
peak=   -3.210 closest distance to " NE1 TRP A 266 " =    2.335
peak=   -3.206 closest distance to " CG  ASP A 286 " =    1.347
peak=   -3.204 closest distance to " O   HOH Z 265 " =    1.071
peak=   -3.202 closest distance to " O   HOH Z 374 " =    2.042
peak=   -3.201 closest distance to " O   HOH Z 196 " =    1.536
peak=   -3.196 closest distance to " CG2 THR A  18 " =    2.862
peak=   -3.196 closest distance to " CD  ARG A 139 " =    1.063
peak=   -3.194 closest distance to " O   HOH Z  31 " =    2.128
peak=   -3.193 closest distance to " O   HOH Z 266 " =    1.559
peak=   -3.193 closest distance to " CG  PHE A  59 " =    1.628
peak=   -3.191 closest distance to " OD2 ASP A 140 " =    1.057
peak=   -3.186 closest distance to " NH2 ARG A  79 " =    2.091
peak=   -3.181 closest distance to " NE1 TRP A 150 " =    0.882
peak=   -3.180 closest distance to " O   HOH Z  35 " =    1.226
peak=   -3.178 closest distance to " O   HOH Z 407 " =    2.318
peak=   -3.177 closest distance to " O   HOH Z 431 " =    2.553
peak=   -3.174 closest distance to " CB  ALA A 129 " =    2.462
peak=   -3.174 closest distance to " N   ALA A   1 " =    2.409
peak=   -3.174 closest distance to " CD1 TYR A 247 " =    2.650
peak=   -3.172 closest distance to " O   HOH Z 246 " =    0.993
peak=   -3.171 closest distance to " CH2 TRP A 274 " =    1.121
peak=   -3.165 closest distance to " CE1 HIS A  81 " =    1.422
peak=   -3.165 closest distance to " ND2 ASN A  39 " =    1.360
peak=   -3.165 closest distance to " O   HOH Z 214 " =    2.608
peak=   -3.162 closest distance to " O   HOH Z 403 " =    1.256
peak=   -3.154 closest distance to " CD1 TRP A 179 " =    1.119
peak=   -3.148 closest distance to " N   ARG A  66 " =    1.899
peak=   -3.147 closest distance to " O   HOH Z 297 " =    2.594
peak=   -3.146 closest distance to " O   HOH Z  41 " =    1.752
peak=   -3.140 closest distance to " NE2 GLN A 278 " =    1.951
peak=   -3.138 closest distance to " CD2 LEU A 167 " =    1.812
peak=   -3.135 closest distance to " CB  ASN A  45 " =    2.000
peak=   -3.135 closest distance to " C   ASN A 285 " =    2.071
peak=   -3.131 closest distance to " O   TYR A  15 " =    1.869
peak=   -3.130 closest distance to " O   HOH Z 377 " =    1.995
peak=   -3.129 closest distance to " OXT GLY A 302 " =    3.543
peak=   -3.128 closest distance to " O   SER A   3 " =    0.862
peak=   -3.125 closest distance to " CG  ASN A  45 " =    0.706
peak=   -3.113 closest distance to " O   LYS A 289 " =    1.077
peak=   -3.111 closest distance to " O   HOH Z 208 " =    1.719
peak=   -3.106 closest distance to " O   HOH Z  78 " =    1.904
peak=   -3.097 closest distance to " CZ  ARG A 156 " =    1.683
peak=   -3.096 closest distance to " O   HOH Z 259 " =    1.394
peak=   -3.088 closest distance to " CG1 VAL A  78 " =    2.498
peak=   -3.082 closest distance to " O   HOH Z 214 " =    1.107
peak=   -3.080 closest distance to " O   GLY A  80 " =    2.710
peak=   -3.063 closest distance to " NE2 GLN A  11 " =    0.954
peak=   -3.061 closest distance to " CZ  PHE A  38 " =    2.361
peak=   -3.044 closest distance to " O   HOH Z 216 " =    3.868
peak=   -3.007 closest distance to " O   ASP A 107 " =    1.945

================= 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    :  0.5212 0.5172   6.312964e+00   6.310178e+00
   1_bss:  0.5143 0.5136   6.307937e+00   6.310601e+00
   1_xyz:  0.4569 0.4802   6.256382e+00   6.283448e+00
   1_adp:  0.4155 0.4800   6.216425e+00   6.280243e+00
   1_occ:  0.4151 0.4802   6.216187e+00   6.281291e+00
   2_bss:  0.4132 0.4746   6.216010e+00   6.280661e+00
   2_xyz:  0.3419 0.4088   6.078422e+00   6.198227e+00
   2_adp:  0.3193 0.3885   6.029980e+00   6.161866e+00
   2_occ:  0.3190 0.3879   6.029008e+00   6.161091e+00
   3_bss:  0.3158 0.3825   6.026205e+00   6.158212e+00
   3_xyz:  0.2391 0.2949   5.791823e+00   5.964757e+00
   3_adp:  0.2186 0.2713   5.714665e+00   5.891453e+00
   3_occ:  0.2181 0.2710   5.713730e+00   5.891309e+00
   4_bss:  0.2168 0.2705   5.714364e+00   5.891236e+00
   4_xyz:  0.1639 0.2106   5.466363e+00   5.665065e+00
   4_adp:  0.1484 0.1993   5.391551e+00   5.605732e+00
   4_occ:  0.1482 0.1993   5.391080e+00   5.605665e+00
   5_bss:  0.1482 0.1995   5.390639e+00   5.604994e+00
   5_xyz:  0.1330 0.1837   5.303572e+00   5.528304e+00
   5_adp:  0.1319 0.1796   5.289694e+00   5.504990e+00
   5_occ:  0.1317 0.1793   5.288248e+00   5.503346e+00
   5_bss:  0.1316 0.1794   5.288142e+00   5.503219e+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:  0.306   0.000   7.218  10.766   9.271   0.000   0.000   0.000
   1_xyz:  0.306   0.000   7.218  10.766   9.271   0.000   0.000   0.000
   1_adp:  0.306   0.000   7.218  10.766   9.271   0.000   0.000   0.000
   1_occ:  0.306   0.000   7.218  10.766   9.271   0.000   0.000   0.000
   2_bss:  0.300  20.000   3.311   6.311   5.592   0.000   0.000   0.000
   2_xyz:  0.300  20.000   3.311   6.311   5.592   0.000   0.000   0.000
   2_adp:  0.300  20.000   3.311   6.311   5.592   0.000   0.000   0.000
   2_occ:  0.300  20.000   3.311   6.311   5.592   0.000   0.000   0.000
   3_bss:  0.325  48.044   0.738   3.134   2.832   0.000   0.000   0.000
   3_xyz:  0.325  48.044   0.738   3.134   2.832   0.000   0.000   0.000
   3_adp:  0.325  48.044   0.738   3.134   2.832   0.000   0.000   0.000
   3_occ:  0.325  48.044   0.738   3.134   2.832   0.000   0.000   0.000
   4_bss:  0.323  48.044  -0.827   1.373   1.525   0.000   0.000   0.000
   4_xyz:  0.323  48.044  -0.827   1.373   1.525   0.000   0.000   0.000
   4_adp:  0.323  48.044  -0.827   1.373   1.525   0.000   0.000   0.000
   4_occ:  0.323  48.044  -0.827   1.373   1.525   0.000   0.000   0.000
   5_bss:  0.328  59.170  -1.362   0.589   1.180   0.000   0.000   0.000
   5_xyz:  0.328  59.170  -1.362   0.589   1.180   0.000   0.000   0.000
   5_adp:  0.328  59.170  -1.362   0.589   1.180   0.000   0.000   0.000
   5_occ:  0.328  59.170  -1.362   0.589   1.180   0.000   0.000   0.000
   5_bss:  0.327  55.957  -1.531   0.160   0.991   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  66.287 0.3123  0.3776    87689.537
   1_bss:  67.591 0.2940  0.4537    88486.192
   1_xyz:  60.449 0.3859  0.5881    73997.235
   1_adp:  58.648 0.4092  0.7051    72091.328
   1_occ:  58.749 0.4079  0.7014    72308.699
   2_bss:  57.851 0.4196  0.6395    71266.445
   2_xyz:  47.092 0.5557  0.8443    50839.457
   2_adp:  43.198 0.6042  0.9025    44626.980
   2_occ:  43.122 0.6051  0.9034    44469.923
   3_bss:  42.680 0.6104  0.8266    43764.615
   3_xyz:  31.660 0.7380  0.9587    24418.414
   3_adp:  28.146 0.7777  0.9848    20309.792
   3_occ:  28.116 0.7781  0.9848    20250.684
   4_bss:  28.058 0.7788  0.9330    20256.508
   4_xyz:  20.659 0.8550  0.9830    11658.991
   4_adp:  19.144 0.8700  0.9868    10444.441
   4_occ:  19.147 0.8699  0.9869    10450.935
   5_bss:  19.097 0.8703  0.9682    10417.800
   5_xyz:  17.412 0.8858  0.9739     8808.045
   5_adp:  16.819 0.8914  0.9803     8466.842
   5_occ:  16.787 0.8917  0.9806     8448.781
   5_bss:  16.778 0.8918  0.9721     8444.725
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.3809e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.3809e+01
   1_xyz:   1.804  0.014  0.111 18.566  0.007  4.107   1.6248e-01
   1_adp:   1.804  0.014  0.111 18.566  0.007  4.107   1.6248e-01
   1_occ:   1.804  0.014  0.111 18.566  0.007  4.107   1.6248e-01
   2_bss:   1.804  0.014  0.111 18.566  0.007  4.107   1.6248e-01
   2_xyz:   1.440  0.011  0.086 17.165  0.006  4.102   1.2428e-01
   2_adp:   1.440  0.011  0.086 17.165  0.006  4.102   1.2428e-01
   2_occ:   1.440  0.011  0.086 17.165  0.006  4.102   1.2428e-01
   3_bss:   1.440  0.011  0.086 17.165  0.006  4.102   1.2428e-01
   3_xyz:   1.323  0.010  0.089 16.433  0.005  4.106   9.7270e-02
   3_adp:   1.323  0.010  0.089 16.433  0.005  4.106   9.7270e-02
   3_occ:   1.323  0.010  0.089 16.433  0.005  4.106   9.7270e-02
   4_bss:   1.323  0.010  0.089 16.433  0.005  4.106   9.7270e-02
   4_xyz:   1.165  0.009  0.082 15.765  0.004  4.122   8.0666e-02
   4_adp:   1.165  0.009  0.082 15.765  0.004  4.122   8.0666e-02
   4_occ:   1.165  0.009  0.082 15.765  0.004  4.122   8.0666e-02
   5_bss:   1.165  0.009  0.082 15.765  0.004  4.122   8.0666e-02
   5_xyz:   1.081  0.008  0.082 15.417  0.004  4.114   6.7467e-02
   5_adp:   1.081  0.008  0.082 15.417  0.004  4.114   6.7467e-02
   5_occ:   1.081  0.008  0.082 15.417  0.004  4.114   6.7467e-02
   5_bss:   1.081  0.008  0.082 15.417  0.004  4.114   6.7467e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.631   6.9641e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.631   6.9641e+00
   1_xyz:  16.492  0.178  0.519 86.372  0.049  2.182   1.0869e-01
   1_adp:  16.492  0.178  0.519 86.372  0.049  2.182   1.0869e-01
   1_occ:  16.492  0.178  0.519 86.372  0.049  2.182   1.0869e-01
   2_bss:  16.492  0.178  0.519 86.372  0.049  2.182   1.0869e-01
   2_xyz:  10.029  0.117  0.276 84.364  0.047  2.053   9.8310e-02
   2_adp:  10.029  0.117  0.276 84.364  0.047  2.053   9.8310e-02
   2_occ:  10.029  0.117  0.276 84.364  0.047  2.053   9.8310e-02
   3_bss:  10.029  0.117  0.276 84.364  0.047  2.053   9.8310e-02
   3_xyz:   9.876  0.053  0.288 82.260  0.053  2.201   7.6008e-02
   3_adp:   9.876  0.053  0.288 82.260  0.053  2.201   7.6008e-02
   3_occ:   9.876  0.053  0.288 82.260  0.053  2.201   7.6008e-02
   4_bss:   9.876  0.053  0.288 82.260  0.053  2.201   7.6008e-02
   4_xyz:   7.873  0.044  0.354 79.516  0.041  2.079   6.2603e-02
   4_adp:   7.873  0.044  0.354 79.516  0.041  2.079   6.2603e-02
   4_occ:   7.873  0.044  0.354 79.516  0.041  2.079   6.2603e-02
   5_bss:   7.873  0.044  0.354 79.516  0.041  2.079   6.2603e-02
   5_xyz:   7.394  0.047  0.412 82.810  0.043  2.196   4.5499e-02
   5_adp:   7.394  0.047  0.412 82.810  0.043  2.196   4.5499e-02
   5_occ:   7.394  0.047  0.412 82.810  0.043  2.196   4.5499e-02
   5_bss:   7.394  0.047  0.412 82.810  0.043  2.196   4.5499e-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: 102.28   0.00  18.20  82.98   0.00  16.54 102.28   0.00  27.23
   1_occ: 102.28   0.00  18.20  82.98   0.00  16.54 102.28   0.00  27.23
   2_bss: 102.28   0.00  18.20  82.98   0.00  16.54 102.28   0.00  27.23
   2_xyz: 102.28   0.00  18.20  82.98   0.00  16.54 102.28   0.00  27.23
   2_adp:  86.62   0.00  16.26  83.17   0.00  13.73  86.62   0.00  30.02
   2_occ:  86.62   0.00  16.26  83.17   0.00  13.73  86.62   0.00  30.02
   3_bss:  86.62   0.00  16.26  83.17   0.00  13.73  86.62   0.00  30.02
   3_xyz:  86.62   0.00  16.26  83.17   0.00  13.73  86.62   0.00  30.02
   3_adp:  81.05   0.00  15.53  81.05   0.00  12.02  77.21   3.53  34.63
   3_occ:  81.05   0.00  15.53  81.05   0.00  12.02  77.21   3.53  34.63
   4_bss:  81.05   0.00  15.53  81.05   0.00  12.02  77.21   3.53  34.63
   4_xyz:  81.05   0.00  15.53  81.05   0.00  12.02  77.21   3.53  34.63
   4_adp:  91.75   0.00  16.29  91.75   0.00  11.58  84.85   4.16  41.96
   4_occ:  91.75   0.00  16.29  91.75   0.00  11.58  84.85   4.16  41.96
   5_bss:  91.75   0.00  16.29  91.75   0.00  11.58  84.85   4.16  41.96
   5_xyz:  91.75   0.00  16.29  91.75   0.00  11.58  84.85   4.16  41.96
   5_adp:  91.50   0.00  16.25  91.50   0.00  11.63  84.43   4.13  41.42
   5_occ:  91.50   0.00  16.25  91.50   0.00  11.63  84.43   4.13  41.42
   5_bss:  91.50   0.00  16.26  91.50   0.00  11.63  84.43   4.14  41.42
------------------------------------------------------------------------
 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:    1.276    0.027    0.418
   1_adp:    1.276    0.027    0.418
   1_occ:    1.276    0.027    0.418
   2_bss:    1.276    0.027    0.418
   2_xyz:    1.900    0.048    0.643
   2_adp:    1.900    0.048    0.643
   2_occ:    1.900    0.048    0.643
   3_bss:    1.900    0.048    0.643
   3_xyz:    2.026    0.039    0.786
   3_adp:    2.026    0.039    0.786
   3_occ:    2.026    0.039    0.786
   4_bss:    2.026    0.039    0.786
   4_xyz:    2.196    0.056    0.886
   4_adp:    2.196    0.056    0.886
   4_occ:    2.196    0.056    0.886
   5_bss:    2.196    0.056    0.886
   5_xyz:    2.248    0.060    0.915
   5_adp:    2.248    0.060    0.915
   5_occ:    2.248    0.060    0.915
   5_bss:    2.248    0.060    0.915
------------------------------------------------------------------------

CPU time actual refinement: 359.86


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_107/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_107/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_107/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_107/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_107/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 359.71 
  Macro-tasks:
    bulk solvent and scale       = 45.77  
    individual site refinement   = 156.23 
    weights calculation          = 31.61  
    collect and process          = 6.27   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 239.99 
  Micro-tasks:
    mask                            = 2.43   
    f_calc                          = 113.35 
    alpha_beta                      = 8.06   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 124.94 
    fmodel                         = 8.07   
    r_factors                      = 0.19   
    phase_errors                   = 9.91   
    foms                           = 0.33   
    TOTAL for micro-tasks          = 268.40 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.004 micro seconds
Total CPU time: 6.23 minutes
from_scatterers_fft:    651 calls, 113.15 s
gradients_fft:          595 calls, 111.38 s

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

# Date 2008-01-16 Time 00:45:52 PST -0800 (1200473152.87 s)
Start R-work = 0.5212, R-free = 0.5172 (no bulk solvent and anisotropic scale)
Final R-work = 0.1503, R-free = 0.1940 (no bulk solvent and anisotropic scale)

Start R-work = 0.5143, R-free = 0.5136
Final R-work = 0.1316, R-free = 0.1794