# Date 2008-01-16 Time 04:36:37 PST -0800 (1200486997.55 s)
#phil __OFF__

Command line arguments: "../384.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 24137
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 384

-------------------------------------------------------------------------------
  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.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 45.9914, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.33, 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: (69.5475, 45.9914, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.981 1.96276
Completeness in resolution range: 0.937497
Completeness with d_max=infinity: 0.934723

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9810
                             d_min =   1.9628

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 45.9914, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.981 1.96276
Completeness in resolution range: 0.937497
Completeness with d_max=infinity: 0.934723

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9814 -  4.2005 [2196/2221]  1974   222  10.1%
  bin  2:  4.2005 -  3.3463 [2109/2129]  1902   207   9.8%
  bin  3:  3.3463 -  2.9269 [2089/2108]  1881   208  10.0%
  bin  4:  2.9269 -  2.6609 [2049/2079]  1833   216  10.5%
  bin  5:  2.6609 -  2.4711 [2061/2080]  1858   203   9.8%
  bin  6:  2.4711 -  2.3259 [2037/2062]  1835   202   9.9%
  bin  7:  2.3259 -  2.2098 [2024/2052]  1826   198   9.8%
  bin  8:  2.2098 -  2.1139 [2017/2053]  1814   203  10.1%
  bin  9:  2.1139 -  2.0327 [1989/2059]  1796   193   9.7%
  bin 10:  2.0327 -  1.9628 [1018/2052]   911   107  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_384/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:
        1.06 -     1.82: 7
        1.82 -     2.59: 74
        2.59 -     3.36: 4166
        3.36 -     4.13: 9437
        4.13 -     4.90: 14771
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.056 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.498 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.572 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  53 " - " O   HOH Z 102 "  1.600 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 104 "  1.644 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28450 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 =====================


==================== 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/noshake/run_384/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_384/model_refine_001.geo

CPU time processing inputs: 9.48


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 45.9914 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4762   r_free= 0.4772   ksol= 0.00   Bsol= 0.00   scale= 0.886    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.286812                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.6853 0.99   1426  156 0.3774 0.3636      6.5902      6.5314|
|  2:  4.6853 -  3.7379 0.99   1372  155 0.4136 0.4443      6.8063      6.8255|
|  3:  3.7379 -  3.2710 0.99   1347  149 0.4491 0.4190      6.6903      6.6792|
|  4:  3.2710 -  2.9745 0.99   1326  150 0.4753 0.4931      6.5373      6.5502|
|  5:  2.9745 -  2.7627 0.99   1335  145 0.5100 0.4782      6.3641      6.3919|
|  6:  2.7627 -  2.6007 0.99   1326  147 0.5122 0.5217      6.2808      6.1802|
|  7:  2.6007 -  2.4711 0.99   1316  154 0.5043 0.5211      6.2247      6.1699|
|  8:  2.4711 -  2.3639 0.98   1312  148 0.5285 0.5427      6.1849      6.1889|
|  9:  2.3639 -  2.2733 0.98   1295  133 0.5170 0.5175      6.1171      6.1701|
| 10:  2.2733 -  2.1951 1.00   1319  149 0.5293 0.5371      6.0871      6.1133|
| 11:  2.1951 -  2.1266 0.98   1294  144 0.5221 0.5015      6.0232      6.0238|
| 12:  2.1266 -  2.0660 0.98   1287  144 0.5225 0.4739      5.9656      5.9392|
| 13:  2.0660 -  2.0117 0.90   1187  128 0.5134 0.5309      5.8876       5.831|
| 14:  2.0117 -  1.9628 0.37    488   57 0.5367 0.5117      5.8988      5.8114|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9814 -  4.6853  1426   156  0.72  32.65   0.82     0.78      69050.47|
|  2:  4.6853 -  3.7379  1372   155  0.68  37.07   0.90     0.79     116995.46|
|  3:  3.7379 -  3.2710  1347   149  0.56  47.36   0.91     0.74     126644.27|
|  4:  3.2710 -  2.9745  1326   150  0.45  55.99   0.89     0.64     118276.60|
|  5:  2.9745 -  2.7627  1335   145  0.40  59.90   0.87     0.57      83931.09|
|  6:  2.7627 -  2.6007  1326   147  0.36  62.50   0.89     0.52      73502.67|
|  7:  2.6007 -  2.4711  1316   154  0.36  63.04   0.90     0.50      64751.19|
|  8:  2.4711 -  2.3639  1312   148  0.33  65.12   0.90     0.48      60252.45|
|  9:  2.3639 -  2.2733  1295   133  0.34  64.60   0.92     0.50      54922.53|
| 10:  2.2733 -  2.1951  1319   149  0.35  64.01   0.91     0.51      48681.53|
| 11:  2.1951 -  2.1266  1294   144  0.33  65.31   0.93     0.52      48716.46|
| 12:  2.1266 -  2.0660  1287   144  0.32  66.01   0.93     0.52      43859.35|
| 13:  2.0660 -  2.0117  1187   128  0.33  65.56   0.93     0.53      37668.60|
| 14:  2.0117 -  1.9628   488    57  0.41  59.11   0.99     0.58      26935.55|
|alpha:            min =        0.48 max =            0.79 mean =         0.59|
|beta:             min =    26935.55 max =       126644.27 mean =     72198.73|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           89.99 mean =        57.34|
|phase err.(test): min =        0.00 max =           89.92 mean =        57.72|
|-----------------------------------------------------------------------------|

============================== 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 = 11.015319             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.793   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.876531              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.613   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.056 -  1.440:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.440 -  1.825:        6 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.825 -  2.209:       22 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.209 -  2.594:       52 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.594 -  2.978:     1781 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.978 -  3.362:     2385 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.362 -  3.747:     3916 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.747 -  4.131:     5521 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.131 -  4.516:     6548 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.516 -  4.900:     8223 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.194 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.056 |       0.655 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.698)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    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:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4762   r_free= 0.4772   ksol= 0.00   Bsol= 0.00   scale= 0.886    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.286812                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4662   r_free= 0.4667   ksol= 0.32   Bsol= 29.03   scale= 0.931   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,1.29,3.98,0.00,0.00,0.00); trace/3= 0.81                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.280063                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.453466              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.811   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.322907              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.368   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4662      final r-factor (work) = 0.3906          |
| start r-factor (free) = 0.4667      final r-factor (free) = 0.4274          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.7151 = 8.45 * 0.50 * 6.2746 + 1.00 * 0.1942                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.2838 = 8.45 * 0.50 * 6.1923 + 1.00 * 0.1104                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3906      final r-factor (work) = 0.3592          |
| start r-factor (free) = 0.4274      final r-factor (free) = 0.4346          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1980 = 1.32 * 1.00 * 6.1923 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1267 = 1.32 * 1.00 * 6.1244 + 1.00 * 0.0246                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.698)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.32  18.63    None  None   None       |
|    all(noH): 2823   0      0.00    103.32  18.63    None  None   None       |
|    Sol.    : 438    0      0.00    72.25   35.68    None  None   None       |
|    Mac.    : 2385   0      0.00    103.32  15.49    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 -  10.333:  855   |   5:    51.662 -  61.995:   48        |
|      1:    10.333 -  20.665:  941   |   6:    61.995 -  72.327:   11        |
|      2:    20.665 -  30.997:  561   |   7:    72.327 -  82.660:    0        |
|      3:    30.997 -  41.330:  257   |   8:    82.660 -  92.992:    0        |
|      4:    41.330 -  51.662:  149   |   9:    92.992 - 103.324:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3592 r_free = 0.4346             target_work(ml) = 6.128         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3591 r_free = 0.4361             target_work(ml) = 6.128         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3591   r_free= 0.4361   ksol= 0.32   Bsol= 29.03   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,1.29,3.98,0.00,0.00,0.00); trace/3= 0.81                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.127656                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3590   r_free= 0.4351   ksol= 0.34   Bsol= 56.91   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.57,0.35,2.59,0.00,0.00,0.00); trace/3= 0.46                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.130841                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.725668              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.823   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.703361              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.703  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3590      final r-factor (work) = 0.2953          |
| start r-factor (free) = 0.4351      final r-factor (free) = 0.3710          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.7742 = 7.73 * 0.50 * 6.1261 + 1.00 * 0.1101                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.5088 = 7.73 * 0.50 * 6.0608 + 1.00 * 0.0969                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2953      final r-factor (work) = 0.2800          |
| start r-factor (free) = 0.3710      final r-factor (free) = 0.3610          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2837 = 0.70 * 1.00 * 6.0608 + 1.00 * 0.0208                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2085 = 0.70 * 1.00 * 5.9639 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.698)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.32   18.35    None  None   None       |
|    all(noH): 2823   0      0.00    87.32   18.35    None  None   None       |
|    Sol.    : 438    0      0.00    87.32   36.73    None  None   None       |
|    Mac.    : 2385   0      0.00    67.68   14.98    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 -   8.732:  744   |   5:    43.660 -  52.393:  106        |
|      1:     8.732 -  17.464:  941   |   6:    52.393 -  61.125:   52        |
|      2:    17.464 -  26.196:  506   |   7:    61.125 -  69.857:   17        |
|      3:    26.196 -  34.928:  254   |   8:    69.857 -  78.589:    6        |
|      4:    34.928 -  43.660:  196   |   9:    78.589 -  87.321:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2800 r_free = 0.3610             target_work(ml) = 5.955         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2798 r_free = 0.3612             target_work(ml) = 5.955         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2798   r_free= 0.3612   ksol= 0.34   Bsol= 56.91   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.57,0.35,2.59,0.00,0.00,0.00); trace/3= 0.46                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.954933                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2804   r_free= 0.3603   ksol= 0.32   Bsol= 50.52   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.15,0.03,2.11,0.00,0.00,0.00); trace/3= 0.33                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.954782                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.492335              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.670   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 8.216301              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.462  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2804      final r-factor (work) = 0.2089          |
| start r-factor (free) = 0.3603      final r-factor (free) = 0.2721          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.4074 = 9.49 * 0.50 * 5.9649 + 1.00 * 0.0969                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.8700 = 9.49 * 0.50 * 5.8510 + 1.00 * 0.1003                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2089      final r-factor (work) = 0.1811          |
| start r-factor (free) = 0.2721      final r-factor (free) = 0.2494          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 48.0872 = 8.22 * 1.00 * 5.8510 + 1.00 * 0.0137                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 46.2530 = 8.22 * 1.00 * 5.6272 + 1.00 * 0.0184                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.698)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.11  19.23    None  None   None       |
|    all(noH): 2823   0      0.00    105.11  19.23    None  None   None       |
|    Sol.    : 438    0      3.37    105.11  48.79    None  None   None       |
|    Mac.    : 2385   0      0.00    99.73   13.80    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 -  10.511: 1160   |   5:    52.553 -  63.064:  100        |
|      1:    10.511 -  21.021:  905   |   6:    63.064 -  73.575:   79        |
|      2:    21.021 -  31.532:  264   |   7:    73.575 -  84.085:   37        |
|      3:    31.532 -  42.043:  142   |   8:    84.085 -  94.596:   18        |
|      4:    42.043 -  52.553:  114   |   9:    94.596 - 105.107:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1811 r_free = 0.2494             target_work(ml) = 5.581         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1809 r_free = 0.2496             target_work(ml) = 5.581         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1809   r_free= 0.2496   ksol= 0.32   Bsol= 50.52   scale= 1.050   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.15,0.03,2.11,0.00,0.00,0.00); trace/3= 0.33                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.580511                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1802   r_free= 0.2495   ksol= 0.32   Bsol= 60.16   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-1.30,0.86,-0.00,0.00,0.00); trace/3= -0.79                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.577182                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.182368              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.098   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.435778              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 109.875  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1802      final r-factor (work) = 0.1494          |
| start r-factor (free) = 0.2495      final r-factor (free) = 0.2083          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.8791 = 4.18 * 0.50 * 5.6326 + 1.00 * 0.1003                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.5826 = 4.18 * 0.50 * 5.5070 + 1.00 * 0.0665                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1494      final r-factor (work) = 0.1394          |
| start r-factor (free) = 0.2083      final r-factor (free) = 0.1915          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4182 = 0.44 * 1.00 * 5.5070 + 1.00 * 0.0184                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3584 = 0.44 * 1.00 * 5.3832 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.698)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.16  18.01    None  None   None       |
|    all(noH): 2823   0      0.00    101.16  18.01    None  None   None       |
|    Sol.    : 438    0      5.34    101.16  46.59    None  None   None       |
|    Mac.    : 2385   0      0.00    95.46   12.77    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 -  10.116: 1182   |   5:    50.581 -  60.698:   84        |
|      1:    10.116 -  20.233:  981   |   6:    60.698 -  70.814:   82        |
|      2:    20.233 -  30.349:  216   |   7:    70.814 -  80.930:   36        |
|      3:    30.349 -  40.465:  105   |   8:    80.930 -  91.047:   20        |
|      4:    40.465 -  50.581:  113   |   9:    91.047 - 101.163:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1394 r_free = 0.1915             target_work(ml) = 5.336         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1393 r_free = 0.1913             target_work(ml) = 5.335         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1393   r_free= 0.1913   ksol= 0.32   Bsol= 60.16   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-1.30,0.86,-0.00,0.00,0.00); trace/3= -0.79                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.335481                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1395   r_free= 0.1909   ksol= 0.32   Bsol= 60.16   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-1.70,0.48,-0.00,0.00,0.00); trace/3= -1.11                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.334285                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.017166              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.146  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.086585              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.997  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1395      final r-factor (work) = 0.1300          |
| start r-factor (free) = 0.1909      final r-factor (free) = 0.1776          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4966 = 2.02 * 0.50 * 5.3839 + 1.00 * 0.0665                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4075 = 2.02 * 0.50 * 5.3080 + 1.00 * 0.0539                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1300      final r-factor (work) = 0.1272          |
| start r-factor (free) = 0.1776      final r-factor (free) = 0.1759          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7801 = 1.09 * 1.00 * 5.3080 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7251 = 1.09 * 1.00 * 5.2572 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.698)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.27  17.76    None  None   None       |
|    all(noH): 2823   0      0.00    101.27  17.76    None  None   None       |
|    Sol.    : 438    0      5.18    101.27  46.27    None  None   None       |
|    Mac.    : 2385   0      0.00    94.74   12.52    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 -  10.127: 1236   |   5:    50.637 -  60.764:   83        |
|      1:    10.127 -  20.255:  947   |   6:    60.764 -  70.891:   77        |
|      2:    20.255 -  30.382:  213   |   7:    70.891 -  81.019:   40        |
|      3:    30.382 -  40.509:  103   |   8:    81.019 -  91.146:   18        |
|      4:    40.509 -  50.637:   98   |   9:    91.146 - 101.273:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1272 r_free = 0.1759             target_work(ml) = 5.252         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1270 r_free = 0.1758             target_work(ml) = 5.252         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1270   r_free= 0.1758   ksol= 0.32   Bsol= 60.16   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-1.70,0.48,-0.00,0.00,0.00); trace/3= -1.11                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.251726                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.6853 0.99   1426  156 0.0992 0.1284       5.398      5.5892|
|  2:  4.6853 -  3.7379 0.99   1372  155 0.0879 0.1178      5.4734      5.6874|
|  3:  3.7379 -  3.2710 0.99   1347  149 0.1204 0.1594      5.5714      5.8781|
|  4:  3.2710 -  2.9745 0.99   1326  150 0.1449 0.1933      5.5798      5.7476|
|  5:  2.9745 -  2.7627 0.99   1335  145 0.1573 0.1909      5.4788      5.6704|
|  6:  2.7627 -  2.6007 0.99   1326  147 0.1471 0.2440      5.3551      5.6327|
|  7:  2.6007 -  2.4711 0.99   1316  154 0.1501 0.1847      5.3131      5.4474|
|  8:  2.4711 -  2.3639 0.98   1312  148 0.1436 0.1953      5.2323      5.4647|
|  9:  2.3639 -  2.2733 0.98   1295  133 0.1384 0.1926      5.1487      5.4032|
| 10:  2.2733 -  2.1951 1.00   1319  149 0.1284 0.1824      5.0432      5.2437|
| 11:  2.1951 -  2.1266 0.98   1294  144 0.1267 0.2059      5.0192      5.3854|
| 12:  2.1266 -  2.0660 0.98   1287  144 0.1341 0.1919      4.9786      5.2684|
| 13:  2.0660 -  2.0117 0.90   1187  128 0.1142 0.1708      4.8133      4.9802|
| 14:  2.0117 -  1.9628 0.37    488   57 0.0958 0.1719      4.6527      4.9661|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9814 -  4.6853  1426   156  0.93   9.77   0.97     0.95       7760.97|
|  2:  4.6853 -  3.7379  1372   155  0.95   8.47   1.02     1.01       9836.02|
|  3:  3.7379 -  3.2710  1347   149  0.92  12.92   1.05     1.05      12300.75|
|  4:  3.2710 -  2.9745  1326   150  0.90  16.25   1.02     1.00      12961.02|
|  5:  2.9745 -  2.7627  1335   145  0.88  18.88   1.01     0.99      11545.89|
|  6:  2.7627 -  2.6007  1326   147  0.87  19.29   0.98     0.93       9319.49|
|  7:  2.6007 -  2.4711  1316   154  0.87  19.27   1.00     0.96       8669.68|
|  8:  2.4711 -  2.3639  1312   148  0.88  18.55   1.00     0.97       7344.61|
|  9:  2.3639 -  2.2733  1295   133  0.89  17.96   1.00     0.94       6107.80|
| 10:  2.2733 -  2.1951  1319   149  0.89  17.30   1.01     0.97       5157.93|
| 11:  2.1951 -  2.1266  1294   144  0.89  17.95   1.00     0.95       5156.72|
| 12:  2.1266 -  2.0660  1287   144  0.89  17.88   1.01     1.00       4744.20|
| 13:  2.0660 -  2.0117  1187   128  0.89  17.37   1.00     0.98       3662.65|
| 14:  2.0117 -  1.9628   488    57  0.94  12.45   0.99     0.96       2479.70|
|alpha:            min =        0.93 max =            1.05 mean =         0.98|
|beta:             min =     2479.70 max =        12961.02 mean =      7951.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.90 mean =        16.11|
|phase err.(test): min =        0.00 max =           89.91 mean =        15.61|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1270   r_free= 0.1758   ksol= 0.32   Bsol= 60.16   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-1.78,0.48,-0.00,0.00,0.00); trace/3= -1.12                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.251554                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1270   r_free= 0.1758   ksol= 0.32   Bsol= 60.16   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-1.78,0.48,-0.00,0.00,0.00); trace/3= -1.12                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.251554                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.6853 0.99   1426  156 0.0991 0.1283      5.3972      5.5898|
|  2:  4.6853 -  3.7379 0.99   1372  155 0.0880 0.1178      5.4739      5.6879|
|  3:  3.7379 -  3.2710 0.99   1347  149 0.1204 0.1594      5.5721      5.8788|
|  4:  3.2710 -  2.9745 0.99   1326  150 0.1449 0.1933      5.5799      5.7477|
|  5:  2.9745 -  2.7627 0.99   1335  145 0.1573 0.1908      5.4786      5.6701|
|  6:  2.7627 -  2.6007 0.99   1326  147 0.1471 0.2438      5.3545      5.6322|
|  7:  2.6007 -  2.4711 0.99   1316  154 0.1501 0.1848      5.3129      5.4478|
|  8:  2.4711 -  2.3639 0.98   1312  148 0.1436 0.1953      5.2323      5.4641|
|  9:  2.3639 -  2.2733 0.98   1295  133 0.1384 0.1926      5.1487      5.4034|
| 10:  2.2733 -  2.1951 1.00   1319  149 0.1284 0.1825      5.0429      5.2446|
| 11:  2.1951 -  2.1266 0.98   1294  144 0.1267 0.2058      5.0191      5.3858|
| 12:  2.1266 -  2.0660 0.98   1287  144 0.1340 0.1917      4.9785      5.2679|
| 13:  2.0660 -  2.0117 0.90   1187  128 0.1142 0.1705      4.8123      4.9782|
| 14:  2.0117 -  1.9628 0.37    488   57 0.0959 0.1714      4.6511      4.9636|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9814 -  4.6853  1426   156  0.93   9.77   0.97     0.94       7758.29|
|  2:  4.6853 -  3.7379  1372   155  0.95   8.48   1.02     1.01       9843.14|
|  3:  3.7379 -  3.2710  1347   149  0.92  12.94   1.05     1.05      12320.83|
|  4:  3.2710 -  2.9745  1326   150  0.90  16.25   1.02     1.00      12963.56|
|  5:  2.9745 -  2.7627  1335   145  0.88  18.88   1.01     0.99      11541.04|
|  6:  2.7627 -  2.6007  1326   147  0.87  19.27   0.98     0.93       9309.21|
|  7:  2.6007 -  2.4711  1316   154  0.87  19.26   1.00     0.96       8665.85|
|  8:  2.4711 -  2.3639  1312   148  0.88  18.55   1.00     0.97       7343.20|
|  9:  2.3639 -  2.2733  1295   133  0.89  17.97   1.00     0.94       6113.79|
| 10:  2.2733 -  2.1951  1319   149  0.89  17.31   1.01     0.97       5160.40|
| 11:  2.1951 -  2.1266  1294   144  0.89  17.96   1.00     0.95       5160.09|
| 12:  2.1266 -  2.0660  1287   144  0.89  17.88   1.01     1.00       4742.81|
| 13:  2.0660 -  2.0117  1187   128  0.89  17.35   1.00     0.98       3651.41|
| 14:  2.0117 -  1.9628   488    57  0.94  12.40   0.99     0.96       2464.92|
|alpha:            min =        0.93 max =            1.05 mean =         0.98|
|beta:             min =     2464.92 max =        12963.56 mean =      7951.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.90 mean =        16.11|
|phase err.(test): min =        0.00 max =           89.91 mean =        15.61|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.698)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.28  17.76    None  None   None       |
|    all(noH): 2823   0      0.00    101.28  17.76    None  None   None       |
|    Sol.    : 438    0      5.18    101.28  46.27    None  None   None       |
|    Mac.    : 2385   0      0.00    94.74   12.52    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 -  10.130: 1236   |   5:    50.640 -  60.767:   83        |
|      1:    10.130 -  20.258:  947   |   6:    60.767 -  70.894:   77        |
|      2:    20.258 -  30.385:  213   |   7:    70.894 -  81.022:   40        |
|      3:    30.385 -  40.512:  103   |   8:    81.022 -  91.149:   18        |
|      4:    40.512 -  50.640:   98   |   9:    91.149 - 101.276:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 330         
Filter by distance & map next to the model:
   mapped sites are within: 0.585 - 4.632
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 322 from: 330
   mapped sites are within: 0.701 - 4.632

peak=    6.625 closest distance to " O   HOH Z 245 " =    1.141
peak=    6.587 closest distance to " O   HOH Z 385 " =    1.256
peak=    5.717 closest distance to " O   HOH Z 103 " =    1.155
peak=    5.536 closest distance to " CG  PRO A  54 " =    1.478
peak=    5.491 closest distance to " O   HOH Z 222 " =    1.151
peak=    5.440 closest distance to " NE2 GLN A  11 " =    1.223
peak=    5.425 closest distance to " O   HOH Z 422 " =    1.083
peak=    5.412 closest distance to " O   HOH Z 287 " =    1.998
peak=    5.386 closest distance to " O   HOH Z 417 " =    2.554
peak=    5.362 closest distance to " O   HOH Z  65 " =    1.369
peak=    5.311 closest distance to " O   HOH Z 105 " =    1.263
peak=    5.263 closest distance to " O   HOH Z 130 " =    1.111
peak=    5.216 closest distance to " O   HOH Z  63 " =    1.802
peak=    5.164 closest distance to " O   HOH Z 142 " =    1.934
peak=    5.150 closest distance to " O   HOH Z   7 " =    1.788
peak=    5.134 closest distance to " O   HOH Z  49 " =    1.622
peak=    4.923 closest distance to " O   HOH Z  69 " =    1.600
peak=    4.920 closest distance to " CG2 ILE A 120 " =    1.101
peak=    4.895 closest distance to " O   HOH Z 427 " =    2.151
peak=    4.863 closest distance to " O   HOH Z 126 " =    2.059
peak=    4.835 closest distance to " O   HOH Z 423 " =    1.849
peak=    4.714 closest distance to " O   HOH Z  39 " =    1.214
peak=    4.709 closest distance to " O   HOH Z 419 " =    2.376
peak=    4.603 closest distance to " OE1 GLN A  55 " =    1.788
peak=    4.585 closest distance to " O   HOH Z 127 " =    1.071
peak=    4.573 closest distance to " CG  PRO A  90 " =    1.419
peak=    4.565 closest distance to " O   HOH Z 112 " =    1.193
peak=    4.511 closest distance to " O   HOH Z   9 " =    2.197
peak=    4.509 closest distance to " O   HOH Z 117 " =    1.176
peak=    4.493 closest distance to " O   HOH Z 380 " =    1.971
peak=    4.457 closest distance to " CG  GLN A  58 " =    1.211
peak=    4.424 closest distance to " O   HOH Z 232 " =    2.152
peak=    4.398 closest distance to " O   HOH Z  83 " =    1.086
peak=    4.397 closest distance to " O   HOH Z 425 " =    1.462
peak=    4.367 closest distance to " CB  ARG A 275 " =    1.119
peak=    4.351 closest distance to " O   HOH Z 293 " =    1.492
peak=    4.329 closest distance to " CB  PRO A  54 " =    1.113
peak=    4.323 closest distance to " CB  SER A  63 " =    1.268
peak=    4.287 closest distance to " O   HOH Z 371 " =    1.926
peak=    4.287 closest distance to " CB  ASN A 148 " =    1.461
peak=    4.278 closest distance to " O   HOH Z 236 " =    1.462
peak=    4.261 closest distance to " O   HOH Z 130 " =    2.406
peak=    4.238 closest distance to " CG2 VAL A 257 " =    0.913
peak=    4.233 closest distance to " ND2BASN A 224 " =    0.927
peak=    4.229 closest distance to " CA  VAL A 125 " =    1.167
peak=    4.220 closest distance to " CB  SER A 216 " =    1.055
peak=    4.210 closest distance to " O   HOH Z 258 " =    1.073
peak=    4.202 closest distance to " O   HOH Z 211 " =    1.138
peak=    4.196 closest distance to " O   HOH Z 414 " =    1.378
peak=    4.188 closest distance to " O   HOH Z 303 " =    2.157
peak=    4.187 closest distance to " NH1AARG A 145 " =    1.238
peak=    4.175 closest distance to " O   HOH Z 427 " =    1.163
peak=    4.168 closest distance to " CE  LYS A 119 " =    1.299
peak=    4.161 closest distance to " O   PRO A 198 " =    1.399
peak=    4.154 closest distance to " CA  TYR A  30 " =    1.067
peak=    4.151 closest distance to " O   HOH Z 298 " =    1.851
peak=    4.142 closest distance to " CZ3 TRP A 266 " =    1.231
peak=    4.129 closest distance to " CG  PRO A 198 " =    1.226
peak=    4.117 closest distance to " CD  GLN A  77 " =    1.346
peak=    4.102 closest distance to " NH2AARG A 190 " =    1.989
peak=    4.099 closest distance to " O   HOH Z 193 " =    1.214
peak=    4.076 closest distance to " O   HOH Z  46 " =    1.092
peak=    4.061 closest distance to " O   HOH Z 145 " =    1.373
peak=    4.060 closest distance to " NH2 ARG A  56 " =    2.086
peak=    4.041 closest distance to " CB  GLN A 223 " =    1.554
peak=    4.035 closest distance to " NZ  LYS A 117 " =    2.895
peak=    4.019 closest distance to " O   HOH Z 132 " =    1.051
peak=    4.014 closest distance to " NZ  LYS A 166 " =    1.104
peak=    4.012 closest distance to " CB  PRO A  90 " =    1.102
peak=    4.011 closest distance to " CB  ASP A 191 " =    1.237
peak=    4.010 closest distance to " O   HOH Z  78 " =    1.585
peak=    4.006 closest distance to " O   HOH Z  26 " =    1.632
peak=    4.001 closest distance to " CG AARG A 275 " =    1.198
peak=    3.999 closest distance to " CA  ARG A 195 " =    1.359
peak=    3.996 closest distance to " O   HOH Z 431 " =    1.163
peak=    3.996 closest distance to " CB  GLU A 277 " =    3.552
peak=    3.995 closest distance to " OG ASER A 258 " =    3.109
peak=    3.982 closest distance to " O   HOH Z 139 " =    1.267
peak=    3.980 closest distance to " CD2 TRP A 179 " =    1.271
peak=    3.971 closest distance to " O   HOH Z 392 " =    1.275
peak=    3.967 closest distance to " O   HOH Z 411 " =    3.772
peak=    3.956 closest distance to " O   HOH Z 278 " =    1.092
peak=    3.954 closest distance to " O   HOH Z  91 " =    2.393
peak=    3.949 closest distance to " O   HOH Z 406 " =    1.673
peak=    3.942 closest distance to " O   HOH Z  30 " =    1.869
peak=    3.915 closest distance to " CB  ASN A  39 " =    0.972
peak=    3.906 closest distance to " CA  ALA A 160 " =    1.126
peak=    3.906 closest distance to " O   HOH Z  76 " =    1.224
peak=    3.904 closest distance to " CB  VAL A 202 " =    1.720
peak=    3.904 closest distance to " CB  ASN A 142 " =    0.933
peak=    3.904 closest distance to " O   HOH Z 359 " =    1.523
peak=    3.891 closest distance to " O   HOH Z 218 " =    1.753
peak=    3.863 closest distance to " CB  ALA A 114 " =    0.854
peak=    3.850 closest distance to " O   HOH Z 251 " =    1.418
peak=    3.844 closest distance to " O   HOH Z  11 " =    1.035
peak=    3.843 closest distance to " CG  LEU A 167 " =    1.279
peak=    3.834 closest distance to " N   TYR A  15 " =    1.269
peak=    3.834 closest distance to " O   HOH Z 346 " =    1.621
peak=    3.832 closest distance to " O   HOH Z 368 " =    3.674
peak=    3.831 closest distance to " CB  TRP A 179 " =    1.404
peak=    3.827 closest distance to " ND2 ASN A 249 " =    0.850
peak=    3.822 closest distance to " NH2AARG A 145 " =    1.139
peak=    3.819 closest distance to " CA  ALA A  51 " =    1.034
peak=    3.811 closest distance to " O   HOH Z 124 " =    1.387
peak=    3.809 closest distance to " CB  SER A  62 " =    0.995
peak=    3.806 closest distance to " OE2 GLU A  53 " =    1.991
peak=    3.805 closest distance to " O   HOH Z 394 " =    1.770
peak=    3.783 closest distance to " O   HOH Z 380 " =    1.532
peak=    3.781 closest distance to " CB  SER A  99 " =    0.873
peak=    3.778 closest distance to " O   HOH Z 215 " =    1.553
peak=    3.776 closest distance to " CB  ARG A  79 " =    1.112
peak=    3.771 closest distance to " O   HOH Z  61 " =    1.700
peak=    3.764 closest distance to " O   HOH Z 258 " =    1.930
peak=    3.763 closest distance to " O   HOH Z  59 " =    1.779
peak=    3.760 closest distance to " O   HOH Z 327 " =    1.688
peak=    3.753 closest distance to " N   GLN A 278 " =    1.390
peak=    3.749 closest distance to " O   HOH Z 378 " =    1.004
peak=    3.746 closest distance to " CB  THR A  31 " =    1.598
peak=    3.742 closest distance to " O   HOH Z  40 " =    1.652
peak=    3.734 closest distance to " CA  ASN A 127 " =    1.181
peak=    3.733 closest distance to " CD  ARG A 159 " =    0.861
peak=    3.731 closest distance to " O   HOH Z 272 " =    1.826
peak=    3.721 closest distance to " CZ  PHE A  38 " =    1.253
peak=    3.719 closest distance to " CG  PRO A 213 " =    1.247
peak=    3.706 closest distance to " CE3 TRP A 150 " =    1.191
peak=    3.706 closest distance to " NZ  LYS A 119 " =    2.482
peak=    3.697 closest distance to " O   HOH Z 203 " =    1.657
peak=    3.694 closest distance to " O   HOH Z 357 " =    2.031
peak=    3.692 closest distance to " O   HOH Z 201 " =    1.546
peak=    3.685 closest distance to " O   HOH Z 296 " =    1.058
peak=    3.683 closest distance to " CG  LYS A  76 " =    1.840
peak=    3.681 closest distance to " O   HOH Z 437 " =    1.725
peak=    3.680 closest distance to " CB  VAL A 265 " =    1.335
peak=    3.678 closest distance to " O   HOH Z  66 " =    0.978
peak=    3.677 closest distance to " O   HOH Z 153 " =    3.694
peak=    3.673 closest distance to " CB  SER A 210 " =    0.866
peak=    3.673 closest distance to " CB  ASP A 124 " =    0.869
peak=    3.671 closest distance to " O   HOH Z  68 " =    2.166
peak=    3.669 closest distance to " O   TYR A 116 " =    1.276
peak=    3.649 closest distance to " O   HOH Z 193 " =    1.581
peak=    3.648 closest distance to " CB  ALA A   1 " =    1.024
peak=    3.647 closest distance to " CG  GLN A  11 " =    2.306
peak=    3.641 closest distance to " O   HOH Z 425 " =    1.975
peak=    3.639 closest distance to " O  BHOH Z  74 " =    1.156
peak=    3.635 closest distance to " O   HOH Z  42 " =    1.428
peak=    3.632 closest distance to " O   HOH Z  67 " =    1.151
peak=    3.632 closest distance to " O   HOH Z  71 " =    1.504
peak=    3.626 closest distance to " CB  LEU A 300 " =    0.954
peak=    3.624 closest distance to " CG  GLN A  89 " =    1.566
peak=    3.618 closest distance to " O   HOH Z 126 " =    1.525
peak=    3.618 closest distance to " CB  ASN A 110 " =    1.085
peak=    3.606 closest distance to " O   HOH Z 365 " =    2.543
peak=    3.605 closest distance to " O   HOH Z 132 " =    2.295
peak=    3.594 closest distance to " CZ  PHE A 218 " =    1.200
peak=    3.590 closest distance to " O   HOH Z 234 " =    3.602
peak=    3.589 closest distance to " NE2 HIS A 207 " =    1.094
peak=    3.580 closest distance to " ND2 ASN A  60 " =    2.934
peak=    3.578 closest distance to " CG  PRO A 243 " =    1.122
peak=    3.576 closest distance to " CD  ARG A  66 " =    2.184
peak=    3.575 closest distance to " O   HOH Z  88 " =    3.681
peak=    3.570 closest distance to " CE  LYS A  76 " =    0.879
peak=    3.565 closest distance to " OG BSER A 164 " =    2.207
peak=    3.548 closest distance to " O   HOH Z 362 " =    2.076
peak=    3.531 closest distance to " O   HOH Z 290 " =    1.008
peak=    3.528 closest distance to " O   HOH Z 222 " =    2.462
peak=    3.526 closest distance to " CB  ARG A 190 " =    1.660
peak=    3.524 closest distance to " O   HOH Z 246 " =    1.150
peak=    3.513 closest distance to " OE2 GLU A  44 " =    1.116
peak=    3.513 closest distance to " CB  PHE A 130 " =    0.915
peak=    3.508 closest distance to " CB  SER A 212 " =    1.469
peak=    3.507 closest distance to " O   HOH Z 374 " =    1.218
peak=    3.504 closest distance to " O   HOH Z 119 " =    4.317
peak=    3.495 closest distance to " CB  TYR A 116 " =    1.120
peak=    3.487 closest distance to " O   HOH Z 402 " =    1.441
peak=    3.485 closest distance to " CA  ASN A 215 " =    0.954
peak=    3.484 closest distance to " O   HOH Z   1 " =    1.662
peak=    3.482 closest distance to " O   HOH Z 368 " =    4.333
peak=    3.480 closest distance to " CB  GLU A 128 " =    1.011
peak=    3.476 closest distance to " CG2 VAL A 197 " =    1.144
peak=    3.472 closest distance to " CG2 ILE A  20 " =    1.576
peak=    3.469 closest distance to " O   HOH Z 434 " =    1.560
peak=    3.464 closest distance to " CG2 THR A 221 " =    1.226
peak=    3.457 closest distance to " N   TYR A 116 " =    1.368
peak=    3.457 closest distance to " O   HOH Z 361 " =    1.297
peak=    3.455 closest distance to " CA  PHE A 283 " =    1.258
peak=    3.450 closest distance to " O   HOH Z 369 " =    1.793
peak=    3.449 closest distance to " O   HOH Z 193 " =    1.435
peak=    3.447 closest distance to " O   HOH Z 199 " =    1.271
peak=    3.438 closest distance to " O   HOH Z  70 " =    1.118
peak=    3.437 closest distance to " CB  GLU A  46 " =    1.163
peak=    3.431 closest distance to " O   HOH Z 421 " =    2.161
peak=    3.429 closest distance to " N   VAL A 296 " =    1.848
peak=    3.427 closest distance to " O   HOH Z 143 " =    1.300
peak=    3.425 closest distance to " O   HOH Z 213 " =    2.012
peak=    3.424 closest distance to " CB  LYS A 117 " =    1.232
peak=    3.419 closest distance to " O   HOH Z  77 " =    1.243
peak=    3.419 closest distance to " CB  GLU A 152 " =    1.198
peak=    3.415 closest distance to " O   HOH Z 180 " =    2.311
peak=    3.405 closest distance to " O   HOH Z   1 " =    1.670
peak=    3.404 closest distance to " NE2 GLN A  58 " =    4.632
peak=    3.403 closest distance to " CB  SER A 276 " =    1.130
peak=    3.400 closest distance to " CD1 ILE A 199 " =    1.321
peak=    3.397 closest distance to " CA  ARG A 156 " =    1.068
peak=    3.395 closest distance to " N   ARG A 156 " =    1.250
peak=    3.395 closest distance to " O   HOH Z 157 " =    1.622
peak=    3.393 closest distance to " CG2 ILE A 239 " =    0.942
peak=    3.393 closest distance to " CB  ALA A  43 " =    0.832
peak=    3.389 closest distance to " CA  TYR A 116 " =    1.329
peak=    3.388 closest distance to " CB  ASN A 215 " =    1.090
peak=    3.385 closest distance to " O   MET A 105 " =    1.853
peak=    3.384 closest distance to " O   HOH Z 365 " =    1.444
peak=    3.378 closest distance to " CD2 LEU A   5 " =    1.203
peak=    3.373 closest distance to " CB  ASN A 148 " =    2.040
peak=    3.368 closest distance to " O   HOH Z 295 " =    1.243
peak=    3.368 closest distance to " O   HOH Z 185 " =    1.579
peak=    3.354 closest distance to " CE BMET A  47 " =    1.145
peak=    3.353 closest distance to " O   HOH Z  40 " =    2.171
peak=    3.353 closest distance to " O   HOH Z 259 " =    2.338
peak=    3.353 closest distance to " O   HOH Z 248 " =    1.630
peak=    3.352 closest distance to " N   CYS A 260 " =    0.949
peak=    3.351 closest distance to " CA  ALA A 291 " =    0.911
peak=    3.351 closest distance to " CB  ARG A 219 " =    0.924
peak=    3.350 closest distance to " O   HOH Z  78 " =    0.948
peak=    3.344 closest distance to " O   HOH Z  51 " =    1.690
peak=    3.340 closest distance to " O   HOH Z 216 " =    3.889
peak=    3.337 closest distance to " O   HOH Z 116 " =    1.113
peak=    3.336 closest distance to " CB  SER A   3 " =    1.453
peak=    3.334 closest distance to " N   SER A  97 " =    0.812
peak=    3.334 closest distance to " O   HOH Z 220 " =    1.325
peak=    3.333 closest distance to " O   HOH Z 329 " =    4.150
peak=    3.330 closest distance to " O   HOH Z 287 " =    2.136
peak=    3.325 closest distance to " O   HOH Z  60 " =    1.335
peak=    3.323 closest distance to " CB  ASN A 285 " =    1.027
peak=    3.319 closest distance to " O   HOH Z 214 " =    2.695
peak=    3.318 closest distance to " O   HOH Z 394 " =    3.790
peak=    3.316 closest distance to " CZ3 TRP A 274 " =    1.360
peak=    3.308 closest distance to " CA  ALA A 129 " =    1.153
peak=    3.304 closest distance to " O   HOH Z 331 " =    1.035
peak=    3.302 closest distance to " CB  ASP A 200 " =    0.830
peak=    3.301 closest distance to " O   HOH Z 158 " =    3.072
peak=    3.289 closest distance to " CA  ILE A 234 " =    1.150
peak=    3.284 closest distance to " CB  HIS A 108 " =    0.840
peak=    3.281 closest distance to " N   GLU A   2 " =    1.413
peak=    3.270 closest distance to " O   HOH Z 393 " =    1.421
peak=    3.269 closest distance to " O   HOH Z 284 " =    1.456
peak=    3.268 closest distance to " N   ASN A 127 " =    1.392
peak=    3.267 closest distance to " N   TRP A  70 " =    0.830
peak=    3.266 closest distance to " CB  GLN A 183 " =    1.173
peak=    3.262 closest distance to " O   ASN A  74 " =    1.380
peak=    3.259 closest distance to " O   HOH Z  58 " =    1.797
peak=    3.254 closest distance to " CB  GLN A  88 " =    1.344
peak=    3.249 closest distance to " CB  GLU A 236 " =    1.401
peak=    3.247 closest distance to " N   PHE A 130 " =    1.351
peak=    3.246 closest distance to " O   HOH Z 379 " =    1.506
peak=    3.241 closest distance to " CB  ASP A 140 " =    1.105
peak=    3.241 closest distance to " NE1 TRP A 274 " =    0.959
peak=    3.239 closest distance to " O   HOH Z 344 " =    3.091
peak=    3.235 closest distance to " O   HOH Z 375 " =    1.101
peak=    3.235 closest distance to " ND1 HIS A  86 " =    1.785
peak=    3.234 closest distance to " CB  TYR A  30 " =    1.510
peak=    3.234 closest distance to " CB AVAL A  41 " =    1.057
peak=    3.233 closest distance to " CG1 ILE A 120 " =    1.420
peak=    3.232 closest distance to " CB  ALA A 160 " =    1.361
peak=    3.226 closest distance to " O   HOH Z 191 " =    3.061
peak=    3.223 closest distance to " O   HOH Z 146 " =    1.459
peak=    3.223 closest distance to " O   HOH Z  88 " =    3.070
peak=    3.222 closest distance to " CB  ASN A 187 " =    1.018
peak=    3.222 closest distance to " O   HOH Z 422 " =    2.237
peak=    3.217 closest distance to " O   HOH Z 280 " =    1.545
peak=    3.217 closest distance to " O   HOH Z  61 " =    1.750
peak=    3.214 closest distance to " CA  MET A 105 " =    0.971
peak=    3.213 closest distance to " NZ  LYS A 117 " =    1.227
peak=    3.212 closest distance to " O   HOH Z 207 " =    2.619
peak=    3.209 closest distance to " NH2 ARG A  56 " =    1.059
peak=    3.205 closest distance to " NE2 GLN A  73 " =    1.724
peak=    3.203 closest distance to " O   HOH Z  47 " =    1.973
peak=    3.202 closest distance to " CD  LYS A 119 " =    1.753
peak=    3.201 closest distance to " O   HOH Z 225 " =    1.692
peak=    3.199 closest distance to " CA  TRP A 150 " =    0.939
peak=    3.199 closest distance to " O   HOH Z   1 " =    1.786
peak=    3.198 closest distance to " O   HOH Z  41 " =    2.528
peak=    3.194 closest distance to " CG  GLU A  37 " =    1.087
peak=    3.183 closest distance to " CB  ASP A 272 " =    1.137
peak=    3.181 closest distance to " CB  ARG A 138 " =    0.920
peak=    3.180 closest distance to " CE  LYS A  48 " =    1.156
peak=    3.175 closest distance to " O   HOH Z  48 " =    1.662
peak=    3.175 closest distance to " C   GLN A  73 " =    1.091
peak=    3.175 closest distance to " OG  SER A 135 " =    1.168
peak=    3.173 closest distance to " O   HOH Z   7 " =    3.228
peak=    3.173 closest distance to " C   PHE A 208 " =    1.177
peak=    3.171 closest distance to " O   HOH Z 371 " =    3.220
peak=    3.171 closest distance to " CA  SER A  87 " =    1.134
peak=    3.169 closest distance to " O   HOH Z 111 " =    1.547
peak=    3.167 closest distance to " CB  ASN A 176 " =    1.010
peak=    3.165 closest distance to " CB  LEU A 237 " =    0.752
peak=    3.165 closest distance to " CB  PRO A 243 " =    1.141
peak=    3.163 closest distance to " CB  ARG A 156 " =    1.271
peak=    3.149 closest distance to " CG2BVAL A  41 " =    0.754
peak=    3.147 closest distance to " CD  ARG A 269 " =    0.989
peak=    3.135 closest distance to " O   GLY A 211 " =    1.193
peak=    3.133 closest distance to " CB  MET A  40 " =    0.797
peak=    3.133 closest distance to " O   ALA A 242 " =    1.076
peak=    3.126 closest distance to " O   HOH Z 136 " =    0.967
peak=    3.123 closest distance to " O   HOH Z 172 " =    2.242
peak=    3.119 closest distance to " NH1AARG A 102 " =    1.003
peak=    3.118 closest distance to " O   HOH Z  88 " =    2.629
peak=    3.109 closest distance to " O   HOH Z 162 " =    1.195
peak=    3.104 closest distance to " CB  ASP A 107 " =    1.084
peak=    3.104 closest distance to " O   HOH Z  44 " =    1.726
peak=    3.099 closest distance to " O   HOH Z 119 " =    1.593
peak=    3.098 closest distance to " O   HOH Z 353 " =    1.778
peak=    3.085 closest distance to " OD1 ASP A 238 " =    0.932
peak=    3.076 closest distance to " O   HOH Z 285 " =    2.403
peak=    3.073 closest distance to " CA  ALA A 158 " =    1.178
peak=    3.073 closest distance to " O   HOH Z  78 " =    1.694
peak=    3.072 closest distance to " O   HOH Z  90 " =    2.203
peak=    3.069 closest distance to " NH2BARG A 102 " =    0.919
peak=    3.067 closest distance to " N   ASN A 224 " =    1.736
peak=    3.065 closest distance to " N   GLU A 152 " =    1.460
peak=    3.058 closest distance to " OE1 GLU A   2 " =    1.415
peak=    3.056 closest distance to " CB  LEU A  83 " =    0.701
peak=    3.054 closest distance to " CA  GLY A 133 " =    3.917

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 215         
Filter by distance & map next to the model:
   mapped sites are within: 0.699 - 5.346
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 213 from: 215
   mapped sites are within: 0.771 - 5.346

peak=   -4.842 closest distance to " O   PRO A 198 " =    1.226
peak=   -4.570 closest distance to " CZ2 TRP A  92 " =    2.823
peak=   -4.534 closest distance to " CB  GLN A  55 " =    1.196
peak=   -4.284 closest distance to " CD  ARG A  14 " =    3.304
peak=   -4.253 closest distance to " O   HOH Z  69 " =    1.767
peak=   -4.222 closest distance to " O   HOH Z 276 " =    1.202
peak=   -4.208 closest distance to " CD2 TYR A 293 " =    1.802
peak=   -4.202 closest distance to " O   GLU A 152 " =    1.396
peak=   -4.102 closest distance to " O   HOH Z 385 " =    1.353
peak=   -4.067 closest distance to " NE2 GLN A  55 " =    1.253
peak=   -4.033 closest distance to " O   HOH Z 131 " =    3.977
peak=   -4.017 closest distance to " O   HOH Z 105 " =    1.926
peak=   -4.013 closest distance to " CA  HIS A 207 " =    1.157
peak=   -3.983 closest distance to " CB  ALA A  43 " =    2.422
peak=   -3.979 closest distance to " O   HOH Z  60 " =    1.732
peak=   -3.978 closest distance to " OG BSER A 134 " =    1.492
peak=   -3.959 closest distance to " O   HOH Z 298 " =    2.603
peak=   -3.948 closest distance to " CD1 LEU A 101 " =    2.269
peak=   -3.933 closest distance to " O   HOH Z  32 " =    2.094
peak=   -3.895 closest distance to " O   ALA A  10 " =    1.550
peak=   -3.891 closest distance to " O   HOH Z 377 " =    1.947
peak=   -3.862 closest distance to " CE BMET A  47 " =    1.143
peak=   -3.819 closest distance to " O   HOH Z 231 " =    0.874
peak=   -3.814 closest distance to " CG  GLN A  58 " =    1.146
peak=   -3.794 closest distance to " O   HOH Z 100 " =    1.097
peak=   -3.771 closest distance to " O   SER A  22 " =    2.583
peak=   -3.765 closest distance to " O   HOH Z  39 " =    1.022
peak=   -3.747 closest distance to " O   HOH Z 415 " =    1.322
peak=   -3.746 closest distance to " OE1 GLU A 277 " =    2.102
peak=   -3.734 closest distance to " OD2 ASP A 171 " =    2.104
peak=   -3.733 closest distance to " CB  PRO A 243 " =    2.616
peak=   -3.733 closest distance to " O   HOH Z  24 " =    0.995
peak=   -3.727 closest distance to " C   HIS A 108 " =    1.177
peak=   -3.705 closest distance to " CE1 TYR A 247 " =    2.717
peak=   -3.702 closest distance to " CG2AVAL A  41 " =    2.682
peak=   -3.698 closest distance to " N   THR A 157 " =    1.567
peak=   -3.682 closest distance to " O   HOH Z   5 " =    1.137
peak=   -3.678 closest distance to " CD  ARG A 156 " =    1.993
peak=   -3.661 closest distance to " CZ2 TRP A 274 " =    0.961
peak=   -3.637 closest distance to " O   HOH Z  70 " =    1.010
peak=   -3.626 closest distance to " O   SER A 135 " =    1.452
peak=   -3.620 closest distance to " O   HOH Z 166 " =    1.743
peak=   -3.611 closest distance to " O   HOH Z 278 " =    1.056
peak=   -3.606 closest distance to " O   HOH Z 165 " =    2.315
peak=   -3.605 closest distance to " O   HOH Z 266 " =    5.346
peak=   -3.604 closest distance to " O   HOH Z 105 " =    1.568
peak=   -3.597 closest distance to " O   HOH Z 201 " =    2.037
peak=   -3.591 closest distance to " CD1 TYR A 247 " =    2.863
peak=   -3.591 closest distance to " O   HOH Z  71 " =    0.998
peak=   -3.589 closest distance to " O   HOH Z 231 " =    2.113
peak=   -3.589 closest distance to " CA  GLY A  98 " =    1.805
peak=   -3.588 closest distance to " OG  SER A  87 " =    1.803
peak=   -3.588 closest distance to " O   HOH Z  28 " =    1.288
peak=   -3.588 closest distance to " NE2 GLN A 223 " =    1.706
peak=   -3.581 closest distance to " NE2 GLN A 194 " =    1.988
peak=   -3.581 closest distance to " CB  SER A 210 " =    1.120
peak=   -3.579 closest distance to " CB  ALA A 291 " =    2.256
peak=   -3.572 closest distance to " O   HOH Z 198 " =    1.169
peak=   -3.571 closest distance to " OD1 ASP A 191 " =    1.857
peak=   -3.567 closest distance to " CG  MET A 105 " =    1.019
peak=   -3.564 closest distance to " CB  ASP A 132 " =    2.494
peak=   -3.560 closest distance to " CA  GLY A 241 " =    2.232
peak=   -3.558 closest distance to " O   HOH Z 286 " =    1.631
peak=   -3.557 closest distance to " CB  ASP A  27 " =    2.431
peak=   -3.554 closest distance to " O   ILE A  49 " =    1.639
peak=   -3.532 closest distance to " CA  GLY A 133 " =    1.924
peak=   -3.523 closest distance to " O   HOH Z 313 " =    1.440
peak=   -3.523 closest distance to " CD  PRO A 213 " =    2.060
peak=   -3.520 closest distance to " CD1 LEU A 255 " =    2.922
peak=   -3.515 closest distance to " CG  GLN A  88 " =    0.809
peak=   -3.506 closest distance to " O   PRO A 163 " =    1.398
peak=   -3.500 closest distance to " O   HOH Z 285 " =    1.757
peak=   -3.496 closest distance to " O   HOH Z 216 " =    1.454
peak=   -3.494 closest distance to " CG  LEU A  83 " =    2.261
peak=   -3.487 closest distance to " CG2 ILE A 120 " =    1.013
peak=   -3.483 closest distance to " ND2 ASN A 285 " =    2.097
peak=   -3.473 closest distance to " O   HOH Z 185 " =    1.988
peak=   -3.470 closest distance to " O   HOH Z 348 " =    1.881
peak=   -3.470 closest distance to " O   HOH Z 111 " =    2.087
peak=   -3.467 closest distance to " OG  SER A 245 " =    1.560
peak=   -3.465 closest distance to " CZ  PHE A  59 " =    1.553
peak=   -3.464 closest distance to " O   HOH Z 151 " =    2.280
peak=   -3.462 closest distance to " O   HOH Z 193 " =    0.849
peak=   -3.459 closest distance to " O   HOH Z  67 " =    1.347
peak=   -3.450 closest distance to " CZ3 TRP A 179 " =    1.384
peak=   -3.444 closest distance to " O   HOH Z 351 " =    1.632
peak=   -3.443 closest distance to " OE2 GLU A 152 " =    1.265
peak=   -3.440 closest distance to " CE2 TYR A  30 " =    2.546
peak=   -3.438 closest distance to " NH2BARG A 102 " =    0.891
peak=   -3.437 closest distance to " O   HOH Z 238 " =    1.065
peak=   -3.437 closest distance to " CG2 ILE A  20 " =    2.762
peak=   -3.435 closest distance to " O   HOH Z 389 " =    1.157
peak=   -3.426 closest distance to " CD2 PHE A  61 " =    2.027
peak=   -3.425 closest distance to " CD2 HIS A 207 " =    2.070
peak=   -3.418 closest distance to " OG  SER A  97 " =    2.163
peak=   -3.414 closest distance to " O   HOH Z 359 " =    3.119
peak=   -3.408 closest distance to " O   HOH Z 438 " =    1.262
peak=   -3.405 closest distance to " CB  ALA A 114 " =    2.624
peak=   -3.394 closest distance to " O   HOH Z 147 " =    1.998
peak=   -3.393 closest distance to " CB  ASP A 200 " =    2.624
peak=   -3.390 closest distance to " NZ  LYS A 119 " =    0.771
peak=   -3.387 closest distance to " O   GLY A  80 " =    2.629
peak=   -3.386 closest distance to " ND2 ASN A 249 " =    2.157
peak=   -3.377 closest distance to " OE1 GLN A  88 " =    0.982
peak=   -3.368 closest distance to " CA  GLN A  58 " =    1.171
peak=   -3.367 closest distance to " CG2 THR A  52 " =    3.122
peak=   -3.363 closest distance to " O   HOH Z 275 " =    1.695
peak=   -3.354 closest distance to " CZ  PHE A 130 " =    1.024
peak=   -3.352 closest distance to " O   GLN A 240 " =    1.832
peak=   -3.352 closest distance to " CD1 TRP A 179 " =    1.168
peak=   -3.348 closest distance to " O   HOH Z 425 " =    1.005
peak=   -3.339 closest distance to " CA  ASN A 127 " =    1.313
peak=   -3.327 closest distance to " O   HOH Z  11 " =    1.586
peak=   -3.325 closest distance to " OG  SER A  63 " =    1.459
peak=   -3.319 closest distance to " O   HOH Z 412 " =    3.906
peak=   -3.319 closest distance to " CG1BVAL A  72 " =    2.257
peak=   -3.314 closest distance to " C   SER A 276 " =    1.564
peak=   -3.311 closest distance to " O   HOH Z 359 " =    1.640
peak=   -3.310 closest distance to " CZ  TYR A 169 " =    2.015
peak=   -3.309 closest distance to " O   ARG A 145 " =    1.283
peak=   -3.306 closest distance to " N   GLN A  58 " =    1.329
peak=   -3.305 closest distance to " CD  GLU A 236 " =    1.138
peak=   -3.305 closest distance to " SG BCYS A 201 " =    2.201
peak=   -3.302 closest distance to " C   ALA A 158 " =    1.718
peak=   -3.300 closest distance to " CG  ARG A 219 " =    2.221
peak=   -3.298 closest distance to " CG1 VAL A 112 " =    2.636
peak=   -3.297 closest distance to " CD  GLU A 277 " =    1.181
peak=   -3.295 closest distance to " CG2BVAL A  41 " =    1.286
peak=   -3.289 closest distance to " O   HOH Z 426 " =    1.623
peak=   -3.287 closest distance to " C   VAL A 257 " =    1.326
peak=   -3.283 closest distance to " O   HOH Z 414 " =    1.336
peak=   -3.279 closest distance to " O   HOH Z 102 " =    1.542
peak=   -3.272 closest distance to " O   HOH Z 421 " =    2.814
peak=   -3.267 closest distance to " NZ  LYS A 166 " =    1.263
peak=   -3.260 closest distance to " O   HOH Z 129 " =    3.362
peak=   -3.259 closest distance to " NH2 ARG A 219 " =    1.783
peak=   -3.257 closest distance to " O   HOH Z 357 " =    1.822
peak=   -3.257 closest distance to " O   HOH Z  64 " =    1.145
peak=   -3.256 closest distance to " CG  TRP A 266 " =    1.752
peak=   -3.254 closest distance to " O   HOH Z 428 " =    2.630
peak=   -3.254 closest distance to " O   PHE A 218 " =    1.441
peak=   -3.254 closest distance to " O   HOH Z  52 " =    1.986
peak=   -3.252 closest distance to " O   HOH Z 219 " =    4.465
peak=   -3.251 closest distance to " CB  ALA A   9 " =    2.358
peak=   -3.249 closest distance to " O   PRO A 243 " =    2.567
peak=   -3.246 closest distance to " O   HOH Z  77 " =    1.794
peak=   -3.244 closest distance to " CD2 TYR A 116 " =    2.193
peak=   -3.244 closest distance to " N   ASP A 270 " =    1.309
peak=   -3.243 closest distance to " O   HOH Z 407 " =    2.796
peak=   -3.239 closest distance to " O   TRP A  70 " =    1.396
peak=   -3.238 closest distance to " O   LYS A  76 " =    2.048
peak=   -3.235 closest distance to " CG2BVAL A  72 " =    1.733
peak=   -3.228 closest distance to " O   HOH Z 143 " =    1.407
peak=   -3.227 closest distance to " CE3 TRP A 274 " =    2.218
peak=   -3.222 closest distance to " O   TYR A 186 " =    1.470
peak=   -3.221 closest distance to " O   HOH Z  68 " =    1.454
peak=   -3.220 closest distance to " NH2 ARG A  79 " =    2.424
peak=   -3.217 closest distance to " O   LYS A 117 " =    1.734
peak=   -3.214 closest distance to " NE2 GLN A 122 " =    0.995
peak=   -3.214 closest distance to " CB  TYR A  68 " =    1.074
peak=   -3.208 closest distance to " O   HOH Z 368 " =    1.412
peak=   -3.207 closest distance to " OG BSER A  99 " =    1.081
peak=   -3.206 closest distance to " O   HOH Z 109 " =    0.937
peak=   -3.206 closest distance to " O   HOH Z 295 " =    2.165
peak=   -3.204 closest distance to " N   GLN A 223 " =    2.099
peak=   -3.201 closest distance to " OG  SER A   3 " =    1.722
peak=   -3.199 closest distance to " O   VAL A  67 " =    2.797
peak=   -3.195 closest distance to " CA  SER A  26 " =    0.988
peak=   -3.193 closest distance to " OE1 GLN A 183 " =    1.613
peak=   -3.191 closest distance to " O   HOH Z 256 " =    1.371
peak=   -3.189 closest distance to " OD1 ASP A 171 " =    1.600
peak=   -3.183 closest distance to " CB  ALA A 291 " =    1.994
peak=   -3.180 closest distance to " O   HOH Z 352 " =    1.198
peak=   -3.178 closest distance to " O   HOH Z 253 " =    3.717
peak=   -3.176 closest distance to " OG  SER A  97 " =    1.730
peak=   -3.175 closest distance to " O   HOH Z 217 " =    1.618
peak=   -3.174 closest distance to " OD2 ASP A 191 " =    1.399
peak=   -3.167 closest distance to " O   ALA A   1 " =    2.050
peak=   -3.161 closest distance to " CE  MET A 105 " =    2.595
peak=   -3.158 closest distance to " O   HOH Z  66 " =    1.055
peak=   -3.157 closest distance to " O   ASN A 187 " =    1.367
peak=   -3.156 closest distance to " CB  ASP A 132 " =    2.490
peak=   -3.154 closest distance to " ND2 ASN A  45 " =    2.347
peak=   -3.154 closest distance to " CZ  PHE A  38 " =    2.512
peak=   -3.153 closest distance to " O   HOH Z 427 " =    1.801
peak=   -3.151 closest distance to " CG  PRO A 243 " =    1.767
peak=   -3.147 closest distance to " OD2 ASP A 171 " =    1.601
peak=   -3.143 closest distance to " O   HOH Z  37 " =    1.542
peak=   -3.143 closest distance to " CB  GLN A  11 " =    1.599
peak=   -3.142 closest distance to " O   HOH Z 263 " =    2.966
peak=   -3.138 closest distance to " O   HOH Z 389 " =    2.257
peak=   -3.136 closest distance to " ND2 ASN A 187 " =    1.556
peak=   -3.131 closest distance to " CD2 LEU A  25 " =    2.172
peak=   -3.119 closest distance to " CG2 THR A 221 " =    2.220
peak=   -3.116 closest distance to " CB  TRP A  85 " =    2.138
peak=   -3.111 closest distance to " OD2 ASP A 270 " =    1.166
peak=   -3.106 closest distance to " O   ASN A 249 " =    1.582
peak=   -3.105 closest distance to " OE2 GLU A 152 " =    2.408
peak=   -3.103 closest distance to " C   GLN A  58 " =    1.978
peak=   -3.099 closest distance to " N   ALA A  43 " =    2.471
peak=   -3.097 closest distance to " O   HOH Z 179 " =    1.792
peak=   -3.095 closest distance to " O   ALA A  34 " =    2.653
peak=   -3.095 closest distance to " O   ASP A 253 " =    1.890
peak=   -3.089 closest distance to " N   LYS A 166 " =    1.891
peak=   -3.089 closest distance to " OG  SER A  32 " =    1.059
peak=   -3.085 closest distance to " CG  GLU A 128 " =    1.501
peak=   -3.084 closest distance to " CG2 ILE A 263 " =    2.322
peak=   -3.079 closest distance to " N   SER A 212 " =    1.874
peak=   -3.077 closest distance to " CD2 LEU A 237 " =    2.383
peak=   -3.070 closest distance to " O   HOH Z 134 " =    3.899
peak=   -3.050 closest distance to " CA  GLY A  57 " =    2.180
peak=   -3.049 closest distance to " O   HOH Z 174 " =    2.415
peak=   -3.046 closest distance to " O   GLY A 196 " =    1.326

================= 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    :  0.4762 0.4772   6.286812e+00   6.272497e+00
   1_bss:  0.4662 0.4667   6.280063e+00   6.263358e+00
   1_xyz:  0.3906 0.4274   6.166396e+00   6.209575e+00
   1_adp:  0.3592 0.4346   6.127675e+00   6.216677e+00
   1_occ:  0.3591 0.4361   6.127656e+00   6.217804e+00
   2_bss:  0.3590 0.4351   6.130841e+00   6.220101e+00
   2_xyz:  0.2953 0.3710   5.981916e+00   6.118808e+00
   2_adp:  0.2800 0.3610   5.954955e+00   6.102975e+00
   2_occ:  0.2798 0.3612   5.954933e+00   6.103012e+00
   3_bss:  0.2804 0.3603   5.954782e+00   6.101785e+00
   3_xyz:  0.2089 0.2721   5.692050e+00   5.886086e+00
   3_adp:  0.1811 0.2494   5.580997e+00   5.804025e+00
   3_occ:  0.1809 0.2496   5.580511e+00   5.803831e+00
   4_bss:  0.1802 0.2495   5.577182e+00   5.801253e+00
   4_xyz:  0.1494 0.2083   5.407101e+00   5.646599e+00
   4_adp:  0.1394 0.1915   5.336428e+00   5.568840e+00
   4_occ:  0.1393 0.1913   5.335481e+00   5.567706e+00
   5_bss:  0.1395 0.1909   5.334285e+00   5.565713e+00
   5_xyz:  0.1300 0.1776   5.266747e+00   5.494670e+00
   5_adp:  0.1272 0.1759   5.252105e+00   5.484973e+00
   5_occ:  0.1270 0.1758   5.251726e+00   5.484407e+00
   5_bss:  0.1270 0.1758   5.251554e+00   5.484340e+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:  0.322  29.027  -2.835   1.291   3.984   0.000   0.000   0.000
   1_xyz:  0.322  29.027  -2.835   1.291   3.984   0.000   0.000   0.000
   1_adp:  0.322  29.027  -2.835   1.291   3.984   0.000   0.000   0.000
   1_occ:  0.322  29.027  -2.835   1.291   3.984   0.000   0.000   0.000
   2_bss:  0.341  56.913  -1.567   0.350   2.588   0.000   0.000   0.000
   2_xyz:  0.341  56.913  -1.567   0.350   2.588   0.000   0.000   0.000
   2_adp:  0.341  56.913  -1.567   0.350   2.588   0.000   0.000   0.000
   2_occ:  0.341  56.913  -1.567   0.350   2.588   0.000   0.000   0.000
   3_bss:  0.320  50.517  -1.150   0.025   2.109   0.000   0.000   0.000
   3_xyz:  0.320  50.517  -1.150   0.025   2.109   0.000   0.000   0.000
   3_adp:  0.320  50.517  -1.150   0.025   2.109   0.000   0.000   0.000
   3_occ:  0.320  50.517  -1.150   0.025   2.109   0.000   0.000   0.000
   4_bss:  0.324  60.155  -1.944  -1.297   0.861  -0.000   0.000   0.000
   4_xyz:  0.324  60.155  -1.944  -1.297   0.861  -0.000   0.000   0.000
   4_adp:  0.324  60.155  -1.944  -1.297   0.861  -0.000   0.000   0.000
   4_occ:  0.324  60.155  -1.944  -1.297   0.861  -0.000   0.000   0.000
   5_bss:  0.324  60.155  -2.123  -1.702   0.485  -0.000   0.000   0.000
   5_xyz:  0.324  60.155  -2.123  -1.702   0.485  -0.000   0.000   0.000
   5_adp:  0.324  60.155  -2.123  -1.702   0.485  -0.000   0.000   0.000
   5_occ:  0.324  60.155  -2.123  -1.702   0.485  -0.000   0.000   0.000
   5_bss:  0.321  60.158  -2.042  -1.784   0.481  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.378 0.4278  0.5868    72208.444
   1_bss:  56.008 0.4442  0.6288    68952.782
   1_xyz:  48.960 0.5324  0.7369    54046.187
   1_adp:  49.780 0.5215  0.7300    55217.454
   1_occ:  49.924 0.5197  0.7269    55478.927
   2_bss:  49.893 0.5202  0.7221    55704.630
   2_xyz:  40.786 0.6313  0.8600    38192.230
   2_adp:  39.034 0.6532  0.8683    36567.970
   2_occ:  39.073 0.6527  0.8676    36614.179
   3_bss:  38.972 0.6538  0.8645    36358.499
   3_xyz:  27.918 0.7798  0.9916    19726.027
   3_adp:  24.992 0.8109  0.9984    16270.854
   3_occ:  24.981 0.8110  0.9982    16252.355
   4_bss:  24.837 0.8122  0.9606    16096.993
   4_xyz:  20.409 0.8564  0.9836    11195.998
   4_adp:  18.258 0.8777  0.9827     9607.772
   4_occ:  18.236 0.8779  0.9828     9576.285
   5_bss:  18.177 0.8784  0.9719     9512.809
   5_xyz:  16.437 0.8940  0.9811     8135.674
   5_adp:  16.072 0.8977  0.9758     7963.933
   5_occ:  16.060 0.8978  0.9757     7952.364
   5_bss:  16.058 0.8979  0.9758     7952.497
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.9417e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.9417e-01
   1_xyz:   1.440  0.010  0.094 15.641  0.006  4.104   1.1040e-01
   1_adp:   1.440  0.010  0.094 15.641  0.006  4.104   1.1040e-01
   1_occ:   1.440  0.010  0.094 15.641  0.006  4.104   1.1040e-01
   2_bss:   1.440  0.010  0.094 15.641  0.006  4.104   1.1040e-01
   2_xyz:   1.362  0.009  0.093 15.399  0.005  4.113   9.6884e-02
   2_adp:   1.362  0.009  0.093 15.399  0.005  4.113   9.6884e-02
   2_occ:   1.362  0.009  0.093 15.399  0.005  4.113   9.6884e-02
   3_bss:   1.362  0.009  0.093 15.399  0.005  4.113   9.6884e-02
   3_xyz:   1.294  0.011  0.092 15.556  0.005  4.110   1.0028e-01
   3_adp:   1.294  0.011  0.092 15.556  0.005  4.110   1.0028e-01
   3_occ:   1.294  0.011  0.092 15.556  0.005  4.110   1.0028e-01
   4_bss:   1.294  0.011  0.092 15.556  0.005  4.110   1.0028e-01
   4_xyz:   1.068  0.008  0.074 14.903  0.004  4.121   6.6456e-02
   4_adp:   1.068  0.008  0.074 14.903  0.004  4.121   6.6456e-02
   4_occ:   1.068  0.008  0.074 14.903  0.004  4.121   6.6456e-02
   5_bss:   1.068  0.008  0.074 14.903  0.004  4.121   6.6456e-02
   5_xyz:   0.939  0.006  0.071 14.581  0.004  4.117   5.3927e-02
   5_adp:   0.939  0.006  0.071 14.581  0.004  4.117   5.3927e-02
   5_occ:   0.939  0.006  0.071 14.581  0.004  4.117   5.3927e-02
   5_bss:   0.939  0.006  0.071 14.581  0.004  4.117   5.3927e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.056   2.4192e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.056   2.4192e-01
   1_xyz:   9.657  0.059  0.320 81.985  0.045  1.986   9.2991e-02
   1_adp:   9.657  0.059  0.320 81.985  0.045  1.986   9.2991e-02
   1_occ:   9.657  0.059  0.320 81.985  0.045  1.986   9.2991e-02
   2_bss:   9.657  0.059  0.320 81.985  0.045  1.986   9.2991e-02
   2_xyz:   8.947  0.094  0.288 86.342  0.035  2.134   9.2186e-02
   2_adp:   8.947  0.094  0.288 86.342  0.035  2.134   9.2186e-02
   2_occ:   8.947  0.094  0.288 86.342  0.035  2.134   9.2186e-02
   3_bss:   8.947  0.094  0.288 86.342  0.035  2.134   9.2186e-02
   3_xyz:  11.573  0.067  0.333 85.207  0.032  2.225   1.8438e-01
   3_adp:  11.573  0.067  0.333 85.207  0.032  2.225   1.8438e-01
   3_occ:  11.573  0.067  0.333 85.207  0.032  2.225   1.8438e-01
   4_bss:  11.573  0.067  0.333 85.207  0.032  2.225   1.8438e-01
   4_xyz:   6.635  0.046  0.244 79.529  0.038  2.283   6.4938e-02
   4_adp:   6.635  0.046  0.244 79.529  0.038  2.283   6.4938e-02
   4_occ:   6.635  0.046  0.244 79.529  0.038  2.283   6.4938e-02
   5_bss:   6.635  0.046  0.244 79.529  0.038  2.283   6.4938e-02
   5_xyz:   6.506  0.039  0.237 80.969  0.034  2.386   4.1890e-02
   5_adp:   6.506  0.039  0.237 80.969  0.034  2.386   4.1890e-02
   5_occ:   6.506  0.039  0.237 80.969  0.034  2.386   4.1890e-02
   5_bss:   6.506  0.039  0.237 80.969  0.034  2.386   4.1890e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp: 103.32   0.00  18.63 103.32   0.00  15.49  72.25   0.00  35.68
   1_occ: 103.32   0.00  18.63 103.32   0.00  15.49  72.25   0.00  35.68
   2_bss: 103.32   0.00  18.63 103.32   0.00  15.49  72.25   0.00  35.68
   2_xyz: 103.32   0.00  18.63 103.32   0.00  15.49  72.25   0.00  35.68
   2_adp:  87.32   0.00  18.35  67.68   0.00  14.98  87.32   0.00  36.73
   2_occ:  87.32   0.00  18.35  67.68   0.00  14.98  87.32   0.00  36.73
   3_bss:  87.32   0.00  18.35  67.68   0.00  14.98  87.32   0.00  36.73
   3_xyz:  87.32   0.00  18.35  67.68   0.00  14.98  87.32   0.00  36.73
   3_adp: 105.11   0.00  19.23  99.73   0.00  13.80 105.11   3.37  48.79
   3_occ: 105.11   0.00  19.23  99.73   0.00  13.80 105.11   3.37  48.79
   4_bss: 105.11   0.00  19.23  99.73   0.00  13.80 105.11   3.37  48.79
   4_xyz: 105.11   0.00  19.23  99.73   0.00  13.80 105.11   3.37  48.79
   4_adp: 101.16   0.00  18.01  95.46   0.00  12.77 101.16   5.34  46.59
   4_occ: 101.16   0.00  18.01  95.46   0.00  12.77 101.16   5.34  46.59
   5_bss: 101.16   0.00  18.01  95.46   0.00  12.77 101.16   5.34  46.59
   5_xyz: 101.16   0.00  18.01  95.46   0.00  12.77 101.16   5.34  46.59
   5_adp: 101.27   0.00  17.76  94.74   0.00  12.52 101.27   5.18  46.27
   5_occ: 101.27   0.00  17.76  94.74   0.00  12.52 101.27   5.18  46.27
   5_bss: 101.28   0.00  17.76  94.74   0.00  12.52 101.28   5.18  46.27
------------------------------------------------------------------------
 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:    2.934    0.018    0.284
   1_adp:    2.934    0.018    0.284
   1_occ:    2.934    0.018    0.284
   2_bss:    2.934    0.018    0.284
   2_xyz:    2.415    0.017    0.488
   2_adp:    2.415    0.017    0.488
   2_occ:    2.415    0.017    0.488
   3_bss:    2.415    0.017    0.488
   3_xyz:    2.112    0.053    0.725
   3_adp:    2.112    0.053    0.725
   3_occ:    2.112    0.053    0.725
   4_bss:    2.112    0.053    0.725
   4_xyz:    1.814    0.055    0.782
   4_adp:    1.814    0.055    0.782
   4_occ:    1.814    0.055    0.782
   5_bss:    1.814    0.055    0.782
   5_xyz:    1.800    0.037    0.805
   5_adp:    1.800    0.037    0.805
   5_occ:    1.800    0.037    0.805
   5_bss:    1.800    0.037    0.805
------------------------------------------------------------------------

CPU time actual refinement: 342.68


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_384/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/noshake/run_384/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_384/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_384/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_384/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 342.53 
  Macro-tasks:
    bulk solvent and scale       = 37.98  
    individual site refinement   = 144.06 
    weights calculation          = 30.87  
    collect and process          = 6.55   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 219.59 
  Micro-tasks:
    mask                            = 2.47   
    f_calc                          = 109.76 
    alpha_beta                      = 8.81   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 118.75 
    fmodel                         = 6.85   
    r_factors                      = 0.21   
    phase_errors                   = 10.00  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 258.32 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.862 micro seconds
Total CPU time: 5.94 minutes
from_scatterers_fft:    649 calls, 109.42 s
gradients_fft:          594 calls, 105.37 s

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

# Date 2008-01-16 Time 04:42:32 PST -0800 (1200487352.85 s)
Start R-work = 0.4762, R-free = 0.4772 (no bulk solvent and anisotropic scale)
Final R-work = 0.1467, R-free = 0.1911 (no bulk solvent and anisotropic scale)

Start R-work = 0.4662, R-free = 0.4667
Final R-work = 0.1270, R-free = 0.1758