# Date 2008-01-16 Time 04:34:03 PST -0800 (1200486843.78 s)
#phil __OFF__

Command line arguments: "../372.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 523
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 372

-------------------------------------------------------------------------------
  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, 45.7567, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.82, per 1000 atoms: 1.00


================================== 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, 45.7567, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.962 1.95303
Completeness in resolution range: 0.933076
Completeness with d_max=infinity: 0.930329

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9620
                             d_min =   1.9530

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, 45.7567, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.962 1.95303
Completeness in resolution range: 0.933076
Completeness with d_max=infinity: 0.930329

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9625 -  4.1800 [2202/2227]  1980   222  10.1%
  bin  2:  4.1800 -  3.3298 [2117/2137]  1908   209   9.9%
  bin  3:  3.3298 -  2.9124 [2098/2117]  1890   208   9.9%
  bin  4:  2.9124 -  2.6477 [2073/2103]  1856   217  10.5%
  bin  5:  2.6477 -  2.4588 [2061/2080]  1856   205   9.9%
  bin  6:  2.4588 -  2.3144 [2040/2065]  1840   200   9.8%
  bin  7:  2.3144 -  2.1989 [2042/2070]  1839   203   9.9%
  bin  8:  2.1989 -  2.1035 [2040/2076]  1830   210  10.3%
  bin  9:  2.1035 -  2.0227 [1985/2059]  1796   189   9.5%
  bin 10:  2.0227 -  1.9530 [ 931/2060]   835    96  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_372/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: 0.12 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:
        1.20 -     1.94: 19
        1.94 -     2.68: 141
        2.68 -     3.42: 4513
        3.42 -     4.16: 9464
        4.16 -     4.90: 14447
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.195 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.580 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  53 " - " O   HOH Z 102 "  1.700 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.716 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28579 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_372/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_372/model_refine_001.geo

CPU time processing inputs: 7.84


============================ 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 45.75675 88.1178 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: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4787   r_free= 0.4800   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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.290348                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9625 -  4.6626 0.99   1433  156 0.3869 0.3828       6.611      6.5838|
|  2:  4.6626 -  3.7195 0.99   1384  158 0.4229 0.4295       6.825      6.8113|
|  3:  3.7195 -  3.2549 0.99   1340  147 0.4553 0.4405         6.7       6.699|
|  4:  3.2549 -  2.9598 0.99   1345  151 0.4817 0.4849      6.5475      6.5447|
|  5:  2.9598 -  2.7491 0.99   1335  148 0.5138 0.4959      6.3641      6.4062|
|  6:  2.7491 -  2.5879 0.99   1340  144 0.5056 0.5066      6.2801      6.1745|
|  7:  2.5879 -  2.4588 0.99   1313  157 0.5087 0.5303      6.2248        6.18|
|  8:  2.4588 -  2.3522 0.98   1319  149 0.5307 0.5281      6.1797      6.1726|
|  9:  2.3522 -  2.2620 0.98   1306  134 0.5161 0.5491      6.1234      6.1878|
| 10:  2.2620 -  2.1842 1.00   1328  149 0.5243 0.5704      6.0795      6.1085|
| 11:  2.1842 -  2.1161 0.98   1299  145 0.5191 0.4688      6.0225      6.0231|
| 12:  2.1161 -  2.0558 0.98   1290  143 0.5114 0.5032      5.9445       5.945|
| 13:  2.0558 -  2.0018 0.89   1184  131 0.5132 0.4940      5.8857      5.7924|
| 14:  2.0018 -  1.9530 0.31    414   47 0.5306 0.5187      5.8662      5.8667|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9625 -  4.6626  1433   156  0.70  33.91   0.81     0.77      74072.52|
|  2:  4.6626 -  3.7195  1384   158  0.66  38.94   0.89     0.77     125730.98|
|  3:  3.7195 -  3.2549  1340   147  0.52  50.23   0.91     0.70     137324.26|
|  4:  3.2549 -  2.9598  1345   151  0.40  59.47   0.90     0.59     128107.40|
|  5:  2.9598 -  2.7491  1335   148  0.37  62.30   0.87     0.55      88872.84|
|  6:  2.7491 -  2.5879  1340   144  0.36  62.62   0.90     0.52      74366.06|
|  7:  2.5879 -  2.4588  1313   157  0.37  62.36   0.91     0.51      63779.74|
|  8:  2.4588 -  2.3522  1319   149  0.34  64.79   0.90     0.49      60166.70|
|  9:  2.3522 -  2.2620  1306   134  0.32  66.01   0.92     0.48      56432.67|
| 10:  2.2620 -  2.1842  1328   149  0.32  66.28   0.92     0.47      50743.38|
| 11:  2.1842 -  2.1161  1299   145  0.31  66.60   0.94     0.50      49666.02|
| 12:  2.1161 -  2.0558  1290   143  0.33  65.61   0.96     0.52      42692.92|
| 13:  2.0558 -  2.0018  1184   131  0.33  65.63   0.94     0.54      37537.99|
| 14:  2.0018 -  1.9530   414    47  0.36  63.07   1.00     0.53      30401.91|
|alpha:            min =        0.47 max =            0.77 mean =         0.57|
|beta:             min =    30401.91 max =       137324.26 mean =     75756.36|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           90.00 mean =        58.62|
|phase err.(test): min =        0.00 max =           89.93 mean =        58.96|
|-----------------------------------------------------------------------------|

============================== 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 = 12.889475             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.605   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.100329              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.524   (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 |  1.195 -  1.566:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.566 -  1.936:       18 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.936 -  2.307:       25 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.307 -  2.677:      116 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.677 -  3.048:     2187 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.048 -  3.418:     2326 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.418 -  3.789:     4056 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.789 -  4.159:     5408 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.159 -  4.530:     6476 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.530 -  4.900:     7971 |
|-----------------------------------------------------------------------------|
|-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 |        0.200 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.107    4.900  1.195 |       0.751 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.589)------------------------------------------|
|    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: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4787   r_free= 0.4800   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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.290348                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4689   r_free= 0.4708   ksol= 0.34   Bsol= 28.37   scale= 0.921   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,1.61,2.40,0.00,0.00,0.00); trace/3= 0.37                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.285311                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.804824              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.494   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.408447              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.287   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4689      final r-factor (work) = 0.4027          |
| start r-factor (free) = 0.4708      final r-factor (free) = 0.4439          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.9872 = 9.80 * 0.50 * 6.2800 + 1.00 * 0.2000                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.5625 = 9.80 * 0.50 * 6.2118 + 1.00 * 0.1096                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4027      final r-factor (work) = 0.3725          |
| start r-factor (free) = 0.4439      final r-factor (free) = 0.4491          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7551 = 1.41 * 1.00 * 6.2118 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.6945 = 1.41 * 1.00 * 6.1594 + 1.00 * 0.0193                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.589)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.89   18.78    None  None   None       |
|    all(noH): 2823   0      0.00    89.89   18.78    None  None   None       |
|    Sol.    : 438    0      0.00    89.89   32.65    None  None   None       |
|    Mac.    : 2385   0      0.00    87.47   16.24    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 -   8.989:  735   |   5:    44.946 -  53.935:   83        |
|      1:     8.989 -  17.979:  861   |   6:    53.935 -  62.925:   44        |
|      2:    17.979 -  26.968:  589   |   7:    62.925 -  71.914:   17        |
|      3:    26.968 -  35.957:  331   |   8:    71.914 -  80.903:    8        |
|      4:    35.957 -  44.946:  149   |   9:    80.903 -  89.892:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3725 r_free = 0.4491             target_work(ml) = 6.163         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3722 r_free = 0.4505             target_work(ml) = 6.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3722   r_free= 0.4505   ksol= 0.34   Bsol= 28.37   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,1.61,2.40,0.00,0.00,0.00); trace/3= 0.37                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.163489                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3727   r_free= 0.4476   ksol= 0.35   Bsol= 52.95   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.94,1.37,2.10,0.00,0.00,0.00); trace/3= 0.84                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.166297                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.753594             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.714  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.755328              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.667  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3727      final r-factor (work) = 0.3118          |
| start r-factor (free) = 0.4476      final r-factor (free) = 0.3994          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 48.6556 = 15.75 * 0.50 * 6.1632 + 1.00 * 0.1096                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 48.2176 = 15.75 * 0.50 * 6.1069 + 1.00 * 0.1144                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3118      final r-factor (work) = 0.2972          |
| start r-factor (free) = 0.3994      final r-factor (free) = 0.3912          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6322 = 0.76 * 1.00 * 6.1069 + 1.00 * 0.0195                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5637 = 0.76 * 1.00 * 6.0233 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.589)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.76   18.30    None  None   None       |
|    all(noH): 2823   0      0.00    90.76   18.30    None  None   None       |
|    Sol.    : 438    0      0.00    90.76   33.85    None  None   None       |
|    Mac.    : 2385   0      0.00    82.78   15.44    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.076:  758   |   5:    45.379 -  54.454:   74        |
|      1:     9.076 -  18.151:  918   |   6:    54.454 -  63.530:   38        |
|      2:    18.151 -  27.227:  559   |   7:    63.530 -  72.606:   16        |
|      3:    27.227 -  36.303:  311   |   8:    72.606 -  81.681:    3        |
|      4:    36.303 -  45.379:  140   |   9:    81.681 -  90.757:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2972 r_free = 0.3912             target_work(ml) = 6.011         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2969 r_free = 0.3914             target_work(ml) = 6.011         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2969   r_free= 0.3914   ksol= 0.35   Bsol= 52.95   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.94,1.37,2.10,0.00,0.00,0.00); trace/3= 0.84                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.011194                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2975   r_free= 0.3908   ksol= 0.33   Bsol= 57.85   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.81,0.38,1.59,0.00,0.00,0.00); trace/3= 0.38                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.011350                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.739165              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.279  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 12.238562             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.350  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2975      final r-factor (work) = 0.2435          |
| start r-factor (free) = 0.3908      final r-factor (free) = 0.3156          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.4480 = 9.74 * 0.50 * 6.0238 + 1.00 * 0.1144                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.0381 = 9.74 * 0.50 * 5.9456 + 1.00 * 0.0854                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2435      final r-factor (work) = 0.2150          |
| start r-factor (free) = 0.3156      final r-factor (free) = 0.3004          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 72.7799 = 12.24 * 1.00 * 5.9456 + 1.00 * 0.0140                             |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 70.7032 = 12.24 * 1.00 * 5.7752 + 1.00 * 0.0233                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.589)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.04  19.84    None  None   None       |
|    all(noH): 2823   0      0.00    107.04  19.84    None  None   None       |
|    Sol.    : 438    0      1.36    107.04  47.67    None  None   None       |
|    Mac.    : 2385   0      0.00    105.99  14.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.704: 1147   |   5:    53.522 -  64.226:  100        |
|      1:    10.704 -  21.409:  818   |   6:    64.226 -  74.931:   64        |
|      2:    21.409 -  32.113:  334   |   7:    74.931 -  85.635:   35        |
|      3:    32.113 -  42.818:  170   |   8:    85.635 -  96.339:   20        |
|      4:    42.818 -  53.522:  125   |   9:    96.339 - 107.044:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2150 r_free = 0.3004             target_work(ml) = 5.752         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2147 r_free = 0.3000             target_work(ml) = 5.751         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2147   r_free= 0.3000   ksol= 0.33   Bsol= 57.85   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.81,0.38,1.59,0.00,0.00,0.00); trace/3= 0.38                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.750830                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2145   r_free= 0.3001   ksol= 0.33   Bsol= 65.23   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.24,-0.55,1.06,-0.00,0.00,0.00); trace/3= -0.24                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.748264                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.340648              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.123  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.442177              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.616  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2145      final r-factor (work) = 0.1825          |
| start r-factor (free) = 0.3001      final r-factor (free) = 0.2514          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7322 = 3.34 * 0.50 * 5.7754 + 1.00 * 0.0854                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5596 = 3.34 * 0.50 * 5.6902 + 1.00 * 0.0552                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1825      final r-factor (work) = 0.1700          |
| start r-factor (free) = 0.2514      final r-factor (free) = 0.2270          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5392 = 0.44 * 1.00 * 5.6902 + 1.00 * 0.0232                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4773 = 0.44 * 1.00 * 5.5729 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.589)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.79  18.11    None  None   None       |
|    all(noH): 2823   0      0.00    109.79  18.11    None  None   None       |
|    Sol.    : 438    0      3.87    109.79  46.04    None  None   None       |
|    Mac.    : 2385   0      0.00    106.00  12.98    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 -  10.979: 1339   |   5:    54.893 -  65.872:   83        |
|      1:    10.979 -  21.957:  844   |   6:    65.872 -  76.850:   45        |
|      2:    21.957 -  32.936:  210   |   7:    76.850 -  87.829:   33        |
|      3:    32.936 -  43.915:  129   |   8:    87.829 -  98.808:    4        |
|      4:    43.915 -  54.893:  132   |   9:    98.808 - 109.786:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1700 r_free = 0.2270             target_work(ml) = 5.516         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1698 r_free = 0.2266             target_work(ml) = 5.514         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1698   r_free= 0.2266   ksol= 0.33   Bsol= 65.23   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.24,-0.55,1.06,-0.00,0.00,0.00); trace/3= -0.24                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.514429                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1700   r_free= 0.2269   ksol= 0.32   Bsol= 57.47   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.48,-1.25,0.84,-0.00,0.00,0.00); trace/3= -0.63                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.513914                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.527473              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.561  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.886020              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.404  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1700      final r-factor (work) = 0.1387          |
| start r-factor (free) = 0.2269      final r-factor (free) = 0.1916          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.6708 = 4.53 * 0.50 * 5.5729 + 1.00 * 0.0552                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.3675 = 4.53 * 0.50 * 5.4334 + 1.00 * 0.0676                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1387      final r-factor (work) = 0.1305          |
| start r-factor (free) = 0.1916      final r-factor (free) = 0.1834          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2605 = 1.89 * 1.00 * 5.4334 + 1.00 * 0.0129                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0220 = 1.89 * 1.00 * 5.3066 + 1.00 * 0.0136                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.589)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.48  17.78    None  None   None       |
|    all(noH): 2823   0      0.00    113.48  17.78    None  None   None       |
|    Sol.    : 438    0      5.22    113.48  47.49    None  None   None       |
|    Mac.    : 2385   0      0.00    106.40  12.33    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 -  11.348: 1493   |   5:    56.738 -  68.085:   85        |
|      1:    11.348 -  22.695:  762   |   6:    68.085 -  79.433:   60        |
|      2:    22.695 -  34.043:  180   |   7:    79.433 -  90.780:   29        |
|      3:    34.043 -  45.390:   97   |   8:    90.780 - 102.128:    9        |
|      4:    45.390 -  56.738:  105   |   9:   102.128 - 113.475:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1305 r_free = 0.1834             target_work(ml) = 5.282         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1304 r_free = 0.1833             target_work(ml) = 5.282         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1304   r_free= 0.1833   ksol= 0.32   Bsol= 57.47   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.48,-1.25,0.84,-0.00,0.00,0.00); trace/3= -0.63                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.281740                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9625 -  4.6626 0.99   1433  156 0.0991 0.1417      5.4243      5.6632|
|  2:  4.6626 -  3.7195 0.99   1384  158 0.0898 0.1241      5.5064       5.742|
|  3:  3.7195 -  3.2549 0.99   1340  147 0.1228 0.1622      5.5971      5.9002|
|  4:  3.2549 -  2.9598 0.99   1345  151 0.1504 0.2096      5.6091      5.8212|
|  5:  2.9598 -  2.7491 0.99   1335  148 0.1582 0.2022      5.4922      5.7318|
|  6:  2.7491 -  2.5879 0.99   1340  144 0.1496 0.2360      5.3706      5.5952|
|  7:  2.5879 -  2.4588 0.99   1313  157 0.1489 0.1959      5.3136      5.4877|
|  8:  2.4588 -  2.3522 0.98   1319  149 0.1502 0.1939      5.2618      5.4868|
|  9:  2.3522 -  2.2620 0.98   1306  134 0.1419 0.2075      5.1778      5.4498|
| 10:  2.2620 -  2.1842 1.00   1328  149 0.1298 0.1849      5.0523      5.2653|
| 11:  2.1842 -  2.1161 0.98   1299  145 0.1297 0.2197      5.0435      5.4938|
| 12:  2.1161 -  2.0558 0.98   1290  143 0.1369 0.2017      5.0063       5.253|
| 13:  2.0558 -  2.0018 0.89   1184  131 0.1253 0.1703       4.884      5.0296|
| 14:  2.0018 -  1.9530 0.31    414   47 0.1225 0.1821      4.7561      5.0661|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9625 -  4.6626  1433   156  0.93  10.52   0.97     0.95       8877.41|
|  2:  4.6626 -  3.7195  1384   158  0.94   9.30   1.03     1.02      10992.81|
|  3:  3.7195 -  3.2549  1340   147  0.92  13.87   1.06     1.05      13641.21|
|  4:  3.2549 -  2.9598  1345   151  0.88  17.73   1.03     1.01      14602.06|
|  5:  2.9598 -  2.7491  1335   148  0.87  19.75   1.02     0.99      12267.30|
|  6:  2.7491 -  2.5879  1340   144  0.86  20.08   0.99     0.94       9866.74|
|  7:  2.5879 -  2.4588  1313   157  0.87  19.70   1.02     0.98       8824.85|
|  8:  2.4588 -  2.3522  1319   149  0.87  20.02   1.02     0.98       8021.03|
|  9:  2.3522 -  2.2620  1306   134  0.88  18.96   1.01     0.95       6593.12|
| 10:  2.2620 -  2.1842  1328   149  0.88  18.29   1.01     0.98       5478.13|
| 11:  2.1842 -  2.1161  1299   145  0.88  18.62   1.01     0.95       5392.78|
| 12:  2.1161 -  2.0558  1290   143  0.87  19.22   1.03     1.02       5257.08|
| 13:  2.0558 -  2.0018  1184   131  0.88  18.81   1.01     0.99       4169.83|
| 14:  2.0018 -  1.9530   414    47  0.92  14.08   1.00     0.98       2791.28|
|alpha:            min =        0.94 max =            1.05 mean =         0.98|
|beta:             min =     2791.28 max =        14602.06 mean =      8700.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.98 mean =        17.13|
|phase err.(test): min =        0.00 max =           89.72 mean =        16.39|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1310   r_free= 0.1827   ksol= 0.32   Bsol= 57.47   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.64,-1.53,0.64,-0.00,0.00,0.00); trace/3= -0.84                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.281462                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1310   r_free= 0.1827   ksol= 0.32   Bsol= 57.47   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.64,-1.53,0.64,-0.00,0.00,0.00); trace/3= -0.84                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.281462                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9625 -  4.6626 0.99   1433  156 0.1015 0.1375      5.4217      5.6445|
|  2:  4.6626 -  3.7195 0.99   1384  158 0.0910 0.1233      5.5076      5.7436|
|  3:  3.7195 -  3.2549 0.99   1340  147 0.1233 0.1620      5.5992       5.898|
|  4:  3.2549 -  2.9598 0.99   1345  151 0.1506 0.2099      5.6104      5.8232|
|  5:  2.9598 -  2.7491 0.99   1335  148 0.1584 0.2026      5.4924      5.7318|
|  6:  2.7491 -  2.5879 0.99   1340  144 0.1497 0.2355      5.3701      5.5929|
|  7:  2.5879 -  2.4588 0.99   1313  157 0.1491 0.1960      5.3131      5.4872|
|  8:  2.4588 -  2.3522 0.98   1319  149 0.1499 0.1935      5.2607      5.4849|
|  9:  2.3522 -  2.2620 0.98   1306  134 0.1418 0.2075       5.177      5.4493|
| 10:  2.2620 -  2.1842 1.00   1328  149 0.1296 0.1850      5.0513      5.2661|
| 11:  2.1842 -  2.1161 0.98   1299  145 0.1295 0.2196      5.0428      5.4937|
| 12:  2.1161 -  2.0558 0.98   1290  143 0.1368 0.2017      5.0062      5.2529|
| 13:  2.0558 -  2.0018 0.89   1184  131 0.1253 0.1697      4.8832      5.0277|
| 14:  2.0018 -  1.9530 0.31    414   47 0.1225 0.1817      4.7547      5.0634|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9625 -  4.6626  1433   156  0.93  10.36   0.97     0.95       8529.13|
|  2:  4.6626 -  3.7195  1384   158  0.94   9.21   1.03     1.01      10830.95|
|  3:  3.7195 -  3.2549  1340   147  0.91  13.88   1.06     1.05      13653.95|
|  4:  3.2549 -  2.9598  1345   151  0.88  17.76   1.03     1.00      14644.09|
|  5:  2.9598 -  2.7491  1335   148  0.87  19.75   1.01     0.98      12266.47|
|  6:  2.7491 -  2.5879  1340   144  0.86  20.06   0.98     0.94       9843.70|
|  7:  2.5879 -  2.4588  1313   157  0.87  19.67   1.01     0.97       8800.70|
|  8:  2.4588 -  2.3522  1319   149  0.87  19.99   1.01     0.97       7999.56|
|  9:  2.3522 -  2.2620  1306   134  0.88  18.95   1.00     0.94       6592.26|
| 10:  2.2620 -  2.1842  1328   149  0.88  18.27   1.00     0.97       5471.10|
| 11:  2.1842 -  2.1161  1299   145  0.88  18.61   1.00     0.94       5389.98|
| 12:  2.1161 -  2.0558  1290   143  0.87  19.20   1.01     1.01       5250.84|
| 13:  2.0558 -  2.0018  1184   131  0.88  18.77   1.00     0.98       4155.87|
| 14:  2.0018 -  1.9530   414    47  0.92  14.00   0.99     0.97       2772.06|
|alpha:            min =        0.94 max =            1.05 mean =         0.98|
|beta:             min =     2772.06 max =        14644.09 mean =      8655.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.88 mean =        17.10|
|phase err.(test): min =        0.00 max =           88.42 mean =        16.35|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.589)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.48  17.79    None  None   None       |
|    all(noH): 2823   0      0.00    113.48  17.79    None  None   None       |
|    Sol.    : 438    0      5.22    113.48  47.49    None  None   None       |
|    Mac.    : 2385   0      0.00    106.41  12.33    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 -  11.351: 1493   |   5:    56.741 -  68.088:   85        |
|      1:    11.351 -  22.698:  762   |   6:    68.088 -  79.436:   60        |
|      2:    22.698 -  34.046:  180   |   7:    79.436 -  90.783:   29        |
|      3:    34.046 -  45.393:   97   |   8:    90.783 - 102.131:    9        |
|      4:    45.393 -  56.741:  105   |   9:   102.131 - 113.478:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 329         
Filter by distance & map next to the model:
   mapped sites are within: 0.602 - 4.522
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 325 from: 329
   mapped sites are within: 0.711 - 4.522

peak=    9.561 closest distance to " O   HOH Z 390 " =    1.413
peak=    7.228 closest distance to " O   HOH Z 385 " =    2.023
peak=    6.938 closest distance to " O   HOH Z 130 " =    1.306
peak=    6.603 closest distance to " O   HOH Z 245 " =    1.306
peak=    6.190 closest distance to " O   HOH Z 431 " =    1.853
peak=    6.180 closest distance to " O   HOH Z  77 " =    1.181
peak=    6.175 closest distance to " O   HOH Z 422 " =    1.554
peak=    5.774 closest distance to " O   HOH Z 415 " =    1.239
peak=    5.666 closest distance to " O   HOH Z  69 " =    2.133
peak=    5.660 closest distance to " O   HOH Z 105 " =    1.337
peak=    5.620 closest distance to " O   HOH Z   7 " =    2.030
peak=    5.585 closest distance to " O   HOH Z 222 " =    1.525
peak=    5.569 closest distance to " O   HOH Z  66 " =    1.232
peak=    5.546 closest distance to " O   HOH Z 109 " =    2.875
peak=    5.502 closest distance to " O   HOH Z 287 " =    1.938
peak=    5.483 closest distance to " O   HOH Z  65 " =    1.762
peak=    5.312 closest distance to " NE2 GLN A  11 " =    1.318
peak=    5.266 closest distance to " O   HOH Z  29 " =    2.080
peak=    5.196 closest distance to " O   HOH Z 427 " =    1.387
peak=    4.978 closest distance to " O   HOH Z 403 " =    1.910
peak=    4.965 closest distance to " O   HOH Z  63 " =    2.008
peak=    4.951 closest distance to " O   ASP A 286 " =    2.517
peak=    4.950 closest distance to " O   HOH Z 293 " =    1.588
peak=    4.935 closest distance to " O   HOH Z 117 " =    1.388
peak=    4.904 closest distance to " O   HOH Z 427 " =    1.886
peak=    4.885 closest distance to " O   HOH Z  46 " =    1.217
peak=    4.871 closest distance to " O   HOH Z  63 " =    1.826
peak=    4.815 closest distance to " O   HOH Z 142 " =    1.570
peak=    4.782 closest distance to " O   HOH Z 359 " =    1.716
peak=    4.773 closest distance to " CG  PRO A  54 " =    1.425
peak=    4.770 closest distance to " O   HOH Z  49 " =    1.453
peak=    4.768 closest distance to " CG2 ILE A 120 " =    1.047
peak=    4.763 closest distance to " O   HOH Z 295 " =    1.237
peak=    4.724 closest distance to " O   HOH Z 418 " =    1.181
peak=    4.715 closest distance to " O   HOH Z  43 " =    1.383
peak=    4.588 closest distance to " O   HOH Z 145 " =    1.639
peak=    4.585 closest distance to " O   HOH Z   9 " =    2.025
peak=    4.566 closest distance to " CB  ARG A 275 " =    1.145
peak=    4.542 closest distance to " O   HOH Z 278 " =    1.252
peak=    4.541 closest distance to " CG  PRO A  90 " =    1.611
peak=    4.517 closest distance to " CB  PRO A  54 " =    1.126
peak=    4.502 closest distance to " O   HOH Z 124 " =    1.470
peak=    4.486 closest distance to " O   HOH Z 425 " =    1.307
peak=    4.470 closest distance to " O   HOH Z  57 " =    2.151
peak=    4.456 closest distance to " O   HOH Z 112 " =    1.327
peak=    4.405 closest distance to " O   HOH Z 358 " =    1.295
peak=    4.402 closest distance to " O   HOH Z 232 " =    2.304
peak=    4.382 closest distance to " O   PRO A 198 " =    1.381
peak=    4.344 closest distance to " O   HOH Z  30 " =    2.125
peak=    4.343 closest distance to " O   HOH Z  39 " =    1.453
peak=    4.324 closest distance to " CB  SER A 216 " =    1.078
peak=    4.296 closest distance to " O   HOH Z  67 " =    1.432
peak=    4.256 closest distance to " CB  GLN A 223 " =    1.580
peak=    4.253 closest distance to " O   HOH Z 316 " =    3.079
peak=    4.246 closest distance to " O   HOH Z 380 " =    2.225
peak=    4.227 closest distance to " O   HOH Z 298 " =    1.821
peak=    4.171 closest distance to " O   HOH Z 368 " =    3.580
peak=    4.161 closest distance to " CG  PRO A 280 " =    0.975
peak=    4.136 closest distance to " O   HOH Z 193 " =    1.499
peak=    4.127 closest distance to " O   HOH Z 225 " =    1.847
peak=    4.125 closest distance to " O   HOH Z 405 " =    1.897
peak=    4.117 closest distance to " O   HOH Z  76 " =    1.333
peak=    4.109 closest distance to " O   HOH Z 119 " =    1.506
peak=    4.101 closest distance to " CD  ARG A  66 " =    2.346
peak=    4.097 closest distance to " NH1AARG A 145 " =    1.215
peak=    4.095 closest distance to " CE  LYS A 119 " =    1.373
peak=    4.094 closest distance to " CB  SER A  63 " =    1.330
peak=    4.089 closest distance to " O   HOH Z 424 " =    1.206
peak=    4.089 closest distance to " NE1 TRP A 274 " =    1.096
peak=    4.079 closest distance to " NZ  LYS A 117 " =    2.836
peak=    4.073 closest distance to " CD  GLN A  77 " =    1.211
peak=    4.072 closest distance to " CZ3 TRP A 266 " =    1.123
peak=    4.067 closest distance to " O   HOH Z 139 " =    1.130
peak=    4.054 closest distance to " O   HOH Z 276 " =    1.496
peak=    4.047 closest distance to " O   HOH Z 375 " =    1.053
peak=    4.041 closest distance to " O   HOH Z  11 " =    1.121
peak=    4.034 closest distance to " NZ  LYS A 119 " =    2.331
peak=    4.026 closest distance to " CB  SER A 276 " =    1.241
peak=    4.025 closest distance to " O   HOH Z 365 " =    2.397
peak=    4.024 closest distance to " O   HOH Z  78 " =    1.849
peak=    4.012 closest distance to " O   HOH Z 303 " =    2.095
peak=    4.000 closest distance to " CG  GLN A  58 " =    1.001
peak=    3.992 closest distance to " O   HOH Z 392 " =    1.302
peak=    3.982 closest distance to " O   HOH Z  91 " =    2.455
peak=    3.970 closest distance to " O   HOH Z 236 " =    1.461
peak=    3.961 closest distance to " CG2 VAL A 257 " =    0.857
peak=    3.960 closest distance to " O   HOH Z 423 " =    2.212
peak=    3.934 closest distance to " CB  GLU A 277 " =    3.586
peak=    3.904 closest distance to " CB  PHE A 130 " =    1.009
peak=    3.904 closest distance to " NH2 ARG A  56 " =    2.118
peak=    3.892 closest distance to " CA  VAL A 125 " =    1.104
peak=    3.890 closest distance to " C   GLN A  73 " =    1.060
peak=    3.887 closest distance to " N   ALA A   1 " =    1.572
peak=    3.882 closest distance to " CA  TYR A  30 " =    1.100
peak=    3.876 closest distance to " CB  THR A  31 " =    1.562
peak=    3.874 closest distance to " O   HOH Z  51 " =    1.713
peak=    3.873 closest distance to " O   HOH Z 400 " =    0.758
peak=    3.864 closest distance to " CG AARG A 275 " =    1.258
peak=    3.847 closest distance to " O   HOH Z 244 " =    1.585
peak=    3.846 closest distance to " O   HOH Z  83 " =    1.111
peak=    3.835 closest distance to " O   HOH Z  88 " =    3.635
peak=    3.832 closest distance to " O   HOH Z 248 " =    1.836
peak=    3.830 closest distance to " CZ3 TRP A 274 " =    1.377
peak=    3.820 closest distance to " O   VAL A  72 " =    0.937
peak=    3.811 closest distance to " O   HOH Z 378 " =    1.047
peak=    3.791 closest distance to " NH2AARG A 145 " =    1.280
peak=    3.788 closest distance to " CB  SER A  99 " =    0.871
peak=    3.783 closest distance to " SD BMET A  47 " =    1.179
peak=    3.781 closest distance to " O   HOH Z 158 " =    1.075
peak=    3.780 closest distance to " CA  PHE A 283 " =    1.307
peak=    3.777 closest distance to " O   HOH Z   7 " =    2.833
peak=    3.774 closest distance to " O   HOH Z 272 " =    1.902
peak=    3.763 closest distance to " O   HOH Z  71 " =    1.420
peak=    3.763 closest distance to " O   HOH Z 181 " =    1.481
peak=    3.762 closest distance to " O   HOH Z 215 " =    1.647
peak=    3.758 closest distance to " OE2 GLU A  53 " =    2.056
peak=    3.748 closest distance to " O   HOH Z 406 " =    1.525
peak=    3.737 closest distance to " O   HOH Z 258 " =    2.074
peak=    3.735 closest distance to " O   HOH Z  68 " =    1.911
peak=    3.715 closest distance to " N   GLN A 278 " =    1.132
peak=    3.700 closest distance to " CB  PRO A  90 " =    1.134
peak=    3.696 closest distance to " CB  ASN A 148 " =    1.392
peak=    3.691 closest distance to " CB  GLU A 128 " =    1.051
peak=    3.691 closest distance to " CB  ASP A 124 " =    0.941
peak=    3.690 closest distance to " O   HOH Z 153 " =    3.532
peak=    3.688 closest distance to " NH1AARG A 275 " =    1.045
peak=    3.682 closest distance to " O   HOH Z 365 " =    1.539
peak=    3.682 closest distance to " O  BHOH Z  74 " =    1.146
peak=    3.676 closest distance to " O   HOH Z 211 " =    1.098
peak=    3.674 closest distance to " N   TYR A  15 " =    1.132
peak=    3.671 closest distance to " O   HOH Z 218 " =    1.867
peak=    3.670 closest distance to " CD2 TRP A 179 " =    1.432
peak=    3.668 closest distance to " O   ALA A 165 " =    1.340
peak=    3.664 closest distance to " O   HOH Z 393 " =    1.325
peak=    3.662 closest distance to " NZ  LYS A 166 " =    1.075
peak=    3.651 closest distance to " OG BSER A 164 " =    2.337
peak=    3.649 closest distance to " CB  ASN A  39 " =    0.864
peak=    3.637 closest distance to " CA  LEU A 282 " =    1.027
peak=    3.635 closest distance to " CB  LEU A 300 " =    0.939
peak=    3.625 closest distance to " ND2 ASN A  60 " =    2.920
peak=    3.623 closest distance to " O   HOH Z  30 " =    1.398
peak=    3.615 closest distance to " CB  ALA A 114 " =    0.952
peak=    3.608 closest distance to " O   HOH Z  26 " =    1.565
peak=    3.607 closest distance to " CA  PRO A 280 " =    1.359
peak=    3.603 closest distance to " CB  TRP A 266 " =    1.014
peak=    3.600 closest distance to " O   HOH Z 426 " =    1.088
peak=    3.600 closest distance to " NH2AARG A 145 " =    2.295
peak=    3.596 closest distance to " O   HOH Z   6 " =    1.631
peak=    3.585 closest distance to " O   HOH Z 146 " =    1.570
peak=    3.583 closest distance to " CB  TRP A 179 " =    1.456
peak=    3.583 closest distance to " O   HOH Z 219 " =    3.484
peak=    3.577 closest distance to " CA  ALA A  51 " =    1.056
peak=    3.577 closest distance to " CG  PRO A 213 " =    1.207
peak=    3.576 closest distance to " O   HOH Z 214 " =    2.576
peak=    3.576 closest distance to " O   HOH Z  61 " =    1.668
peak=    3.575 closest distance to " O   HOH Z 368 " =    1.806
peak=    3.569 closest distance to " O   HOH Z  44 " =    1.848
peak=    3.569 closest distance to " CG2AVAL A  72 " =    0.861
peak=    3.563 closest distance to " O   HOH Z 220 " =    1.300
peak=    3.557 closest distance to " CB  SER A 273 " =    0.932
peak=    3.555 closest distance to " O   ASN A 142 " =    1.027
peak=    3.549 closest distance to " O   HOH Z 201 " =    1.673
peak=    3.546 closest distance to " CG1 ILE A 120 " =    1.571
peak=    3.546 closest distance to " CB  ARG A 190 " =    1.692
peak=    3.542 closest distance to " O   HOH Z 425 " =    2.057
peak=    3.542 closest distance to " CB  GLN A 183 " =    1.164
peak=    3.539 closest distance to " CA  ILE A 234 " =    1.159
peak=    3.536 closest distance to " CE3 TRP A 150 " =    1.148
peak=    3.533 closest distance to " CB  MET A 105 " =    1.367
peak=    3.532 closest distance to " CG  LYS A 119 " =    0.963
peak=    3.530 closest distance to " ND2 ASN A 249 " =    0.797
peak=    3.527 closest distance to " O   HOH Z 327 " =    1.685
peak=    3.523 closest distance to " O   HOH Z 119 " =    4.174
peak=    3.517 closest distance to " CB  GLU A 152 " =    1.245
peak=    3.502 closest distance to " CZ  PHE A  38 " =    1.371
peak=    3.496 closest distance to " O   HOH Z 116 " =    1.196
peak=    3.495 closest distance to " O   HOH Z 424 " =    3.134
peak=    3.492 closest distance to " CB  VAL A 202 " =    1.722
peak=    3.487 closest distance to " O   HOH Z 156 " =    3.504
peak=    3.478 closest distance to " N   ARG A 275 " =    0.949
peak=    3.475 closest distance to " O   HOH Z  40 " =    1.767
peak=    3.474 closest distance to " O   HOH Z 434 " =    1.511
peak=    3.472 closest distance to " O   HOH Z 128 " =    1.981
peak=    3.471 closest distance to " CB  ASP A 140 " =    1.053
peak=    3.471 closest distance to " OD1 ASP A 286 " =    1.148
peak=    3.468 closest distance to " CG2 THR A 221 " =    1.155
peak=    3.460 closest distance to " O   HOH Z 357 " =    2.074
peak=    3.456 closest distance to " CA  ALA A 291 " =    0.941
peak=    3.452 closest distance to " O   HOH Z 180 " =    2.336
peak=    3.436 closest distance to " CG AASN A 224 " =    0.987
peak=    3.431 closest distance to " CG  GLN A  89 " =    1.576
peak=    3.430 closest distance to " O   HOH Z 411 " =    3.683
peak=    3.418 closest distance to " N   ASP A 162 " =    1.009
peak=    3.418 closest distance to " O   HOH Z  50 " =    1.788
peak=    3.410 closest distance to " O   HOH Z 394 " =    1.577
peak=    3.409 closest distance to " CB  ARG A  79 " =    1.209
peak=    3.409 closest distance to " O   HOH Z  92 " =    1.191
peak=    3.406 closest distance to " O   HOH Z 193 " =    2.260
peak=    3.405 closest distance to " O   HOH Z 410 " =    1.475
peak=    3.404 closest distance to " O   HOH Z 380 " =    1.733
peak=    3.404 closest distance to " O   HOH Z  44 " =    2.945
peak=    3.399 closest distance to " O   HOH Z 361 " =    1.321
peak=    3.398 closest distance to " O   HOH Z 292 " =    2.472
peak=    3.397 closest distance to " OG  SER A  22 " =    2.600
peak=    3.397 closest distance to " O   HOH Z 248 " =    2.249
peak=    3.395 closest distance to " O   HOH Z 258 " =    1.051
peak=    3.395 closest distance to " CB  TYR A 116 " =    1.226
peak=    3.392 closest distance to " N   GLU A   2 " =    1.507
peak=    3.387 closest distance to " O   HOH Z  11 " =    1.952
peak=    3.376 closest distance to " O   HOH Z 371 " =    1.676
peak=    3.376 closest distance to " O   HOH Z  21 " =    1.427
peak=    3.375 closest distance to " CA  TYR A 116 " =    1.518
peak=    3.374 closest distance to " CG  ARG A 159 " =    0.862
peak=    3.367 closest distance to " O   HOH Z 194 " =    2.329
peak=    3.366 closest distance to " O   HOH Z 106 " =    4.001
peak=    3.364 closest distance to " O   HOH Z 156 " =    3.089
peak=    3.360 closest distance to " CA  ALA A 129 " =    1.176
peak=    3.358 closest distance to " CB  LYS A 117 " =    1.233
peak=    3.357 closest distance to " CB  ASN A 142 " =    1.040
peak=    3.355 closest distance to " O   HOH Z 369 " =    1.755
peak=    3.353 closest distance to " CG  PRO A 198 " =    1.310
peak=    3.352 closest distance to " CG  GLU A  37 " =    1.021
peak=    3.351 closest distance to " CA  SER A  87 " =    1.102
peak=    3.345 closest distance to " CE  MET A  93 " =    1.333
peak=    3.344 closest distance to " O   HOH Z 386 " =    2.738
peak=    3.342 closest distance to " N   CYS A 260 " =    0.953
peak=    3.342 closest distance to " O   HOH Z 330 " =    1.056
peak=    3.330 closest distance to " CB  ALA A  43 " =    0.893
peak=    3.326 closest distance to " O   HOH Z  59 " =    2.011
peak=    3.323 closest distance to " O   HOH Z  58 " =    1.620
peak=    3.322 closest distance to " O   HOH Z 280 " =    1.371
peak=    3.316 closest distance to " C   VAL A 153 " =    1.152
peak=    3.316 closest distance to " CH2 TRP A 274 " =    2.199
peak=    3.314 closest distance to " OG BSER A 212 " =    2.622
peak=    3.314 closest distance to " O   HOH Z 362 " =    1.891
peak=    3.314 closest distance to " O   HOH Z 104 " =    1.605
peak=    3.313 closest distance to " CA  ASN A 127 " =    1.163
peak=    3.313 closest distance to " CG2 VAL A 197 " =    1.194
peak=    3.303 closest distance to " CB  PHE A 225 " =    1.249
peak=    3.302 closest distance to " NH1 ARG A  14 " =    0.712
peak=    3.296 closest distance to " O   HOH Z 289 " =    1.084
peak=    3.286 closest distance to " O   HOH Z 173 " =    1.919
peak=    3.286 closest distance to " O   HOH Z 143 " =    1.325
peak=    3.283 closest distance to " O   HOH Z 185 " =    1.489
peak=    3.283 closest distance to " CB  ASP A 171 " =    0.711
peak=    3.280 closest distance to " O   HOH Z 323 " =    1.628
peak=    3.277 closest distance to " O   HOH Z 172 " =    1.866
peak=    3.277 closest distance to " CG2 THR A 178 " =    1.075
peak=    3.274 closest distance to " O   HOH Z 423 " =    2.051
peak=    3.267 closest distance to " O   HOH Z  88 " =    2.987
peak=    3.267 closest distance to " CA  MET A 105 " =    0.917
peak=    3.267 closest distance to " CA  ALA A 160 " =    0.939
peak=    3.265 closest distance to " CB  THR A 157 " =    0.994
peak=    3.263 closest distance to " CB  ASN A 215 " =    1.127
peak=    3.263 closest distance to " O   HOH Z 356 " =    1.288
peak=    3.262 closest distance to " CB  LYS A 290 " =    0.978
peak=    3.262 closest distance to " CG  LYS A  76 " =    1.665
peak=    3.259 closest distance to " O   HOH Z 352 " =    1.685
peak=    3.252 closest distance to " CD  ARG A 159 " =    0.909
peak=    3.252 closest distance to " O   HOH Z  90 " =    4.354
peak=    3.250 closest distance to " CD2 LEU A   5 " =    1.251
peak=    3.244 closest distance to " O   HOH Z 345 " =    2.000
peak=    3.236 closest distance to " CG  GLN A  11 " =    2.278
peak=    3.236 closest distance to " OG ASER A 212 " =    1.430
peak=    3.236 closest distance to " O   HOH Z  40 " =    2.281
peak=    3.235 closest distance to " CB  ARG A 219 " =    0.785
peak=    3.233 closest distance to " CB  ASN A  74 " =    1.251
peak=    3.232 closest distance to " NE2 GLN A  73 " =    1.504
peak=    3.232 closest distance to " CD  LYS A 166 " =    1.530
peak=    3.227 closest distance to " O   HOH Z 222 " =    2.341
peak=    3.223 closest distance to " OG BSER A  99 " =    2.176
peak=    3.222 closest distance to " O   HOH Z 274 " =    2.504
peak=    3.217 closest distance to " O   HOH Z 343 " =    3.107
peak=    3.215 closest distance to " CE1 PHE A  61 " =    1.579
peak=    3.215 closest distance to " CB  ALA A 114 " =    1.558
peak=    3.213 closest distance to " O   HOH Z 328 " =    1.576
peak=    3.213 closest distance to " O   HOH Z 163 " =    2.064
peak=    3.211 closest distance to " CB  ASN A 110 " =    1.059
peak=    3.209 closest distance to " O   HOH Z 324 " =    1.197
peak=    3.203 closest distance to " CA  LEU A  83 " =    1.699
peak=    3.203 closest distance to " CD  ARG A 138 " =    0.865
peak=    3.202 closest distance to " CB  VAL A 265 " =    1.308
peak=    3.200 closest distance to " NE2 GLN A  58 " =    4.522
peak=    3.199 closest distance to " N   GLN A  73 " =    1.132
peak=    3.199 closest distance to " NZ  LYS A 117 " =    1.330
peak=    3.191 closest distance to " CA  ARG A  36 " =    1.064
peak=    3.190 closest distance to " NH2AARG A 190 " =    1.890
peak=    3.188 closest distance to " CB  GLN A  88 " =    1.368
peak=    3.188 closest distance to " O   HOH Z 326 " =    1.348
peak=    3.184 closest distance to " O   HOH Z  42 " =    1.436
peak=    3.181 closest distance to " CG2 VAL A 202 " =    1.495
peak=    3.180 closest distance to " O   HOH Z 251 " =    1.482
peak=    3.179 closest distance to " O   HOH Z 303 " =    1.533
peak=    3.178 closest distance to " O   GLN A 278 " =    1.319
peak=    3.178 closest distance to " CD1 LEU A 167 " =    1.104
peak=    3.173 closest distance to " CE  LYS A  48 " =    1.177
peak=    3.171 closest distance to " O   HOH Z 416 " =    1.328
peak=    3.166 closest distance to " O   HOH Z   1 " =    1.567
peak=    3.164 closest distance to " CB  SER A   3 " =    1.396
peak=    3.162 closest distance to " CB  ALA A 242 " =    1.378
peak=    3.155 closest distance to " O   HOH Z 353 " =    1.928
peak=    3.154 closest distance to " O   HOH Z 128 " =    2.749
peak=    3.153 closest distance to " O   HOH Z 118 " =    3.012
peak=    3.150 closest distance to " NH1AARG A 102 " =    0.982
peak=    3.147 closest distance to " CG  LEU A 167 " =    1.274
peak=    3.141 closest distance to " OE1 GLU A   2 " =    1.391
peak=    3.134 closest distance to " OD2 ASP A 286 " =    2.192
peak=    3.131 closest distance to " CD1 ILE A  33 " =    1.764
peak=    3.126 closest distance to " O   HOH Z 157 " =    1.627
peak=    3.119 closest distance to " O   GLN A  55 " =    1.643
peak=    3.118 closest distance to " O   HOH Z 342 " =    0.929
peak=    3.115 closest distance to " O   HOH Z 296 " =    0.971
peak=    3.115 closest distance to " O   HOH Z 384 " =    0.955
peak=    3.112 closest distance to " O   HOH Z 379 " =    1.625
peak=    3.106 closest distance to " CB  ARG A 138 " =    0.849
peak=    3.095 closest distance to " O   HOH Z 225 " =    2.236
peak=    3.090 closest distance to " O   GLY A 147 " =    1.257
peak=    3.088 closest distance to " O   HOH Z  40 " =    1.332
peak=    3.079 closest distance to " O   THR A 220 " =    1.282
peak=    3.078 closest distance to " CA  ALA A 158 " =    1.132
peak=    3.063 closest distance to " CD  ARG A  56 " =    0.815
peak=    3.047 closest distance to " CE  LYS A  76 " =    0.882
peak=    3.047 closest distance to " O   HOH Z 394 " =    3.608
peak=    3.027 closest distance to " O   HOH Z 151 " =    1.513
peak=    3.021 closest distance to " NH2 ARG A  56 " =    0.946

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 214         
Filter by distance & map next to the model:
   mapped sites are within: 0.759 - 5.064
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 213 from: 214
   mapped sites are within: 0.759 - 5.064

peak=   -4.543 closest distance to " O   PRO A 198 " =    1.156
peak=   -4.330 closest distance to " O   HOH Z 385 " =    1.404
peak=   -4.230 closest distance to " O   HOH Z  69 " =    1.581
peak=   -4.187 closest distance to " O   HOH Z 415 " =    0.963
peak=   -4.182 closest distance to " O   HOH Z 313 " =    1.074
peak=   -4.175 closest distance to " O   HOH Z 100 " =    0.989
peak=   -4.175 closest distance to " O   SER A  22 " =    2.585
peak=   -4.162 closest distance to " OE1 GLU A 277 " =    2.135
peak=   -4.062 closest distance to " CG2 ILE A  49 " =    2.770
peak=   -4.047 closest distance to " CD  ARG A  14 " =    3.241
peak=   -4.004 closest distance to " OD2 ASP A 171 " =    2.173
peak=   -3.975 closest distance to " O   ASP A 191 " =    1.915
peak=   -3.900 closest distance to " CB  ALA A  43 " =    2.415
peak=   -3.888 closest distance to " CD1 TRP A 179 " =    1.286
peak=   -3.873 closest distance to " O   HOH Z  24 " =    0.911
peak=   -3.872 closest distance to " O   HOH Z 131 " =    3.909
peak=   -3.870 closest distance to " N   GLN A  58 " =    1.264
peak=   -3.853 closest distance to " CB  ALA A 291 " =    2.206
peak=   -3.820 closest distance to " O   ALA A  10 " =    1.562
peak=   -3.811 closest distance to " OG BSER A 134 " =    1.505
peak=   -3.811 closest distance to " CE3 TRP A 274 " =    2.265
peak=   -3.809 closest distance to " O   HOH Z 377 " =    2.088
peak=   -3.796 closest distance to " CZ2 TRP A 274 " =    0.959
peak=   -3.768 closest distance to " CD2 TYR A 116 " =    2.189
peak=   -3.764 closest distance to " CD2 TYR A 293 " =    1.781
peak=   -3.759 closest distance to " N   ARG A 275 " =    1.100
peak=   -3.754 closest distance to " NH2 ARG A 219 " =    2.036
peak=   -3.743 closest distance to " CA  GLY A 133 " =    2.012
peak=   -3.741 closest distance to " O   GLY A  80 " =    2.621
peak=   -3.741 closest distance to " N   THR A 157 " =    1.580
peak=   -3.728 closest distance to " CZ  PHE A  59 " =    1.507
peak=   -3.721 closest distance to " O   HOH Z 242 " =    1.483
peak=   -3.721 closest distance to " CG2AVAL A  41 " =    2.750
peak=   -3.701 closest distance to " O   GLU A 152 " =    1.599
peak=   -3.700 closest distance to " CB  GLN A  55 " =    1.256
peak=   -3.691 closest distance to " CG  TRP A 266 " =    1.803
peak=   -3.691 closest distance to " O   HOH Z  60 " =    1.979
peak=   -3.659 closest distance to " O   HOH Z  52 " =    0.759
peak=   -3.643 closest distance to " NE2 GLN A 223 " =    1.804
peak=   -3.638 closest distance to " O   HOH Z 216 " =    1.530
peak=   -3.629 closest distance to " CG  MET A 105 " =    0.946
peak=   -3.622 closest distance to " O   HOH Z  52 " =    1.090
peak=   -3.621 closest distance to " ND2 ASN A 209 " =    1.748
peak=   -3.613 closest distance to " OE2 GLU A 152 " =    1.382
peak=   -3.588 closest distance to " O   ASN A 170 " =    1.977
peak=   -3.586 closest distance to " OE1 GLN A 223 " =    2.392
peak=   -3.577 closest distance to " O   HOH Z 105 " =    1.844
peak=   -3.576 closest distance to " O   PHE A 218 " =    1.430
peak=   -3.576 closest distance to " OG  SER A  87 " =    1.879
peak=   -3.572 closest distance to " O   HOH Z  39 " =    0.976
peak=   -3.571 closest distance to " C   HIS A 207 " =    1.259
peak=   -3.571 closest distance to " N   ALA A   1 " =    1.376
peak=   -3.570 closest distance to " OG  SER A  97 " =    2.155
peak=   -3.565 closest distance to " OD2 ASP A  27 " =    1.655
peak=   -3.560 closest distance to " O   HOH Z  28 " =    1.280
peak=   -3.559 closest distance to " O   HOH Z 198 " =    1.411
peak=   -3.554 closest distance to " CG2 ILE A  20 " =    2.660
peak=   -3.550 closest distance to " CA  ASN A 127 " =    1.174
peak=   -3.549 closest distance to " OG  SER A 245 " =    1.579
peak=   -3.548 closest distance to " CD1 LEU A 101 " =    2.192
peak=   -3.545 closest distance to " O   ILE A  49 " =    1.714
peak=   -3.542 closest distance to " O   HOH Z 276 " =    1.347
peak=   -3.541 closest distance to " O   HOH Z 129 " =    3.507
peak=   -3.537 closest distance to " CB  ASN A  45 " =    2.041
peak=   -3.534 closest distance to " CB  PRO A 243 " =    2.573
peak=   -3.523 closest distance to " NZ  LYS A 166 " =    1.620
peak=   -3.510 closest distance to " O   HOH Z 323 " =    2.239
peak=   -3.510 closest distance to " ND2 ASN A 285 " =    2.166
peak=   -3.506 closest distance to " O   HOH Z 147 " =    1.175
peak=   -3.500 closest distance to " C   VAL A  72 " =    0.909
peak=   -3.496 closest distance to " CB  ASP A  27 " =    2.373
peak=   -3.487 closest distance to " CD2 HIS A 207 " =    1.617
peak=   -3.472 closest distance to " CZ  PHE A  38 " =    2.312
peak=   -3.469 closest distance to " CA  GLY A 241 " =    2.244
peak=   -3.457 closest distance to " O   HOH Z 111 " =    1.944
peak=   -3.455 closest distance to " NE2 GLN A 278 " =    1.516
peak=   -3.452 closest distance to " O   HOH Z 292 " =    1.538
peak=   -3.451 closest distance to " C   HIS A 108 " =    1.264
peak=   -3.440 closest distance to " O   HOH Z  22 " =    2.887
peak=   -3.432 closest distance to " O   HOH Z 211 " =    0.928
peak=   -3.426 closest distance to " NE  ARG A  36 " =    1.966
peak=   -3.424 closest distance to " O   PRO A 163 " =    1.375
peak=   -3.416 closest distance to " N   ALA A  43 " =    2.674
peak=   -3.415 closest distance to " OE1 GLU A  44 " =    2.008
peak=   -3.409 closest distance to " O   HOH Z 244 " =    1.635
peak=   -3.408 closest distance to " O   HOH Z 266 " =    5.064
peak=   -3.401 closest distance to " O   HOH Z 357 " =    1.914
peak=   -3.397 closest distance to " O   HOH Z   5 " =    1.245
peak=   -3.394 closest distance to " O   HOH Z  49 " =    1.097
peak=   -3.392 closest distance to " N   ARG A 138 " =    1.724
peak=   -3.392 closest distance to " O   HOH Z 364 " =    1.159
peak=   -3.391 closest distance to " OG  SER A  63 " =    1.305
peak=   -3.384 closest distance to " N   ARG A 159 " =    2.007
peak=   -3.383 closest distance to " CG2 VAL A 189 " =    1.904
peak=   -3.379 closest distance to " C   ASN A 285 " =    2.036
peak=   -3.373 closest distance to " CB  ALA A 114 " =    2.431
peak=   -3.372 closest distance to " O   HOH Z 359 " =    1.646
peak=   -3.371 closest distance to " O   HOH Z 163 " =    1.975
peak=   -3.370 closest distance to " O   HOH Z 126 " =    1.903
peak=   -3.370 closest distance to " O   HOH Z 231 " =    1.857
peak=   -3.341 closest distance to " CG2 ILE A 120 " =    0.962
peak=   -3.329 closest distance to " OD2 ASP A 272 " =    1.511
peak=   -3.326 closest distance to " CE BMET A  47 " =    1.328
peak=   -3.314 closest distance to " CE3 TRP A 179 " =    1.461
peak=   -3.313 closest distance to " NE2 GLN A  55 " =    1.218
peak=   -3.313 closest distance to " O   HOH Z  71 " =    1.318
peak=   -3.312 closest distance to " O   HOH Z 372 " =    2.553
peak=   -3.310 closest distance to " CG2 ILE A 120 " =    1.295
peak=   -3.309 closest distance to " N   VAL A 232 " =    2.076
peak=   -3.304 closest distance to " CB  ALA A 233 " =    2.473
peak=   -3.289 closest distance to " CA  GLY A 203 " =    2.375
peak=   -3.288 closest distance to " O   HOH Z 201 " =    1.881
peak=   -3.284 closest distance to " O   HOH Z 298 " =    2.582
peak=   -3.282 closest distance to " O   VAL A 125 " =    2.088
peak=   -3.282 closest distance to " O   HOH Z 428 " =    2.437
peak=   -3.280 closest distance to " O   HOH Z 426 " =    1.558
peak=   -3.280 closest distance to " O   HOH Z 275 " =    1.841
peak=   -3.277 closest distance to " O   HOH Z 251 " =    0.865
peak=   -3.274 closest distance to " CD2 PHE A  61 " =    2.526
peak=   -3.271 closest distance to " CG  ARG A  66 " =    1.758
peak=   -3.268 closest distance to " O   HOH Z 348 " =    1.900
peak=   -3.268 closest distance to " O   HOH Z 404 " =    1.221
peak=   -3.267 closest distance to " CB  GLN A  11 " =    1.675
peak=   -3.266 closest distance to " CA  TYR A  68 " =    0.950
peak=   -3.265 closest distance to " CG  GLN A 240 " =    2.368
peak=   -3.263 closest distance to " O   HOH Z 231 " =    0.940
peak=   -3.262 closest distance to " O   HOH Z 100 " =    1.591
peak=   -3.260 closest distance to " NE2 GLN A 194 " =    1.878
peak=   -3.259 closest distance to " CG2 THR A 178 " =    2.222
peak=   -3.258 closest distance to " CG1 VAL A 112 " =    3.133
peak=   -3.257 closest distance to " CB  PRO A  54 " =    2.262
peak=   -3.256 closest distance to " O   SER A 271 " =    1.778
peak=   -3.256 closest distance to " CB  ALA A 131 " =    1.751
peak=   -3.255 closest distance to " O   LYS A  76 " =    2.351
peak=   -3.255 closest distance to " CD1 TRP A 274 " =    1.131
peak=   -3.249 closest distance to " O   HOH Z  60 " =    1.591
peak=   -3.249 closest distance to " C   GLU A   2 " =    1.849
peak=   -3.247 closest distance to " CD  LYS A 166 " =    2.562
peak=   -3.245 closest distance to " O   HOH Z 181 " =    1.545
peak=   -3.243 closest distance to " O   HOH Z 278 " =    1.408
peak=   -3.241 closest distance to " O   HOH Z 359 " =    3.164
peak=   -3.234 closest distance to " CG  PRO A 243 " =    1.666
peak=   -3.232 closest distance to " O   LEU A 261 " =    1.272
peak=   -3.228 closest distance to " O   HOH Z 151 " =    1.072
peak=   -3.223 closest distance to " CA  GLY A  98 " =    1.693
peak=   -3.220 closest distance to " N   GLU A 277 " =    1.416
peak=   -3.216 closest distance to " CA  GLY A  57 " =    2.176
peak=   -3.214 closest distance to " O   HOH Z 185 " =    1.991
peak=   -3.212 closest distance to " O   HOH Z 429 " =    1.609
peak=   -3.211 closest distance to " CB  ALA A 248 " =    2.027
peak=   -3.210 closest distance to " CH2 TRP A 177 " =    2.217
peak=   -3.210 closest distance to " O   HOH Z 324 " =    0.883
peak=   -3.209 closest distance to " CG1 VAL A 126 " =    2.519
peak=   -3.205 closest distance to " O   HOH Z  88 " =    2.164
peak=   -3.205 closest distance to " O   HOH Z 102 " =    1.664
peak=   -3.205 closest distance to " NE2 GLN A  77 " =    1.470
peak=   -3.205 closest distance to " OE1 GLN A 183 " =    1.600
peak=   -3.203 closest distance to " CG1BVAL A  41 " =    2.713
peak=   -3.202 closest distance to " C   GLN A 205 " =    1.895
peak=   -3.197 closest distance to " CE1 TYR A  15 " =    2.136
peak=   -3.195 closest distance to " CH2 TRP A 123 " =    1.698
peak=   -3.194 closest distance to " O   HOH Z 414 " =    1.343
peak=   -3.194 closest distance to " O   HOH Z 356 " =    3.890
peak=   -3.194 closest distance to " O   HOH Z 286 " =    1.784
peak=   -3.194 closest distance to " O   HOH Z 407 " =    2.910
peak=   -3.194 closest distance to " O   HOH Z  56 " =    1.660
peak=   -3.182 closest distance to " O   HOH Z 218 " =    3.912
peak=   -3.178 closest distance to " CB  ASP A 132 " =    2.451
peak=   -3.177 closest distance to " O   ALA A  84 " =    1.547
peak=   -3.177 closest distance to " O   HOH Z  73 " =    2.323
peak=   -3.174 closest distance to " O   HOH Z 253 " =    3.654
peak=   -3.172 closest distance to " O   ARG A 156 " =    1.019
peak=   -3.171 closest distance to " O   HOH Z  97 " =    1.206
peak=   -3.165 closest distance to " CB  SER A 276 " =    1.603
peak=   -3.164 closest distance to " OE2 GLU A 152 " =    2.190
peak=   -3.162 closest distance to " CG1 VAL A 265 " =    2.304
peak=   -3.154 closest distance to " O   HOH Z 179 " =    1.691
peak=   -3.152 closest distance to " OE1 GLN A 223 " =    2.035
peak=   -3.150 closest distance to " O   HOH Z 328 " =    1.048
peak=   -3.150 closest distance to " O   HOH Z 368 " =    1.538
peak=   -3.150 closest distance to " O   HOH Z 238 " =    1.186
peak=   -3.140 closest distance to " O   HOH Z 389 " =    1.042
peak=   -3.140 closest distance to " CD  PRO A 213 " =    2.140
peak=   -3.139 closest distance to " CB  ALA A   9 " =    2.372
peak=   -3.132 closest distance to " OD1 ASN A 249 " =    1.678
peak=   -3.132 closest distance to " C   VAL A 257 " =    1.305
peak=   -3.127 closest distance to " O   HOH Z  67 " =    1.510
peak=   -3.126 closest distance to " O   HOH Z 380 " =    4.668
peak=   -3.123 closest distance to " CZ2 TRP A 179 " =    2.765
peak=   -3.123 closest distance to " ND2 ASN A 187 " =    1.486
peak=   -3.119 closest distance to " CB  ALA A 100 " =    1.913
peak=   -3.116 closest distance to " NE2 GLN A 278 " =    1.460
peak=   -3.116 closest distance to " CD  ARG A 156 " =    1.956
peak=   -3.107 closest distance to " ND2 ASN A  60 " =    1.900
peak=   -3.106 closest distance to " O   HOH Z 177 " =    1.746
peak=   -3.103 closest distance to " CB  ASP A 132 " =    2.597
peak=   -3.100 closest distance to " CB  ASN A  39 " =    2.280
peak=   -3.098 closest distance to " O   HOH Z 105 " =    1.589
peak=   -3.097 closest distance to " CE1 TYR A 247 " =    2.675
peak=   -3.094 closest distance to " ND2 ASN A  69 " =    1.591
peak=   -3.089 closest distance to " CE  MET A 105 " =    2.604
peak=   -3.083 closest distance to " CD2 LEU A  25 " =    2.139
peak=   -3.074 closest distance to " O   GLY A 196 " =    1.267
peak=   -3.071 closest distance to " O   HOH Z 427 " =    2.015
peak=   -3.069 closest distance to " O   GLN A 240 " =    3.237
peak=   -3.066 closest distance to " CG  GLU A 128 " =    1.653
peak=   -3.063 closest distance to " O   HOH Z 217 " =    1.752
peak=   -3.062 closest distance to " O   HOH Z 325 " =    1.443
peak=   -3.052 closest distance to " C   PHE A  59 " =    1.136
peak=   -3.039 closest distance to " CD2 LEU A 237 " =    2.525
peak=   -3.038 closest distance to " C   ALA A 158 " =    1.585
peak=   -3.032 closest distance to " OD1 ASP A 238 " =    1.825
peak=   -3.019 closest distance to " OG  SER A   3 " =    1.589

================= 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    :  0.4787 0.4800   6.290348e+00   6.279142e+00
   1_bss:  0.4689 0.4708   6.285311e+00   6.269859e+00
   1_xyz:  0.4027 0.4439   6.196379e+00   6.239739e+00
   1_adp:  0.3725 0.4491   6.163180e+00   6.246302e+00
   1_occ:  0.3722 0.4505   6.163489e+00   6.247386e+00
   2_bss:  0.3727 0.4476   6.166297e+00   6.248018e+00
   2_xyz:  0.3118 0.3994   6.037999e+00   6.176454e+00
   2_adp:  0.2972 0.3912   6.011231e+00   6.157729e+00
   2_occ:  0.2969 0.3914   6.011194e+00   6.157713e+00
   3_bss:  0.2975 0.3908   6.011350e+00   6.156464e+00
   3_xyz:  0.2435 0.3156   5.830238e+00   6.003024e+00
   3_adp:  0.2150 0.3004   5.751652e+00   5.963854e+00
   3_occ:  0.2147 0.3000   5.750830e+00   5.963371e+00
   4_bss:  0.2145 0.3001   5.748264e+00   5.961647e+00
   4_xyz:  0.1825 0.2514   5.593874e+00   5.826416e+00
   4_adp:  0.1700 0.2270   5.515613e+00   5.734620e+00
   4_occ:  0.1698 0.2266   5.514429e+00   5.733091e+00
   5_bss:  0.1700 0.2269   5.513914e+00   5.732462e+00
   5_xyz:  0.1387 0.1916   5.332211e+00   5.572072e+00
   5_adp:  0.1305 0.1834   5.282318e+00   5.528931e+00
   5_occ:  0.1304 0.1833   5.281740e+00   5.528176e+00
   5_bss:  0.1310 0.1827   5.281462e+00   5.526268e+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:  0.342  28.372  -2.904   1.614   2.400   0.000   0.000   0.000
   1_xyz:  0.342  28.372  -2.904   1.614   2.400   0.000   0.000   0.000
   1_adp:  0.342  28.372  -2.904   1.614   2.400   0.000   0.000   0.000
   1_occ:  0.342  28.372  -2.904   1.614   2.400   0.000   0.000   0.000
   2_bss:  0.347  52.954  -0.937   1.371   2.100   0.000   0.000   0.000
   2_xyz:  0.347  52.954  -0.937   1.371   2.100   0.000   0.000   0.000
   2_adp:  0.347  52.954  -0.937   1.371   2.100   0.000   0.000   0.000
   2_occ:  0.347  52.954  -0.937   1.371   2.100   0.000   0.000   0.000
   3_bss:  0.326  57.853  -0.813   0.377   1.587   0.000   0.000   0.000
   3_xyz:  0.326  57.853  -0.813   0.377   1.587   0.000   0.000   0.000
   3_adp:  0.326  57.853  -0.813   0.377   1.587   0.000   0.000   0.000
   3_occ:  0.326  57.853  -0.813   0.377   1.587   0.000   0.000   0.000
   4_bss:  0.328  65.234  -1.238  -0.554   1.058  -0.000   0.000   0.000
   4_xyz:  0.328  65.234  -1.238  -0.554   1.058  -0.000   0.000   0.000
   4_adp:  0.328  65.234  -1.238  -0.554   1.058  -0.000   0.000   0.000
   4_occ:  0.328  65.234  -1.238  -0.554   1.058  -0.000   0.000   0.000
   5_bss:  0.321  57.469  -1.480  -1.252   0.835  -0.000   0.000   0.000
   5_xyz:  0.321  57.469  -1.480  -1.252   0.835  -0.000   0.000   0.000
   5_adp:  0.321  57.469  -1.480  -1.252   0.835  -0.000   0.000   0.000
   5_occ:  0.321  57.469  -1.480  -1.252   0.835  -0.000   0.000   0.000
   5_bss:  0.321  57.472  -1.640  -1.531   0.640  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.651 0.4117  0.5716    75764.577
   1_bss:  57.210 0.4291  0.6054    72267.390
   1_xyz:  53.134 0.4799  0.6639    62323.325
   1_adp:  53.769 0.4716  0.6557    64235.983
   1_occ:  53.925 0.4697  0.6524    64619.260
   2_bss:  53.845 0.4706  0.6662    64506.230
   2_xyz:  45.089 0.5796  0.8186    46950.882
   2_adp:  43.152 0.6038  0.8394    44503.363
   2_occ:  43.186 0.6034  0.8387    44539.718
   3_bss:  43.098 0.6044  0.8267    44317.697
   3_xyz:  33.164 0.7215  0.9505    27410.169
   3_adp:  31.186 0.7439  0.9470    24489.948
   3_occ:  31.151 0.7443  0.9472    24425.350
   4_bss:  31.043 0.7453  0.9275    24240.286
   4_xyz:  25.787 0.8017  0.9702    16827.760
   4_adp:  22.411 0.8378  0.9816    13599.051
   4_occ:  22.375 0.8381  0.9815    13541.467
   5_bss:  22.343 0.8383  0.9679    13496.292
   5_xyz:  18.221 0.8779  0.9890     9486.575
   5_adp:  17.079 0.8888  0.9836     8717.117
   5_occ:  17.058 0.8890  0.9835     8701.021
   5_bss:  17.026 0.8892  0.9764     8656.331
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.107   2.0001e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.107   2.0001e-01
   1_xyz:   1.408  0.010  0.096 15.561  0.006  4.102   1.0962e-01
   1_adp:   1.408  0.010  0.096 15.561  0.006  4.102   1.0962e-01
   1_occ:   1.408  0.010  0.096 15.561  0.006  4.102   1.0962e-01
   2_bss:   1.408  0.010  0.096 15.561  0.006  4.102   1.0962e-01
   2_xyz:   1.426  0.010  0.093 16.033  0.005  4.103   1.1440e-01
   2_adp:   1.426  0.010  0.093 16.033  0.005  4.103   1.1440e-01
   2_occ:   1.426  0.010  0.093 16.033  0.005  4.103   1.1440e-01
   3_bss:   1.426  0.010  0.093 16.033  0.005  4.103   1.1440e-01
   3_xyz:   1.202  0.010  0.092 15.374  0.004  4.110   8.5406e-02
   3_adp:   1.202  0.010  0.092 15.374  0.004  4.110   8.5406e-02
   3_occ:   1.202  0.010  0.092 15.374  0.004  4.110   8.5406e-02
   4_bss:   1.202  0.010  0.092 15.374  0.004  4.110   8.5406e-02
   4_xyz:   0.968  0.006  0.071 14.286  0.003  4.115   5.5203e-02
   4_adp:   0.968  0.006  0.071 14.286  0.003  4.115   5.5203e-02
   4_occ:   0.968  0.006  0.071 14.286  0.003  4.115   5.5203e-02
   5_bss:   0.968  0.006  0.071 14.286  0.003  4.115   5.5203e-02
   5_xyz:   1.093  0.008  0.077 14.575  0.004  4.109   6.7620e-02
   5_adp:   1.093  0.008  0.077 14.575  0.004  4.109   6.7620e-02
   5_occ:   1.093  0.008  0.077 14.575  0.004  4.109   6.7620e-02
   5_bss:   1.093  0.008  0.077 14.575  0.004  4.109   6.7620e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.195   2.4113e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.195   2.4113e-01
   1_xyz:   9.473  0.058  0.349 77.594  0.044  2.041   8.9634e-02
   1_adp:   9.473  0.058  0.349 77.594  0.044  2.041   8.9634e-02
   1_occ:   9.473  0.058  0.349 77.594  0.044  2.041   8.9634e-02
   2_bss:   9.473  0.058  0.349 77.594  0.044  2.041   8.9634e-02
   2_xyz:   9.687  0.060  0.323 77.947  0.038  1.955   1.0419e-01
   2_adp:   9.687  0.060  0.323 77.947  0.038  1.955   1.0419e-01
   2_occ:   9.687  0.060  0.323 77.947  0.038  1.955   1.0419e-01
   3_bss:   9.687  0.060  0.323 77.947  0.038  1.955   1.0419e-01
   3_xyz:   7.627  0.084  0.296 80.820  0.037  2.127   7.0681e-02
   3_adp:   7.627  0.084  0.296 80.820  0.037  2.127   7.0681e-02
   3_occ:   7.627  0.084  0.296 80.820  0.037  2.127   7.0681e-02
   4_bss:   7.627  0.084  0.296 80.820  0.037  2.127   7.0681e-02
   4_xyz:   6.276  0.046  0.221 81.598  0.026  2.323   3.9250e-02
   4_adp:   6.276  0.046  0.221 81.598  0.026  2.323   3.9250e-02
   4_occ:   6.276  0.046  0.221 81.598  0.026  2.323   3.9250e-02
   5_bss:   6.276  0.046  0.221 81.598  0.026  2.323   3.9250e-02
   5_xyz:   6.783  0.054  0.262 83.533  0.030  2.332   5.5632e-02
   5_adp:   6.783  0.054  0.262 83.533  0.030  2.332   5.5632e-02
   5_occ:   6.783  0.054  0.262 83.533  0.030  2.332   5.5632e-02
   5_bss:   6.783  0.054  0.262 83.533  0.030  2.332   5.5632e-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:  89.89   0.00  18.78  87.47   0.00  16.24  89.89   0.00  32.65
   1_occ:  89.89   0.00  18.78  87.47   0.00  16.24  89.89   0.00  32.65
   2_bss:  89.89   0.00  18.78  87.47   0.00  16.24  89.89   0.00  32.65
   2_xyz:  89.89   0.00  18.78  87.47   0.00  16.24  89.89   0.00  32.65
   2_adp:  90.76   0.00  18.30  82.78   0.00  15.44  90.76   0.00  33.85
   2_occ:  90.76   0.00  18.30  82.78   0.00  15.44  90.76   0.00  33.85
   3_bss:  90.76   0.00  18.30  82.78   0.00  15.44  90.76   0.00  33.85
   3_xyz:  90.76   0.00  18.30  82.78   0.00  15.44  90.76   0.00  33.85
   3_adp: 107.04   0.00  19.84 105.99   0.00  14.73 107.04   1.36  47.67
   3_occ: 107.04   0.00  19.84 105.99   0.00  14.73 107.04   1.36  47.67
   4_bss: 107.04   0.00  19.84 105.99   0.00  14.73 107.04   1.36  47.67
   4_xyz: 107.04   0.00  19.84 105.99   0.00  14.73 107.04   1.36  47.67
   4_adp: 109.79   0.00  18.11 106.00   0.00  12.98 109.79   3.87  46.04
   4_occ: 109.79   0.00  18.11 106.00   0.00  12.98 109.79   3.87  46.04
   5_bss: 109.79   0.00  18.11 106.00   0.00  12.98 109.79   3.87  46.04
   5_xyz: 109.79   0.00  18.11 106.00   0.00  12.98 109.79   3.87  46.04
   5_adp: 113.48   0.00  17.78 106.40   0.00  12.33 113.48   5.22  47.49
   5_occ: 113.48   0.00  17.78 106.40   0.00  12.33 113.48   5.22  47.49
   5_bss: 113.48   0.00  17.79 106.41   0.00  12.33 113.48   5.22  47.49
------------------------------------------------------------------------
 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:    2.667    0.019    0.278
   1_adp:    2.667    0.019    0.278
   1_occ:    2.667    0.019    0.278
   2_bss:    2.667    0.019    0.278
   2_xyz:    2.223    0.013    0.533
   2_adp:    2.223    0.013    0.533
   2_occ:    2.223    0.013    0.533
   3_bss:    2.223    0.013    0.533
   3_xyz:    2.079    0.037    0.737
   3_adp:    2.079    0.037    0.737
   3_occ:    2.079    0.037    0.737
   4_bss:    2.079    0.037    0.737
   4_xyz:    2.021    0.091    0.799
   4_adp:    2.021    0.091    0.799
   4_occ:    2.021    0.091    0.799
   5_bss:    2.021    0.091    0.799
   5_xyz:    1.942    0.109    0.870
   5_adp:    1.942    0.109    0.870
   5_occ:    1.942    0.109    0.870
   5_bss:    1.942    0.109    0.870
------------------------------------------------------------------------

CPU time actual refinement: 282.67


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_372/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_372/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_372/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_372/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_372/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 282.55 
  Macro-tasks:
    bulk solvent and scale       = 32.22  
    individual site refinement   = 115.62 
    weights calculation          = 25.52  
    collect and process          = 5.39   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 178.86 
  Micro-tasks:
    mask                            = 2.55   
    f_calc                          = 90.33  
    alpha_beta                      = 7.12   
    target                          = 0.95   
    gradients_wrt_atomic_parameters = 97.27  
    fmodel                         = 5.58   
    r_factors                      = 0.18   
    phase_errors                   = 8.26   
    foms                           = 0.17   
    TOTAL for micro-tasks          = 212.41 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.053 micro seconds
Total CPU time: 4.90 minutes
from_scatterers_fft:    643 calls, 90.04 s
gradients_fft:          588 calls, 86.16 s

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

# Date 2008-01-16 Time 04:38:56 PST -0800 (1200487136.92 s)
Start R-work = 0.4787, R-free = 0.4800 (no bulk solvent and anisotropic scale)
Final R-work = 0.1489, R-free = 0.1976 (no bulk solvent and anisotropic scale)

Start R-work = 0.4689, R-free = 0.4708
Final R-work = 0.1310, R-free = 0.1827