# Date 2008-01-16 Time 04:50:21 PST -0800 (1200487821.22 s)
#phil __OFF__

Command line arguments: "../486.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31098
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 486

-------------------------------------------------------------------------------
  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: (69.8988, 45.7567, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 45.7567, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8779 1.95275
Completeness in resolution range: 0.961235
Completeness with d_max=infinity: 0.958319

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8779
                             d_min =   1.9527

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: (69.8988, 45.7567, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8779 1.95275
Completeness in resolution range: 0.961235
Completeness with d_max=infinity: 0.958319

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8783 -  4.1789 [2139/2164]  1926   213  10.0%
  bin  2:  4.1789 -  3.3291 [2049/2069]  1844   205  10.0%
  bin  3:  3.3291 -  2.9119 [2045/2064]  1840   205  10.0%
  bin  4:  2.9119 -  2.6473 [2007/2037]  1807   200  10.0%
  bin  5:  2.6473 -  2.4585 [2014/2033]  1818   196   9.7%
  bin  6:  2.4585 -  2.3141 [1978/2003]  1772   206  10.4%
  bin  7:  2.3141 -  2.1986 [1978/2006]  1780   198  10.0%
  bin  8:  2.1986 -  2.1031 [1970/2006]  1772   198  10.1%
  bin  9:  2.1031 -  2.0224 [1970/2012]  1777   193   9.8%
  bin 10:  2.0224 -  1.9527 [1439/1985]  1294   145  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_486/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.66 -     2.31: 39
        2.31 -     2.96: 1757
        2.96 -     3.60: 4676
        3.60 -     4.25: 9373
        4.25 -     4.90: 13121
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.661 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 204 " - " O   HOH Z 296 "  1.711 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.737 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  ... (remaining 28961 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_486/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_486/model_refine_001.geo

CPU time processing inputs: 9.19


============================ 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 = 69.89875 45.75675 85.09415 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 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4595   r_free= 0.4557   ksol= 0.00   Bsol= 0.00   scale= 0.909    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.273888                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8783 -  4.6612 0.99   1390  155 0.3830 0.3918      6.5772      6.6002|
|  2:  4.6612 -  3.7187 0.99   1341  150 0.4051 0.3798      6.8118      6.7413|
|  3:  3.7187 -  3.2543 0.99   1313  141 0.4369 0.4194      6.6965      6.7704|
|  4:  3.2543 -  2.9593 0.99   1304  152 0.4439 0.4386      6.5346      6.4825|
|  5:  2.9593 -  2.7486 0.99   1299  144 0.4877 0.4786      6.3639      6.3847|
|  6:  2.7486 -  2.5874 0.99   1295  137 0.4824 0.5146      6.2766      6.2115|
|  7:  2.5874 -  2.4585 0.99   1293  140 0.4830 0.4892      6.2296       6.222|
|  8:  2.4585 -  2.3519 0.98   1263  148 0.5025 0.4624      6.1748      6.1507|
|  9:  2.3519 -  2.2617 0.98   1257  145 0.5019 0.5189      6.1161      6.1596|
| 10:  2.2617 -  2.1839 1.00   1295  138 0.4948 0.5267      6.0881      6.1162|
| 11:  2.1839 -  2.1158 0.98   1268  140 0.4983 0.4786      6.0218      6.0477|
| 12:  2.1158 -  2.0555 0.98   1255  141 0.4802 0.4508      5.9641      5.9848|
| 13:  2.0555 -  2.0015 0.99   1274  139 0.4945 0.4790      5.8632       5.804|
| 14:  2.0015 -  1.9527 0.61    783   89 0.5224 0.4389      5.8842      5.7671|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8783 -  4.6612  1390   155  0.67  36.88   0.82     0.73      81461.39|
|  2:  4.6612 -  3.7187  1341   150  0.69  36.38   0.91     0.81     112626.71|
|  3:  3.7187 -  3.2543  1313   141  0.60  44.08   0.93     0.79     116928.11|
|  4:  3.2543 -  2.9593  1304   152  0.51  51.25   0.95     0.70     105584.39|
|  5:  2.9593 -  2.7486  1299   144  0.42  58.25   0.90     0.60      82722.73|
|  6:  2.7486 -  2.5874  1295   137  0.39  60.43   0.90     0.54      72638.55|
|  7:  2.5874 -  2.4585  1293   140  0.37  62.11   0.94     0.52      65164.29|
|  8:  2.4585 -  2.3519  1263   148  0.36  62.88   0.94     0.54      60145.52|
|  9:  2.3519 -  2.2617  1257   145  0.37  61.99   0.92     0.55      53486.77|
| 10:  2.2617 -  2.1839  1295   138  0.40  59.99   0.96     0.58      46133.89|
| 11:  2.1839 -  2.1158  1268   140  0.40  59.84   0.99     0.62      42881.02|
| 12:  2.1158 -  2.0555  1255   141  0.43  57.67   1.03     0.67      37904.17|
| 13:  2.0555 -  2.0015  1274   139  0.44  56.81   0.97     0.70      30936.47|
| 14:  2.0015 -  1.9527   783    89  0.53  49.93   0.99     0.75      21371.68|
|alpha:            min =        0.52 max =            0.81 mean =         0.65|
|beta:             min =    21371.68 max =       116928.11 mean =     68195.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           89.99 mean =        54.10|
|phase err.(test): min =        0.00 max =           89.92 mean =        54.07|
|-----------------------------------------------------------------------------|

============================== 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 = 16.104350             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.895   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.308910              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.324   (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 |  1.661 -  1.985:       16 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.985 -  2.309:       23 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.309 -  2.633:       85 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.633 -  2.957:     1672 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.957 -  3.281:     1990 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.281 -  3.605:     2686 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.605 -  3.928:     4842 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.928 -  4.252:     4531 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.252 -  4.576:     5973 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.576 -  4.900:     7148 |
|-----------------------------------------------------------------------------|
|-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 |        0.191 |
| 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  1.661 |       0.642 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.367)------------------------------------------|
|    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 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4595   r_free= 0.4557   ksol= 0.00   Bsol= 0.00   scale= 0.909    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.273888                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4484   r_free= 0.4429   ksol= 0.36   Bsol= 29.73   scale= 0.925   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.52,2.54,-0.08,0.00,-0.00,-0.00); trace/3= -0.35                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.266880                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.658705             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.778   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.306788              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.330   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4484      final r-factor (work) = 0.3508          |
| start r-factor (free) = 0.4429      final r-factor (free) = 0.3850          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.9766 = 13.66 * 0.50 * 6.2650 + 1.00 * 0.1906                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.1538 = 13.66 * 0.50 * 6.1501 + 1.00 * 0.1524                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3508      final r-factor (work) = 0.3188          |
| start r-factor (free) = 0.3850      final r-factor (free) = 0.3992          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0432 = 1.31 * 1.00 * 6.1501 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9270 = 1.31 * 1.00 * 6.0513 + 1.00 * 0.0192                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.367)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.09   18.33    None  None   None       |
|    all(noH): 2823   0      0.00    92.09   18.33    None  None   None       |
|    Sol.    : 438    0      0.00    92.09   35.22    None  None   None       |
|    Mac.    : 2385   0      0.00    89.78   15.23    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 -   9.209:  821   |   5:    46.045 -  55.254:   79        |
|      1:     9.209 -  18.418:  902   |   6:    55.254 -  64.462:   47        |
|      2:    18.418 -  27.627:  505   |   7:    64.462 -  73.671:   13        |
|      3:    27.627 -  36.836:  285   |   8:    73.671 -  82.880:    7        |
|      4:    36.836 -  46.045:  161   |   9:    82.880 -  92.089:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3188 r_free = 0.3992             target_work(ml) = 6.058         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3182 r_free = 0.3990             target_work(ml) = 6.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3182   r_free= 0.3990   ksol= 0.36   Bsol= 29.73   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.52,2.54,-0.08,0.00,-0.00,-0.00); trace/3= -0.35                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.057495                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3179   r_free= 0.3989   ksol= 0.35   Bsol= 54.62   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.44,0.79,-0.16,0.00,-0.00,-0.00); trace/3= -0.27                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.057880                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.745221              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.595  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.548247              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.910  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3179      final r-factor (work) = 0.2816          |
| start r-factor (free) = 0.3989      final r-factor (free) = 0.3542          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.5409 = 5.75 * 0.50 * 6.0532 + 1.00 * 0.1524                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.3463 = 5.75 * 0.50 * 6.0144 + 1.00 * 0.0694                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2816      final r-factor (work) = 0.2749          |
| start r-factor (free) = 0.3542      final r-factor (free) = 0.3470          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3161 = 0.55 * 1.00 * 6.0144 + 1.00 * 0.0188                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2773 = 0.55 * 1.00 * 5.9558 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.367)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.67   17.56    None  None   None       |
|    all(noH): 2823   0      0.00    90.67   17.56    None  None   None       |
|    Sol.    : 438    0      0.00    89.96   34.05    None  None   None       |
|    Mac.    : 2385   0      0.00    90.67   14.54    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.067:  814   |   5:    45.334 -  54.401:   80        |
|      1:     9.067 -  18.134:  972   |   6:    54.401 -  63.468:   31        |
|      2:    18.134 -  27.200:  487   |   7:    63.468 -  72.534:   10        |
|      3:    27.200 -  36.267:  270   |   8:    72.534 -  81.601:    7        |
|      4:    36.267 -  45.334:  149   |   9:    81.601 -  90.668:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2749 r_free = 0.3470             target_work(ml) = 5.948         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2747 r_free = 0.3471             target_work(ml) = 5.948         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2747   r_free= 0.3471   ksol= 0.35   Bsol= 54.62   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.44,0.79,-0.16,0.00,-0.00,-0.00); trace/3= -0.27                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.947565                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2750   r_free= 0.3467   ksol= 0.34   Bsol= 49.88   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.94,0.21,-0.04,0.00,-0.00,-0.00); trace/3= -0.26                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.946931                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.760699              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.634   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.464300              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 164.216  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2750      final r-factor (work) = 0.2092          |
| start r-factor (free) = 0.3467      final r-factor (free) = 0.2752          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.1376 = 9.76 * 0.50 * 5.9562 + 1.00 * 0.0694                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.5924 = 9.76 * 0.50 * 5.8396 + 1.00 * 0.0933                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2092      final r-factor (work) = 0.1861          |
| start r-factor (free) = 0.2752      final r-factor (free) = 0.2479          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7234 = 0.46 * 1.00 * 5.8396 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6318 = 0.46 * 1.00 * 5.6464 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.367)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.85   17.19    None  None   None       |
|    all(noH): 2823   0      0.00    91.85   17.19    None  None   None       |
|    Sol.    : 438    0      4.83    86.79   39.92    None  None   None       |
|    Mac.    : 2385   0      0.00    91.85   13.02    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.185:  952   |   5:    45.924 -  55.108:  122        |
|      1:     9.185 -  18.370: 1055   |   6:    55.108 -  64.293:   55        |
|      2:    18.370 -  27.554:  319   |   7:    64.293 -  73.478:   13        |
|      3:    27.554 -  36.739:  157   |   8:    73.478 -  82.663:    6        |
|      4:    36.739 -  45.924:  141   |   9:    82.663 -  91.847:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1861 r_free = 0.2479             target_work(ml) = 5.595         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1856 r_free = 0.2470             target_work(ml) = 5.593         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1856   r_free= 0.2470   ksol= 0.34   Bsol= 49.88   scale= 1.041   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.94,0.21,-0.04,0.00,-0.00,-0.00); trace/3= -0.26                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.592883                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1854   r_free= 0.2445   ksol= 0.33   Bsol= 44.58   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.49,-1.21,-0.57,-0.00,-0.00,-0.00); trace/3= -1.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.587929                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.588610              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.463  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.383206              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.406  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1854      final r-factor (work) = 0.1493          |
| start r-factor (free) = 0.2445      final r-factor (free) = 0.2021          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2287 = 3.59 * 0.50 * 5.6486 + 1.00 * 0.0933                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9234 = 3.59 * 0.50 * 5.4977 + 1.00 * 0.0588                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1493      final r-factor (work) = 0.1387          |
| start r-factor (free) = 0.2021      final r-factor (free) = 0.1924          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1168 = 0.38 * 1.00 * 5.4977 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0642 = 0.38 * 1.00 * 5.3622 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.367)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.39    92.92   16.99    None  None   None       |
|    all(noH): 2823   0      0.39    92.92   16.99    None  None   None       |
|    Sol.    : 438    0      4.73    84.50   41.65    None  None   None       |
|    Mac.    : 2385   0      0.39    92.92   12.46    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:     0.393 -   9.645: 1089   |   5:    46.654 -  55.907:  112        |
|      1:     9.645 -  18.898: 1040   |   6:    55.907 -  65.159:   71        |
|      2:    18.898 -  28.150:  235   |   7:    65.159 -  74.411:   28        |
|      3:    28.150 -  37.402:  128   |   8:    74.411 -  83.663:    5        |
|      4:    37.402 -  46.654:  112   |   9:    83.663 -  92.915:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1387 r_free = 0.1924             target_work(ml) = 5.335         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1385 r_free = 0.1920             target_work(ml) = 5.334         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1385   r_free= 0.1920   ksol= 0.33   Bsol= 44.58   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.49,-1.21,-0.57,-0.00,-0.00,-0.00); trace/3= -1.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.333648                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1385   r_free= 0.1920   ksol= 0.33   Bsol= 44.58   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.75,-1.79,-0.80,-0.00,-0.00,-0.00); trace/3= -1.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.332677                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.123719              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.186  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.346494              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.508  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1385      final r-factor (work) = 0.1200          |
| start r-factor (free) = 0.1920      final r-factor (free) = 0.1716          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1161 = 4.12 * 0.50 * 5.3628 + 1.00 * 0.0588                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.9451 = 4.12 * 0.50 * 5.2750 + 1.00 * 0.0688                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1200      final r-factor (work) = 0.1153          |
| start r-factor (free) = 0.1716      final r-factor (free) = 0.1682          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1121 = 1.35 * 1.00 * 5.2750 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0017 = 1.35 * 1.00 * 5.1922 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.367)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.97   17.05    None  None   None       |
|    all(noH): 2823   0      0.00    99.97   17.05    None  None   None       |
|    Sol.    : 438    0      4.64    87.91   43.11    None  None   None       |
|    Mac.    : 2385   0      0.00    99.97   12.27    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 -   9.997: 1207   |   5:    49.985 -  59.982:   92        |
|      1:     9.997 -  19.994:  987   |   6:    59.982 -  69.979:   68        |
|      2:    19.994 -  29.991:  211   |   7:    69.979 -  79.976:   29        |
|      3:    29.991 -  39.988:  118   |   8:    79.976 -  89.973:    8        |
|      4:    39.988 -  49.985:  100   |   9:    89.973 -  99.970:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1153 r_free = 0.1682             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1152 r_free = 0.1680             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1680   ksol= 0.33   Bsol= 44.58   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.75,-1.79,-0.80,-0.00,-0.00,-0.00); trace/3= -1.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.180915                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8783 -  4.6612 0.99   1390  155 0.0995 0.1335      5.3822      5.5705|
|  2:  4.6612 -  3.7187 0.99   1341  150 0.0837 0.1212      5.4538       5.689|
|  3:  3.7187 -  3.2543 0.99   1313  141 0.1109 0.1539      5.5296      5.9085|
|  4:  3.2543 -  2.9593 0.99   1304  152 0.1274 0.1797      5.5166      5.6817|
|  5:  2.9593 -  2.7486 0.99   1299  144 0.1366 0.1928      5.3726      5.6291|
|  6:  2.7486 -  2.5874 0.99   1295  137 0.1229 0.1775      5.2375      5.4302|
|  7:  2.5874 -  2.4585 0.99   1293  140 0.1294 0.1732       5.189       5.422|
|  8:  2.4585 -  2.3519 0.98   1263  148 0.1225 0.1846      5.0975       5.394|
|  9:  2.3519 -  2.2617 0.98   1257  145 0.1229 0.1804      5.0641      5.2907|
| 10:  2.2617 -  2.1839 1.00   1295  138 0.1183 0.1935      5.0104      5.2889|
| 11:  2.1839 -  2.1158 0.98   1268  140 0.1194 0.1944      4.9988      5.3402|
| 12:  2.1158 -  2.0555 0.98   1255  141 0.1162 0.1761       4.926      5.1938|
| 13:  2.0555 -  2.0015 0.99   1274  139 0.1156 0.1950      4.8126      5.1394|
| 14:  2.0015 -  1.9527 0.61    783   89 0.1039 0.1627      4.6947      4.9199|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8783 -  4.6612  1390   155  0.94   9.37   0.99     0.96       7328.85|
|  2:  4.6612 -  3.7187  1341   150  0.95   8.65   1.04     1.02       9986.61|
|  3:  3.7187 -  3.2543  1313   141  0.93  12.48   1.05     1.04      12078.94|
|  4:  3.2543 -  2.9593  1304   152  0.90  15.38   1.03     1.01      12310.98|
|  5:  2.9593 -  2.7486  1299   144  0.89  16.73   1.01     0.98       9253.39|
|  6:  2.7486 -  2.5874  1295   137  0.89  17.17   1.00     0.97       7764.70|
|  7:  2.5874 -  2.4585  1293   140  0.90  16.52   1.01     0.98       6656.16|
|  8:  2.4585 -  2.3519  1263   148  0.90  16.19   1.01     0.99       5655.30|
|  9:  2.3519 -  2.2617  1257   145  0.90  16.09   1.01     0.98       5349.55|
| 10:  2.2617 -  2.1839  1295   138  0.89  16.93   1.01     0.97       4999.47|
| 11:  2.1839 -  2.1158  1268   140  0.89  17.71   1.01     0.96       5007.64|
| 12:  2.1158 -  2.0555  1255   141  0.90  16.44   1.02     1.01       4468.00|
| 13:  2.0555 -  2.0015  1274   139  0.89  17.29   1.02     1.01       3618.86|
| 14:  2.0015 -  1.9527   783    89  0.91  15.02   1.00     0.98       2831.84|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2831.84 max =        12310.98 mean =      7107.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.08|
|phase err.(test): min =        0.00 max =           89.42 mean =        14.63|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1679   ksol= 0.32   Bsol= 44.07   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.67,-1.80,-0.71,-0.00,-0.00,-0.00); trace/3= -1.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.180507                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1679   ksol= 0.32   Bsol= 44.07   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.67,-1.80,-0.71,-0.00,-0.00,-0.00); trace/3= -1.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.180507                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8783 -  4.6612 0.99   1390  155 0.0993 0.1333      5.3786      5.5683|
|  2:  4.6612 -  3.7187 0.99   1341  150 0.0838 0.1213      5.4538      5.6897|
|  3:  3.7187 -  3.2543 0.99   1313  141 0.1109 0.1539      5.5302      5.9089|
|  4:  3.2543 -  2.9593 0.99   1304  152 0.1274 0.1797      5.5167      5.6818|
|  5:  2.9593 -  2.7486 0.99   1299  144 0.1365 0.1927      5.3723      5.6288|
|  6:  2.7486 -  2.5874 0.99   1295  137 0.1229 0.1772       5.237      5.4291|
|  7:  2.5874 -  2.4585 0.99   1293  140 0.1294 0.1732      5.1888      5.4221|
|  8:  2.4585 -  2.3519 0.98   1263  148 0.1225 0.1845      5.0975      5.3938|
|  9:  2.3519 -  2.2617 0.98   1257  145 0.1230 0.1804       5.064      5.2903|
| 10:  2.2617 -  2.1839 1.00   1295  138 0.1182 0.1938      5.0104      5.2897|
| 11:  2.1839 -  2.1158 0.98   1268  140 0.1194 0.1945      4.9987      5.3404|
| 12:  2.1158 -  2.0555 0.98   1255  141 0.1162 0.1759      4.9258      5.1936|
| 13:  2.0555 -  2.0015 0.99   1274  139 0.1156 0.1950      4.8121      5.1387|
| 14:  2.0015 -  1.9527 0.61    783   89 0.1039 0.1622      4.6935      4.9182|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8783 -  4.6612  1390   155  0.94   9.32   0.99     0.96       7264.65|
|  2:  4.6612 -  3.7187  1341   150  0.95   8.63   1.04     1.02       9962.97|
|  3:  3.7187 -  3.2543  1313   141  0.93  12.50   1.05     1.04      12102.05|
|  4:  3.2543 -  2.9593  1304   152  0.90  15.39   1.03     1.01      12314.24|
|  5:  2.9593 -  2.7486  1299   144  0.89  16.72   1.01     0.98       9243.52|
|  6:  2.7486 -  2.5874  1295   137  0.89  17.16   1.00     0.97       7756.19|
|  7:  2.5874 -  2.4585  1293   140  0.90  16.51   1.01     0.98       6649.33|
|  8:  2.4585 -  2.3519  1263   148  0.90  16.18   1.01     0.99       5654.31|
|  9:  2.3519 -  2.2617  1257   145  0.90  16.09   1.02     0.98       5349.02|
| 10:  2.2617 -  2.1839  1295   138  0.89  16.94   1.01     0.98       5002.68|
| 11:  2.1839 -  2.1158  1268   140  0.89  17.72   1.01     0.97       5007.87|
| 12:  2.1158 -  2.0555  1255   141  0.90  16.44   1.02     1.01       4467.81|
| 13:  2.0555 -  2.0015  1274   139  0.89  17.28   1.02     1.01       3613.42|
| 14:  2.0015 -  1.9527   783    89  0.91  15.00   1.00     0.98       2822.76|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2822.76 max =        12314.24 mean =      7099.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.07|
|phase err.(test): min =        0.00 max =           89.41 mean =        14.63|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.367)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.97   17.06    None  None   None       |
|    all(noH): 2823   0      0.00    99.97   17.06    None  None   None       |
|    Sol.    : 438    0      4.65    87.91   43.11    None  None   None       |
|    Mac.    : 2385   0      0.00    99.97   12.27    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.000: 1207   |   5:    49.988 -  59.985:   92        |
|      1:    10.000 -  19.997:  987   |   6:    59.985 -  69.982:   68        |
|      2:    19.997 -  29.994:  211   |   7:    69.982 -  79.979:   29        |
|      3:    29.994 -  39.991:  118   |   8:    79.979 -  89.976:    8        |
|      4:    39.991 -  49.988:  100   |   9:    89.976 -  99.973:    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)= 302         
Filter by distance & map next to the model:
   mapped sites are within: 0.410 - 4.179
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 297 from: 302
   mapped sites are within: 0.754 - 4.179

peak=    7.363 closest distance to " O   HOH Z 390 " =    1.176
peak=    7.266 closest distance to " O   HOH Z 431 " =    2.190
peak=    7.008 closest distance to " O   HOH Z 385 " =    1.818
peak=    6.751 closest distance to " O   HOH Z 289 " =    1.417
peak=    6.645 closest distance to " NE2 GLN A  11 " =    1.384
peak=    6.401 closest distance to " O   HOH Z  65 " =    1.689
peak=    6.056 closest distance to " O   HOH Z   7 " =    1.818
peak=    5.962 closest distance to " O   HOH Z 130 " =    1.003
peak=    5.940 closest distance to " O   HOH Z 427 " =    1.401
peak=    5.583 closest distance to " O   HOH Z 222 " =    1.373
peak=    5.399 closest distance to " O   HOH Z 112 " =    1.567
peak=    5.393 closest distance to " O   HOH Z 142 " =    1.815
peak=    5.326 closest distance to " O   HOH Z 417 " =    2.066
peak=    5.268 closest distance to " O   HOH Z  63 " =    2.071
peak=    5.232 closest distance to " O   HOH Z 124 " =    1.555
peak=    5.215 closest distance to " CG  PRO A  54 " =    1.213
peak=    5.204 closest distance to " O   HOH Z  28 " =    1.514
peak=    5.170 closest distance to " O   HOH Z 245 " =    1.209
peak=    5.164 closest distance to " O   HOH Z 403 " =    1.467
peak=    5.142 closest distance to " O   HOH Z  49 " =    1.456
peak=    5.073 closest distance to " O   HOH Z 287 " =    1.964
peak=    5.003 closest distance to " NH2 ARG A  56 " =    1.990
peak=    4.994 closest distance to " O   HOH Z 427 " =    1.789
peak=    4.860 closest distance to " O   HOH Z  78 " =    1.632
peak=    4.855 closest distance to " CB  PRO A  54 " =    1.038
peak=    4.843 closest distance to " O   HOH Z 236 " =    1.489
peak=    4.719 closest distance to " O   HOH Z 214 " =    1.505
peak=    4.709 closest distance to " O   HOH Z 193 " =    1.843
peak=    4.670 closest distance to " O   HOH Z 139 " =    1.444
peak=    4.659 closest distance to " O   HOH Z  57 " =    2.600
peak=    4.634 closest distance to " O   HOH Z  29 " =    1.125
peak=    4.612 closest distance to " CB  ARG A 275 " =    0.981
peak=    4.586 closest distance to " O   HOH Z 145 " =    1.597
peak=    4.562 closest distance to " O   HOH Z 392 " =    1.348
peak=    4.544 closest distance to " O   HOH Z 232 " =    2.201
peak=    4.524 closest distance to " O   HOH Z 158 " =    1.441
peak=    4.502 closest distance to " CB  GLN A 183 " =    1.173
peak=    4.499 closest distance to " O   HOH Z 166 " =    1.673
peak=    4.451 closest distance to " CA  TYR A  30 " =    1.005
peak=    4.444 closest distance to " O   HOH Z 352 " =    1.539
peak=    4.403 closest distance to " O   HOH Z 380 " =    1.806
peak=    4.372 closest distance to " O   HOH Z 369 " =    2.071
peak=    4.343 closest distance to " O   HOH Z 211 " =    1.137
peak=    4.342 closest distance to " CB  SER A   3 " =    1.272
peak=    4.330 closest distance to " O   HOH Z 316 " =    2.862
peak=    4.322 closest distance to " O   HOH Z 402 " =    1.482
peak=    4.317 closest distance to " O   PRO A 198 " =    1.245
peak=    4.308 closest distance to " O   HOH Z 298 " =    2.033
peak=    4.288 closest distance to " O   HOH Z 261 " =    1.972
peak=    4.279 closest distance to " O   HOH Z 272 " =    1.866
peak=    4.277 closest distance to " NZ  LYS A 117 " =    1.266
peak=    4.274 closest distance to " O   HOH Z 414 " =    1.251
peak=    4.253 closest distance to " O   HOH Z  63 " =    1.884
peak=    4.222 closest distance to " O   HOH Z 363 " =    1.124
peak=    4.214 closest distance to " CB  SER A  63 " =    1.333
peak=    4.206 closest distance to " CG  PRO A 213 " =    1.197
peak=    4.193 closest distance to " CB  GLN A 223 " =    1.426
peak=    4.184 closest distance to " O   SER A  87 " =    2.341
peak=    4.184 closest distance to " O   HOH Z 371 " =    3.151
peak=    4.164 closest distance to " O   HOH Z 423 " =    1.790
peak=    4.161 closest distance to " O   HOH Z 394 " =    1.754
peak=    4.139 closest distance to " O   HOH Z   9 " =    1.060
peak=    4.113 closest distance to " CB  ASN A 148 " =    1.349
peak=    4.109 closest distance to " O   HOH Z 371 " =    2.105
peak=    4.073 closest distance to " O   HOH Z 368 " =    3.651
peak=    4.046 closest distance to " O   HOH Z 217 " =    2.943
peak=    4.045 closest distance to " O   HOH Z 152 " =    2.091
peak=    4.042 closest distance to " OG BSER A  99 " =    2.240
peak=    4.041 closest distance to " O   HOH Z   2 " =    1.874
peak=    4.038 closest distance to " O   HOH Z  44 " =    1.868
peak=    4.022 closest distance to " O   HOH Z 412 " =    1.849
peak=    4.016 closest distance to " CG  ARG A  66 " =    2.399
peak=    4.016 closest distance to " O   HOH Z 424 " =    1.216
peak=    3.969 closest distance to " O   HOH Z 302 " =    1.344
peak=    3.955 closest distance to " O   HOH Z 405 " =    1.367
peak=    3.955 closest distance to " CB  GLU A 128 " =    1.049
peak=    3.943 closest distance to " CA  PHE A 283 " =    1.403
peak=    3.931 closest distance to " O   HOH Z 119 " =    4.179
peak=    3.930 closest distance to " O   HOH Z  88 " =    2.890
peak=    3.929 closest distance to " O   HOH Z 415 " =    1.166
peak=    3.903 closest distance to " O   HOH Z 171 " =    2.353
peak=    3.900 closest distance to " O   HOH Z 327 " =    1.829
peak=    3.897 closest distance to " O   HOH Z 425 " =    1.451
peak=    3.882 closest distance to " O   HOH Z 151 " =    1.754
peak=    3.876 closest distance to " O   HOH Z 222 " =    2.109
peak=    3.852 closest distance to " CG  TRP A 179 " =    2.136
peak=    3.851 closest distance to " O   HOH Z 155 " =    1.789
peak=    3.851 closest distance to " O   HOH Z 244 " =    1.567
peak=    3.819 closest distance to " O   HOH Z 378 " =    0.962
peak=    3.815 closest distance to " O   HOH Z 278 " =    1.018
peak=    3.815 closest distance to " CG  LEU A 167 " =    1.267
peak=    3.814 closest distance to " O   HOH Z 425 " =    2.164
peak=    3.807 closest distance to " NE2 GLN A  58 " =    3.697
peak=    3.807 closest distance to " O   HOH Z 215 " =    1.291
peak=    3.794 closest distance to " CG2 THR A 221 " =    1.282
peak=    3.792 closest distance to " N   ALA A   1 " =    2.750
peak=    3.781 closest distance to " O   HOH Z 250 " =    1.472
peak=    3.780 closest distance to " CB  GLU A 152 " =    1.220
peak=    3.772 closest distance to " O   HOH Z 413 " =    1.494
peak=    3.772 closest distance to " NE AARG A 275 " =    1.395
peak=    3.750 closest distance to " CG1BVAL A 121 " =    2.097
peak=    3.742 closest distance to " CB  TRP A 179 " =    1.401
peak=    3.736 closest distance to " CB  LYS A 290 " =    1.465
peak=    3.734 closest distance to " O   HOH Z 435 " =    1.796
peak=    3.733 closest distance to " N   ALA A   1 " =    1.378
peak=    3.732 closest distance to " O   HOH Z  59 " =    1.537
peak=    3.731 closest distance to " CB  ILE A 120 " =    1.442
peak=    3.727 closest distance to " OG1 THR A 221 " =    1.359
peak=    3.715 closest distance to " O   HOH Z 385 " =    3.250
peak=    3.714 closest distance to " CB  GLU A 277 " =    3.391
peak=    3.711 closest distance to " OG  SER A  62 " =    3.045
peak=    3.708 closest distance to " O   HOH Z 365 " =    2.631
peak=    3.702 closest distance to " CG2 VAL A 257 " =    0.857
peak=    3.701 closest distance to " CA  ASN A 215 " =    1.188
peak=    3.699 closest distance to " CB  TYR A 169 " =    0.754
peak=    3.698 closest distance to " O   HOH Z 108 " =    1.687
peak=    3.697 closest distance to " OD1 ASN A  69 " =    2.532
peak=    3.683 closest distance to " OD2 ASP A 286 " =    2.536
peak=    3.682 closest distance to " O   HOH Z 213 " =    1.657
peak=    3.680 closest distance to " O   HOH Z 234 " =    3.705
peak=    3.674 closest distance to " O   HOH Z 291 " =    1.468
peak=    3.664 closest distance to " CD1 ILE A 263 " =    1.237
peak=    3.658 closest distance to " NE1 TRP A 274 " =    1.006
peak=    3.658 closest distance to " O   HOH Z 422 " =    2.572
peak=    3.656 closest distance to " CA  ASN A  74 " =    1.200
peak=    3.653 closest distance to " CB  TRP A 266 " =    1.136
peak=    3.647 closest distance to " CB  SER A 216 " =    0.870
peak=    3.647 closest distance to " CD2 TRP A 179 " =    1.428
peak=    3.629 closest distance to " CG  PRO A  90 " =    1.091
peak=    3.629 closest distance to " O   HOH Z  61 " =    1.505
peak=    3.623 closest distance to " CG2AVAL A 121 " =    2.530
peak=    3.623 closest distance to " O   HOH Z 128 " =    2.083
peak=    3.618 closest distance to " O   HOH Z   9 " =    2.110
peak=    3.617 closest distance to " O   HOH Z   6 " =    1.973
peak=    3.615 closest distance to " CG  GLN A  11 " =    2.136
peak=    3.610 closest distance to " O   HOH Z 258 " =    2.001
peak=    3.610 closest distance to " O   HOH Z  30 " =    1.858
peak=    3.599 closest distance to " CB  VAL A 202 " =    1.658
peak=    3.596 closest distance to " CB  MET A 105 " =    1.253
peak=    3.595 closest distance to " CA  GLY A 241 " =    3.682
peak=    3.591 closest distance to " O   HOH Z 311 " =    2.378
peak=    3.587 closest distance to " O   HOH Z 108 " =    1.696
peak=    3.586 closest distance to " ND1 HIS A  81 " =    1.496
peak=    3.584 closest distance to " O   HOH Z 416 " =    1.181
peak=    3.575 closest distance to " O   HOH Z 329 " =    3.328
peak=    3.573 closest distance to " NH2 ARG A 219 " =    1.730
peak=    3.569 closest distance to " OG BSER A 164 " =    2.184
peak=    3.557 closest distance to " CE  MET A  93 " =    1.478
peak=    3.553 closest distance to " O   HOH Z 227 " =    1.897
peak=    3.553 closest distance to " O   HOH Z   7 " =    3.178
peak=    3.549 closest distance to " O   HOH Z 175 " =    2.038
peak=    3.547 closest distance to " O   HOH Z 313 " =    1.943
peak=    3.544 closest distance to " NE2 GLN A 278 " =    3.562
peak=    3.540 closest distance to " CA  ALA A 160 " =    0.787
peak=    3.539 closest distance to " O   HOH Z 282 " =    1.560
peak=    3.531 closest distance to " O   HOH Z  32 " =    2.016
peak=    3.527 closest distance to " O   HOH Z 358 " =    1.217
peak=    3.521 closest distance to " CB  VAL A 265 " =    1.404
peak=    3.518 closest distance to " OG  SER A  22 " =    2.770
peak=    3.517 closest distance to " NH1AARG A 145 " =    1.031
peak=    3.499 closest distance to " CD  LYS A 166 " =    1.629
peak=    3.485 closest distance to " O   HOH Z 106 " =    2.467
peak=    3.485 closest distance to " O   HOH Z 115 " =    1.333
peak=    3.485 closest distance to " O   HOH Z 368 " =    1.894
peak=    3.483 closest distance to " O   HOH Z  44 " =    2.891
peak=    3.480 closest distance to " OE1 GLU A  37 " =    1.208
peak=    3.474 closest distance to " CA  ASN A 127 " =    1.049
peak=    3.472 closest distance to " O   HOH Z  97 " =    1.868
peak=    3.471 closest distance to " O   HOH Z  10 " =    1.637
peak=    3.469 closest distance to " O   HOH Z 419 " =    1.811
peak=    3.466 closest distance to " O   HOH Z 207 " =    2.174
peak=    3.460 closest distance to " CB  SER A 276 " =    1.099
peak=    3.460 closest distance to " O   HOH Z 193 " =    1.739
peak=    3.457 closest distance to " CB  LYS A 117 " =    1.157
peak=    3.450 closest distance to " CB  LEU A 300 " =    0.955
peak=    3.438 closest distance to " CB  THR A 157 " =    1.088
peak=    3.437 closest distance to " O   HOH Z  92 " =    1.241
peak=    3.434 closest distance to " CB  MET A 105 " =    1.030
peak=    3.430 closest distance to " O   HOH Z 119 " =    1.575
peak=    3.429 closest distance to " O   HOH Z   2 " =    1.187
peak=    3.417 closest distance to " O   HOH Z  50 " =    1.866
peak=    3.413 closest distance to " OG BSER A 212 " =    2.768
peak=    3.411 closest distance to " CA  ALA A  21 " =    1.124
peak=    3.406 closest distance to " O   HOH Z 209 " =    2.484
peak=    3.405 closest distance to " O   HOH Z 389 " =    1.646
peak=    3.403 closest distance to " O   ALA A 165 " =    1.295
peak=    3.402 closest distance to " O   HOH Z 126 " =    1.435
peak=    3.402 closest distance to " CG1 VAL A 202 " =    1.905
peak=    3.402 closest distance to " N   GLN A 278 " =    1.196
peak=    3.400 closest distance to " O   HOH Z  40 " =    1.955
peak=    3.397 closest distance to " O   HOH Z 426 " =    1.908
peak=    3.392 closest distance to " N   TYR A  15 " =    1.101
peak=    3.391 closest distance to " O   HOH Z  73 " =    1.690
peak=    3.391 closest distance to " O   HOH Z 272 " =    2.032
peak=    3.391 closest distance to " NZ  LYS A 119 " =    2.776
peak=    3.390 closest distance to " O   HOH Z 288 " =    2.017
peak=    3.388 closest distance to " O   HOH Z 290 " =    0.907
peak=    3.386 closest distance to " O   HOH Z 361 " =    2.624
peak=    3.385 closest distance to " O   HOH Z 434 " =    1.196
peak=    3.383 closest distance to " O   HOH Z  17 " =    2.100
peak=    3.379 closest distance to " O   HOH Z 214 " =    1.675
peak=    3.377 closest distance to " O   HOH Z 393 " =    1.353
peak=    3.377 closest distance to " O   HOH Z  57 " =    1.829
peak=    3.373 closest distance to " O   HOH Z  65 " =    1.389
peak=    3.370 closest distance to " CB  PHE A 225 " =    1.449
peak=    3.367 closest distance to " CE AMET A  47 " =    1.248
peak=    3.359 closest distance to " O   HOH Z 116 " =    2.535
peak=    3.352 closest distance to " CB  TYR A 116 " =    0.991
peak=    3.352 closest distance to " O   HOH Z  93 " =    1.828
peak=    3.352 closest distance to " CB  ARG A 190 " =    1.727
peak=    3.351 closest distance to " O   HOH Z 430 " =    1.863
peak=    3.347 closest distance to " CB  GLU A 277 " =    1.087
peak=    3.346 closest distance to " O   HOH Z 112 " =    2.201
peak=    3.346 closest distance to " O   HOH Z 156 " =    2.723
peak=    3.344 closest distance to " O   GLY A 147 " =    1.546
peak=    3.343 closest distance to " N   GLU A   2 " =    1.326
peak=    3.341 closest distance to " O   ALA A   1 " =    1.636
peak=    3.340 closest distance to " CA  ALA A 299 " =    0.918
peak=    3.338 closest distance to " CB  LEU A 228 " =    1.063
peak=    3.334 closest distance to " O   HOH Z  80 " =    2.004
peak=    3.333 closest distance to " O   HOH Z  61 " =    1.581
peak=    3.314 closest distance to " CA  ILE A 234 " =    1.019
peak=    3.313 closest distance to " CG2BVAL A  41 " =    0.946
peak=    3.306 closest distance to " NZ  LYS A  76 " =    1.497
peak=    3.306 closest distance to " O   HOH Z 158 " =    2.379
peak=    3.304 closest distance to " CG2 THR A 220 " =    0.969
peak=    3.298 closest distance to " O   HOH Z 419 " =    1.844
peak=    3.295 closest distance to " O   HOH Z 359 " =    1.386
peak=    3.295 closest distance to " O   HOH Z 122 " =    1.684
peak=    3.290 closest distance to " O   HOH Z 130 " =    2.116
peak=    3.289 closest distance to " O   HOH Z 409 " =    2.051
peak=    3.287 closest distance to " O   HOH Z 344 " =    2.976
peak=    3.286 closest distance to " CZ3 TRP A 274 " =    2.090
peak=    3.283 closest distance to " CA  LEU A 282 " =    1.089
peak=    3.277 closest distance to " ND2 ASN A 187 " =    1.476
peak=    3.274 closest distance to " O   HOH Z 142 " =    1.569
peak=    3.273 closest distance to " O   HOH Z 193 " =    1.965
peak=    3.268 closest distance to " CG  PRO A 198 " =    1.247
peak=    3.268 closest distance to " O   HOH Z  47 " =    1.375
peak=    3.260 closest distance to " CB  ASP A 200 " =    0.960
peak=    3.257 closest distance to " O   HOH Z 421 " =    2.796
peak=    3.255 closest distance to " O   HOH Z 248 " =    1.936
peak=    3.254 closest distance to " CG  LYS A 166 " =    1.287
peak=    3.253 closest distance to " O   HOH Z 214 " =    3.265
peak=    3.247 closest distance to " O   HOH Z 293 " =    1.304
peak=    3.243 closest distance to " CA  GLU A 152 " =    1.324
peak=    3.240 closest distance to " O   HOH Z 263 " =    2.350
peak=    3.235 closest distance to " O   HOH Z 147 " =    1.262
peak=    3.233 closest distance to " O   HOH Z 336 " =    1.860
peak=    3.219 closest distance to " CB  ALA A   1 " =    0.988
peak=    3.217 closest distance to " O   HOH Z  11 " =    1.318
peak=    3.216 closest distance to " CG2 ILE A  20 " =    1.723
peak=    3.214 closest distance to " O   HOH Z   1 " =    1.959
peak=    3.210 closest distance to " CG  GLN A  89 " =    1.354
peak=    3.210 closest distance to " O   HOH Z 424 " =    3.093
peak=    3.208 closest distance to " CG  LYS A  76 " =    1.682
peak=    3.200 closest distance to " O   HOH Z 325 " =    3.179
peak=    3.198 closest distance to " O   HOH Z 369 " =    1.567
peak=    3.191 closest distance to " CB  ARG A 138 " =    0.902
peak=    3.187 closest distance to " CB  ARG A 139 " =    1.083
peak=    3.186 closest distance to " O   HOH Z 128 " =    2.279
peak=    3.183 closest distance to " O   HOH Z 158 " =    3.069
peak=    3.182 closest distance to " CG  LYS A 119 " =    1.024
peak=    3.179 closest distance to " O   HOH Z 357 " =    1.695
peak=    3.177 closest distance to " O   HOH Z 326 " =    1.830
peak=    3.174 closest distance to " CE  LYS A  76 " =    0.916
peak=    3.171 closest distance to " O   HOH Z 216 " =    1.439
peak=    3.165 closest distance to " O   HOH Z 384 " =    1.587
peak=    3.162 closest distance to " CZ  ARG A  14 " =    1.561
peak=    3.158 closest distance to " OG  SER A  62 " =    2.932
peak=    3.157 closest distance to " O   HOH Z 431 " =    0.997
peak=    3.147 closest distance to " NH1BARG A 145 " =    1.256
peak=    3.143 closest distance to " O   HOH Z 153 " =    3.661
peak=    3.137 closest distance to " O   HOH Z 258 " =    1.600
peak=    3.136 closest distance to " O   HOH Z 213 " =    1.814
peak=    3.135 closest distance to " CA  MET A 105 " =    0.836
peak=    3.131 closest distance to " O   HOH Z 196 " =    1.663
peak=    3.121 closest distance to " O   HOH Z 311 " =    1.501
peak=    3.115 closest distance to " CB  ARG A  79 " =    1.252
peak=    3.110 closest distance to " CB  ALA A  34 " =    1.140
peak=    3.110 closest distance to " CG  GLN A 240 " =    3.524
peak=    3.104 closest distance to " O   HOH Z 287 " =    1.822
peak=    3.102 closest distance to " CE3 TRP A 274 " =    2.357
peak=    3.099 closest distance to " CD1 PHE A  16 " =    1.028
peak=    3.096 closest distance to " O  BHOH Z  74 " =    1.404
peak=    3.088 closest distance to " CE3 TRP A 274 " =    1.244
peak=    3.085 closest distance to " O   HOH Z 189 " =    2.867
peak=    3.079 closest distance to " CG2 VAL A 232 " =    1.094
peak=    3.078 closest distance to " O   HOH Z  87 " =    1.092
peak=    3.067 closest distance to " O   HOH Z 227 " =    2.061
peak=    3.064 closest distance to " O   HOH Z 123 " =    2.046
peak=    3.063 closest distance to " CG2 THR A 251 " =    1.798
peak=    3.054 closest distance to " O   HOH Z  99 " =    2.407
peak=    3.045 closest distance to " O   HOH Z  43 " =    2.389
peak=    3.041 closest distance to " O   HOH Z  94 " =    2.054
peak=    3.032 closest distance to " CB  ASN A 187 " =    0.995
peak=    3.031 closest distance to " O   HOH Z 172 " =    2.157

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.785 - 5.263
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 197
   mapped sites are within: 0.785 - 5.263

peak=   -4.614 closest distance to " O   HOH Z 409 " =    3.246
peak=   -4.381 closest distance to " O   HOH Z  60 " =    2.080
peak=   -4.273 closest distance to " O   HOH Z 385 " =    1.062
peak=   -4.170 closest distance to " CD  ARG A  14 " =    3.170
peak=   -4.159 closest distance to " CA  GLY A  98 " =    1.805
peak=   -4.068 closest distance to " CZ  PHE A  59 " =    1.452
peak=   -4.065 closest distance to " CB  PRO A 243 " =    2.531
peak=   -4.007 closest distance to " O   HOH Z  43 " =    1.834
peak=   -3.989 closest distance to " O   MET A  40 " =    2.818
peak=   -3.974 closest distance to " OG BSER A 134 " =    1.398
peak=   -3.951 closest distance to " CD  ARG A 156 " =    2.020
peak=   -3.936 closest distance to " O   HOH Z 185 " =    1.846
peak=   -3.924 closest distance to " CB  TYR A  15 " =    2.061
peak=   -3.922 closest distance to " CB  ALA A 248 " =    1.982
peak=   -3.879 closest distance to " O   SER A  22 " =    2.585
peak=   -3.875 closest distance to " NH2 ARG A 219 " =    1.846
peak=   -3.859 closest distance to " O   ARG A 145 " =    1.458
peak=   -3.848 closest distance to " CD2 TYR A 293 " =    1.692
peak=   -3.840 closest distance to " O   HOH Z 197 " =    3.231
peak=   -3.813 closest distance to " N   THR A 157 " =    1.553
peak=   -3.809 closest distance to " O   PRO A 198 " =    1.327
peak=   -3.805 closest distance to " CG  GLN A  58 " =    1.390
peak=   -3.795 closest distance to " O   HOH Z  88 " =    2.053
peak=   -3.789 closest distance to " O   HOH Z 388 " =    2.275
peak=   -3.787 closest distance to " O   HOH Z 393 " =    2.912
peak=   -3.754 closest distance to " CG  MET A 105 " =    0.963
peak=   -3.753 closest distance to " OG  SER A  87 " =    1.168
peak=   -3.743 closest distance to " OE1 GLU A 277 " =    2.079
peak=   -3.708 closest distance to " O   HOH Z 415 " =    1.139
peak=   -3.703 closest distance to " O   PRO A 243 " =    2.396
peak=   -3.702 closest distance to " O   HOH Z  56 " =    1.833
peak=   -3.697 closest distance to " C   HIS A 108 " =    1.229
peak=   -3.694 closest distance to " CZ2 TRP A 274 " =    0.996
peak=   -3.692 closest distance to " O   HOH Z 372 " =    2.538
peak=   -3.686 closest distance to " O   SER A 216 " =    1.884
peak=   -3.685 closest distance to " OD2 ASP A 191 " =    1.527
peak=   -3.684 closest distance to " NH1 ARG A  56 " =    2.241
peak=   -3.665 closest distance to " O   HOH Z 427 " =    1.846
peak=   -3.661 closest distance to " O   HOH Z  52 " =    1.213
peak=   -3.655 closest distance to " O   SER A  95 " =    1.203
peak=   -3.653 closest distance to " O   HOH Z 298 " =    1.082
peak=   -3.651 closest distance to " O   HOH Z 390 " =    1.034
peak=   -3.646 closest distance to " O   HOH Z  37 " =    1.550
peak=   -3.644 closest distance to " NH2 ARG A  79 " =    1.938
peak=   -3.640 closest distance to " N   GLN A  58 " =    1.733
peak=   -3.632 closest distance to " N   VAL A  72 " =    1.503
peak=   -3.630 closest distance to " O   HOH Z  65 " =    0.821
peak=   -3.622 closest distance to " OG  SER A  97 " =    1.969
peak=   -3.618 closest distance to " CD1 LEU A 101 " =    2.246
peak=   -3.609 closest distance to " O   HOH Z 425 " =    1.043
peak=   -3.608 closest distance to " CB  ALA A 291 " =    2.157
peak=   -3.605 closest distance to " OG BSER A 134 " =    1.698
peak=   -3.593 closest distance to " CB  ALA A 100 " =    1.887
peak=   -3.588 closest distance to " O   HOH Z 290 " =    1.286
peak=   -3.585 closest distance to " CD2 LEU A 237 " =    2.488
peak=   -3.585 closest distance to " O   HOH Z 418 " =    1.611
peak=   -3.573 closest distance to " O   HOH Z 438 " =    1.006
peak=   -3.570 closest distance to " O   SER A 135 " =    1.527
peak=   -3.562 closest distance to " O   HOH Z 198 " =    1.967
peak=   -3.561 closest distance to " O   SER A 146 " =    1.239
peak=   -3.555 closest distance to " NE1 TRP A 179 " =    1.295
peak=   -3.552 closest distance to " O   HOH Z 416 " =    0.935
peak=   -3.549 closest distance to " N   HIS A 115 " =    1.742
peak=   -3.548 closest distance to " CA  GLY A 133 " =    1.885
peak=   -3.545 closest distance to " O   HOH Z  22 " =    2.508
peak=   -3.539 closest distance to " O   HOH Z 351 " =    1.602
peak=   -3.535 closest distance to " CA  GLY A 203 " =    2.261
peak=   -3.534 closest distance to " O   PHE A 218 " =    1.344
peak=   -3.531 closest distance to " O   HOH Z  28 " =    2.222
peak=   -3.527 closest distance to " O   ALA A   1 " =    1.337
peak=   -3.520 closest distance to " ND2 ASN A 209 " =    1.867
peak=   -3.519 closest distance to " O   HOH Z 313 " =    1.566
peak=   -3.512 closest distance to " C   ALA A 158 " =    1.424
peak=   -3.511 closest distance to " O   HOH Z  60 " =    2.434
peak=   -3.507 closest distance to " O   VAL A 189 " =    2.361
peak=   -3.501 closest distance to " CE3 TRP A 274 " =    2.393
peak=   -3.496 closest distance to " O   HOH Z 166 " =    1.561
peak=   -3.494 closest distance to " O   HOH Z 435 " =    3.080
peak=   -3.494 closest distance to " NE  ARG A  36 " =    1.890
peak=   -3.482 closest distance to " CA  ASP A  27 " =    2.345
peak=   -3.472 closest distance to " O   VAL A  67 " =    2.957
peak=   -3.471 closest distance to " N   GLN A  88 " =    1.721
peak=   -3.470 closest distance to " O   HOH Z 250 " =    1.337
peak=   -3.454 closest distance to " OE1 GLN A 223 " =    2.103
peak=   -3.447 closest distance to " CD  GLN A  88 " =    0.845
peak=   -3.446 closest distance to " O   HOH Z  90 " =    2.340
peak=   -3.435 closest distance to " O   HOH Z 213 " =    1.151
peak=   -3.426 closest distance to " O   HOH Z 236 " =    2.173
peak=   -3.421 closest distance to " CD  LYS A 166 " =    2.326
peak=   -3.420 closest distance to " O   HOH Z  72 " =    1.577
peak=   -3.419 closest distance to " CG  ARG A 219 " =    2.227
peak=   -3.415 closest distance to " CG  ASN A 301 " =    2.032
peak=   -3.411 closest distance to " OH  TYR A 214 " =    1.296
peak=   -3.404 closest distance to " OD2 ASP A 171 " =    1.957
peak=   -3.401 closest distance to " OE1 GLN A 183 " =    1.408
peak=   -3.400 closest distance to " O   HOH Z   4 " =    0.814
peak=   -3.393 closest distance to " CB  ASP A 132 " =    2.403
peak=   -3.391 closest distance to " O   HOH Z  13 " =    1.485
peak=   -3.390 closest distance to " O   HOH Z 131 " =    4.104
peak=   -3.390 closest distance to " ND2 ASN A  60 " =    1.303
peak=   -3.389 closest distance to " CG  PHE A 283 " =    2.509
peak=   -3.378 closest distance to " O   HOH Z 385 " =    2.464
peak=   -3.377 closest distance to " CA  GLY A 241 " =    2.180
peak=   -3.375 closest distance to " ND2 ASN A 252 " =    1.731
peak=   -3.373 closest distance to " O   HOH Z   1 " =    3.733
peak=   -3.373 closest distance to " CB  ILE A  33 " =    2.835
peak=   -3.371 closest distance to " CG  ASP A 231 " =    0.785
peak=   -3.359 closest distance to " OD1 ASN A 148 " =    1.749
peak=   -3.357 closest distance to " CG  PRO A 163 " =    2.527
peak=   -3.353 closest distance to " O   HOH Z 211 " =    1.457
peak=   -3.347 closest distance to " O   HOH Z 426 " =    2.047
peak=   -3.346 closest distance to " OG ASER A 134 " =    1.037
peak=   -3.343 closest distance to " O   VAL A 232 " =    1.957
peak=   -3.340 closest distance to " O   ILE A  49 " =    1.620
peak=   -3.330 closest distance to " O   HOH Z  51 " =    1.211
peak=   -3.325 closest distance to " O   HOH Z 137 " =    1.395
peak=   -3.324 closest distance to " O   PRO A 198 " =    1.173
peak=   -3.323 closest distance to " O   TRP A  70 " =    1.400
peak=   -3.316 closest distance to " CD  GLN A 223 " =    1.560
peak=   -3.314 closest distance to " N   GLY A 302 " =    1.540
peak=   -3.311 closest distance to " O   HOH Z  93 " =    1.738
peak=   -3.309 closest distance to " CB  ALA A  43 " =    2.154
peak=   -3.305 closest distance to " OG BSER A  99 " =    1.745
peak=   -3.297 closest distance to " CB  SER A  62 " =    2.402
peak=   -3.296 closest distance to " ND2 ASN A 285 " =    1.736
peak=   -3.294 closest distance to " O   HOH Z 429 " =    2.043
peak=   -3.293 closest distance to " C   ARG A 190 " =    1.083
peak=   -3.291 closest distance to " O   HOH Z 412 " =    5.091
peak=   -3.286 closest distance to " CB  SER A 245 " =    2.508
peak=   -3.282 closest distance to " OXT GLY A 302 " =    2.901
peak=   -3.280 closest distance to " CA  VAL A 153 " =    2.303
peak=   -3.279 closest distance to " C   ASN A 285 " =    2.180
peak=   -3.278 closest distance to " CE2 TYR A 116 " =    3.002
peak=   -3.277 closest distance to " CE3 TRP A  70 " =    2.105
peak=   -3.275 closest distance to " OG ASER A 216 " =    1.165
peak=   -3.274 closest distance to " O   HOH Z 288 " =    1.313
peak=   -3.271 closest distance to " NE2 GLN A  58 " =    3.019
peak=   -3.271 closest distance to " O   HOH Z 234 " =    3.918
peak=   -3.269 closest distance to " CD2 LEU A 237 " =    2.624
peak=   -3.268 closest distance to " ND2 ASN A 187 " =    1.375
peak=   -3.262 closest distance to " CB  ALA A  10 " =    2.257
peak=   -3.254 closest distance to " O   ALA A  10 " =    1.648
peak=   -3.253 closest distance to " O   ILE A 239 " =    1.391
peak=   -3.253 closest distance to " O   HOH Z 137 " =    1.498
peak=   -3.247 closest distance to " CE  MET A 105 " =    2.395
peak=   -3.247 closest distance to " CG2 THR A 178 " =    2.056
peak=   -3.243 closest distance to " O   HOH Z 266 " =    4.374
peak=   -3.242 closest distance to " O   HOH Z 143 " =    2.124
peak=   -3.241 closest distance to " CB  ALA A   7 " =    1.905
peak=   -3.239 closest distance to " CZ3 TRP A 123 " =    1.815
peak=   -3.227 closest distance to " O   HOH Z 102 " =    1.662
peak=   -3.222 closest distance to " O   HOH Z  24 " =    1.216
peak=   -3.221 closest distance to " CD2 LEU A  25 " =    1.897
peak=   -3.219 closest distance to " OG  SER A 206 " =    1.859
peak=   -3.216 closest distance to " OD2 ASP A 298 " =    1.021
peak=   -3.214 closest distance to " O   HOH Z  68 " =    1.520
peak=   -3.213 closest distance to " CA  ALA A 227 " =    2.326
peak=   -3.202 closest distance to " OG  SER A   3 " =    1.626
peak=   -3.201 closest distance to " O   HOH Z  54 " =    0.839
peak=   -3.200 closest distance to " C   ILE A 239 " =    2.118
peak=   -3.189 closest distance to " CZ  TYR A 169 " =    1.846
peak=   -3.181 closest distance to " O   ALA A  51 " =    1.324
peak=   -3.177 closest distance to " O   HOH Z  14 " =    1.664
peak=   -3.174 closest distance to " N   ALA A   1 " =    1.351
peak=   -3.173 closest distance to " O   HOH Z 231 " =    1.877
peak=   -3.169 closest distance to " CD2 TYR A 293 " =    2.134
peak=   -3.161 closest distance to " OE2 GLU A 152 " =    1.029
peak=   -3.161 closest distance to " O   GLN A 194 " =    1.449
peak=   -3.157 closest distance to " N   ALA A 137 " =    1.583
peak=   -3.152 closest distance to " O   HOH Z 359 " =    1.536
peak=   -3.146 closest distance to " O   HOH Z 147 " =    1.406
peak=   -3.144 closest distance to " N   LYS A 166 " =    1.874
peak=   -3.143 closest distance to " O   HOH Z 414 " =    1.824
peak=   -3.136 closest distance to " CE  LYS A  76 " =    2.814
peak=   -3.136 closest distance to " CB  CYS A 201 " =    2.248
peak=   -3.135 closest distance to " CG  ASP A  65 " =    1.558
peak=   -3.133 closest distance to " O   ALA A 161 " =    1.817
peak=   -3.133 closest distance to " O   VAL A  67 " =    2.781
peak=   -3.130 closest distance to " OG  SER A  63 " =    1.408
peak=   -3.126 closest distance to " O   VAL A 174 " =    2.240
peak=   -3.126 closest distance to " O   VAL A 125 " =    2.321
peak=   -3.109 closest distance to " O   TRP A  92 " =    1.773
peak=   -3.107 closest distance to " O   HOH Z 318 " =    1.564
peak=   -3.100 closest distance to " O   HOH Z 265 " =    1.874
peak=   -3.098 closest distance to " O   HOH Z 337 " =    1.653
peak=   -3.096 closest distance to " NE2 GLN A  55 " =    0.881
peak=   -3.094 closest distance to " O   HOH Z  64 " =    1.214
peak=   -3.091 closest distance to " O   HOH Z 359 " =    3.418
peak=   -3.085 closest distance to " OXT GLY A 302 " =    5.263
peak=   -3.085 closest distance to " O   HOH Z 292 " =    1.658
peak=   -3.074 closest distance to " CG  ARG A 269 " =    2.020
peak=   -3.071 closest distance to " O   HOH Z  88 " =    2.437
peak=   -3.064 closest distance to " CG  ARG A 259 " =    2.650
peak=   -3.052 closest distance to " O   ASN A 301 " =    1.401
peak=   -3.026 closest distance to " OG  SER A  32 " =    1.259
peak=   -3.024 closest distance to " N   ALA A   1 " =    2.944
peak=   -3.018 closest distance to " N   ARG A 159 " =    1.578

================= 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    :  0.4595 0.4557   6.273888e+00   6.265289e+00
   1_bss:  0.4484 0.4429   6.266880e+00   6.250214e+00
   1_xyz:  0.3508 0.3850   6.102351e+00   6.172377e+00
   1_adp:  0.3188 0.3992   6.058222e+00   6.185544e+00
   1_occ:  0.3182 0.3990   6.057495e+00   6.185296e+00
   2_bss:  0.3179 0.3989   6.057880e+00   6.185112e+00
   2_xyz:  0.2816 0.3542   5.961787e+00   6.111532e+00
   2_adp:  0.2749 0.3470   5.947530e+00   6.098160e+00
   2_occ:  0.2747 0.3471   5.947565e+00   6.098226e+00
   3_bss:  0.2750 0.3467   5.946931e+00   6.098449e+00
   3_xyz:  0.2092 0.2752   5.701969e+00   5.891500e+00
   3_adp:  0.1861 0.2479   5.594844e+00   5.801737e+00
   3_occ:  0.1856 0.2470   5.592883e+00   5.799407e+00
   4_bss:  0.1854 0.2445   5.587929e+00   5.792286e+00
   4_xyz:  0.1493 0.2021   5.392259e+00   5.618947e+00
   4_adp:  0.1387 0.1924   5.334602e+00   5.569682e+00
   4_occ:  0.1385 0.1920   5.333648e+00   5.568714e+00
   5_bss:  0.1385 0.1920   5.332677e+00   5.567337e+00
   5_xyz:  0.1200 0.1716   5.207637e+00   5.458431e+00
   5_adp:  0.1153 0.1682   5.181488e+00   5.439576e+00
   5_occ:  0.1152 0.1680   5.180915e+00   5.438799e+00
   5_bss:  0.1152 0.1679   5.180507e+00   5.438508e+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:  0.358  29.729  -3.517   2.537  -0.076   0.000  -0.000  -0.000
   1_xyz:  0.358  29.729  -3.517   2.537  -0.076   0.000  -0.000  -0.000
   1_adp:  0.358  29.729  -3.517   2.537  -0.076   0.000  -0.000  -0.000
   1_occ:  0.358  29.729  -3.517   2.537  -0.076   0.000  -0.000  -0.000
   2_bss:  0.354  54.621  -1.441   0.786  -0.157   0.000  -0.000  -0.000
   2_xyz:  0.354  54.621  -1.441   0.786  -0.157   0.000  -0.000  -0.000
   2_adp:  0.354  54.621  -1.441   0.786  -0.157   0.000  -0.000  -0.000
   2_occ:  0.354  54.621  -1.441   0.786  -0.157   0.000  -0.000  -0.000
   3_bss:  0.340  49.877  -0.942   0.209  -0.045   0.000  -0.000  -0.000
   3_xyz:  0.340  49.877  -0.942   0.209  -0.045   0.000  -0.000  -0.000
   3_adp:  0.340  49.877  -0.942   0.209  -0.045   0.000  -0.000  -0.000
   3_occ:  0.340  49.877  -0.942   0.209  -0.045   0.000  -0.000  -0.000
   4_bss:  0.325  44.577  -1.493  -1.212  -0.567  -0.000  -0.000  -0.000
   4_xyz:  0.325  44.577  -1.493  -1.212  -0.567  -0.000  -0.000  -0.000
   4_adp:  0.325  44.577  -1.493  -1.212  -0.567  -0.000  -0.000  -0.000
   4_occ:  0.325  44.577  -1.493  -1.212  -0.567  -0.000  -0.000  -0.000
   5_bss:  0.325  44.577  -1.745  -1.792  -0.798  -0.000  -0.000  -0.000
   5_xyz:  0.325  44.577  -1.745  -1.792  -0.798  -0.000  -0.000  -0.000
   5_adp:  0.325  44.577  -1.745  -1.792  -0.798  -0.000  -0.000  -0.000
   5_occ:  0.325  44.577  -1.745  -1.792  -0.798  -0.000  -0.000  -0.000
   5_bss:  0.319  44.070  -1.675  -1.803  -0.706  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.094 0.4707  0.6505    68196.438
   1_bss:  53.028 0.4829  0.6595    64223.759
   1_xyz:  43.830 0.5967  0.7926    45568.544
   1_adp:  44.709 0.5855  0.7765    47436.538
   1_occ:  44.692 0.5858  0.7764    47470.551
   2_bss:  44.446 0.5887  0.7865    47236.133
   2_xyz:  38.749 0.6570  0.8668    36776.083
   2_adp:  37.522 0.6718  0.8721    35205.750
   2_occ:  37.555 0.6714  0.8714    35213.800
   3_bss:  37.451 0.6725  0.8729    34998.319
   3_xyz:  27.836 0.7811  0.9811    19978.401
   3_adp:  24.338 0.8188  0.9966    15929.834
   3_occ:  24.251 0.8197  0.9970    15808.922
   4_bss:  24.036 0.8215  0.9688    15422.285
   4_xyz:  19.311 0.8677  0.9963    10321.816
   4_adp:  17.971 0.8809  0.9948     9391.544
   4_occ:  17.946 0.8811  0.9945     9352.936
   5_bss:  17.912 0.8814  0.9816     9322.918
   5_xyz:  15.535 0.9018  0.9930     7362.594
   5_adp:  15.051 0.9063  0.9895     7123.324
   5_occ:  15.036 0.9064  0.9894     7107.329
   5_bss:  15.028 0.9065  0.9914     7099.908
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.107   1.9062e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.107   1.9062e-01
   1_xyz:   1.712  0.014  0.116 16.022  0.007  4.103   1.5235e-01
   1_adp:   1.712  0.014  0.116 16.022  0.007  4.103   1.5235e-01
   1_occ:   1.712  0.014  0.116 16.022  0.007  4.103   1.5235e-01
   2_bss:   1.712  0.014  0.116 16.022  0.007  4.103   1.5235e-01
   2_xyz:   1.082  0.007  0.073 14.453  0.004  4.103   6.9362e-02
   2_adp:   1.082  0.007  0.073 14.453  0.004  4.103   6.9362e-02
   2_occ:   1.082  0.007  0.073 14.453  0.004  4.103   6.9362e-02
   3_bss:   1.082  0.007  0.073 14.453  0.004  4.103   6.9362e-02
   3_xyz:   1.297  0.011  0.085 14.971  0.005  4.107   9.3307e-02
   3_adp:   1.297  0.011  0.085 14.971  0.005  4.107   9.3307e-02
   3_occ:   1.297  0.011  0.085 14.971  0.005  4.107   9.3307e-02
   4_bss:   1.297  0.011  0.085 14.971  0.005  4.107   9.3307e-02
   4_xyz:   0.996  0.006  0.069 14.433  0.004  4.107   5.8787e-02
   4_adp:   0.996  0.006  0.069 14.433  0.004  4.107   5.8787e-02
   4_occ:   0.996  0.006  0.069 14.433  0.004  4.107   5.8787e-02
   5_bss:   0.996  0.006  0.069 14.433  0.004  4.107   5.8787e-02
   5_xyz:   1.094  0.008  0.076 14.709  0.005  4.110   6.8759e-02
   5_adp:   1.094  0.008  0.076 14.709  0.005  4.110   6.8759e-02
   5_occ:   1.094  0.008  0.076 14.709  0.005  4.110   6.8759e-02
   5_bss:   1.094  0.008  0.076 14.709  0.005  4.110   6.8759e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.661   2.3764e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.661   2.3764e-01
   1_xyz:   9.505  0.096  0.506 84.944  0.048  2.051   1.2389e-01
   1_adp:   9.505  0.096  0.506 84.944  0.048  2.051   1.2389e-01
   1_occ:   9.505  0.096  0.506 84.944  0.048  2.051   1.2389e-01
   2_bss:   9.505  0.096  0.506 84.944  0.048  2.051   1.2389e-01
   2_xyz:   8.030  0.079  0.293 82.464  0.031  2.211   1.1967e-01
   2_adp:   8.030  0.079  0.293 82.464  0.031  2.211   1.1967e-01
   2_occ:   8.030  0.079  0.293 82.464  0.031  2.211   1.1967e-01
   3_bss:   8.030  0.079  0.293 82.464  0.031  2.211   1.1967e-01
   3_xyz:   9.544  0.064  0.317 82.473  0.026  2.165   8.6227e-02
   3_adp:   9.544  0.064  0.317 82.473  0.026  2.165   8.6227e-02
   3_occ:   9.544  0.064  0.317 82.473  0.026  2.165   8.6227e-02
   4_bss:   9.544  0.064  0.317 82.473  0.026  2.165   8.6227e-02
   4_xyz:   8.383  0.050  0.230 80.328  0.035  2.259   5.3190e-02
   4_adp:   8.383  0.050  0.230 80.328  0.035  2.259   5.3190e-02
   4_occ:   8.383  0.050  0.230 80.328  0.035  2.259   5.3190e-02
   5_bss:   8.383  0.050  0.230 80.328  0.035  2.259   5.3190e-02
   5_xyz:   7.575  0.042  0.233 82.476  0.036  2.261   6.3310e-02
   5_adp:   7.575  0.042  0.233 82.476  0.036  2.261   6.3310e-02
   5_occ:   7.575  0.042  0.233 82.476  0.036  2.261   6.3310e-02
   5_bss:   7.575  0.042  0.233 82.476  0.036  2.261   6.3310e-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:  92.09   0.00  18.33  89.78   0.00  15.23  92.09   0.00  35.22
   1_occ:  92.09   0.00  18.33  89.78   0.00  15.23  92.09   0.00  35.22
   2_bss:  92.09   0.00  18.33  89.78   0.00  15.23  92.09   0.00  35.22
   2_xyz:  92.09   0.00  18.33  89.78   0.00  15.23  92.09   0.00  35.22
   2_adp:  90.67   0.00  17.56  90.67   0.00  14.54  89.96   0.00  34.05
   2_occ:  90.67   0.00  17.56  90.67   0.00  14.54  89.96   0.00  34.05
   3_bss:  90.67   0.00  17.56  90.67   0.00  14.54  89.96   0.00  34.05
   3_xyz:  90.67   0.00  17.56  90.67   0.00  14.54  89.96   0.00  34.05
   3_adp:  91.85   0.00  17.19  91.85   0.00  13.02  86.79   4.83  39.92
   3_occ:  91.85   0.00  17.19  91.85   0.00  13.02  86.79   4.83  39.92
   4_bss:  91.85   0.00  17.19  91.85   0.00  13.02  86.79   4.83  39.92
   4_xyz:  91.85   0.00  17.19  91.85   0.00  13.02  86.79   4.83  39.92
   4_adp:  92.92   0.39  16.99  92.92   0.39  12.46  84.50   4.73  41.65
   4_occ:  92.92   0.39  16.99  92.92   0.39  12.46  84.50   4.73  41.65
   5_bss:  92.92   0.39  16.99  92.92   0.39  12.46  84.50   4.73  41.65
   5_xyz:  92.92   0.39  16.99  92.92   0.39  12.46  84.50   4.73  41.65
   5_adp:  99.97   0.00  17.05  99.97   0.00  12.27  87.91   4.64  43.11
   5_occ:  99.97   0.00  17.05  99.97   0.00  12.27  87.91   4.64  43.11
   5_bss:  99.97   0.00  17.06  99.97   0.00  12.27  87.91   4.65  43.11
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.646    0.020    0.411
   1_adp:    1.646    0.020    0.411
   1_occ:    1.646    0.020    0.411
   2_bss:    1.646    0.020    0.411
   2_xyz:    1.430    0.057    0.478
   2_adp:    1.430    0.057    0.478
   2_occ:    1.430    0.057    0.478
   3_bss:    1.430    0.057    0.478
   3_xyz:    1.649    0.035    0.704
   3_adp:    1.649    0.035    0.704
   3_occ:    1.649    0.035    0.704
   4_bss:    1.649    0.035    0.704
   4_xyz:    1.621    0.028    0.779
   4_adp:    1.621    0.028    0.779
   4_occ:    1.621    0.028    0.779
   5_bss:    1.621    0.028    0.779
   5_xyz:    1.615    0.071    0.823
   5_adp:    1.615    0.071    0.823
   5_occ:    1.615    0.071    0.823
   5_bss:    1.615    0.071    0.823
------------------------------------------------------------------------

CPU time actual refinement: 336.67


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_486/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_486/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_486/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_486/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_486/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.52 
  Macro-tasks:
    bulk solvent and scale       = 38.31  
    individual site refinement   = 144.19 
    weights calculation          = 29.50  
    collect and process          = 6.47   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 218.59 
  Micro-tasks:
    mask                            = 2.43   
    f_calc                          = 107.89 
    alpha_beta                      = 8.17   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 117.91 
    fmodel                         = 6.33   
    r_factors                      = 0.24   
    phase_errors                   = 10.36  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 254.78 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.756 micro seconds
Total CPU time: 5.83 minutes
from_scatterers_fft:    640 calls, 107.64 s
gradients_fft:          585 calls, 104.25 s

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

# Date 2008-01-16 Time 04:56:10 PST -0800 (1200488170.09 s)
Start R-work = 0.4595, R-free = 0.4557 (no bulk solvent and anisotropic scale)
Final R-work = 0.1358, R-free = 0.1840 (no bulk solvent and anisotropic scale)

Start R-work = 0.4484, R-free = 0.4429
Final R-work = 0.1152, R-free = 0.1679