# Date 2008-01-16 Time 04:02:50 PST -0800 (1200484970.25 s)
#phil __OFF__

Command line arguments: "../153.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 22247
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 153

-------------------------------------------------------------------------------
  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: (68.845, 46.2261, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.2261, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9067 1.96088
Completeness in resolution range: 0.940061
Completeness with d_max=infinity: 0.937228

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9067
                             d_min =   1.9609

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.2261, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9067 1.96088
Completeness in resolution range: 0.940061
Completeness with d_max=infinity: 0.937228

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9071 -  4.1961 [2192/2217]  1969   223  10.2%
  bin  2:  4.1961 -  3.3429 [2110/2129]  1900   210  10.0%
  bin  3:  3.3429 -  2.9240 [2081/2100]  1879   202   9.7%
  bin  4:  2.9240 -  2.6583 [2049/2079]  1832   217  10.6%
  bin  5:  2.6583 -  2.4687 [2035/2054]  1835   200   9.8%
  bin  6:  2.4687 -  2.3237 [2043/2068]  1841   202   9.9%
  bin  7:  2.3237 -  2.2077 [2011/2039]  1814   197   9.8%
  bin  8:  2.2077 -  2.1119 [2036/2072]  1831   205  10.1%
  bin  9:  2.1119 -  2.0308 [1961/2037]  1767   194   9.9%
  bin 10:  2.0308 -  1.9609 [1071/2043]   962   109  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_153/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: 0.13 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:
        1.03 -     1.80: 9
        1.80 -     2.58: 83
        2.58 -     3.35: 4090
        3.35 -     4.13: 9495
        4.13 -     4.90: 14932
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.026 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.161 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.193 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  94 " - " NH1BARG A 145 "  1.657 3.120 -x+1,y+1/2,-z+1/2
  " NH1BARG A 145 " - " O   HOH Z  94 "  1.657 3.120 -x+1,y-1/2,-z+1/2
  ... (remaining 28604 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_153/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_153/model_refine_001.geo

CPU time processing inputs: 9.06


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 46.22605 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4789   r_free= 0.4757   ksol= 0.00   Bsol= 0.00   scale= 0.890    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.284329                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9071 -  4.6803 0.99   1421  157 0.3690 0.3574      6.5649      6.5027|
|  2:  4.6803 -  3.7341 0.99   1370  153 0.4064 0.4352      6.7795      6.8318|
|  3:  3.7341 -  3.2678 0.99   1337  151 0.4567 0.4418      6.6942      6.6971|
|  4:  3.2678 -  2.9716 0.99   1332  144 0.4791 0.5113      6.5301      6.5511|
|  5:  2.9716 -  2.7600 0.99   1334  147 0.5047 0.4470       6.354      6.3809|
|  6:  2.7600 -  2.5982 0.99   1321  149 0.5196 0.5249      6.2816      6.1886|
|  7:  2.5982 -  2.4687 0.99   1300  151 0.5124 0.4943      6.2333      6.1383|
|  8:  2.4687 -  2.3617 0.98   1324  146 0.5251 0.5353      6.1823      6.2123|
|  9:  2.3617 -  2.2711 0.98   1290  140 0.5373 0.5322      6.1236       6.187|
| 10:  2.2711 -  2.1929 0.99   1332  142 0.5376 0.5171      6.1041      6.0815|
| 11:  2.1929 -  2.1246 0.98   1257  146 0.5283 0.4947      6.0231      5.9905|
| 12:  2.1246 -  2.0640 0.97   1302  140 0.5359 0.5113      5.9783      6.0147|
| 13:  2.0640 -  2.0098 0.90   1169  128 0.5244 0.5603      5.8941      5.8083|
| 14:  2.0098 -  1.9609 0.41    541   65 0.5355 0.5043      5.8961       5.838|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9071 -  4.6803  1421   157  0.72  32.49   0.82     0.78      67337.34|
|  2:  4.6803 -  3.7341  1370   153  0.68  36.92   0.91     0.79     115203.45|
|  3:  3.7341 -  3.2678  1337   151  0.56  47.34   0.91     0.74     126158.86|
|  4:  3.2678 -  2.9716  1332   144  0.45  55.46   0.89     0.65     116064.05|
|  5:  2.9716 -  2.7600  1334   147  0.41  58.77   0.88     0.59      81959.16|
|  6:  2.7600 -  2.5982  1321   149  0.40  60.07   0.89     0.56      69249.13|
|  7:  2.5982 -  2.4687  1300   151  0.39  60.52   0.89     0.54      61371.45|
|  8:  2.4687 -  2.3617  1324   146  0.35  63.39   0.91     0.51      58058.90|
|  9:  2.3617 -  2.2711  1290   140  0.35  63.41   0.89     0.52      53443.38|
| 10:  2.2711 -  2.1929  1332   142  0.37  62.09   0.92     0.55      46896.96|
| 11:  2.1929 -  2.1246  1257   146  0.37  62.43   0.91     0.60      46714.66|
| 12:  2.1246 -  2.0640  1302   140  0.34  64.27   0.93     0.57      42713.16|
| 13:  2.0640 -  2.0098  1169   128  0.31  67.09   0.94     0.50      38629.61|
| 14:  2.0098 -  1.9609   541    65  0.30  67.28   0.98     0.43      30780.27|
|alpha:            min =        0.43 max =            0.79 mean =         0.60|
|beta:             min =    30780.27 max =       126158.86 mean =     70436.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.95 mean =        56.48|
|phase err.(test): min =        0.00 max =           89.79 mean =        56.37|
|-----------------------------------------------------------------------------|

============================== 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 = 10.493416             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.980   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.463820              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.139   (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 |  1.026 -  1.413:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.413 -  1.801:        6 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.801 -  2.188:       19 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.188 -  2.575:       64 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.575 -  2.963:     1713 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.963 -  3.350:     2377 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.350 -  3.738:     3893 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.738 -  4.125:     5602 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.125 -  4.513:     6589 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.513 -  4.900:     8343 |
|-----------------------------------------------------------------------------|
|-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 |        0.210 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.026 |       0.896 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.605)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4789   r_free= 0.4757   ksol= 0.00   Bsol= 0.00   scale= 0.890    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.284329                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4712   r_free= 0.4661   ksol= 0.31   Bsol= 20.05   scale= 0.940   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.27,0.36,3.96,0.00,0.00,0.00); trace/3= 1.02                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.278010                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.341434              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.729   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.279544              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.847   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4712      final r-factor (work) = 0.3742          |
| start r-factor (free) = 0.4661      final r-factor (free) = 0.4059          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.3740 = 8.34 * 0.50 * 6.2733 + 1.00 * 0.2097                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.8711 = 8.34 * 0.50 * 6.1721 + 1.00 * 0.1292                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3742      final r-factor (work) = 0.3439          |
| start r-factor (free) = 0.4059      final r-factor (free) = 0.4142          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9036 = 1.28 * 1.00 * 6.1721 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8250 = 1.28 * 1.00 * 6.0829 + 1.00 * 0.0417                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.605)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.28   17.94    None  None   None       |
|    all(noH): 2823   0      0.00    90.28   17.94    None  None   None       |
|    Sol.    : 438    0      0.00    64.58   36.50    None  None   None       |
|    Mac.    : 2385   0      0.00    90.28   14.53    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 -   9.028:  757   |   5:    45.139 -  54.167:   99        |
|      1:     9.028 -  18.056:  947   |   6:    54.167 -  63.195:   30        |
|      2:    18.056 -  27.083:  541   |   7:    63.195 -  72.222:    3        |
|      3:    27.083 -  36.111:  272   |   8:    72.222 -  81.250:    0        |
|      4:    36.111 -  45.139:  173   |   9:    81.250 -  90.278:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3439 r_free = 0.4142             target_work(ml) = 6.088         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3436 r_free = 0.4144             target_work(ml) = 6.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3436   r_free= 0.4144   ksol= 0.31   Bsol= 20.05   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.27,0.36,3.96,0.00,0.00,0.00); trace/3= 1.02                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.088078                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3427   r_free= 0.4134   ksol= 0.33   Bsol= 50.00   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.63,-0.36,2.33,-0.00,0.00,0.00); trace/3= 0.11                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.087956                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.571335              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.415   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.758931              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.752   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3427      final r-factor (work) = 0.2477          |
| start r-factor (free) = 0.4134      final r-factor (free) = 0.3060          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.2382 = 9.57 * 0.50 * 6.0826 + 1.00 * 0.1290                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.7079 = 9.57 * 0.50 * 5.9767 + 1.00 * 0.1056                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2477      final r-factor (work) = 0.2207          |
| start r-factor (free) = 0.3060      final r-factor (free) = 0.2894          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5555 = 0.76 * 1.00 * 5.9767 + 1.00 * 0.0196                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3964 = 0.76 * 1.00 * 5.7700 + 1.00 * 0.0173                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.605)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.09   18.35    None  None   None       |
|    all(noH): 2823   0      0.00    83.09   18.35    None  None   None       |
|    Sol.    : 438    0      3.16    83.09   42.00    None  None   None       |
|    Mac.    : 2385   0      0.00    75.38   14.01    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.309:  729   |   5:    41.543 -  49.852:  124        |
|      1:     8.309 -  16.617: 1017   |   6:    49.852 -  58.160:   81        |
|      2:    16.617 -  24.926:  439   |   7:    58.160 -  66.469:   63        |
|      3:    24.926 -  33.234:  204   |   8:    66.469 -  74.777:   19        |
|      4:    33.234 -  41.543:  140   |   9:    74.777 -  83.086:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2207 r_free = 0.2894             target_work(ml) = 5.741         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2205 r_free = 0.2893             target_work(ml) = 5.741         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2205   r_free= 0.2893   ksol= 0.33   Bsol= 50.00   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.63,-0.36,2.33,-0.00,0.00,0.00); trace/3= 0.11                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.740669                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2204   r_free= 0.2888   ksol= 0.32   Bsol= 50.00   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-1.08,1.24,-0.00,0.00,0.00); trace/3= -0.61                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.740411                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.991030              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.860   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.382410              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.410  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2204      final r-factor (work) = 0.1683          |
| start r-factor (free) = 0.2888      final r-factor (free) = 0.2307          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.5088 = 4.99 * 0.50 * 5.7717 + 1.00 * 0.1056                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.1439 = 4.99 * 0.50 * 5.6405 + 1.00 * 0.0680                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1683      final r-factor (work) = 0.1547          |
| start r-factor (free) = 0.2307      final r-factor (free) = 0.2128          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1725 = 0.38 * 1.00 * 5.6405 + 1.00 * 0.0155                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1035 = 0.38 * 1.00 * 5.4738 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.605)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.06   17.66    None  None   None       |
|    all(noH): 2823   0      0.00    88.06   17.66    None  None   None       |
|    Sol.    : 438    0      5.19    88.06   42.92    None  None   None       |
|    Mac.    : 2385   0      0.00    82.67   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 -   8.807:  809   |   5:    44.032 -  52.839:  101        |
|      1:     8.807 -  17.613: 1199   |   6:    52.839 -  61.645:   95        |
|      2:    17.613 -  26.419:  303   |   7:    61.645 -  70.451:   43        |
|      3:    26.419 -  35.226:  132   |   8:    70.451 -  79.258:   13        |
|      4:    35.226 -  44.032:  119   |   9:    79.258 -  88.064:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1547 r_free = 0.2128             target_work(ml) = 5.431         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1544 r_free = 0.2126             target_work(ml) = 5.430         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1544   r_free= 0.2126   ksol= 0.32   Bsol= 50.00   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-1.08,1.24,-0.00,0.00,0.00); trace/3= -0.61                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.429697                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1542   r_free= 0.2122   ksol= 0.33   Bsol= 58.50   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-1.95,0.28,-0.00,0.00,0.00); trace/3= -1.46                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.427238                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.118626              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.782  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.141897              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.424  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1542      final r-factor (work) = 0.1362          |
| start r-factor (free) = 0.2122      final r-factor (free) = 0.1851          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8709 = 2.12 * 0.50 * 5.4780 + 1.00 * 0.0680                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7529 = 2.12 * 0.50 * 5.3798 + 1.00 * 0.0540                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1362      final r-factor (work) = 0.1348          |
| start r-factor (free) = 0.1851      final r-factor (free) = 0.1794          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7736 = 0.14 * 1.00 * 5.3798 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7605 = 0.14 * 1.00 * 5.3048 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.605)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.42    85.38   16.90    None  None   None       |
|    all(noH): 2823   0      2.42    85.38   16.90    None  None   None       |
|    Sol.    : 438    0      5.69    85.38   39.95    None  None   None       |
|    Mac.    : 2385   0      2.42    85.19   12.67    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:     2.421 -  10.716: 1235   |   5:    43.900 -  52.195:  100        |
|      1:    10.716 -  19.012:  914   |   6:    52.195 -  60.491:   78        |
|      2:    19.012 -  27.308:  227   |   7:    60.491 -  68.787:   23        |
|      3:    27.308 -  35.604:  123   |   8:    68.787 -  77.083:   13        |
|      4:    35.604 -  43.900:  103   |   9:    77.083 -  85.379:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1348 r_free = 0.1794             target_work(ml) = 5.291         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1346 r_free = 0.1791             target_work(ml) = 5.290         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1346   r_free= 0.1791   ksol= 0.33   Bsol= 58.50   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-1.95,0.28,-0.00,0.00,0.00); trace/3= -1.46                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.290050                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1346   r_free= 0.1792   ksol= 0.32   Bsol= 50.89   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-2.18,0.04,-0.00,0.00,0.00); trace/3= -1.66                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.289977                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.737946              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 127.330  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.177069              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 165.154  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1346      final r-factor (work) = 0.1215          |
| start r-factor (free) = 0.1792      final r-factor (free) = 0.1665          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3152 = 2.74 * 0.50 * 5.3041 + 1.00 * 0.0540                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2484 = 2.74 * 0.50 * 5.2455 + 1.00 * 0.0674                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1215      final r-factor (work) = 0.1198          |
| start r-factor (free) = 0.1665      final r-factor (free) = 0.1654          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9366 = 0.18 * 1.00 * 5.2455 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9289 = 0.18 * 1.00 * 5.2026 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.605)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.19    86.04   16.64    None  None   None       |
|    all(noH): 2823   0      2.19    86.04   16.64    None  None   None       |
|    Sol.    : 438    0      5.93    84.87   39.20    None  None   None       |
|    Mac.    : 2385   0      2.19    86.04   12.49    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.194 -  10.579: 1223   |   5:    44.119 -  52.504:  106        |
|      1:    10.579 -  18.964:  944   |   6:    52.504 -  60.889:   69        |
|      2:    18.964 -  27.349:  218   |   7:    60.889 -  69.274:   22        |
|      3:    27.349 -  35.734:  127   |   8:    69.274 -  77.659:    8        |
|      4:    35.734 -  44.119:  100   |   9:    77.659 -  86.044:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1198 r_free = 0.1654             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1197 r_free = 0.1654             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1197   r_free= 0.1654   ksol= 0.32   Bsol= 50.89   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-2.18,0.04,-0.00,0.00,0.00); trace/3= -1.66                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.199693                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9071 -  4.6803 0.99   1421  157 0.1021 0.1358      5.4219      5.6072|
|  2:  4.6803 -  3.7341 0.99   1370  153 0.0891 0.1178       5.479      5.6825|
|  3:  3.7341 -  3.2678 0.99   1337  151 0.1154 0.1530      5.5389      5.8652|
|  4:  3.2678 -  2.9716 0.99   1332  144 0.1356 0.1706       5.512      5.6276|
|  5:  2.9716 -  2.7600 0.99   1334  147 0.1449 0.1726      5.4182      5.5907|
|  6:  2.7600 -  2.5982 0.99   1321  149 0.1358 0.2196      5.2888      5.5843|
|  7:  2.5982 -  2.4687 0.99   1300  151 0.1413 0.1824      5.2587      5.4187|
|  8:  2.4687 -  2.3617 0.98   1324  146 0.1296 0.1756      5.1562      5.3862|
|  9:  2.3617 -  2.2711 0.98   1290  140 0.1236 0.1899      5.0615      5.3768|
| 10:  2.2711 -  2.1929 0.99   1332  142 0.1190 0.1671      4.9911      5.1673|
| 11:  2.1929 -  2.1246 0.98   1257  146 0.1170 0.2050      4.9414      5.3552|
| 12:  2.1246 -  2.0640 0.97   1302  140 0.1232 0.1481      4.9195      5.1242|
| 13:  2.0640 -  2.0098 0.90   1169  128 0.1053 0.1715      4.7446      4.9734|
| 14:  2.0098 -  1.9609 0.41    541   65 0.0936 0.1627       4.611      4.9058|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9071 -  4.6803  1421   157  0.93   9.99   0.98     0.95       8085.14|
|  2:  4.6803 -  3.7341  1370   153  0.95   8.58   1.02     1.01      10004.89|
|  3:  3.7341 -  3.2678  1337   151  0.93  12.21   1.03     1.03      11414.28|
|  4:  3.2678 -  2.9716  1332   144  0.91  14.66   1.01     1.00      11117.09|
|  5:  2.9716 -  2.7600  1334   147  0.88  17.82   0.99     0.97      10143.49|
|  6:  2.7600 -  2.5982  1321   149  0.88  17.80   0.97     0.92       7949.27|
|  7:  2.5982 -  2.4687  1300   151  0.88  17.86   0.99     0.96       7600.91|
|  8:  2.4687 -  2.3617  1324   146  0.90  16.62   1.00     0.96       6213.73|
|  9:  2.3617 -  2.2711  1290   140  0.90  16.37   1.00     0.96       5276.72|
| 10:  2.2711 -  2.1929  1332   142  0.89  16.52   1.01     0.99       4734.77|
| 11:  2.1929 -  2.1246  1257   146  0.90  16.88   1.00     0.97       4545.05|
| 12:  2.1246 -  2.0640  1302   140  0.89  16.90   1.01     1.01       4251.42|
| 13:  2.0640 -  2.0098  1169   128  0.91  15.43   1.00     0.97       3127.32|
| 14:  2.0098 -  1.9609   541    65  0.94  12.07   0.99     0.96       2217.86|
|alpha:            min =        0.92 max =            1.03 mean =         0.98|
|beta:             min =     2217.86 max =        11414.28 mean =      7182.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.04|
|phase err.(test): min =        0.00 max =           89.97 mean =        14.49|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1197   r_free= 0.1654   ksol= 0.32   Bsol= 50.81   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-2.18,0.03,-0.00,-0.00,-0.00); trace/3= -1.64                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.198509                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1197   r_free= 0.1654   ksol= 0.32   Bsol= 50.81   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-2.18,0.03,-0.00,-0.00,-0.00); trace/3= -1.64                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.198509                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9071 -  4.6803 0.99   1421  157 0.1007 0.1355       5.409       5.593|
|  2:  4.6803 -  3.7341 0.99   1370  153 0.0891 0.1200      5.4789      5.6874|
|  3:  3.7341 -  3.2678 0.99   1337  151 0.1167 0.1526      5.5443      5.8636|
|  4:  3.2678 -  2.9716 0.99   1332  144 0.1356 0.1713      5.5127       5.632|
|  5:  2.9716 -  2.7600 0.99   1334  147 0.1447 0.1714      5.4172      5.5848|
|  6:  2.7600 -  2.5982 0.99   1321  149 0.1359 0.2183       5.287      5.5803|
|  7:  2.5982 -  2.4687 0.99   1300  151 0.1411 0.1835      5.2574      5.4195|
|  8:  2.4687 -  2.3617 0.98   1324  146 0.1296 0.1748      5.1556      5.3829|
|  9:  2.3617 -  2.2711 0.98   1290  140 0.1232 0.1902      5.0604      5.3788|
| 10:  2.2711 -  2.1929 0.99   1332  142 0.1188 0.1673      4.9911      5.1697|
| 11:  2.1929 -  2.1246 0.98   1257  146 0.1169 0.2043      4.9407      5.3528|
| 12:  2.1246 -  2.0640 0.97   1302  140 0.1229 0.1478      4.9188      5.1236|
| 13:  2.0640 -  2.0098 0.90   1169  128 0.1053 0.1718      4.7439      4.9742|
| 14:  2.0098 -  1.9609 0.41    541   65 0.0936 0.1623      4.6101      4.9044|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9071 -  4.6803  1421   157  0.93   9.86   0.98     0.95       8003.41|
|  2:  4.6803 -  3.7341  1370   153  0.95   8.55   1.02     1.01       9930.54|
|  3:  3.7341 -  3.2678  1337   151  0.93  12.25   1.03     1.03      11457.12|
|  4:  3.2678 -  2.9716  1332   144  0.91  14.68   1.01     1.00      11155.76|
|  5:  2.9716 -  2.7600  1334   147  0.88  17.78   0.99     0.96      10125.47|
|  6:  2.7600 -  2.5982  1321   149  0.88  17.74   0.97     0.92       7905.94|
|  7:  2.5982 -  2.4687  1300   151  0.89  17.82   0.99     0.96       7569.76|
|  8:  2.4687 -  2.3617  1324   146  0.90  16.61   1.00     0.96       6207.41|
|  9:  2.3617 -  2.2711  1290   140  0.90  16.37   1.00     0.95       5282.05|
| 10:  2.2711 -  2.1929  1332   142  0.89  16.54   1.01     0.98       4746.19|
| 11:  2.1929 -  2.1246  1257   146  0.90  16.87   1.00     0.96       4542.03|
| 12:  2.1246 -  2.0640  1302   140  0.89  16.89   1.01     1.01       4251.08|
| 13:  2.0640 -  2.0098  1169   128  0.91  15.41   0.99     0.97       3121.12|
| 14:  2.0098 -  1.9609   541    65  0.94  12.04   0.99     0.96       2212.66|
|alpha:            min =        0.92 max =            1.03 mean =         0.97|
|beta:             min =     2212.66 max =        11457.12 mean =      7169.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.02|
|phase err.(test): min =        0.00 max =           88.82 mean =        14.49|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.605)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.11    85.97   16.56    None  None   None       |
|    all(noH): 2823   0      2.11    85.97   16.56    None  None   None       |
|    Sol.    : 438    0      5.85    84.79   39.12    None  None   None       |
|    Mac.    : 2385   0      2.11    85.97   12.41    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:     2.115 -  10.500: 1223   |   5:    44.040 -  52.425:  106        |
|      1:    10.500 -  18.885:  944   |   6:    52.425 -  60.810:   69        |
|      2:    18.885 -  27.270:  218   |   7:    60.810 -  69.195:   22        |
|      3:    27.270 -  35.655:  127   |   8:    69.195 -  77.580:    8        |
|      4:    35.655 -  44.040:  100   |   9:    77.580 -  85.965:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 309         
Filter by distance & map next to the model:
   mapped sites are within: 0.575 - 4.549
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 304 from: 309
   mapped sites are within: 0.703 - 4.549

peak=    9.956 closest distance to " O   HOH Z 103 " =    1.368
peak=    6.278 closest distance to " O   HOH Z 403 " =    1.214
peak=    5.810 closest distance to " O   HOH Z 142 " =    1.912
peak=    5.479 closest distance to " OE1 GLN A  55 " =    2.263
peak=    5.419 closest distance to " O   HOH Z 417 " =    2.156
peak=    5.400 closest distance to " CG  PRO A  54 " =    1.359
peak=    5.270 closest distance to " NE2 GLN A  11 " =    1.198
peak=    5.264 closest distance to " O   HOH Z 375 " =    1.288
peak=    5.221 closest distance to " O   HOH Z   9 " =    1.822
peak=    5.196 closest distance to " CB  ARG A 275 " =    0.905
peak=    5.045 closest distance to " O   HOH Z  70 " =    1.138
peak=    4.940 closest distance to " O   HOH Z 112 " =    1.274
peak=    4.887 closest distance to " O   HOH Z 369 " =    2.086
peak=    4.880 closest distance to " O   HOH Z 117 " =    1.375
peak=    4.871 closest distance to " O   HOH Z  49 " =    1.145
peak=    4.866 closest distance to " O   HOH Z 287 " =    1.923
peak=    4.850 closest distance to " O   HOH Z  40 " =    1.684
peak=    4.806 closest distance to " NH2 ARG A  56 " =    2.106
peak=    4.760 closest distance to " CB  PRO A  54 " =    0.976
peak=    4.744 closest distance to " O   HOH Z 402 " =    1.508
peak=    4.691 closest distance to " O   SER A  87 " =    2.316
peak=    4.629 closest distance to " O   HOH Z  69 " =    1.274
peak=    4.628 closest distance to " O   HOH Z 126 " =    1.997
peak=    4.597 closest distance to " O   HOH Z 406 " =    1.816
peak=    4.558 closest distance to " CB  GLN A 223 " =    1.428
peak=    4.524 closest distance to " CB  ASN A 148 " =    1.524
peak=    4.520 closest distance to " O   HOH Z 232 " =    2.325
peak=    4.514 closest distance to " O   HOH Z 427 " =    2.659
peak=    4.466 closest distance to " O   HOH Z 403 " =    2.144
peak=    4.458 closest distance to " O   HOH Z 126 " =    1.592
peak=    4.436 closest distance to " CG2 VAL A 257 " =    0.883
peak=    4.391 closest distance to " CG  GLN A  58 " =    1.069
peak=    4.344 closest distance to " CD2 TRP A 179 " =    1.239
peak=    4.317 closest distance to " CB  ASN A 142 " =    0.992
peak=    4.310 closest distance to " CB  SER A  63 " =    1.219
peak=    4.293 closest distance to " CG  GLN A  11 " =    2.164
peak=    4.290 closest distance to " O   HOH Z 298 " =    1.923
peak=    4.269 closest distance to " O   HOH Z 419 " =    2.265
peak=    4.262 closest distance to " O   HOH Z 248 " =    1.604
peak=    4.253 closest distance to " O   HOH Z 380 " =    1.770
peak=    4.240 closest distance to " O   HOH Z 365 " =    2.608
peak=    4.237 closest distance to " CB  ARG A  79 " =    1.305
peak=    4.225 closest distance to " ND2 ASN A 187 " =    1.710
peak=    4.204 closest distance to " CB  GLU A 152 " =    1.213
peak=    4.202 closest distance to " O   HOH Z 236 " =    1.514
peak=    4.192 closest distance to " O   HOH Z 272 " =    1.849
peak=    4.174 closest distance to " CA  ARG A 195 " =    1.261
peak=    4.163 closest distance to " O   HOH Z  26 " =    1.367
peak=    4.146 closest distance to " O   HOH Z 389 " =    1.444
peak=    4.117 closest distance to " CG  TRP A 179 " =    2.203
peak=    4.077 closest distance to " O   HOH Z  30 " =    1.838
peak=    4.071 closest distance to " CE  LYS A 119 " =    1.332
peak=    4.053 closest distance to " O   HOH Z 132 " =    1.072
peak=    4.049 closest distance to " O   PRO A 198 " =    1.581
peak=    4.026 closest distance to " CB  PRO A  90 " =    1.098
peak=    4.009 closest distance to " CG2AVAL A 121 " =    2.451
peak=    3.994 closest distance to " O   HOH Z 425 " =    1.426
peak=    3.971 closest distance to " O   HOH Z 423 " =    1.386
peak=    3.967 closest distance to " O   HOH Z   1 " =    1.613
peak=    3.957 closest distance to " O   HOH Z 215 " =    1.533
peak=    3.955 closest distance to " CG  PRO A 243 " =    1.125
peak=    3.942 closest distance to " O   HOH Z 250 " =    1.455
peak=    3.929 closest distance to " O   HOH Z 234 " =    3.577
peak=    3.927 closest distance to " CB  VAL A 265 " =    1.365
peak=    3.925 closest distance to " CG AARG A 275 " =    1.254
peak=    3.897 closest distance to " O   HOH Z 405 " =    1.600
peak=    3.890 closest distance to " O   HOH Z  63 " =    1.378
peak=    3.890 closest distance to " O   HOH Z 185 " =    1.552
peak=    3.888 closest distance to " CB  ASN A 110 " =    1.017
peak=    3.878 closest distance to " NH2AARG A 190 " =    2.010
peak=    3.876 closest distance to " CA  TYR A  30 " =    1.024
peak=    3.873 closest distance to " CB  VAL A 202 " =    1.571
peak=    3.873 closest distance to " CG  PRO A 280 " =    0.778
peak=    3.863 closest distance to " O   HOH Z 362 " =    2.378
peak=    3.862 closest distance to " O   HOH Z   1 " =    1.962
peak=    3.861 closest distance to " CG  PRO A  90 " =    1.417
peak=    3.857 closest distance to " CZ  PHE A 218 " =    1.214
peak=    3.843 closest distance to " O   HOH Z 203 " =    1.701
peak=    3.839 closest distance to " NZ  LYS A 119 " =    2.498
peak=    3.829 closest distance to " O   HOH Z 214 " =    2.504
peak=    3.829 closest distance to " O   HOH Z  78 " =    1.571
peak=    3.812 closest distance to " O   HOH Z   7 " =    1.389
peak=    3.802 closest distance to " O   HOH Z  61 " =    1.626
peak=    3.792 closest distance to " O   HOH Z 305 " =    3.683
peak=    3.786 closest distance to " CB  GLN A 183 " =    1.131
peak=    3.763 closest distance to " NH1AARG A 145 " =    1.196
peak=    3.759 closest distance to " N   ASN A  39 " =    1.264
peak=    3.758 closest distance to " CA  VAL A 125 " =    1.050
peak=    3.754 closest distance to " O   HOH Z 371 " =    2.156
peak=    3.753 closest distance to " NZ  LYS A 117 " =    2.902
peak=    3.719 closest distance to " O   HOH Z 359 " =    1.608
peak=    3.717 closest distance to " O   HOH Z 368 " =    3.446
peak=    3.701 closest distance to " CD1 ILE A 199 " =    1.231
peak=    3.699 closest distance to " O   HOH Z 124 " =    1.185
peak=    3.699 closest distance to " O   HOH Z 261 " =    1.902
peak=    3.698 closest distance to " O   HOH Z 346 " =    1.575
peak=    3.695 closest distance to " CB  GLN A  88 " =    1.231
peak=    3.689 closest distance to " CB  ASP A 191 " =    1.132
peak=    3.686 closest distance to " CB  SER A  62 " =    0.815
peak=    3.682 closest distance to " CE  LYS A  76 " =    0.926
peak=    3.677 closest distance to " CG  LYS A  76 " =    1.699
peak=    3.673 closest distance to " O   HOH Z 368 " =    1.859
peak=    3.673 closest distance to " O   HOH Z 193 " =    1.557
peak=    3.672 closest distance to " CB  LEU A 300 " =    1.022
peak=    3.657 closest distance to " O   HOH Z 180 " =    2.266
peak=    3.649 closest distance to " CB  GLU A 277 " =    3.578
peak=    3.640 closest distance to " CB  ASN A 285 " =    1.032
peak=    3.637 closest distance to " O   HOH Z 394 " =    1.767
peak=    3.627 closest distance to " CG  PRO A 198 " =    1.367
peak=    3.626 closest distance to " CG  PRO A 213 " =    1.227
peak=    3.626 closest distance to " N   TYR A 116 " =    1.453
peak=    3.622 closest distance to " O   HOH Z  10 " =    1.797
peak=    3.607 closest distance to " CB  ASN A 187 " =    1.031
peak=    3.605 closest distance to " CA  ALA A  51 " =    0.964
peak=    3.599 closest distance to " CB  THR A  31 " =    1.552
peak=    3.599 closest distance to " CA  TYR A 116 " =    1.325
peak=    3.597 closest distance to " OG BSER A 164 " =    2.297
peak=    3.588 closest distance to " O   HOH Z 143 " =    1.427
peak=    3.586 closest distance to " O   HOH Z 251 " =    1.417
peak=    3.582 closest distance to " O   HOH Z 109 " =    1.598
peak=    3.581 closest distance to " O   HOH Z  71 " =    1.659
peak=    3.577 closest distance to " O   HOH Z 213 " =    2.156
peak=    3.574 closest distance to " O  BHOH Z  74 " =    1.301
peak=    3.574 closest distance to " O   HOH Z  59 " =    1.741
peak=    3.561 closest distance to " O   HOH Z 327 " =    1.643
peak=    3.560 closest distance to " O   HOH Z 148 " =    3.461
peak=    3.560 closest distance to " O   HOH Z 153 " =    3.786
peak=    3.556 closest distance to " CB  ALA A 160 " =    1.435
peak=    3.551 closest distance to " CB  ASN A  39 " =    0.844
peak=    3.549 closest distance to " O   HOH Z  43 " =    1.414
peak=    3.545 closest distance to " O   HOH Z  44 " =    1.774
peak=    3.544 closest distance to " CA  GLU A  46 " =    1.225
peak=    3.539 closest distance to " O   HOH Z 368 " =    4.303
peak=    3.537 closest distance to " CZ3 TRP A 266 " =    1.061
peak=    3.532 closest distance to " N   PHE A 130 " =    1.335
peak=    3.532 closest distance to " OD1 ASN A  69 " =    2.404
peak=    3.527 closest distance to " O   HOH Z 188 " =    2.581
peak=    3.527 closest distance to " CA  ASN A 127 " =    1.109
peak=    3.525 closest distance to " O   HOH Z 193 " =    1.751
peak=    3.525 closest distance to " O   HOH Z  88 " =    2.469
peak=    3.525 closest distance to " N   GLN A 278 " =    1.456
peak=    3.524 closest distance to " O   HOH Z 425 " =    1.841
peak=    3.520 closest distance to " O   HOH Z 216 " =    3.937
peak=    3.517 closest distance to " O   HOH Z 411 " =    3.956
peak=    3.512 closest distance to " O   HOH Z  80 " =    1.645
peak=    3.511 closest distance to " O   HOH Z 258 " =    1.150
peak=    3.510 closest distance to " CB  ARG A 156 " =    1.155
peak=    3.509 closest distance to " O   HOH Z 132 " =    2.231
peak=    3.507 closest distance to " CD  ARG A  66 " =    2.375
peak=    3.505 closest distance to " O   HOH Z  66 " =    2.262
peak=    3.497 closest distance to " NZ  LYS A 117 " =    1.340
peak=    3.496 closest distance to " O   HOH Z 415 " =    3.702
peak=    3.486 closest distance to " CB  ILE A 120 " =    1.273
peak=    3.484 closest distance to " CB  ARG A 190 " =    1.520
peak=    3.483 closest distance to " O   HOH Z 218 " =    1.673
peak=    3.483 closest distance to " CB  SER A 212 " =    1.358
peak=    3.480 closest distance to " O   HOH Z  97 " =    2.214
peak=    3.479 closest distance to " CE3 TRP A 150 " =    1.071
peak=    3.478 closest distance to " O   HOH Z 385 " =    3.940
peak=    3.476 closest distance to " CG2 ILE A  20 " =    1.638
peak=    3.472 closest distance to " CB  TRP A 266 " =    1.184
peak=    3.470 closest distance to " O   HOH Z 394 " =    3.720
peak=    3.463 closest distance to " CB  SER A 216 " =    0.882
peak=    3.459 closest distance to " CB  TRP A 179 " =    1.340
peak=    3.458 closest distance to " O   HOH Z 188 " =    1.510
peak=    3.447 closest distance to " CE BMET A  47 " =    0.803
peak=    3.445 closest distance to " OG ASER A 258 " =    2.938
peak=    3.445 closest distance to " O   HOH Z 422 " =    1.061
peak=    3.441 closest distance to " N   ASP A 162 " =    1.106
peak=    3.439 closest distance to " O   HOH Z 193 " =    1.653
peak=    3.436 closest distance to " CB  MET A  40 " =    0.798
peak=    3.436 closest distance to " NH1BARG A 145 " =    1.371
peak=    3.422 closest distance to " ND2 ASN A 249 " =    0.836
peak=    3.420 closest distance to " O   HOH Z  61 " =    1.667
peak=    3.417 closest distance to " O   HOH Z  40 " =    1.819
peak=    3.413 closest distance to " O   HOH Z  88 " =    2.556
peak=    3.412 closest distance to " CG1BVAL A  72 " =    1.540
peak=    3.406 closest distance to " O   HOH Z 191 " =    2.940
peak=    3.399 closest distance to " O   HOH Z 111 " =    1.560
peak=    3.396 closest distance to " OG1 THR A 264 " =    0.758
peak=    3.385 closest distance to " CG2 VAL A 197 " =    1.037
peak=    3.378 closest distance to " O   GLN A 194 " =    1.524
peak=    3.375 closest distance to " N   ALA A   1 " =    1.931
peak=    3.374 closest distance to " O   HOH Z 234 " =    4.385
peak=    3.371 closest distance to " CB  ARG A 219 " =    0.936
peak=    3.369 closest distance to " O   HOH Z 119 " =    4.250
peak=    3.369 closest distance to " O   HOH Z 422 " =    2.358
peak=    3.361 closest distance to " CA  ALA A 129 " =    1.450
peak=    3.357 closest distance to " CG  LYS A 119 " =    1.065
peak=    3.354 closest distance to " O   HOH Z 255 " =    1.762
peak=    3.349 closest distance to " CG  LEU A 167 " =    1.310
peak=    3.348 closest distance to " O   GLN A 240 " =    1.781
peak=    3.343 closest distance to " O   HOH Z 357 " =    2.016
peak=    3.343 closest distance to " CG  GLU A  37 " =    1.061
peak=    3.342 closest distance to " CB  PRO A 198 " =    1.248
peak=    3.340 closest distance to " O   ASN A  74 " =    1.393
peak=    3.339 closest distance to " O   HOH Z 438 " =    3.064
peak=    3.335 closest distance to " O   HOH Z 325 " =    2.359
peak=    3.330 closest distance to " O   HOH Z 207 " =    2.695
peak=    3.326 closest distance to " CB  ARG A 139 " =    1.317
peak=    3.324 closest distance to " CD  GLN A  77 " =    1.387
peak=    3.322 closest distance to " CB  SER A  99 " =    0.842
peak=    3.316 closest distance to " O   HOH Z 211 " =    1.043
peak=    3.314 closest distance to " O   HOH Z 369 " =    1.724
peak=    3.311 closest distance to " O   HOH Z 213 " =    1.984
peak=    3.307 closest distance to " O   HOH Z  78 " =    1.897
peak=    3.304 closest distance to " CG1 ILE A  49 " =    1.499
peak=    3.303 closest distance to " CA  ALA A 233 " =    1.092
peak=    3.296 closest distance to " O   HOH Z 124 " =    1.595
peak=    3.293 closest distance to " CA  ASN A 215 " =    0.949
peak=    3.288 closest distance to " CD  ARG A 159 " =    0.711
peak=    3.287 closest distance to " OE1 GLN A 223 " =    2.386
peak=    3.283 closest distance to " CA  ALA A 100 " =    1.052
peak=    3.282 closest distance to " O   TYR A 116 " =    1.332
peak=    3.278 closest distance to " CB  GLU A 128 " =    0.908
peak=    3.278 closest distance to " O   THR A 220 " =    1.262
peak=    3.275 closest distance to " O   HOH Z   2 " =    1.652
peak=    3.272 closest distance to " CB  ASP A 107 " =    1.188
peak=    3.269 closest distance to " CG2 ILE A 234 " =    0.966
peak=    3.269 closest distance to " CG2 ILE A 239 " =    0.703
peak=    3.267 closest distance to " O   HOH Z 158 " =    3.129
peak=    3.267 closest distance to " O   HOH Z  54 " =    1.696
peak=    3.267 closest distance to " O   PHE A 192 " =    1.439
peak=    3.265 closest distance to " O   HOH Z  48 " =    1.636
peak=    3.265 closest distance to " CA  ASP A 162 " =    1.039
peak=    3.260 closest distance to " O   HOH Z 116 " =    2.617
peak=    3.248 closest distance to " O   HOH Z 128 " =    1.833
peak=    3.246 closest distance to " CG BARG A 275 " =    1.674
peak=    3.245 closest distance to " O   HOH Z 421 " =    2.256
peak=    3.244 closest distance to " O   HOH Z   6 " =    1.660
peak=    3.244 closest distance to " CB  PHE A 130 " =    0.817
peak=    3.243 closest distance to " CD  ARG A 269 " =    0.880
peak=    3.242 closest distance to " O   HOH Z 287 " =    2.232
peak=    3.240 closest distance to " O   HOH Z  21 " =    1.733
peak=    3.240 closest distance to " O   HOH Z 173 " =    2.178
peak=    3.239 closest distance to " OG  SER A  62 " =    2.812
peak=    3.237 closest distance to " O   HOH Z  94 " =    2.269
peak=    3.235 closest distance to " O   HOH Z 435 " =    1.944
peak=    3.235 closest distance to " O   HOH Z  44 " =    2.657
peak=    3.232 closest distance to " CB  ASP A 140 " =    0.823
peak=    3.231 closest distance to " O   PRO A 198 " =    1.398
peak=    3.231 closest distance to " O   HOH Z  41 " =    2.600
peak=    3.228 closest distance to " CA  SER A  87 " =    0.990
peak=    3.228 closest distance to " CB  ASP A 124 " =    0.768
peak=    3.227 closest distance to " CB  ASN A 215 " =    1.038
peak=    3.224 closest distance to " O   HOH Z  28 " =    1.865
peak=    3.223 closest distance to " O   HOH Z 434 " =    1.364
peak=    3.220 closest distance to " CG1 VAL A 153 " =    0.956
peak=    3.211 closest distance to " CG2 ILE A 120 " =    1.481
peak=    3.207 closest distance to " CG  GLN A  73 " =    1.802
peak=    3.205 closest distance to " O   HOH Z 393 " =    1.558
peak=    3.200 closest distance to " O   HOH Z 281 " =    1.654
peak=    3.198 closest distance to " O   THR A 182 " =    1.459
peak=    3.196 closest distance to " O   HOH Z 184 " =    1.484
peak=    3.192 closest distance to " O   HOH Z 188 " =    2.029
peak=    3.191 closest distance to " O   HOH Z 298 " =    2.472
peak=    3.188 closest distance to " CB  ALA A 291 " =    1.174
peak=    3.185 closest distance to " ND1 HIS A  86 " =    1.723
peak=    3.184 closest distance to " O   HOH Z 303 " =    2.224
peak=    3.184 closest distance to " CE  LYS A 166 " =    1.869
peak=    3.183 closest distance to " O   HOH Z  41 " =    1.863
peak=    3.182 closest distance to " CG1 VAL A 202 " =    1.789
peak=    3.182 closest distance to " NH1 ARG A 138 " =    1.243
peak=    3.178 closest distance to " O   HOH Z 390 " =    2.555
peak=    3.175 closest distance to " CZ  PHE A  38 " =    1.203
peak=    3.170 closest distance to " O   ALA A 165 " =    1.452
peak=    3.164 closest distance to " N   TYR A  15 " =    1.136
peak=    3.158 closest distance to " CB  LEU A 228 " =    1.022
peak=    3.157 closest distance to " CD  LYS A 166 " =    1.168
peak=    3.156 closest distance to " O   HOH Z 194 " =    2.245
peak=    3.153 closest distance to " O   HOH Z 261 " =    1.871
peak=    3.146 closest distance to " CB  ALA A 114 " =    1.251
peak=    3.145 closest distance to " O   HOH Z 172 " =    2.655
peak=    3.145 closest distance to " CG  GLN A  77 " =    1.183
peak=    3.145 closest distance to " N   CYS A 260 " =    0.899
peak=    3.145 closest distance to " CB  LYS A 290 " =    0.882
peak=    3.144 closest distance to " NE2 GLN A  58 " =    4.549
peak=    3.138 closest distance to " CA  LYS A 117 " =    1.230
peak=    3.136 closest distance to " O   HOH Z 119 " =    1.763
peak=    3.132 closest distance to " NZ  LYS A  48 " =    1.108
peak=    3.132 closest distance to " CA  MET A 105 " =    0.895
peak=    3.128 closest distance to " O   HOH Z 154 " =    1.834
peak=    3.124 closest distance to " O   HOH Z 303 " =    1.612
peak=    3.124 closest distance to " O   HOH Z 128 " =    3.123
peak=    3.122 closest distance to " CG  MET A 113 " =    1.011
peak=    3.120 closest distance to " CB  SER A   3 " =    1.290
peak=    3.116 closest distance to " O   HOH Z 222 " =    1.426
peak=    3.116 closest distance to " CG2 THR A 221 " =    1.123
peak=    3.100 closest distance to " NH2AARG A 275 " =    3.649
peak=    3.094 closest distance to " CB  SER A 276 " =    1.214
peak=    3.093 closest distance to " O   HOH Z  60 " =    1.458
peak=    3.092 closest distance to " N   TYR A 247 " =    1.432
peak=    3.089 closest distance to " NH2 ARG A  56 " =    1.385
peak=    3.088 closest distance to " O   HOH Z 294 " =    1.518
peak=    3.084 closest distance to " O   HOH Z 156 " =    2.592
peak=    3.070 closest distance to " O   HOH Z 183 " =    1.718
peak=    3.054 closest distance to " O   HOH Z 407 " =    2.290
peak=    3.050 closest distance to " CB  TYR A 116 " =    0.961
peak=    3.048 closest distance to " O   HOH Z 298 " =    4.091
peak=    3.044 closest distance to " O   HOH Z 218 " =    1.696
peak=    3.040 closest distance to " CB  SER A  62 " =    1.192
peak=    3.037 closest distance to " CA  ASP A 149 " =    1.165
peak=    3.033 closest distance to " CE1 PHE A  61 " =    1.387
peak=    3.008 closest distance to " O   HOH Z 419 " =    2.233

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.587 - 5.876
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 199
   mapped sites are within: 0.703 - 5.876

peak=   -4.820 closest distance to " NE2 GLN A  55 " =    1.036
peak=   -4.807 closest distance to " CD  ARG A  14 " =    3.233
peak=   -4.773 closest distance to " O   HOH Z 211 " =    0.761
peak=   -4.573 closest distance to " O   PRO A 198 " =    1.234
peak=   -4.537 closest distance to " O   HOH Z 290 " =    0.941
peak=   -4.306 closest distance to " O   HOH Z 131 " =    3.972
peak=   -4.285 closest distance to " O   HOH Z 193 " =    0.883
peak=   -4.226 closest distance to " CZ2 TRP A  92 " =    2.826
peak=   -4.196 closest distance to " CG2 ILE A  20 " =    2.868
peak=   -4.145 closest distance to " O   HOH Z 387 " =    2.626
peak=   -4.125 closest distance to " O   HOH Z  69 " =    1.571
peak=   -4.095 closest distance to " CG  GLN A  88 " =    0.883
peak=   -4.093 closest distance to " CE  MET A 105 " =    2.576
peak=   -4.047 closest distance to " CD  GLU A 277 " =    1.182
peak=   -4.027 closest distance to " CG  GLN A  58 " =    0.918
peak=   -4.006 closest distance to " O   HOH Z 278 " =    0.889
peak=   -3.998 closest distance to " O   SER A  22 " =    2.527
peak=   -3.992 closest distance to " CB  ALA A  43 " =    2.349
peak=   -3.976 closest distance to " O   HOH Z  60 " =    1.527
peak=   -3.948 closest distance to " CD1 LEU A 101 " =    2.248
peak=   -3.942 closest distance to " O   HOH Z   5 " =    0.891
peak=   -3.935 closest distance to " C   HIS A 108 " =    1.138
peak=   -3.924 closest distance to " O   HOH Z 377 " =    2.129
peak=   -3.921 closest distance to " OG BSER A 134 " =    1.351
peak=   -3.915 closest distance to " CG2 THR A  18 " =    2.711
peak=   -3.914 closest distance to " O   HOH Z  26 " =    0.894
peak=   -3.896 closest distance to " CB  PHE A 192 " =    1.951
peak=   -3.876 closest distance to " O   HOH Z 109 " =    0.703
peak=   -3.860 closest distance to " CA  GLY A 241 " =    2.304
peak=   -3.837 closest distance to " CD1 LEU A 255 " =    2.807
peak=   -3.820 closest distance to " CD2 TYR A 293 " =    1.998
peak=   -3.810 closest distance to " CG1 VAL A 112 " =    3.032
peak=   -3.797 closest distance to " O   HOH Z 298 " =    2.501
peak=   -3.792 closest distance to " O   HOH Z 421 " =    2.946
peak=   -3.775 closest distance to " O   ALA A  10 " =    1.604
peak=   -3.753 closest distance to " O   HOH Z  24 " =    1.195
peak=   -3.739 closest distance to " OD2 ASP A 191 " =    1.372
peak=   -3.735 closest distance to " CD  ARG A 156 " =    2.158
peak=   -3.722 closest distance to " CD2 LEU A 237 " =    2.734
peak=   -3.720 closest distance to " O   VAL A  67 " =    2.617
peak=   -3.717 closest distance to " O   HOH Z 313 " =    1.843
peak=   -3.709 closest distance to " CB  GLN A  11 " =    1.743
peak=   -3.706 closest distance to " CB  ALA A 114 " =    2.546
peak=   -3.703 closest distance to " O   SER A 210 " =    1.887
peak=   -3.661 closest distance to " O   HOH Z 372 " =    2.431
peak=   -3.660 closest distance to " OD1 ASP A 171 " =    1.594
peak=   -3.654 closest distance to " O   HOH Z 359 " =    3.228
peak=   -3.645 closest distance to " O   HOH Z 351 " =    1.513
peak=   -3.641 closest distance to " OD1 ASN A 187 " =    1.532
peak=   -3.639 closest distance to " SG BCYS A 201 " =    2.082
peak=   -3.618 closest distance to " CG  GLN A  55 " =    1.266
peak=   -3.603 closest distance to " NZ  LYS A 119 " =    0.857
peak=   -3.598 closest distance to " O   GLU A 152 " =    1.357
peak=   -3.568 closest distance to " O   HOH Z 165 " =    2.212
peak=   -3.565 closest distance to " O   HOH Z 362 " =    5.876
peak=   -3.563 closest distance to " C   ALA A 114 " =    2.281
peak=   -3.549 closest distance to " O   HOH Z  15 " =    1.429
peak=   -3.544 closest distance to " O   HOH Z 414 " =    1.278
peak=   -3.539 closest distance to " O   HOH Z 140 " =    1.134
peak=   -3.535 closest distance to " O   PRO A 198 " =    1.285
peak=   -3.533 closest distance to " CZ2 TRP A 274 " =    0.977
peak=   -3.531 closest distance to " O   HOH Z 187 " =    1.711
peak=   -3.526 closest distance to " CB  ALA A 291 " =    2.174
peak=   -3.522 closest distance to " CA  GLY A 133 " =    2.004
peak=   -3.519 closest distance to " CB  ASN A  39 " =    2.434
peak=   -3.514 closest distance to " CD  GLU A 152 " =    0.776
peak=   -3.511 closest distance to " CE BMET A  47 " =    1.318
peak=   -3.503 closest distance to " NE2 GLN A 278 " =    1.372
peak=   -3.497 closest distance to " O   GLN A 240 " =    2.079
peak=   -3.496 closest distance to " O   HOH Z 219 " =    4.350
peak=   -3.489 closest distance to " CG1 VAL A 265 " =    2.752
peak=   -3.487 closest distance to " O   PRO A 243 " =    2.540
peak=   -3.482 closest distance to " C   GLN A  58 " =    1.978
peak=   -3.473 closest distance to " ND2 ASN A 285 " =    2.124
peak=   -3.463 closest distance to " CG  MET A 105 " =    1.008
peak=   -3.463 closest distance to " OE1 GLN A 183 " =    1.624
peak=   -3.459 closest distance to " O   ALA A 161 " =    1.781
peak=   -3.454 closest distance to " O   HOH Z 139 " =    4.867
peak=   -3.447 closest distance to " O   HOH Z  70 " =    0.945
peak=   -3.446 closest distance to " CB  ASP A 132 " =    2.423
peak=   -3.438 closest distance to " O   HOH Z 374 " =    1.744
peak=   -3.431 closest distance to " O   HOH Z 429 " =    1.836
peak=   -3.427 closest distance to " CD2 PHE A  61 " =    2.360
peak=   -3.422 closest distance to " O   HOH Z  71 " =    0.986
peak=   -3.412 closest distance to " O   LYS A  76 " =    2.099
peak=   -3.412 closest distance to " O   HOH Z 281 " =    3.122
peak=   -3.407 closest distance to " O   HOH Z  91 " =    1.742
peak=   -3.407 closest distance to " CZ  TYR A 169 " =    1.817
peak=   -3.403 closest distance to " OXT GLY A 302 " =    3.111
peak=   -3.391 closest distance to " CB  ASN A  45 " =    1.974
peak=   -3.381 closest distance to " O   HOH Z 174 " =    2.577
peak=   -3.381 closest distance to " O   HOH Z 185 " =    2.038
peak=   -3.377 closest distance to " O   HOH Z 428 " =    2.785
peak=   -3.372 closest distance to " CD1 ILE A 199 " =    2.452
peak=   -3.371 closest distance to " O   HOH Z   5 " =    0.978
peak=   -3.362 closest distance to " O   VAL A 174 " =    2.259
peak=   -3.361 closest distance to " CG2 THR A  42 " =    1.937
peak=   -3.357 closest distance to " ND2 ASN A 249 " =    2.216
peak=   -3.347 closest distance to " O   HOH Z 385 " =    1.837
peak=   -3.347 closest distance to " CA  GLY A  57 " =    2.143
peak=   -3.340 closest distance to " CG1 VAL A 126 " =    2.469
peak=   -3.338 closest distance to " O   HOH Z 171 " =    1.279
peak=   -3.338 closest distance to " O   HOH Z   9 " =    2.619
peak=   -3.336 closest distance to " O   ALA A 227 " =    1.543
peak=   -3.336 closest distance to " O   HOH Z 286 " =    1.742
peak=   -3.335 closest distance to " O   HOH Z 116 " =    1.848
peak=   -3.334 closest distance to " O   HOH Z 276 " =    1.622
peak=   -3.313 closest distance to " OG  SER A  87 " =    1.380
peak=   -3.312 closest distance to " O   VAL A 189 " =    2.622
peak=   -3.310 closest distance to " O   HOH Z 331 " =    0.784
peak=   -3.308 closest distance to " O   HOH Z 100 " =    0.868
peak=   -3.306 closest distance to " O   HOH Z 103 " =    1.097
peak=   -3.306 closest distance to " O   HOH Z  20 " =    1.361
peak=   -3.304 closest distance to " CB  ALA A 158 " =    1.608
peak=   -3.301 closest distance to " O   HOH Z   5 " =    1.499
peak=   -3.299 closest distance to " O   ASN A 187 " =    1.541
peak=   -3.296 closest distance to " ND2 ASN A  45 " =    2.056
peak=   -3.296 closest distance to " CD2 PHE A 225 " =    1.106
peak=   -3.296 closest distance to " O   HOH Z 134 " =    3.987
peak=   -3.289 closest distance to " O   PRO A 163 " =    1.786
peak=   -3.287 closest distance to " OH  TYR A 172 " =    1.909
peak=   -3.274 closest distance to " O   HOH Z  63 " =    2.159
peak=   -3.274 closest distance to " CG1 VAL A 230 " =    2.088
peak=   -3.267 closest distance to " OD1 ASP A 191 " =    1.699
peak=   -3.266 closest distance to " O   HOH Z  39 " =    1.268
peak=   -3.261 closest distance to " CB  ASP A  27 " =    2.389
peak=   -3.258 closest distance to " CB  SER A 210 " =    1.167
peak=   -3.258 closest distance to " O   LEU A 167 " =    1.459
peak=   -3.254 closest distance to " O   HOH Z 394 " =    1.546
peak=   -3.251 closest distance to " O   HOH Z 136 " =    0.795
peak=   -3.250 closest distance to " O   HOH Z 369 " =    2.281
peak=   -3.241 closest distance to " O   HOH Z  97 " =    1.116
peak=   -3.236 closest distance to " O   HOH Z 266 " =    5.446
peak=   -3.235 closest distance to " O   HOH Z  37 " =    1.363
peak=   -3.233 closest distance to " N   ALA A 226 " =    1.984
peak=   -3.233 closest distance to " CB  ALA A 161 " =    2.341
peak=   -3.231 closest distance to " O   HOH Z  64 " =    1.196
peak=   -3.230 closest distance to " O   HOH Z 216 " =    1.255
peak=   -3.225 closest distance to " CZ3 TRP A 179 " =    1.232
peak=   -3.224 closest distance to " OG  SER A  97 " =    2.298
peak=   -3.220 closest distance to " CD2 PHE A  61 " =    2.646
peak=   -3.220 closest distance to " ND2 ASN A 187 " =    1.439
peak=   -3.219 closest distance to " O   SER A 135 " =    1.496
peak=   -3.218 closest distance to " O   HOH Z 103 " =    1.306
peak=   -3.214 closest distance to " C   ARG A 195 " =    1.706
peak=   -3.212 closest distance to " O   ASP A  27 " =    1.584
peak=   -3.209 closest distance to " CD  PRO A 213 " =    2.046
peak=   -3.208 closest distance to " CA  ASP A 298 " =    1.137
peak=   -3.205 closest distance to " O   HOH Z 179 " =    2.086
peak=   -3.204 closest distance to " CE  LYS A  76 " =    2.786
peak=   -3.203 closest distance to " O   TRP A  70 " =    1.464
peak=   -3.202 closest distance to " O   HOH Z 412 " =    0.834
peak=   -3.198 closest distance to " C   HIS A 207 " =    1.222
peak=   -3.193 closest distance to " O   ASN A 249 " =    1.638
peak=   -3.193 closest distance to " CD  GLN A  77 " =    1.092
peak=   -3.192 closest distance to " O   HOH Z 348 " =    2.191
peak=   -3.191 closest distance to " CA  GLY A  98 " =    1.720
peak=   -3.188 closest distance to " CG  ARG A 219 " =    2.592
peak=   -3.184 closest distance to " NZ  LYS A 166 " =    1.052
peak=   -3.182 closest distance to " N   SER A 276 " =    1.370
peak=   -3.174 closest distance to " O   HOH Z 389 " =    1.313
peak=   -3.173 closest distance to " ND2 ASN A  45 " =    1.302
peak=   -3.172 closest distance to " CG1 VAL A 250 " =    2.725
peak=   -3.164 closest distance to " O   HOH Z 236 " =    1.502
peak=   -3.162 closest distance to " N   ALA A  43 " =    2.441
peak=   -3.161 closest distance to " O   HOH Z  20 " =    1.615
peak=   -3.159 closest distance to " O   HOH Z 126 " =    1.801
peak=   -3.158 closest distance to " O   HOH Z 137 " =    1.453
peak=   -3.155 closest distance to " C   VAL A 265 " =    0.831
peak=   -3.153 closest distance to " O   HOH Z 113 " =    1.499
peak=   -3.149 closest distance to " O   SER A 276 " =    1.677
peak=   -3.144 closest distance to " OE1 GLN A 223 " =    2.248
peak=   -3.143 closest distance to " CB  PRO A 163 " =    2.601
peak=   -3.140 closest distance to " O   HOH Z  49 " =    1.115
peak=   -3.137 closest distance to " CB  PHE A  59 " =    2.173
peak=   -3.133 closest distance to " C   ARG A 269 " =    1.414
peak=   -3.133 closest distance to " CE2 TYR A  30 " =    2.705
peak=   -3.125 closest distance to " O   HOH Z 137 " =    1.460
peak=   -3.123 closest distance to " OD1 ASN A 173 " =    1.317
peak=   -3.119 closest distance to " CG2 VAL A 296 " =    1.972
peak=   -3.119 closest distance to " CE3 TRP A 274 " =    2.422
peak=   -3.115 closest distance to " CB  TRP A  85 " =    2.507
peak=   -3.112 closest distance to " O   HOH Z 281 " =    1.117
peak=   -3.104 closest distance to " NH2 ARG A  79 " =    2.254
peak=   -3.101 closest distance to " O   HOH Z 166 " =    1.814
peak=   -3.089 closest distance to " O   HOH Z 397 " =    1.177
peak=   -3.075 closest distance to " O   HOH Z 438 " =    1.182
peak=   -3.071 closest distance to " O   PHE A 218 " =    1.769
peak=   -3.064 closest distance to " C   ASN A 285 " =    2.066
peak=   -3.052 closest distance to " CZ  PHE A  59 " =    1.512
peak=   -3.039 closest distance to " O   HOH Z  51 " =    1.065
peak=   -3.038 closest distance to " O   HOH Z  11 " =    1.599
peak=   -3.033 closest distance to " O   GLN A  77 " =    1.836

================= 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    :  0.4789 0.4757   6.284329e+00   6.270618e+00
   1_bss:  0.4712 0.4661   6.278010e+00   6.259616e+00
   1_xyz:  0.3742 0.4059   6.128574e+00   6.175836e+00
   1_adp:  0.3439 0.4142   6.088103e+00   6.185395e+00
   1_occ:  0.3436 0.4144   6.088078e+00   6.185941e+00
   2_bss:  0.3427 0.4134   6.087956e+00   6.186304e+00
   2_xyz:  0.2477 0.3060   5.819277e+00   5.984773e+00
   2_adp:  0.2207 0.2894   5.741072e+00   5.931680e+00
   2_occ:  0.2205 0.2893   5.740669e+00   5.931347e+00
   3_bss:  0.2204 0.2888   5.740411e+00   5.930863e+00
   3_xyz:  0.1683 0.2307   5.508915e+00   5.732773e+00
   3_adp:  0.1547 0.2128   5.430536e+00   5.656610e+00
   3_occ:  0.1544 0.2126   5.429697e+00   5.655763e+00
   4_bss:  0.1542 0.2122   5.427238e+00   5.654066e+00
   4_xyz:  0.1362 0.1851   5.307789e+00   5.530663e+00
   4_adp:  0.1348 0.1794   5.290692e+00   5.503767e+00
   4_occ:  0.1346 0.1791   5.290050e+00   5.503302e+00
   5_bss:  0.1346 0.1792   5.289977e+00   5.503158e+00
   5_xyz:  0.1215 0.1665   5.209554e+00   5.439258e+00
   5_adp:  0.1198 0.1654   5.200334e+00   5.434773e+00
   5_occ:  0.1197 0.1654   5.199693e+00   5.434141e+00
   5_bss:  0.1197 0.1654   5.198509e+00   5.432769e+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:  0.314  20.051  -1.271   0.360   3.962   0.000   0.000   0.000
   1_xyz:  0.314  20.051  -1.271   0.360   3.962   0.000   0.000   0.000
   1_adp:  0.314  20.051  -1.271   0.360   3.962   0.000   0.000   0.000
   1_occ:  0.314  20.051  -1.271   0.360   3.962   0.000   0.000   0.000
   2_bss:  0.333  50.000  -1.627  -0.364   2.331  -0.000   0.000   0.000
   2_xyz:  0.333  50.000  -1.627  -0.364   2.331  -0.000   0.000   0.000
   2_adp:  0.333  50.000  -1.627  -0.364   2.331  -0.000   0.000   0.000
   2_occ:  0.333  50.000  -1.627  -0.364   2.331  -0.000   0.000   0.000
   3_bss:  0.325  50.000  -1.994  -1.080   1.244  -0.000   0.000   0.000
   3_xyz:  0.325  50.000  -1.994  -1.080   1.244  -0.000   0.000   0.000
   3_adp:  0.325  50.000  -1.994  -1.080   1.244  -0.000   0.000   0.000
   3_occ:  0.325  50.000  -1.994  -1.080   1.244  -0.000   0.000   0.000
   4_bss:  0.327  58.495  -2.699  -1.954   0.276  -0.000   0.000   0.000
   4_xyz:  0.327  58.495  -2.699  -1.954   0.276  -0.000   0.000   0.000
   4_adp:  0.327  58.495  -2.699  -1.954   0.276  -0.000   0.000   0.000
   4_occ:  0.327  58.495  -2.699  -1.954   0.276  -0.000   0.000   0.000
   5_bss:  0.323  50.891  -2.829  -2.183   0.037  -0.000   0.000   0.000
   5_xyz:  0.323  50.891  -2.829  -2.183   0.037  -0.000   0.000   0.000
   5_adp:  0.323  50.891  -2.829  -2.183   0.037  -0.000   0.000   0.000
   5_occ:  0.323  50.891  -2.829  -2.183   0.037  -0.000   0.000   0.000
   5_bss:  0.323  50.812  -2.763  -2.179   0.035  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.470 0.4396  0.6047    70435.502
   1_bss:  55.033 0.4569  0.6545    67223.606
   1_xyz:  44.895 0.5833  0.8057    47157.214
   1_adp:  46.089 0.5678  0.7892    49013.547
   1_occ:  46.175 0.5668  0.7876    49168.570
   2_bss:  45.990 0.5689  0.7688    48803.259
   2_xyz:  32.264 0.7311  0.9522    25261.108
   2_adp:  29.467 0.7632  0.9657    22127.788
   2_occ:  29.469 0.7632  0.9656    22127.298
   3_bss:  29.374 0.7642  0.9418    22018.613
   3_xyz:  22.708 0.8343  0.9947    13680.208
   3_adp:  20.406 0.8577  0.9973    11750.717
   3_occ:  20.391 0.8578  0.9974    11734.748
   4_bss:  20.282 0.8587  0.9684    11632.214
   4_xyz:  17.251 0.8869  0.9822     8810.579
   4_adp:  16.571 0.8934  0.9811     8395.460
   4_occ:  16.558 0.8935  0.9811     8384.199
   5_bss:  16.561 0.8934  0.9741     8382.218
   5_xyz:  15.172 0.9053  0.9801     7287.301
   5_adp:  15.002 0.9069  0.9765     7195.902
   5_occ:  14.988 0.9070  0.9765     7182.208
   5_bss:  14.969 0.9072  0.9745     7169.052
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   2.0967e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   2.0967e-01
   1_xyz:   1.558  0.011  0.098 15.803  0.006  4.105   1.2921e-01
   1_adp:   1.558  0.011  0.098 15.803  0.006  4.105   1.2921e-01
   1_occ:   1.558  0.011  0.098 15.803  0.006  4.105   1.2921e-01
   2_bss:   1.558  0.011  0.098 15.803  0.006  4.105   1.2921e-01
   2_xyz:   1.376  0.011  0.096 15.816  0.005  4.111   1.0558e-01
   2_adp:   1.376  0.011  0.096 15.816  0.005  4.111   1.0558e-01
   2_occ:   1.376  0.011  0.096 15.816  0.005  4.111   1.0558e-01
   3_bss:   1.376  0.011  0.096 15.816  0.005  4.111   1.0558e-01
   3_xyz:   1.071  0.008  0.074 14.996  0.004  4.112   6.8035e-02
   3_adp:   1.071  0.008  0.074 14.996  0.004  4.112   6.8035e-02
   3_occ:   1.071  0.008  0.074 14.996  0.004  4.112   6.8035e-02
   4_bss:   1.071  0.008  0.074 14.996  0.004  4.112   6.8035e-02
   4_xyz:   0.952  0.006  0.069 14.559  0.004  4.119   5.3964e-02
   4_adp:   0.952  0.006  0.069 14.559  0.004  4.119   5.3964e-02
   4_occ:   0.952  0.006  0.069 14.559  0.004  4.119   5.3964e-02
   5_bss:   0.952  0.006  0.069 14.559  0.004  4.119   5.3964e-02
   5_xyz:   1.068  0.008  0.077 14.899  0.004  4.109   6.7419e-02
   5_adp:   1.068  0.008  0.077 14.899  0.004  4.109   6.7419e-02
   5_occ:   1.068  0.008  0.077 14.899  0.004  4.109   6.7419e-02
   5_bss:   1.068  0.008  0.077 14.899  0.004  4.109   6.7419e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.026   2.4264e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.026   2.4264e-01
   1_xyz:  10.778  0.064  0.331 87.400  0.042  1.831   9.9579e-02
   1_adp:  10.778  0.064  0.331 87.400  0.042  1.831   9.9579e-02
   1_occ:  10.778  0.064  0.331 87.400  0.042  1.831   9.9579e-02
   2_bss:  10.778  0.064  0.331 87.400  0.042  1.831   9.9579e-02
   2_xyz:   7.382  0.111  0.297 86.980  0.035  2.034   1.0189e-01
   2_adp:   7.382  0.111  0.297 86.980  0.035  2.034   1.0189e-01
   2_occ:   7.382  0.111  0.297 86.980  0.035  2.034   1.0189e-01
   3_bss:   7.382  0.111  0.297 86.980  0.035  2.034   1.0189e-01
   3_xyz:   7.666  0.047  0.235 82.845  0.029  2.294   9.5764e-02
   3_adp:   7.666  0.047  0.235 82.845  0.029  2.294   9.5764e-02
   3_occ:   7.666  0.047  0.235 82.845  0.029  2.294   9.5764e-02
   4_bss:   7.666  0.047  0.235 82.845  0.029  2.294   9.5764e-02
   4_xyz:   6.629  0.039  0.216 81.041  0.031  2.372   3.8270e-02
   4_adp:   6.629  0.039  0.216 81.041  0.031  2.372   3.8270e-02
   4_occ:   6.629  0.039  0.216 81.041  0.031  2.372   3.8270e-02
   5_bss:   6.629  0.039  0.216 81.041  0.031  2.372   3.8270e-02
   5_xyz:   6.653  0.049  0.276 82.351  0.029  2.212   8.1032e-02
   5_adp:   6.653  0.049  0.276 82.351  0.029  2.212   8.1032e-02
   5_occ:   6.653  0.049  0.276 82.351  0.029  2.212   8.1032e-02
   5_bss:   6.653  0.049  0.276 82.351  0.029  2.212   8.1032e-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:  90.28   0.00  17.94  90.28   0.00  14.53  64.58   0.00  36.50
   1_occ:  90.28   0.00  17.94  90.28   0.00  14.53  64.58   0.00  36.50
   2_bss:  90.28   0.00  17.94  90.28   0.00  14.53  64.58   0.00  36.50
   2_xyz:  90.28   0.00  17.94  90.28   0.00  14.53  64.58   0.00  36.50
   2_adp:  83.09   0.00  18.35  75.38   0.00  14.01  83.09   3.16  42.00
   2_occ:  83.09   0.00  18.35  75.38   0.00  14.01  83.09   3.16  42.00
   3_bss:  83.09   0.00  18.35  75.38   0.00  14.01  83.09   3.16  42.00
   3_xyz:  83.09   0.00  18.35  75.38   0.00  14.01  83.09   3.16  42.00
   3_adp:  88.06   0.00  17.66  82.67   0.00  13.02  88.06   5.19  42.92
   3_occ:  88.06   0.00  17.66  82.67   0.00  13.02  88.06   5.19  42.92
   4_bss:  88.06   0.00  17.66  82.67   0.00  13.02  88.06   5.19  42.92
   4_xyz:  88.06   0.00  17.66  82.67   0.00  13.02  88.06   5.19  42.92
   4_adp:  85.38   2.42  16.90  85.19   2.42  12.67  85.38   5.69  39.95
   4_occ:  85.38   2.42  16.90  85.19   2.42  12.67  85.38   5.69  39.95
   5_bss:  85.38   2.42  16.90  85.19   2.42  12.67  85.38   5.69  39.95
   5_xyz:  85.38   2.42  16.90  85.19   2.42  12.67  85.38   5.69  39.95
   5_adp:  86.04   2.19  16.64  86.04   2.19  12.49  84.87   5.93  39.20
   5_occ:  86.04   2.19  16.64  86.04   2.19  12.49  84.87   5.93  39.20
   5_bss:  85.97   2.11  16.56  85.97   2.11  12.41  84.79   5.85  39.12
------------------------------------------------------------------------
 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:    3.233    0.009    0.326
   1_adp:    3.233    0.009    0.326
   1_occ:    3.233    0.009    0.326
   2_bss:    3.233    0.009    0.326
   2_xyz:    1.908    0.065    0.605
   2_adp:    1.908    0.065    0.605
   2_occ:    1.908    0.065    0.605
   3_bss:    1.908    0.065    0.605
   3_xyz:    1.793    0.061    0.710
   3_adp:    1.793    0.061    0.710
   3_occ:    1.793    0.061    0.710
   4_bss:    1.793    0.061    0.710
   4_xyz:    1.927    0.075    0.750
   4_adp:    1.927    0.075    0.750
   4_occ:    1.927    0.075    0.750
   5_bss:    1.927    0.075    0.750
   5_xyz:    2.220    0.065    0.781
   5_adp:    2.220    0.065    0.781
   5_occ:    2.220    0.065    0.781
   5_bss:    2.220    0.065    0.781
------------------------------------------------------------------------

CPU time actual refinement: 349.44


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_153/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_153/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_153/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_153/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_153/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 349.29 
  Macro-tasks:
    bulk solvent and scale       = 44.40  
    individual site refinement   = 148.83 
    weights calculation          = 30.13  
    collect and process          = 6.62   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 230.07 
  Micro-tasks:
    mask                            = 2.44   
    f_calc                          = 108.47 
    alpha_beta                      = 8.54   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 119.40 
    fmodel                         = 7.85   
    r_factors                      = 0.16   
    phase_errors                   = 10.53  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 258.85 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.839 micro seconds
Total CPU time: 6.04 minutes
from_scatterers_fft:    664 calls, 107.98 s
gradients_fft:          609 calls, 105.09 s

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

# Date 2008-01-16 Time 04:08:52 PST -0800 (1200485332.02 s)
Start R-work = 0.4789, R-free = 0.4757 (no bulk solvent and anisotropic scale)
Final R-work = 0.1437, R-free = 0.1835 (no bulk solvent and anisotropic scale)

Start R-work = 0.4712, R-free = 0.4661
Final R-work = 0.1197, R-free = 0.1654