# Date 2008-01-16 Time 05:45:53 PST -0800 (1200491153.33 s)
#phil __OFF__

Command line arguments: "../866.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27954
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 866

-------------------------------------------------------------------------------
  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: (70.9525, 45.9914, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, 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: (70.9525, 45.9914, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1641 1.96371
Completeness in resolution range: 0.930019
Completeness with d_max=infinity: 0.927334

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1641
                             d_min =   1.9637

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: (70.9525, 45.9914, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1641 1.96371
Completeness in resolution range: 0.930019
Completeness with d_max=infinity: 0.927334

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1646 -  4.2035 [2212/2238]  1991   221  10.0%
  bin  2:  4.2035 -  3.3482 [2135/2155]  1921   214  10.0%
  bin  3:  3.3482 -  2.9285 [2090/2109]  1883   207   9.9%
  bin  4:  2.9285 -  2.6623 [2077/2107]  1862   215  10.4%
  bin  5:  2.6623 -  2.4723 [2069/2088]  1870   199   9.6%
  bin  6:  2.4723 -  2.3271 [2079/2104]  1869   210  10.1%
  bin  7:  2.3271 -  2.2109 [2025/2053]  1815   210  10.4%
  bin  8:  2.2109 -  2.1150 [2042/2078]  1838   204  10.0%
  bin  9:  2.1150 -  2.0337 [2030/2072]  1838   192   9.5%
  bin 10:  2.0337 -  1.9637 [ 830/2059]   743    87  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_866/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:
        1.81 -     2.42: 38
        2.42 -     3.04: 2198
        3.04 -     3.66: 4696
        3.66 -     4.28: 8999
        4.28 -     4.90: 12301
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.973 3.040 -x+1/2,-y+1,z+1/2
  " N   ASN A 148 " - " O   HOH Z 138 "  2.019 3.120 x,y-1,z
  ... (remaining 28227 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_866/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_866/model_refine_001.geo

CPU time processing inputs: 8.83


============================ 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 = 70.9525 45.9914 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4436   r_free= 0.4427   ksol= 0.00   Bsol= 0.00   scale= 0.904    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.257000                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1646 -  4.6891 0.99   1435  158 0.3590 0.3401      6.5425       6.484|
|  2:  4.6891 -  3.7403 0.99   1387  155 0.3716 0.3575       6.764      6.7006|
|  3:  3.7403 -  3.2729 0.99   1357  148 0.4003 0.3807      6.6091      6.6179|
|  4:  3.2729 -  2.9761 0.99   1342  154 0.4358 0.4692       6.496      6.5286|
|  5:  2.9761 -  2.7642 0.99   1338  151 0.4728 0.4417      6.3339       6.328|
|  6:  2.7642 -  2.6021 0.99   1345  146 0.4691 0.4945      6.2297      6.1929|
|  7:  2.6021 -  2.4723 0.99   1323  144 0.4797 0.4737      6.2127      6.1595|
|  8:  2.4723 -  2.3651 0.98   1318  153 0.4983 0.5053      6.1583      6.1518|
|  9:  2.3651 -  2.2744 0.98   1316  145 0.4856 0.5217      6.0999      6.1718|
| 10:  2.2744 -  2.1961 1.00   1325  145 0.5107 0.5012      6.0716      6.0605|
| 11:  2.1961 -  2.1277 0.98   1308  145 0.4927 0.5300      6.0166      6.0318|
| 12:  2.1277 -  2.0670 0.98   1312  142 0.5042 0.4915      5.9267       5.944|
| 13:  2.0670 -  2.0127 0.92   1221  137 0.4979 0.4784      5.8699      5.7965|
| 14:  2.0127 -  1.9637 0.23    303   36 0.5378 0.5854      5.8736      5.8957|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1646 -  4.6891  1435   158  0.76  29.34   0.83     0.80      55971.26|
|  2:  4.6891 -  3.7403  1387   155  0.75  30.78   0.91     0.85      87988.44|
|  3:  3.7403 -  3.2729  1357   148  0.63  41.25   0.94     0.82      98849.54|
|  4:  3.2729 -  2.9761  1342   154  0.54  48.41   0.91     0.73      94122.86|
|  5:  2.9761 -  2.7642  1338   151  0.47  54.52   0.90     0.66      74732.72|
|  6:  2.7642 -  2.6021  1345   146  0.44  56.74   0.91     0.61      64443.01|
|  7:  2.6021 -  2.4723  1323   144  0.42  58.63   0.92     0.57      59811.64|
|  8:  2.4723 -  2.3651  1318   153  0.39  60.67   0.91     0.56      55151.24|
|  9:  2.3651 -  2.2744  1316   145  0.39  60.42   0.93     0.57      51693.37|
| 10:  2.2744 -  2.1961  1325   145  0.39  60.43   0.93     0.58      45506.13|
| 11:  2.1961 -  2.1277  1308   145  0.36  62.96   0.97     0.55      46155.94|
| 12:  2.1277 -  2.0670  1312   142  0.34  64.90   0.93     0.53      42324.13|
| 13:  2.0670 -  2.0127  1221   137  0.32  65.99   0.96     0.54      37521.70|
| 14:  2.0127 -  1.9637   303    36  0.43  58.01   0.94     0.61      28010.46|
|alpha:            min =        0.53 max =            0.85 mean =         0.65|
|beta:             min =    28010.46 max =        98849.54 mean =     62383.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           90.00 mean =        53.19|
|phase err.(test): min =        0.00 max =           89.73 mean =        53.61|
|-----------------------------------------------------------------------------|

============================== 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 = 7.911740              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.893   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.321091              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.700   (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 |  1.806 -  2.115:       10 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       28 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      196 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2002 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1865 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2831 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4634 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4365 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5619 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6682 |
|-----------------------------------------------------------------------------|
|-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 |        0.172 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.806 |       0.312 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.905)------------------------------------------|
|    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 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4436   r_free= 0.4427   ksol= 0.00   Bsol= 0.00   scale= 0.904    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.257000                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4342   r_free= 0.4374   ksol= 0.30   Bsol= 50.00   scale= 0.938   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,2.09,1.31,0.00,0.00,0.00); trace/3= 0.40                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.250300                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.538522              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.872   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.114364              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.417   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4342      final r-factor (work) = 0.3368          |
| start r-factor (free) = 0.4374      final r-factor (free) = 0.3724          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.5852 = 6.54 * 0.50 * 6.2440 + 1.00 * 0.1719                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.1491 = 6.54 * 0.50 * 6.1297 + 1.00 * 0.1097                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3368      final r-factor (work) = 0.3061          |
| start r-factor (free) = 0.3724      final r-factor (free) = 0.3890          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8367 = 1.11 * 1.00 * 6.1297 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7248 = 1.11 * 1.00 * 6.0177 + 1.00 * 0.0189                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.905)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.17  19.02    None  None   None       |
|    all(noH): 2823   0      0.00    106.17  19.02    None  None   None       |
|    Sol.    : 438    0      0.68    106.17  39.05    None  None   None       |
|    Mac.    : 2385   0      0.00    67.21   15.34    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.617:  964   |   5:    53.086 -  63.703:   75        |
|      1:    10.617 -  21.234:  909   |   6:    63.703 -  74.320:   34        |
|      2:    21.234 -  31.851:  491   |   7:    74.320 -  84.937:   12        |
|      3:    31.851 -  42.469:  216   |   8:    84.937 -  95.554:    1        |
|      4:    42.469 -  53.086:  120   |   9:    95.554 - 106.171:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3061 r_free = 0.3890             target_work(ml) = 6.030         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3057 r_free = 0.3899             target_work(ml) = 6.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3057   r_free= 0.3899   ksol= 0.30   Bsol= 50.00   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,2.09,1.31,0.00,0.00,0.00); trace/3= 0.40                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.030371                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3056   r_free= 0.3881   ksol= 0.35   Bsol= 81.63   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.62,-0.03,0.43,-0.00,0.00,0.00); trace/3= -0.41                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.032156                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.036136              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.973   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.388756              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.853  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3056      final r-factor (work) = 0.2313          |
| start r-factor (free) = 0.3881      final r-factor (free) = 0.2955          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.2931 = 8.04 * 0.50 * 6.0187 + 1.00 * 0.1097                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.9343 = 8.04 * 0.50 * 5.9330 + 1.00 * 0.0952                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2313      final r-factor (work) = 0.2103          |
| start r-factor (free) = 0.2955      final r-factor (free) = 0.2690          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3253 = 0.39 * 1.00 * 5.9330 + 1.00 * 0.0188                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2418 = 0.39 * 1.00 * 5.7391 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.905)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.41  18.30    None  None   None       |
|    all(noH): 2823   0      0.00    104.41  18.30    None  None   None       |
|    Sol.    : 438    0      4.35    104.41  41.39    None  None   None       |
|    Mac.    : 2385   0      0.00    77.16   14.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.441: 1001   |   5:    52.204 -  62.644:   76        |
|      1:    10.441 -  20.881: 1054   |   6:    62.644 -  73.085:   28        |
|      2:    20.881 -  31.322:  310   |   7:    73.085 -  83.526:   13        |
|      3:    31.322 -  41.763:  197   |   8:    83.526 -  93.966:    0        |
|      4:    41.763 -  52.204:  143   |   9:    93.966 - 104.407:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2103 r_free = 0.2690             target_work(ml) = 5.700         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2102 r_free = 0.2683             target_work(ml) = 5.699         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2102   r_free= 0.2683   ksol= 0.35   Bsol= 81.63   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.62,-0.03,0.43,-0.00,0.00,0.00); trace/3= -0.41                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.699130                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2098   r_free= 0.2677   ksol= 0.35   Bsol= 80.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.25,-1.69,-0.33,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.697566                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.974749              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.766   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.786017              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.110  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2098      final r-factor (work) = 0.1689          |
| start r-factor (free) = 0.2677      final r-factor (free) = 0.2199          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6349 = 2.97 * 0.50 * 5.7414 + 1.00 * 0.0952                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3882 = 2.97 * 0.50 * 5.6035 + 1.00 * 0.0538                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1689      final r-factor (work) = 0.1557          |
| start r-factor (free) = 0.2199      final r-factor (free) = 0.2122          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4151 = 0.79 * 1.00 * 5.6035 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3064 = 0.79 * 1.00 * 5.4625 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.905)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.55  18.75    None  None   None       |
|    all(noH): 2823   0      0.00    105.55  18.75    None  None   None       |
|    Sol.    : 438    0      6.24    105.55  46.69    None  None   None       |
|    Mac.    : 2385   0      0.00    88.22   13.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.555: 1110   |   5:    52.777 -  63.333:   93        |
|      1:    10.555 -  21.111: 1033   |   6:    63.333 -  73.888:   69        |
|      2:    21.111 -  31.666:  239   |   7:    73.888 -  84.443:   37        |
|      3:    31.666 -  42.222:  129   |   8:    84.443 -  94.999:    9        |
|      4:    42.222 -  52.777:  103   |   9:    94.999 - 105.554:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1557 r_free = 0.2122             target_work(ml) = 5.444         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1556 r_free = 0.2119             target_work(ml) = 5.443         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1556   r_free= 0.2119   ksol= 0.35   Bsol= 80.00   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.25,-1.69,-0.33,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.443318                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1558   r_free= 0.2117   ksol= 0.34   Bsol= 80.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.36,-0.56,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.441959                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.666732              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.558  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.232294              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.290  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1558      final r-factor (work) = 0.1323          |
| start r-factor (free) = 0.2117      final r-factor (free) = 0.1847          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3380 = 2.67 * 0.50 * 5.4630 + 1.00 * 0.0538                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2214 = 2.67 * 0.50 * 5.3743 + 1.00 * 0.0555                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1323      final r-factor (work) = 0.1283          |
| start r-factor (free) = 0.1847      final r-factor (free) = 0.1755          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2610 = 0.23 * 1.00 * 5.3743 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2372 = 0.23 * 1.00 * 5.2859 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.905)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.64    97.75   17.74    None  None   None       |
|    all(noH): 2823   0      0.64    97.75   17.74    None  None   None       |
|    Sol.    : 438    0      6.05    97.75   43.21    None  None   None       |
|    Mac.    : 2385   0      0.64    90.53   13.06    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:     0.639 -  10.351: 1089   |   5:    49.196 -  58.907:   86        |
|      1:    10.351 -  20.062: 1068   |   6:    58.907 -  68.618:   65        |
|      2:    20.062 -  29.773:  231   |   7:    68.618 -  78.329:   32        |
|      3:    29.773 -  39.484:  129   |   8:    78.329 -  88.041:   10        |
|      4:    39.484 -  49.196:  109   |   9:    88.041 -  97.752:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1283 r_free = 0.1755             target_work(ml) = 5.261         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1282 r_free = 0.1754             target_work(ml) = 5.261         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1282   r_free= 0.1754   ksol= 0.34   Bsol= 80.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.36,-0.56,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.260533                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1284   r_free= 0.1755   ksol= 0.32   Bsol= 64.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.66,-0.78,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.259165                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.092994              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.832  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.232097              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.193  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1284      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1755      final r-factor (free) = 0.1638          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8724 = 4.09 * 0.50 * 5.2856 + 1.00 * 0.0555                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7470 = 4.09 * 0.50 * 5.2138 + 1.00 * 0.0770                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1152      final r-factor (work) = 0.1135          |
| start r-factor (free) = 0.1638      final r-factor (free) = 0.1613          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2193 = 0.23 * 1.00 * 5.2138 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2078 = 0.23 * 1.00 * 5.1682 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.905)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.94    91.90   17.24    None  None   None       |
|    all(noH): 2823   0      0.94    91.90   17.24    None  None   None       |
|    Sol.    : 438    0      6.41    91.76   41.01    None  None   None       |
|    Mac.    : 2385   0      0.94    91.90   12.88    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:     0.941 -  10.037: 1041   |   5:    46.420 -  55.516:   97        |
|      1:    10.037 -  19.133: 1102   |   6:    55.516 -  64.612:   62        |
|      2:    19.133 -  28.229:  240   |   7:    64.612 -  73.708:   27        |
|      3:    28.229 -  37.325:  139   |   8:    73.708 -  82.803:   11        |
|      4:    37.325 -  46.420:   98   |   9:    82.803 -  91.899:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1135 r_free = 0.1613             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1134 r_free = 0.1613             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1613   ksol= 0.32   Bsol= 64.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.66,-0.78,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163481                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1646 -  4.6891 0.99   1435  158 0.0938 0.1306      5.3502      5.5894|
|  2:  4.6891 -  3.7403 0.99   1387  155 0.0838 0.1130      5.4326      5.6515|
|  3:  3.7403 -  3.2729 0.99   1357  148 0.1096 0.1587      5.4912       5.828|
|  4:  3.2729 -  2.9761 0.99   1342  154 0.1267 0.1733      5.4755      5.6264|
|  5:  2.9761 -  2.7642 0.99   1338  151 0.1383 0.1783      5.3482       5.578|
|  6:  2.7642 -  2.6021 0.99   1345  146 0.1269 0.1956      5.2087      5.4793|
|  7:  2.6021 -  2.4723 0.99   1323  144 0.1299 0.1577      5.1848      5.3116|
|  8:  2.4723 -  2.3651 0.98   1318  153 0.1188 0.1812      5.0747      5.3824|
|  9:  2.3651 -  2.2744 0.98   1316  145 0.1230 0.1849      5.0563      5.3266|
| 10:  2.2744 -  2.1961 1.00   1325  145 0.1114 0.1690      4.9417      5.1803|
| 11:  2.1961 -  2.1277 0.98   1308  145 0.1119 0.1824      4.9445      5.3182|
| 12:  2.1277 -  2.0670 0.98   1312  142 0.1193 0.1763      4.8904      5.1273|
| 13:  2.0670 -  2.0127 0.92   1221  137 0.1092 0.1620      4.7686      4.9978|
| 14:  2.0127 -  1.9637 0.23    303   36 0.0938 0.1549      4.6285      4.9231|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1646 -  4.6891  1435   158  0.94   8.80   0.97     0.94       6846.03|
|  2:  4.6891 -  3.7403  1387   155  0.95   8.07   1.01     1.00       9276.57|
|  3:  3.7403 -  3.2729  1357   148  0.93  12.05   1.03     1.02      10956.88|
|  4:  3.2729 -  2.9761  1342   154  0.91  14.84   1.01     0.98      10958.19|
|  5:  2.9761 -  2.7642  1338   151  0.90  16.05   1.00     0.98       8390.77|
|  6:  2.7642 -  2.6021  1345   146  0.89  16.57   0.98     0.96       7008.63|
|  7:  2.6021 -  2.4723  1323   144  0.91  15.53   1.00     0.96       6317.79|
|  8:  2.4723 -  2.3651  1318   153  0.90  15.96   0.99     0.96       5413.47|
|  9:  2.3651 -  2.2744  1316   145  0.90  16.12   1.00     0.96       5202.97|
| 10:  2.2744 -  2.1961  1325   145  0.90  15.89   1.01     0.98       4390.10|
| 11:  2.1961 -  2.1277  1308   145  0.90  16.18   0.99     0.94       4383.27|
| 12:  2.1277 -  2.0670  1312   142  0.90  16.58   1.00     1.01       4080.18|
| 13:  2.0670 -  2.0127  1221   137  0.90  16.78   1.00     0.98       3356.90|
| 14:  2.0127 -  1.9637   303    36  0.94  12.57   0.99     0.96       2452.61|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2452.61 max =        10958.19 mean =      6636.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.46|
|phase err.(test): min =        0.00 max =           89.24 mean =        13.92|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1613   ksol= 0.31   Bsol= 55.83   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.63,-0.75,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163432                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1613   ksol= 0.31   Bsol= 55.83   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.63,-0.75,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163432                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1646 -  4.6891 0.99   1435  158 0.0934 0.1301      5.3477      5.5855|
|  2:  4.6891 -  3.7403 0.99   1387  155 0.0834 0.1127      5.4282      5.6463|
|  3:  3.7403 -  3.2729 0.99   1357  148 0.1093 0.1582      5.4884      5.8257|
|  4:  3.2729 -  2.9761 0.99   1342  154 0.1268 0.1736      5.4757      5.6276|
|  5:  2.9761 -  2.7642 0.99   1338  151 0.1386 0.1786      5.3494      5.5799|
|  6:  2.7642 -  2.6021 0.99   1345  146 0.1271 0.1958      5.2102       5.481|
|  7:  2.6021 -  2.4723 0.99   1323  144 0.1301 0.1577      5.1866       5.313|
|  8:  2.4723 -  2.3651 0.98   1318  153 0.1189 0.1815      5.0762      5.3842|
|  9:  2.3651 -  2.2744 0.98   1316  145 0.1231 0.1849      5.0574      5.3264|
| 10:  2.2744 -  2.1961 1.00   1325  145 0.1115 0.1692      4.9429      5.1812|
| 11:  2.1961 -  2.1277 0.98   1308  145 0.1118 0.1824       4.945      5.3184|
| 12:  2.1277 -  2.0670 0.98   1312  142 0.1194 0.1763      4.8907      5.1274|
| 13:  2.0670 -  2.0127 0.92   1221  137 0.1092 0.1621      4.7689      4.9979|
| 14:  2.0127 -  1.9637 0.23    303   36 0.0938 0.1552      4.6287      4.9245|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1646 -  4.6891  1435   158  0.94   8.76   0.97     0.94       6796.11|
|  2:  4.6891 -  3.7403  1387   155  0.95   8.04   1.01     1.00       9207.74|
|  3:  3.7403 -  3.2729  1357   148  0.93  11.99   1.03     1.02      10881.34|
|  4:  3.2729 -  2.9761  1342   154  0.91  14.83   1.01     0.98      10941.10|
|  5:  2.9761 -  2.7642  1338   151  0.90  16.07   1.00     0.98       8409.22|
|  6:  2.7642 -  2.6021  1345   146  0.89  16.60   0.98     0.96       7032.77|
|  7:  2.6021 -  2.4723  1323   144  0.91  15.56   0.99     0.96       6343.83|
|  8:  2.4723 -  2.3651  1318   153  0.90  16.00   0.99     0.96       5431.55|
|  9:  2.3651 -  2.2744  1316   145  0.90  16.15   1.00     0.96       5217.53|
| 10:  2.2744 -  2.1961  1325   145  0.90  15.91   1.01     0.98       4400.49|
| 11:  2.1961 -  2.1277  1308   145  0.90  16.19   0.99     0.93       4390.23|
| 12:  2.1277 -  2.0670  1312   142  0.90  16.59   1.00     1.01       4084.88|
| 13:  2.0670 -  2.0127  1221   137  0.90  16.78   1.00     0.98       3359.05|
| 14:  2.0127 -  1.9637   303    36  0.94  12.57   0.99     0.96       2454.18|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2454.18 max =        10941.10 mean =      6629.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.46|
|phase err.(test): min =        0.00 max =           89.39 mean =        13.92|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.905)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.91    91.87   17.21    None  None   None       |
|    all(noH): 2823   0      0.91    91.87   17.21    None  None   None       |
|    Sol.    : 438    0      6.38    91.72   40.98    None  None   None       |
|    Mac.    : 2385   0      0.91    91.87   12.84    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:     0.909 -  10.005: 1041   |   5:    46.388 -  55.484:   97        |
|      1:    10.005 -  19.101: 1102   |   6:    55.484 -  64.580:   62        |
|      2:    19.101 -  28.196:  240   |   7:    64.580 -  73.675:   27        |
|      3:    28.196 -  37.292:  139   |   8:    73.675 -  82.771:   11        |
|      4:    37.292 -  46.388:   98   |   9:    82.771 -  91.867:    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)= 318         
Filter by distance & map next to the model:
   mapped sites are within: 0.611 - 4.750
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 313 from: 318
   mapped sites are within: 0.708 - 4.750

peak=    6.483 closest distance to " NE2 GLN A  11 " =    1.281
peak=    5.440 closest distance to " O   HOH Z 144 " =    1.948
peak=    5.403 closest distance to " NH2 ARG A  56 " =    2.126
peak=    5.389 closest distance to " O   HOH Z  63 " =    1.753
peak=    5.357 closest distance to " O   HOH Z   7 " =    1.595
peak=    5.264 closest distance to " CB  GLN A 223 " =    1.565
peak=    5.206 closest distance to " O   HOH Z 126 " =    2.100
peak=    5.164 closest distance to " O   HOH Z 287 " =    2.226
peak=    5.094 closest distance to " CG  PRO A  54 " =    1.318
peak=    5.047 closest distance to " O   HOH Z 417 " =    2.150
peak=    4.923 closest distance to " O   HOH Z 232 " =    2.206
peak=    4.896 closest distance to " O   HOH Z 423 " =    1.941
peak=    4.867 closest distance to " O   HOH Z 369 " =    2.094
peak=    4.728 closest distance to " CB  SER A  63 " =    1.261
peak=    4.716 closest distance to " O   HOH Z   9 " =    1.744
peak=    4.630 closest distance to " O   HOH Z 427 " =    2.391
peak=    4.489 closest distance to " O   HOH Z  78 " =    1.610
peak=    4.462 closest distance to " CB  ARG A 190 " =    1.516
peak=    4.419 closest distance to " O   HOH Z   1 " =    1.880
peak=    4.419 closest distance to " CB  ASN A 148 " =    1.433
peak=    4.383 closest distance to " O   HOH Z 419 " =    2.217
peak=    4.374 closest distance to " CD  ARG A 159 " =    0.784
peak=    4.369 closest distance to " O   HOH Z 298 " =    2.085
peak=    4.335 closest distance to " CB  PRO A  54 " =    1.020
peak=    4.328 closest distance to " O   HOH Z 380 " =    1.873
peak=    4.312 closest distance to " CB  GLN A 183 " =    1.223
peak=    4.259 closest distance to " CG  TRP A 179 " =    2.154
peak=    4.248 closest distance to " ND2 ASN A 187 " =    1.559
peak=    4.236 closest distance to " O   HOH Z 133 " =    2.457
peak=    4.217 closest distance to " CB  ARG A 275 " =    0.947
peak=    4.184 closest distance to " O   HOH Z   2 " =    1.818
peak=    4.172 closest distance to " CB  ASN A 187 " =    1.013
peak=    4.156 closest distance to " O   HOH Z 425 " =    1.468
peak=    4.133 closest distance to " O   HOH Z  49 " =    1.105
peak=    4.090 closest distance to " O   HOH Z 214 " =    2.264
peak=    4.088 closest distance to " O   HOH Z  61 " =    1.643
peak=    4.083 closest distance to " O   HOH Z 316 " =    3.092
peak=    4.080 closest distance to " CD  ARG A  66 " =    2.079
peak=    4.027 closest distance to " O   HOH Z 437 " =    1.794
peak=    4.025 closest distance to " CB  GLU A 128 " =    1.004
peak=    4.006 closest distance to " O   HOH Z  88 " =    3.940
peak=    3.979 closest distance to " CA  TYR A  30 " =    1.046
peak=    3.978 closest distance to " CG  LEU A 167 " =    1.250
peak=    3.977 closest distance to " ND1 HIS A  86 " =    1.686
peak=    3.976 closest distance to " O   HOH Z  91 " =    2.418
peak=    3.967 closest distance to " O   HOH Z  61 " =    1.601
peak=    3.958 closest distance to " CD2 TRP A 179 " =    1.184
peak=    3.940 closest distance to " O   PRO A 198 " =    1.576
peak=    3.939 closest distance to " O   HOH Z 327 " =    1.744
peak=    3.927 closest distance to " O   HOH Z 222 " =    1.184
peak=    3.921 closest distance to " O   HOH Z 201 " =    1.612
peak=    3.912 closest distance to " O   HOH Z 258 " =    2.066
peak=    3.887 closest distance to " CG2 THR A 221 " =    1.030
peak=    3.880 closest distance to " O   HOH Z 225 " =    1.598
peak=    3.874 closest distance to " CB  GLU A 277 " =    3.574
peak=    3.874 closest distance to " O   HOH Z  78 " =    1.805
peak=    3.872 closest distance to " CG  PRO A 213 " =    1.248
peak=    3.871 closest distance to " CB  ARG A  79 " =    1.249
peak=    3.858 closest distance to " CB  LEU A 228 " =    1.095
peak=    3.857 closest distance to " O   HOH Z   1 " =    1.618
peak=    3.853 closest distance to " O   HOH Z 126 " =    1.469
peak=    3.850 closest distance to " O   HOH Z 195 " =    1.432
peak=    3.822 closest distance to " O   HOH Z 116 " =    3.074
peak=    3.821 closest distance to " CB  ASN A  39 " =    0.921
peak=    3.818 closest distance to " O   HOH Z  10 " =    1.690
peak=    3.813 closest distance to " O   HOH Z 145 " =    1.538
peak=    3.800 closest distance to " CA  ARG A 195 " =    1.270
peak=    3.797 closest distance to " CB  ASN A 142 " =    0.952
peak=    3.793 closest distance to " CZ3 TRP A 266 " =    1.115
peak=    3.792 closest distance to " O   HOH Z  40 " =    1.999
peak=    3.787 closest distance to " O   HOH Z 158 " =    2.873
peak=    3.782 closest distance to " O   HOH Z 218 " =    1.755
peak=    3.778 closest distance to " CB  VAL A 265 " =    1.375
peak=    3.772 closest distance to " CB  SER A 216 " =    0.942
peak=    3.762 closest distance to " CB  SER A 212 " =    1.257
peak=    3.753 closest distance to " O   HOH Z 345 " =    1.793
peak=    3.744 closest distance to " CB  SER A   3 " =    1.488
peak=    3.736 closest distance to " CG  PRO A 280 " =    0.736
peak=    3.732 closest distance to " CB  ALA A   1 " =    4.750
peak=    3.723 closest distance to " O   HOH Z  21 " =    1.724
peak=    3.721 closest distance to " CB  TYR A 169 " =    0.904
peak=    3.716 closest distance to " CB  GLU A 152 " =    1.251
peak=    3.712 closest distance to " CG  PRO A  90 " =    1.619
peak=    3.697 closest distance to " O   HOH Z 422 " =    2.680
peak=    3.694 closest distance to " O   HOH Z 346 " =    1.696
peak=    3.694 closest distance to " O   HOH Z 325 " =    3.874
peak=    3.691 closest distance to " O   HOH Z 145 " =    2.080
peak=    3.688 closest distance to " OD1 ASN A  69 " =    2.607
peak=    3.686 closest distance to " O   HOH Z 365 " =    2.679
peak=    3.677 closest distance to " O   HOH Z 352 " =    1.646
peak=    3.663 closest distance to " N   ALA A   1 " =    2.159
peak=    3.662 closest distance to " CB  GLN A  88 " =    1.250
peak=    3.659 closest distance to " CB  THR A 157 " =    1.156
peak=    3.656 closest distance to " O   HOH Z 362 " =    1.821
peak=    3.655 closest distance to " O   HOH Z 368 " =    3.775
peak=    3.640 closest distance to " O   HOH Z  69 " =    2.180
peak=    3.639 closest distance to " O   HOH Z 183 " =    1.474
peak=    3.638 closest distance to " NH1AARG A 145 " =    1.219
peak=    3.637 closest distance to " CA  TYR A 116 " =    1.342
peak=    3.632 closest distance to " CG2 VAL A 257 " =    0.840
peak=    3.632 closest distance to " O   HOH Z 132 " =    2.483
peak=    3.625 closest distance to " CG  PRO A 198 " =    1.259
peak=    3.616 closest distance to " O   TYR A 116 " =    1.292
peak=    3.615 closest distance to " CA  ALA A 233 " =    1.160
peak=    3.606 closest distance to " CA  ASN A 127 " =    1.113
peak=    3.600 closest distance to " NZ  LYS A 117 " =    3.015
peak=    3.599 closest distance to " CE  LYS A  76 " =    0.877
peak=    3.595 closest distance to " CD1 LEU A 300 " =    1.156
peak=    3.594 closest distance to " O   HOH Z 175 " =    2.212
peak=    3.591 closest distance to " O   ASN A 209 " =    1.475
peak=    3.588 closest distance to " CB  GLU A  46 " =    0.990
peak=    3.584 closest distance to " O   HOH Z 188 " =    2.074
peak=    3.580 closest distance to " CB  TRP A 266 " =    1.038
peak=    3.577 closest distance to " O   HOH Z 405 " =    1.510
peak=    3.574 closest distance to " CA  PRO A  54 " =    1.346
peak=    3.563 closest distance to " O   HOH Z 411 " =    3.866
peak=    3.562 closest distance to " O   HOH Z 171 " =    2.894
peak=    3.557 closest distance to " CA  SER A  87 " =    1.014
peak=    3.555 closest distance to " N   CYS A 260 " =    0.847
peak=    3.553 closest distance to " O   HOH Z 406 " =    1.635
peak=    3.551 closest distance to " CB  ASP A 124 " =    0.746
peak=    3.550 closest distance to " OG  SER A  62 " =    3.031
peak=    3.545 closest distance to " O   HOH Z 371 " =    2.898
peak=    3.542 closest distance to " O   HOH Z  58 " =    1.729
peak=    3.542 closest distance to " O   HOH Z 180 " =    2.139
peak=    3.541 closest distance to " O   HOH Z 421 " =    2.104
peak=    3.534 closest distance to " CB  SER A 276 " =    1.137
peak=    3.533 closest distance to " CG AARG A 275 " =    1.172
peak=    3.529 closest distance to " O   ASN A  74 " =    1.376
peak=    3.527 closest distance to " N   SER A  97 " =    0.914
peak=    3.523 closest distance to " CA  VAL A 125 " =    1.176
peak=    3.515 closest distance to " O   HOH Z 130 " =    2.065
peak=    3.515 closest distance to " OG BSER A  99 " =    2.284
peak=    3.508 closest distance to " O   HOH Z 234 " =    3.823
peak=    3.507 closest distance to " O   HOH Z 414 " =    1.263
peak=    3.506 closest distance to " O   HOH Z 357 " =    2.021
peak=    3.501 closest distance to " O   HOH Z 286 " =    2.125
peak=    3.500 closest distance to " O   HOH Z 403 " =    1.463
peak=    3.497 closest distance to " O   HOH Z 367 " =    2.446
peak=    3.497 closest distance to " NZ  LYS A 119 " =    1.407
peak=    3.490 closest distance to " O   HOH Z 272 " =    1.736
peak=    3.487 closest distance to " O   HOH Z  30 " =    1.799
peak=    3.485 closest distance to " CB  LYS A 117 " =    1.210
peak=    3.484 closest distance to " CG1 ILE A 151 " =    1.069
peak=    3.481 closest distance to " CA  ALA A  51 " =    0.955
peak=    3.480 closest distance to " O   HOH Z  68 " =    2.051
peak=    3.476 closest distance to " CB  ILE A 120 " =    1.385
peak=    3.471 closest distance to " NE2 HIS A 207 " =    1.204
peak=    3.470 closest distance to " CB  TRP A 150 " =    1.178
peak=    3.469 closest distance to " CZ  PHE A 218 " =    1.086
peak=    3.464 closest distance to " CG  LYS A  76 " =    1.963
peak=    3.464 closest distance to " CA  SER A  95 " =    0.990
peak=    3.463 closest distance to " N   PHE A 130 " =    1.322
peak=    3.459 closest distance to " OE2 GLU A  53 " =    2.083
peak=    3.456 closest distance to " CD  PRO A 243 " =    1.736
peak=    3.455 closest distance to " CG2 ILE A  20 " =    1.512
peak=    3.453 closest distance to " O   HOH Z 139 " =    1.034
peak=    3.450 closest distance to " O   HOH Z  44 " =    1.750
peak=    3.448 closest distance to " O   HOH Z 274 " =    2.149
peak=    3.447 closest distance to " O   HOH Z 371 " =    1.859
peak=    3.440 closest distance to " CB  ALA A 114 " =    1.067
peak=    3.440 closest distance to " CB  ASP A 140 " =    0.845
peak=    3.436 closest distance to " O   HOH Z 272 " =    2.196
peak=    3.436 closest distance to " O   HOH Z 122 " =    1.888
peak=    3.436 closest distance to " O   HOH Z  51 " =    1.886
peak=    3.433 closest distance to " O   HOH Z 368 " =    1.828
peak=    3.427 closest distance to " O   HOH Z 305 " =    3.630
peak=    3.420 closest distance to " CA  ILE A 234 " =    1.002
peak=    3.419 closest distance to " CA  ALA A 160 " =    1.043
peak=    3.416 closest distance to " NH2AARG A 190 " =    1.827
peak=    3.411 closest distance to " CB  TYR A  30 " =    1.299
peak=    3.408 closest distance to " CA  LEU A 101 " =    1.521
peak=    3.408 closest distance to " O   HOH Z 193 " =    1.824
peak=    3.405 closest distance to " N   ASN A 127 " =    1.396
peak=    3.403 closest distance to " O   HOH Z 147 " =    1.778
peak=    3.400 closest distance to " O   HOH Z  59 " =    1.746
peak=    3.400 closest distance to " CA  THR A 264 " =    0.864
peak=    3.397 closest distance to " CB  ARG A 138 " =    0.969
peak=    3.396 closest distance to " CE3 TRP A 274 " =    1.263
peak=    3.393 closest distance to " CE  LYS A 119 " =    1.179
peak=    3.392 closest distance to " O   HOH Z 392 " =    1.250
peak=    3.391 closest distance to " O   HOH Z 148 " =    3.406
peak=    3.390 closest distance to " O   HOH Z 394 " =    1.777
peak=    3.385 closest distance to " CD2 LEU A 297 " =    1.044
peak=    3.384 closest distance to " CB  SER A  97 " =    0.892
peak=    3.383 closest distance to " O   HOH Z 128 " =    1.844
peak=    3.380 closest distance to " O   HOH Z 359 " =    1.365
peak=    3.377 closest distance to " O   HOH Z  88 " =    3.078
peak=    3.375 closest distance to " O   HOH Z 368 " =    4.280
peak=    3.375 closest distance to " O   HOH Z 248 " =    1.608
peak=    3.369 closest distance to " CB  TYR A 116 " =    0.933
peak=    3.365 closest distance to " O   HOH Z 236 " =    1.573
peak=    3.364 closest distance to " OG BSER A 164 " =    2.345
peak=    3.362 closest distance to " O   HOH Z  17 " =    1.697
peak=    3.362 closest distance to " CD  ARG A 269 " =    0.903
peak=    3.361 closest distance to " CA  ALA A 180 " =    1.418
peak=    3.360 closest distance to " CA  ALA A 129 " =    1.215
peak=    3.359 closest distance to " CB  ALA A 114 " =    1.428
peak=    3.358 closest distance to " O   HOH Z 115 " =    1.650
peak=    3.355 closest distance to " O   HOH Z  44 " =    2.710
peak=    3.354 closest distance to " CB  ASN A 110 " =    1.017
peak=    3.351 closest distance to " O   HOH Z 109 " =    2.507
peak=    3.347 closest distance to " CD2 LEU A 255 " =    1.734
peak=    3.346 closest distance to " O   HOH Z 215 " =    1.468
peak=    3.345 closest distance to " O   HOH Z 128 " =    2.211
peak=    3.343 closest distance to " CB  ARG A 139 " =    1.152
peak=    3.341 closest distance to " NE AARG A 275 " =    1.494
peak=    3.340 closest distance to " CB  ALA A 160 " =    1.440
peak=    3.338 closest distance to " N   GLN A 278 " =    1.334
peak=    3.338 closest distance to " O   HOH Z 432 " =    1.825
peak=    3.326 closest distance to " CA  ASP A 162 " =    1.072
peak=    3.324 closest distance to " O   HOH Z 385 " =    3.867
peak=    3.324 closest distance to " CG  LYS A 119 " =    1.094
peak=    3.323 closest distance to " O   HOH Z 291 " =    1.524
peak=    3.318 closest distance to " O   HOH Z 389 " =    1.856
peak=    3.316 closest distance to " CE3 TRP A 150 " =    1.030
peak=    3.315 closest distance to " O   HOH Z  22 " =    2.677
peak=    3.313 closest distance to " CA  MET A 105 " =    0.886
peak=    3.307 closest distance to " CG1 VAL A 202 " =    1.743
peak=    3.306 closest distance to " O   HOH Z 386 " =    2.834
peak=    3.304 closest distance to " CA  ARG A 102 " =    1.159
peak=    3.301 closest distance to " O   HOH Z 193 " =    2.069
peak=    3.299 closest distance to " CG2 VAL A 197 " =    1.024
peak=    3.296 closest distance to " O   HOH Z 273 " =    2.874
peak=    3.296 closest distance to " CA  ALA A 158 " =    1.159
peak=    3.293 closest distance to " O   HOH Z 235 " =    1.734
peak=    3.290 closest distance to " O   HOH Z 250 " =    1.429
peak=    3.288 closest distance to " CD2 PHE A  59 " =    1.791
peak=    3.288 closest distance to " O   HOH Z  85 " =    2.109
peak=    3.286 closest distance to " O   HOH Z 218 " =    1.905
peak=    3.286 closest distance to " O   HOH Z 219 " =    4.364
peak=    3.286 closest distance to " CB  TYR A  30 " =    1.037
peak=    3.281 closest distance to " O   HOH Z 434 " =    1.474
peak=    3.277 closest distance to " CB  SER A 210 " =    0.799
peak=    3.275 closest distance to " OG BSER A 134 " =    3.005
peak=    3.271 closest distance to " O   PRO A 198 " =    1.275
peak=    3.269 closest distance to " CB  VAL A 202 " =    1.618
peak=    3.267 closest distance to " CB  ASP A 171 " =    0.708
peak=    3.266 closest distance to " O   HOH Z 130 " =    3.608
peak=    3.264 closest distance to " O   HOH Z 189 " =    2.662
peak=    3.262 closest distance to " CA  TYR A  30 " =    1.061
peak=    3.262 closest distance to " O   HOH Z 146 " =    1.548
peak=    3.261 closest distance to " CB  GLU A 236 " =    1.176
peak=    3.260 closest distance to " CA  ILE A 106 " =    0.770
peak=    3.257 closest distance to " O   HOH Z 393 " =    1.221
peak=    3.256 closest distance to " ND1 HIS A  81 " =    1.740
peak=    3.253 closest distance to " CA  ALA A 291 " =    0.904
peak=    3.250 closest distance to " O   HOH Z 193 " =    1.618
peak=    3.244 closest distance to " O   HOH Z 358 " =    3.900
peak=    3.244 closest distance to " O   HOH Z 369 " =    1.768
peak=    3.242 closest distance to " O   HOH Z 219 " =    1.910
peak=    3.242 closest distance to " O   MET A 105 " =    1.698
peak=    3.242 closest distance to " CA  ALA A 299 " =    0.845
peak=    3.241 closest distance to " O   HOH Z 373 " =    1.477
peak=    3.241 closest distance to " O   HOH Z 172 " =    2.358
peak=    3.240 closest distance to " CB  LEU A 237 " =    0.786
peak=    3.238 closest distance to " O   ILE A  20 " =    2.094
peak=    3.237 closest distance to " CG1 VAL A 189 " =    1.758
peak=    3.232 closest distance to " CB  ALA A 248 " =    0.972
peak=    3.229 closest distance to " CE3 TRP A  85 " =    0.901
peak=    3.227 closest distance to " O   HOH Z 430 " =    1.734
peak=    3.227 closest distance to " O   THR A 220 " =    1.564
peak=    3.223 closest distance to " O   HOH Z 213 " =    1.809
peak=    3.218 closest distance to " O   HOH Z 409 " =    3.159
peak=    3.214 closest distance to " CB  PRO A 243 " =    1.304
peak=    3.214 closest distance to " CA  THR A 221 " =    1.080
peak=    3.213 closest distance to " CD  LYS A 166 " =    1.277
peak=    3.210 closest distance to " O   HOH Z 325 " =    2.219
peak=    3.206 closest distance to " O   HOH Z  28 " =    1.725
peak=    3.205 closest distance to " O   HOH Z 386 " =    3.096
peak=    3.196 closest distance to " O   HOH Z 181 " =    2.122
peak=    3.194 closest distance to " CG  LEU A 101 " =    1.154
peak=    3.194 closest distance to " CD2 TYR A 186 " =    1.118
peak=    3.193 closest distance to " O   HOH Z  80 " =    1.586
peak=    3.188 closest distance to " O   HOH Z 302 " =    1.637
peak=    3.186 closest distance to " O   HOH Z 313 " =    1.521
peak=    3.185 closest distance to " OD2 ASP A 286 " =    2.822
peak=    3.173 closest distance to " O   HOH Z 344 " =    3.097
peak=    3.167 closest distance to " OG  SER A  22 " =    2.894
peak=    3.164 closest distance to " O   HOH Z  97 " =    1.940
peak=    3.163 closest distance to " CB  SER A  22 " =    0.922
peak=    3.162 closest distance to " O   HOH Z 132 " =    3.919
peak=    3.162 closest distance to " CD1 ILE A  49 " =    1.397
peak=    3.159 closest distance to " O   HOH Z 128 " =    2.019
peak=    3.158 closest distance to " CA  ARG A 159 " =    1.288
peak=    3.157 closest distance to " O   HOH Z 135 " =    1.796
peak=    3.153 closest distance to " O   HOH Z 426 " =    1.997
peak=    3.153 closest distance to " N   VAL A 296 " =    1.729
peak=    3.148 closest distance to " NH1BARG A 145 " =    1.281
peak=    3.148 closest distance to " O   HOH Z 381 " =    1.725
peak=    3.146 closest distance to " O   HOH Z   3 " =    2.586
peak=    3.143 closest distance to " CA  GLY A 136 " =    0.952
peak=    3.141 closest distance to " O   PHE A 192 " =    1.357
peak=    3.133 closest distance to " CG  GLN A  73 " =    1.511
peak=    3.132 closest distance to " CB  THR A  31 " =    1.625
peak=    3.130 closest distance to " CB  PRO A  90 " =    1.141
peak=    3.127 closest distance to " CA  ASN A 217 " =    1.168
peak=    3.127 closest distance to " CB  ASN A 215 " =    1.107
peak=    3.124 closest distance to " NH2 ARG A 219 " =    1.829
peak=    3.122 closest distance to " O   HOH Z 409 " =    2.098
peak=    3.120 closest distance to " CA  ALA A 100 " =    1.082
peak=    3.119 closest distance to " CE AMET A  47 " =    1.356
peak=    3.118 closest distance to " N   SER A 134 " =    1.409
peak=    3.116 closest distance to " O   HOH Z 425 " =    1.954
peak=    3.105 closest distance to " NE2 GLN A 278 " =    3.619
peak=    3.088 closest distance to " O   HOH Z 213 " =    2.092
peak=    3.082 closest distance to " OE1 GLU A  37 " =    1.261
peak=    3.079 closest distance to " NZ  LYS A 117 " =    1.421
peak=    3.067 closest distance to " CG BARG A 102 " =    1.861
peak=    3.060 closest distance to " CD  ARG A 138 " =    0.824
peak=    3.054 closest distance to " O   HOH Z 359 " =    4.151
peak=    3.048 closest distance to " O   HOH Z 133 " =    1.532
peak=    3.036 closest distance to " O   HOH Z 415 " =    3.882

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.513 - 5.466
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 202
   mapped sites are within: 0.788 - 5.466

peak=   -4.695 closest distance to " CD  ARG A  14 " =    3.363
peak=   -4.565 closest distance to " CB  PRO A 243 " =    2.582
peak=   -4.416 closest distance to " O   HOH Z 377 " =    1.943
peak=   -4.409 closest distance to " O   HOH Z  52 " =    1.106
peak=   -4.386 closest distance to " O   HOH Z 231 " =    0.860
peak=   -4.314 closest distance to " CA  GLY A  98 " =    1.823
peak=   -4.294 closest distance to " CB  ALA A  43 " =    2.447
peak=   -4.233 closest distance to " O   PRO A 198 " =    1.243
peak=   -4.233 closest distance to " CD  ARG A 156 " =    2.094
peak=   -4.201 closest distance to " O   HOH Z  65 " =    1.092
peak=   -4.175 closest distance to " O   HOH Z 131 " =    4.099
peak=   -4.139 closest distance to " ND2 ASN A 249 " =    2.116
peak=   -4.118 closest distance to " O   HOH Z 185 " =    2.074
peak=   -4.113 closest distance to " O   HOH Z 290 " =    1.143
peak=   -4.096 closest distance to " O   SER A  22 " =    2.742
peak=   -4.026 closest distance to " CD1 LEU A 255 " =    2.935
peak=   -3.996 closest distance to " CE2 PHE A 218 " =    2.515
peak=   -3.992 closest distance to " CE BMET A  47 " =    1.376
peak=   -3.985 closest distance to " O   VAL A  67 " =    2.701
peak=   -3.969 closest distance to " O   HOH Z  60 " =    1.478
peak=   -3.966 closest distance to " O   HOH Z 231 " =    2.005
peak=   -3.963 closest distance to " O   HOH Z 351 " =    1.650
peak=   -3.873 closest distance to " N   THR A 157 " =    1.577
peak=   -3.869 closest distance to " CB  ALA A 291 " =    2.176
peak=   -3.855 closest distance to " O   HOH Z  24 " =    1.030
peak=   -3.842 closest distance to " O   HOH Z 211 " =    1.173
peak=   -3.837 closest distance to " O   HOH Z 389 " =    2.152
peak=   -3.812 closest distance to " CZ3 TRP A 179 " =    1.229
peak=   -3.798 closest distance to " O   HOH Z 298 " =    2.521
peak=   -3.787 closest distance to " CG2 THR A  18 " =    2.790
peak=   -3.786 closest distance to " OG BSER A 134 " =    1.461
peak=   -3.785 closest distance to " N   ALA A  43 " =    2.706
peak=   -3.776 closest distance to " OD1 ASP A 191 " =    1.964
peak=   -3.771 closest distance to " CA  GLY A 241 " =    2.271
peak=   -3.757 closest distance to " CD1 LEU A 101 " =    2.253
peak=   -3.737 closest distance to " O   PRO A 163 " =    1.968
peak=   -3.725 closest distance to " O   ALA A  10 " =    1.685
peak=   -3.725 closest distance to " ND2 ASN A  45 " =    2.176
peak=   -3.712 closest distance to " O   HOH Z 407 " =    3.163
peak=   -3.706 closest distance to " O   HOH Z 111 " =    1.664
peak=   -3.671 closest distance to " O   HOH Z 266 " =    5.104
peak=   -3.666 closest distance to " O   PRO A 243 " =    2.361
peak=   -3.664 closest distance to " O   HOH Z  39 " =    1.022
peak=   -3.662 closest distance to " O   HOH Z 313 " =    1.677
peak=   -3.642 closest distance to " CB  ASP A  27 " =    2.402
peak=   -3.642 closest distance to " N   ASP A 171 " =    2.458
peak=   -3.631 closest distance to " CB  ALA A   9 " =    2.410
peak=   -3.619 closest distance to " CG2 ILE A  49 " =    2.761
peak=   -3.618 closest distance to " O   HOH Z 174 " =    2.733
peak=   -3.618 closest distance to " NE2 GLN A  55 " =    1.141
peak=   -3.609 closest distance to " O   HOH Z 357 " =    2.107
peak=   -3.606 closest distance to " CA  GLY A 203 " =    2.339
peak=   -3.601 closest distance to " CB  ALA A 158 " =    1.711
peak=   -3.600 closest distance to " O   HOH Z 372 " =    2.523
peak=   -3.591 closest distance to " O   PRO A 198 " =    1.373
peak=   -3.587 closest distance to " N   SER A 141 " =    1.870
peak=   -3.586 closest distance to " O   SER A 135 " =    1.457
peak=   -3.582 closest distance to " O   HOH Z 286 " =    1.647
peak=   -3.580 closest distance to " NE2 GLN A 194 " =    1.826
peak=   -3.575 closest distance to " CD2 LEU A 237 " =    2.899
peak=   -3.569 closest distance to " OG  SER A  97 " =    2.228
peak=   -3.568 closest distance to " O   HOH Z 275 " =    1.750
peak=   -3.551 closest distance to " CD2 LEU A 143 " =    2.563
peak=   -3.550 closest distance to " C   HIS A 108 " =    1.230
peak=   -3.548 closest distance to " CE2 TYR A  30 " =    2.584
peak=   -3.546 closest distance to " O   ILE A  49 " =    1.610
peak=   -3.546 closest distance to " O   HOH Z 412 " =    4.373
peak=   -3.544 closest distance to " CG  MET A 105 " =    0.978
peak=   -3.542 closest distance to " CG  GLN A 240 " =    2.369
peak=   -3.539 closest distance to " CZ2 TRP A 274 " =    0.990
peak=   -3.536 closest distance to " O   HOH Z  51 " =    0.899
peak=   -3.529 closest distance to " NE2 GLN A 278 " =    1.708
peak=   -3.523 closest distance to " CG  PHE A 283 " =    2.621
peak=   -3.515 closest distance to " CD2 TYR A 293 " =    1.928
peak=   -3.508 closest distance to " O   HOH Z  73 " =    2.163
peak=   -3.501 closest distance to " CG  LEU A  83 " =    2.032
peak=   -3.501 closest distance to " CA  GLY A 133 " =    2.014
peak=   -3.500 closest distance to " O   HOH Z 414 " =    1.300
peak=   -3.497 closest distance to " NH2 ARG A  79 " =    2.134
peak=   -3.497 closest distance to " OG BSER A 134 " =    1.786
peak=   -3.489 closest distance to " O   HOH Z 140 " =    1.281
peak=   -3.484 closest distance to " CG  GLN A 223 " =    2.118
peak=   -3.483 closest distance to " O   HOH Z 318 " =    1.708
peak=   -3.481 closest distance to " O   HOH Z  69 " =    1.774
peak=   -3.479 closest distance to " CD  LYS A 289 " =    2.339
peak=   -3.478 closest distance to " CB  PRO A 163 " =    2.477
peak=   -3.478 closest distance to " CG1 VAL A 112 " =    2.577
peak=   -3.478 closest distance to " O   HOH Z  11 " =    1.728
peak=   -3.474 closest distance to " O   HOH Z 337 " =    1.266
peak=   -3.467 closest distance to " CB  PRO A  54 " =    2.380
peak=   -3.460 closest distance to " ND2 ASN A 285 " =    2.176
peak=   -3.457 closest distance to " NH2AARG A 275 " =    5.466
peak=   -3.455 closest distance to " CB  TRP A  85 " =    2.449
peak=   -3.454 closest distance to " CG1 VAL A 112 " =    3.175
peak=   -3.448 closest distance to " CB  ASP A 132 " =    2.385
peak=   -3.439 closest distance to " O   HOH Z 152 " =    4.711
peak=   -3.434 closest distance to " CG2 ILE A  20 " =    3.004
peak=   -3.433 closest distance to " CE  MET A 105 " =    2.528
peak=   -3.431 closest distance to " OD2 ASP A 171 " =    2.212
peak=   -3.430 closest distance to " O   HOH Z  90 " =    2.752
peak=   -3.427 closest distance to " CD2 PHE A  61 " =    2.020
peak=   -3.416 closest distance to " O   HOH Z 292 " =    1.472
peak=   -3.413 closest distance to " CD  GLN A  58 " =    0.875
peak=   -3.410 closest distance to " CD  GLU A 277 " =    1.039
peak=   -3.404 closest distance to " O   VAL A 189 " =    2.567
peak=   -3.403 closest distance to " CD  LYS A 166 " =    2.512
peak=   -3.400 closest distance to " O   HOH Z 295 " =    1.676
peak=   -3.399 closest distance to " O   HOH Z 166 " =    1.239
peak=   -3.393 closest distance to " CG1 VAL A  78 " =    2.540
peak=   -3.380 closest distance to " O   ASP A 162 " =    2.257
peak=   -3.376 closest distance to " ND2 ASN A  60 " =    4.090
peak=   -3.375 closest distance to " CB  ALA A 248 " =    2.129
peak=   -3.372 closest distance to " O   HOH Z   1 " =    1.377
peak=   -3.370 closest distance to " O   HOH Z 359 " =    3.202
peak=   -3.368 closest distance to " NZ  LYS A 166 " =    1.027
peak=   -3.368 closest distance to " O   ARG A 145 " =    1.398
peak=   -3.363 closest distance to " O   HOH Z  38 " =    1.496
peak=   -3.361 closest distance to " CG  ASN A  39 " =    1.705
peak=   -3.358 closest distance to " CE3 TRP A 274 " =    2.441
peak=   -3.355 closest distance to " O   HOH Z  60 " =    1.182
peak=   -3.352 closest distance to " CD  GLN A  88 " =    0.820
peak=   -3.333 closest distance to " O   HOH Z 219 " =    4.605
peak=   -3.331 closest distance to " O   HOH Z 253 " =    3.952
peak=   -3.327 closest distance to " CB  PHE A 192 " =    1.815
peak=   -3.327 closest distance to " O   HOH Z 247 " =    0.939
peak=   -3.323 closest distance to " OG  SER A 245 " =    1.320
peak=   -3.312 closest distance to " CG1 VAL A 230 " =    2.127
peak=   -3.306 closest distance to " O   HOH Z  15 " =    1.516
peak=   -3.305 closest distance to " O   PHE A 218 " =    1.451
peak=   -3.302 closest distance to " OG  SER A  87 " =    1.273
peak=   -3.302 closest distance to " CA  ASP A 298 " =    1.128
peak=   -3.301 closest distance to " CB  CYS A 254 " =    2.231
peak=   -3.296 closest distance to " O   HOH Z 384 " =    3.027
peak=   -3.294 closest distance to " OH  TYR A 172 " =    1.826
peak=   -3.294 closest distance to " CB  ALA A 114 " =    2.466
peak=   -3.286 closest distance to " N   PRO A 163 " =    1.524
peak=   -3.284 closest distance to " O   HOH Z 281 " =    2.614
peak=   -3.280 closest distance to " C   ALA A 114 " =    2.196
peak=   -3.275 closest distance to " O   HOH Z 147 " =    1.163
peak=   -3.263 closest distance to " O   HOH Z 191 " =    5.465
peak=   -3.257 closest distance to " C   LEU A 143 " =    1.405
peak=   -3.252 closest distance to " O   HOH Z 251 " =    0.960
peak=   -3.251 closest distance to " CG2 THR A 157 " =    2.126
peak=   -3.250 closest distance to " O   HOH Z 166 " =    1.957
peak=   -3.249 closest distance to " O   HOH Z 352 " =    2.230
peak=   -3.249 closest distance to " OD1 ASP A 171 " =    1.649
peak=   -3.245 closest distance to " O   HOH Z  32 " =    2.143
peak=   -3.239 closest distance to " O   HOH Z 198 " =    1.886
peak=   -3.238 closest distance to " CA  GLY A 241 " =    3.358
peak=   -3.237 closest distance to " SD  MET A 188 " =    2.337
peak=   -3.237 closest distance to " N   LYS A 166 " =    1.796
peak=   -3.234 closest distance to " CD1 ILE A 239 " =    2.284
peak=   -3.232 closest distance to " CG  PRO A 163 " =    2.652
peak=   -3.228 closest distance to " NE  ARG A  36 " =    1.908
peak=   -3.225 closest distance to " O   HOH Z  96 " =    3.990
peak=   -3.221 closest distance to " O   HOH Z 378 " =    1.057
peak=   -3.216 closest distance to " CG1 VAL A 197 " =    2.223
peak=   -3.211 closest distance to " O   HOH Z 348 " =    2.142
peak=   -3.210 closest distance to " O   HOH Z 128 " =    2.600
peak=   -3.206 closest distance to " O   GLN A 240 " =    2.137
peak=   -3.205 closest distance to " OE1 GLN A 183 " =    1.568
peak=   -3.204 closest distance to " O   SER A 210 " =    1.945
peak=   -3.200 closest distance to " CD  PRO A 213 " =    2.021
peak=   -3.200 closest distance to " CE  LYS A  76 " =    2.830
peak=   -3.198 closest distance to " O   HOH Z 410 " =    2.347
peak=   -3.196 closest distance to " O   HOH Z 218 " =    3.878
peak=   -3.192 closest distance to " NH1AARG A 275 " =    1.959
peak=   -3.190 closest distance to " O   HOH Z 193 " =    1.501
peak=   -3.187 closest distance to " O   HOH Z 134 " =    3.639
peak=   -3.186 closest distance to " O   VAL A 125 " =    2.292
peak=   -3.185 closest distance to " CB  ALA A 291 " =    1.990
peak=   -3.184 closest distance to " O   SER A  95 " =    1.437
peak=   -3.182 closest distance to " O   HOH Z 216 " =    1.633
peak=   -3.174 closest distance to " O   GLU A 152 " =    1.496
peak=   -3.167 closest distance to " O   HOH Z 317 " =    1.416
peak=   -3.164 closest distance to " O   HOH Z  53 " =    1.715
peak=   -3.164 closest distance to " ND2 ASN A  45 " =    1.327
peak=   -3.164 closest distance to " O   HOH Z 200 " =    3.475
peak=   -3.162 closest distance to " CZ  PHE A  16 " =    2.237
peak=   -3.162 closest distance to " C   LEU A 222 " =    0.788
peak=   -3.152 closest distance to " CG1 VAL A 250 " =    2.767
peak=   -3.148 closest distance to " C   LYS A  76 " =    1.543
peak=   -3.142 closest distance to " OD1 ASN A 148 " =    1.604
peak=   -3.142 closest distance to " N   ALA A 226 " =    2.055
peak=   -3.141 closest distance to " CG2 ILE A 151 " =    2.553
peak=   -3.141 closest distance to " O   HOH Z   9 " =    1.859
peak=   -3.138 closest distance to " CB  ALA A 129 " =    2.363
peak=   -3.128 closest distance to " CB  ASN A  39 " =    2.290
peak=   -3.124 closest distance to " O   HOH Z   2 " =    1.713
peak=   -3.122 closest distance to " O   HOH Z 394 " =    1.576
peak=   -3.119 closest distance to " CB  PHE A 130 " =    1.325
peak=   -3.116 closest distance to " ND2BASN A 224 " =    1.656
peak=   -3.111 closest distance to " O   ALA A  34 " =    2.506
peak=   -3.094 closest distance to " O   HOH Z 346 " =    1.622
peak=   -3.091 closest distance to " CG  TRP A 266 " =    1.729
peak=   -3.068 closest distance to " O   HOH Z 389 " =    1.506
peak=   -3.064 closest distance to " O   HOH Z 143 " =    1.810
peak=   -3.055 closest distance to " OE1 GLN A  88 " =    1.228
peak=   -3.055 closest distance to " O   HOH Z 426 " =    2.323
peak=   -3.034 closest distance to " O   ASP A 272 " =    2.362

================= 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    :  0.4436 0.4427   6.257000e+00   6.245274e+00
   1_bss:  0.4342 0.4374   6.250300e+00   6.237182e+00
   1_xyz:  0.3368 0.3724   6.074356e+00   6.130325e+00
   1_adp:  0.3061 0.3890   6.030324e+00   6.154870e+00
   1_occ:  0.3057 0.3899   6.030371e+00   6.155821e+00
   2_bss:  0.3056 0.3881   6.032156e+00   6.155667e+00
   2_xyz:  0.2313 0.2955   5.780963e+00   5.949707e+00
   2_adp:  0.2103 0.2690   5.700081e+00   5.879160e+00
   2_occ:  0.2102 0.2683   5.699130e+00   5.877861e+00
   3_bss:  0.2098 0.2677   5.697566e+00   5.875446e+00
   3_xyz:  0.1689 0.2199   5.500346e+00   5.702990e+00
   3_adp:  0.1557 0.2122   5.444106e+00   5.663277e+00
   3_occ:  0.1556 0.2119   5.443318e+00   5.662231e+00
   4_bss:  0.1558 0.2117   5.441959e+00   5.660283e+00
   4_xyz:  0.1323 0.1847   5.294760e+00   5.530952e+00
   4_adp:  0.1283 0.1755   5.260872e+00   5.486467e+00
   4_occ:  0.1282 0.1754   5.260533e+00   5.486027e+00
   5_bss:  0.1284 0.1755   5.259165e+00   5.483967e+00
   5_xyz:  0.1152 0.1638   5.173129e+00   5.421962e+00
   5_adp:  0.1135 0.1613   5.163612e+00   5.412864e+00
   5_occ:  0.1134 0.1613   5.163481e+00   5.412658e+00
   5_bss:  0.1134 0.1613   5.163432e+00   5.412491e+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:  0.300  50.000  -2.205   2.093   1.311   0.000   0.000   0.000
   1_xyz:  0.300  50.000  -2.205   2.093   1.311   0.000   0.000   0.000
   1_adp:  0.300  50.000  -2.205   2.093   1.311   0.000   0.000   0.000
   1_occ:  0.300  50.000  -2.205   2.093   1.311   0.000   0.000   0.000
   2_bss:  0.349  81.626  -1.615  -0.031   0.432  -0.000   0.000   0.000
   2_xyz:  0.349  81.626  -1.615  -0.031   0.432  -0.000   0.000   0.000
   2_adp:  0.349  81.626  -1.615  -0.031   0.432  -0.000   0.000   0.000
   2_occ:  0.349  81.626  -1.615  -0.031   0.432  -0.000   0.000   0.000
   3_bss:  0.345  80.000  -2.249  -1.686  -0.326  -0.000  -0.000  -0.000
   3_xyz:  0.345  80.000  -2.249  -1.686  -0.326  -0.000  -0.000  -0.000
   3_adp:  0.345  80.000  -2.249  -1.686  -0.326  -0.000  -0.000  -0.000
   3_occ:  0.345  80.000  -2.249  -1.686  -0.326  -0.000  -0.000  -0.000
   4_bss:  0.336  80.000  -2.207  -2.361  -0.555  -0.000  -0.000  -0.000
   4_xyz:  0.336  80.000  -2.207  -2.361  -0.555  -0.000  -0.000  -0.000
   4_adp:  0.336  80.000  -2.207  -2.361  -0.555  -0.000  -0.000  -0.000
   4_occ:  0.336  80.000  -2.207  -2.361  -0.555  -0.000  -0.000  -0.000
   5_bss:  0.321  63.998  -2.401  -2.663  -0.784  -0.000  -0.000  -0.000
   5_xyz:  0.321  63.998  -2.401  -2.663  -0.784  -0.000  -0.000  -0.000
   5_adp:  0.321  63.998  -2.401  -2.663  -0.784  -0.000  -0.000  -0.000
   5_occ:  0.321  63.998  -2.401  -2.663  -0.784  -0.000  -0.000  -0.000
   5_bss:  0.314  55.829  -2.368  -2.631  -0.751  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.234 0.4798  0.6461    62388.144
   1_bss:  52.582 0.4867  0.6690    60471.283
   1_xyz:  40.701 0.6344  0.8409    39907.134
   1_adp:  42.801 0.6079  0.8202    43403.397
   1_occ:  42.927 0.6064  0.8175    43597.703
   2_bss:  42.711 0.6091  0.8001    43416.653
   2_xyz:  30.521 0.7508  0.9537    23150.403
   2_adp:  27.226 0.7878  0.9724    19195.865
   2_occ:  27.183 0.7882  0.9726    19127.597
   3_bss:  27.024 0.7898  0.9402    18956.341
   3_xyz:  21.542 0.8459  0.9763    12478.604
   3_adp:  20.449 0.8571  0.9734    11517.335
   3_occ:  20.420 0.8574  0.9732    11481.703
   4_bss:  20.352 0.8579  0.9640    11413.276
   4_xyz:  17.259 0.8866  0.9801     8491.292
   4_adp:  16.110 0.8974  0.9801     7815.137
   4_occ:  16.102 0.8974  0.9800     7802.212
   5_bss:  16.074 0.8976  0.9715     7750.501
   5_xyz:  14.642 0.9096  0.9781     6735.934
   5_adp:  14.406 0.9118  0.9752     6641.678
   5_occ:  14.406 0.9118  0.9752     6637.165
   5_bss:  14.408 0.9118  0.9749     6630.034
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.7192e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.7192e-01
   1_xyz:   1.426  0.010  0.095 15.733  0.006  4.108   1.0969e-01
   1_adp:   1.426  0.010  0.095 15.733  0.006  4.108   1.0969e-01
   1_occ:   1.426  0.010  0.095 15.733  0.006  4.108   1.0969e-01
   2_bss:   1.426  0.010  0.095 15.733  0.006  4.108   1.0969e-01
   2_xyz:   1.320  0.010  0.096 15.182  0.005  4.109   9.5212e-02
   2_adp:   1.320  0.010  0.096 15.182  0.005  4.109   9.5212e-02
   2_occ:   1.320  0.010  0.096 15.182  0.005  4.109   9.5212e-02
   3_bss:   1.320  0.010  0.096 15.182  0.005  4.109   9.5212e-02
   3_xyz:   0.961  0.006  0.069 14.498  0.003  4.118   5.3779e-02
   3_adp:   0.961  0.006  0.069 14.498  0.003  4.118   5.3779e-02
   3_occ:   0.961  0.006  0.069 14.498  0.003  4.118   5.3779e-02
   4_bss:   0.961  0.006  0.069 14.498  0.003  4.118   5.3779e-02
   4_xyz:   0.958  0.007  0.072 14.360  0.003  4.111   5.5531e-02
   4_adp:   0.958  0.007  0.072 14.360  0.003  4.111   5.5531e-02
   4_occ:   0.958  0.007  0.072 14.360  0.003  4.111   5.5531e-02
   5_bss:   0.958  0.007  0.072 14.360  0.003  4.111   5.5531e-02
   5_xyz:   1.139  0.010  0.085 14.840  0.004  4.117   7.7002e-02
   5_adp:   1.139  0.010  0.085 14.840  0.004  4.117   7.7002e-02
   5_occ:   1.139  0.010  0.085 14.840  0.004  4.117   7.7002e-02
   5_bss:   1.139  0.010  0.085 14.840  0.004  4.117   7.7002e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4158e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4158e-01
   1_xyz:   8.836  0.059  0.319 83.895  0.049  2.036   9.0155e-02
   1_adp:   8.836  0.059  0.319 83.895  0.049  2.036   9.0155e-02
   1_occ:   8.836  0.059  0.319 83.895  0.049  2.036   9.0155e-02
   2_bss:   8.836  0.059  0.319 83.895  0.049  2.036   9.0155e-02
   2_xyz:   7.289  0.068  0.297 83.141  0.031  2.058   9.9878e-02
   2_adp:   7.289  0.068  0.297 83.141  0.031  2.058   9.9878e-02
   2_occ:   7.289  0.068  0.297 83.141  0.031  2.058   9.9878e-02
   3_bss:   7.289  0.068  0.297 83.141  0.031  2.058   9.9878e-02
   3_xyz:   7.237  0.035  0.236 80.341  0.022  2.300   5.4520e-02
   3_adp:   7.237  0.035  0.236 80.341  0.022  2.300   5.4520e-02
   3_occ:   7.237  0.035  0.236 80.341  0.022  2.300   5.4520e-02
   4_bss:   7.237  0.035  0.236 80.341  0.022  2.300   5.4520e-02
   4_xyz:   7.267  0.040  0.224 81.621  0.031  2.374   4.8938e-02
   4_adp:   7.267  0.040  0.224 81.621  0.031  2.374   4.8938e-02
   4_occ:   7.267  0.040  0.224 81.621  0.031  2.374   4.8938e-02
   5_bss:   7.267  0.040  0.224 81.621  0.031  2.374   4.8938e-02
   5_xyz:   7.532  0.056  0.292 83.818  0.031  2.255   6.6232e-02
   5_adp:   7.532  0.056  0.292 83.818  0.031  2.255   6.6232e-02
   5_occ:   7.532  0.056  0.292 83.818  0.031  2.255   6.6232e-02
   5_bss:   7.532  0.056  0.292 83.818  0.031  2.255   6.6232e-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: 106.17   0.00  19.02  67.21   0.00  15.34 106.17   0.68  39.05
   1_occ: 106.17   0.00  19.02  67.21   0.00  15.34 106.17   0.68  39.05
   2_bss: 106.17   0.00  19.02  67.21   0.00  15.34 106.17   0.68  39.05
   2_xyz: 106.17   0.00  19.02  67.21   0.00  15.34 106.17   0.68  39.05
   2_adp: 104.41   0.00  18.30  77.16   0.00  14.06 104.41   4.35  41.39
   2_occ: 104.41   0.00  18.30  77.16   0.00  14.06 104.41   4.35  41.39
   3_bss: 104.41   0.00  18.30  77.16   0.00  14.06 104.41   4.35  41.39
   3_xyz: 104.41   0.00  18.30  77.16   0.00  14.06 104.41   4.35  41.39
   3_adp: 105.55   0.00  18.75  88.22   0.00  13.62 105.55   6.24  46.69
   3_occ: 105.55   0.00  18.75  88.22   0.00  13.62 105.55   6.24  46.69
   4_bss: 105.55   0.00  18.75  88.22   0.00  13.62 105.55   6.24  46.69
   4_xyz: 105.55   0.00  18.75  88.22   0.00  13.62 105.55   6.24  46.69
   4_adp:  97.75   0.64  17.74  90.53   0.64  13.06  97.75   6.05  43.21
   4_occ:  97.75   0.64  17.74  90.53   0.64  13.06  97.75   6.05  43.21
   5_bss:  97.75   0.64  17.74  90.53   0.64  13.06  97.75   6.05  43.21
   5_xyz:  97.75   0.64  17.74  90.53   0.64  13.06  97.75   6.05  43.21
   5_adp:  91.90   0.94  17.24  91.90   0.94  12.88  91.76   6.41  41.01
   5_occ:  91.90   0.94  17.24  91.90   0.94  12.88  91.76   6.41  41.01
   5_bss:  91.87   0.91  17.21  91.87   0.91  12.84  91.72   6.38  40.98
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.730    0.014    0.311
   1_adp:    1.730    0.014    0.311
   1_occ:    1.730    0.014    0.311
   2_bss:    1.730    0.014    0.311
   2_xyz:    1.356    0.046    0.544
   2_adp:    1.356    0.046    0.544
   2_occ:    1.356    0.046    0.544
   3_bss:    1.356    0.046    0.544
   3_xyz:    1.430    0.023    0.628
   3_adp:    1.430    0.023    0.628
   3_occ:    1.430    0.023    0.628
   4_bss:    1.430    0.023    0.628
   4_xyz:    1.408    0.037    0.684
   4_adp:    1.408    0.037    0.684
   4_occ:    1.408    0.037    0.684
   5_bss:    1.408    0.037    0.684
   5_xyz:    1.491    0.057    0.713
   5_adp:    1.491    0.057    0.713
   5_occ:    1.491    0.057    0.713
   5_bss:    1.491    0.057    0.713
------------------------------------------------------------------------

CPU time actual refinement: 361.81


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_866/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_866/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_866/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_866/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_866/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 361.67 
  Macro-tasks:
    bulk solvent and scale       = 57.95  
    individual site refinement   = 136.86 
    weights calculation          = 30.75  
    collect and process          = 6.69   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 232.34 
  Micro-tasks:
    mask                            = 2.33   
    f_calc                          = 114.02 
    alpha_beta                      = 8.48   
    target                          = 1.24   
    gradients_wrt_atomic_parameters = 115.44 
    fmodel                         = 9.28   
    r_factors                      = 0.23   
    phase_errors                   = 11.49  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 262.75 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.182 micro seconds
Total CPU time: 6.25 minutes
from_scatterers_fft:    622 calls, 113.58 s
gradients_fft:          567 calls, 104.76 s

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

# Date 2008-01-16 Time 05:52:08 PST -0800 (1200491528.44 s)
Start R-work = 0.4436, R-free = 0.4427 (no bulk solvent and anisotropic scale)
Final R-work = 0.1375, R-free = 0.1821 (no bulk solvent and anisotropic scale)

Start R-work = 0.4342, R-free = 0.4374
Final R-work = 0.1134, R-free = 0.1613