# Date 2008-01-16 Time 06:01:28 PST -0800 (1200492088.26 s)
#phil __OFF__

Command line arguments: "../978.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25080
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 978

-------------------------------------------------------------------------------
  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: (71.3037, 45.7567, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


================================== 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: (71.3037, 45.7567, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2591 1.95446
Completeness in resolution range: 0.907823
Completeness with d_max=infinity: 0.905264

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2591
                             d_min =   1.9545

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: (71.3037, 45.7567, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2591 1.95446
Completeness in resolution range: 0.907823
Completeness with d_max=infinity: 0.905264

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2596 -  4.1845 [2269/2295]  2040   229  10.1%
  bin  2:  4.1845 -  3.3328 [2181/2201]  1971   210   9.6%
  bin  3:  3.3328 -  2.9148 [2143/2162]  1922   221  10.3%
  bin  4:  2.9148 -  2.6498 [2112/2142]  1895   217  10.3%
  bin  5:  2.6498 -  2.4607 [2136/2155]  1920   216  10.1%
  bin  6:  2.4607 -  2.3162 [2098/2123]  1892   206   9.8%
  bin  7:  2.3162 -  2.2005 [2114/2142]  1901   213  10.1%
  bin  8:  2.2005 -  2.1050 [2081/2117]  1876   205   9.9%
  bin  9:  2.1050 -  2.0242 [1941/2118]  1757   184   9.5%
  bin 10:  2.0242 -  1.9545 [ 514/2123]   456    58  11.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_978/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.68 -     2.32: 31
        2.32 -     2.97: 1780
        2.97 -     3.61: 4544
        3.61 -     4.26: 9120
        4.26 -     4.90: 12685
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 324 " - " O   HOH Z 374 "  1.854 3.040 -x,y-1/2,-z+1/2
  ... (remaining 28155 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_978/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_978/model_refine_001.geo

CPU time processing inputs: 9.22


============================ 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 = 71.30375 45.75675 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5008   r_free= 0.5059   ksol= 0.00   Bsol= 0.00   scale= 0.857    |
|                                                                             |
| 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:   0.94 A                  |
| x-ray target function (ml) for work reflections: 6.310377                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2596 -  4.6684 0.99   1473  165 0.4214 0.4000      6.6642      6.6276|
|  2:  4.6684 -  3.7232 0.99   1414  156 0.4547 0.4591      6.8752      6.8884|
|  3:  3.7232 -  3.2577 0.99   1383  155 0.4732 0.4511      6.6954      6.6812|
|  4:  3.2577 -  2.9623 0.99   1393  152 0.5056 0.5384      6.5508       6.542|
|  5:  2.9623 -  2.7513 0.99   1368  159 0.5344 0.5708      6.3777      6.4137|
|  6:  2.7513 -  2.5899 0.99   1370  148 0.5360 0.5229      6.3019      6.2286|
|  7:  2.5899 -  2.4607 0.99   1347  158 0.5362 0.5466      6.2347      6.1864|
|  8:  2.4607 -  2.3540 0.98   1354  142 0.5374 0.5669      6.1665      6.1402|
|  9:  2.3540 -  2.2637 0.98   1350  155 0.5419 0.5593      6.1368      6.2285|
| 10:  2.2637 -  2.1858 1.00   1358  149 0.5370 0.5529      6.0625      6.0474|
| 11:  2.1858 -  2.1177 0.98   1323  150 0.5205 0.5123      6.0144      6.0325|
| 12:  2.1177 -  2.0573 0.98   1360  138 0.5336 0.5555      5.9265      5.9296|
| 13:  2.0573 -  2.0032 0.69    926  109 0.5342 0.4942      5.8939      5.7845|
| 14:  2.0032 -  1.9545 0.15    211   23 0.5056 0.4823      5.8333      5.9421|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2596 -  4.6684  1473   165  0.68  36.12   0.79     0.73      81515.73|
|  2:  4.6684 -  3.7232  1414   156  0.63  41.55   0.87     0.73     141703.86|
|  3:  3.7232 -  3.2577  1383   155  0.45  56.14   0.88     0.62     156726.00|
|  4:  3.2577 -  2.9623  1393   152  0.29  68.39   0.85     0.43     148145.43|
|  5:  2.9623 -  2.7513  1368   159  0.23  72.88   0.84     0.35     107861.86|
|  6:  2.7513 -  2.5899  1370   148  0.20  74.74   0.87     0.31      90153.58|
|  7:  2.5899 -  2.4607  1347   158  0.22  73.30   0.87     0.32      76058.12|
|  8:  2.4607 -  2.3540  1354   142  0.19  75.71   0.88     0.29      69630.52|
|  9:  2.3540 -  2.2637  1350   155  0.18  76.69   0.89     0.28      65884.07|
| 10:  2.2637 -  2.1858  1358   149  0.17  77.06   0.88     0.27      58187.59|
| 11:  2.1858 -  2.1177  1323   150  0.20  75.39   0.94     0.32      54667.42|
| 12:  2.1177 -  2.0573  1360   138  0.23  72.88   0.88     0.39      46997.87|
| 13:  2.0573 -  2.0032   926   109  0.26  70.42   0.93     0.44      40390.87|
| 14:  2.0032 -  1.9545   211    23  0.34  64.89   1.03     0.49      30656.97|
|alpha:            min =        0.27 max =            0.73 mean =         0.43|
|beta:             min =    30656.97 max =       156726.00 mean =     88453.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.31|
|phase err.(work): min =        0.00 max =           90.00 mean =        66.60|
|phase err.(test): min =        0.00 max =           89.81 mean =        66.98|
|-----------------------------------------------------------------------------|

============================== 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 = 22.913453             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.897   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.982141              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.790   (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 |  1.681 -  2.003:       11 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.003 -  2.325:       20 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.325 -  2.647:       78 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.647 -  2.969:     1702 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.969 -  3.290:     1899 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.290 -  3.612:     2645 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.612 -  3.934:     4716 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.934 -  4.256:     4404 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.256 -  4.578:     5764 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.578 -  4.900:     6921 |
|-----------------------------------------------------------------------------|
|-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 |        0.185 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.681 |       0.494 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.949)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5008   r_free= 0.5059   ksol= 0.00   Bsol= 0.00   scale= 0.857    |
|                                                                             |
| 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:   0.94 A                  |
| x-ray target function (ml) for work reflections: 6.310377                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4930   r_free= 0.5026   ksol= 0.30   Bsol= 50.00   scale= 0.892   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.82,0.20,2.87,0.00,0.00,0.00); trace/3= 0.41                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.94 A                  |
| x-ray target function (ml) for work reflections: 6.310051                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.690317             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.694   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.168524              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.272   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4930      final r-factor (work) = 0.4298          |
| start r-factor (free) = 0.5026      final r-factor (free) = 0.4734          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 55.9406 = 17.69 * 0.50 * 6.3035 + 1.00 * 0.1848                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 55.4307 = 17.69 * 0.50 * 6.2508 + 1.00 * 0.1416                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4298      final r-factor (work) = 0.3985          |
| start r-factor (free) = 0.4734      final r-factor (free) = 0.4835          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.5610 = 2.17 * 1.00 * 6.2508 + 1.00 * 0.0060                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.4722 = 2.17 * 1.00 * 6.2017 + 1.00 * 0.0237                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.949)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.39   20.74    None  None   None       |
|    all(noH): 2823   0      0.00    97.39   20.74    None  None   None       |
|    Sol.    : 438    0      0.00    97.39   35.30    None  None   None       |
|    Mac.    : 2385   0      0.00    93.90   18.06    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 -   9.739:  711   |   5:    48.695 -  58.434:   89        |
|      1:     9.739 -  19.478:  843   |   6:    58.434 -  68.173:   50        |
|      2:    19.478 -  29.217:  620   |   7:    68.173 -  77.913:   28        |
|      3:    29.217 -  38.956:  319   |   8:    77.913 -  87.652:   10        |
|      4:    38.956 -  48.695:  150   |   9:    87.652 -  97.391:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3985 r_free = 0.4835             target_work(ml) = 6.206         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3980 r_free = 0.4849             target_work(ml) = 6.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3980   r_free= 0.4849   ksol= 0.30   Bsol= 50.00   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.82,0.20,2.87,0.00,0.00,0.00); trace/3= 0.41                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.205304                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3986   r_free= 0.4841   ksol= 0.36   Bsol= 88.40   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.24,0.17,2.35,0.00,0.00,0.00); trace/3= 0.76                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.208427                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 25.863703             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.407  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.945565              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.185  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3986      final r-factor (work) = 0.3430          |
| start r-factor (free) = 0.4841      final r-factor (free) = 0.4294          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 80.3763 = 25.86 * 0.50 * 6.2044 + 1.00 * 0.1413                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 79.8867 = 25.86 * 0.50 * 6.1671 + 1.00 * 0.1349                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3430      final r-factor (work) = 0.3253          |
| start r-factor (free) = 0.4294      final r-factor (free) = 0.4182          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8552 = 0.95 * 1.00 * 6.1671 + 1.00 * 0.0238                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7643 = 0.95 * 1.00 * 6.0805 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.949)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.19   19.87    None  None   None       |
|    all(noH): 2823   0      0.00    87.19   19.87    None  None   None       |
|    Sol.    : 438    0      0.00    87.19   35.94    None  None   None       |
|    Mac.    : 2385   0      0.00    79.37   16.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.719:  614   |   5:    43.595 -  52.314:  103        |
|      1:     8.719 -  17.438:  890   |   6:    52.314 -  61.034:   61        |
|      2:    17.438 -  26.157:  607   |   7:    61.034 -  69.753:   36        |
|      3:    26.157 -  34.876:  321   |   8:    69.753 -  78.472:   13        |
|      4:    34.876 -  43.595:  173   |   9:    78.472 -  87.191:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3253 r_free = 0.4182             target_work(ml) = 6.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3251 r_free = 0.4178             target_work(ml) = 6.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3251   r_free= 0.4178   ksol= 0.36   Bsol= 88.40   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.24,0.17,2.35,0.00,0.00,0.00); trace/3= 0.76                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.067912                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3254   r_free= 0.4169   ksol= 0.37   Bsol= 100.38   scale= 1.014  |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.53,-0.70,1.18,-0.00,0.00,0.00); trace/3= -0.01                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.066856                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.440790             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.008  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.015903              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.393  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3254      final r-factor (work) = 0.2700          |
| start r-factor (free) = 0.4169      final r-factor (free) = 0.3475          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.9195 = 11.44 * 0.50 * 6.0808 + 1.00 * 0.1351                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.4859 = 11.44 * 0.50 * 6.0136 + 1.00 * 0.0860                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2700      final r-factor (work) = 0.2435          |
| start r-factor (free) = 0.3475      final r-factor (free) = 0.3332          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.1375 = 2.02 * 1.00 * 6.0136 + 1.00 * 0.0147                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.8698 = 2.02 * 1.00 * 5.8775 + 1.00 * 0.0213                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.949)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.71   20.79    None  None   None       |
|    all(noH): 2823   0      0.00    96.71   20.79    None  None   None       |
|    Sol.    : 438    0      0.00    95.14   46.15    None  None   None       |
|    Mac.    : 2385   0      0.00    96.71   16.13    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.671:  869   |   5:    48.357 -  58.028:  120        |
|      1:     9.671 -  19.343:  865   |   6:    58.028 -  67.700:   66        |
|      2:    19.343 -  29.014:  428   |   7:    67.700 -  77.371:   47        |
|      3:    29.014 -  38.686:  238   |   8:    77.371 -  87.043:   27        |
|      4:    38.686 -  48.357:  149   |   9:    87.043 -  96.714:   14        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2435 r_free = 0.3332             target_work(ml) = 5.856         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2433 r_free = 0.3329             target_work(ml) = 5.855         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2433   r_free= 0.3329   ksol= 0.37   Bsol= 100.38   scale= 1.038  |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.53,-0.70,1.18,-0.00,0.00,0.00); trace/3= -0.01                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.855269                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2434   r_free= 0.3331   ksol= 0.36   Bsol= 107.75   scale= 1.017  |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.26,-1.43,0.47,-0.00,0.00,0.00); trace/3= -0.74                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.854349                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.919315              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.100  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.560597              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.840  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2434      final r-factor (work) = 0.2099          |
| start r-factor (free) = 0.3331      final r-factor (free) = 0.2877          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6041 = 3.92 * 0.50 * 5.8776 + 1.00 * 0.0860                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4294 = 3.92 * 0.50 * 5.8013 + 1.00 * 0.0609                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2099      final r-factor (work) = 0.1983          |
| start r-factor (free) = 0.2877      final r-factor (free) = 0.2683          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2732 = 0.56 * 1.00 * 5.8013 + 1.00 * 0.0210                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2105 = 0.56 * 1.00 * 5.6995 + 1.00 * 0.0154                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.949)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.52   19.92    None  None   None       |
|    all(noH): 2823   0      0.00    97.52   19.92    None  None   None       |
|    Sol.    : 438    0      3.34    94.74   46.85    None  None   None       |
|    Mac.    : 2385   0      0.00    97.52   14.97    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.752:  959   |   5:    48.761 -  58.514:  106        |
|      1:     9.752 -  19.505:  935   |   6:    58.514 -  68.266:   74        |
|      2:    19.505 -  29.257:  328   |   7:    68.266 -  78.018:   44        |
|      3:    29.257 -  39.009:  199   |   8:    78.018 -  87.771:   21        |
|      4:    39.009 -  48.761:  144   |   9:    87.771 -  97.523:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1983 r_free = 0.2683             target_work(ml) = 5.665         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1982 r_free = 0.2682             target_work(ml) = 5.664         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1982   r_free= 0.2682   ksol= 0.36   Bsol= 107.75   scale= 1.026  |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.26,-1.43,0.47,-0.00,0.00,0.00); trace/3= -0.74                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.664497                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1981   r_free= 0.2674   ksol= 0.33   Bsol= 78.53   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.63,-2.13,0.10,-0.00,0.00,0.00); trace/3= -1.22                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.661649                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.899302              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.343  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 6.155408              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.367  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1981      final r-factor (work) = 0.1680          |
| start r-factor (free) = 0.2674      final r-factor (free) = 0.2298          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1707 = 3.90 * 0.50 * 5.6983 + 1.00 * 0.0609                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.9722 = 3.90 * 0.50 * 5.5945 + 1.00 * 0.0649                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1680      final r-factor (work) = 0.1547          |
| start r-factor (free) = 0.2298      final r-factor (free) = 0.2171          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 34.4517 = 6.16 * 1.00 * 5.5945 + 1.00 * 0.0154                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 33.7206 = 6.16 * 1.00 * 5.4754 + 1.00 * 0.0173                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.949)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.49  19.91    None  None   None       |
|    all(noH): 2823   0      0.00    111.49  19.91    None  None   None       |
|    Sol.    : 438    0      5.54    111.49  52.44    None  None   None       |
|    Mac.    : 2385   0      0.00    101.70  13.94    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.149: 1231   |   5:    55.747 -  66.896:   94        |
|      1:    11.149 -  22.299:  907   |   6:    66.896 -  78.045:   88        |
|      2:    22.299 -  33.448:  236   |   7:    78.045 -  89.194:   35        |
|      3:    33.448 -  44.597:   99   |   8:    89.194 - 100.344:   26        |
|      4:    44.597 -  55.747:  102   |   9:   100.344 - 111.493:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1547 r_free = 0.2171             target_work(ml) = 5.444         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1546 r_free = 0.2170             target_work(ml) = 5.444         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1546   r_free= 0.2170   ksol= 0.33   Bsol= 78.53   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.63,-2.13,0.10,-0.00,0.00,0.00); trace/3= -1.22                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.444098                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2596 -  4.6684 0.99   1473  165 0.0974 0.1409      5.4178      5.6855|
|  2:  4.6684 -  3.7232 0.99   1414  156 0.0988 0.1471      5.5981      5.9325|
|  3:  3.7232 -  3.2577 0.99   1383  155 0.1426 0.2181      5.7345      6.0753|
|  4:  3.2577 -  2.9623 0.99   1393  152 0.1808 0.2372      5.7608      5.9494|
|  5:  2.9623 -  2.7513 0.99   1368  159 0.1817 0.2360       5.624      5.8416|
|  6:  2.7513 -  2.5899 0.99   1370  148 0.1804 0.2525      5.5265      5.7353|
|  7:  2.5899 -  2.4607 0.99   1347  158 0.1746 0.2441      5.4416      5.6576|
|  8:  2.4607 -  2.3540 0.98   1354  142 0.1852 0.2662      5.4383      5.6564|
|  9:  2.3540 -  2.2637 0.98   1350  155 0.1832 0.2531      5.3862      5.6378|
| 10:  2.2637 -  2.1858 1.00   1358  149 0.1696 0.2486      5.2949      5.4972|
| 11:  2.1858 -  2.1177 0.98   1323  150 0.1669 0.2463      5.2473      5.5582|
| 12:  2.1177 -  2.0573 0.98   1360  138 0.1640 0.2275      5.1399      5.3396|
| 13:  2.0573 -  2.0032 0.69    926  109 0.1578 0.2347      5.0848       5.266|
| 14:  2.0032 -  1.9545 0.15    211   23 0.1657 0.2541      5.0553      5.4344|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2596 -  4.6684  1473   165  0.93  10.35   0.96     0.93       8623.19|
|  2:  4.6684 -  3.7232  1414   156  0.93  10.84   1.04     1.02      13317.89|
|  3:  3.7232 -  3.2577  1383   155  0.89  17.04   1.06     1.06      18608.03|
|  4:  3.2577 -  2.9623  1393   152  0.84  22.44   1.04     1.01      21142.16|
|  5:  2.9623 -  2.7513  1368   159  0.83  23.61   1.02     1.00      16847.22|
|  6:  2.7513 -  2.5899  1370   148  0.82  24.76   1.00     0.94      13924.78|
|  7:  2.5899 -  2.4607  1347   158  0.83  23.36   1.02     0.95      11669.05|
|  8:  2.4607 -  2.3540  1354   142  0.82  24.34   1.01     0.97      11707.30|
|  9:  2.3540 -  2.2637  1350   155  0.81  25.18   1.00     0.93      10596.83|
| 10:  2.2637 -  2.1858  1358   149  0.82  24.98   1.01     0.97       9614.69|
| 11:  2.1858 -  2.1177  1323   150  0.83  23.93   1.00     0.92       8488.81|
| 12:  2.1177 -  2.0573  1360   138  0.83  24.29   1.01     0.98       7253.96|
| 13:  2.0573 -  2.0032   926   109  0.83  24.01   1.00     0.95       6426.80|
| 14:  2.0032 -  1.9545   211    23  0.86  20.94   0.96     0.94       5612.27|
|alpha:            min =        0.92 max =            1.06 mean =         0.97|
|beta:             min =     5612.27 max =        21142.16 mean =     12252.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.85|
|phase err.(work): min =        0.00 max =           89.95 mean =        21.29|
|phase err.(test): min =        0.00 max =           89.89 mean =        20.07|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1552   r_free= 0.2171   ksol= 0.33   Bsol= 80.00   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.69,-2.39,-0.05,-0.00,-0.00,-0.00); trace/3= -1.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.444248                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1552   r_free= 0.2171   ksol= 0.33   Bsol= 80.00   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.69,-2.39,-0.05,-0.00,-0.00,-0.00); trace/3= -1.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.444248                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2596 -  4.6684 0.99   1473  165 0.0995 0.1385      5.4178      5.6694|
|  2:  4.6684 -  3.7232 0.99   1414  156 0.0997 0.1473       5.599      5.9333|
|  3:  3.7232 -  3.2577 0.99   1383  155 0.1429 0.2189       5.736      6.0797|
|  4:  3.2577 -  2.9623 0.99   1393  152 0.1808 0.2371      5.7619       5.949|
|  5:  2.9623 -  2.7513 0.99   1368  159 0.1814 0.2356      5.6238       5.841|
|  6:  2.7513 -  2.5899 0.99   1370  148 0.1804 0.2528       5.526      5.7353|
|  7:  2.5899 -  2.4607 0.99   1347  158 0.1746 0.2440      5.4411      5.6569|
|  8:  2.4607 -  2.3540 0.98   1354  142 0.1852 0.2665       5.438       5.657|
|  9:  2.3540 -  2.2637 0.98   1350  155 0.1830 0.2529      5.3857      5.6372|
| 10:  2.2637 -  2.1858 1.00   1358  149 0.1694 0.2484      5.2947      5.4977|
| 11:  2.1858 -  2.1177 0.98   1323  150 0.1667 0.2468      5.2471      5.5593|
| 12:  2.1177 -  2.0573 0.98   1360  138 0.1640 0.2279      5.1406      5.3406|
| 13:  2.0573 -  2.0032 0.69    926  109 0.1578 0.2341      5.0849      5.2645|
| 14:  2.0032 -  1.9545 0.15    211   23 0.1657 0.2538      5.0552      5.4322|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2596 -  4.6684  1473   165  0.93  10.23   0.96     0.93       8378.22|
|  2:  4.6684 -  3.7232  1414   156  0.93  10.72   1.04     1.02      13118.15|
|  3:  3.7232 -  3.2577  1383   155  0.89  17.05   1.06     1.06      18625.49|
|  4:  3.2577 -  2.9623  1393   152  0.84  22.49   1.03     1.00      21212.84|
|  5:  2.9623 -  2.7513  1368   159  0.83  23.61   1.02     0.99      16868.02|
|  6:  2.7513 -  2.5899  1370   148  0.82  24.73   0.99     0.93      13904.29|
|  7:  2.5899 -  2.4607  1347   158  0.83  23.35   1.01     0.95      11659.04|
|  8:  2.4607 -  2.3540  1354   142  0.82  24.34   1.01     0.97      11700.75|
|  9:  2.3540 -  2.2637  1350   155  0.81  25.16   1.00     0.92      10587.63|
| 10:  2.2637 -  2.1858  1358   149  0.82  24.98   1.00     0.96       9615.43|
| 11:  2.1858 -  2.1177  1323   150  0.83  23.93   0.99     0.92       8501.87|
| 12:  2.1177 -  2.0573  1360   138  0.82  24.32   1.00     0.97       7269.98|
| 13:  2.0573 -  2.0032   926   109  0.83  24.00   0.98     0.95       6429.27|
| 14:  2.0032 -  1.9545   211    23  0.86  20.84   0.94     0.94       5582.01|
|alpha:            min =        0.92 max =            1.06 mean =         0.97|
|beta:             min =     5582.01 max =        21212.84 mean =     12222.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.85|
|phase err.(work): min =        0.00 max =           89.97 mean =        21.27|
|phase err.(test): min =        0.00 max =           89.96 mean =        20.05|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.949)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.50  19.91    None  None   None       |
|    all(noH): 2823   0      0.00    111.50  19.91    None  None   None       |
|    Sol.    : 438    0      5.54    111.50  52.44    None  None   None       |
|    Mac.    : 2385   0      0.00    101.71  13.94    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  11.152: 1231   |   5:    55.749 -  66.899:   94        |
|      1:    11.152 -  22.302:  907   |   6:    66.899 -  78.048:   88        |
|      2:    22.302 -  33.451:  236   |   7:    78.048 -  89.197:   35        |
|      3:    33.451 -  44.600:   99   |   8:    89.197 - 100.347:   26        |
|      4:    44.600 -  55.749:  102   |   9:   100.347 - 111.496:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 357         
Filter by distance & map next to the model:
   mapped sites are within: 0.610 - 4.037
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 351 from: 357
   mapped sites are within: 0.763 - 4.037

peak=    7.550 closest distance to " O   HOH Z 103 " =    1.331
peak=    6.872 closest distance to " O   HOH Z 396 " =    1.197
peak=    6.538 closest distance to " O   HOH Z 381 " =    1.498
peak=    5.999 closest distance to " O   HOH Z 385 " =    1.581
peak=    5.712 closest distance to " O   HOH Z 130 " =    1.193
peak=    5.675 closest distance to " O   HOH Z 131 " =    1.859
peak=    5.536 closest distance to " O   HOH Z 245 " =    1.484
peak=    5.431 closest distance to " CG  PRO A  90 " =    1.301
peak=    5.239 closest distance to " NE2 GLN A 103 " =    0.904
peak=    5.225 closest distance to " O   HOH Z 351 " =    1.029
peak=    5.026 closest distance to " O   HOH Z 431 " =    2.005
peak=    4.995 closest distance to " O   HOH Z 390 " =    1.245
peak=    4.874 closest distance to " O   HOH Z 424 " =    2.062
peak=    4.835 closest distance to " O   HOH Z 117 " =    0.946
peak=    4.824 closest distance to " O   HOH Z 403 " =    1.834
peak=    4.813 closest distance to " O   HOH Z 359 " =    1.889
peak=    4.780 closest distance to " O   HOH Z  27 " =    1.203
peak=    4.770 closest distance to " O   HOH Z  70 " =    1.351
peak=    4.740 closest distance to " O   HOH Z  29 " =    1.644
peak=    4.731 closest distance to " NH1AARG A 145 " =    1.274
peak=    4.723 closest distance to " C   PRO A  54 " =    0.992
peak=    4.723 closest distance to " O   HOH Z  11 " =    1.424
peak=    4.694 closest distance to " O   HOH Z 127 " =    1.227
peak=    4.662 closest distance to " O   HOH Z 287 " =    1.850
peak=    4.637 closest distance to " O  BHOH Z  74 " =    1.149
peak=    4.608 closest distance to " CB  SER A  63 " =    1.615
peak=    4.596 closest distance to " O   HOH Z  21 " =    1.334
peak=    4.589 closest distance to " C   PRO A 198 " =    1.313
peak=    4.572 closest distance to " N   SER A  63 " =    0.876
peak=    4.555 closest distance to " O   HOH Z  67 " =    1.684
peak=    4.554 closest distance to " O   HOH Z 147 " =    1.459
peak=    4.550 closest distance to " O   HOH Z 182 " =    1.501
peak=    4.533 closest distance to " N   ALA A 165 " =    1.343
peak=    4.508 closest distance to " O   HOH Z 144 " =    2.141
peak=    4.458 closest distance to " C   VAL A  72 " =    1.006
peak=    4.457 closest distance to " O   HOH Z  66 " =    1.298
peak=    4.435 closest distance to " O   HOH Z 350 " =    1.336
peak=    4.409 closest distance to " O   HOH Z 295 " =    1.712
peak=    4.403 closest distance to " O   HOH Z 255 " =    1.045
peak=    4.403 closest distance to " O   HOH Z  46 " =    1.547
peak=    4.386 closest distance to " CB  SER A 216 " =    1.167
peak=    4.385 closest distance to " O   HOH Z  65 " =    1.951
peak=    4.373 closest distance to " O   HOH Z 422 " =    1.175
peak=    4.354 closest distance to " NE2 GLN A  11 " =    1.255
peak=    4.351 closest distance to " O   HOH Z 105 " =    1.501
peak=    4.346 closest distance to " O   HOH Z 181 " =    1.568
peak=    4.336 closest distance to " O   HOH Z 417 " =    2.914
peak=    4.323 closest distance to " N   PHE A  59 " =    0.870
peak=    4.311 closest distance to " O   HOH Z  92 " =    1.419
peak=    4.287 closest distance to " O   HOH Z 360 " =    1.263
peak=    4.286 closest distance to " O   HOH Z  49 " =    2.086
peak=    4.283 closest distance to " CE3 TRP A 274 " =    1.413
peak=    4.280 closest distance to " CB  ASN A  60 " =    0.862
peak=    4.277 closest distance to " OG ASER A 258 " =    2.977
peak=    4.256 closest distance to " O   HOH Z 131 " =    2.013
peak=    4.255 closest distance to " N   GLN A  73 " =    1.041
peak=    4.250 closest distance to " O   HOH Z  69 " =    2.083
peak=    4.247 closest distance to " O   ASN A 285 " =    0.882
peak=    4.247 closest distance to " O   HOH Z 126 " =    1.709
peak=    4.231 closest distance to " O   HOH Z 181 " =    2.075
peak=    4.223 closest distance to " NH2 ARG A 269 " =    1.020
peak=    4.206 closest distance to " O   HOH Z 427 " =    1.293
peak=    4.204 closest distance to " O   HOH Z 120 " =    1.097
peak=    4.203 closest distance to " O   HOH Z 179 " =    0.930
peak=    4.188 closest distance to " O   HOH Z 139 " =    1.326
peak=    4.164 closest distance to " O   HOH Z 155 " =    2.043
peak=    4.150 closest distance to " O   HOH Z 410 " =    1.664
peak=    4.146 closest distance to " CB  PRO A  90 " =    1.222
peak=    4.135 closest distance to " CG2 THR A 221 " =    1.261
peak=    4.132 closest distance to " O   HOH Z  91 " =    2.401
peak=    4.126 closest distance to " CB  ARG A 275 " =    1.119
peak=    4.122 closest distance to " CZ3 TRP A 266 " =    1.249
peak=    4.098 closest distance to " O   HOH Z 217 " =    2.768
peak=    4.095 closest distance to " O   HOH Z  63 " =    1.578
peak=    4.087 closest distance to " O   HOH Z 415 " =    1.245
peak=    4.086 closest distance to " CB  PHE A  61 " =    1.190
peak=    4.075 closest distance to " CE  MET A  93 " =    1.618
peak=    4.048 closest distance to " O   HOH Z 427 " =    2.249
peak=    4.040 closest distance to " O   HOH Z 400 " =    0.889
peak=    4.038 closest distance to " O   HOH Z  97 " =    1.706
peak=    4.031 closest distance to " CA  VAL A 125 " =    1.090
peak=    4.029 closest distance to " O   HOH Z 419 " =    2.009
peak=    4.000 closest distance to " O   HOH Z 280 " =    1.721
peak=    3.996 closest distance to " N   TYR A  15 " =    1.292
peak=    3.988 closest distance to " O   HOH Z 250 " =    2.297
peak=    3.963 closest distance to " O   PHE A  59 " =    0.903
peak=    3.954 closest distance to " O   HOH Z 248 " =    1.565
peak=    3.949 closest distance to " CD2 PHE A  59 " =    2.039
peak=    3.940 closest distance to " C   HIS A 115 " =    0.928
peak=    3.938 closest distance to " O   HOH Z 333 " =    1.003
peak=    3.927 closest distance to " O   GLN A  55 " =    1.241
peak=    3.924 closest distance to " C   GLN A  73 " =    1.086
peak=    3.921 closest distance to " O   HOH Z  77 " =    1.397
peak=    3.913 closest distance to " CD2 LEU A   5 " =    1.666
peak=    3.910 closest distance to " O   HOH Z 346 " =    1.200
peak=    3.893 closest distance to " CZ  PHE A 218 " =    1.158
peak=    3.890 closest distance to " O   HOH Z 205 " =    1.017
peak=    3.875 closest distance to " CZ  PHE A  16 " =    0.763
peak=    3.874 closest distance to " O   HOH Z  28 " =    1.132
peak=    3.868 closest distance to " O   ASN A 142 " =    1.067
peak=    3.866 closest distance to " CB  PRO A  54 " =    1.310
peak=    3.849 closest distance to " O   HOH Z  53 " =    2.184
peak=    3.841 closest distance to " CB  SER A 210 " =    1.292
peak=    3.829 closest distance to " CG  GLN A  55 " =    0.875
peak=    3.820 closest distance to " CD  ARG A 195 " =    3.500
peak=    3.813 closest distance to " CG2 VAL A 257 " =    1.012
peak=    3.797 closest distance to " O   HOH Z 411 " =    3.424
peak=    3.796 closest distance to " CG  PRO A  54 " =    1.368
peak=    3.793 closest distance to " NE2 HIS A 207 " =    0.986
peak=    3.789 closest distance to " CB  GLN A 223 " =    1.686
peak=    3.783 closest distance to " CG  PRO A 243 " =    1.215
peak=    3.781 closest distance to " OG  SER A 276 " =    1.199
peak=    3.778 closest distance to " O   HOH Z  39 " =    1.365
peak=    3.776 closest distance to " O   HOH Z 128 " =    1.805
peak=    3.775 closest distance to " O   HOH Z 296 " =    1.476
peak=    3.770 closest distance to " O   HOH Z 143 " =    1.479
peak=    3.769 closest distance to " O   HOH Z 244 " =    1.482
peak=    3.763 closest distance to " CB  MET A  40 " =    1.066
peak=    3.752 closest distance to " O   HOH Z 102 " =    1.319
peak=    3.750 closest distance to " N   PHE A 130 " =    1.352
peak=    3.738 closest distance to " CD  GLN A  77 " =    1.432
peak=    3.737 closest distance to " ND2BASN A 224 " =    1.077
peak=    3.727 closest distance to " CA  TYR A  30 " =    1.193
peak=    3.727 closest distance to " CA  ASN A  69 " =    0.858
peak=    3.721 closest distance to " N   ARG A 156 " =    1.292
peak=    3.717 closest distance to " O   HOH Z 189 " =    3.342
peak=    3.715 closest distance to " CB  ASP A 124 " =    0.997
peak=    3.714 closest distance to " N   ALA A   1 " =    1.533
peak=    3.708 closest distance to " O   HOH Z 257 " =    1.130
peak=    3.698 closest distance to " O   HOH Z 233 " =    1.240
peak=    3.696 closest distance to " CB  TRP A 179 " =    1.380
peak=    3.695 closest distance to " OG BSER A  12 " =    1.007
peak=    3.695 closest distance to " O   HOH Z 100 " =    1.165
peak=    3.694 closest distance to " O   HOH Z 414 " =    1.810
peak=    3.693 closest distance to " O   HOH Z 119 " =    1.616
peak=    3.690 closest distance to " CA  PRO A  54 " =    0.996
peak=    3.682 closest distance to " O   HOH Z 158 " =    2.727
peak=    3.681 closest distance to " CG  LEU A 101 " =    1.092
peak=    3.679 closest distance to " CG2 ILE A 120 " =    0.962
peak=    3.675 closest distance to " O   HOH Z  33 " =    1.900
peak=    3.673 closest distance to " O   HOH Z 375 " =    1.221
peak=    3.667 closest distance to " O   HOH Z 349 " =    1.919
peak=    3.664 closest distance to " CE2 PHE A  61 " =    0.845
peak=    3.663 closest distance to " O   HOH Z 225 " =    1.979
peak=    3.661 closest distance to " O   HOH Z 363 " =    1.270
peak=    3.661 closest distance to " CG1 VAL A 296 " =    1.164
peak=    3.659 closest distance to " CB  ASN A 148 " =    1.294
peak=    3.657 closest distance to " O   GLY A 302 " =    1.887
peak=    3.653 closest distance to " CB  ASN A 187 " =    0.916
peak=    3.651 closest distance to " O   HOH Z  58 " =    2.202
peak=    3.643 closest distance to " O   HOH Z 357 " =    2.315
peak=    3.637 closest distance to " O   HOH Z 298 " =    2.397
peak=    3.637 closest distance to " NH2 ARG A  56 " =    1.119
peak=    3.630 closest distance to " NZ ALYS A 290 " =    1.168
peak=    3.622 closest distance to " N   VAL A 296 " =    1.956
peak=    3.618 closest distance to " CB  ALA A 233 " =    1.257
peak=    3.610 closest distance to " O   HOH Z 374 " =    1.190
peak=    3.610 closest distance to " O   HOH Z  61 " =    1.763
peak=    3.610 closest distance to " O   HOH Z 222 " =    2.023
peak=    3.604 closest distance to " CB  SER A  99 " =    0.920
peak=    3.591 closest distance to " CB  SER A  62 " =    1.445
peak=    3.590 closest distance to " CB  VAL A 202 " =    1.559
peak=    3.589 closest distance to " CB  ALA A 131 " =    1.581
peak=    3.584 closest distance to " O   HOH Z 180 " =    2.282
peak=    3.572 closest distance to " OE1 GLN A 240 " =    1.685
peak=    3.569 closest distance to " OD1 ASN A  69 " =    1.166
peak=    3.563 closest distance to " CD  LYS A  76 " =    1.768
peak=    3.562 closest distance to " CG  ARG A 159 " =    1.151
peak=    3.554 closest distance to " CB  GLU A 128 " =    1.150
peak=    3.552 closest distance to " CA  LEU A 282 " =    0.990
peak=    3.549 closest distance to " CB  LYS A 290 " =    1.012
peak=    3.545 closest distance to " O   HOH Z 380 " =    2.298
peak=    3.545 closest distance to " O   HOH Z   9 " =    2.219
peak=    3.544 closest distance to " O   HOH Z 284 " =    1.583
peak=    3.543 closest distance to " CB  SER A 276 " =    1.475
peak=    3.540 closest distance to " O   HOH Z 126 " =    1.604
peak=    3.539 closest distance to " CA  ALA A  51 " =    1.221
peak=    3.525 closest distance to " O   HOH Z  51 " =    2.300
peak=    3.523 closest distance to " CE2 PHE A  16 " =    0.813
peak=    3.518 closest distance to " O   HOH Z 220 " =    1.538
peak=    3.509 closest distance to " CB  ALA A 114 " =    0.904
peak=    3.508 closest distance to " O   ALA A 165 " =    1.497
peak=    3.506 closest distance to " NE1 TRP A 266 " =    1.735
peak=    3.505 closest distance to " O   HOH Z 392 " =    1.232
peak=    3.504 closest distance to " O   HOH Z  88 " =    3.562
peak=    3.500 closest distance to " NH1 ARG A  36 " =    2.033
peak=    3.492 closest distance to " N   GLU A  53 " =    1.738
peak=    3.492 closest distance to " O   HOH Z 158 " =    1.439
peak=    3.490 closest distance to " CG  PRO A 198 " =    1.355
peak=    3.490 closest distance to " O   HOH Z 330 " =    1.166
peak=    3.488 closest distance to " CB  ILE A 120 " =    1.372
peak=    3.480 closest distance to " O   HOH Z 416 " =    1.447
peak=    3.478 closest distance to " CB  PHE A 225 " =    1.513
peak=    3.478 closest distance to " O   HOH Z 171 " =    1.924
peak=    3.462 closest distance to " O   HOH Z 176 " =    1.468
peak=    3.461 closest distance to " CB  ALA A 114 " =    1.471
peak=    3.460 closest distance to " CA  GLU A 152 " =    1.104
peak=    3.456 closest distance to " CD  ARG A 259 " =    1.443
peak=    3.453 closest distance to " CG  GLN A  89 " =    1.549
peak=    3.453 closest distance to " O   HOH Z 389 " =    1.773
peak=    3.452 closest distance to " O   HOH Z 204 " =    1.039
peak=    3.452 closest distance to " O   HOH Z 296 " =    1.398
peak=    3.449 closest distance to " O   HOH Z 239 " =    1.830
peak=    3.446 closest distance to " CB  ASN A 285 " =    1.149
peak=    3.440 closest distance to " CG2 ILE A 239 " =    1.028
peak=    3.439 closest distance to " CB  GLU A 152 " =    1.219
peak=    3.438 closest distance to " O   HOH Z   7 " =    2.469
peak=    3.428 closest distance to " O   HOH Z  30 " =    1.743
peak=    3.425 closest distance to " O   HOH Z 424 " =    3.346
peak=    3.423 closest distance to " CB  GLU A 175 " =    1.049
peak=    3.417 closest distance to " CB  LEU A  83 " =    0.791
peak=    3.413 closest distance to " OG  SER A  32 " =    1.074
peak=    3.407 closest distance to " C   ASN A 209 " =    1.862
peak=    3.404 closest distance to " ND2 ASN A  60 " =    2.658
peak=    3.404 closest distance to " CB  VAL A 230 " =    1.024
peak=    3.402 closest distance to " CG2BVAL A  41 " =    1.098
peak=    3.398 closest distance to " NH2BARG A 190 " =    1.292
peak=    3.394 closest distance to " O   HOH Z 278 " =    1.061
peak=    3.394 closest distance to " N   GLY A 302 " =    1.011
peak=    3.393 closest distance to " N   GLN A 278 " =    1.192
peak=    3.392 closest distance to " CB  VAL A 296 " =    1.512
peak=    3.387 closest distance to " CA  ARG A  36 " =    1.290
peak=    3.386 closest distance to " NZ  LYS A 119 " =    2.446
peak=    3.382 closest distance to " OD1 ASP A  65 " =    1.841
peak=    3.381 closest distance to " CD2 TRP A 179 " =    2.063
peak=    3.375 closest distance to " CE  LYS A 119 " =    1.237
peak=    3.375 closest distance to " O   HOH Z 153 " =    4.037
peak=    3.367 closest distance to " O   HOH Z 175 " =    3.709
peak=    3.364 closest distance to " CG  LEU A 167 " =    1.389
peak=    3.360 closest distance to " CA  ILE A 234 " =    1.238
peak=    3.359 closest distance to " O   HOH Z 368 " =    2.155
peak=    3.357 closest distance to " O   HOH Z 212 " =    1.997
peak=    3.356 closest distance to " N   ALA A 295 " =    1.736
peak=    3.355 closest distance to " O   HOH Z 124 " =    1.062
peak=    3.354 closest distance to " NE2 GLN A  73 " =    1.670
peak=    3.350 closest distance to " CB  SER A   3 " =    1.189
peak=    3.349 closest distance to " CB  ALA A  10 " =    1.019
peak=    3.342 closest distance to " O   HOH Z 362 " =    2.107
peak=    3.341 closest distance to " O   HOH Z 286 " =    2.042
peak=    3.341 closest distance to " CB  SER A 273 " =    1.172
peak=    3.340 closest distance to " CA  TRP A  92 " =    1.172
peak=    3.335 closest distance to " CB  ARG A  66 " =    0.904
peak=    3.333 closest distance to " O   HOH Z 422 " =    2.184
peak=    3.331 closest distance to " OD1 ASP A  27 " =    0.937
peak=    3.326 closest distance to " O   ALA A 158 " =    1.210
peak=    3.324 closest distance to " NZ  LYS A  48 " =    2.349
peak=    3.324 closest distance to " CB  TYR A  30 " =    1.841
peak=    3.323 closest distance to " CG  ASN A 252 " =    1.350
peak=    3.317 closest distance to " CA  ARG A  24 " =    1.048
peak=    3.315 closest distance to " O   HOH Z 115 " =    1.671
peak=    3.315 closest distance to " CG1 VAL A 125 " =    2.169
peak=    3.315 closest distance to " CA  GLY A 196 " =    0.876
peak=    3.311 closest distance to " O   HOH Z 213 " =    1.896
peak=    3.309 closest distance to " O   HOH Z 207 " =    1.417
peak=    3.308 closest distance to " CB  ALA A  43 " =    0.970
peak=    3.307 closest distance to " CB  ASN A  39 " =    0.870
peak=    3.304 closest distance to " CA  ALA A   7 " =    1.056
peak=    3.303 closest distance to " CD  GLU A  53 " =    1.175
peak=    3.303 closest distance to " O   HOH Z 153 " =    3.420
peak=    3.300 closest distance to " O   HOH Z 197 " =    1.994
peak=    3.299 closest distance to " O   HOH Z 132 " =    1.522
peak=    3.298 closest distance to " O   HOH Z 170 " =    1.308
peak=    3.297 closest distance to " CB  ARG A 102 " =    0.920
peak=    3.297 closest distance to " N   GLU A   2 " =    1.452
peak=    3.297 closest distance to " CA  LEU A  83 " =    1.634
peak=    3.296 closest distance to " O   HOH Z  76 " =    1.496
peak=    3.287 closest distance to " O   HOH Z 368 " =    3.517
peak=    3.285 closest distance to " CE3 TRP A 150 " =    1.238
peak=    3.284 closest distance to " NZ  LYS A 166 " =    0.975
peak=    3.283 closest distance to " O   HOH Z   6 " =    1.653
peak=    3.277 closest distance to " O   HOH Z 240 " =    1.972
peak=    3.275 closest distance to " O   HOH Z 365 " =    2.542
peak=    3.274 closest distance to " CG2AVAL A 121 " =    1.653
peak=    3.273 closest distance to " CB  ASP A  50 " =    1.069
peak=    3.262 closest distance to " O   HOH Z 313 " =    1.768
peak=    3.260 closest distance to " O   HOH Z  54 " =    1.215
peak=    3.252 closest distance to " O   ASN A  69 " =    1.232
peak=    3.251 closest distance to " CB  THR A   4 " =    1.280
peak=    3.251 closest distance to " O   HOH Z 424 " =    1.400
peak=    3.248 closest distance to " CB  VAL A 265 " =    1.383
peak=    3.246 closest distance to " O   HOH Z 284 " =    1.377
peak=    3.245 closest distance to " CA  VAL A 202 " =    1.245
peak=    3.244 closest distance to " CD1BILE A 234 " =    1.129
peak=    3.242 closest distance to " N   SER A 210 " =    1.194
peak=    3.238 closest distance to " O   HOH Z 356 " =    1.445
peak=    3.238 closest distance to " O   HOH Z 293 " =    1.338
peak=    3.236 closest distance to " CE BMET A  47 " =    1.074
peak=    3.231 closest distance to " CA  ALA A 184 " =    1.589
peak=    3.230 closest distance to " OE1 GLU A  37 " =    1.178
peak=    3.225 closest distance to " CB  ARG A 219 " =    0.834
peak=    3.218 closest distance to " CA  ARG A 195 " =    1.450
peak=    3.218 closest distance to " CG1 VAL A 265 " =    0.976
peak=    3.216 closest distance to " CB  HIS A  86 " =    1.079
peak=    3.212 closest distance to " CD1 LEU A 228 " =    1.837
peak=    3.211 closest distance to " CZ  PHE A  38 " =    1.209
peak=    3.210 closest distance to " C   LEU A  25 " =    0.967
peak=    3.206 closest distance to " CB  ALA A 161 " =    1.950
peak=    3.202 closest distance to " CB  TYR A  30 " =    1.464
peak=    3.200 closest distance to " CB  PHE A 130 " =    1.599
peak=    3.192 closest distance to " O   HOH Z  43 " =    1.236
peak=    3.189 closest distance to " CZ3 TRP A 123 " =    1.689
peak=    3.189 closest distance to " O   HOH Z 434 " =    1.816
peak=    3.189 closest distance to " OD1 ASP A 238 " =    1.093
peak=    3.188 closest distance to " CB  GLU A 277 " =    3.644
peak=    3.184 closest distance to " CG  ASP A  65 " =    1.072
peak=    3.180 closest distance to " N   TRP A  70 " =    0.873
peak=    3.180 closest distance to " O   HOH Z 341 " =    1.193
peak=    3.179 closest distance to " N   MET A 185 " =    1.179
peak=    3.174 closest distance to " CB  ALA A 114 " =    0.768
peak=    3.168 closest distance to " CE3 TRP A  85 " =    1.021
peak=    3.167 closest distance to " CA  LYS A 289 " =    0.805
peak=    3.166 closest distance to " CB  TRP A 274 " =    1.069
peak=    3.165 closest distance to " O   HOH Z 371 " =    3.062
peak=    3.164 closest distance to " CA  PRO A 280 " =    1.389
peak=    3.161 closest distance to " CD2 LEU A 300 " =    1.368
peak=    3.161 closest distance to " O   HOH Z 358 " =    1.372
peak=    3.160 closest distance to " CA  VAL A 153 " =    0.983
peak=    3.159 closest distance to " N   MET A 113 " =    1.092
peak=    3.159 closest distance to " O   HOH Z 430 " =    2.401
peak=    3.155 closest distance to " CB  ASN A 176 " =    1.133
peak=    3.154 closest distance to " NH2 ARG A 269 " =    1.221
peak=    3.152 closest distance to " O   HOH Z 301 " =    1.881
peak=    3.152 closest distance to " CG  GLN A 183 " =    1.647
peak=    3.151 closest distance to " O   HOH Z 171 " =    1.636
peak=    3.150 closest distance to " O   HOH Z 298 " =    2.386
peak=    3.148 closest distance to " O   HOH Z  28 " =    1.343
peak=    3.147 closest distance to " CD1 ILE A 199 " =    1.151
peak=    3.145 closest distance to " O   HOH Z  59 " =    3.383
peak=    3.144 closest distance to " O   TRP A  70 " =    1.256
peak=    3.144 closest distance to " O   HOH Z 139 " =    2.779
peak=    3.143 closest distance to " CG  LYS A 119 " =    1.006
peak=    3.142 closest distance to " CB  ARG A  79 " =    1.127
peak=    3.138 closest distance to " CB  ARG A 138 " =    1.016
peak=    3.132 closest distance to " O   HOH Z 274 " =    2.487
peak=    3.122 closest distance to " CA  SER A  12 " =    1.484
peak=    3.122 closest distance to " O   HOH Z 218 " =    1.727
peak=    3.120 closest distance to " O   HOH Z 352 " =    1.993
peak=    3.120 closest distance to " CA  GLY A  57 " =    1.522
peak=    3.113 closest distance to " N   TRP A  85 " =    0.836
peak=    3.113 closest distance to " CB  ASP A 286 " =    1.871
peak=    3.108 closest distance to " CA  ARG A 102 " =    1.146
peak=    3.107 closest distance to " O   HOH Z 111 " =    1.648
peak=    3.095 closest distance to " CB  ALA A  43 " =    0.974
peak=    3.092 closest distance to " CG1 VAL A 153 " =    1.161
peak=    3.084 closest distance to " CA  VAL A 202 " =    1.701
peak=    3.078 closest distance to " CG2 ILE A  20 " =    1.571
peak=    3.062 closest distance to " OG BSER A 210 " =    1.222
peak=    3.048 closest distance to " O   HOH Z 288 " =    2.212
peak=    3.042 closest distance to " N   ARG A  66 " =    0.851
peak=    3.022 closest distance to " O   ASN A 284 " =    1.456
peak=    3.016 closest distance to " O   HOH Z 287 " =    2.147

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 220         
Filter by distance & map next to the model:
   mapped sites are within: 0.380 - 5.621
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 216 from: 220
   mapped sites are within: 0.770 - 5.621

peak=   -4.769 closest distance to " OE1 GLU A  44 " =    1.682
peak=   -4.462 closest distance to " CG  MET A 105 " =    0.936
peak=   -4.448 closest distance to " O   ASN A  69 " =    0.939
peak=   -4.326 closest distance to " O   PHE A  59 " =    1.027
peak=   -4.311 closest distance to " N   PRO A  54 " =    0.927
peak=   -4.281 closest distance to " C   PHE A  61 " =    0.923
peak=   -4.206 closest distance to " O   HOH Z 242 " =    1.554
peak=   -4.176 closest distance to " C   ASP A  65 " =    1.103
peak=   -4.125 closest distance to " O   HOH Z 181 " =    1.004
peak=   -4.113 closest distance to " C   VAL A  72 " =    0.822
peak=   -4.071 closest distance to " O   ALA A  10 " =    1.551
peak=   -4.069 closest distance to " O   GLN A 240 " =    3.177
peak=   -4.068 closest distance to " OG  SER A  97 " =    1.812
peak=   -4.053 closest distance to " CB  GLN A  55 " =    1.202
peak=   -4.051 closest distance to " O   HOH Z  28 " =    0.825
peak=   -4.050 closest distance to " O   VAL A 125 " =    2.430
peak=   -3.994 closest distance to " O   GLY A  80 " =    2.603
peak=   -3.988 closest distance to " O   GLY A 203 " =    2.402
peak=   -3.986 closest distance to " O   HOH Z  54 " =    1.339
peak=   -3.970 closest distance to " O   HOH Z 313 " =    1.130
peak=   -3.969 closest distance to " CB  ASN A 285 " =    1.976
peak=   -3.964 closest distance to " O   HOH Z 216 " =    1.271
peak=   -3.948 closest distance to " O   HOH Z  27 " =    1.143
peak=   -3.947 closest distance to " CB  ALA A   9 " =    2.641
peak=   -3.935 closest distance to " CD2 HIS A 207 " =    1.410
peak=   -3.924 closest distance to " NE2 GLN A 223 " =    1.414
peak=   -3.920 closest distance to " O   HOH Z 231 " =    0.770
peak=   -3.911 closest distance to " OE2 GLU A 152 " =    1.140
peak=   -3.908 closest distance to " O   PRO A 198 " =    1.195
peak=   -3.896 closest distance to " CG  GLN A  88 " =    1.234
peak=   -3.889 closest distance to " O   HOH Z 257 " =    1.101
peak=   -3.877 closest distance to " O   ASP A 191 " =    1.872
peak=   -3.877 closest distance to " NH2AARG A 275 " =    5.621
peak=   -3.856 closest distance to " CA  ILE A 120 " =    1.118
peak=   -3.838 closest distance to " OG BSER A 134 " =    1.888
peak=   -3.807 closest distance to " CZ  TYR A 169 " =    2.001
peak=   -3.805 closest distance to " CD2 TYR A 293 " =    1.960
peak=   -3.805 closest distance to " CA  ASN A 110 " =    0.999
peak=   -3.801 closest distance to " ND2 ASN A  39 " =    1.278
peak=   -3.799 closest distance to " O   HOH Z 389 " =    2.694
peak=   -3.793 closest distance to " CA  GLY A 133 " =    2.042
peak=   -3.791 closest distance to " CB  PHE A  61 " =    1.247
peak=   -3.787 closest distance to " O   HOH Z 179 " =    1.146
peak=   -3.783 closest distance to " O   HOH Z 385 " =    1.282
peak=   -3.782 closest distance to " O   HOH Z 415 " =    1.110
peak=   -3.776 closest distance to " OG  SER A  63 " =    1.500
peak=   -3.772 closest distance to " O   HOH Z 119 " =    0.787
peak=   -3.743 closest distance to " O   HOH Z 357 " =    1.308
peak=   -3.733 closest distance to " CB  ALA A 291 " =    2.166
peak=   -3.728 closest distance to " O   ASN A 285 " =    1.188
peak=   -3.710 closest distance to " CA  GLY A 203 " =    2.667
peak=   -3.697 closest distance to " NE  ARG A 195 " =    1.310
peak=   -3.697 closest distance to " OH  TYR A 247 " =    1.366
peak=   -3.691 closest distance to " OE1 GLN A  88 " =    0.888
peak=   -3.690 closest distance to " NZ  LYS A 166 " =    1.771
peak=   -3.688 closest distance to " CG  GLN A  55 " =    1.135
peak=   -3.686 closest distance to " N   GLN A 122 " =    1.341
peak=   -3.678 closest distance to " CB  ASP A 132 " =    2.567
peak=   -3.676 closest distance to " CD  ARG A  14 " =    3.182
peak=   -3.670 closest distance to " O   PHE A 218 " =    1.684
peak=   -3.665 closest distance to " CD1 TYR A 247 " =    2.689
peak=   -3.662 closest distance to " CG  ARG A 259 " =    2.458
peak=   -3.657 closest distance to " CB  PHE A 208 " =    2.231
peak=   -3.644 closest distance to " CG1 VAL A 265 " =    2.558
peak=   -3.641 closest distance to " O   GLN A  58 " =    0.887
peak=   -3.625 closest distance to " N   ARG A 138 " =    1.885
peak=   -3.616 closest distance to " O   HOH Z  70 " =    1.950
peak=   -3.615 closest distance to " O   HOH Z 426 " =    1.722
peak=   -3.610 closest distance to " ND2 ASN A 209 " =    1.760
peak=   -3.606 closest distance to " CG2BVAL A  41 " =    1.340
peak=   -3.593 closest distance to " CA  GLY A  57 " =    2.065
peak=   -3.568 closest distance to " N   ALA A  19 " =    2.192
peak=   -3.568 closest distance to " CG2 ILE A 120 " =    1.609
peak=   -3.566 closest distance to " N   ALA A  43 " =    2.604
peak=   -3.561 closest distance to " NH2 ARG A 195 " =    2.452
peak=   -3.543 closest distance to " C   ASP A  50 " =    1.599
peak=   -3.537 closest distance to " CA  GLY A 241 " =    2.337
peak=   -3.531 closest distance to " O   HOH Z 103 " =    1.493
peak=   -3.526 closest distance to " O   HOH Z 111 " =    1.675
peak=   -3.524 closest distance to " CB  PRO A 243 " =    2.574
peak=   -3.521 closest distance to " O   HOH Z 163 " =    1.619
peak=   -3.517 closest distance to " CZ  PHE A  38 " =    2.372
peak=   -3.503 closest distance to " O   HOH Z 417 " =    3.648
peak=   -3.500 closest distance to " O   HOH Z 285 " =    2.903
peak=   -3.492 closest distance to " O   HOH Z  24 " =    0.899
peak=   -3.491 closest distance to " CG  GLN A 122 " =    2.396
peak=   -3.488 closest distance to " CB  PHE A 130 " =    1.152
peak=   -3.487 closest distance to " O   HOH Z 438 " =    1.359
peak=   -3.486 closest distance to " O   HOH Z  67 " =    1.282
peak=   -3.485 closest distance to " N   GLU A 277 " =    1.605
peak=   -3.483 closest distance to " O   THR A 178 " =    1.151
peak=   -3.482 closest distance to " CD1 TYR A 214 " =    1.468
peak=   -3.475 closest distance to " O   LEU A 261 " =    1.127
peak=   -3.464 closest distance to " O   HOH Z 179 " =    1.903
peak=   -3.457 closest distance to " C   HIS A 108 " =    1.413
peak=   -3.450 closest distance to " O   HOH Z 139 " =    2.957
peak=   -3.449 closest distance to " OG BSER A 164 " =    1.472
peak=   -3.445 closest distance to " O   HOH Z 285 " =    1.565
peak=   -3.439 closest distance to " O   SER A  22 " =    2.762
peak=   -3.429 closest distance to " O   HOH Z 100 " =    1.031
peak=   -3.429 closest distance to " O   HOH Z  68 " =    1.421
peak=   -3.425 closest distance to " CA  MET A 113 " =    1.109
peak=   -3.424 closest distance to " O   HOH Z 368 " =    1.679
peak=   -3.423 closest distance to " O   HOH Z  32 " =    2.269
peak=   -3.422 closest distance to " NE1 TRP A 179 " =    1.166
peak=   -3.421 closest distance to " O   HOH Z 435 " =    3.186
peak=   -3.420 closest distance to " O   LEU A 167 " =    1.616
peak=   -3.417 closest distance to " O   ALA A 100 " =    1.421
peak=   -3.410 closest distance to " O   HOH Z  49 " =    1.086
peak=   -3.394 closest distance to " CE2 TYR A  30 " =    2.397
peak=   -3.394 closest distance to " O   HOH Z  97 " =    2.270
peak=   -3.392 closest distance to " O   TRP A  70 " =    1.376
peak=   -3.390 closest distance to " OD2 ASP A 171 " =    2.424
peak=   -3.388 closest distance to " O   HOH Z  60 " =    1.444
peak=   -3.388 closest distance to " N   ASP A  65 " =    1.168
peak=   -3.387 closest distance to " O   HOH Z 358 " =    1.291
peak=   -3.386 closest distance to " O   SER A  99 " =    1.306
peak=   -3.385 closest distance to " O   HOH Z  37 " =    2.088
peak=   -3.383 closest distance to " O   HOH Z 409 " =    2.267
peak=   -3.382 closest distance to " OD2 ASP A 272 " =    1.644
peak=   -3.380 closest distance to " O   HOH Z 102 " =    1.871
peak=   -3.368 closest distance to " CG  ARG A 219 " =    2.377
peak=   -3.363 closest distance to " NH1 ARG A  36 " =    0.923
peak=   -3.362 closest distance to " O   SER A 141 " =    1.596
peak=   -3.356 closest distance to " CD2 TYR A 116 " =    2.291
peak=   -3.354 closest distance to " O   HOH Z 371 " =    2.240
peak=   -3.350 closest distance to " O   HOH Z 131 " =    1.167
peak=   -3.348 closest distance to " CD  GLU A 277 " =    1.139
peak=   -3.347 closest distance to " OG  SER A  32 " =    0.807
peak=   -3.346 closest distance to " CD  ARG A 156 " =    1.973
peak=   -3.345 closest distance to " NE2 GLN A  77 " =    1.547
peak=   -3.338 closest distance to " O   HOH Z 143 " =    0.950
peak=   -3.326 closest distance to " CA  GLY A 133 " =    2.178
peak=   -3.319 closest distance to " O   VAL A 174 " =    2.335
peak=   -3.314 closest distance to " O   HOH Z 411 " =    5.209
peak=   -3.310 closest distance to " O   HOH Z  69 " =    1.336
peak=   -3.308 closest distance to " O   HOH Z 405 " =    2.337
peak=   -3.308 closest distance to " O   HOH Z 256 " =    1.133
peak=   -3.306 closest distance to " CA  THR A  29 " =    1.290
peak=   -3.287 closest distance to " O   SER A  62 " =    1.197
peak=   -3.286 closest distance to " CE3 TRP A 274 " =    2.214
peak=   -3.283 closest distance to " O   HOH Z 358 " =    3.515
peak=   -3.275 closest distance to " OE1 GLN A 278 " =    1.308
peak=   -3.275 closest distance to " N   GLN A  11 " =    1.134
peak=   -3.269 closest distance to " CZ3 TRP A 179 " =    1.417
peak=   -3.269 closest distance to " O   ARG A  24 " =    1.974
peak=   -3.263 closest distance to " O   HOH Z  15 " =    1.254
peak=   -3.262 closest distance to " OG  SER A  87 " =    1.740
peak=   -3.255 closest distance to " OE2 GLU A 175 " =    1.408
peak=   -3.253 closest distance to " CD2 LEU A 167 " =    1.928
peak=   -3.252 closest distance to " CG2 THR A 221 " =    2.175
peak=   -3.248 closest distance to " CB  ALA A   7 " =    1.792
peak=   -3.242 closest distance to " CB  SER A  62 " =    5.107
peak=   -3.238 closest distance to " O   THR A  52 " =    1.236
peak=   -3.237 closest distance to " O   HOH Z  21 " =    0.885
peak=   -3.232 closest distance to " O   HOH Z 105 " =    2.049
peak=   -3.231 closest distance to " CA  HIS A  86 " =    2.013
peak=   -3.225 closest distance to " NE2 GLN A 205 " =    2.098
peak=   -3.225 closest distance to " CD1 ILE A  33 " =    2.191
peak=   -3.224 closest distance to " C   ILE A 239 " =    1.948
peak=   -3.223 closest distance to " CB  GLN A 144 " =    1.119
peak=   -3.223 closest distance to " O   ASP A 171 " =    0.909
peak=   -3.221 closest distance to " NE2 GLN A 194 " =    1.879
peak=   -3.218 closest distance to " O   HOH Z 353 " =    4.135
peak=   -3.217 closest distance to " O   HOH Z 261 " =    1.245
peak=   -3.207 closest distance to " SG BCYS A 201 " =    2.608
peak=   -3.204 closest distance to " CG1BVAL A  41 " =    2.739
peak=   -3.203 closest distance to " NH2BARG A 275 " =    1.466
peak=   -3.202 closest distance to " O   HOH Z 165 " =    1.753
peak=   -3.192 closest distance to " CB  ASN A  39 " =    2.335
peak=   -3.186 closest distance to " CG  GLN A  73 " =    1.329
peak=   -3.186 closest distance to " CB  PRO A  54 " =    2.351
peak=   -3.182 closest distance to " CE BMET A  47 " =    1.560
peak=   -3.181 closest distance to " O   HOH Z  25 " =    1.957
peak=   -3.181 closest distance to " ND2 ASN A  45 " =    2.975
peak=   -3.176 closest distance to " CG  TRP A 266 " =    1.559
peak=   -3.175 closest distance to " O   HOH Z 394 " =    1.738
peak=   -3.169 closest distance to " O   HOH Z 300 " =    2.659
peak=   -3.169 closest distance to " CB  TRP A  85 " =    1.968
peak=   -3.169 closest distance to " CD  GLN A  55 " =    1.299
peak=   -3.168 closest distance to " CB  ALA A  43 " =    2.517
peak=   -3.165 closest distance to " O   HOH Z 200 " =    3.439
peak=   -3.164 closest distance to " N   SER A  26 " =    0.872
peak=   -3.160 closest distance to " CB  ALA A 129 " =    2.786
peak=   -3.159 closest distance to " CB  ALA A 131 " =    1.786
peak=   -3.158 closest distance to " O   HOH Z 155 " =    0.960
peak=   -3.157 closest distance to " O   HOH Z 381 " =    1.440
peak=   -3.154 closest distance to " O   HOH Z 297 " =    1.464
peak=   -3.153 closest distance to " CA  GLY A  57 " =    2.009
peak=   -3.152 closest distance to " O   GLY A 136 " =    1.711
peak=   -3.151 closest distance to " O   HOH Z 166 " =    1.769
peak=   -3.149 closest distance to " N   TRP A 274 " =    1.307
peak=   -3.147 closest distance to " O   HOH Z 324 " =    1.073
peak=   -3.145 closest distance to " OE1 GLN A 223 " =    5.159
peak=   -3.140 closest distance to " O   HOH Z 140 " =    1.082
peak=   -3.133 closest distance to " N   GLN A 223 " =    2.005
peak=   -3.131 closest distance to " CZ  PHE A  16 " =    0.947
peak=   -3.127 closest distance to " OG BSER A 210 " =    2.277
peak=   -3.121 closest distance to " O   HOH Z 323 " =    1.988
peak=   -3.120 closest distance to " O   HOH Z 205 " =    0.877
peak=   -3.115 closest distance to " CB  TYR A  68 " =    1.065
peak=   -3.114 closest distance to " OG BSER A 212 " =    1.297
peak=   -3.114 closest distance to " O   HOH Z 387 " =    2.040
peak=   -3.114 closest distance to " CA  ARG A 156 " =    1.126
peak=   -3.113 closest distance to " ND2 ASN A 285 " =    2.015
peak=   -3.109 closest distance to " O   HOH Z 210 " =    2.041
peak=   -3.107 closest distance to " C   LEU A 222 " =    1.449
peak=   -3.104 closest distance to " CG2 THR A 178 " =    2.118
peak=   -3.091 closest distance to " O   HOH Z 434 " =    1.966
peak=   -3.089 closest distance to " O   HOH Z 378 " =    1.832
peak=   -3.086 closest distance to " CZ  ARG A  66 " =    2.089
peak=   -3.055 closest distance to " O   PRO A 163 " =    1.840
peak=   -3.051 closest distance to " O   HOH Z 236 " =    1.249
peak=   -3.031 closest distance to " CB  ASP A  27 " =    2.594
peak=   -3.014 closest distance to " O   HOH Z 174 " =    2.563
peak=   -3.001 closest distance to " O   HOH Z 333 " =    0.801

================= 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    :  0.5008 0.5059   6.310377e+00   6.302151e+00
   1_bss:  0.4930 0.5026   6.310051e+00   6.300111e+00
   1_xyz:  0.4298 0.4734   6.230291e+00   6.272071e+00
   1_adp:  0.3985 0.4835   6.205548e+00   6.278409e+00
   1_occ:  0.3980 0.4849   6.205304e+00   6.278738e+00
   2_bss:  0.3986 0.4841   6.208427e+00   6.279374e+00
   2_xyz:  0.3430 0.4294   6.093913e+00   6.214058e+00
   2_adp:  0.3253 0.4182   6.068580e+00   6.196484e+00
   2_occ:  0.3251 0.4178   6.067912e+00   6.196111e+00
   3_bss:  0.3254 0.4169   6.066856e+00   6.194644e+00
   3_xyz:  0.2700 0.3475   5.914607e+00   6.081461e+00
   3_adp:  0.2435 0.3332   5.855985e+00   6.050867e+00
   3_occ:  0.2433 0.3329   5.855269e+00   6.050498e+00
   4_bss:  0.2434 0.3331   5.854349e+00   6.050160e+00
   4_xyz:  0.2099 0.2877   5.717145e+00   5.931279e+00
   4_adp:  0.1983 0.2683   5.664930e+00   5.875999e+00
   4_occ:  0.1982 0.2682   5.664497e+00   5.875480e+00
   5_bss:  0.1981 0.2674   5.661649e+00   5.873440e+00
   5_xyz:  0.1680 0.2298   5.509367e+00   5.748285e+00
   5_adp:  0.1547 0.2171   5.444280e+00   5.690141e+00
   5_occ:  0.1546 0.2170   5.444098e+00   5.690069e+00
   5_bss:  0.1552 0.2171   5.444248e+00   5.689045e+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  -1.825   0.199   2.867   0.000   0.000   0.000
   1_xyz:  0.300  50.000  -1.825   0.199   2.867   0.000   0.000   0.000
   1_adp:  0.300  50.000  -1.825   0.199   2.867   0.000   0.000   0.000
   1_occ:  0.300  50.000  -1.825   0.199   2.867   0.000   0.000   0.000
   2_bss:  0.365  88.400  -0.236   0.170   2.347   0.000   0.000   0.000
   2_xyz:  0.365  88.400  -0.236   0.170   2.347   0.000   0.000   0.000
   2_adp:  0.365  88.400  -0.236   0.170   2.347   0.000   0.000   0.000
   2_occ:  0.365  88.400  -0.236   0.170   2.347   0.000   0.000   0.000
   3_bss:  0.375 100.382  -0.526  -0.703   1.184  -0.000   0.000   0.000
   3_xyz:  0.375 100.382  -0.526  -0.703   1.184  -0.000   0.000   0.000
   3_adp:  0.375 100.382  -0.526  -0.703   1.184  -0.000   0.000   0.000
   3_occ:  0.375 100.382  -0.526  -0.703   1.184  -0.000   0.000   0.000
   4_bss:  0.363 107.746  -1.265  -1.427   0.473  -0.000   0.000   0.000
   4_xyz:  0.363 107.746  -1.265  -1.427   0.473  -0.000   0.000   0.000
   4_adp:  0.363 107.746  -1.265  -1.427   0.473  -0.000   0.000   0.000
   4_occ:  0.363 107.746  -1.265  -1.427   0.473  -0.000   0.000   0.000
   5_bss:  0.335  78.534  -1.633  -2.126   0.099  -0.000   0.000   0.000
   5_xyz:  0.335  78.534  -1.633  -2.126   0.099  -0.000   0.000   0.000
   5_adp:  0.335  78.534  -1.633  -2.126   0.099  -0.000   0.000   0.000
   5_occ:  0.335  78.534  -1.633  -2.126   0.099  -0.000   0.000   0.000
   5_bss:  0.332  80.003  -1.686  -2.393  -0.045  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  66.637 0.3068  0.4256    88461.405
   1_bss:  66.287 0.3106  0.4458    88112.877
   1_xyz:  59.557 0.3976  0.5600    74312.872
   1_adp:  60.807 0.3810  0.5537    77278.481
   1_occ:  60.819 0.3809  0.5533    77390.359
   2_bss:  60.893 0.3799  0.5587    77740.141
   2_xyz:  49.946 0.5193  0.7597    55469.427
   2_adp:  47.825 0.5462  0.7862    52146.707
   2_occ:  47.818 0.5462  0.7861    52060.003
   3_bss:  47.635 0.5483  0.7684    51611.777
   3_xyz:  37.724 0.6683  0.9078    34359.907
   3_adp:  35.546 0.6939  0.9086    31030.230
   3_occ:  35.522 0.6941  0.9086    30959.663
   4_bss:  35.461 0.6948  0.8868    30870.311
   4_xyz:  29.964 0.7560  0.9422    22070.274
   4_adp:  27.344 0.7856  0.9555    19264.404
   4_occ:  27.327 0.7858  0.9554    19226.798
   5_bss:  27.214 0.7867  0.9401    19030.456
   5_xyz:  22.854 0.8321  0.9720    13837.834
   5_adp:  21.175 0.8494  0.9721    12256.284
   5_occ:  21.166 0.8495  0.9721    12253.319
   5_bss:  21.146 0.8496  0.9672    12223.861
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.8477e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.8477e-01
   1_xyz:   1.577  0.011  0.105 16.199  0.006  4.106   1.4158e-01
   1_adp:   1.577  0.011  0.105 16.199  0.006  4.106   1.4158e-01
   1_occ:   1.577  0.011  0.105 16.199  0.006  4.106   1.4158e-01
   2_bss:   1.577  0.011  0.105 16.199  0.006  4.106   1.4158e-01
   2_xyz:   1.492  0.012  0.098 16.471  0.006  4.110   1.3493e-01
   2_adp:   1.492  0.012  0.098 16.471  0.006  4.110   1.3493e-01
   2_occ:   1.492  0.012  0.098 16.471  0.006  4.110   1.3493e-01
   3_bss:   1.492  0.012  0.098 16.471  0.006  4.110   1.3493e-01
   3_xyz:   1.166  0.009  0.085 15.445  0.004  4.121   8.6017e-02
   3_adp:   1.166  0.009  0.085 15.445  0.004  4.121   8.6017e-02
   3_occ:   1.166  0.009  0.085 15.445  0.004  4.121   8.6017e-02
   4_bss:   1.166  0.009  0.085 15.445  0.004  4.121   8.6017e-02
   4_xyz:   1.007  0.007  0.073 14.438  0.003  4.112   6.0896e-02
   4_adp:   1.007  0.007  0.073 14.438  0.003  4.112   6.0896e-02
   4_occ:   1.007  0.007  0.073 14.438  0.003  4.112   6.0896e-02
   5_bss:   1.007  0.007  0.073 14.438  0.003  4.112   6.0896e-02
   5_xyz:   1.039  0.008  0.074 14.531  0.003  4.121   6.4902e-02
   5_adp:   1.039  0.008  0.074 14.531  0.003  4.121   6.4902e-02
   5_occ:   1.039  0.008  0.074 14.531  0.003  4.121   6.4902e-02
   5_bss:   1.039  0.008  0.074 14.531  0.003  4.121   6.4902e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.681   2.4271e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.681   2.4271e-01
   1_xyz:   9.140  0.050  0.381 81.684  0.041  1.948   1.0125e-01
   1_adp:   9.140  0.050  0.381 81.684  0.041  1.948   1.0125e-01
   1_occ:   9.140  0.050  0.381 81.684  0.041  1.948   1.0125e-01
   2_bss:   9.140  0.050  0.381 81.684  0.041  1.948   1.0125e-01
   2_xyz:   7.946  0.057  0.317 78.750  0.064  1.855   1.2299e-01
   2_adp:   7.946  0.057  0.317 78.750  0.064  1.855   1.2299e-01
   2_occ:   7.946  0.057  0.317 78.750  0.064  1.855   1.2299e-01
   3_bss:   7.946  0.057  0.317 78.750  0.064  1.855   1.2299e-01
   3_xyz:   7.101  0.075  0.287 88.119  0.029  2.136   8.0864e-02
   3_adp:   7.101  0.075  0.287 88.119  0.029  2.136   8.0864e-02
   3_occ:   7.101  0.075  0.287 88.119  0.029  2.136   8.0864e-02
   4_bss:   7.101  0.075  0.287 88.119  0.029  2.136   8.0864e-02
   4_xyz:   7.262  0.055  0.297 89.033  0.036  2.358   8.3122e-02
   4_adp:   7.262  0.055  0.297 89.033  0.036  2.358   8.3122e-02
   4_occ:   7.262  0.055  0.297 89.033  0.036  2.358   8.3122e-02
   5_bss:   7.262  0.055  0.297 89.033  0.036  2.358   8.3122e-02
   5_xyz:   7.475  0.042  0.241 80.992  0.029  2.279   5.4206e-02
   5_adp:   7.475  0.042  0.241 80.992  0.029  2.279   5.4206e-02
   5_occ:   7.475  0.042  0.241 80.992  0.029  2.279   5.4206e-02
   5_bss:   7.475  0.042  0.241 80.992  0.029  2.279   5.4206e-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:  97.39   0.00  20.74  93.90   0.00  18.06  97.39   0.00  35.30
   1_occ:  97.39   0.00  20.74  93.90   0.00  18.06  97.39   0.00  35.30
   2_bss:  97.39   0.00  20.74  93.90   0.00  18.06  97.39   0.00  35.30
   2_xyz:  97.39   0.00  20.74  93.90   0.00  18.06  97.39   0.00  35.30
   2_adp:  87.19   0.00  19.87  79.37   0.00  16.92  87.19   0.00  35.94
   2_occ:  87.19   0.00  19.87  79.37   0.00  16.92  87.19   0.00  35.94
   3_bss:  87.19   0.00  19.87  79.37   0.00  16.92  87.19   0.00  35.94
   3_xyz:  87.19   0.00  19.87  79.37   0.00  16.92  87.19   0.00  35.94
   3_adp:  96.71   0.00  20.79  96.71   0.00  16.13  95.14   0.00  46.15
   3_occ:  96.71   0.00  20.79  96.71   0.00  16.13  95.14   0.00  46.15
   4_bss:  96.71   0.00  20.79  96.71   0.00  16.13  95.14   0.00  46.15
   4_xyz:  96.71   0.00  20.79  96.71   0.00  16.13  95.14   0.00  46.15
   4_adp:  97.52   0.00  19.92  97.52   0.00  14.97  94.74   3.34  46.85
   4_occ:  97.52   0.00  19.92  97.52   0.00  14.97  94.74   3.34  46.85
   5_bss:  97.52   0.00  19.92  97.52   0.00  14.97  94.74   3.34  46.85
   5_xyz:  97.52   0.00  19.92  97.52   0.00  14.97  94.74   3.34  46.85
   5_adp: 111.49   0.00  19.91 101.70   0.00  13.94 111.49   5.54  52.44
   5_occ: 111.49   0.00  19.91 101.70   0.00  13.94 111.49   5.54  52.44
   5_bss: 111.50   0.00  19.91 101.71   0.00  13.94 111.50   5.54  52.44
------------------------------------------------------------------------
 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:    1.704    0.027    0.331
   1_adp:    1.704    0.027    0.331
   1_occ:    1.704    0.027    0.331
   2_bss:    1.704    0.027    0.331
   2_xyz:    1.639    0.050    0.591
   2_adp:    1.639    0.050    0.591
   2_occ:    1.639    0.050    0.591
   3_bss:    1.639    0.050    0.591
   3_xyz:    1.643    0.051    0.761
   3_adp:    1.643    0.051    0.761
   3_occ:    1.643    0.051    0.761
   4_bss:    1.643    0.051    0.761
   4_xyz:    1.636    0.030    0.847
   4_adp:    1.636    0.030    0.847
   4_occ:    1.636    0.030    0.847
   5_bss:    1.636    0.030    0.847
   5_xyz:    1.815    0.056    0.921
   5_adp:    1.815    0.056    0.921
   5_occ:    1.815    0.056    0.921
   5_bss:    1.815    0.056    0.921
------------------------------------------------------------------------

CPU time actual refinement: 352.87


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_978/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_978/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_978/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_978/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_978/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 352.73 
  Macro-tasks:
    bulk solvent and scale       = 61.01  
    individual site refinement   = 145.56 
    weights calculation          = 30.94  
    collect and process          = 6.31   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 243.94 
  Micro-tasks:
    mask                            = 3.08   
    f_calc                          = 105.60 
    alpha_beta                      = 8.35   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 113.86 
    fmodel                         = 9.13   
    r_factors                      = 0.35   
    phase_errors                   = 9.64   
    foms                           = 0.27   
    TOTAL for micro-tasks          = 251.43 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.025 micro seconds
Total CPU time: 6.11 minutes
from_scatterers_fft:    575 calls, 105.26 s
gradients_fft:          520 calls, 101.22 s

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

# Date 2008-01-16 Time 06:07:33 PST -0800 (1200492453.68 s)
Start R-work = 0.5008, R-free = 0.5059 (no bulk solvent and anisotropic scale)
Final R-work = 0.1728, R-free = 0.2331 (no bulk solvent and anisotropic scale)

Start R-work = 0.4930, R-free = 0.5026
Final R-work = 0.1552, R-free = 0.2171