# Date 2008-01-16 Time 04:14:58 PST -0800 (1200485698.16 s)
#phil __OFF__

Command line arguments: "../238.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28298
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 238

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 48.1033, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 48.1033, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0501 1.96089
Completeness in resolution range: 0.916916
Completeness with d_max=infinity: 0.91422

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0501
                             d_min =   1.9609

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 48.1033, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0501 1.96089
Completeness in resolution range: 0.916916
Completeness with d_max=infinity: 0.91422

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0505 -  4.1969 [2239/2268]  2011   228  10.2%
  bin  2:  4.1969 -  3.3432 [2154/2177]  1937   217  10.1%
  bin  3:  3.3432 -  2.9242 [2123/2148]  1920   203   9.6%
  bin  4:  2.9242 -  2.6584 [2102/2129]  1887   215  10.2%
  bin  5:  2.6584 -  2.4687 [2078/2111]  1867   211  10.2%
  bin  6:  2.4687 -  2.3237 [2085/2113]  1878   207   9.9%
  bin  7:  2.3237 -  2.2077 [2071/2107]  1871   200   9.7%
  bin  8:  2.2077 -  2.1119 [2072/2114]  1863   209  10.1%
  bin  9:  2.1119 -  2.0308 [1994/2092]  1795   199  10.0%
  bin 10:  2.0308 -  1.9609 [ 671/2105]   601    70  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_238/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.14 -     1.89: 7
        1.89 -     2.64: 88
        2.64 -     3.40: 4342
        3.40 -     4.15: 9286
        4.15 -     4.90: 14469
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.140 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.276 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.388 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 296 "  1.566 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.713 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28187 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_238/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_238/model_refine_001.geo

CPU time processing inputs: 9.03


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 48.10325 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4741   r_free= 0.4647   ksol= 0.00   Bsol= 0.00   scale= 0.880    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.285953                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0505 -  4.6816 0.99   1458  161 0.3833 0.4104      6.5875       6.633|
|  2:  4.6816 -  3.7346 0.99   1406  154 0.4195 0.4222      6.8394      6.8392|
|  3:  3.7346 -  3.2680 0.99   1361  153 0.4604 0.4391      6.6843      6.6686|
|  4:  3.2680 -  2.9717 0.98   1374  148 0.4692 0.4111      6.5017      6.4683|
|  5:  2.9717 -  2.7601 0.99   1337  155 0.5084 0.4863      6.3597        6.36|
|  6:  2.7601 -  2.5983 0.99   1374  149 0.5016 0.5136      6.2747      6.1788|
|  7:  2.5983 -  2.4687 0.98   1312  154 0.4949 0.4298      6.2166      6.1357|
|  8:  2.4687 -  2.3617 0.98   1339  144 0.5234 0.5046      6.1668      6.1851|
|  9:  2.3617 -  2.2711 0.99   1347  139 0.5233 0.4962      6.1102      6.1397|
| 10:  2.2711 -  2.1930 0.99   1349  148 0.5082 0.5123      6.0801      6.0872|
| 11:  2.1930 -  2.1246 0.97   1307  156 0.5305 0.5544      6.0129      6.0599|
| 12:  2.1246 -  2.0640 0.98   1316  150 0.5175 0.4689      5.9434       5.939|
| 13:  2.0640 -  2.0098 0.81   1087  115 0.5061 0.5762      5.8585      5.7997|
| 14:  2.0098 -  1.9609 0.20    263   33 0.4816 0.3980      5.8968      5.7128|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0505 -  4.6816  1458   161  0.66  38.00   0.82     0.68      83840.86|
|  2:  4.6816 -  3.7346  1406   154  0.69  36.53   0.90     0.78     112912.87|
|  3:  3.7346 -  3.2680  1361   153  0.59  44.92   0.89     0.77     114950.29|
|  4:  3.2680 -  2.9717  1374   148  0.51  50.72   0.90     0.71      95920.01|
|  5:  2.9717 -  2.7601  1337   155  0.44  56.66   0.85     0.63      77215.27|
|  6:  2.7601 -  2.5983  1374   149  0.43  57.70   0.89     0.59      64914.42|
|  7:  2.5983 -  2.4687  1312   154  0.41  59.22   0.91     0.56      60125.62|
|  8:  2.4687 -  2.3617  1339   144  0.39  60.29   0.89     0.56      53928.42|
|  9:  2.3617 -  2.2711  1347   139  0.37  61.95   0.90     0.56      52706.36|
| 10:  2.2711 -  2.1930  1349   148  0.38  61.74   0.92     0.55      47750.03|
| 11:  2.1930 -  2.1246  1307   156  0.33  65.77   0.91     0.52      47705.21|
| 12:  2.1246 -  2.0640  1316   150  0.28  69.43   0.91     0.45      45898.64|
| 13:  2.0640 -  2.0098  1087   115  0.24  71.98   0.93     0.40      40490.06|
| 14:  2.0098 -  1.9609   263    33  0.29  68.01   0.98     0.36      30547.69|
|alpha:            min =        0.36 max =            0.78 mean =         0.60|
|beta:             min =    30547.69 max =       114950.29 mean =     69368.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.99 mean =        56.23|
|phase err.(test): min =        0.00 max =           89.82 mean =        56.31|
|-----------------------------------------------------------------------------|

============================== 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 = 15.176311             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.210   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.244795              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.683   (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 |  1.140 -  1.516:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.516 -  1.892:        4 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.892 -  2.268:       14 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.268 -  2.644:       74 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.644 -  3.020:     1994 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.020 -  3.396:     2348 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.396 -  3.772:     3918 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.772 -  4.148:     5368 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.148 -  4.524:     6444 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.524 -  4.900:     8025 |
|-----------------------------------------------------------------------------|
|-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 |        0.194 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.140 |       0.633 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.918)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4741   r_free= 0.4647   ksol= 0.00   Bsol= 0.00   scale= 0.880    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.285953                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4675   r_free= 0.4544   ksol= 0.29   Bsol= 24.67   scale= 0.918   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.55,4.27,-0.45,0.00,-0.00,-0.00); trace/3= 0.76                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.280496                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.139038             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.694   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.218857              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.402   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4675      final r-factor (work) = 0.3595          |
| start r-factor (free) = 0.4544      final r-factor (free) = 0.3906          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.4492 = 13.14 * 0.50 * 6.2798 + 1.00 * 0.1941                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.6499 = 13.14 * 0.50 * 6.1639 + 1.00 * 0.1557                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3595      final r-factor (work) = 0.3261          |
| start r-factor (free) = 0.3906      final r-factor (free) = 0.3980          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5189 = 1.22 * 1.00 * 6.1639 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4169 = 1.22 * 1.00 * 6.0642 + 1.00 * 0.0254                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.918)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.72   19.40    None  None   None       |
|    all(noH): 2823   0      0.00    91.72   19.40    None  None   None       |
|    Sol.    : 438    0      0.00    91.72   38.04    None  None   None       |
|    Mac.    : 2385   0      0.00    79.87   15.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.172:  816   |   5:    45.860 -  55.032:  119        |
|      1:     9.172 -  18.344:  854   |   6:    55.032 -  64.205:   65        |
|      2:    18.344 -  27.516:  483   |   7:    64.205 -  73.377:   21        |
|      3:    27.516 -  36.688:  282   |   8:    73.377 -  82.549:    9        |
|      4:    36.688 -  45.860:  171   |   9:    82.549 -  91.721:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3261 r_free = 0.3980             target_work(ml) = 6.069         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3258 r_free = 0.3975             target_work(ml) = 6.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3258   r_free= 0.3975   ksol= 0.29   Bsol= 24.67   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.55,4.27,-0.45,0.00,-0.00,-0.00); trace/3= 0.76                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.068326                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3242   r_free= 0.3939   ksol= 0.30   Bsol= 50.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,2.26,0.04,0.00,0.00,0.00); trace/3= 0.21                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.066574                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.862000              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.468   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.837397              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.292   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3242      final r-factor (work) = 0.2802          |
| start r-factor (free) = 0.3939      final r-factor (free) = 0.3467          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.9305 = 5.86 * 0.50 * 6.0645 + 1.00 * 0.1555                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.6928 = 5.86 * 0.50 * 6.0131 + 1.00 * 0.0683                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2802      final r-factor (work) = 0.2695          |
| start r-factor (free) = 0.3467      final r-factor (free) = 0.3417          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0587 = 0.84 * 1.00 * 6.0131 + 1.00 * 0.0234                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9870 = 0.84 * 1.00 * 5.9355 + 1.00 * 0.0166                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.918)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.12   19.28    None  None   None       |
|    all(noH): 2823   0      0.00    95.12   19.28    None  None   None       |
|    Sol.    : 438    0      2.42    95.12   38.58    None  None   None       |
|    Mac.    : 2385   0      0.00    84.80   15.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.512:  874   |   5:    47.562 -  57.074:  108        |
|      1:     9.512 -  19.025:  911   |   6:    57.074 -  66.587:   58        |
|      2:    19.025 -  28.537:  423   |   7:    66.587 -  76.099:   22        |
|      3:    28.537 -  38.050:  264   |   8:    76.099 -  85.612:   14        |
|      4:    38.050 -  47.562:  147   |   9:    85.612 -  95.124:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2695 r_free = 0.3417             target_work(ml) = 5.931         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2693 r_free = 0.3413             target_work(ml) = 5.931         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2693   r_free= 0.3413   ksol= 0.30   Bsol= 50.00   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,2.26,0.04,0.00,0.00,0.00); trace/3= 0.21                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.930510                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2695   r_free= 0.3416   ksol= 0.31   Bsol= 52.04   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.81,1.74,0.25,0.00,0.00,0.00); trace/3= 0.06                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.932171                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.023337              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.622  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.105316              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.061  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2695      final r-factor (work) = 0.2205          |
| start r-factor (free) = 0.3416      final r-factor (free) = 0.2798          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.9770 = 5.02 * 0.50 * 5.9358 + 1.00 * 0.0683                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.7675 = 5.02 * 0.50 * 5.8509 + 1.00 * 0.0720                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2205      final r-factor (work) = 0.2004          |
| start r-factor (free) = 0.2798      final r-factor (free) = 0.2668          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.1855 = 3.11 * 1.00 * 5.8509 + 1.00 * 0.0167                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.6960 = 3.11 * 1.00 * 5.6918 + 1.00 * 0.0210                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.918)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    117.67  20.04    None  None   None       |
|    all(noH): 2823   0      0.00    117.67  20.04    None  None   None       |
|    Sol.    : 438    0      2.90    117.67  47.72    None  None   None       |
|    Mac.    : 2385   0      0.00    112.67  14.96    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 -  11.767: 1288   |   5:    58.836 -  70.603:   83        |
|      1:    11.767 -  23.534:  821   |   6:    70.603 -  82.370:   46        |
|      2:    23.534 -  35.301:  262   |   7:    82.370 -  94.137:   32        |
|      3:    35.301 -  47.068:  151   |   8:    94.137 - 105.904:   23        |
|      4:    47.068 -  58.836:  110   |   9:   105.904 - 117.671:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2004 r_free = 0.2668             target_work(ml) = 5.672         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2003 r_free = 0.2668             target_work(ml) = 5.671         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2003   r_free= 0.2668   ksol= 0.31   Bsol= 52.04   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.81,1.74,0.25,0.00,0.00,0.00); trace/3= 0.06                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.671422                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2001   r_free= 0.2664   ksol= 0.32   Bsol= 69.84   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.93,0.48,0.02,0.00,0.00,0.00); trace/3= -0.48                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.671399                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.005258              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.731  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.382815              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.200  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2001      final r-factor (work) = 0.1690          |
| start r-factor (free) = 0.2664      final r-factor (free) = 0.2288          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6274 = 3.01 * 0.50 * 5.6936 + 1.00 * 0.0720                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4789 = 3.01 * 0.50 * 5.6051 + 1.00 * 0.0565                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1690      final r-factor (work) = 0.1608          |
| start r-factor (free) = 0.2288      final r-factor (free) = 0.2086          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1668 = 0.38 * 1.00 * 5.6051 + 1.00 * 0.0211                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1198 = 0.38 * 1.00 * 5.5016 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.918)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.48    111.37  18.64    None  None   None       |
|    all(noH): 2823   0      0.48    111.37  18.64    None  None   None       |
|    Sol.    : 438    0      5.55    111.37  46.02    None  None   None       |
|    Mac.    : 2385   0      0.48    109.74  13.61    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:     0.478 -  11.568: 1394   |   5:    55.924 -  67.013:   79        |
|      1:    11.568 -  22.657:  820   |   6:    67.013 -  78.103:   43        |
|      2:    22.657 -  33.746:  176   |   7:    78.103 -  89.192:   30        |
|      3:    33.746 -  44.835:  135   |   8:    89.192 - 100.281:   19        |
|      4:    44.835 -  55.924:  118   |   9:   100.281 - 111.370:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1608 r_free = 0.2086             target_work(ml) = 5.455         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1605 r_free = 0.2083             target_work(ml) = 5.454         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1605   r_free= 0.2083   ksol= 0.32   Bsol= 69.84   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.93,0.48,0.02,0.00,0.00,0.00); trace/3= -0.48                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.454290                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1611   r_free= 0.2082   ksol= 0.33   Bsol= 69.84   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-0.23,-0.29,-0.00,-0.00,-0.00); trace/3= -0.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.455911                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.947303              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.346  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.248087              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.886  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1611      final r-factor (work) = 0.1419          |
| start r-factor (free) = 0.2082      final r-factor (free) = 0.1895          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4151 = 1.95 * 0.50 * 5.5036 + 1.00 * 0.0565                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3105 = 1.95 * 0.50 * 5.3987 + 1.00 * 0.0541                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1419      final r-factor (work) = 0.1367          |
| start r-factor (free) = 0.1895      final r-factor (free) = 0.1894          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.1504 = 2.25 * 1.00 * 5.3987 + 1.00 * 0.0137                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.0074 = 2.25 * 1.00 * 5.3344 + 1.00 * 0.0153                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.918)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.57    118.32  18.56    None  None   None       |
|    all(noH): 2823   0      0.57    118.32  18.56    None  None   None       |
|    Sol.    : 438    0      5.22    118.32  48.08    None  None   None       |
|    Mac.    : 2385   0      0.57    117.64  13.14    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:     0.566 -  12.341: 1539   |   5:    59.441 -  71.216:   71        |
|      1:    12.341 -  24.116:  728   |   6:    71.216 -  82.992:   49        |
|      2:    24.116 -  35.891:  165   |   7:    82.992 -  94.767:   27        |
|      3:    35.891 -  47.666:  118   |   8:    94.767 - 106.542:   14        |
|      4:    47.666 -  59.441:  103   |   9:   106.542 - 118.317:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1367 r_free = 0.1894             target_work(ml) = 5.329         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1367 r_free = 0.1893             target_work(ml) = 5.329         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1367   r_free= 0.1893   ksol= 0.33   Bsol= 69.84   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-0.23,-0.29,-0.00,-0.00,-0.00); trace/3= -0.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.329146                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0505 -  4.6816 0.99   1458  161 0.1029 0.1450      5.4351      5.6682|
|  2:  4.6816 -  3.7346 0.99   1406  154 0.0940 0.1158      5.5213      5.7186|
|  3:  3.7346 -  3.2680 0.99   1361  153 0.1284 0.1806      5.6353      5.9356|
|  4:  3.2680 -  2.9717 0.98   1374  148 0.1526 0.1955      5.6117      5.7869|
|  5:  2.9717 -  2.7601 0.99   1337  155 0.1680 0.2037       5.525      5.7101|
|  6:  2.7601 -  2.5983 0.99   1374  149 0.1552 0.2392      5.3925      5.5732|
|  7:  2.5983 -  2.4687 0.98   1312  154 0.1514 0.1866      5.3281      5.4887|
|  8:  2.4687 -  2.3617 0.98   1339  144 0.1515 0.2322      5.2909      5.5578|
|  9:  2.3617 -  2.2711 0.99   1347  139 0.1451 0.2233      5.2109      5.4798|
| 10:  2.2711 -  2.1930 0.99   1349  148 0.1476 0.2146      5.1825      5.3632|
| 11:  2.1930 -  2.1246 0.97   1307  156 0.1426 0.2163      5.0972      5.4529|
| 12:  2.1246 -  2.0640 0.98   1316  150 0.1462 0.1952      5.0615      5.2515|
| 13:  2.0640 -  2.0098 0.81   1087  115 0.1419 0.2167      4.9573      5.1971|
| 14:  2.0098 -  1.9609 0.20    263   33 0.1315 0.2199      4.9142      5.1259|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0505 -  4.6816  1458   161  0.93   9.95   0.96     0.93       8029.21|
|  2:  4.6816 -  3.7346  1406   154  0.95   9.22   1.02     1.01      10897.69|
|  3:  3.7346 -  3.2680  1361   153  0.92  13.80   1.04     1.03      13817.24|
|  4:  3.2680 -  2.9717  1374   148  0.89  17.45   1.02     1.01      14064.06|
|  5:  2.9717 -  2.7601  1337   155  0.87  19.60   1.02     1.01      12414.73|
|  6:  2.7601 -  2.5983  1374   149  0.87  19.85   0.98     0.93       9796.70|
|  7:  2.5983 -  2.4687  1312   154  0.87  19.18   1.01     0.97       8778.37|
|  8:  2.4687 -  2.3617  1339   144  0.86  20.42   1.01     0.97       8537.55|
|  9:  2.3617 -  2.2711  1347   139  0.86  20.22   0.99     0.92       7122.23|
| 10:  2.2711 -  2.1930  1349   148  0.86  20.80   1.00     0.96       7202.41|
| 11:  2.1930 -  2.1246  1307   156  0.87  20.03   0.99     0.94       6095.70|
| 12:  2.1246 -  2.0640  1316   150  0.87  19.97   0.99     0.98       5681.04|
| 13:  2.0640 -  2.0098  1087   115  0.86  20.58   0.99     0.96       4815.16|
| 14:  2.0098 -  1.9609   263    33  0.88  18.49   0.97     0.90       4057.24|
|alpha:            min =        0.90 max =            1.03 mean =         0.97|
|beta:             min =     4057.24 max =        14064.06 mean =      9031.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.93 mean =        17.65|
|phase err.(test): min =        0.00 max =           89.88 mean =        17.14|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1367   r_free= 0.1895   ksol= 0.33   Bsol= 71.84   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-0.47,-0.21,-0.00,-0.00,-0.00); trace/3= -1.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.329234                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1367   r_free= 0.1895   ksol= 0.33   Bsol= 71.84   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-0.47,-0.21,-0.00,-0.00,-0.00); trace/3= -1.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.329234                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0505 -  4.6816 0.99   1458  161 0.1030 0.1450      5.4358      5.6689|
|  2:  4.6816 -  3.7346 0.99   1406  154 0.0941 0.1160      5.5221      5.7201|
|  3:  3.7346 -  3.2680 0.99   1361  153 0.1285 0.1807       5.636      5.9357|
|  4:  3.2680 -  2.9717 0.98   1374  148 0.1525 0.1954      5.6115      5.7866|
|  5:  2.9717 -  2.7601 0.99   1337  155 0.1680 0.2034      5.5243      5.7085|
|  6:  2.7601 -  2.5983 0.99   1374  149 0.1550 0.2390      5.3917      5.5722|
|  7:  2.5983 -  2.4687 0.98   1312  154 0.1514 0.1874      5.3275      5.4893|
|  8:  2.4687 -  2.3617 0.98   1339  144 0.1516 0.2322      5.2911      5.5589|
|  9:  2.3617 -  2.2711 0.99   1347  139 0.1450 0.2234       5.211       5.479|
| 10:  2.2711 -  2.1930 0.99   1349  148 0.1474 0.2152      5.1823      5.3649|
| 11:  2.1930 -  2.1246 0.97   1307  156 0.1424 0.2168      5.0973      5.4537|
| 12:  2.1246 -  2.0640 0.98   1316  150 0.1463 0.1951      5.0623      5.2525|
| 13:  2.0640 -  2.0098 0.81   1087  115 0.1421 0.2162      4.9577      5.1958|
| 14:  2.0098 -  1.9609 0.20    263   33 0.1314 0.2199      4.9136       5.126|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0505 -  4.6816  1458   161  0.93   9.95   0.96     0.93       8037.81|
|  2:  4.6816 -  3.7346  1406   154  0.95   9.23   1.02     1.01      10914.31|
|  3:  3.7346 -  3.2680  1361   153  0.92  13.81   1.03     1.03      13844.02|
|  4:  3.2680 -  2.9717  1374   148  0.89  17.46   1.02     1.01      14069.11|
|  5:  2.9717 -  2.7601  1337   155  0.87  19.57   1.02     1.01      12384.75|
|  6:  2.7601 -  2.5983  1374   149  0.87  19.83   0.98     0.93       9785.07|
|  7:  2.5983 -  2.4687  1312   154  0.87  19.16   1.00     0.97       8767.32|
|  8:  2.4687 -  2.3617  1339   144  0.86  20.43   1.01     0.96       8546.08|
|  9:  2.3617 -  2.2711  1347   139  0.86  20.23   0.99     0.91       7131.12|
| 10:  2.2711 -  2.1930  1349   148  0.86  20.80   1.00     0.95       7208.29|
| 11:  2.1930 -  2.1246  1307   156  0.87  20.05   0.99     0.93       6110.35|
| 12:  2.1246 -  2.0640  1316   150  0.87  19.98   0.99     0.98       5690.10|
| 13:  2.0640 -  2.0098  1087   115  0.86  20.59   0.98     0.95       4815.78|
| 14:  2.0098 -  1.9609   263    33  0.88  18.48   0.97     0.90       4048.06|
|alpha:            min =        0.90 max =            1.03 mean =         0.97|
|beta:             min =     4048.06 max =        14069.11 mean =      9035.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.96 mean =        17.65|
|phase err.(test): min =        0.00 max =           89.98 mean =        17.14|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.918)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.55    118.30  18.55    None  None   None       |
|    all(noH): 2823   0      0.55    118.30  18.55    None  None   None       |
|    Sol.    : 438    0      5.20    118.30  48.06    None  None   None       |
|    Mac.    : 2385   0      0.55    117.62  13.13    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:     0.547 -  12.322: 1539   |   5:    59.423 -  71.198:   71        |
|      1:    12.322 -  24.098:  728   |   6:    71.198 -  82.973:   49        |
|      2:    24.098 -  35.873:  165   |   7:    82.973 -  94.749:   27        |
|      3:    35.873 -  47.648:  118   |   8:    94.749 - 106.524:   14        |
|      4:    47.648 -  59.423:  103   |   9:   106.524 - 118.299:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 317         
Filter by distance & map next to the model:
   mapped sites are within: 0.611 - 4.369
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 314 from: 317
   mapped sites are within: 0.750 - 4.369

peak=   10.229 closest distance to " O  BHOH Z  74 " =    1.500
peak=    8.502 closest distance to " O   GLN A  11 " =    1.140
peak=    7.521 closest distance to " O   HOH Z 203 " =    1.039
peak=    6.519 closest distance to " O   HOH Z 117 " =    1.539
peak=    6.046 closest distance to " O   HOH Z 178 " =    1.127
peak=    5.840 closest distance to " O   HOH Z 159 " =    1.133
peak=    5.681 closest distance to " O   HOH Z 124 " =    1.389
peak=    5.625 closest distance to " O   HOH Z 255 " =    1.141
peak=    5.362 closest distance to " O   HOH Z 403 " =    2.175
peak=    5.336 closest distance to " OD1 ASN A 301 " =    1.073
peak=    5.323 closest distance to " O   HOH Z 102 " =    1.627
peak=    5.267 closest distance to " O   HOH Z 210 " =    1.360
peak=    5.227 closest distance to " O   HOH Z 248 " =    1.557
peak=    5.191 closest distance to " CA  TYR A  30 " =    0.914
peak=    5.002 closest distance to " CD2 TRP A 179 " =    1.385
peak=    4.996 closest distance to " NH2 ARG A  36 " =    1.190
peak=    4.894 closest distance to " O   HOH Z  49 " =    1.589
peak=    4.835 closest distance to " CB  ASN A 285 " =    1.027
peak=    4.811 closest distance to " CG  PRO A  54 " =    1.323
peak=    4.758 closest distance to " CB  ARG A 275 " =    0.919
peak=    4.622 closest distance to " CD  ARG A  36 " =    1.183
peak=    4.614 closest distance to " O   HOH Z 433 " =    2.046
peak=    4.608 closest distance to " O   HOH Z 113 " =    2.159
peak=    4.595 closest distance to " O   HOH Z 404 " =    1.378
peak=    4.587 closest distance to " NE  ARG A  36 " =    1.049
peak=    4.574 closest distance to " O   HOH Z 422 " =    0.926
peak=    4.571 closest distance to " O   HOH Z  46 " =    1.097
peak=    4.565 closest distance to " NH2 ARG A 156 " =    1.173
peak=    4.558 closest distance to " O   HOH Z  80 " =    2.173
peak=    4.532 closest distance to " O   HOH Z 128 " =    1.591
peak=    4.528 closest distance to " CG  PRO A 280 " =    0.947
peak=    4.509 closest distance to " O   HOH Z 130 " =    1.073
peak=    4.496 closest distance to " ND2 ASN A 249 " =    2.225
peak=    4.420 closest distance to " O   HOH Z 116 " =    1.277
peak=    4.405 closest distance to " O   HOH Z  65 " =    1.043
peak=    4.365 closest distance to " NH1 ARG A  36 " =    1.305
peak=    4.360 closest distance to " O   HOH Z 394 " =    1.780
peak=    4.346 closest distance to " O   HOH Z  44 " =    2.285
peak=    4.344 closest distance to " CZ3 TRP A 266 " =    0.986
peak=    4.338 closest distance to " CB  SER A  62 " =    1.105
peak=    4.332 closest distance to " CB  SER A  63 " =    1.298
peak=    4.289 closest distance to " CG  GLN A  77 " =    0.833
peak=    4.265 closest distance to " O   HOH Z 272 " =    1.399
peak=    4.237 closest distance to " O   HOH Z 414 " =    1.780
peak=    4.237 closest distance to " N   SER A 164 " =    0.991
peak=    4.235 closest distance to " O   HOH Z 403 " =    1.586
peak=    4.209 closest distance to " CG  ARG A  66 " =    1.004
peak=    4.199 closest distance to " O   HOH Z 261 " =    2.365
peak=    4.198 closest distance to " O   HOH Z  54 " =    0.989
peak=    4.185 closest distance to " O   HOH Z 298 " =    1.943
peak=    4.183 closest distance to " CA  GLN A  73 " =    1.391
peak=    4.171 closest distance to " O   HOH Z 154 " =    1.726
peak=    4.171 closest distance to " CA  ALA A 100 " =    1.281
peak=    4.169 closest distance to " O   HOH Z 402 " =    1.716
peak=    4.155 closest distance to " CB  GLN A 223 " =    1.348
peak=    4.135 closest distance to " O   HOH Z  43 " =    2.213
peak=    4.116 closest distance to " CG  PRO A  90 " =    1.319
peak=    4.094 closest distance to " CG2BVAL A  41 " =    0.918
peak=    4.087 closest distance to " O   HOH Z  97 " =    1.329
peak=    4.073 closest distance to " CB  GLN A  73 " =    1.190
peak=    4.038 closest distance to " NE2 GLN A  11 " =    1.043
peak=    4.033 closest distance to " O   HOH Z 130 " =    2.471
peak=    4.029 closest distance to " CB  TRP A 179 " =    1.307
peak=    4.029 closest distance to " O   HOH Z 186 " =    2.230
peak=    4.018 closest distance to " NH1AARG A 275 " =    1.095
peak=    4.014 closest distance to " O   PRO A 198 " =    1.544
peak=    3.994 closest distance to " CA  ARG A 195 " =    1.109
peak=    3.983 closest distance to " O   HOH Z  63 " =    1.789
peak=    3.983 closest distance to " O   HOH Z 132 " =    2.969
peak=    3.974 closest distance to " O   HOH Z 369 " =    1.945
peak=    3.964 closest distance to " O   HOH Z 431 " =    1.383
peak=    3.949 closest distance to " CZ  PHE A 218 " =    1.248
peak=    3.944 closest distance to " NZ  LYS A 117 " =    3.045
peak=    3.933 closest distance to " O   HOH Z 134 " =    1.993
peak=    3.932 closest distance to " CA  ARG A  36 " =    1.045
peak=    3.926 closest distance to " CB  THR A  52 " =    0.791
peak=    3.925 closest distance to " CB  PRO A  54 " =    1.086
peak=    3.921 closest distance to " O   HOH Z  69 " =    1.270
peak=    3.920 closest distance to " O   HOH Z 189 " =    2.842
peak=    3.920 closest distance to " CB  GLU A 128 " =    1.142
peak=    3.917 closest distance to " CA  GLN A  11 " =    1.047
peak=    3.913 closest distance to " CB  SER A 141 " =    1.036
peak=    3.908 closest distance to " O   HOH Z 412 " =    3.572
peak=    3.905 closest distance to " O   HOH Z 357 " =    2.064
peak=    3.882 closest distance to " O   HOH Z 126 " =    1.547
peak=    3.881 closest distance to " CG  PRO A 243 " =    1.117
peak=    3.878 closest distance to " CB  GLU A   2 " =    1.025
peak=    3.858 closest distance to " CG AARG A 275 " =    1.293
peak=    3.855 closest distance to " CA  ARG A 156 " =    1.002
peak=    3.850 closest distance to " CB  MET A  40 " =    1.018
peak=    3.835 closest distance to " OE1 GLU A   2 " =    1.336
peak=    3.826 closest distance to " CG2 VAL A 197 " =    1.204
peak=    3.820 closest distance to " CZ  PHE A  38 " =    1.103
peak=    3.820 closest distance to " O   HOH Z 146 " =    1.234
peak=    3.814 closest distance to " O   GLY A  23 " =    2.499
peak=    3.797 closest distance to " O   HOH Z 193 " =    1.384
peak=    3.792 closest distance to " O   HOH Z  67 " =    1.124
peak=    3.790 closest distance to " CG  PRO A 198 " =    1.344
peak=    3.786 closest distance to " CD  ARG A 269 " =    0.958
peak=    3.785 closest distance to " O   HOH Z 209 " =    2.144
peak=    3.779 closest distance to " CG  GLN A  58 " =    0.859
peak=    3.778 closest distance to " O   HOH Z 141 " =    2.029
peak=    3.775 closest distance to " O   HOH Z 428 " =    1.108
peak=    3.770 closest distance to " O   HOH Z 120 " =    0.939
peak=    3.767 closest distance to " N   HIS A 108 " =    1.774
peak=    3.766 closest distance to " CG1 ILE A 120 " =    1.096
peak=    3.755 closest distance to " CB  GLN A 183 " =    1.265
peak=    3.751 closest distance to " O   HOH Z 417 " =    1.521
peak=    3.744 closest distance to " OE1 GLN A  11 " =    2.318
peak=    3.744 closest distance to " O   ASP A 200 " =    1.490
peak=    3.744 closest distance to " O   HOH Z 427 " =    3.476
peak=    3.715 closest distance to " O   HOH Z 214 " =    1.296
peak=    3.714 closest distance to " O   ALA A 165 " =    1.469
peak=    3.713 closest distance to " CB  SER A 273 " =    0.965
peak=    3.712 closest distance to " O   HOH Z  40 " =    1.966
peak=    3.710 closest distance to " O   HOH Z 368 " =    3.301
peak=    3.707 closest distance to " NH2BARG A 145 " =    2.258
peak=    3.690 closest distance to " O   HOH Z 426 " =    1.256
peak=    3.684 closest distance to " O   HOH Z 406 " =    1.630
peak=    3.679 closest distance to " O   HOH Z 370 " =    2.166
peak=    3.674 closest distance to " O   HOH Z  88 " =    3.387
peak=    3.667 closest distance to " O   HOH Z 358 " =    1.450
peak=    3.660 closest distance to " O   HOH Z 247 " =    1.546
peak=    3.656 closest distance to " CB  ARG A 190 " =    1.890
peak=    3.646 closest distance to " O   HOH Z 282 " =    2.356
peak=    3.638 closest distance to " CD  ARG A  24 " =    1.210
peak=    3.638 closest distance to " CB  MET A 105 " =    1.013
peak=    3.628 closest distance to " O   HOH Z 234 " =    3.514
peak=    3.620 closest distance to " O   HOH Z 146 " =    1.528
peak=    3.618 closest distance to " O   HOH Z 344 " =    3.170
peak=    3.616 closest distance to " CA  ILE A 120 " =    1.276
peak=    3.613 closest distance to " N   GLU A  44 " =    1.320
peak=    3.608 closest distance to " O   HOH Z 423 " =    1.866
peak=    3.594 closest distance to " O  BHOH Z 338 " =    1.136
peak=    3.587 closest distance to " CA  GLU A 152 " =    0.919
peak=    3.583 closest distance to " CA  VAL A  41 " =    0.963
peak=    3.581 closest distance to " CA  CYS A 260 " =    1.596
peak=    3.581 closest distance to " O   HOH Z 377 " =    1.134
peak=    3.578 closest distance to " O   HOH Z 340 " =    1.455
peak=    3.575 closest distance to " OE1 GLN A  58 " =    3.051
peak=    3.569 closest distance to " O   HOH Z  22 " =    2.723
peak=    3.569 closest distance to " O   HOH Z 418 " =    3.019
peak=    3.568 closest distance to " CA  THR A 246 " =    1.066
peak=    3.565 closest distance to " CB  ASN A 148 " =    1.344
peak=    3.561 closest distance to " O   HOH Z 365 " =    2.530
peak=    3.557 closest distance to " CB  PRO A 243 " =    1.159
peak=    3.555 closest distance to " CG2 THR A  42 " =    0.803
peak=    3.550 closest distance to " CB  GLU A 175 " =    1.278
peak=    3.545 closest distance to " O   THR A 251 " =    1.273
peak=    3.543 closest distance to " O   HOH Z 132 " =    2.220
peak=    3.541 closest distance to " O   HOH Z 425 " =    1.572
peak=    3.539 closest distance to " CG2 ILE A  20 " =    1.335
peak=    3.537 closest distance to " CB  SER A  26 " =    1.695
peak=    3.527 closest distance to " ND2 ASN A 249 " =    0.914
peak=    3.522 closest distance to " O   HOH Z 111 " =    1.547
peak=    3.522 closest distance to " CB  VAL A 265 " =    1.153
peak=    3.520 closest distance to " O   ASN A 285 " =    0.851
peak=    3.518 closest distance to " CB  ALA A 114 " =    0.768
peak=    3.515 closest distance to " O   HOH Z 277 " =    2.812
peak=    3.511 closest distance to " CA  VAL A 112 " =    1.238
peak=    3.507 closest distance to " O   HOH Z 250 " =    2.416
peak=    3.500 closest distance to " CD  LYS A 119 " =    1.825
peak=    3.498 closest distance to " CD  LYS A 166 " =    1.604
peak=    3.496 closest distance to " CG1 ILE A  33 " =    1.374
peak=    3.495 closest distance to " O   HOH Z  39 " =    1.788
peak=    3.487 closest distance to " O   HOH Z 358 " =    2.177
peak=    3.478 closest distance to " O   HOH Z 219 " =    2.071
peak=    3.473 closest distance to " O   HOH Z 299 " =    4.075
peak=    3.468 closest distance to " CB  PHE A  16 " =    1.171
peak=    3.465 closest distance to " CA  ALA A 160 " =    0.975
peak=    3.464 closest distance to " CB  TRP A 179 " =    1.797
peak=    3.462 closest distance to " N   ALA A   1 " =    1.112
peak=    3.459 closest distance to " O   HOH Z 284 " =    2.879
peak=    3.458 closest distance to " CG  GLN A  11 " =    1.209
peak=    3.457 closest distance to " CE1 TYR A 186 " =    1.361
peak=    3.454 closest distance to " CA  SER A  12 " =    1.409
peak=    3.453 closest distance to " O   ASP A 191 " =    1.655
peak=    3.452 closest distance to " O   THR A 220 " =    1.112
peak=    3.450 closest distance to " CB  SER A 288 " =    0.851
peak=    3.449 closest distance to " O   VAL A  72 " =    0.997
peak=    3.447 closest distance to " CA  THR A  82 " =    1.660
peak=    3.445 closest distance to " CD2 TYR A  68 " =    0.855
peak=    3.441 closest distance to " O   HOH Z 298 " =    4.369
peak=    3.436 closest distance to " O   HOH Z 380 " =    1.994
peak=    3.433 closest distance to " O   HOH Z 289 " =    1.712
peak=    3.422 closest distance to " O   HOH Z  68 " =    1.989
peak=    3.422 closest distance to " N   ASN A  39 " =    1.304
peak=    3.415 closest distance to " CB  TYR A 116 " =    1.168
peak=    3.415 closest distance to " O   HOH Z 437 " =    1.996
peak=    3.414 closest distance to " O   HOH Z 394 " =    3.895
peak=    3.412 closest distance to " O   HOH Z 236 " =    1.669
peak=    3.411 closest distance to " O   HOH Z 423 " =    3.282
peak=    3.406 closest distance to " N   TRP A 150 " =    1.126
peak=    3.403 closest distance to " O   HOH Z  90 " =    3.896
peak=    3.399 closest distance to " CA  ASN A 217 " =    1.331
peak=    3.399 closest distance to " N   ASN A 252 " =    1.203
peak=    3.397 closest distance to " CE3 TRP A  85 " =    1.230
peak=    3.393 closest distance to " CE  LYS A 119 " =    1.215
peak=    3.392 closest distance to " O   HOH Z 109 " =    2.936
peak=    3.379 closest distance to " O   HOH Z 401 " =    0.954
peak=    3.378 closest distance to " CB  ASN A  39 " =    0.815
peak=    3.376 closest distance to " NE2 GLN A  77 " =    3.012
peak=    3.376 closest distance to " CE3 TRP A 274 " =    3.428
peak=    3.369 closest distance to " CB  GLU A  46 " =    1.236
peak=    3.367 closest distance to " CB  ALA A 114 " =    1.064
peak=    3.367 closest distance to " CA  ALA A  51 " =    0.986
peak=    3.366 closest distance to " CB  VAL A 202 " =    1.498
peak=    3.365 closest distance to " O   HOH Z  35 " =    1.832
peak=    3.365 closest distance to " CB  GLN A 194 " =    0.979
peak=    3.363 closest distance to " OG1 THR A 221 " =    1.447
peak=    3.361 closest distance to " O   HOH Z  89 " =    2.255
peak=    3.356 closest distance to " O   HOH Z 176 " =    1.339
peak=    3.356 closest distance to " CD1 LEU A  96 " =    0.838
peak=    3.349 closest distance to " CB  GLN A  88 " =    1.253
peak=    3.345 closest distance to " NH1AARG A 275 " =    2.315
peak=    3.343 closest distance to " CB  ASN A 187 " =    2.419
peak=    3.343 closest distance to " N   THR A  52 " =    1.142
peak=    3.342 closest distance to " OG  SER A  62 " =    2.667
peak=    3.335 closest distance to " O   SER A  87 " =    2.202
peak=    3.333 closest distance to " O   HOH Z 371 " =    2.939
peak=    3.329 closest distance to " CG2AVAL A 121 " =    2.010
peak=    3.329 closest distance to " CA  GLU A   2 " =    0.750
peak=    3.326 closest distance to " O   HOH Z 421 " =    2.116
peak=    3.324 closest distance to " O   HOH Z  85 " =    1.295
peak=    3.324 closest distance to " NE2 HIS A 115 " =    1.126
peak=    3.321 closest distance to " O   HOH Z 393 " =    3.592
peak=    3.315 closest distance to " CG2 THR A 220 " =    0.758
peak=    3.312 closest distance to " O   HOH Z 365 " =    1.459
peak=    3.312 closest distance to " CA  ALA A 129 " =    0.859
peak=    3.308 closest distance to " CG2BVAL A 121 " =    0.892
peak=    3.304 closest distance to " O   GLY A  57 " =    1.255
peak=    3.303 closest distance to " CB  ARG A 219 " =    1.310
peak=    3.294 closest distance to " CA  SER A  62 " =    0.927
peak=    3.291 closest distance to " CD  ARG A 159 " =    0.833
peak=    3.290 closest distance to " CB  VAL A 230 " =    1.042
peak=    3.290 closest distance to " CD  ARG A 195 " =    1.179
peak=    3.289 closest distance to " O   HOH Z 185 " =    1.748
peak=    3.287 closest distance to " O   HOH Z  41 " =    1.977
peak=    3.278 closest distance to " O   HOH Z  48 " =    1.831
peak=    3.276 closest distance to " O   HOH Z 156 " =    2.749
peak=    3.274 closest distance to " CA  LEU A  83 " =    1.361
peak=    3.272 closest distance to " CA  GLU A   2 " =    1.072
peak=    3.269 closest distance to " CD  LYS A  76 " =    1.755
peak=    3.268 closest distance to " CB  THR A  31 " =    1.525
peak=    3.263 closest distance to " O   HOH Z 250 " =    1.536
peak=    3.262 closest distance to " CB  ASN A 187 " =    1.378
peak=    3.259 closest distance to " O   HOH Z  15 " =    2.473
peak=    3.258 closest distance to " OD1 ASP A 231 " =    1.978
peak=    3.257 closest distance to " CB  ARG A 269 " =    1.267
peak=    3.257 closest distance to " CB  GLU A 152 " =    1.135
peak=    3.251 closest distance to " O   PRO A  90 " =    1.511
peak=    3.249 closest distance to " O   HOH Z 281 " =    2.700
peak=    3.249 closest distance to " OD1 ASN A 217 " =    1.578
peak=    3.245 closest distance to " CA  ALA A 248 " =    1.203
peak=    3.239 closest distance to " CB  ALA A 292 " =    0.821
peak=    3.239 closest distance to " O   HOH Z 196 " =    1.459
peak=    3.231 closest distance to " O   HOH Z 213 " =    1.417
peak=    3.227 closest distance to " O   HOH Z 214 " =    2.276
peak=    3.226 closest distance to " OE1 GLN A  73 " =    1.379
peak=    3.225 closest distance to " CB  ASN A  45 " =    1.158
peak=    3.224 closest distance to " O   HOH Z 339 " =    1.381
peak=    3.219 closest distance to " O   HOH Z 258 " =    2.064
peak=    3.218 closest distance to " CG2 ILE A 234 " =    1.255
peak=    3.217 closest distance to " CE  LYS A  76 " =    0.851
peak=    3.216 closest distance to " N   CYS A 260 " =    0.862
peak=    3.213 closest distance to " CB  TYR A 247 " =    0.954
peak=    3.212 closest distance to " CD  GLN A  73 " =    1.292
peak=    3.210 closest distance to " O   HOH Z 279 " =    1.216
peak=    3.207 closest distance to " O   HOH Z 221 " =    0.988
peak=    3.205 closest distance to " OG1 THR A  82 " =    1.222
peak=    3.199 closest distance to " O  BHOH Z 338 " =    2.065
peak=    3.199 closest distance to " CG  ARG A 138 " =    1.431
peak=    3.195 closest distance to " CD  PRO A  54 " =    1.113
peak=    3.194 closest distance to " O   HOH Z 195 " =    1.136
peak=    3.190 closest distance to " OE1 GLN A  73 " =    1.513
peak=    3.185 closest distance to " O   HOH Z 316 " =    3.096
peak=    3.183 closest distance to " O   HOH Z 424 " =    1.369
peak=    3.182 closest distance to " O   ARG A 275 " =    0.934
peak=    3.181 closest distance to " CB  GLU A 277 " =    3.708
peak=    3.179 closest distance to " ND1 HIS A  81 " =    1.292
peak=    3.179 closest distance to " O   HOH Z 172 " =    2.945
peak=    3.176 closest distance to " O   ASN A 301 " =    1.539
peak=    3.176 closest distance to " OD2 ASP A 298 " =    3.297
peak=    3.174 closest distance to " O   HOH Z 245 " =    1.243
peak=    3.166 closest distance to " O   HOH Z 217 " =    2.723
peak=    3.158 closest distance to " CB  ASP A 286 " =    1.058
peak=    3.154 closest distance to " CA  PRO A  90 " =    0.862
peak=    3.144 closest distance to " CD2 LEU A 255 " =    1.532
peak=    3.143 closest distance to " CD  GLN A 144 " =    1.554
peak=    3.142 closest distance to " OG BSER A  99 " =    2.725
peak=    3.141 closest distance to " CZ3 TRP A  85 " =    1.001
peak=    3.128 closest distance to " O   LYS A 289 " =    0.947
peak=    3.128 closest distance to " OG  SER A 245 " =    1.420
peak=    3.128 closest distance to " CG2 VAL A  78 " =    0.787
peak=    3.126 closest distance to " O   HOH Z 415 " =    1.060
peak=    3.126 closest distance to " O   HOH Z 154 " =    1.973
peak=    3.124 closest distance to " CB  ASP A 191 " =    1.247
peak=    3.116 closest distance to " O   HOH Z 251 " =    1.504
peak=    3.101 closest distance to " CA  ASN A 209 " =    1.212
peak=    3.088 closest distance to " CB  ARG A 156 " =    0.976
peak=    3.088 closest distance to " O   HOH Z 298 " =    2.056
peak=    3.087 closest distance to " CG  GLN A  11 " =    0.952
peak=    3.085 closest distance to " O   HOH Z  78 " =    2.249
peak=    3.076 closest distance to " CB  ARG A 138 " =    0.953
peak=    3.075 closest distance to " O   HOH Z 163 " =    2.031
peak=    3.072 closest distance to " OE2 GLU A  53 " =    1.408
peak=    3.068 closest distance to " O   HOH Z 435 " =    1.689
peak=    3.067 closest distance to " O   HOH Z  78 " =    1.633
peak=    3.062 closest distance to " CD  GLN A 194 " =    1.706
peak=    3.055 closest distance to " CD1 LEU A 222 " =    0.854
peak=    3.043 closest distance to " O   HOH Z 200 " =    3.530
peak=    3.043 closest distance to " CG  MET A 185 " =    1.200
peak=    3.038 closest distance to " O   HOH Z 109 " =    2.879
peak=    3.031 closest distance to " O   HOH Z 297 " =    1.000

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.640 - 5.973
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 201
   mapped sites are within: 0.716 - 5.973

peak=   -4.847 closest distance to " NH2 ARG A  36 " =    1.013
peak=   -4.738 closest distance to " O   GLN A  11 " =    1.161
peak=   -4.709 closest distance to " O   HOH Z 411 " =    5.440
peak=   -4.592 closest distance to " CG  PRO A 243 " =    1.670
peak=   -4.372 closest distance to " CA  SER A 288 " =    1.178
peak=   -4.361 closest distance to " CD  ARG A  14 " =    3.314
peak=   -4.296 closest distance to " OD1 ASN A 301 " =    0.812
peak=   -4.273 closest distance to " O   HOH Z 120 " =    1.029
peak=   -4.271 closest distance to " O   PRO A 198 " =    1.372
peak=   -4.245 closest distance to " CD2 TYR A  30 " =    2.766
peak=   -4.200 closest distance to " CG2 VAL A 189 " =    2.160
peak=   -4.146 closest distance to " CD  GLN A 223 " =    1.768
peak=   -4.140 closest distance to " O   PHE A 218 " =    1.364
peak=   -4.095 closest distance to " O   HOH Z 418 " =    1.322
peak=   -4.094 closest distance to " NE2 GLN A 223 " =    1.258
peak=   -4.065 closest distance to " O   HOH Z   7 " =    1.064
peak=   -3.974 closest distance to " O   HOH Z  67 " =    1.466
peak=   -3.970 closest distance to " O   HOH Z 166 " =    1.630
peak=   -3.970 closest distance to " O   HOH Z 423 " =    2.614
peak=   -3.955 closest distance to " O   HOH Z 203 " =    0.716
peak=   -3.931 closest distance to " O   HOH Z 150 " =    1.861
peak=   -3.925 closest distance to " CD2 LEU A 237 " =    2.214
peak=   -3.916 closest distance to " CD  GLN A  58 " =    1.033
peak=   -3.913 closest distance to " CG  GLU A  53 " =    1.278
peak=   -3.908 closest distance to " C   HIS A 108 " =    0.988
peak=   -3.901 closest distance to " CA  GLY A 133 " =    1.959
peak=   -3.892 closest distance to " O   HOH Z 130 " =    1.016
peak=   -3.883 closest distance to " C   THR A 279 " =    1.177
peak=   -3.879 closest distance to " O   HOH Z  38 " =    1.343
peak=   -3.877 closest distance to " O   HOH Z 155 " =    1.749
peak=   -3.867 closest distance to " CD1 TRP A 179 " =    1.160
peak=   -3.855 closest distance to " O   HOH Z 422 " =    1.081
peak=   -3.851 closest distance to " O   ILE A 109 " =    2.579
peak=   -3.829 closest distance to " CG2 ILE A  20 " =    2.804
peak=   -3.803 closest distance to " O   HOH Z  35 " =    2.015
peak=   -3.802 closest distance to " CA  GLU A 277 " =    1.110
peak=   -3.801 closest distance to " CG2 THR A 279 " =    1.817
peak=   -3.790 closest distance to " O   HOH Z  56 " =    1.025
peak=   -3.787 closest distance to " CG2 ILE A  49 " =    2.795
peak=   -3.776 closest distance to " CD1 ILE A 106 " =    2.118
peak=   -3.773 closest distance to " CD2 PHE A  61 " =    2.039
peak=   -3.770 closest distance to " NE  ARG A 156 " =    1.958
peak=   -3.766 closest distance to " O   HOH Z 234 " =    4.036
peak=   -3.751 closest distance to " C   ASN A 285 " =    2.216
peak=   -3.745 closest distance to " O   HOH Z  37 " =    1.438
peak=   -3.735 closest distance to " O   VAL A  67 " =    2.746
peak=   -3.725 closest distance to " CD1 PHE A  59 " =    1.811
peak=   -3.717 closest distance to " O   HOH Z 159 " =    0.908
peak=   -3.716 closest distance to " O   HOH Z 250 " =    1.732
peak=   -3.711 closest distance to " CD  LYS A 289 " =    2.316
peak=   -3.709 closest distance to " O   HOH Z 203 " =    1.151
peak=   -3.670 closest distance to " O   VAL A 174 " =    1.985
peak=   -3.654 closest distance to " O   HOH Z 171 " =    2.478
peak=   -3.647 closest distance to " O   HOH Z 165 " =    1.868
peak=   -3.644 closest distance to " CB  LEU A 167 " =    2.049
peak=   -3.609 closest distance to " CA  SER A 276 " =    1.423
peak=   -3.595 closest distance to " O   SER A  95 " =    1.650
peak=   -3.584 closest distance to " O   HOH Z  46 " =    1.280
peak=   -3.571 closest distance to " CB  ALA A 248 " =    2.214
peak=   -3.557 closest distance to " O   HOH Z 377 " =    2.294
peak=   -3.555 closest distance to " O   HOH Z 369 " =    2.268
peak=   -3.552 closest distance to " OD2 ASP A 298 " =    1.103
peak=   -3.549 closest distance to " O   ASP A 171 " =    0.951
peak=   -3.548 closest distance to " O   LYS A  76 " =    1.236
peak=   -3.539 closest distance to " O   HOH Z 109 " =    2.801
peak=   -3.530 closest distance to " O   HOH Z 109 " =    2.997
peak=   -3.525 closest distance to " O   HOH Z 368 " =    2.077
peak=   -3.521 closest distance to " O   HOH Z 102 " =    1.772
peak=   -3.519 closest distance to " CD  GLN A  11 " =    1.323
peak=   -3.517 closest distance to " O   HOH Z 233 " =    2.488
peak=   -3.511 closest distance to " O   HOH Z 157 " =    3.673
peak=   -3.510 closest distance to " O   PRO A  54 " =    1.820
peak=   -3.509 closest distance to " O   ARG A  79 " =    0.975
peak=   -3.509 closest distance to " O   SER A 273 " =    1.007
peak=   -3.506 closest distance to " CD2 PHE A 225 " =    1.385
peak=   -3.505 closest distance to " O   HOH Z 197 " =    1.742
peak=   -3.500 closest distance to " O   HOH Z 196 " =    1.679
peak=   -3.499 closest distance to " CA  ALA A 114 " =    1.028
peak=   -3.498 closest distance to " NH2 ARG A  66 " =    1.957
peak=   -3.497 closest distance to " N   ALA A  43 " =    2.661
peak=   -3.492 closest distance to " O   GLY A 241 " =    2.222
peak=   -3.487 closest distance to " OD2 ASP A 171 " =    1.800
peak=   -3.487 closest distance to " N   ALA A 226 " =    1.987
peak=   -3.480 closest distance to " O   HOH Z 151 " =    1.187
peak=   -3.460 closest distance to " N   VAL A  72 " =    1.192
peak=   -3.453 closest distance to " O   HOH Z  41 " =    1.959
peak=   -3.440 closest distance to " O   TRP A  92 " =    2.118
peak=   -3.437 closest distance to " O   HOH Z 191 " =    5.973
peak=   -3.422 closest distance to " CD  ARG A  36 " =    0.948
peak=   -3.420 closest distance to " O   HOH Z 166 " =    1.536
peak=   -3.418 closest distance to " OG  SER A  32 " =    1.128
peak=   -3.418 closest distance to " O   HOH Z  88 " =    4.327
peak=   -3.414 closest distance to " O   ASN A 110 " =    2.410
peak=   -3.407 closest distance to " C   VAL A 265 " =    0.936
peak=   -3.400 closest distance to " CA  ASN A 127 " =    0.999
peak=   -3.399 closest distance to " CZ3 TRP A  70 " =    1.449
peak=   -3.388 closest distance to " CB  ALA A  43 " =    2.765
peak=   -3.385 closest distance to " O   HOH Z  52 " =    1.932
peak=   -3.383 closest distance to " O   HOH Z 176 " =    1.742
peak=   -3.381 closest distance to " O   GLN A 122 " =    1.058
peak=   -3.375 closest distance to " OG BSER A 134 " =    1.527
peak=   -3.368 closest distance to " OG1 THR A  82 " =    1.441
peak=   -3.368 closest distance to " O   HOH Z  38 " =    1.760
peak=   -3.363 closest distance to " OH  TYR A 169 " =    0.881
peak=   -3.363 closest distance to " CE3 TRP A 150 " =    2.183
peak=   -3.358 closest distance to " SD  MET A  93 " =    1.741
peak=   -3.354 closest distance to " O   HOH Z 366 " =    1.737
peak=   -3.354 closest distance to " O   HOH Z 248 " =    1.242
peak=   -3.353 closest distance to " CA  ASP A 298 " =    1.169
peak=   -3.351 closest distance to " CG2 THR A 182 " =    2.254
peak=   -3.350 closest distance to " O   HOH Z 221 " =    1.225
peak=   -3.348 closest distance to " CD2 HIS A 115 " =    1.042
peak=   -3.340 closest distance to " O   HOH Z 118 " =    4.814
peak=   -3.339 closest distance to " O   ALA A  34 " =    2.201
peak=   -3.338 closest distance to " O   HOH Z   2 " =    2.081
peak=   -3.336 closest distance to " O   HOH Z 417 " =    1.002
peak=   -3.327 closest distance to " CG  ARG A  24 " =    2.062
peak=   -3.326 closest distance to " C   ASP A  65 " =    1.145
peak=   -3.326 closest distance to " CZ  PHE A  59 " =    1.863
peak=   -3.322 closest distance to " O   HOH Z 114 " =    5.513
peak=   -3.317 closest distance to " ND2 ASN A  74 " =    1.285
peak=   -3.315 closest distance to " ND2 ASN A  45 " =    1.437
peak=   -3.303 closest distance to " O   THR A  52 " =    1.878
peak=   -3.294 closest distance to " CE2 PHE A  61 " =    2.766
peak=   -3.294 closest distance to " CD2 TYR A 293 " =    1.561
peak=   -3.289 closest distance to " CG2 VAL A 232 " =    1.860
peak=   -3.286 closest distance to " C   GLY A 133 " =    1.157
peak=   -3.282 closest distance to " CA  VAL A 197 " =    0.978
peak=   -3.281 closest distance to " O   HOH Z 326 " =    4.421
peak=   -3.279 closest distance to " OXT GLY A 302 " =    2.927
peak=   -3.276 closest distance to " O   HOH Z 148 " =    3.566
peak=   -3.274 closest distance to " N   ASP A 272 " =    1.279
peak=   -3.270 closest distance to " O   HOH Z 198 " =    1.448
peak=   -3.268 closest distance to " CA  GLY A 203 " =    2.289
peak=   -3.268 closest distance to " O   ASP A 298 " =    1.952
peak=   -3.261 closest distance to " N   LEU A 237 " =    1.974
peak=   -3.258 closest distance to " CH2 TRP A 150 " =    0.978
peak=   -3.253 closest distance to " N   GLN A 223 " =    0.955
peak=   -3.253 closest distance to " CG  LYS A 181 " =    2.343
peak=   -3.252 closest distance to " O   HOH Z 242 " =    1.641
peak=   -3.252 closest distance to " ND2 ASN A  69 " =    1.526
peak=   -3.251 closest distance to " CB  ASP A 132 " =    2.395
peak=   -3.242 closest distance to " O   HOH Z  37 " =    1.729
peak=   -3.240 closest distance to " CG1 VAL A 189 " =    2.527
peak=   -3.237 closest distance to " O   HOH Z 326 " =    5.064
peak=   -3.230 closest distance to " OH  TYR A  30 " =    1.050
peak=   -3.226 closest distance to " NE2 GLN A  88 " =    1.745
peak=   -3.224 closest distance to " NE2 GLN A  88 " =    0.988
peak=   -3.220 closest distance to " O   HOH Z   1 " =    4.469
peak=   -3.220 closest distance to " O   HOH Z 219 " =    4.233
peak=   -3.217 closest distance to " O   HOH Z 313 " =    1.276
peak=   -3.210 closest distance to " O   HOH Z 208 " =    1.938
peak=   -3.198 closest distance to " CE  MET A 105 " =    2.010
peak=   -3.197 closest distance to " OG BSER A 134 " =    4.038
peak=   -3.193 closest distance to " OXT GLY A 302 " =    3.219
peak=   -3.193 closest distance to " O   HOH Z 119 " =    1.351
peak=   -3.189 closest distance to " CZ3 TRP A 150 " =    1.889
peak=   -3.186 closest distance to " O   HOH Z  52 " =    2.333
peak=   -3.183 closest distance to " CE1 HIS A 207 " =    1.761
peak=   -3.182 closest distance to " N   ARG A 275 " =    1.038
peak=   -3.182 closest distance to " CD  GLN A  58 " =    1.133
peak=   -3.178 closest distance to " CD1 ILE A 109 " =    2.672
peak=   -3.177 closest distance to " O   HOH Z 351 " =    1.609
peak=   -3.174 closest distance to " CA  PRO A 280 " =    0.989
peak=   -3.172 closest distance to " O   HOH Z 388 " =    2.042
peak=   -3.168 closest distance to " O   HOH Z 298 " =    3.537
peak=   -3.165 closest distance to " O   SER A 141 " =    2.297
peak=   -3.163 closest distance to " O   HOH Z 424 " =    3.268
peak=   -3.162 closest distance to " SD  MET A 105 " =    2.182
peak=   -3.161 closest distance to " OG  SER A  87 " =    1.774
peak=   -3.159 closest distance to " OE1 GLN A 223 " =    2.194
peak=   -3.154 closest distance to " O   HOH Z 134 " =    2.586
peak=   -3.152 closest distance to " CE1 TYR A 247 " =    2.867
peak=   -3.149 closest distance to " O   HOH Z 434 " =    2.216
peak=   -3.145 closest distance to " CA  ALA A 137 " =    2.807
peak=   -3.143 closest distance to " O   HOH Z 135 " =    1.923
peak=   -3.137 closest distance to " NE2 GLN A 278 " =    1.870
peak=   -3.135 closest distance to " O   HOH Z 200 " =    1.167
peak=   -3.133 closest distance to " NE1 TRP A 177 " =    2.009
peak=   -3.133 closest distance to " O   HOH Z   6 " =    1.655
peak=   -3.133 closest distance to " CD1 PHE A  59 " =    1.632
peak=   -3.128 closest distance to " O   TRP A  85 " =    2.186
peak=   -3.124 closest distance to " CD1 ILE A 239 " =    2.323
peak=   -3.123 closest distance to " CG  GLN A 103 " =    2.347
peak=   -3.120 closest distance to " O   HOH Z 196 " =    2.092
peak=   -3.119 closest distance to " CG2BVAL A  41 " =    1.450
peak=   -3.111 closest distance to " OG  SER A  97 " =    2.154
peak=   -3.108 closest distance to " O   HOH Z 166 " =    1.157
peak=   -3.108 closest distance to " CB  GLN A  55 " =    1.650
peak=   -3.106 closest distance to " O   HOH Z 130 " =    2.083
peak=   -3.102 closest distance to " OE2 GLU A 128 " =    1.878
peak=   -3.081 closest distance to " O   HOH Z 108 " =    1.953
peak=   -3.080 closest distance to " CE1 PHE A 218 " =    2.597
peak=   -3.050 closest distance to " O   HOH Z 278 " =    1.340
peak=   -3.047 closest distance to " O   THR A 251 " =    1.720
peak=   -3.046 closest distance to " CD1 LEU A  96 " =    2.155
peak=   -3.036 closest distance to " CG1 VAL A 112 " =    2.494
peak=   -3.032 closest distance to " O   HOH Z 320 " =    1.629
peak=   -3.024 closest distance to " NZ  LYS A 289 " =    1.721

================= 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    :  0.4741 0.4647   6.285953e+00   6.271954e+00
   1_bss:  0.4675 0.4544   6.280496e+00   6.264768e+00
   1_xyz:  0.3595 0.3906   6.117389e+00   6.171952e+00
   1_adp:  0.3261 0.3980   6.069151e+00   6.184439e+00
   1_occ:  0.3258 0.3975   6.068326e+00   6.184033e+00
   2_bss:  0.3242 0.3939   6.066574e+00   6.182372e+00
   2_xyz:  0.2802 0.3467   5.947943e+00   6.091214e+00
   2_adp:  0.2695 0.3417   5.930764e+00   6.081064e+00
   2_occ:  0.2693 0.3413   5.930510e+00   6.081167e+00
   3_bss:  0.2695 0.3416   5.932171e+00   6.081710e+00
   3_xyz:  0.2205 0.2798   5.733998e+00   5.916689e+00
   3_adp:  0.2004 0.2668   5.671847e+00   5.879568e+00
   3_occ:  0.2003 0.2668   5.671422e+00   5.879441e+00
   4_bss:  0.2001 0.2664   5.671399e+00   5.877900e+00
   4_xyz:  0.1690 0.2288   5.517125e+00   5.745170e+00
   4_adp:  0.1608 0.2086   5.455090e+00   5.657814e+00
   4_occ:  0.1605 0.2083   5.454290e+00   5.657258e+00
   5_bss:  0.1611 0.2082   5.455911e+00   5.657377e+00
   5_xyz:  0.1419 0.1895   5.351697e+00   5.569190e+00
   5_adp:  0.1367 0.1894   5.329438e+00   5.554061e+00
   5_occ:  0.1367 0.1893   5.329146e+00   5.553641e+00
   5_bss:  0.1367 0.1895   5.329234e+00   5.553847e+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:  0.287  24.671  -1.549   4.267  -0.452   0.000  -0.000  -0.000
   1_xyz:  0.287  24.671  -1.549   4.267  -0.452   0.000  -0.000  -0.000
   1_adp:  0.287  24.671  -1.549   4.267  -0.452   0.000  -0.000  -0.000
   1_occ:  0.287  24.671  -1.549   4.267  -0.452   0.000  -0.000  -0.000
   2_bss:  0.300  50.000  -1.684   2.262   0.041   0.000   0.000   0.000
   2_xyz:  0.300  50.000  -1.684   2.262   0.041   0.000   0.000   0.000
   2_adp:  0.300  50.000  -1.684   2.262   0.041   0.000   0.000   0.000
   2_occ:  0.300  50.000  -1.684   2.262   0.041   0.000   0.000   0.000
   3_bss:  0.309  52.039  -1.806   1.735   0.255   0.000   0.000   0.000
   3_xyz:  0.309  52.039  -1.806   1.735   0.255   0.000   0.000   0.000
   3_adp:  0.309  52.039  -1.806   1.735   0.255   0.000   0.000   0.000
   3_occ:  0.309  52.039  -1.806   1.735   0.255   0.000   0.000   0.000
   4_bss:  0.323  69.843  -1.925   0.475   0.022   0.000   0.000   0.000
   4_xyz:  0.323  69.843  -1.925   0.475   0.022   0.000   0.000   0.000
   4_adp:  0.323  69.843  -1.925   0.475   0.022   0.000   0.000   0.000
   4_occ:  0.323  69.843  -1.925   0.475   0.022   0.000   0.000   0.000
   5_bss:  0.329  69.843  -2.332  -0.226  -0.286  -0.000  -0.000  -0.000
   5_xyz:  0.329  69.843  -2.332  -0.226  -0.286  -0.000  -0.000  -0.000
   5_adp:  0.329  69.843  -2.332  -0.226  -0.286  -0.000  -0.000  -0.000
   5_occ:  0.329  69.843  -2.332  -0.226  -0.286  -0.000  -0.000  -0.000
   5_bss:  0.333  71.836  -2.365  -0.475  -0.211  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.234 0.4428  0.5979    69359.948
   1_bss:  55.194 0.4550  0.6336    66719.176
   1_xyz:  44.559 0.5875  0.7956    45912.445
   1_adp:  45.416 0.5767  0.7920    47840.380
   1_occ:  45.384 0.5771  0.7906    47658.007
   2_bss:  45.012 0.5815  0.7845    46898.076
   2_xyz:  38.508 0.6591  0.8720    34765.940
   2_adp:  37.661 0.6695  0.8725    33797.740
   2_occ:  37.648 0.6696  0.8723    33783.652
   3_bss:  37.694 0.6692  0.8670    33910.433
   3_xyz:  29.390 0.7630  0.9561    20689.989
   3_adp:  27.457 0.7848  0.9503    18835.639
   3_occ:  27.437 0.7850  0.9505    18825.875
   4_bss:  27.329 0.7862  0.9354    18739.066
   4_xyz:  22.783 0.8331  0.9710    13390.503
   4_adp:  20.105 0.8608  0.9815    11170.402
   4_occ:  20.082 0.8610  0.9819    11153.918
   5_bss:  20.065 0.8612  0.9661    11142.885
   5_xyz:  17.955 0.8810  0.9755     9221.814
   5_adp:  17.610 0.8843  0.9691     9034.499
   5_occ:  17.599 0.8844  0.9692     9030.514
   5_bss:  17.602 0.8844  0.9665     9034.437
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.9410e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.9410e-01
   1_xyz:   1.713  0.013  0.101 15.964  0.006  4.104   1.5575e-01
   1_adp:   1.713  0.013  0.101 15.964  0.006  4.104   1.5575e-01
   1_occ:   1.713  0.013  0.101 15.964  0.006  4.104   1.5575e-01
   2_bss:   1.713  0.013  0.101 15.964  0.006  4.104   1.5575e-01
   2_xyz:   1.114  0.007  0.077 14.645  0.004  4.119   6.8340e-02
   2_adp:   1.114  0.007  0.077 14.645  0.004  4.119   6.8340e-02
   2_occ:   1.114  0.007  0.077 14.645  0.004  4.119   6.8340e-02
   3_bss:   1.114  0.007  0.077 14.645  0.004  4.119   6.8340e-02
   3_xyz:   1.118  0.009  0.072 14.296  0.004  4.110   7.1998e-02
   3_adp:   1.118  0.009  0.072 14.296  0.004  4.110   7.1998e-02
   3_occ:   1.118  0.009  0.072 14.296  0.004  4.110   7.1998e-02
   4_bss:   1.118  0.009  0.072 14.296  0.004  4.110   7.1998e-02
   4_xyz:   0.986  0.006  0.069 14.054  0.004  4.121   5.6529e-02
   4_adp:   0.986  0.006  0.069 14.054  0.004  4.121   5.6529e-02
   4_occ:   0.986  0.006  0.069 14.054  0.004  4.121   5.6529e-02
   5_bss:   0.986  0.006  0.069 14.054  0.004  4.121   5.6529e-02
   5_xyz:   0.963  0.006  0.068 14.118  0.003  4.114   5.4094e-02
   5_adp:   0.963  0.006  0.068 14.118  0.003  4.114   5.4094e-02
   5_occ:   0.963  0.006  0.068 14.118  0.003  4.114   5.4094e-02
   5_bss:   0.963  0.006  0.068 14.118  0.003  4.114   5.4094e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.140   2.4373e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.140   2.4373e-01
   1_xyz:  10.118  0.080  0.419 81.829  0.024  1.893   1.5784e-01
   1_adp:  10.118  0.080  0.419 81.829  0.024  1.893   1.5784e-01
   1_occ:  10.118  0.080  0.419 81.829  0.024  1.893   1.5784e-01
   2_bss:  10.118  0.080  0.419 81.829  0.024  1.893   1.5784e-01
   2_xyz:   7.207  0.046  0.226 86.793  0.020  2.275   6.1341e-02
   2_adp:   7.207  0.046  0.226 86.793  0.020  2.275   6.1341e-02
   2_occ:   7.207  0.046  0.226 86.793  0.020  2.275   6.1341e-02
   3_bss:   7.207  0.046  0.226 86.793  0.020  2.275   6.1341e-02
   3_xyz:   6.973  0.067  0.284 79.423  0.029  2.185   6.8405e-02
   3_adp:   6.973  0.067  0.284 79.423  0.029  2.185   6.8405e-02
   3_occ:   6.973  0.067  0.284 79.423  0.029  2.185   6.8405e-02
   4_bss:   6.973  0.067  0.284 79.423  0.029  2.185   6.8405e-02
   4_xyz:   7.603  0.048  0.207 79.842  0.038  2.357   6.4162e-02
   4_adp:   7.603  0.048  0.207 79.842  0.038  2.357   6.4162e-02
   4_occ:   7.603  0.048  0.207 79.842  0.038  2.357   6.4162e-02
   5_bss:   7.603  0.048  0.207 79.842  0.038  2.357   6.4162e-02
   5_xyz:   6.805  0.041  0.200 79.298  0.029  2.388   3.4116e-02
   5_adp:   6.805  0.041  0.200 79.298  0.029  2.388   3.4116e-02
   5_occ:   6.805  0.041  0.200 79.298  0.029  2.388   3.4116e-02
   5_bss:   6.805  0.041  0.200 79.298  0.029  2.388   3.4116e-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:  91.72   0.00  19.40  79.87   0.00  15.98  91.72   0.00  38.04
   1_occ:  91.72   0.00  19.40  79.87   0.00  15.98  91.72   0.00  38.04
   2_bss:  91.72   0.00  19.40  79.87   0.00  15.98  91.72   0.00  38.04
   2_xyz:  91.72   0.00  19.40  79.87   0.00  15.98  91.72   0.00  38.04
   2_adp:  95.12   0.00  19.28  84.80   0.00  15.73  95.12   2.42  38.58
   2_occ:  95.12   0.00  19.28  84.80   0.00  15.73  95.12   2.42  38.58
   3_bss:  95.12   0.00  19.28  84.80   0.00  15.73  95.12   2.42  38.58
   3_xyz:  95.12   0.00  19.28  84.80   0.00  15.73  95.12   2.42  38.58
   3_adp: 117.67   0.00  20.04 112.67   0.00  14.96 117.67   2.90  47.72
   3_occ: 117.67   0.00  20.04 112.67   0.00  14.96 117.67   2.90  47.72
   4_bss: 117.67   0.00  20.04 112.67   0.00  14.96 117.67   2.90  47.72
   4_xyz: 117.67   0.00  20.04 112.67   0.00  14.96 117.67   2.90  47.72
   4_adp: 111.37   0.48  18.64 109.74   0.48  13.61 111.37   5.55  46.02
   4_occ: 111.37   0.48  18.64 109.74   0.48  13.61 111.37   5.55  46.02
   5_bss: 111.37   0.48  18.64 109.74   0.48  13.61 111.37   5.55  46.02
   5_xyz: 111.37   0.48  18.64 109.74   0.48  13.61 111.37   5.55  46.02
   5_adp: 118.32   0.57  18.56 117.64   0.57  13.14 118.32   5.22  48.08
   5_occ: 118.32   0.57  18.56 117.64   0.57  13.14 118.32   5.22  48.08
   5_bss: 118.30   0.55  18.55 117.62   0.55  13.13 118.30   5.20  48.06
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    2.974    0.029    0.443
   1_adp:    2.974    0.029    0.443
   1_occ:    2.974    0.029    0.443
   2_bss:    2.974    0.029    0.443
   2_xyz:    2.932    0.038    0.518
   2_adp:    2.932    0.038    0.518
   2_occ:    2.932    0.038    0.518
   3_bss:    2.932    0.038    0.518
   3_xyz:    2.872    0.067    0.705
   3_adp:    2.872    0.067    0.705
   3_occ:    2.872    0.067    0.705
   4_bss:    2.872    0.067    0.705
   4_xyz:    2.870    0.096    0.769
   4_adp:    2.870    0.096    0.769
   4_occ:    2.870    0.096    0.769
   5_bss:    2.870    0.096    0.769
   5_xyz:    2.875    0.104    0.825
   5_adp:    2.875    0.104    0.825
   5_occ:    2.875    0.104    0.825
   5_bss:    2.875    0.104    0.825
------------------------------------------------------------------------

CPU time actual refinement: 342.01


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_238/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_238/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_238/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_238/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_238/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 341.87 
  Macro-tasks:
    bulk solvent and scale       = 43.48  
    individual site refinement   = 140.51 
    weights calculation          = 29.16  
    collect and process          = 6.37   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 219.62 
  Micro-tasks:
    mask                            = 2.33   
    f_calc                          = 108.99 
    alpha_beta                      = 8.42   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 117.56 
    fmodel                         = 7.17   
    r_factors                      = 0.23   
    phase_errors                   = 10.34  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 256.53 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.855 micro seconds
Total CPU time: 5.92 minutes
from_scatterers_fft:    645 calls, 108.73 s
gradients_fft:          590 calls, 104.59 s

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

# Date 2008-01-16 Time 04:20:51 PST -0800 (1200486051.86 s)
Start R-work = 0.4741, R-free = 0.4647 (no bulk solvent and anisotropic scale)
Final R-work = 0.1550, R-free = 0.2035 (no bulk solvent and anisotropic scale)

Start R-work = 0.4675, R-free = 0.4544
Final R-work = 0.1367, R-free = 0.1895