# Date 2008-01-16 Time 05:57:35 PST -0800 (1200491855.25 s)
#phil __OFF__

Command line arguments: "../947.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4150
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 947

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 47.8686, 84.6622, 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: 3.30, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.8686, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.96151
Completeness in resolution range: 0.921749
Completeness with d_max=infinity: 0.919024

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0179
                             d_min =   1.9615

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.8686, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.96151
Completeness in resolution range: 0.921749
Completeness with d_max=infinity: 0.919024

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0183 -  4.1981 [2235/2264]  2012   223  10.0%
  bin  2:  4.1981 -  3.3442 [2130/2153]  1917   213  10.0%
  bin  3:  3.3442 -  2.9250 [2111/2136]  1898   213  10.1%
  bin  4:  2.9250 -  2.6592 [2090/2107]  1888   202   9.7%
  bin  5:  2.6592 -  2.4695 [2088/2131]  1876   212  10.2%
  bin  6:  2.4695 -  2.3245 [2063/2091]  1861   202   9.8%
  bin  7:  2.3245 -  2.2084 [2055/2091]  1846   209  10.2%
  bin  8:  2.2084 -  2.1126 [2057/2099]  1851   206  10.0%
  bin  9:  2.1126 -  2.0315 [2014/2074]  1812   202  10.0%
  bin 10:  2.0315 -  1.9615 [ 746/2106]   669    77  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_947/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:
        1.57 -     2.24: 22
        2.24 -     2.90: 1389
        2.90 -     3.57: 4433
        3.57 -     4.23: 9176
        4.23 -     4.90: 13215
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.569 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.582 3.040 -x+1/2,-y+1,z+1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.625 3.040 -x+1/2,-y+1,z-1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.652 3.120 -x+1/2,-y+1,z-1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.715 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28230 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_947/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_947/model_refine_001.geo

CPU time processing inputs: 9.17


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 47.8686 84.6622 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 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4523   r_free= 0.4440   ksol= 0.00   Bsol= 0.00   scale= 0.899    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.263349                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6827 0.99   1449  164 0.3534 0.3633      6.5234      6.5183|
|  2:  4.6827 -  3.7357 0.99   1386  147 0.3800 0.3820      6.7844      6.7433|
|  3:  3.7357 -  3.2690 0.99   1373  155 0.4190 0.3848      6.6266      6.6469|
|  4:  3.2690 -  2.9726 0.99   1349  151 0.4409 0.4364      6.4828      6.4704|
|  5:  2.9726 -  2.7610 0.99   1343  149 0.4640 0.4614      6.3324      6.3171|
|  6:  2.7610 -  2.5991 0.99   1349  151 0.4941 0.4579      6.2608      6.1502|
|  7:  2.5991 -  2.4695 0.98   1342  146 0.4818 0.4239      6.2291      6.1609|
|  8:  2.4695 -  2.3624 0.98   1317  144 0.5153 0.5276      6.1418      6.2059|
|  9:  2.3624 -  2.2718 0.99   1329  149 0.5241 0.5057      6.1307      6.0964|
| 10:  2.2718 -  2.1937 0.98   1328  148 0.5017 0.5451        6.07      6.1158|
| 11:  2.1937 -  2.1253 0.97   1307  143 0.5176 0.5349      6.0194      6.0024|
| 12:  2.1253 -  2.0647 0.99   1322  149 0.5022 0.5356      5.9267      5.9872|
| 13:  2.0647 -  2.0105 0.85   1131  131 0.5053 0.4242      5.8683      5.8142|
| 14:  2.0105 -  1.9615 0.22    305   32 0.5731 0.5030      5.8271      5.7901|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.6827  1449   164  0.72  32.83   0.83     0.74      66686.34|
|  2:  4.6827 -  3.7357  1386   147  0.73  32.88   0.92     0.81      91061.15|
|  3:  3.7357 -  3.2690  1373   155  0.64  40.84   0.91     0.80      98066.54|
|  4:  3.2690 -  2.9726  1349   151  0.56  47.36   0.92     0.75      88251.09|
|  5:  2.9726 -  2.7610  1343   149  0.49  52.45   0.88     0.69      71602.99|
|  6:  2.7610 -  2.5991  1349   151  0.47  54.67   0.90     0.66      60798.72|
|  7:  2.5991 -  2.4695  1342   146  0.46  55.16   0.93     0.62      55444.90|
|  8:  2.4695 -  2.3624  1317   144  0.40  60.18   0.88     0.59      55216.05|
|  9:  2.3624 -  2.2718  1329   149  0.38  61.71   0.91     0.55      51502.10|
| 10:  2.2718 -  2.1937  1328   148  0.35  64.05   0.95     0.52      50984.11|
| 11:  2.1937 -  2.1253  1307   143  0.32  66.40   0.92     0.48      47452.87|
| 12:  2.1253 -  2.0647  1322   149  0.28  69.00   0.94     0.46      45161.31|
| 13:  2.0647 -  2.0105  1131   131  0.32  66.40   0.94     0.49      36740.75|
| 14:  2.0105 -  1.9615   305    32  0.37  61.86   0.88     0.59      28610.81|
|alpha:            min =        0.46 max =            0.81 mean =         0.63|
|beta:             min =    28610.81 max =        98066.54 mean =     62960.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           89.99 mean =        53.86|
|phase err.(test): min =        0.00 max =           89.98 mean =        54.03|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.616342              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.338   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.520333              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.252   (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 |  1.569 -  1.902:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.902 -  2.235:       13 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.235 -  2.569:       35 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.569 -  2.902:     1354 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.902 -  3.235:     1910 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.235 -  3.568:     2523 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.568 -  3.901:     4673 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.901 -  4.234:     4503 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.234 -  4.567:     6042 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.567 -  4.900:     7173 |
|-----------------------------------------------------------------------------|
|-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 |        0.183 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.569 |       0.469 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.991)------------------------------------------|
|    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 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4523   r_free= 0.4440   ksol= 0.00   Bsol= 0.00   scale= 0.899    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.263349                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4432   r_free= 0.4340   ksol= 0.29   Bsol= 26.35   scale= 0.941   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,3.66,1.02,0.00,0.00,0.00); trace/3= 0.83                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.256025                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.220220              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.228   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.105183              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.023   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4432      final r-factor (work) = 0.3567          |
| start r-factor (free) = 0.4340      final r-factor (free) = 0.3834          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.6322 = 6.22 * 0.50 * 6.2537 + 1.00 * 0.1826                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.2037 = 6.22 * 0.50 * 6.1399 + 1.00 * 0.1080                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3567      final r-factor (work) = 0.3253          |
| start r-factor (free) = 0.3834      final r-factor (free) = 0.3926          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7917 = 1.11 * 1.00 * 6.1399 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7091 = 1.11 * 1.00 * 6.0541 + 1.00 * 0.0182                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.991)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.25  19.09    None  None   None       |
|    all(noH): 2823   0      0.00    103.25  19.09    None  None   None       |
|    Sol.    : 438    0      0.00    103.25  38.21    None  None   None       |
|    Mac.    : 2385   0      0.00    89.73   15.58    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.326:  948   |   5:    51.627 -  61.953:   74        |
|      1:    10.326 -  20.651:  927   |   6:    61.953 -  72.278:   43        |
|      2:    20.651 -  30.976:  443   |   7:    72.278 -  82.604:   20        |
|      3:    30.976 -  41.302:  249   |   8:    82.604 -  92.929:    5        |
|      4:    41.302 -  51.627:  113   |   9:    92.929 - 103.255:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3253 r_free = 0.3926             target_work(ml) = 6.061         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3249 r_free = 0.3928             target_work(ml) = 6.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3249   r_free= 0.3928   ksol= 0.29   Bsol= 26.35   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,3.66,1.02,0.00,0.00,0.00); trace/3= 0.83                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.059894                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3243   r_free= 0.3901   ksol= 0.32   Bsol= 54.28   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.51,1.77,-0.06,0.00,-0.00,-0.00); trace/3= 0.06                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.060269                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.742850             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.969   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.553646              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.936  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3243      final r-factor (work) = 0.2422          |
| start r-factor (free) = 0.3901      final r-factor (free) = 0.3018          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.6285 = 10.74 * 0.50 * 6.0543 + 1.00 * 0.1080                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.0832 = 10.74 * 0.50 * 5.9543 + 1.00 * 0.1002                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2422      final r-factor (work) = 0.2171          |
| start r-factor (free) = 0.3018      final r-factor (free) = 0.2803          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3148 = 0.55 * 1.00 * 5.9543 + 1.00 * 0.0182                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2027 = 0.55 * 1.00 * 5.7638 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.991)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.49   18.20    None  None   None       |
|    all(noH): 2823   0      0.00    97.49   18.20    None  None   None       |
|    Sol.    : 438    0      3.92    97.49   40.35    None  None   None       |
|    Mac.    : 2385   0      0.00    86.80   14.13    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.749:  973   |   5:    48.746 -  58.495:   94        |
|      1:     9.749 -  19.498: 1018   |   6:    58.495 -  68.244:   50        |
|      2:    19.498 -  29.247:  326   |   7:    68.244 -  77.993:   23        |
|      3:    29.247 -  38.997:  194   |   8:    77.993 -  87.742:   10        |
|      4:    38.997 -  48.746:  134   |   9:    87.742 -  97.491:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2171 r_free = 0.2803             target_work(ml) = 5.728         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2170 r_free = 0.2802             target_work(ml) = 5.728         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2170   r_free= 0.2802   ksol= 0.32   Bsol= 54.28   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.51,1.77,-0.06,0.00,-0.00,-0.00); trace/3= 0.06                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.727796                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2163   r_free= 0.2793   ksol= 0.32   Bsol= 57.54   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.62,-0.00,-1.12,-0.00,-0.00,-0.00); trace/3= -0.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.725196                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.965032              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.954   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.927956              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.236  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2163      final r-factor (work) = 0.1614          |
| start r-factor (free) = 0.2793      final r-factor (free) = 0.2084          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.2950 = 5.97 * 0.50 * 5.7652 + 1.00 * 0.1002                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.8318 = 5.97 * 0.50 * 5.6194 + 1.00 * 0.0718                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1614      final r-factor (work) = 0.1449          |
| start r-factor (free) = 0.2084      final r-factor (free) = 0.1911          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2261 = 0.93 * 1.00 * 5.6194 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0261 = 0.93 * 1.00 * 5.4031 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.991)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.93  18.28    None  None   None       |
|    all(noH): 2823   0      0.00    101.93  18.28    None  None   None       |
|    Sol.    : 438    0      5.67    98.23   44.66    None  None   None       |
|    Mac.    : 2385   0      0.00    101.93  13.44    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.193: 1106   |   5:    50.963 -  61.155:   93        |
|      1:    10.193 -  20.385: 1025   |   6:    61.155 -  71.348:   62        |
|      2:    20.385 -  30.578:  238   |   7:    71.348 -  81.540:   35        |
|      3:    30.578 -  40.770:  132   |   8:    81.540 -  91.733:   11        |
|      4:    40.770 -  50.963:  115   |   9:    91.733 - 101.925:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1449 r_free = 0.1911             target_work(ml) = 5.362         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1447 r_free = 0.1909             target_work(ml) = 5.362         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1447   r_free= 0.1909   ksol= 0.32   Bsol= 57.54   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.62,-0.00,-1.12,-0.00,-0.00,-0.00); trace/3= -0.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.361663                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1450   r_free= 0.1913   ksol= 0.33   Bsol= 64.81   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-0.97,-1.59,-0.00,-0.00,-0.00); trace/3= -1.55                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.364953                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.654000              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.055  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.323094              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.323  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1450      final r-factor (work) = 0.1257          |
| start r-factor (free) = 0.1913      final r-factor (free) = 0.1730          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9524 = 3.65 * 0.50 * 5.4081 + 1.00 * 0.0718                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7589 = 3.65 * 0.50 * 5.3028 + 1.00 * 0.0707                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1257      final r-factor (work) = 0.1217          |
| start r-factor (free) = 0.1730      final r-factor (free) = 0.1676          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7255 = 0.32 * 1.00 * 5.3028 + 1.00 * 0.0122                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7012 = 0.32 * 1.00 * 5.2345 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.991)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.34    102.70  17.57    None  None   None       |
|    all(noH): 2823   0      1.34    102.70  17.57    None  None   None       |
|    Sol.    : 438    0      5.21    95.16   42.73    None  None   None       |
|    Mac.    : 2385   0      1.34    102.70  12.95    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:     1.343 -  11.479: 1387   |   5:    52.022 -  62.158:   88        |
|      1:    11.479 -  21.615:  853   |   6:    62.158 -  72.294:   48        |
|      2:    21.615 -  31.751:  185   |   7:    72.294 -  82.429:   22        |
|      3:    31.751 -  41.886:  118   |   8:    82.429 -  92.565:    8        |
|      4:    41.886 -  52.022:  108   |   9:    92.565 - 102.701:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1217 r_free = 0.1676             target_work(ml) = 5.218         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1216 r_free = 0.1676             target_work(ml) = 5.218         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1216   r_free= 0.1676   ksol= 0.33   Bsol= 64.81   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-0.97,-1.59,-0.00,-0.00,-0.00); trace/3= -1.55                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.217682                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1219   r_free= 0.1673   ksol= 0.32   Bsol= 58.95   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-1.32,-1.68,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.219226                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.832502              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.243  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.325161              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.658  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1219      final r-factor (work) = 0.1155          |
| start r-factor (free) = 0.1673      final r-factor (free) = 0.1628          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4854 = 2.83 * 0.50 * 5.2354 + 1.00 * 0.0707                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4316 = 2.83 * 0.50 * 5.1997 + 1.00 * 0.0675                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1155      final r-factor (work) = 0.1145          |
| start r-factor (free) = 0.1628      final r-factor (free) = 0.1627          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7006 = 0.33 * 1.00 * 5.1997 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6929 = 0.33 * 1.00 * 5.1783 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.991)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.69    103.76  17.10    None  None   None       |
|    all(noH): 2823   0      1.69    103.76  17.10    None  None   None       |
|    Sol.    : 438    0      5.15    91.06   41.16    None  None   None       |
|    Mac.    : 2385   0      1.69    103.76  12.69    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:     1.691 -  11.898: 1501   |   5:    52.727 -  62.934:   75        |
|      1:    11.898 -  22.106:  769   |   6:    62.934 -  73.141:   36        |
|      2:    22.106 -  32.313:  178   |   7:    73.141 -  83.349:   16        |
|      3:    32.313 -  42.520:  120   |   8:    83.349 -  93.556:    5        |
|      4:    42.520 -  52.727:  117   |   9:    93.556 - 103.763:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1145 r_free = 0.1627             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1143 r_free = 0.1626             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1626   ksol= 0.32   Bsol= 58.95   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-1.32,-1.68,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.177410                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6827 0.99   1449  164 0.0972 0.1273      5.3642        5.54|
|  2:  4.6827 -  3.7357 0.99   1386  147 0.0836 0.1052      5.4119      5.6046|
|  3:  3.7357 -  3.2690 0.99   1373  155 0.1072 0.1622      5.4722      5.8804|
|  4:  3.2690 -  2.9726 0.99   1349  151 0.1318 0.1579      5.4963      5.6177|
|  5:  2.9726 -  2.7610 0.99   1343  149 0.1376 0.1951      5.3668      5.5648|
|  6:  2.7610 -  2.5991 0.99   1349  151 0.1295 0.1952      5.2472      5.4763|
|  7:  2.5991 -  2.4695 0.98   1342  146 0.1253 0.1778      5.1868      5.4038|
|  8:  2.4695 -  2.3624 0.98   1317  144 0.1257 0.1712       5.109       5.326|
|  9:  2.3624 -  2.2718 0.99   1329  149 0.1186 0.1954      5.0545       5.338|
| 10:  2.2718 -  2.1937 0.98   1328  148 0.1171 0.1750      4.9912      5.2625|
| 11:  2.1937 -  2.1253 0.97   1307  143 0.1132 0.1885      4.9298      5.2477|
| 12:  2.1253 -  2.0647 0.99   1322  149 0.1143 0.1752      4.8791      5.1295|
| 13:  2.0647 -  2.0105 0.85   1131  131 0.1182 0.1816      4.8059      5.0465|
| 14:  2.0105 -  1.9615 0.22    305   32 0.1138 0.1654       4.676      4.9393|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.6827  1449   164  0.94   8.64   0.97     0.95       6816.17|
|  2:  4.6827 -  3.7357  1386   147  0.95   7.85   1.01     0.99       8608.07|
|  3:  3.7357 -  3.2690  1373   155  0.93  11.64   1.02     1.01      10413.75|
|  4:  3.2690 -  2.9726  1349   151  0.91  15.09   1.00     0.98      11264.09|
|  5:  2.9726 -  2.7610  1343   149  0.89  17.48   0.99     0.96       9324.31|
|  6:  2.7610 -  2.5991  1349   151  0.89  17.06   0.99     0.96       7718.23|
|  7:  2.5991 -  2.4695  1342   146  0.90  15.99   0.98     0.95       6588.37|
|  8:  2.4695 -  2.3624  1317   144  0.89  17.24   1.00     0.97       6072.28|
|  9:  2.3624 -  2.2718  1329   149  0.89  16.83   0.99     0.95       5413.62|
| 10:  2.2718 -  2.1937  1328   148  0.90  15.91   0.99     0.94       4721.77|
| 11:  2.1937 -  2.1253  1307   143  0.90  16.47   0.98     0.94       4353.94|
| 12:  2.1253 -  2.0647  1322   149  0.90  16.31   0.99     0.98       4084.56|
| 13:  2.0647 -  2.0105  1131   131  0.89  16.97   0.98     0.97       3504.93|
| 14:  2.0105 -  1.9615   305    32  0.89  16.73   0.98     0.94       2719.69|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2719.69 max =        11264.09 mean =      6830.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.82|
|phase err.(test): min =        0.00 max =           88.82 mean =        14.25|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1626   ksol= 0.32   Bsol= 58.89   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,-1.29,-1.53,-0.00,-0.00,-0.00); trace/3= -1.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.177473                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1626   ksol= 0.32   Bsol= 58.89   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,-1.29,-1.53,-0.00,-0.00,-0.00); trace/3= -1.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.177473                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6827 0.99   1449  164 0.0973 0.1274      5.3649      5.5403|
|  2:  4.6827 -  3.7357 0.99   1386  147 0.0837 0.1052      5.4121      5.6046|
|  3:  3.7357 -  3.2690 0.99   1373  155 0.1072 0.1622      5.4723      5.8806|
|  4:  3.2690 -  2.9726 0.99   1349  151 0.1318 0.1579      5.4964      5.6176|
|  5:  2.9726 -  2.7610 0.99   1343  149 0.1375 0.1951      5.3665      5.5645|
|  6:  2.7610 -  2.5991 0.99   1349  151 0.1294 0.1950       5.247      5.4758|
|  7:  2.5991 -  2.4695 0.98   1342  146 0.1253 0.1778      5.1866      5.4036|
|  8:  2.4695 -  2.3624 0.98   1317  144 0.1257 0.1710      5.1089      5.3258|
|  9:  2.3624 -  2.2718 0.99   1329  149 0.1185 0.1955      5.0545      5.3386|
| 10:  2.2718 -  2.1937 0.98   1328  148 0.1172 0.1749      4.9915      5.2627|
| 11:  2.1937 -  2.1253 0.97   1307  143 0.1132 0.1884      4.9297      5.2475|
| 12:  2.1253 -  2.0647 0.99   1322  149 0.1143 0.1755      4.8795      5.1305|
| 13:  2.0647 -  2.0105 0.85   1131  131 0.1181 0.1816      4.8059      5.0459|
| 14:  2.0105 -  1.9615 0.22    305   32 0.1138 0.1652      4.6758      4.9379|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.6827  1449   164  0.94   8.64   0.97     0.95       6819.82|
|  2:  4.6827 -  3.7357  1386   147  0.95   7.85   1.01     0.99       8610.14|
|  3:  3.7357 -  3.2690  1373   155  0.93  11.64   1.02     1.02      10417.36|
|  4:  3.2690 -  2.9726  1349   151  0.91  15.09   1.00     0.98      11265.29|
|  5:  2.9726 -  2.7610  1343   149  0.89  17.47   0.99     0.96       9316.95|
|  6:  2.7610 -  2.5991  1349   151  0.89  17.05   0.99     0.96       7710.81|
|  7:  2.5991 -  2.4695  1342   146  0.90  15.99   0.99     0.96       6583.85|
|  8:  2.4695 -  2.3624  1317   144  0.89  17.24   1.00     0.97       6070.99|
|  9:  2.3624 -  2.2718  1329   149  0.89  16.84   0.99     0.96       5418.26|
| 10:  2.2718 -  2.1937  1328   148  0.90  15.92   0.99     0.95       4724.06|
| 11:  2.1937 -  2.1253  1307   143  0.90  16.47   0.99     0.95       4354.67|
| 12:  2.1253 -  2.0647  1322   149  0.90  16.32   0.99     0.98       4088.50|
| 13:  2.0647 -  2.0105  1131   131  0.89  16.97   0.99     0.97       3504.41|
| 14:  2.0105 -  1.9615   305    32  0.89  16.73   0.98     0.95       2715.07|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2715.07 max =        11265.29 mean =      6830.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.82|
|phase err.(test): min =        0.00 max =           88.82 mean =        14.25|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.991)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.63    103.70  17.04    None  None   None       |
|    all(noH): 2823   0      1.63    103.70  17.04    None  None   None       |
|    Sol.    : 438    0      5.09    91.00   41.10    None  None   None       |
|    Mac.    : 2385   0      1.63    103.70  12.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.631 -  11.838: 1501   |   5:    52.667 -  62.874:   75        |
|      1:    11.838 -  22.045:  769   |   6:    62.874 -  73.081:   36        |
|      2:    22.045 -  32.252:  178   |   7:    73.081 -  83.288:   16        |
|      3:    32.252 -  42.459:  120   |   8:    83.288 -  93.495:    5        |
|      4:    42.459 -  52.667:  117   |   9:    93.495 - 103.702:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 334         
Filter by distance & map next to the model:
   mapped sites are within: 0.516 - 5.997
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 331 from: 334
   mapped sites are within: 0.719 - 5.997

peak=    5.835 closest distance to " NH2 ARG A  56 " =    2.308
peak=    5.587 closest distance to " CB  SER A  63 " =    1.225
peak=    5.531 closest distance to " CB  GLN A 223 " =    1.427
peak=    5.279 closest distance to " CG  PRO A  54 " =    1.239
peak=    5.006 closest distance to " O   HOH Z  15 " =    2.071
peak=    4.741 closest distance to " O   PRO A 198 " =    1.530
peak=    4.740 closest distance to " O   HOH Z 126 " =    1.724
peak=    4.733 closest distance to " O   HOH Z 134 " =    1.865
peak=    4.685 closest distance to " O   HOH Z  80 " =    1.860
peak=    4.675 closest distance to " CA  TYR A  30 " =    0.970
peak=    4.520 closest distance to " CG  PRO A 198 " =    1.290
peak=    4.491 closest distance to " CG  PRO A  90 " =    1.154
peak=    4.489 closest distance to " O   HOH Z  59 " =    2.442
peak=    4.453 closest distance to " O   HOH Z 232 " =    2.401
peak=    4.443 closest distance to " CB  GLN A 183 " =    1.313
peak=    4.411 closest distance to " CG  PRO A 213 " =    1.248
peak=    4.400 closest distance to " CB  GLU A 152 " =    1.145
peak=    4.400 closest distance to " CB  SER A   3 " =    1.321
peak=    4.383 closest distance to " CB  TYR A 169 " =    0.957
peak=    4.360 closest distance to " CB  PRO A  54 " =    0.792
peak=    4.353 closest distance to " O   HOH Z  47 " =    1.467
peak=    4.353 closest distance to " O   HOH Z 108 " =    2.206
peak=    4.341 closest distance to " O   HOH Z 132 " =    1.132
peak=    4.335 closest distance to " CB  ARG A  79 " =    1.352
peak=    4.326 closest distance to " O   HOH Z 234 " =    3.755
peak=    4.325 closest distance to " O   HOH Z  20 " =    1.776
peak=    4.322 closest distance to " O   HOH Z 193 " =    1.942
peak=    4.321 closest distance to " CB  ARG A 275 " =    0.859
peak=    4.321 closest distance to " O   HOH Z 154 " =    1.486
peak=    4.295 closest distance to " O   HOH Z  40 " =    1.880
peak=    4.271 closest distance to " CG1 ILE A  33 " =    1.207
peak=    4.261 closest distance to " O   SER A  87 " =    2.165
peak=    4.231 closest distance to " O   HOH Z 247 " =    1.384
peak=    4.222 closest distance to " O   HOH Z 124 " =    1.428
peak=    4.215 closest distance to " O   HOH Z 196 " =    1.212
peak=    4.215 closest distance to " CB  VAL A 202 " =    1.587
peak=    4.194 closest distance to " O   HOH Z 389 " =    1.943
peak=    4.174 closest distance to " O   HOH Z 374 " =    2.690
peak=    4.170 closest distance to " OD2 ASP A 286 " =    2.911
peak=    4.168 closest distance to " CB  GLU A 277 " =    3.628
peak=    4.167 closest distance to " CB  GLU A 128 " =    1.128
peak=    4.159 closest distance to " O   HOH Z 298 " =    1.972
peak=    4.144 closest distance to " O   HOH Z  67 " =    1.962
peak=    4.138 closest distance to " O   HOH Z  97 " =    1.900
peak=    4.124 closest distance to " O   HOH Z 433 " =    1.576
peak=    4.121 closest distance to " O   HOH Z  43 " =    1.647
peak=    4.115 closest distance to " CB  ARG A 190 " =    1.676
peak=    4.110 closest distance to " OD1 ASN A  69 " =    2.513
peak=    4.094 closest distance to " O   HOH Z 133 " =    1.608
peak=    4.089 closest distance to " O   HOH Z 423 " =    1.908
peak=    4.087 closest distance to " CG  PRO A 280 " =    0.719
peak=    4.081 closest distance to " O   HOH Z 369 " =    2.210
peak=    4.073 closest distance to " O   HOH Z 403 " =    1.772
peak=    4.054 closest distance to " NH2BARG A 145 " =    1.991
peak=    4.050 closest distance to " O   HOH Z  78 " =    1.880
peak=    4.043 closest distance to " O   HOH Z  39 " =    1.188
peak=    4.041 closest distance to " O   HOH Z 260 " =    1.331
peak=    4.037 closest distance to " N   ASN A  39 " =    1.280
peak=    4.029 closest distance to " CA  ASP A 191 " =    0.865
peak=    4.018 closest distance to " O   HOH Z 163 " =    1.597
peak=    4.015 closest distance to " CG  PRO A 243 " =    1.166
peak=    4.012 closest distance to " O   HOH Z 108 " =    1.314
peak=    4.010 closest distance to " O   HOH Z  88 " =    3.525
peak=    4.009 closest distance to " CG  ARG A  66 " =    2.686
peak=    3.985 closest distance to " CB  LEU A 228 " =    1.129
peak=    3.977 closest distance to " O   HOH Z 287 " =    2.035
peak=    3.976 closest distance to " O   HOH Z 313 " =    1.841
peak=    3.974 closest distance to " O   HOH Z 352 " =    1.824
peak=    3.974 closest distance to " O   HOH Z  44 " =    2.387
peak=    3.973 closest distance to " O   HOH Z 316 " =    3.051
peak=    3.968 closest distance to " NH2 ARG A 156 " =    1.193
peak=    3.947 closest distance to " CA  ALA A  21 " =    1.339
peak=    3.946 closest distance to " O   HOH Z 189 " =    2.221
peak=    3.928 closest distance to " O   HOH Z 145 " =    2.204
peak=    3.919 closest distance to " NZ  LYS A 117 " =    3.173
peak=    3.914 closest distance to " O   HOH Z 394 " =    1.710
peak=    3.913 closest distance to " OE1 GLN A  11 " =    1.942
peak=    3.900 closest distance to " O   HOH Z  48 " =    1.668
peak=    3.891 closest distance to " NE2 GLN A  11 " =    1.034
peak=    3.891 closest distance to " CA  ALA A  51 " =    0.942
peak=    3.882 closest distance to " CB  TRP A 179 " =    1.334
peak=    3.876 closest distance to " O   HOH Z 426 " =    1.478
peak=    3.873 closest distance to " O   HOH Z 368 " =    2.153
peak=    3.868 closest distance to " O   HOH Z  30 " =    1.626
peak=    3.867 closest distance to " O   HOH Z 132 " =    2.535
peak=    3.864 closest distance to " O   HOH Z 132 " =    2.015
peak=    3.858 closest distance to " OG BSER A 164 " =    2.391
peak=    3.856 closest distance to " O   GLY A  23 " =    2.413
peak=    3.855 closest distance to " CD1 LEU A 300 " =    1.223
peak=    3.850 closest distance to " CB  SER A 141 " =    1.018
peak=    3.841 closest distance to " O   HOH Z 272 " =    1.918
peak=    3.828 closest distance to " CD  ARG A 269 " =    0.941
peak=    3.827 closest distance to " O   HOH Z  63 " =    1.795
peak=    3.822 closest distance to " O   HOH Z 326 " =    1.481
peak=    3.820 closest distance to " O   HOH Z  49 " =    1.863
peak=    3.794 closest distance to " CA  ARG A  36 " =    1.164
peak=    3.791 closest distance to " NZ  LYS A  76 " =    1.387
peak=    3.788 closest distance to " O   HOH Z 118 " =    1.663
peak=    3.787 closest distance to " O   HOH Z 174 " =    2.332
peak=    3.786 closest distance to " CD  LYS A 166 " =    1.410
peak=    3.784 closest distance to " CG2 THR A 221 " =    1.029
peak=    3.783 closest distance to " O   HOH Z 255 " =    1.719
peak=    3.782 closest distance to " O   HOH Z 279 " =    2.285
peak=    3.780 closest distance to " CB  ASN A 148 " =    1.191
peak=    3.777 closest distance to " O   HOH Z 142 " =    1.539
peak=    3.777 closest distance to " ND2 ASN A 187 " =    1.575
peak=    3.777 closest distance to " CB  ARG A 139 " =    0.896
peak=    3.767 closest distance to " O   HOH Z 193 " =    2.380
peak=    3.767 closest distance to " O   HOH Z 345 " =    3.000
peak=    3.758 closest distance to " O   HOH Z 265 " =    2.259
peak=    3.755 closest distance to " CA  ASN A 176 " =    1.847
peak=    3.726 closest distance to " O   HOH Z 180 " =    2.280
peak=    3.715 closest distance to " CB  PRO A  54 " =    1.302
peak=    3.712 closest distance to " O   HOH Z 371 " =    3.381
peak=    3.704 closest distance to " O   HOH Z  21 " =    1.781
peak=    3.700 closest distance to " O   HOH Z 411 " =    3.455
peak=    3.692 closest distance to " O   HOH Z 406 " =    1.633
peak=    3.691 closest distance to " O   HOH Z 344 " =    2.879
peak=    3.684 closest distance to " O   HOH Z 128 " =    2.228
peak=    3.681 closest distance to " O   HOH Z 358 " =    2.033
peak=    3.680 closest distance to " CA  THR A 221 " =    0.972
peak=    3.675 closest distance to " O   HOH Z  54 " =    1.682
peak=    3.674 closest distance to " O   HOH Z 147 " =    1.786
peak=    3.669 closest distance to " O   ALA A 165 " =    1.299
peak=    3.665 closest distance to " O   HOH Z   6 " =    2.056
peak=    3.641 closest distance to " CD BLYS A 290 " =    1.077
peak=    3.635 closest distance to " O   HOH Z 334 " =    1.359
peak=    3.623 closest distance to " O   HOH Z 284 " =    2.889
peak=    3.615 closest distance to " O   HOH Z 207 " =    2.159
peak=    3.602 closest distance to " O   HOH Z 345 " =    1.802
peak=    3.597 closest distance to " O   HOH Z 227 " =    1.725
peak=    3.593 closest distance to " O   HOH Z 402 " =    1.533
peak=    3.589 closest distance to " CG2 VAL A 197 " =    1.163
peak=    3.580 closest distance to " O   HOH Z 336 " =    1.668
peak=    3.579 closest distance to " O   HOH Z 261 " =    1.918
peak=    3.572 closest distance to " O   HOH Z 130 " =    2.198
peak=    3.572 closest distance to " O   HOH Z 214 " =    0.923
peak=    3.572 closest distance to " O   MET A 105 " =    1.881
peak=    3.571 closest distance to " CG AARG A 275 " =    1.098
peak=    3.563 closest distance to " CB  ASN A 187 " =    1.054
peak=    3.562 closest distance to " O   HOH Z 419 " =    1.688
peak=    3.552 closest distance to " O   HOH Z 173 " =    2.119
peak=    3.551 closest distance to " CB  ALA A 100 " =    1.304
peak=    3.531 closest distance to " C   SER A  32 " =    1.038
peak=    3.531 closest distance to " O   HOH Z 245 " =    1.385
peak=    3.509 closest distance to " O   HOH Z 234 " =    1.841
peak=    3.505 closest distance to " CA  ASP A 124 " =    0.739
peak=    3.503 closest distance to " O   GLY A 211 " =    1.241
peak=    3.501 closest distance to " O   HOH Z 362 " =    3.513
peak=    3.490 closest distance to " O   HOH Z 192 " =    1.762
peak=    3.487 closest distance to " CG2BVAL A  41 " =    0.886
peak=    3.485 closest distance to " O   HOH Z  61 " =    1.502
peak=    3.478 closest distance to " CD2 LEU A 297 " =    0.883
peak=    3.476 closest distance to " CA  ASP A 162 " =    1.201
peak=    3.468 closest distance to " CB  ASN A 285 " =    0.912
peak=    3.460 closest distance to " NH2AARG A 190 " =    1.384
peak=    3.447 closest distance to " O   ALA A 158 " =    1.225
peak=    3.445 closest distance to " O   HOH Z 128 " =    2.168
peak=    3.440 closest distance to " O   HOH Z 227 " =    1.780
peak=    3.437 closest distance to " CB  ALA A  71 " =    1.246
peak=    3.435 closest distance to " CB  PRO A 198 " =    1.004
peak=    3.435 closest distance to " O   HOH Z 357 " =    2.005
peak=    3.434 closest distance to " ND2 ASN A 110 " =    1.671
peak=    3.433 closest distance to " O   HOH Z 263 " =    2.199
peak=    3.432 closest distance to " O   HOH Z 387 " =    2.333
peak=    3.430 closest distance to " OG  SER A  62 " =    3.047
peak=    3.429 closest distance to " O   HOH Z 425 " =    1.357
peak=    3.426 closest distance to " CA  GLU A 152 " =    0.902
peak=    3.420 closest distance to " O   HOH Z 368 " =    2.573
peak=    3.420 closest distance to " CD2 HIS A  81 " =    1.233
peak=    3.417 closest distance to " CD2 LEU A 255 " =    1.170
peak=    3.410 closest distance to " NZ  LYS A 166 " =    3.005
peak=    3.408 closest distance to " CD  ARG A 195 " =    0.981
peak=    3.407 closest distance to " CB  TRP A 266 " =    0.913
peak=    3.405 closest distance to " CG1BVAL A  72 " =    1.654
peak=    3.404 closest distance to " O   HOH Z 150 " =    1.612
peak=    3.397 closest distance to " O   HOH Z 303 " =    2.183
peak=    3.395 closest distance to " CG  GLN A  58 " =    2.435
peak=    3.392 closest distance to " O   SER A  26 " =    1.720
peak=    3.392 closest distance to " CA  ALA A 160 " =    0.860
peak=    3.389 closest distance to " CB  ASN A 148 " =    1.960
peak=    3.386 closest distance to " CG2 VAL A  78 " =    0.943
peak=    3.385 closest distance to " CB  MET A  47 " =    0.983
peak=    3.384 closest distance to " CD  ARG A  66 " =    3.086
peak=    3.366 closest distance to " CA  GLY A 196 " =    1.055
peak=    3.366 closest distance to " CA  GLU A 152 " =    1.397
peak=    3.363 closest distance to " CB  ASN A  39 " =    0.854
peak=    3.359 closest distance to " O   HOH Z 286 " =    2.220
peak=    3.357 closest distance to " O   HOH Z  93 " =    2.616
peak=    3.353 closest distance to " O   HOH Z 327 " =    2.361
peak=    3.348 closest distance to " CZ  PHE A 192 " =    0.934
peak=    3.347 closest distance to " O   HOH Z 346 " =    1.556
peak=    3.346 closest distance to " O   HOH Z 214 " =    2.275
peak=    3.344 closest distance to " O   HOH Z 420 " =    1.972
peak=    3.342 closest distance to " O   HOH Z 295 " =    1.437
peak=    3.339 closest distance to " CZ  PHE A 218 " =    1.071
peak=    3.339 closest distance to " O   HOH Z 383 " =    2.024
peak=    3.339 closest distance to " ND1 HIS A  81 " =    1.555
peak=    3.337 closest distance to " O   TRP A 274 " =    1.806
peak=    3.336 closest distance to " CD  ARG A 195 " =    3.603
peak=    3.335 closest distance to " O   HOH Z 280 " =    2.697
peak=    3.335 closest distance to " CA  ASP A 140 " =    1.173
peak=    3.333 closest distance to " OD1 ASP A 238 " =    0.899
peak=    3.328 closest distance to " O   HOH Z  48 " =    2.004
peak=    3.325 closest distance to " O   HOH Z 416 " =    2.848
peak=    3.324 closest distance to " O   HOH Z  44 " =    1.803
peak=    3.314 closest distance to " O   HOH Z 438 " =    2.417
peak=    3.314 closest distance to " O   HOH Z 102 " =    1.221
peak=    3.311 closest distance to " O   HOH Z 421 " =    1.724
peak=    3.310 closest distance to " O   HOH Z 156 " =    2.514
peak=    3.309 closest distance to " CA  ARG A 195 " =    1.280
peak=    3.308 closest distance to " CD2 TRP A 179 " =    1.317
peak=    3.307 closest distance to " CB  ALA A 291 " =    1.341
peak=    3.307 closest distance to " CB  PHE A  16 " =    1.038
peak=    3.306 closest distance to " O   HOH Z 432 " =    1.764
peak=    3.304 closest distance to " O   HOH Z 281 " =    4.156
peak=    3.301 closest distance to " CA  ASN A 215 " =    1.107
peak=    3.298 closest distance to " NZ  LYS A 117 " =    1.662
peak=    3.294 closest distance to " CA  GLN A 223 " =    0.902
peak=    3.293 closest distance to " CG2 ILE A 106 " =    1.082
peak=    3.292 closest distance to " O   HOH Z 437 " =    1.606
peak=    3.287 closest distance to " CD  ARG A 159 " =    0.824
peak=    3.286 closest distance to " NZ  LYS A 119 " =    1.682
peak=    3.285 closest distance to " CA  LEU A  83 " =    1.442
peak=    3.284 closest distance to " O   HOH Z  11 " =    1.228
peak=    3.278 closest distance to " CD  LYS A 119 " =    1.510
peak=    3.278 closest distance to " CE  LYS A 119 " =    1.066
peak=    3.273 closest distance to " O   HOH Z 427 " =    2.747
peak=    3.272 closest distance to " NH1 ARG A 269 " =    0.747
peak=    3.269 closest distance to " CB  THR A  52 " =    1.145
peak=    3.266 closest distance to " O   HOH Z 197 " =    1.955
peak=    3.266 closest distance to " O   HOH Z  10 " =    1.798
peak=    3.266 closest distance to " CG  MET A 185 " =    1.205
peak=    3.265 closest distance to " O   HOH Z 215 " =    1.494
peak=    3.264 closest distance to " OG1 THR A 294 " =    2.496
peak=    3.262 closest distance to " CA  ALA A 295 " =    1.043
peak=    3.262 closest distance to " CG2 VAL A 257 " =    0.815
peak=    3.261 closest distance to " CD1 TRP A 266 " =    1.165
peak=    3.259 closest distance to " O   HOH Z 250 " =    1.780
peak=    3.251 closest distance to " CD  PRO A  54 " =    1.224
peak=    3.247 closest distance to " O   HOH Z 427 " =    3.019
peak=    3.247 closest distance to " CA  GLU A  46 " =    0.761
peak=    3.246 closest distance to " CB  LEU A 143 " =    1.128
peak=    3.243 closest distance to " O   HOH Z 104 " =    3.099
peak=    3.242 closest distance to " OG  SER A  97 " =    3.539
peak=    3.241 closest distance to " O   PHE A 155 " =    1.374
peak=    3.236 closest distance to " O   GLY A  57 " =    2.543
peak=    3.233 closest distance to " O   HOH Z 409 " =    3.048
peak=    3.233 closest distance to " CA  TYR A 116 " =    1.436
peak=    3.233 closest distance to " CB  SER A  62 " =    1.275
peak=    3.229 closest distance to " O   HOH Z 110 " =    1.607
peak=    3.229 closest distance to " CD1 ILE A 106 " =    0.902
peak=    3.228 closest distance to " O   HOH Z  19 " =    1.640
peak=    3.219 closest distance to " OD1 ASP A 231 " =    1.908
peak=    3.217 closest distance to " O   HOH Z 365 " =    2.999
peak=    3.216 closest distance to " CB  SER A  62 " =    0.795
peak=    3.215 closest distance to " O   HOH Z 299 " =    2.327
peak=    3.213 closest distance to " NH1BARG A 145 " =    0.928
peak=    3.207 closest distance to " O   HOH Z 116 " =    1.799
peak=    3.206 closest distance to " CB  MET A  40 " =    0.839
peak=    3.203 closest distance to " CB  SER A 216 " =    0.802
peak=    3.200 closest distance to " OG  SER A 276 " =    1.397
peak=    3.198 closest distance to " CG2 ILE A  20 " =    1.289
peak=    3.197 closest distance to " O   THR A 251 " =    1.256
peak=    3.194 closest distance to " CB  ALA A 256 " =    1.143
peak=    3.193 closest distance to " O   HOH Z 418 " =    1.404
peak=    3.193 closest distance to " CG  ARG A 219 " =    1.317
peak=    3.190 closest distance to " CG1 VAL A 202 " =    2.112
peak=    3.189 closest distance to " O   HOH Z  50 " =    3.440
peak=    3.187 closest distance to " O   HOH Z   1 " =    2.840
peak=    3.186 closest distance to " O   HOH Z 185 " =    1.713
peak=    3.186 closest distance to " CA  ASN A  74 " =    1.200
peak=    3.186 closest distance to " CB  SER A 273 " =    0.790
peak=    3.186 closest distance to " O   HOH Z 285 " =    2.008
peak=    3.183 closest distance to " O   VAL A  72 " =    3.246
peak=    3.183 closest distance to " NH1AARG A 145 " =    1.083
peak=    3.181 closest distance to " CB  ILE A 120 " =    1.265
peak=    3.176 closest distance to " CE  LYS A 193 " =    1.878
peak=    3.171 closest distance to " O   HOH Z 123 " =    2.075
peak=    3.171 closest distance to " O   HOH Z 183 " =    1.529
peak=    3.169 closest distance to " O   HOH Z 420 " =    5.646
peak=    3.169 closest distance to " CA  LYS A 117 " =    1.252
peak=    3.168 closest distance to " CB  TYR A 116 " =    1.112
peak=    3.164 closest distance to " O   HOH Z 155 " =    2.811
peak=    3.164 closest distance to " N   ARG A 156 " =    1.403
peak=    3.156 closest distance to " CA  VAL A  41 " =    0.801
peak=    3.155 closest distance to " O   HOH Z 291 " =    1.541
peak=    3.155 closest distance to " N   ASN A 127 " =    1.242
peak=    3.152 closest distance to " CD  ARG A 219 " =    0.920
peak=    3.147 closest distance to " O   HOH Z 248 " =    1.524
peak=    3.147 closest distance to " NE2 GLN A  58 " =    4.508
peak=    3.147 closest distance to " CB  TYR A  30 " =    1.430
peak=    3.146 closest distance to " CB  ALA A 248 " =    0.911
peak=    3.134 closest distance to " O   HOH Z 238 " =    5.384
peak=    3.134 closest distance to " O   HOH Z 434 " =    1.479
peak=    3.131 closest distance to " O   GLN A 278 " =    1.255
peak=    3.123 closest distance to " OE1 GLN A  58 " =    5.997
peak=    3.119 closest distance to " O   GLY A  91 " =    1.247
peak=    3.117 closest distance to " O   HOH Z 210 " =    1.077
peak=    3.111 closest distance to " CA  MET A  40 " =    1.056
peak=    3.110 closest distance to " O   HOH Z 162 " =    1.671
peak=    3.109 closest distance to " CZ  PHE A  38 " =    1.399
peak=    3.103 closest distance to " O   HOH Z 215 " =    1.374
peak=    3.103 closest distance to " CG BARG A 102 " =    1.860
peak=    3.099 closest distance to " O   HOH Z  28 " =    2.290
peak=    3.097 closest distance to " CG  LEU A 167 " =    1.157
peak=    3.097 closest distance to " NH2AARG A 275 " =    3.785
peak=    3.093 closest distance to " O   HOH Z 280 " =    2.519
peak=    3.092 closest distance to " O   HOH Z 171 " =    3.807
peak=    3.091 closest distance to " OD2 ASP A 298 " =    4.093
peak=    3.090 closest distance to " O   HOH Z 244 " =    1.739
peak=    3.090 closest distance to " O   HOH Z 435 " =    3.019
peak=    3.089 closest distance to " CB  PRO A 163 " =    3.995
peak=    3.088 closest distance to " O   HOH Z 261 " =    1.537
peak=    3.088 closest distance to " N   GLY A  57 " =    1.523
peak=    3.086 closest distance to " O   HOH Z 359 " =    1.467
peak=    3.085 closest distance to " O   HOH Z  22 " =    2.437
peak=    3.084 closest distance to " O   HOH Z 273 " =    3.342
peak=    3.084 closest distance to " O   HOH Z 166 " =    1.517
peak=    3.078 closest distance to " O   HOH Z 258 " =    2.320
peak=    3.075 closest distance to " CB  GLN A  58 " =    0.809
peak=    3.071 closest distance to " O   HOH Z 211 " =    2.645
peak=    3.069 closest distance to " CA  VAL A 126 " =    1.059
peak=    3.068 closest distance to " O   HOH Z 109 " =    2.394
peak=    3.061 closest distance to " CA  GLY A 241 " =    0.857
peak=    3.060 closest distance to " OH  TYR A  30 " =    1.335
peak=    3.056 closest distance to " NE2 HIS A 115 " =    0.984
peak=    3.056 closest distance to " CG  ASP A 231 " =    0.966
peak=    3.052 closest distance to " CA  THR A 264 " =    0.833
peak=    3.037 closest distance to " CA  ALA A 248 " =    1.212
peak=    3.020 closest distance to " O   HOH Z 194 " =    2.196

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.774 - 5.564
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 199
   mapped sites are within: 0.774 - 5.564

peak=   -4.517 closest distance to " O   HOH Z 266 " =    4.409
peak=   -4.490 closest distance to " O   HOH Z 210 " =    0.775
peak=   -4.309 closest distance to " CD  ARG A 156 " =    1.976
peak=   -4.238 closest distance to " O   VAL A  67 " =    2.669
peak=   -4.205 closest distance to " O   HOH Z  52 " =    1.719
peak=   -4.188 closest distance to " OXT GLY A 302 " =    2.720
peak=   -4.137 closest distance to " O   HOH Z 377 " =    1.067
peak=   -4.088 closest distance to " O   HOH Z 155 " =    1.622
peak=   -3.969 closest distance to " O   HOH Z 407 " =    3.708
peak=   -3.962 closest distance to " CD2 LEU A 237 " =    2.601
peak=   -3.951 closest distance to " CH2 TRP A 179 " =    1.162
peak=   -3.944 closest distance to " OG  SER A  97 " =    2.193
peak=   -3.934 closest distance to " O   HOH Z  19 " =    2.202
peak=   -3.931 closest distance to " CD2 LEU A 300 " =    2.894
peak=   -3.928 closest distance to " NH2 ARG A  66 " =    1.462
peak=   -3.926 closest distance to " O   PRO A 163 " =    2.138
peak=   -3.902 closest distance to " O   HOH Z 290 " =    1.010
peak=   -3.895 closest distance to " O   PRO A 198 " =    1.328
peak=   -3.893 closest distance to " CA  SER A 276 " =    1.481
peak=   -3.888 closest distance to " N   ALA A  43 " =    2.579
peak=   -3.855 closest distance to " O   HOH Z  10 " =    1.573
peak=   -3.850 closest distance to " O   HOH Z 353 " =    2.413
peak=   -3.837 closest distance to " ND2 ASN A  45 " =    1.021
peak=   -3.837 closest distance to " O   HOH Z 372 " =    2.624
peak=   -3.817 closest distance to " CG  MET A  93 " =    2.549
peak=   -3.803 closest distance to " CB  LEU A 167 " =    2.163
peak=   -3.790 closest distance to " CD1 LEU A 228 " =    2.384
peak=   -3.786 closest distance to " O   HOH Z 292 " =    4.512
peak=   -3.781 closest distance to " CG2 THR A   4 " =    1.866
peak=   -3.780 closest distance to " O   HOH Z  17 " =    1.217
peak=   -3.769 closest distance to " CD  ARG A 139 " =    1.506
peak=   -3.767 closest distance to " C   ALA A 158 " =    1.232
peak=   -3.767 closest distance to " O   HOH Z 377 " =    2.026
peak=   -3.759 closest distance to " O   HOH Z 166 " =    1.826
peak=   -3.749 closest distance to " O   HOH Z 234 " =    4.222
peak=   -3.744 closest distance to " OG ASER A 134 " =    1.294
peak=   -3.740 closest distance to " CE2 TYR A  30 " =    2.712
peak=   -3.730 closest distance to " O   HOH Z 151 " =    1.471
peak=   -3.718 closest distance to " ND2 ASN A  60 " =    1.484
peak=   -3.704 closest distance to " O   SER A 210 " =    1.843
peak=   -3.684 closest distance to " C   HIS A 108 " =    1.081
peak=   -3.678 closest distance to " O   HOH Z 165 " =    2.089
peak=   -3.674 closest distance to " OD1 ASP A 191 " =    1.796
peak=   -3.671 closest distance to " CD1 PHE A  59 " =    1.913
peak=   -3.662 closest distance to " O   HOH Z 283 " =    1.856
peak=   -3.657 closest distance to " N   MET A 188 " =    1.866
peak=   -3.655 closest distance to " O   HOH Z  43 " =    1.815
peak=   -3.648 closest distance to " CG  GLN A  58 " =    1.209
peak=   -3.631 closest distance to " CG2 ILE A  20 " =    2.965
peak=   -3.608 closest distance to " N   GLN A  58 " =    1.680
peak=   -3.595 closest distance to " O   HOH Z 236 " =    1.521
peak=   -3.594 closest distance to " O   ILE A 109 " =    2.647
peak=   -3.585 closest distance to " CG1 VAL A 112 " =    2.599
peak=   -3.584 closest distance to " CG  ASP A  50 " =    2.466
peak=   -3.582 closest distance to " CB  ASN A  39 " =    2.225
peak=   -3.580 closest distance to " OE2 GLU A   2 " =    1.541
peak=   -3.579 closest distance to " CD2 PHE A  59 " =    2.492
peak=   -3.575 closest distance to " O   HOH Z  93 " =    1.415
peak=   -3.567 closest distance to " CD1 PHE A 130 " =    2.269
peak=   -3.562 closest distance to " O   HOH Z 111 " =    1.353
peak=   -3.555 closest distance to " OH  TYR A 169 " =    1.039
peak=   -3.552 closest distance to " CG  GLU A  53 " =    1.433
peak=   -3.544 closest distance to " O   HOH Z 118 " =    3.239
peak=   -3.537 closest distance to " O   GLY A 196 " =    1.093
peak=   -3.535 closest distance to " NE2 GLN A  58 " =    0.924
peak=   -3.531 closest distance to " O   ALA A 256 " =    1.524
peak=   -3.530 closest distance to " OG  SER A  62 " =    1.375
peak=   -3.524 closest distance to " O   ALA A 160 " =    1.529
peak=   -3.523 closest distance to " O   HOH Z 196 " =    2.431
peak=   -3.520 closest distance to " CG  ASP A 231 " =    0.822
peak=   -3.513 closest distance to " O   HOH Z 185 " =    2.441
peak=   -3.506 closest distance to " O   HOH Z 380 " =    4.801
peak=   -3.506 closest distance to " CG  ARG A  66 " =    2.394
peak=   -3.504 closest distance to " O   HOH Z 221 " =    1.243
peak=   -3.501 closest distance to " O   HOH Z  58 " =    1.098
peak=   -3.501 closest distance to " OD2 ASP A 171 " =    2.243
peak=   -3.500 closest distance to " CB  ALA A 248 " =    1.996
peak=   -3.500 closest distance to " CD1 TYR A 247 " =    2.242
peak=   -3.494 closest distance to " ND2 ASN A 187 " =    1.701
peak=   -3.492 closest distance to " NH1 ARG A 195 " =    2.275
peak=   -3.484 closest distance to " CB  PHE A 208 " =    2.256
peak=   -3.482 closest distance to " O   HOH Z 417 " =    2.784
peak=   -3.481 closest distance to " OG BSER A 134 " =    1.843
peak=   -3.480 closest distance to " NH2AARG A 275 " =    5.281
peak=   -3.479 closest distance to " CA  GLY A 203 " =    2.284
peak=   -3.469 closest distance to " CA  ASP A 298 " =    1.095
peak=   -3.463 closest distance to " CE  MET A 105 " =    1.926
peak=   -3.462 closest distance to " CB  ALA A 291 " =    2.451
peak=   -3.455 closest distance to " CD  ARG A  14 " =    3.263
peak=   -3.452 closest distance to " CZ  TYR A 169 " =    1.831
peak=   -3.447 closest distance to " CB  CYS A 254 " =    2.471
peak=   -3.445 closest distance to " CB  PRO A 243 " =    2.556
peak=   -3.439 closest distance to " O   HOH Z  91 " =    2.055
peak=   -3.437 closest distance to " O   HOH Z  97 " =    1.694
peak=   -3.435 closest distance to " C   ASN A 285 " =    2.378
peak=   -3.432 closest distance to " CD2 LEU A 167 " =    1.778
peak=   -3.419 closest distance to " O   VAL A 125 " =    2.088
peak=   -3.416 closest distance to " O   HOH Z 426 " =    1.673
peak=   -3.412 closest distance to " CD  GLN A  88 " =    0.774
peak=   -3.412 closest distance to " OD1 ASN A 148 " =    1.690
peak=   -3.410 closest distance to " CD  GLN A 223 " =    1.294
peak=   -3.410 closest distance to " O   HOH Z  15 " =    1.560
peak=   -3.409 closest distance to " CB  ASP A 132 " =    2.382
peak=   -3.409 closest distance to " O   GLY A 118 " =    2.243
peak=   -3.408 closest distance to " O   HOH Z 128 " =    2.409
peak=   -3.406 closest distance to " C   SER A 206 " =    1.562
peak=   -3.401 closest distance to " CA  VAL A 197 " =    1.003
peak=   -3.400 closest distance to " O   HOH Z  71 " =    1.502
peak=   -3.399 closest distance to " C   THR A 279 " =    1.161
peak=   -3.397 closest distance to " CD  ARG A 195 " =    5.168
peak=   -3.395 closest distance to " N   ALA A 226 " =    2.119
peak=   -3.394 closest distance to " O   HOH Z 150 " =    1.460
peak=   -3.392 closest distance to " O   HOH Z  38 " =    1.330
peak=   -3.390 closest distance to " CD2 TYR A 293 " =    1.995
peak=   -3.383 closest distance to " O   HOH Z 414 " =    1.417
peak=   -3.378 closest distance to " O   HOH Z 399 " =    2.279
peak=   -3.375 closest distance to " CG2 VAL A 189 " =    2.202
peak=   -3.371 closest distance to " CE3 TRP A 150 " =    2.187
peak=   -3.370 closest distance to " NH2 ARG A  79 " =    1.869
peak=   -3.360 closest distance to " O   HOH Z 241 " =    1.200
peak=   -3.357 closest distance to " CB  TYR A  15 " =    2.296
peak=   -3.356 closest distance to " OD2 ASP A 171 " =    1.898
peak=   -3.353 closest distance to " O   HOH Z 423 " =    2.315
peak=   -3.351 closest distance to " CB  TRP A  85 " =    2.424
peak=   -3.348 closest distance to " CG  MET A 105 " =    0.898
peak=   -3.337 closest distance to " ND2 ASN A 249 " =    2.000
peak=   -3.335 closest distance to " O   HOH Z  11 " =    1.698
peak=   -3.333 closest distance to " O   HOH Z   6 " =    1.621
peak=   -3.333 closest distance to " SG  CYS A 168 " =    1.123
peak=   -3.332 closest distance to " O   ALA A   1 " =    1.963
peak=   -3.324 closest distance to " O   HOH Z 427 " =    1.397
peak=   -3.316 closest distance to " O   HOH Z 102 " =    1.627
peak=   -3.310 closest distance to " NE2 GLN A  88 " =    1.957
peak=   -3.306 closest distance to " CD1 LEU A 101 " =    2.705
peak=   -3.306 closest distance to " CB  ASP A 286 " =    2.339
peak=   -3.294 closest distance to " O   HOH Z 259 " =    1.324
peak=   -3.288 closest distance to " O   HOH Z 385 " =    2.066
peak=   -3.288 closest distance to " CZ  ARG A  66 " =    1.118
peak=   -3.287 closest distance to " OG  SER A  87 " =    1.523
peak=   -3.286 closest distance to " O   LEU A 167 " =    1.600
peak=   -3.281 closest distance to " O   HOH Z 313 " =    1.068
peak=   -3.280 closest distance to " OG BSER A 134 " =    1.262
peak=   -3.279 closest distance to " CE  MET A  93 " =    1.188
peak=   -3.274 closest distance to " O   PHE A 218 " =    1.492
peak=   -3.274 closest distance to " CG  ARG A 219 " =    2.368
peak=   -3.274 closest distance to " O   ASN A 187 " =    1.555
peak=   -3.273 closest distance to " O   HOH Z 311 " =    3.600
peak=   -3.268 closest distance to " O   ALA A 158 " =    1.108
peak=   -3.268 closest distance to " OG BSER A 210 " =    2.229
peak=   -3.253 closest distance to " NH2 ARG A  66 " =    5.351
peak=   -3.235 closest distance to " CA  GLY A 241 " =    2.272
peak=   -3.235 closest distance to " C   LEU A 143 " =    1.278
peak=   -3.226 closest distance to " CH2 TRP A 177 " =    1.920
peak=   -3.218 closest distance to " O   HOH Z 350 " =    1.609
peak=   -3.215 closest distance to " O   HOH Z 418 " =    1.375
peak=   -3.214 closest distance to " O   PRO A 198 " =    1.291
peak=   -3.208 closest distance to " O   HOH Z 361 " =    3.397
peak=   -3.208 closest distance to " O   HOH Z 385 " =    3.810
peak=   -3.208 closest distance to " CA  GLY A  98 " =    2.150
peak=   -3.207 closest distance to " N   VAL A 189 " =    1.839
peak=   -3.199 closest distance to " CD2 LEU A 237 " =    2.733
peak=   -3.195 closest distance to " CD  LYS A 289 " =    2.453
peak=   -3.194 closest distance to " O   HOH Z 396 " =    1.784
peak=   -3.193 closest distance to " O   HOH Z 265 " =    2.005
peak=   -3.190 closest distance to " OG  SER A  26 " =    1.413
peak=   -3.187 closest distance to " O   HOH Z  37 " =    1.844
peak=   -3.185 closest distance to " O   HOH Z  76 " =    2.003
peak=   -3.182 closest distance to " NH1 ARG A 195 " =    2.606
peak=   -3.180 closest distance to " CG  ARG A 269 " =    2.326
peak=   -3.177 closest distance to " O   HOH Z 298 " =    2.771
peak=   -3.173 closest distance to " O   HOH Z 275 " =    1.530
peak=   -3.171 closest distance to " CG  PHE A 283 " =    2.855
peak=   -3.168 closest distance to " O   HOH Z  39 " =    1.703
peak=   -3.165 closest distance to " O   HOH Z 351 " =    1.380
peak=   -3.159 closest distance to " O   ALA A  10 " =    1.729
peak=   -3.159 closest distance to " C   ASP A 191 " =    1.382
peak=   -3.157 closest distance to " CB  ALA A 291 " =    2.124
peak=   -3.153 closest distance to " O   HOH Z  90 " =    1.879
peak=   -3.152 closest distance to " OD2 ASP A  65 " =    1.791
peak=   -3.142 closest distance to " CB  PRO A 163 " =    2.788
peak=   -3.127 closest distance to " N   LEU A 261 " =    1.285
peak=   -3.118 closest distance to " O   HOH Z 166 " =    1.878
peak=   -3.115 closest distance to " CG1 VAL A 153 " =    2.253
peak=   -3.113 closest distance to " O   HOH Z  67 " =    2.868
peak=   -3.107 closest distance to " O   HOH Z 407 " =    1.044
peak=   -3.104 closest distance to " CG  PRO A 163 " =    2.547
peak=   -3.098 closest distance to " O   HOH Z 252 " =    4.014
peak=   -3.094 closest distance to " O   VAL A 174 " =    2.114
peak=   -3.094 closest distance to " CB  PRO A 163 " =    2.527
peak=   -3.091 closest distance to " O   ALA A  34 " =    2.491
peak=   -3.082 closest distance to " O   HOH Z 430 " =    5.564
peak=   -3.077 closest distance to " O   PRO A 198 " =    1.762
peak=   -3.070 closest distance to " O   HOH Z 434 " =    4.114
peak=   -3.052 closest distance to " CD  GLN A  58 " =    1.143
peak=   -3.052 closest distance to " CZ  PHE A  59 " =    1.885
peak=   -3.050 closest distance to " O   HOH Z 280 " =    2.115
peak=   -3.049 closest distance to " NE  ARG A 138 " =    2.227
peak=   -3.022 closest distance to " O   HOH Z 424 " =    2.903

================= 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    :  0.4523 0.4440   6.263349e+00   6.248859e+00
   1_bss:  0.4432 0.4340   6.256025e+00   6.234693e+00
   1_xyz:  0.3567 0.3834   6.105735e+00   6.157694e+00
   1_adp:  0.3253 0.3926   6.060570e+00   6.170497e+00
   1_occ:  0.3249 0.3928   6.059894e+00   6.171055e+00
   2_bss:  0.3243 0.3901   6.060269e+00   6.170233e+00
   2_xyz:  0.2422 0.3018   5.808442e+00   5.978205e+00
   2_adp:  0.2171 0.2803   5.728388e+00   5.913676e+00
   2_occ:  0.2170 0.2802   5.727796e+00   5.912989e+00
   3_bss:  0.2163 0.2793   5.725196e+00   5.909932e+00
   3_xyz:  0.1614 0.2084   5.451024e+00   5.659778e+00
   3_adp:  0.1449 0.1911   5.361922e+00   5.578412e+00
   3_occ:  0.1447 0.1909   5.361663e+00   5.578078e+00
   4_bss:  0.1450 0.1913   5.364953e+00   5.580157e+00
   4_xyz:  0.1257 0.1730   5.245255e+00   5.480229e+00
   4_adp:  0.1217 0.1676   5.217878e+00   5.450695e+00
   4_occ:  0.1216 0.1676   5.217682e+00   5.450817e+00
   5_bss:  0.1219 0.1673   5.219226e+00   5.450570e+00
   5_xyz:  0.1155 0.1628   5.182070e+00   5.418838e+00
   5_adp:  0.1145 0.1627   5.177586e+00   5.416918e+00
   5_occ:  0.1143 0.1626   5.177410e+00   5.417149e+00
   5_bss:  0.1143 0.1626   5.177473e+00   5.417176e+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:  0.292  26.351  -2.191   3.656   1.022   0.000   0.000   0.000
   1_xyz:  0.292  26.351  -2.191   3.656   1.022   0.000   0.000   0.000
   1_adp:  0.292  26.351  -2.191   3.656   1.022   0.000   0.000   0.000
   1_occ:  0.292  26.351  -2.191   3.656   1.022   0.000   0.000   0.000
   2_bss:  0.319  54.278  -1.510   1.767  -0.062   0.000  -0.000  -0.000
   2_xyz:  0.319  54.278  -1.510   1.767  -0.062   0.000  -0.000  -0.000
   2_adp:  0.319  54.278  -1.510   1.767  -0.062   0.000  -0.000  -0.000
   2_occ:  0.319  54.278  -1.510   1.767  -0.062   0.000  -0.000  -0.000
   3_bss:  0.319  57.537  -1.619  -0.001  -1.121  -0.000  -0.000  -0.000
   3_xyz:  0.319  57.537  -1.619  -0.001  -1.121  -0.000  -0.000  -0.000
   3_adp:  0.319  57.537  -1.619  -0.001  -1.121  -0.000  -0.000  -0.000
   3_occ:  0.319  57.537  -1.619  -0.001  -1.121  -0.000  -0.000  -0.000
   4_bss:  0.326  64.813  -2.099  -0.968  -1.591  -0.000  -0.000  -0.000
   4_xyz:  0.326  64.813  -2.099  -0.968  -1.591  -0.000  -0.000  -0.000
   4_adp:  0.326  64.813  -2.099  -0.968  -1.591  -0.000  -0.000  -0.000
   4_occ:  0.326  64.813  -2.099  -0.968  -1.591  -0.000  -0.000  -0.000
   5_bss:  0.321  58.947  -2.158  -1.321  -1.675  -0.000  -0.000  -0.000
   5_xyz:  0.321  58.947  -2.158  -1.321  -1.675  -0.000  -0.000  -0.000
   5_adp:  0.321  58.947  -2.158  -1.321  -1.675  -0.000  -0.000  -0.000
   5_occ:  0.321  58.947  -2.158  -1.321  -1.675  -0.000  -0.000  -0.000
   5_bss:  0.323  58.886  -2.019  -1.288  -1.527  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.881 0.4718  0.6316    62954.044
   1_bss:  52.612 0.4861  0.6686    59129.663
   1_xyz:  43.461 0.6003  0.8111    43409.127
   1_adp:  44.858 0.5825  0.7972    45439.887
   1_occ:  44.931 0.5815  0.7940    45438.029
   2_bss:  44.648 0.5850  0.7816    45094.694
   2_xyz:  32.549 0.7274  0.9403    25015.775
   2_adp:  29.280 0.7649  0.9534    21266.425
   2_occ:  29.267 0.7650  0.9531    21228.562
   3_bss:  29.063 0.7671  0.9236    20961.343
   3_xyz:  20.587 0.8546  0.9876    11180.622
   3_adp:  18.378 0.8764  0.9902     9501.903
   3_occ:  18.372 0.8765  0.9902     9506.285
   4_bss:  18.416 0.8762  0.9684     9581.018
   4_xyz:  16.249 0.8954  0.9784     7694.287
   4_adp:  15.540 0.9020  0.9765     7310.807
   4_occ:  15.537 0.9020  0.9764     7318.140
   5_bss:  15.554 0.9019  0.9709     7332.050
   5_xyz:  14.845 0.9079  0.9723     6821.753
   5_adp:  14.763 0.9088  0.9664     6824.782
   5_occ:  14.763 0.9088  0.9664     6830.126
   5_bss:  14.763 0.9088  0.9681     6830.152
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.8262e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.8262e-01
   1_xyz:   1.434  0.011  0.087 15.443  0.005  4.113   1.0805e-01
   1_adp:   1.434  0.011  0.087 15.443  0.005  4.113   1.0805e-01
   1_occ:   1.434  0.011  0.087 15.443  0.005  4.113   1.0805e-01
   2_bss:   1.434  0.011  0.087 15.443  0.005  4.113   1.0805e-01
   2_xyz:   1.384  0.010  0.089 15.037  0.005  4.115   1.0023e-01
   2_adp:   1.384  0.010  0.089 15.037  0.005  4.115   1.0023e-01
   2_occ:   1.384  0.010  0.089 15.037  0.005  4.115   1.0023e-01
   3_bss:   1.384  0.010  0.089 15.037  0.005  4.115   1.0023e-01
   3_xyz:   1.109  0.009  0.073 14.691  0.004  4.113   7.1822e-02
   3_adp:   1.109  0.009  0.073 14.691  0.004  4.113   7.1822e-02
   3_occ:   1.109  0.009  0.073 14.691  0.004  4.113   7.1822e-02
   4_bss:   1.109  0.009  0.073 14.691  0.004  4.113   7.1822e-02
   4_xyz:   1.112  0.009  0.078 14.707  0.004  4.121   7.0732e-02
   4_adp:   1.112  0.009  0.078 14.707  0.004  4.121   7.0732e-02
   4_occ:   1.112  0.009  0.078 14.707  0.004  4.121   7.0732e-02
   5_bss:   1.112  0.009  0.078 14.707  0.004  4.121   7.0732e-02
   5_xyz:   1.087  0.009  0.077 14.685  0.004  4.126   6.7498e-02
   5_adp:   1.087  0.009  0.077 14.685  0.004  4.126   6.7498e-02
   5_occ:   1.087  0.009  0.077 14.685  0.004  4.126   6.7498e-02
   5_bss:   1.087  0.009  0.077 14.685  0.004  4.126   6.7498e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.569   2.4250e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.569   2.4250e-01
   1_xyz:   9.096  0.073  0.388 88.345  0.027  1.934   8.1927e-02
   1_adp:   9.096  0.073  0.388 88.345  0.027  1.934   8.1927e-02
   1_occ:   9.096  0.073  0.388 88.345  0.027  1.934   8.1927e-02
   2_bss:   9.096  0.073  0.388 88.345  0.027  1.934   8.1927e-02
   2_xyz:   8.092  0.057  0.254 84.111  0.035  2.239   1.4376e-01
   2_adp:   8.092  0.057  0.254 84.111  0.035  2.239   1.4376e-01
   2_occ:   8.092  0.057  0.254 84.111  0.035  2.239   1.4376e-01
   3_bss:   8.092  0.057  0.254 84.111  0.035  2.239   1.4376e-01
   3_xyz:   8.058  0.068  0.234 89.666  0.038  2.282   6.7907e-02
   3_adp:   8.058  0.068  0.234 89.666  0.038  2.282   6.7907e-02
   3_occ:   8.058  0.068  0.234 89.666  0.038  2.282   6.7907e-02
   4_bss:   8.058  0.068  0.234 89.666  0.038  2.282   6.7907e-02
   4_xyz:   7.445  0.054  0.264 82.581  0.033  2.307   5.9149e-02
   4_adp:   7.445  0.054  0.264 82.581  0.033  2.307   5.9149e-02
   4_occ:   7.445  0.054  0.264 82.581  0.033  2.307   5.9149e-02
   5_bss:   7.445  0.054  0.264 82.581  0.033  2.307   5.9149e-02
   5_xyz:   7.686  0.045  0.264 82.105  0.034  2.317   4.7918e-02
   5_adp:   7.686  0.045  0.264 82.105  0.034  2.317   4.7918e-02
   5_occ:   7.686  0.045  0.264 82.105  0.034  2.317   4.7918e-02
   5_bss:   7.686  0.045  0.264 82.105  0.034  2.317   4.7918e-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: 103.25   0.00  19.09  89.73   0.00  15.58 103.25   0.00  38.21
   1_occ: 103.25   0.00  19.09  89.73   0.00  15.58 103.25   0.00  38.21
   2_bss: 103.25   0.00  19.09  89.73   0.00  15.58 103.25   0.00  38.21
   2_xyz: 103.25   0.00  19.09  89.73   0.00  15.58 103.25   0.00  38.21
   2_adp:  97.49   0.00  18.20  86.80   0.00  14.13  97.49   3.92  40.35
   2_occ:  97.49   0.00  18.20  86.80   0.00  14.13  97.49   3.92  40.35
   3_bss:  97.49   0.00  18.20  86.80   0.00  14.13  97.49   3.92  40.35
   3_xyz:  97.49   0.00  18.20  86.80   0.00  14.13  97.49   3.92  40.35
   3_adp: 101.93   0.00  18.28 101.93   0.00  13.44  98.23   5.67  44.66
   3_occ: 101.93   0.00  18.28 101.93   0.00  13.44  98.23   5.67  44.66
   4_bss: 101.93   0.00  18.28 101.93   0.00  13.44  98.23   5.67  44.66
   4_xyz: 101.93   0.00  18.28 101.93   0.00  13.44  98.23   5.67  44.66
   4_adp: 102.70   1.34  17.57 102.70   1.34  12.95  95.16   5.21  42.73
   4_occ: 102.70   1.34  17.57 102.70   1.34  12.95  95.16   5.21  42.73
   5_bss: 102.70   1.34  17.57 102.70   1.34  12.95  95.16   5.21  42.73
   5_xyz: 102.70   1.34  17.57 102.70   1.34  12.95  95.16   5.21  42.73
   5_adp: 103.76   1.69  17.10 103.76   1.69  12.69  91.06   5.15  41.16
   5_occ: 103.76   1.69  17.10 103.76   1.69  12.69  91.06   5.15  41.16
   5_bss: 103.70   1.63  17.04 103.70   1.63  12.62  91.00   5.09  41.10
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.919    0.018    0.297
   1_adp:    1.919    0.018    0.297
   1_occ:    1.919    0.018    0.297
   2_bss:    1.919    0.018    0.297
   2_xyz:    1.551    0.020    0.576
   2_adp:    1.551    0.020    0.576
   2_occ:    1.551    0.020    0.576
   3_bss:    1.551    0.020    0.576
   3_xyz:    1.515    0.052    0.695
   3_adp:    1.515    0.052    0.695
   3_occ:    1.515    0.052    0.695
   4_bss:    1.515    0.052    0.695
   4_xyz:    1.404    0.067    0.748
   4_adp:    1.404    0.067    0.748
   4_occ:    1.404    0.067    0.748
   5_bss:    1.404    0.067    0.748
   5_xyz:    1.458    0.058    0.771
   5_adp:    1.458    0.058    0.771
   5_occ:    1.458    0.058    0.771
   5_bss:    1.458    0.058    0.771
------------------------------------------------------------------------

CPU time actual refinement: 348.51


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_947/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_947/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_947/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_947/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_947/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 348.36 
  Macro-tasks:
    bulk solvent and scale       = 39.18  
    individual site refinement   = 143.14 
    weights calculation          = 30.02  
    collect and process          = 6.54   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 219.01 
  Micro-tasks:
    mask                            = 2.51   
    f_calc                          = 115.27 
    alpha_beta                      = 8.12   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 121.94 
    fmodel                         = 6.17   
    r_factors                      = 0.22   
    phase_errors                   = 10.69  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 266.39 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.006 micro seconds
Total CPU time: 6.03 minutes
from_scatterers_fft:    628 calls, 115.01 s
gradients_fft:          573 calls, 109.16 s

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

# Date 2008-01-16 Time 06:03:37 PST -0800 (1200492217.28 s)
Start R-work = 0.4523, R-free = 0.4440 (no bulk solvent and anisotropic scale)
Final R-work = 0.1356, R-free = 0.1813 (no bulk solvent and anisotropic scale)

Start R-work = 0.4432, R-free = 0.4340
Final R-work = 0.1143, R-free = 0.1626