# Date 2008-01-16 Time 06:02:02 PST -0800 (1200492122.36 s)
#phil __OFF__

Command line arguments: "../983.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25818
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 983

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 45.9914, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 45.9914, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1358 1.96366
Completeness in resolution range: 0.942731
Completeness with d_max=infinity: 0.940016

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1358
                             d_min =   1.9637

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 45.9914, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1358 1.96366
Completeness in resolution range: 0.942731
Completeness with d_max=infinity: 0.940016

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1362 -  4.2032 [2184/2211]  1967   217   9.9%
  bin  2:  4.2032 -  3.3481 [2089/2109]  1880   209  10.0%
  bin  3:  3.3481 -  2.9283 [2075/2094]  1864   211  10.2%
  bin  4:  2.9283 -  2.6622 [2033/2063]  1829   204  10.0%
  bin  5:  2.6622 -  2.4723 [2058/2077]  1859   199   9.7%
  bin  6:  2.4723 -  2.3270 [2013/2038]  1803   210  10.4%
  bin  7:  2.3270 -  2.2109 [2031/2059]  1829   202   9.9%
  bin  8:  2.2109 -  2.1149 [1993/2029]  1799   194   9.7%
  bin  9:  2.1149 -  2.0337 [2002/2044]  1801   201  10.0%
  bin 10:  2.0337 -  1.9637 [1111/2055]   999   112  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_983/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: 0.14 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:
        1.78 -     2.40: 32
        2.40 -     3.03: 2093
        3.03 -     3.65: 4695
        3.65 -     4.28: 9137
        4.28 -     4.90: 12471
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.776 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.838 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  ... (remaining 28423 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_983/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_983/model_refine_001.geo

CPU time processing inputs: 9.16


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 45.9914 85.95805 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 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4266   r_free= 0.4260   ksol= 0.00   Bsol= 0.00   scale= 0.919    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.237258                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.6887 0.99   1417  159 0.3517 0.3512      6.5045      6.5013|
|  2:  4.6887 -  3.7401 0.99   1355  151 0.3573 0.3507      6.7365      6.6831|
|  3:  3.7401 -  3.2728 0.99   1335  142 0.3828 0.3599      6.5979      6.6471|
|  4:  3.2728 -  2.9760 0.99   1334  155 0.4160 0.4374      6.4759      6.4732|
|  5:  2.9760 -  2.7641 0.99   1331  149 0.4492 0.4368      6.3222      6.3323|
|  6:  2.7641 -  2.6020 0.99   1316  141 0.4522 0.4690      6.2334      6.1959|
|  7:  2.6020 -  2.4723 0.99   1311  143 0.4623 0.4484      6.2045      6.1505|
|  8:  2.4723 -  2.3651 0.98   1290  146 0.4698 0.4620      6.1325      6.1285|
|  9:  2.3651 -  2.2743 0.98   1291  150 0.4631 0.4853      6.0907      6.1436|
| 10:  2.2743 -  2.1961 1.00   1296  150 0.4751 0.4719      6.0594      6.0453|
| 11:  2.1961 -  2.1276 0.98   1307  132 0.4755 0.4834      6.0079      6.0402|
| 12:  2.1276 -  2.0669 0.98   1266  144 0.4839 0.5027      5.9328      5.9884|
| 13:  2.0669 -  2.0127 0.96   1267  135 0.4905 0.4719      5.8554       5.791|
| 14:  2.0127 -  1.9637 0.39    514   62 0.5105 0.5130      5.8555      5.8068|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.6887  1417   159  0.73  31.69   0.83     0.78      62969.26|
|  2:  4.6887 -  3.7401  1355   151  0.75  30.84   0.93     0.86      86116.44|
|  3:  3.7401 -  3.2728  1335   142  0.66  39.11   0.95     0.84      93945.51|
|  4:  3.2728 -  2.9760  1334   155  0.57  46.23   0.94     0.77      88283.62|
|  5:  2.9760 -  2.7641  1331   149  0.49  52.81   0.91     0.68      72641.43|
|  6:  2.7641 -  2.6020  1316   141  0.48  53.58   0.92     0.67      62638.50|
|  7:  2.6020 -  2.4723  1311   143  0.47  54.60   0.95     0.65      55450.81|
|  8:  2.4723 -  2.3651  1290   146  0.46  55.09   0.93     0.65      50281.70|
|  9:  2.3651 -  2.2743  1291   150  0.46  55.32   0.96     0.65      45465.84|
| 10:  2.2743 -  2.1961  1296   150  0.45  55.90   0.97     0.66      42218.00|
| 11:  2.1961 -  2.1276  1307   132  0.43  57.60   0.99     0.65      41651.48|
| 12:  2.1276 -  2.0669  1266   144  0.41  59.50   0.95     0.63      38550.85|
| 13:  2.0669 -  2.0127  1267   135  0.38  61.73   0.96     0.61      33740.93|
| 14:  2.0127 -  1.9637   514    62  0.42  58.23   0.98     0.59      26841.67|
|alpha:            min =        0.59 max =            0.86 mean =         0.70|
|beta:             min =    26841.67 max =        93945.51 mean =     58932.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           89.96 mean =        50.29|
|phase err.(test): min =        0.00 max =           89.91 mean =        50.57|
|-----------------------------------------------------------------------------|

============================== 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 = 7.055311              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.010   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.967779              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.016   (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 |  1.776 -  2.089:       10 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.089 -  2.401:       22 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.401 -  2.713:      151 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.713 -  3.026:     1942 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.026 -  3.338:     1907 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.338 -  3.650:     2788 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.650 -  3.963:     4720 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.963 -  4.275:     4417 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.275 -  4.588:     5678 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.588 -  4.900:     6793 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.172 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.776 |       0.331 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    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 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4266   r_free= 0.4260   ksol= 0.00   Bsol= 0.00   scale= 0.919    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.237258                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4163   r_free= 0.4178   ksol= 0.35   Bsol= 50.00   scale= 0.949   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,2.79,-1.75,0.00,-0.00,-0.00); trace/3= 0.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.226685                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.151439              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.079   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.988582              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.753   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4163      final r-factor (work) = 0.3154          |
| start r-factor (free) = 0.4178      final r-factor (free) = 0.3512          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.3215 = 6.15 * 0.50 * 6.2259 + 1.00 * 0.1722                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.8620 = 6.15 * 0.50 * 6.0990 + 1.00 * 0.1031                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3154      final r-factor (work) = 0.2876          |
| start r-factor (free) = 0.3512      final r-factor (free) = 0.3621          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0356 = 0.99 * 1.00 * 6.0990 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9231 = 0.99 * 1.00 * 5.9745 + 1.00 * 0.0168                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.93  18.49    None  None   None       |
|    all(noH): 2823   0      0.00    105.93  18.49    None  None   None       |
|    Sol.    : 438    0      1.44    105.93  38.17    None  None   None       |
|    Mac.    : 2385   0      0.00    69.61   14.88    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.593:  970   |   5:    52.965 -  63.558:   62        |
|      1:    10.593 -  21.186:  985   |   6:    63.558 -  74.151:   30        |
|      2:    21.186 -  31.779:  420   |   7:    74.151 -  84.744:    7        |
|      3:    31.779 -  42.372:  225   |   8:    84.744 -  95.337:    0        |
|      4:    42.372 -  52.965:  123   |   9:    95.337 - 105.930:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2876 r_free = 0.3621             target_work(ml) = 5.982         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2872 r_free = 0.3624             target_work(ml) = 5.981         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2872   r_free= 0.3624   ksol= 0.35   Bsol= 50.00   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,2.79,-1.75,0.00,-0.00,-0.00); trace/3= 0.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.981345                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2868   r_free= 0.3594   ksol= 0.35   Bsol= 67.67   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.13,-0.01,-1.08,-0.00,-0.00,-0.00); trace/3= -0.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.980116                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.246742              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.433   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.491126              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.772  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2868      final r-factor (work) = 0.2082          |
| start r-factor (free) = 0.3594      final r-factor (free) = 0.2679          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.7392 = 8.25 * 0.50 * 5.9747 + 1.00 * 0.1031                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.2300 = 8.25 * 0.50 * 5.8555 + 1.00 * 0.0855                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2082      final r-factor (work) = 0.1833          |
| start r-factor (free) = 0.2679      final r-factor (free) = 0.2407          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8925 = 0.49 * 1.00 * 5.8555 + 1.00 * 0.0167                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7766 = 0.49 * 1.00 * 5.6312 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.45  18.02    None  None   None       |
|    all(noH): 2823   0      0.00    102.45  18.02    None  None   None       |
|    Sol.    : 438    0      4.01    102.45  41.97    None  None   None       |
|    Mac.    : 2385   0      0.00    83.55   13.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.245: 1041   |   5:    51.224 -  61.469:  107        |
|      1:    10.245 -  20.490: 1052   |   6:    61.469 -  71.713:   43        |
|      2:    20.490 -  30.734:  274   |   7:    71.713 -  81.958:    9        |
|      3:    30.734 -  40.979:  164   |   8:    81.958 -  92.203:    1        |
|      4:    40.979 -  51.224:  131   |   9:    92.203 - 102.448:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1833 r_free = 0.2407             target_work(ml) = 5.579         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1833 r_free = 0.2402             target_work(ml) = 5.579         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1833   r_free= 0.2402   ksol= 0.35   Bsol= 67.67   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.13,-0.01,-1.08,-0.00,-0.00,-0.00); trace/3= -0.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.578667                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1826   r_free= 0.2386   ksol= 0.33   Bsol= 59.61   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.44,-1.56,-0.96,-0.00,-0.00,-0.00); trace/3= -1.32                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.573446                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.561461              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.590  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.282658              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.871  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1826      final r-factor (work) = 0.1396          |
| start r-factor (free) = 0.2386      final r-factor (free) = 0.1925          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.9283 = 4.56 * 0.50 * 5.6310 + 1.00 * 0.0855                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5279 = 4.56 * 0.50 * 5.4654 + 1.00 * 0.0628                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1396      final r-factor (work) = 0.1300          |
| start r-factor (free) = 0.1925      final r-factor (free) = 0.1803          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5557 = 0.28 * 1.00 * 5.4654 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5102 = 0.28 * 1.00 * 5.3122 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.83    95.30   17.38    None  None   None       |
|    all(noH): 2823   0      0.83    95.30   17.38    None  None   None       |
|    Sol.    : 438    0      2.08    95.30   41.37    None  None   None       |
|    Mac.    : 2385   0      0.83    85.78   12.97    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.831 -  10.278: 1082   |   5:    48.065 -  57.512:  108        |
|      1:    10.278 -  19.724: 1066   |   6:    57.512 -  66.959:   55        |
|      2:    19.724 -  29.171:  236   |   7:    66.959 -  76.406:   22        |
|      3:    29.171 -  38.618:  136   |   8:    76.406 -  85.853:    5        |
|      4:    38.618 -  48.065:  112   |   9:    85.853 -  95.300:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1300 r_free = 0.1803             target_work(ml) = 5.274         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1298 r_free = 0.1802             target_work(ml) = 5.273         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1298   r_free= 0.1802   ksol= 0.33   Bsol= 59.61   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.44,-1.56,-0.96,-0.00,-0.00,-0.00); trace/3= -1.32                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.273150                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1299   r_free= 0.1793   ksol= 0.32   Bsol= 51.75   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-2.45,-1.37,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.270698                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.394910              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.546  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.263790              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.190  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1299      final r-factor (work) = 0.1192          |
| start r-factor (free) = 0.1793      final r-factor (free) = 0.1661          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4279 = 2.39 * 0.50 * 5.3158 + 1.00 * 0.0625                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3266 = 2.39 * 0.50 * 5.2366 + 1.00 * 0.0560                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1192      final r-factor (work) = 0.1164          |
| start r-factor (free) = 0.1661      final r-factor (free) = 0.1629          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3900 = 0.26 * 1.00 * 5.2366 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3764 = 0.26 * 1.00 * 5.1865 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.78    91.29   17.09    None  None   None       |
|    all(noH): 2823   0      0.78    91.29   17.09    None  None   None       |
|    Sol.    : 438    0      3.13    88.45   40.35    None  None   None       |
|    Mac.    : 2385   0      0.78    91.29   12.81    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:     0.778 -   9.829:  997   |   5:    46.032 -  55.083:  104        |
|      1:     9.829 -  18.880: 1141   |   6:    55.083 -  64.134:   57        |
|      2:    18.880 -  27.931:  240   |   7:    64.134 -  73.185:   24        |
|      3:    27.931 -  36.981:  132   |   8:    73.185 -  82.236:   10        |
|      4:    36.981 -  46.032:  114   |   9:    82.236 -  91.286:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1164 r_free = 0.1629             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1163 r_free = 0.1628             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1628   ksol= 0.32   Bsol= 51.75   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-2.45,-1.37,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.178063                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1628   ksol= 0.32   Bsol= 49.23   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-2.58,-1.34,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.177916                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.354535              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.011  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.207037              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.695  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1163      final r-factor (work) = 0.1167          |
| start r-factor (free) = 0.1628      final r-factor (free) = 0.1605          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5684 = 1.35 * 0.50 * 5.1861 + 1.00 * 0.0560                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5545 = 1.35 * 0.50 * 5.1798 + 1.00 * 0.0464                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1167      final r-factor (work) = 0.1167          |
| start r-factor (free) = 0.1605      final r-factor (free) = 0.1603          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0807 = 0.21 * 1.00 * 5.1798 + 1.00 * 0.0083                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0793 = 0.21 * 1.00 * 5.1753 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.78    91.53   16.84    None  None   None       |
|    all(noH): 2823   0      0.78    91.53   16.84    None  None   None       |
|    Sol.    : 438    0      5.74    83.93   39.30    None  None   None       |
|    Mac.    : 2385   0      0.78    91.53   12.72    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:     0.779 -   9.854: 1014   |   5:    46.154 -  55.229:   98        |
|      1:     9.854 -  18.929: 1143   |   6:    55.229 -  64.304:   50        |
|      2:    18.929 -  28.004:  231   |   7:    64.304 -  73.379:   23        |
|      3:    28.004 -  37.079:  134   |   8:    73.379 -  82.454:    7        |
|      4:    37.079 -  46.154:  119   |   9:    82.454 -  91.528:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1167 r_free = 0.1603             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1166 r_free = 0.1602             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1166   r_free= 0.1602   ksol= 0.32   Bsol= 49.23   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-2.58,-1.34,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.175808                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.6887 0.99   1417  159 0.0985 0.1289      5.3718      5.5656|
|  2:  4.6887 -  3.7401 0.99   1355  151 0.0877 0.1100      5.4633      5.6371|
|  3:  3.7401 -  3.2728 0.99   1335  142 0.1133 0.1612      5.5164      5.8646|
|  4:  3.2728 -  2.9760 0.99   1334  155 0.1302 0.1683      5.4901      5.6225|
|  5:  2.9760 -  2.7641 0.99   1331  149 0.1402 0.1761      5.3463       5.564|
|  6:  2.7641 -  2.6020 0.99   1316  141 0.1248 0.1805      5.2198      5.4467|
|  7:  2.6020 -  2.4723 0.99   1311  143 0.1315 0.1715       5.192      5.3837|
|  8:  2.4723 -  2.3651 0.98   1290  146 0.1231 0.1844      5.0931      5.3798|
|  9:  2.3651 -  2.2743 0.98   1291  150 0.1234 0.1792      5.0717      5.3377|
| 10:  2.2743 -  2.1961 1.00   1296  150 0.1181 0.1697      4.9748       5.192|
| 11:  2.1961 -  2.1276 0.98   1307  132 0.1175 0.1850      4.9785      5.3339|
| 12:  2.1276 -  2.0669 0.98   1266  144 0.1174 0.1643      4.8948      5.1117|
| 13:  2.0669 -  2.0127 0.96   1267  135 0.1190 0.1788      4.8092      5.0791|
| 14:  2.0127 -  1.9637 0.39    514   62 0.1032 0.1495      4.6557      4.8677|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.6887  1417   159  0.94   8.67   0.98     0.95       6642.70|
|  2:  4.6887 -  3.7401  1355   151  0.95   7.99   1.01     1.01       9226.02|
|  3:  3.7401 -  3.2728  1335   142  0.93  11.80   1.02     1.02      10973.98|
|  4:  3.2728 -  2.9760  1334   155  0.91  14.55   1.01     0.98      10806.56|
|  5:  2.9760 -  2.7641  1331   149  0.90  15.67   0.99     0.97       8162.59|
|  6:  2.7641 -  2.6020  1316   141  0.90  16.18   0.98     0.96       7068.96|
|  7:  2.6020 -  2.4723  1311   143  0.90  16.04   1.00     0.97       6466.36|
|  8:  2.4723 -  2.3651  1290   146  0.90  16.00   0.98     0.96       5514.59|
|  9:  2.3651 -  2.2743  1291   150  0.90  15.90   1.00     0.97       5303.88|
| 10:  2.2743 -  2.1961  1296   150  0.90  16.14   1.00     0.96       4526.49|
| 11:  2.1961 -  2.1276  1307   132  0.90  16.48   0.99     0.95       4617.11|
| 12:  2.1276 -  2.0669  1266   144  0.90  16.36   1.01     1.00       4176.48|
| 13:  2.0669 -  2.0127  1267   135  0.90  16.23   1.00     0.99       3422.36|
| 14:  2.0127 -  1.9637   514    62  0.92  14.40   0.98     0.95       2530.81|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2530.81 max =        10973.98 mean =      6603.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.74 mean =        14.39|
|phase err.(test): min =        0.00 max =           89.43 mean =        13.94|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1166   r_free= 0.1602   ksol= 0.32   Bsol= 49.21   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-2.57,-1.26,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.175747                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1166   r_free= 0.1602   ksol= 0.32   Bsol= 49.21   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-2.57,-1.26,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.175747                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.6887 0.99   1417  159 0.0985 0.1289      5.3721       5.566|
|  2:  4.6887 -  3.7401 0.99   1355  151 0.0877 0.1100      5.4635      5.6371|
|  3:  3.7401 -  3.2728 0.99   1335  142 0.1133 0.1612      5.5164      5.8645|
|  4:  3.2728 -  2.9760 0.99   1334  155 0.1302 0.1684      5.4901      5.6224|
|  5:  2.9760 -  2.7641 0.99   1331  149 0.1402 0.1761      5.3462      5.5641|
|  6:  2.7641 -  2.6020 0.99   1316  141 0.1248 0.1803      5.2196      5.4461|
|  7:  2.6020 -  2.4723 0.99   1311  143 0.1315 0.1715      5.1918      5.3836|
|  8:  2.4723 -  2.3651 0.98   1290  146 0.1231 0.1844       5.093      5.3798|
|  9:  2.3651 -  2.2743 0.98   1291  150 0.1234 0.1791      5.0716       5.337|
| 10:  2.2743 -  2.1961 1.00   1296  150 0.1180 0.1699      4.9748       5.193|
| 11:  2.1961 -  2.1276 0.98   1307  132 0.1175 0.1850      4.9786       5.334|
| 12:  2.1276 -  2.0669 0.98   1266  144 0.1173 0.1643      4.8947      5.1119|
| 13:  2.0669 -  2.0127 0.96   1267  135 0.1191 0.1786      4.8089      5.0785|
| 14:  2.0127 -  1.9637 0.39    514   62 0.1031 0.1492      4.6545      4.8663|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.6887  1417   159  0.94   8.67   0.98     0.95       6646.40|
|  2:  4.6887 -  3.7401  1355   151  0.95   7.99   1.02     1.01       9229.13|
|  3:  3.7401 -  3.2728  1335   142  0.93  11.80   1.03     1.02      10975.30|
|  4:  3.2728 -  2.9760  1334   155  0.91  14.55   1.01     0.98      10805.28|
|  5:  2.9760 -  2.7641  1331   149  0.90  15.67   0.99     0.98       8157.02|
|  6:  2.7641 -  2.6020  1316   141  0.90  16.18   0.99     0.97       7065.09|
|  7:  2.6020 -  2.4723  1311   143  0.90  16.03   1.00     0.97       6462.22|
|  8:  2.4723 -  2.3651  1290   146  0.90  15.99   0.98     0.96       5512.32|
|  9:  2.3651 -  2.2743  1291   150  0.90  15.90   1.01     0.97       5301.68|
| 10:  2.2743 -  2.1961  1296   150  0.90  16.15   1.00     0.97       4528.57|
| 11:  2.1961 -  2.1276  1307   132  0.90  16.49   0.99     0.95       4620.99|
| 12:  2.1276 -  2.0669  1266   144  0.90  16.37   1.01     1.01       4177.58|
| 13:  2.0669 -  2.0127  1267   135  0.90  16.22   1.00     0.99       3418.92|
| 14:  2.0127 -  1.9637   514    62  0.92  14.38   0.98     0.95       2524.51|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2524.51 max =        10975.30 mean =      6602.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.74 mean =        14.39|
|phase err.(test): min =        0.00 max =           89.43 mean =        13.94|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.75    91.50   16.81    None  None   None       |
|    all(noH): 2823   0      0.75    91.50   16.81    None  None   None       |
|    Sol.    : 438    0      5.71    83.91   39.27    None  None   None       |
|    Mac.    : 2385   0      0.75    91.50   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:     0.753 -   9.828: 1014   |   5:    46.127 -  55.202:   98        |
|      1:     9.828 -  18.902: 1143   |   6:    55.202 -  64.277:   50        |
|      2:    18.902 -  27.977:  231   |   7:    64.277 -  73.352:   23        |
|      3:    27.977 -  37.052:  134   |   8:    73.352 -  82.427:    7        |
|      4:    37.052 -  46.127:  119   |   9:    82.427 -  91.502:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 311         
Filter by distance & map next to the model:
   mapped sites are within: 0.610 - 4.599
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 307 from: 311
   mapped sites are within: 0.706 - 4.599

peak=    6.213 closest distance to " NE2 GLN A  11 " =    1.343
peak=    5.492 closest distance to " O   HOH Z 126 " =    2.105
peak=    5.478 closest distance to " CG  PRO A  54 " =    1.379
peak=    5.270 closest distance to " O   HOH Z   7 " =    1.580
peak=    5.226 closest distance to " CB  GLN A 223 " =    1.484
peak=    5.198 closest distance to " NH2 ARG A  56 " =    2.055
peak=    5.164 closest distance to " CG  PRO A 198 " =    1.285
peak=    5.051 closest distance to " O   HOH Z 423 " =    1.871
peak=    4.987 closest distance to " CG  PRO A  90 " =    1.201
peak=    4.978 closest distance to " CB  PRO A  54 " =    1.010
peak=    4.973 closest distance to " CB  SER A  63 " =    1.317
peak=    4.942 closest distance to " O   HOH Z 427 " =    2.399
peak=    4.929 closest distance to " O   HOH Z 232 " =    2.239
peak=    4.882 closest distance to " O   HOH Z 417 " =    1.549
peak=    4.813 closest distance to " CG  PRO A 213 " =    1.330
peak=    4.807 closest distance to " O   HOH Z  63 " =    1.698
peak=    4.735 closest distance to " O   HOH Z 287 " =    2.062
peak=    4.699 closest distance to " CB  GLU A 128 " =    1.015
peak=    4.689 closest distance to " O   HOH Z 144 " =    1.718
peak=    4.616 closest distance to " CB  ASN A 148 " =    1.342
peak=    4.590 closest distance to " O   HOH Z 298 " =    2.031
peak=    4.571 closest distance to " ND2 ASN A 187 " =    1.538
peak=    4.569 closest distance to " O   HOH Z 369 " =    2.077
peak=    4.558 closest distance to " CB  ARG A 275 " =    0.925
peak=    4.526 closest distance to " O   HOH Z 425 " =    1.458
peak=    4.415 closest distance to " CA  TYR A  30 " =    1.036
peak=    4.406 closest distance to " O   HOH Z   2 " =    1.825
peak=    4.405 closest distance to " CB  ASN A 187 " =    1.075
peak=    4.402 closest distance to " CB  SER A   3 " =    1.484
peak=    4.394 closest distance to " O   HOH Z  78 " =    1.706
peak=    4.367 closest distance to " CG  PRO A 280 " =    0.841
peak=    4.346 closest distance to " CG2 VAL A 257 " =    1.018
peak=    4.342 closest distance to " O   HOH Z 380 " =    1.792
peak=    4.300 closest distance to " CB  SER A 216 " =    0.833
peak=    4.299 closest distance to " CB  GLN A 183 " =    1.197
peak=    4.265 closest distance to " O   HOH Z   1 " =    1.845
peak=    4.250 closest distance to " CD  ARG A 159 " =    0.839
peak=    4.196 closest distance to " O   HOH Z 214 " =    1.327
peak=    4.194 closest distance to " O   HOH Z 419 " =    2.266
peak=    4.168 closest distance to " CG  LEU A 167 " =    1.266
peak=    4.158 closest distance to " O   HOH Z 132 " =    2.394
peak=    4.153 closest distance to " O   HOH Z 261 " =    1.907
peak=    4.147 closest distance to " C   PRO A 198 " =    1.581
peak=    4.115 closest distance to " O   HOH Z 236 " =    1.573
peak=    4.089 closest distance to " O   HOH Z  78 " =    2.338
peak=    4.079 closest distance to " O   HOH Z   1 " =    1.628
peak=    4.072 closest distance to " ND1 HIS A  86 " =    1.806
peak=    4.052 closest distance to " CB  LEU A 228 " =    1.083
peak=    4.017 closest distance to " N   PHE A 130 " =    1.192
peak=    4.015 closest distance to " O   HOH Z 389 " =    1.951
peak=    3.997 closest distance to " O   HOH Z 146 " =    1.748
peak=    3.981 closest distance to " O   HOH Z   9 " =    2.015
peak=    3.980 closest distance to " CB  TRP A 266 " =    0.993
peak=    3.976 closest distance to " O   HOH Z 272 " =    1.830
peak=    3.972 closest distance to " OD1BASN A 224 " =    2.243
peak=    3.965 closest distance to " O   HOH Z  10 " =    1.778
peak=    3.958 closest distance to " CG2 THR A 221 " =    1.040
peak=    3.955 closest distance to " O   HOH Z 316 " =    3.119
peak=    3.944 closest distance to " CG  PRO A 243 " =    1.115
peak=    3.925 closest distance to " O   HOH Z 394 " =    1.670
peak=    3.920 closest distance to " CB  GLU A 152 " =    1.353
peak=    3.914 closest distance to " O   HOH Z 193 " =    1.851
peak=    3.910 closest distance to " CG  TRP A 179 " =    2.248
peak=    3.909 closest distance to " CB  ASP A 124 " =    0.864
peak=    3.906 closest distance to " O   SER A  87 " =    2.231
peak=    3.902 closest distance to " O   HOH Z 371 " =    1.974
peak=    3.901 closest distance to " O   HOH Z 258 " =    2.279
peak=    3.896 closest distance to " CA  THR A 264 " =    0.848
peak=    3.869 closest distance to " O   HOH Z  40 " =    2.210
peak=    3.858 closest distance to " O   HOH Z 193 " =    1.727
peak=    3.842 closest distance to " O   HOH Z 234 " =    3.849
peak=    3.841 closest distance to " O   HOH Z 437 " =    1.975
peak=    3.838 closest distance to " CB  THR A 157 " =    1.144
peak=    3.832 closest distance to " O   HOH Z 133 " =    2.444
peak=    3.822 closest distance to " CB  LEU A 143 " =    1.172
peak=    3.817 closest distance to " N   GLN A 278 " =    1.040
peak=    3.810 closest distance to " CA  ILE A 234 " =    1.019
peak=    3.809 closest distance to " CB  ARG A 190 " =    1.734
peak=    3.806 closest distance to " O   HOH Z  44 " =    2.884
peak=    3.799 closest distance to " CA  GLY A 241 " =    3.716
peak=    3.794 closest distance to " CG1 ILE A  33 " =    1.239
peak=    3.790 closest distance to " O   HOH Z 217 " =    2.776
peak=    3.782 closest distance to " OD1 ASN A  69 " =    2.618
peak=    3.775 closest distance to " O   HOH Z 171 " =    2.777
peak=    3.773 closest distance to " OD2 ASP A 286 " =    2.802
peak=    3.771 closest distance to " O   ASN A 209 " =    1.414
peak=    3.758 closest distance to " CD1 LEU A 300 " =    1.219
peak=    3.747 closest distance to " O   HOH Z 392 " =    1.317
peak=    3.746 closest distance to " CB  ASN A  39 " =    0.873
peak=    3.734 closest distance to " OG BSER A  99 " =    2.255
peak=    3.727 closest distance to " CA  ALA A 233 " =    1.388
peak=    3.720 closest distance to " CA  SER A  87 " =    1.017
peak=    3.718 closest distance to " CA  ARG A 195 " =    1.418
peak=    3.715 closest distance to " CZ  PHE A 192 " =    0.924
peak=    3.705 closest distance to " O   HOH Z  49 " =    1.404
peak=    3.702 closest distance to " O   HOH Z 352 " =    1.666
peak=    3.698 closest distance to " CD BLYS A 290 " =    1.065
peak=    3.689 closest distance to " O   HOH Z   3 " =    2.054
peak=    3.685 closest distance to " CB  VAL A 265 " =    1.287
peak=    3.682 closest distance to " O   HOH Z 403 " =    1.404
peak=    3.681 closest distance to " O   HOH Z  59 " =    2.058
peak=    3.671 closest distance to " O   HOH Z 222 " =    2.464
peak=    3.663 closest distance to " O   HOH Z 116 " =    2.879
peak=    3.657 closest distance to " CB  GLU A 277 " =    3.599
peak=    3.653 closest distance to " CA  ASN A 215 " =    1.128
peak=    3.649 closest distance to " NE AARG A 275 " =    1.469
peak=    3.640 closest distance to " CA  ALA A 299 " =    0.880
peak=    3.632 closest distance to " NH1AARG A 145 " =    1.149
peak=    3.632 closest distance to " O   HOH Z  21 " =    1.673
peak=    3.629 closest distance to " O   THR A 220 " =    1.492
peak=    3.625 closest distance to " O   HOH Z 368 " =    3.643
peak=    3.614 closest distance to " O   HOH Z  44 " =    1.701
peak=    3.608 closest distance to " CA  TYR A  30 " =    1.077
peak=    3.596 closest distance to " O   HOH Z 175 " =    2.124
peak=    3.594 closest distance to " O   HOH Z  17 " =    1.976
peak=    3.590 closest distance to " NZ BLYS A 290 " =    1.032
peak=    3.584 closest distance to " O   HOH Z 250 " =    1.482
peak=    3.578 closest distance to " CD  ARG A  66 " =    2.093
peak=    3.578 closest distance to " CB  ASP A 132 " =    4.020
peak=    3.577 closest distance to " N   TYR A  15 " =    0.898
peak=    3.576 closest distance to " N   SER A  97 " =    0.851
peak=    3.575 closest distance to " O   HOH Z 371 " =    2.714
peak=    3.574 closest distance to " CA  LEU A 101 " =    1.645
peak=    3.572 closest distance to " O   HOH Z 139 " =    1.225
peak=    3.567 closest distance to " CB  ALA A 114 " =    0.917
peak=    3.562 closest distance to " O   TYR A 116 " =    1.346
peak=    3.556 closest distance to " O   HOH Z 365 " =    2.718
peak=    3.556 closest distance to " O   HOH Z  61 " =    1.556
peak=    3.553 closest distance to " CB  LYS A 117 " =    1.241
peak=    3.549 closest distance to " O   HOH Z 219 " =    2.355
peak=    3.546 closest distance to " CB  ASN A 142 " =    0.906
peak=    3.542 closest distance to " O   HOH Z 183 " =    1.486
peak=    3.532 closest distance to " CB  MET A  40 " =    0.830
peak=    3.531 closest distance to " N   ASN A 127 " =    1.385
peak=    3.530 closest distance to " O   HOH Z 313 " =    1.742
peak=    3.526 closest distance to " CG1 ILE A 151 " =    1.051
peak=    3.525 closest distance to " NH1 ARG A  14 " =    0.956
peak=    3.521 closest distance to " CB  ARG A 139 " =    0.955
peak=    3.517 closest distance to " CB  ALA A   1 " =    4.599
peak=    3.511 closest distance to " O   HOH Z  88 " =    3.077
peak=    3.511 closest distance to " CB  SER A 276 " =    1.220
peak=    3.507 closest distance to " O   HOH Z 144 " =    2.279
peak=    3.505 closest distance to " CA  ALA A 154 " =    0.949
peak=    3.500 closest distance to " O   HOH Z  88 " =    2.678
peak=    3.499 closest distance to " CA  GLY A 267 " =    1.267
peak=    3.497 closest distance to " CB  VAL A 202 " =    1.635
peak=    3.497 closest distance to " O   HOH Z 225 " =    1.453
peak=    3.494 closest distance to " O   HOH Z 195 " =    1.396
peak=    3.483 closest distance to " O   HOH Z 272 " =    2.085
peak=    3.472 closest distance to " NZ  LYS A 117 " =    1.247
peak=    3.469 closest distance to " CG  MET A 113 " =    1.248
peak=    3.463 closest distance to " O   HOH Z 115 " =    1.620
peak=    3.458 closest distance to " O   HOH Z 362 " =    2.023
peak=    3.458 closest distance to " CB  TRP A 179 " =    1.439
peak=    3.457 closest distance to " CB  ALA A  34 " =    1.169
peak=    3.455 closest distance to " CE  LYS A  76 " =    0.839
peak=    3.452 closest distance to " O   HOH Z  58 " =    1.792
peak=    3.451 closest distance to " O   HOH Z 327 " =    1.725
peak=    3.450 closest distance to " CB  SER A  62 " =    1.193
peak=    3.446 closest distance to " O   HOH Z 345 " =    1.785
peak=    3.444 closest distance to " CZ  PHE A 218 " =    1.051
peak=    3.443 closest distance to " CB  ALA A 180 " =    1.327
peak=    3.441 closest distance to " O   HOH Z 302 " =    1.649
peak=    3.434 closest distance to " O   HOH Z 213 " =    2.238
peak=    3.426 closest distance to " O   HOH Z 214 " =    1.730
peak=    3.425 closest distance to " O   HOH Z 126 " =    1.432
peak=    3.425 closest distance to " CB  ARG A  79 " =    1.291
peak=    3.423 closest distance to " O   HOH Z 119 " =    1.595
peak=    3.419 closest distance to " NE2 GLN A  73 " =    3.730
peak=    3.411 closest distance to " CB  ALA A  10 " =    0.840
peak=    3.399 closest distance to " O   HOH Z  61 " =    1.661
peak=    3.396 closest distance to " O   HOH Z 108 " =    1.544
peak=    3.395 closest distance to " CA  ARG A 102 " =    1.217
peak=    3.393 closest distance to " O   HOH Z 193 " =    2.053
peak=    3.393 closest distance to " O   HOH Z 180 " =    2.074
peak=    3.392 closest distance to " OG  SER A  62 " =    2.957
peak=    3.391 closest distance to " O   HOH Z  50 " =    1.668
peak=    3.391 closest distance to " CB  GLU A 236 " =    1.215
peak=    3.389 closest distance to " O   HOH Z  67 " =    1.690
peak=    3.386 closest distance to " O   HOH Z 209 " =    2.311
peak=    3.381 closest distance to " CD  PRO A 243 " =    1.735
peak=    3.380 closest distance to " CB  PRO A 198 " =    0.835
peak=    3.377 closest distance to " NE2 GLN A  58 " =    3.729
peak=    3.377 closest distance to " O   HOH Z  68 " =    1.944
peak=    3.376 closest distance to " CB  TYR A 116 " =    0.912
peak=    3.375 closest distance to " CB  GLU A 152 " =    1.403
peak=    3.373 closest distance to " CG  ARG A 159 " =    0.790
peak=    3.367 closest distance to " CB  SER A 210 " =    0.777
peak=    3.363 closest distance to " CB  PRO A 243 " =    1.193
peak=    3.363 closest distance to " CG  GLN A  88 " =    1.109
peak=    3.362 closest distance to " ND2 ASN A  60 " =    3.091
peak=    3.358 closest distance to " O   HOH Z 344 " =    3.254
peak=    3.358 closest distance to " O   HOH Z 135 " =    1.685
peak=    3.356 closest distance to " O   HOH Z 286 " =    2.265
peak=    3.354 closest distance to " O   HOH Z 409 " =    2.282
peak=    3.353 closest distance to " O   HOH Z 305 " =    3.736
peak=    3.350 closest distance to " N   ALA A   1 " =    2.245
peak=    3.350 closest distance to " O   HOH Z 184 " =    1.716
peak=    3.346 closest distance to " O   ALA A   1 " =    1.555
peak=    3.343 closest distance to " CB  ILE A 120 " =    1.173
peak=    3.343 closest distance to " CB  MET A  47 " =    1.015
peak=    3.332 closest distance to " CD2 LEU A 255 " =    1.607
peak=    3.331 closest distance to " CG  GLN A 278 " =    3.747
peak=    3.321 closest distance to " O   HOH Z 108 " =    1.949
peak=    3.321 closest distance to " CA  TYR A 116 " =    1.349
peak=    3.320 closest distance to " O   HOH Z 158 " =    2.710
peak=    3.318 closest distance to " N   SER A 134 " =    1.344
peak=    3.316 closest distance to " NH1BARG A 145 " =    1.339
peak=    3.313 closest distance to " O   HOH Z 172 " =    2.682
peak=    3.310 closest distance to " CB  TYR A 169 " =    0.968
peak=    3.308 closest distance to " OD1 ASN A 217 " =    1.486
peak=    3.306 closest distance to " CB  ALA A  43 " =    0.891
peak=    3.306 closest distance to " O   HOH Z  59 " =    1.552
peak=    3.298 closest distance to " O   HOH Z 145 " =    1.497
peak=    3.298 closest distance to " CB  HIS A 108 " =    0.793
peak=    3.297 closest distance to " CA  ALA A  21 " =    1.215
peak=    3.296 closest distance to " CE3 TRP A 274 " =    1.242
peak=    3.295 closest distance to " O   HOH Z 368 " =    1.870
peak=    3.292 closest distance to " OG BSER A 258 " =    0.811
peak=    3.291 closest distance to " O   HOH Z 207 " =    2.180
peak=    3.291 closest distance to " N   ARG A 156 " =    1.346
peak=    3.278 closest distance to " O   HOH Z 128 " =    2.160
peak=    3.271 closest distance to " O   HOH Z 133 " =    1.608
peak=    3.269 closest distance to " CZ  PHE A  38 " =    1.324
peak=    3.268 closest distance to " CD  ARG A 219 " =    1.045
peak=    3.265 closest distance to " O   HOH Z 405 " =    1.525
peak=    3.264 closest distance to " CA  MET A 105 " =    0.870
peak=    3.264 closest distance to " O   HOH Z 425 " =    1.908
peak=    3.260 closest distance to " O   HOH Z 295 " =    1.563
peak=    3.258 closest distance to " O   HOH Z 422 " =    2.773
peak=    3.255 closest distance to " O   HOH Z 289 " =    1.669
peak=    3.255 closest distance to " N   CYS A 260 " =    0.723
peak=    3.249 closest distance to " O   HOH Z  64 " =    2.370
peak=    3.248 closest distance to " O   HOH Z 134 " =    1.239
peak=    3.247 closest distance to " O   HOH Z 426 " =    1.891
peak=    3.246 closest distance to " CG  GLN A 144 " =    0.918
peak=    3.244 closest distance to " O   HOH Z 216 " =    2.619
peak=    3.241 closest distance to " CE1 TYR A 186 " =    1.418
peak=    3.241 closest distance to " O   HOH Z 345 " =    3.423
peak=    3.239 closest distance to " OE2 GLU A  53 " =    2.079
peak=    3.238 closest distance to " O   HOH Z 288 " =    2.034
peak=    3.237 closest distance to " NH2BARG A 145 " =    2.104
peak=    3.234 closest distance to " CA  THR A 221 " =    0.931
peak=    3.232 closest distance to " CB  SER A 212 " =    1.237
peak=    3.231 closest distance to " O   HOH Z 273 " =    2.751
peak=    3.228 closest distance to " CA  SER A  95 " =    1.026
peak=    3.226 closest distance to " CB  ASP A 171 " =    0.796
peak=    3.224 closest distance to " CB  GLU A 152 " =    1.400
peak=    3.222 closest distance to " O   HOH Z 329 " =    3.765
peak=    3.220 closest distance to " O   HOH Z 122 " =    1.622
peak=    3.219 closest distance to " CG1 VAL A 153 " =    0.886
peak=    3.217 closest distance to " CE AMET A  47 " =    1.388
peak=    3.211 closest distance to " O   HOH Z 109 " =    2.559
peak=    3.204 closest distance to " O   HOH Z 217 " =    1.698
peak=    3.203 closest distance to " O   HOH Z 145 " =    2.141
peak=    3.202 closest distance to " O   HOH Z 148 " =    3.440
peak=    3.201 closest distance to " O   HOH Z 238 " =    3.607
peak=    3.195 closest distance to " N   SER A 271 " =    0.988
peak=    3.190 closest distance to " O   HOH Z 207 " =    1.685
peak=    3.189 closest distance to " N   VAL A 296 " =    1.695
peak=    3.187 closest distance to " CA  ALA A 291 " =    0.944
peak=    3.184 closest distance to " NZ  LYS A  76 " =    1.521
peak=    3.183 closest distance to " CH2 TRP A 150 " =    0.983
peak=    3.179 closest distance to " CB  GLU A 277 " =    0.987
peak=    3.178 closest distance to " NE  ARG A  66 " =    3.653
peak=    3.175 closest distance to " O   MET A 105 " =    1.780
peak=    3.169 closest distance to " CA  ALA A  51 " =    1.030
peak=    3.162 closest distance to " N   SER A 210 " =    1.035
peak=    3.161 closest distance to " O   HOH Z 130 " =    1.989
peak=    3.159 closest distance to " CB  ALA A 114 " =    1.430
peak=    3.158 closest distance to " O   HOH Z 113 " =    1.868
peak=    3.155 closest distance to " O   HOH Z  51 " =    1.742
peak=    3.150 closest distance to " CA  ILE A 263 " =    1.115
peak=    3.144 closest distance to " CA  ASP A 124 " =    0.706
peak=    3.143 closest distance to " O   HOH Z 271 " =    2.317
peak=    3.143 closest distance to " O  BHOH Z 338 " =    2.391
peak=    3.141 closest distance to " CB  LEU A 300 " =    0.961
peak=    3.140 closest distance to " ND1 HIS A  81 " =    1.739
peak=    3.140 closest distance to " OH  TYR A 186 " =    1.048
peak=    3.140 closest distance to " N   ASN A  39 " =    1.372
peak=    3.139 closest distance to " CB  VAL A 250 " =    1.011
peak=    3.131 closest distance to " CB  PRO A  90 " =    1.122
peak=    3.127 closest distance to " O   HOH Z 284 " =    1.433
peak=    3.127 closest distance to " O   HOH Z 227 " =    1.967
peak=    3.126 closest distance to " CD  LYS A 166 " =    1.367
peak=    3.125 closest distance to " CA  ALA A 158 " =    1.088
peak=    3.125 closest distance to " CB  GLU A 175 " =    0.934
peak=    3.123 closest distance to " O   CYS A 168 " =    1.430
peak=    3.123 closest distance to " O   HOH Z 189 " =    2.220
peak=    3.109 closest distance to " CE3 TRP A  85 " =    0.873
peak=    3.099 closest distance to " CB  ARG A 138 " =    0.945
peak=    3.098 closest distance to " O   HOH Z  30 " =    1.755
peak=    3.095 closest distance to " OG  SER A  22 " =    2.854
peak=    3.091 closest distance to " CA  TYR A 186 " =    1.561
peak=    3.087 closest distance to " O   HOH Z 413 " =    1.475
peak=    3.086 closest distance to " O   HOH Z 154 " =    1.961
peak=    3.086 closest distance to " CB  ASN A 215 " =    1.131
peak=    3.084 closest distance to " O   GLY A 302 " =    1.617
peak=    3.084 closest distance to " CG  GLU A 277 " =    2.005
peak=    3.080 closest distance to " O   HOH Z 128 " =    2.053
peak=    3.077 closest distance to " ND2 ASN A  60 " =    3.728
peak=    3.070 closest distance to " O   HOH Z 423 " =    1.995
peak=    3.052 closest distance to " CB  ALA A   7 " =    1.180
peak=    3.047 closest distance to " O   HOH Z  43 " =    2.190
peak=    3.042 closest distance to " O   PRO A 198 " =    1.278
peak=    3.016 closest distance to " O   HOH Z  73 " =    1.779
peak=    3.008 closest distance to " CA  ALA A 233 " =    0.937

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 188         
Filter by distance & map next to the model:
   mapped sites are within: 0.577 - 5.719
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 187 from: 188
   mapped sites are within: 0.729 - 5.719

peak=   -4.672 closest distance to " O   PRO A 198 " =    1.237
peak=   -4.660 closest distance to " CB  PRO A 243 " =    2.522
peak=   -4.573 closest distance to " O   HOH Z  65 " =    0.964
peak=   -4.515 closest distance to " O   HOH Z 290 " =    1.062
peak=   -4.279 closest distance to " O   HOH Z 231 " =    0.864
peak=   -4.260 closest distance to " CA  GLY A  98 " =    1.830
peak=   -4.244 closest distance to " O   HOH Z 377 " =    1.548
peak=   -4.212 closest distance to " O   HOH Z  52 " =    1.290
peak=   -4.163 closest distance to " CD  ARG A  14 " =    3.261
peak=   -4.118 closest distance to " O   HOH Z 407 " =    3.290
peak=   -4.116 closest distance to " C   ALA A 158 " =    1.562
peak=   -4.100 closest distance to " CG  MET A 105 " =    0.924
peak=   -4.019 closest distance to " O   HOH Z 266 " =    4.729
peak=   -3.962 closest distance to " CD1 LEU A 255 " =    3.038
peak=   -3.960 closest distance to " O   HOH Z 351 " =    1.511
peak=   -3.954 closest distance to " O   HOH Z 185 " =    2.034
peak=   -3.945 closest distance to " OG BSER A 134 " =    1.353
peak=   -3.914 closest distance to " O   HOH Z 231 " =    1.870
peak=   -3.893 closest distance to " CZ3 TRP A 179 " =    1.177
peak=   -3.871 closest distance to " N   THR A 157 " =    1.556
peak=   -3.863 closest distance to " OD1 ASP A 191 " =    1.883
peak=   -3.837 closest distance to " N   ALA A  43 " =    2.487
peak=   -3.813 closest distance to " CB  ALA A 291 " =    2.176
peak=   -3.806 closest distance to " CB  ALA A 248 " =    1.988
peak=   -3.752 closest distance to " CG  ASP A 231 " =    0.786
peak=   -3.744 closest distance to " CD  ARG A 156 " =    2.034
peak=   -3.741 closest distance to " O   HOH Z 198 " =    2.084
peak=   -3.732 closest distance to " CB  ASP A  27 " =    2.441
peak=   -3.730 closest distance to " O   HOH Z 389 " =    1.878
peak=   -3.716 closest distance to " O   SER A 135 " =    1.464
peak=   -3.715 closest distance to " O   HOH Z 313 " =    1.807
peak=   -3.711 closest distance to " ND2 ASN A 285 " =    2.112
peak=   -3.700 closest distance to " O   HOH Z 211 " =    1.465
peak=   -3.687 closest distance to " CA  GLY A 203 " =    2.305
peak=   -3.674 closest distance to " OD1 ASN A 148 " =    1.672
peak=   -3.663 closest distance to " O   HOH Z  38 " =    1.445
peak=   -3.648 closest distance to " OE1 GLN A  88 " =    1.064
peak=   -3.646 closest distance to " CG1 VAL A 112 " =    3.019
peak=   -3.644 closest distance to " O   HOH Z 166 " =    1.231
peak=   -3.643 closest distance to " O   TYR A 247 " =    2.850
peak=   -3.629 closest distance to " O   HOH Z  60 " =    2.504
peak=   -3.623 closest distance to " CB  CYS A 254 " =    1.989
peak=   -3.618 closest distance to " O   HOH Z 298 " =    2.556
peak=   -3.618 closest distance to " O   PRO A 243 " =    2.376
peak=   -3.615 closest distance to " CE3 TRP A 123 " =    1.429
peak=   -3.588 closest distance to " OG  SER A  87 " =    1.316
peak=   -3.570 closest distance to " ND2 ASN A  45 " =    1.121
peak=   -3.559 closest distance to " CA  GLY A 241 " =    2.189
peak=   -3.551 closest distance to " O   HOH Z 298 " =    1.127
peak=   -3.544 closest distance to " ND2 ASN A 249 " =    2.306
peak=   -3.537 closest distance to " O   SER A  22 " =    2.638
peak=   -3.527 closest distance to " O   HOH Z 385 " =    1.927
peak=   -3.526 closest distance to " O   HOH Z 384 " =    2.886
peak=   -3.522 closest distance to " OD2 ASP A 191 " =    1.545
peak=   -3.522 closest distance to " CG  ARG A 269 " =    2.530
peak=   -3.521 closest distance to " CB  PHE A 283 " =    2.775
peak=   -3.514 closest distance to " N   ASP A 171 " =    2.514
peak=   -3.511 closest distance to " OG  SER A   3 " =    1.588
peak=   -3.509 closest distance to " CD2 TYR A 293 " =    1.857
peak=   -3.496 closest distance to " C   LEU A 222 " =    0.729
peak=   -3.496 closest distance to " NH1AARG A 275 " =    1.899
peak=   -3.494 closest distance to " O   ARG A 145 " =    1.480
peak=   -3.491 closest distance to " C   HIS A 108 " =    1.139
peak=   -3.490 closest distance to " O   HOH Z  28 " =    1.713
peak=   -3.487 closest distance to " O   HOH Z 111 " =    1.889
peak=   -3.478 closest distance to " O   HOH Z  13 " =    1.608
peak=   -3.476 closest distance to " O   HOH Z  43 " =    1.660
peak=   -3.474 closest distance to " O   HOH Z 282 " =    4.642
peak=   -3.463 closest distance to " O   HOH Z 191 " =    5.399
peak=   -3.463 closest distance to " C   LEU A 143 " =    1.230
peak=   -3.462 closest distance to " CB  ALA A  43 " =    2.413
peak=   -3.458 closest distance to " O   VAL A 189 " =    2.416
peak=   -3.457 closest distance to " CZ  PHE A  59 " =    1.491
peak=   -3.453 closest distance to " CB  ALA A 248 " =    2.507
peak=   -3.452 closest distance to " CG2 THR A  18 " =    2.808
peak=   -3.452 closest distance to " O   HOH Z   1 " =    1.329
peak=   -3.449 closest distance to " CG  GLN A 223 " =    2.186
peak=   -3.434 closest distance to " NH2 ARG A  79 " =    1.894
peak=   -3.432 closest distance to " CG1 VAL A 197 " =    2.272
peak=   -3.428 closest distance to " CE  LYS A  76 " =    2.892
peak=   -3.418 closest distance to " N   GLN A  58 " =    1.788
peak=   -3.418 closest distance to " O   HOH Z 352 " =    2.104
peak=   -3.417 closest distance to " CB  ALA A   9 " =    2.423
peak=   -3.417 closest distance to " O   ASP A 162 " =    2.256
peak=   -3.414 closest distance to " O   HOH Z 152 " =    4.885
peak=   -3.411 closest distance to " O   ILE A  49 " =    1.724
peak=   -3.410 closest distance to " O   HOH Z 281 " =    2.936
peak=   -3.409 closest distance to " CG2 VAL A 232 " =    2.056
peak=   -3.408 closest distance to " CE  MET A  93 " =    1.076
peak=   -3.407 closest distance to " CB  ASN A  39 " =    2.244
peak=   -3.397 closest distance to " NH2AARG A 275 " =    5.520
peak=   -3.396 closest distance to " CD  GLN A  58 " =    1.272
peak=   -3.394 closest distance to " O   VAL A  67 " =    2.492
peak=   -3.386 closest distance to " CD1 LEU A 101 " =    2.300
peak=   -3.366 closest distance to " O   HOH Z 168 " =    1.829
peak=   -3.366 closest distance to " CD  GLN A 223 " =    0.918
peak=   -3.365 closest distance to " O   ALA A 180 " =    1.175
peak=   -3.360 closest distance to " OG BSER A 134 " =    1.680
peak=   -3.359 closest distance to " C   GLY A  13 " =    0.999
peak=   -3.357 closest distance to " ND2 ASN A  45 " =    1.960
peak=   -3.356 closest distance to " O   HOH Z 300 " =    1.994
peak=   -3.351 closest distance to " O   HOH Z  11 " =    1.834
peak=   -3.344 closest distance to " CB  PRO A  54 " =    2.432
peak=   -3.343 closest distance to " O   HOH Z 102 " =    1.609
peak=   -3.341 closest distance to " CG  GLN A  88 " =    0.800
peak=   -3.341 closest distance to " CD1 PHE A  59 " =    1.982
peak=   -3.340 closest distance to " O   PRO A 163 " =    1.932
peak=   -3.340 closest distance to " O   HOH Z 438 " =    1.051
peak=   -3.336 closest distance to " O   HOH Z  39 " =    1.168
peak=   -3.336 closest distance to " O   HOH Z  24 " =    1.167
peak=   -3.335 closest distance to " O   ALA A   1 " =    1.094
peak=   -3.333 closest distance to " CB  PHE A 192 " =    1.668
peak=   -3.330 closest distance to " CE2 TYR A  30 " =    2.617
peak=   -3.326 closest distance to " C   ASN A 285 " =    2.384
peak=   -3.325 closest distance to " O   HOH Z  60 " =    1.915
peak=   -3.305 closest distance to " CB  TYR A  15 " =    2.131
peak=   -3.303 closest distance to " O   PRO A 243 " =    2.143
peak=   -3.299 closest distance to " O   HOH Z  51 " =    0.939
peak=   -3.299 closest distance to " O   VAL A  67 " =    2.735
peak=   -3.295 closest distance to " O   HOH Z 317 " =    1.547
peak=   -3.293 closest distance to " O   ALA A  51 " =    1.505
peak=   -3.290 closest distance to " C   GLU A 236 " =    0.844
peak=   -3.288 closest distance to " O   PHE A 218 " =    1.336
peak=   -3.288 closest distance to " CA  GLY A 133 " =    2.021
peak=   -3.287 closest distance to " ND2 ASN A 187 " =    1.345
peak=   -3.285 closest distance to " O   HOH Z  90 " =    2.775
peak=   -3.281 closest distance to " O   HOH Z  76 " =    1.283
peak=   -3.266 closest distance to " O   HOH Z 222 " =    0.916
peak=   -3.262 closest distance to " CB  CYS A 201 " =    2.338
peak=   -3.257 closest distance to " CE1 TYR A 169 " =    2.508
peak=   -3.250 closest distance to " O   HOH Z 372 " =    2.391
peak=   -3.247 closest distance to " OD2 ASP A  27 " =    1.709
peak=   -3.245 closest distance to " CD  GLN A  58 " =    0.877
peak=   -3.245 closest distance to " CB  ASP A 132 " =    2.307
peak=   -3.240 closest distance to " NE  ARG A  36 " =    1.999
peak=   -3.240 closest distance to " O   VAL A 197 " =    1.748
peak=   -3.234 closest distance to " N   GLN A 122 " =    1.456
peak=   -3.230 closest distance to " N   ASP A 270 " =    1.342
peak=   -3.228 closest distance to " OXT GLY A 302 " =    3.116
peak=   -3.227 closest distance to " CG  LEU A 101 " =    2.478
peak=   -3.226 closest distance to " O   HOH Z 409 " =    5.719
peak=   -3.221 closest distance to " CA  GLY A  57 " =    1.984
peak=   -3.220 closest distance to " NE2 GLN A  58 " =    3.027
peak=   -3.218 closest distance to " ND2BASN A 224 " =    1.556
peak=   -3.214 closest distance to " O   GLN A 240 " =    1.931
peak=   -3.211 closest distance to " O   HOH Z 388 " =    2.139
peak=   -3.209 closest distance to " OD2 ASP A 171 " =    1.992
peak=   -3.207 closest distance to " C   ALA A 114 " =    2.342
peak=   -3.207 closest distance to " O   PRO A 198 " =    1.297
peak=   -3.204 closest distance to " CB  SER A  63 " =    3.401
peak=   -3.203 closest distance to " CB  PRO A 163 " =    2.499
peak=   -3.199 closest distance to " CE  MET A 105 " =    2.401
peak=   -3.196 closest distance to " NE2 GLN A 278 " =    1.906
peak=   -3.188 closest distance to " CG  PRO A 163 " =    2.411
peak=   -3.182 closest distance to " O   HOH Z 390 " =    2.384
peak=   -3.180 closest distance to " O   SER A  62 " =    2.169
peak=   -3.174 closest distance to " CB  TRP A  85 " =    2.391
peak=   -3.168 closest distance to " CG  LEU A 282 " =    2.368
peak=   -3.168 closest distance to " O   HOH Z 359 " =    3.294
peak=   -3.166 closest distance to " OG  SER A  26 " =    1.107
peak=   -3.165 closest distance to " N   ARG A 159 " =    2.042
peak=   -3.161 closest distance to " O   HOH Z  73 " =    2.322
peak=   -3.158 closest distance to " O   GLY A  17 " =    1.217
peak=   -3.157 closest distance to " CA  ALA A  34 " =    2.459
peak=   -3.157 closest distance to " O   HOH Z 417 " =    2.250
peak=   -3.157 closest distance to " O   HOH Z 432 " =    3.622
peak=   -3.155 closest distance to " OD2 ASP A 171 " =    1.730
peak=   -3.153 closest distance to " CD  LYS A 289 " =    2.389
peak=   -3.150 closest distance to " O   HOH Z 247 " =    1.763
peak=   -3.148 closest distance to " O   HOH Z 292 " =    1.452
peak=   -3.143 closest distance to " O   HOH Z 345 " =    2.185
peak=   -3.135 closest distance to " O   HOH Z 426 " =    2.278
peak=   -3.127 closest distance to " O   HOH Z  49 " =    1.765
peak=   -3.115 closest distance to " CA  ILE A 263 " =    0.985
peak=   -3.108 closest distance to " N   SER A 212 " =    1.840
peak=   -3.108 closest distance to " O   LEU A 101 " =    2.420
peak=   -3.106 closest distance to " O   HOH Z 410 " =    2.361
peak=   -3.105 closest distance to " O   HOH Z 198 " =    1.675
peak=   -3.102 closest distance to " OG  SER A  97 " =    2.139
peak=   -3.101 closest distance to " C   MET A 188 " =    1.596
peak=   -3.101 closest distance to " OE1 GLN A  89 " =    1.902
peak=   -3.097 closest distance to " CZ BARG A 275 " =    1.590
peak=   -3.093 closest distance to " NH2 ARG A 219 " =    1.844
peak=   -3.060 closest distance to " CD  GLN A 223 " =    1.333
peak=   -3.051 closest distance to " O   GLY A  80 " =    2.370
peak=   -3.038 closest distance to " CG1 VAL A  78 " =    2.477
peak=   -3.038 closest distance to " CG  TRP A 266 " =    1.764

================= 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    :  0.4266 0.4260   6.237258e+00   6.233419e+00
   1_bss:  0.4163 0.4178   6.226685e+00   6.220152e+00
   1_xyz:  0.3154 0.3512   6.032621e+00   6.088469e+00
   1_adp:  0.2876 0.3621   5.982144e+00   6.106281e+00
   1_occ:  0.2872 0.3624   5.981345e+00   6.106017e+00
   2_bss:  0.2868 0.3594   5.980116e+00   6.103262e+00
   2_xyz:  0.2082 0.2679   5.691684e+00   5.866169e+00
   2_adp:  0.1833 0.2407   5.579442e+00   5.780244e+00
   2_occ:  0.1833 0.2402   5.578667e+00   5.779260e+00
   3_bss:  0.1826 0.2386   5.573446e+00   5.772952e+00
   3_xyz:  0.1396 0.1925   5.339771e+00   5.575944e+00
   3_adp:  0.1300 0.1803   5.273717e+00   5.509705e+00
   3_occ:  0.1298 0.1802   5.273150e+00   5.509143e+00
   4_bss:  0.1299 0.1793   5.270698e+00   5.505958e+00
   4_xyz:  0.1192 0.1661   5.194610e+00   5.434346e+00
   4_adp:  0.1164 0.1629   5.178510e+00   5.420413e+00
   4_occ:  0.1163 0.1628   5.178063e+00   5.420126e+00
   5_bss:  0.1163 0.1628   5.177916e+00   5.419966e+00
   5_xyz:  0.1167 0.1605   5.175203e+00   5.410212e+00
   5_adp:  0.1167 0.1603   5.176208e+00   5.411251e+00
   5_occ:  0.1166 0.1602   5.175808e+00   5.410831e+00
   5_bss:  0.1166 0.1602   5.175747e+00   5.410763e+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:  0.352  50.001  -0.483   2.795  -1.747   0.000  -0.000  -0.000
   1_xyz:  0.352  50.001  -0.483   2.795  -1.747   0.000  -0.000  -0.000
   1_adp:  0.352  50.001  -0.483   2.795  -1.747   0.000  -0.000  -0.000
   1_occ:  0.352  50.001  -0.483   2.795  -1.747   0.000  -0.000  -0.000
   2_bss:  0.350  67.668  -1.132  -0.011  -1.079  -0.000  -0.000  -0.000
   2_xyz:  0.350  67.668  -1.132  -0.011  -1.079  -0.000  -0.000  -0.000
   2_adp:  0.350  67.668  -1.132  -0.011  -1.079  -0.000  -0.000  -0.000
   2_occ:  0.350  67.668  -1.132  -0.011  -1.079  -0.000  -0.000  -0.000
   3_bss:  0.335  59.608  -1.442  -1.558  -0.964  -0.000  -0.000  -0.000
   3_xyz:  0.335  59.608  -1.442  -1.558  -0.964  -0.000  -0.000  -0.000
   3_adp:  0.335  59.608  -1.442  -1.558  -0.964  -0.000  -0.000  -0.000
   3_occ:  0.335  59.608  -1.442  -1.558  -0.964  -0.000  -0.000  -0.000
   4_bss:  0.321  51.747  -2.057  -2.452  -1.366  -0.000  -0.000  -0.000
   4_xyz:  0.321  51.747  -2.057  -2.452  -1.366  -0.000  -0.000  -0.000
   4_adp:  0.321  51.747  -2.057  -2.452  -1.366  -0.000  -0.000  -0.000
   4_occ:  0.321  51.747  -2.057  -2.452  -1.366  -0.000  -0.000  -0.000
   5_bss:  0.319  49.231  -2.071  -2.581  -1.345  -0.000  -0.000  -0.000
   5_xyz:  0.319  49.231  -2.071  -2.581  -1.345  -0.000  -0.000  -0.000
   5_adp:  0.319  49.231  -2.071  -2.581  -1.345  -0.000  -0.000  -0.000
   5_occ:  0.319  49.231  -2.071  -2.581  -1.345  -0.000  -0.000  -0.000
   5_bss:  0.319  49.205  -2.003  -2.568  -1.255  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.320 0.5176  0.6972    58929.432
   1_bss:  49.587 0.5254  0.7158    56433.646
   1_xyz:  37.783 0.6697  0.8765    35410.695
   1_adp:  39.078 0.6532  0.8604    36993.757
   1_occ:  39.103 0.6528  0.8596    37005.365
   2_bss:  38.614 0.6585  0.8410    36331.399
   2_xyz:  27.245 0.7866  0.9669    18667.005
   2_adp:  23.831 0.8235  0.9853    15078.814
   2_occ:  23.806 0.8237  0.9850    15046.310
   3_bss:  23.573 0.8258  0.9663    14738.478
   3_xyz:  18.360 0.8764  0.9971     9363.588
   3_adp:  16.634 0.8927  0.9997     8252.539
   3_occ:  16.626 0.8928  0.9994     8229.924
   4_bss:  16.550 0.8933  0.9770     8126.545
   4_xyz:  14.955 0.9070  0.9824     6931.392
   4_adp:  14.565 0.9105  0.9795     6747.323
   4_occ:  14.559 0.9106  0.9793     6731.613
   5_bss:  14.556 0.9106  0.9779     6727.723
   5_xyz:  14.363 0.9122  0.9784     6588.479
   5_adp:  14.358 0.9124  0.9758     6613.479
   5_occ:  14.348 0.9124  0.9758     6602.731
   5_bss:  14.347 0.9124  0.9769     6602.013
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.7224e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.7224e-01
   1_xyz:   1.387  0.010  0.095 15.401  0.006  4.106   1.0311e-01
   1_adp:   1.387  0.010  0.095 15.401  0.006  4.106   1.0311e-01
   1_occ:   1.387  0.010  0.095 15.401  0.006  4.106   1.0311e-01
   2_bss:   1.387  0.010  0.095 15.401  0.006  4.106   1.0311e-01
   2_xyz:   1.260  0.009  0.089 15.023  0.004  4.107   8.5516e-02
   2_adp:   1.260  0.009  0.089 15.023  0.004  4.107   8.5516e-02
   2_occ:   1.260  0.009  0.089 15.023  0.004  4.107   8.5516e-02
   3_bss:   1.260  0.009  0.089 15.023  0.004  4.107   8.5516e-02
   3_xyz:   1.034  0.007  0.073 14.464  0.004  4.115   6.2792e-02
   3_adp:   1.034  0.007  0.073 14.464  0.004  4.115   6.2792e-02
   3_occ:   1.034  0.007  0.073 14.464  0.004  4.115   6.2792e-02
   4_bss:   1.034  0.007  0.073 14.464  0.004  4.115   6.2792e-02
   4_xyz:   0.968  0.006  0.071 14.361  0.004  4.116   5.5978e-02
   4_adp:   0.968  0.006  0.071 14.361  0.004  4.116   5.5978e-02
   4_occ:   0.968  0.006  0.071 14.361  0.004  4.116   5.5978e-02
   5_bss:   0.968  0.006  0.071 14.361  0.004  4.116   5.5978e-02
   5_xyz:   0.865  0.005  0.065 14.112  0.003  4.115   4.6381e-02
   5_adp:   0.865  0.005  0.065 14.112  0.003  4.115   4.6381e-02
   5_occ:   0.865  0.005  0.065 14.112  0.003  4.115   4.6381e-02
   5_bss:   0.865  0.005  0.065 14.112  0.003  4.115   4.6381e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.776   2.4033e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.776   2.4033e-01
   1_xyz:   8.921  0.073  0.419 88.145  0.042  2.069   8.4507e-02
   1_adp:   8.921  0.073  0.419 88.145  0.042  2.069   8.4507e-02
   1_occ:   8.921  0.073  0.419 88.145  0.042  2.069   8.4507e-02
   2_bss:   8.921  0.073  0.419 88.145  0.042  2.069   8.4507e-02
   2_xyz:   7.381  0.061  0.257 84.919  0.035  2.115   7.2420e-02
   2_adp:   7.381  0.061  0.257 84.919  0.035  2.115   7.2420e-02
   2_occ:   7.381  0.061  0.257 84.919  0.035  2.115   7.2420e-02
   3_bss:   7.381  0.061  0.257 84.919  0.035  2.115   7.2420e-02
   3_xyz:   8.602  0.058  0.210 84.304  0.026  2.241   6.6936e-02
   3_adp:   8.602  0.058  0.210 84.304  0.026  2.241   6.6936e-02
   3_occ:   8.602  0.058  0.210 84.304  0.026  2.241   6.6936e-02
   4_bss:   8.602  0.058  0.210 84.304  0.026  2.241   6.6936e-02
   4_xyz:   7.930  0.044  0.225 84.304  0.030  2.321   3.9186e-02
   4_adp:   7.930  0.044  0.225 84.304  0.030  2.321   3.9186e-02
   4_occ:   7.930  0.044  0.225 84.304  0.030  2.321   3.9186e-02
   5_bss:   7.930  0.044  0.225 84.304  0.030  2.321   3.9186e-02
   5_xyz:   7.839  0.044  0.204 84.459  0.027  2.367   2.6333e-02
   5_adp:   7.839  0.044  0.204 84.459  0.027  2.367   2.6333e-02
   5_occ:   7.839  0.044  0.204 84.459  0.027  2.367   2.6333e-02
   5_bss:   7.839  0.044  0.204 84.459  0.027  2.367   2.6333e-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: 105.93   0.00  18.49  69.61   0.00  14.88 105.93   1.44  38.17
   1_occ: 105.93   0.00  18.49  69.61   0.00  14.88 105.93   1.44  38.17
   2_bss: 105.93   0.00  18.49  69.61   0.00  14.88 105.93   1.44  38.17
   2_xyz: 105.93   0.00  18.49  69.61   0.00  14.88 105.93   1.44  38.17
   2_adp: 102.45   0.00  18.02  83.55   0.00  13.62 102.45   4.01  41.97
   2_occ: 102.45   0.00  18.02  83.55   0.00  13.62 102.45   4.01  41.97
   3_bss: 102.45   0.00  18.02  83.55   0.00  13.62 102.45   4.01  41.97
   3_xyz: 102.45   0.00  18.02  83.55   0.00  13.62 102.45   4.01  41.97
   3_adp:  95.30   0.83  17.38  85.78   0.83  12.97  95.30   2.08  41.37
   3_occ:  95.30   0.83  17.38  85.78   0.83  12.97  95.30   2.08  41.37
   4_bss:  95.30   0.83  17.38  85.78   0.83  12.97  95.30   2.08  41.37
   4_xyz:  95.30   0.83  17.38  85.78   0.83  12.97  95.30   2.08  41.37
   4_adp:  91.29   0.78  17.09  91.29   0.78  12.81  88.45   3.13  40.35
   4_occ:  91.29   0.78  17.09  91.29   0.78  12.81  88.45   3.13  40.35
   5_bss:  91.29   0.78  17.09  91.29   0.78  12.81  88.45   3.13  40.35
   5_xyz:  91.29   0.78  17.09  91.29   0.78  12.81  88.45   3.13  40.35
   5_adp:  91.53   0.78  16.84  91.53   0.78  12.72  83.93   5.74  39.30
   5_occ:  91.53   0.78  16.84  91.53   0.78  12.72  83.93   5.74  39.30
   5_bss:  91.50   0.75  16.81  91.50   0.75  12.69  83.91   5.71  39.27
------------------------------------------------------------------------
 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:    1.723    0.017    0.310
   1_adp:    1.723    0.017    0.310
   1_occ:    1.723    0.017    0.310
   2_bss:    1.723    0.017    0.310
   2_xyz:    1.389    0.045    0.553
   2_adp:    1.389    0.045    0.553
   2_occ:    1.389    0.045    0.553
   3_bss:    1.389    0.045    0.553
   3_xyz:    1.315    0.061    0.640
   3_adp:    1.315    0.061    0.640
   3_occ:    1.315    0.061    0.640
   4_bss:    1.315    0.061    0.640
   4_xyz:    1.454    0.069    0.668
   4_adp:    1.454    0.069    0.668
   4_occ:    1.454    0.069    0.668
   5_bss:    1.454    0.069    0.668
   5_xyz:    1.528    0.097    0.676
   5_adp:    1.528    0.097    0.676
   5_occ:    1.528    0.097    0.676
   5_bss:    1.528    0.097    0.676
------------------------------------------------------------------------

CPU time actual refinement: 338.54


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_983/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_983/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_983/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_983/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_983/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 338.39 
  Macro-tasks:
    bulk solvent and scale       = 35.41  
    individual site refinement   = 137.49 
    weights calculation          = 30.12  
    collect and process          = 6.61   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 209.74 
  Micro-tasks:
    mask                            = 1.87   
    f_calc                          = 112.77 
    alpha_beta                      = 8.50   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 119.12 
    fmodel                         = 6.34   
    r_factors                      = 0.12   
    phase_errors                   = 10.89  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 261.06 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.877 micro seconds
Total CPU time: 5.87 minutes
from_scatterers_fft:    631 calls, 112.43 s
gradients_fft:          576 calls, 106.19 s

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

# Date 2008-01-16 Time 06:07:53 PST -0800 (1200492473.64 s)
Start R-work = 0.4266, R-free = 0.4260 (no bulk solvent and anisotropic scale)
Final R-work = 0.1401, R-free = 0.1804 (no bulk solvent and anisotropic scale)

Start R-work = 0.4163, R-free = 0.4178
Final R-work = 0.1166, R-free = 0.1602