# Date 2008-01-16 Time 03:54:20 PST -0800 (1200484460.62 s)
#phil __OFF__

Command line arguments: "../95.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30293
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 95

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.4938, 47.6339, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.35, per 1000 atoms: 1.19


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 47.6339, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9205 1.95091
Completeness in resolution range: 0.916616
Completeness with d_max=infinity: 0.913879

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9205
                             d_min =   1.9509

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 47.6339, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9205 1.95091
Completeness in resolution range: 0.916616
Completeness with d_max=infinity: 0.913879

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9210 -  4.1753 [2243/2271]  2014   229  10.2%
  bin  2:  4.1753 -  3.3261 [2153/2176]  1935   218  10.1%
  bin  3:  3.3261 -  2.9092 [2129/2154]  1926   203   9.5%
  bin  4:  2.9092 -  2.6448 [2095/2113]  1883   212  10.1%
  bin  5:  2.6448 -  2.4562 [2093/2135]  1881   212  10.1%
  bin  6:  2.4562 -  2.3119 [2084/2112]  1878   206   9.9%
  bin  7:  2.3119 -  2.1965 [2068/2104]  1868   200   9.7%
  bin  8:  2.1965 -  2.1012 [2069/2111]  1859   210  10.1%
  bin  9:  2.1012 -  2.0205 [2027/2099]  1827   200   9.9%
  bin 10:  2.0205 -  1.9509 [ 628/2096]   559    69  11.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_95/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: 0.12 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:
        1.01 -     1.79: 9
        1.79 -     2.57: 61
        2.57 -     3.35: 4031
        3.35 -     4.12: 9406
        4.12 -     4.90: 14940
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.014 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.218 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.275 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.455 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.468 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28442 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_95/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_95/model_refine_001.geo

CPU time processing inputs: 8.95


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.49375 47.63395 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4432   r_free= 0.4366   ksol= 0.00   Bsol= 0.00   scale= 0.911    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.249096                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9210 -  4.6573 0.99   1457  161 0.3451 0.3644      6.5079      6.5649|
|  2:  4.6573 -  3.7154 0.99   1410  154 0.3705 0.3615      6.7244      6.7283|
|  3:  3.7154 -  3.2513 0.99   1365  156 0.4117 0.4032       6.602      6.6258|
|  4:  3.2513 -  2.9566 0.99   1371  146 0.4334 0.4065      6.4515      6.4497|
|  5:  2.9566 -  2.7461 0.99   1344  154 0.4654 0.4387      6.3204      6.3168|
|  6:  2.7461 -  2.5850 0.99   1362  153 0.4693 0.5182      6.2349      6.1728|
|  7:  2.5850 -  2.4562 0.98   1330  150 0.4741 0.4074      6.1866      6.1023|
|  8:  2.4562 -  2.3497 0.98   1341  143 0.5097 0.4865      6.1551      6.1666|
|  9:  2.3497 -  2.2595 0.99   1340  144 0.5041 0.4695      6.1056      6.1301|
| 10:  2.2595 -  2.1818 0.98   1339  150 0.5019 0.4853      6.0787      6.0735|
| 11:  2.1818 -  2.1138 0.97   1316  155 0.5108 0.5231      5.9927      6.0303|
| 12:  2.1138 -  2.0535 0.98   1323  151 0.5137 0.5084      5.9414       5.943|
| 13:  2.0535 -  1.9996 0.80   1085  108 0.4921 0.5614      5.8513      5.7878|
| 14:  1.9996 -  1.9509 0.19    247   34 0.4997 0.5037       5.936      5.7332|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9210 -  4.6573  1457   161  0.71  33.79   0.84     0.72      67974.44|
|  2:  4.6573 -  3.7154  1410   154  0.73  32.46   0.94     0.82      92640.67|
|  3:  3.7154 -  3.2513  1365   156  0.64  40.43   0.93     0.82      96307.54|
|  4:  3.2513 -  2.9566  1371   146  0.56  46.82   0.93     0.75      83510.84|
|  5:  2.9566 -  2.7461  1344   154  0.50  52.04   0.90     0.70      68703.24|
|  6:  2.7461 -  2.5850  1362   153  0.49  53.16   0.91     0.67      58746.90|
|  7:  2.5850 -  2.4562  1330   150  0.48  53.55   0.92     0.67      53781.60|
|  8:  2.4562 -  2.3497  1341   143  0.46  55.15   0.93     0.66      48092.65|
|  9:  2.3497 -  2.2595  1340   144  0.46  55.15   0.91     0.68      45830.33|
| 10:  2.2595 -  2.1818  1339   150  0.45  56.08   0.93     0.66      41874.98|
| 11:  2.1818 -  2.1138  1316   155  0.40  60.39   0.93     0.61      42730.22|
| 12:  2.1138 -  2.0535  1323   151  0.33  65.61   0.95     0.54      42725.50|
| 13:  2.0535 -  1.9996  1085   108  0.30  67.91   0.95     0.49      38504.34|
| 14:  1.9996 -  1.9509   247    34  0.37  62.28   0.98     0.46      28300.91|
|alpha:            min =        0.46 max =            0.82 mean =         0.68|
|beta:             min =    28300.91 max =        96307.54 mean =     60294.78|
|figures of merit: min =        0.00 max =            1.00 mean =         0.50|
|phase err.(work): min =        0.00 max =           90.00 mean =        51.40|
|phase err.(test): min =        0.00 max =           89.85 mean =        51.62|
|-----------------------------------------------------------------------------|

============================== 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 = 10.045802             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.240   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.695500              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.581   (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 |  1.014 -  1.402:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.402 -  1.791:        6 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.791 -  2.180:       14 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.180 -  2.568:       47 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.568 -  2.957:     1670 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.957 -  3.346:     2361 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.346 -  3.734:     3835 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.734 -  4.123:     5571 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.123 -  4.511:     6577 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.511 -  4.900:     8363 |
|-----------------------------------------------------------------------------|
|-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 |        0.220 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.014 |       1.030 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.744)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4432   r_free= 0.4366   ksol= 0.00   Bsol= 0.00   scale= 0.911    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.249096                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4362   r_free= 0.4282   ksol= 0.30   Bsol= 29.14   scale= 0.949   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.12,1.86,-0.04,0.00,-0.00,-0.00); trace/3= 0.65                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.241709                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.786660              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.902   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.933379              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.294   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4362      final r-factor (work) = 0.2917          |
| start r-factor (free) = 0.4282      final r-factor (free) = 0.3224          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.6476 = 8.79 * 0.50 * 6.2431 + 1.00 * 0.2197                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.7994 = 8.79 * 0.50 * 6.0731 + 1.00 * 0.1181                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2917      final r-factor (work) = 0.2605          |
| start r-factor (free) = 0.3224      final r-factor (free) = 0.3283          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6746 = 0.93 * 1.00 * 6.0731 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5032 = 0.93 * 1.00 * 5.8730 + 1.00 * 0.0215                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.744)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.68   18.74    None  None   None       |
|    all(noH): 2823   0      0.00    99.68   18.74    None  None   None       |
|    Sol.    : 438    0      2.95    99.68   41.18    None  None   None       |
|    Mac.    : 2385   0      0.00    85.09   14.62    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 -   9.968:  967   |   5:    49.839 -  59.806:   91        |
|      1:     9.968 -  19.936:  933   |   6:    59.806 -  69.774:   45        |
|      2:    19.936 -  29.903:  408   |   7:    69.774 -  79.742:   28        |
|      3:    29.903 -  39.871:  210   |   8:    79.742 -  89.710:   15        |
|      4:    39.871 -  49.839:  125   |   9:    89.710 -  99.677:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2605 r_free = 0.3283             target_work(ml) = 5.881         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2604 r_free = 0.3281             target_work(ml) = 5.881         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2604   r_free= 0.3281   ksol= 0.30   Bsol= 29.14   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.12,1.86,-0.04,0.00,-0.00,-0.00); trace/3= 0.65                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.880627                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2568   r_free= 0.3226   ksol= 0.32   Bsol= 56.59   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.97,-0.19,-0.66,-0.00,-0.00,-0.00); trace/3= -0.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.872039                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.381594              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.065   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.347348              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.107   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2568      final r-factor (work) = 0.1857          |
| start r-factor (free) = 0.3226      final r-factor (free) = 0.2347          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.9271 = 5.38 * 0.50 * 5.8752 + 1.00 * 0.1181                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.5571 = 5.38 * 0.50 * 5.7548 + 1.00 * 0.0721                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1857      final r-factor (work) = 0.1674          |
| start r-factor (free) = 0.2347      final r-factor (free) = 0.2144          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0241 = 0.35 * 1.00 * 5.7548 + 1.00 * 0.0252                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9302 = 0.35 * 1.00 * 5.5278 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.744)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.51   18.16    None  None   None       |
|    all(noH): 2823   0      0.00    95.51   18.16    None  None   None       |
|    Sol.    : 438    0      5.55    95.51   41.80    None  None   None       |
|    Mac.    : 2385   0      0.00    88.47   13.82    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.551:  891   |   5:    47.753 -  57.303:  106        |
|      1:     9.551 -  19.101: 1164   |   6:    57.303 -  66.854:   58        |
|      2:    19.101 -  28.652:  288   |   7:    66.854 -  76.404:   27        |
|      3:    28.652 -  38.202:  137   |   8:    76.404 -  85.955:   13        |
|      4:    38.202 -  47.753:  137   |   9:    85.955 -  95.505:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1674 r_free = 0.2144             target_work(ml) = 5.486         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1672 r_free = 0.2142             target_work(ml) = 5.485         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1672   r_free= 0.2142   ksol= 0.32   Bsol= 56.59   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.97,-0.19,-0.66,-0.00,-0.00,-0.00); trace/3= -0.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.485255                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1669   r_free= 0.2134   ksol= 0.33   Bsol= 56.59   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-1.32,-1.01,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.483253                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.872955              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.364  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.341990              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.878  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1669      final r-factor (work) = 0.1411          |
| start r-factor (free) = 0.2134      final r-factor (free) = 0.1833          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2523 = 1.87 * 0.50 * 5.5315 + 1.00 * 0.0722                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1182 = 1.87 * 0.50 * 5.4103 + 1.00 * 0.0516                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1411      final r-factor (work) = 0.1353          |
| start r-factor (free) = 0.1833      final r-factor (free) = 0.1790          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8603 = 0.34 * 1.00 * 5.4103 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8276 = 0.34 * 1.00 * 5.3159 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.744)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.18    95.07   17.96    None  None   None       |
|    all(noH): 2823   0      1.18    95.07   17.96    None  None   None       |
|    Sol.    : 438    0      6.23    95.07   42.17    None  None   None       |
|    Mac.    : 2385   0      1.18    90.64   13.51    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.180 -  10.569: 1083   |   5:    48.123 -  57.512:   94        |
|      1:    10.569 -  19.957: 1069   |   6:    57.512 -  66.901:   67        |
|      2:    19.957 -  29.346:  212   |   7:    66.901 -  76.289:   30        |
|      3:    29.346 -  38.735:  131   |   8:    76.289 -  85.678:    7        |
|      4:    38.735 -  48.123:  126   |   9:    85.678 -  95.067:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1353 r_free = 0.1790             target_work(ml) = 5.305         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1352 r_free = 0.1789             target_work(ml) = 5.305         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1352   r_free= 0.1789   ksol= 0.33   Bsol= 56.59   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-1.32,-1.01,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.304548                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1354   r_free= 0.1788   ksol= 0.33   Bsol= 56.59   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.45,-1.82,-1.19,-0.00,-0.00,-0.00); trace/3= -2.16                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.305286                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.640572              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.176  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.416527              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.126  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1354      final r-factor (work) = 0.1240          |
| start r-factor (free) = 0.1788      final r-factor (free) = 0.1662          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4137 = 1.64 * 0.50 * 5.3177 + 1.00 * 0.0516                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3716 = 1.64 * 0.50 * 5.2634 + 1.00 * 0.0541                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1240      final r-factor (work) = 0.1221          |
| start r-factor (free) = 0.1662      final r-factor (free) = 0.1652          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2019 = 0.42 * 1.00 * 5.2634 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1832 = 0.42 * 1.00 * 5.2186 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.744)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.27    94.55   17.74    None  None   None       |
|    all(noH): 2823   0      1.27    94.55   17.74    None  None   None       |
|    Sol.    : 438    0      5.99    94.55   41.83    None  None   None       |
|    Mac.    : 2385   0      1.27    92.27   13.31    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.275 -  10.602: 1117   |   5:    47.910 -  57.237:  100        |
|      1:    10.602 -  19.929: 1053   |   6:    57.237 -  66.564:   58        |
|      2:    19.929 -  29.256:  201   |   7:    66.564 -  75.891:   39        |
|      3:    29.256 -  38.583:  135   |   8:    75.891 -  85.218:    7        |
|      4:    38.583 -  47.910:  108   |   9:    85.218 -  94.545:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1221 r_free = 0.1652             target_work(ml) = 5.215         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1221 r_free = 0.1652             target_work(ml) = 5.215         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1221   r_free= 0.1652   ksol= 0.33   Bsol= 56.59   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.45,-1.82,-1.19,-0.00,-0.00,-0.00); trace/3= -2.16                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.214809                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1221   r_free= 0.1652   ksol= 0.33   Bsol= 56.59   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.38,-1.87,-1.11,-0.00,-0.00,-0.00); trace/3= -2.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.214888                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.080362              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.886  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.701529              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.786  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1221      final r-factor (work) = 0.1155          |
| start r-factor (free) = 0.1652      final r-factor (free) = 0.1597          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4824 = 2.08 * 0.50 * 5.2186 + 1.00 * 0.0541                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4608 = 2.08 * 0.50 * 5.1919 + 1.00 * 0.0603                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1155      final r-factor (work) = 0.1145          |
| start r-factor (free) = 0.1597      final r-factor (free) = 0.1595          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6517 = 0.70 * 1.00 * 5.1919 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6385 = 0.70 * 1.00 * 5.1724 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.744)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.37   17.60    None  None   None       |
|    all(noH): 2823   0      0.00    96.37   17.60    None  None   None       |
|    Sol.    : 438    0      0.00    93.81   41.72    None  None   None       |
|    Mac.    : 2385   0      0.91    96.37   13.17    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.637:  906   |   5:    48.184 -  57.820:   96        |
|      1:     9.637 -  19.273: 1244   |   6:    57.820 -  67.457:   62        |
|      2:    19.273 -  28.910:  228   |   7:    67.457 -  77.094:   36        |
|      3:    28.910 -  38.547:  126   |   8:    77.094 -  86.730:    5        |
|      4:    38.547 -  48.184:  115   |   9:    86.730 -  96.367:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1145 r_free = 0.1595             target_work(ml) = 5.172         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1144 r_free = 0.1594             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1144   r_free= 0.1594   ksol= 0.33   Bsol= 56.59   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.38,-1.87,-1.11,-0.00,-0.00,-0.00); trace/3= -2.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.171292                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9210 -  4.6573 0.99   1457  161 0.0972 0.1281      5.3825      5.5734|
|  2:  4.6573 -  3.7154 0.99   1410  154 0.0830 0.1032      5.4053      5.5896|
|  3:  3.7154 -  3.2513 0.99   1365  156 0.1093 0.1463      5.4661      5.7862|
|  4:  3.2513 -  2.9566 0.99   1371  146 0.1279 0.1642      5.4602      5.6465|
|  5:  2.9566 -  2.7461 0.99   1344  154 0.1357 0.1674      5.3459      5.5228|
|  6:  2.7461 -  2.5850 0.99   1362  153 0.1288 0.2104      5.2358      5.5053|
|  7:  2.5850 -  2.4562 0.98   1330  150 0.1284 0.1668      5.1886      5.3782|
|  8:  2.4562 -  2.3497 0.98   1341  143 0.1232 0.1724      5.1111      5.3024|
|  9:  2.3497 -  2.2595 0.99   1340  144 0.1177 0.1904      5.0329      5.3471|
| 10:  2.2595 -  2.1818 0.98   1339  150 0.1165 0.1826      4.9709      5.2065|
| 11:  2.1818 -  2.1138 0.97   1316  155 0.1193 0.1791      4.9274      5.2478|
| 12:  2.1138 -  2.0535 0.98   1323  151 0.1175 0.1518      4.8656      5.0545|
| 13:  2.0535 -  1.9996 0.80   1085  108 0.1123 0.2114      4.7791      5.1085|
| 14:  1.9996 -  1.9509 0.19    247   34 0.1075 0.1492      4.7801      4.8294|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9210 -  4.6573  1457   161  0.94   9.26   0.97     0.95       7349.70|
|  2:  4.6573 -  3.7154  1410   154  0.95   7.86   1.01     1.00       8666.47|
|  3:  3.7154 -  3.2513  1365   156  0.93  11.29   1.03     1.02      10003.70|
|  4:  3.2513 -  2.9566  1371   146  0.91  14.35   1.01     1.00      10406.56|
|  5:  2.9566 -  2.7461  1344   154  0.90  16.44   1.00     0.98       8806.68|
|  6:  2.7461 -  2.5850  1362   153  0.89  17.04   0.98     0.95       7446.43|
|  7:  2.5850 -  2.4562  1330   150  0.90  16.27   0.99     0.96       6605.56|
|  8:  2.4562 -  2.3497  1341   143  0.90  16.40   1.00     0.97       5911.29|
|  9:  2.3497 -  2.2595  1340   144  0.90  16.45   0.99     0.95       5181.57|
| 10:  2.2595 -  2.1818  1339   150  0.90  16.51   0.99     0.96       4638.21|
| 11:  2.1818 -  2.1138  1316   155  0.90  16.35   0.98     0.94       4281.10|
| 12:  2.1138 -  2.0535  1323   151  0.91  15.91   1.00     1.00       3799.52|
| 13:  2.0535 -  1.9996  1085   108  0.90  16.85   0.98     0.97       3390.08|
| 14:  1.9996 -  1.9509   247    34  0.91  14.70   0.97     0.92       3048.01|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     3048.01 max =        10406.56 mean =      6681.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.59|
|phase err.(test): min =        0.00 max =           88.37 mean =        14.12|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1144   r_free= 0.1594   ksol= 0.32   Bsol= 56.59   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.23,-1.78,-0.94,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.171401                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1144   r_free= 0.1594   ksol= 0.32   Bsol= 56.59   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.23,-1.78,-0.94,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.171401                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9210 -  4.6573 0.99   1457  161 0.0972 0.1282       5.383      5.5748|
|  2:  4.6573 -  3.7154 0.99   1410  154 0.0830 0.1032      5.4059      5.5898|
|  3:  3.7154 -  3.2513 0.99   1365  156 0.1093 0.1464      5.4663      5.7866|
|  4:  3.2513 -  2.9566 0.99   1371  146 0.1279 0.1643      5.4602      5.6463|
|  5:  2.9566 -  2.7461 0.99   1344  154 0.1357 0.1673      5.3456      5.5221|
|  6:  2.7461 -  2.5850 0.99   1362  153 0.1287 0.2104      5.2356      5.5051|
|  7:  2.5850 -  2.4562 0.98   1330  150 0.1284 0.1670      5.1886      5.3783|
|  8:  2.4562 -  2.3497 0.98   1341  143 0.1232 0.1723      5.1111      5.3022|
|  9:  2.3497 -  2.2595 0.99   1340  144 0.1177 0.1905      5.0331      5.3477|
| 10:  2.2595 -  2.1818 0.98   1339  150 0.1164 0.1827      4.9711      5.2068|
| 11:  2.1818 -  2.1138 0.97   1316  155 0.1193 0.1791      4.9277      5.2481|
| 12:  2.1138 -  2.0535 0.98   1323  151 0.1176 0.1518      4.8656      5.0544|
| 13:  2.0535 -  1.9996 0.80   1085  108 0.1123 0.2114      4.7792      5.1073|
| 14:  1.9996 -  1.9509 0.19    247   34 0.1075 0.1492      4.7804      4.8298|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9210 -  4.6573  1457   161  0.94   9.27   0.98     0.95       7356.56|
|  2:  4.6573 -  3.7154  1410   154  0.95   7.87   1.02     1.00       8675.00|
|  3:  3.7154 -  3.2513  1365   156  0.93  11.30   1.03     1.02      10011.45|
|  4:  3.2513 -  2.9566  1371   146  0.91  14.35   1.01     1.00      10407.75|
|  5:  2.9566 -  2.7461  1344   154  0.90  16.44   1.01     0.98       8799.68|
|  6:  2.7461 -  2.5850  1362   153  0.89  17.03   0.98     0.96       7441.89|
|  7:  2.5850 -  2.4562  1330   150  0.90  16.27   0.99     0.96       6602.91|
|  8:  2.4562 -  2.3497  1341   143  0.90  16.39   1.01     0.97       5911.32|
|  9:  2.3497 -  2.2595  1340   144  0.90  16.46   1.00     0.96       5183.75|
| 10:  2.2595 -  2.1818  1339   150  0.90  16.52   1.00     0.96       4639.75|
| 11:  2.1818 -  2.1138  1316   155  0.90  16.36   0.99     0.95       4283.08|
| 12:  2.1138 -  2.0535  1323   151  0.91  15.91   1.01     1.00       3800.44|
| 13:  2.0535 -  1.9996  1085   108  0.90  16.85   0.99     0.97       3389.08|
| 14:  1.9996 -  1.9509   247    34  0.91  14.70   0.98     0.92       3046.02|
|alpha:            min =        0.92 max =            1.02 mean =         0.98|
|beta:             min =     3046.02 max =        10407.75 mean =      6682.32|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.59|
|phase err.(test): min =        0.00 max =           88.40 mean =        14.13|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.744)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.37   17.60    None  None   None       |
|    all(noH): 2823   0      0.00    96.37   17.60    None  None   None       |
|    Sol.    : 438    0      0.00    93.82   41.72    None  None   None       |
|    Mac.    : 2385   0      0.92    96.37   13.18    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.640:  906   |   5:    48.186 -  57.823:   96        |
|      1:     9.640 -  19.276: 1244   |   6:    57.823 -  67.460:   62        |
|      2:    19.276 -  28.913:  228   |   7:    67.460 -  77.097:   36        |
|      3:    28.913 -  38.550:  126   |   8:    77.097 -  86.733:    5        |
|      4:    38.550 -  48.186:  115   |   9:    86.733 -  96.370:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 299         
Filter by distance & map next to the model:
   mapped sites are within: 0.484 - 5.575
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 296 from: 299
   mapped sites are within: 0.702 - 5.575

peak=    6.455 closest distance to " O  BHOH Z  74 " =    1.154
peak=    5.374 closest distance to " NH2 ARG A  56 " =    2.188
peak=    5.218 closest distance to " CB  ARG A 275 " =    0.967
peak=    4.949 closest distance to " CG  PRO A  54 " =    1.289
peak=    4.890 closest distance to " O   HOH Z 417 " =    2.696
peak=    4.864 closest distance to " O   HOH Z 232 " =    2.286
peak=    4.772 closest distance to " O   HOH Z 102 " =    1.420
peak=    4.637 closest distance to " O   HOH Z 234 " =    3.596
peak=    4.632 closest distance to " CB  GLN A 223 " =    1.451
peak=    4.616 closest distance to " CG  PRO A  90 " =    1.204
peak=    4.609 closest distance to " CA  TYR A  30 " =    0.917
peak=    4.600 closest distance to " O   HOH Z  43 " =    1.931
peak=    4.547 closest distance to " CB  GLN A 183 " =    1.248
peak=    4.511 closest distance to " O   HOH Z 401 " =    1.080
peak=    4.498 closest distance to " CB  ARG A 190 " =    1.705
peak=    4.493 closest distance to " O   HOH Z 142 " =    1.523
peak=    4.472 closest distance to " O   HOH Z 186 " =    2.217
peak=    4.440 closest distance to " O   GLY A  23 " =    2.412
peak=    4.430 closest distance to " O   HOH Z 193 " =    1.763
peak=    4.393 closest distance to " O   HOH Z 403 " =    1.815
peak=    4.389 closest distance to " CB  PRO A  54 " =    1.031
peak=    4.387 closest distance to " O   HOH Z  63 " =    1.946
peak=    4.339 closest distance to " O   HOH Z  49 " =    1.100
peak=    4.330 closest distance to " CD2 TRP A 179 " =    1.343
peak=    4.327 closest distance to " NZ  LYS A 117 " =    3.065
peak=    4.326 closest distance to " CG  PRO A 198 " =    1.251
peak=    4.321 closest distance to " C   PRO A 198 " =    1.564
peak=    4.276 closest distance to " O   HOH Z 209 " =    2.240
peak=    4.275 closest distance to " CA  ARG A  36 " =    1.056
peak=    4.254 closest distance to " O   SER A  87 " =    2.215
peak=    4.250 closest distance to " O   HOH Z 402 " =    1.451
peak=    4.242 closest distance to " NH2BARG A 145 " =    2.101
peak=    4.237 closest distance to " O   HOH Z 298 " =    1.724
peak=    4.230 closest distance to " O   HOH Z 272 " =    1.920
peak=    4.229 closest distance to " O   HOH Z  97 " =    1.637
peak=    4.225 closest distance to " O   HOH Z 126 " =    1.820
peak=    4.213 closest distance to " CB  SER A  63 " =    1.100
peak=    4.191 closest distance to " O   HOH Z 369 " =    2.297
peak=    4.184 closest distance to " O   HOH Z 365 " =    2.549
peak=    4.183 closest distance to " CD  ARG A 269 " =    1.054
peak=    4.154 closest distance to " CB  ARG A  79 " =    1.425
peak=    4.151 closest distance to " CZ  PHE A 218 " =    1.178
peak=    4.142 closest distance to " O   HOH Z 188 " =    2.732
peak=    4.137 closest distance to " CB  ASN A 148 " =    1.431
peak=    4.132 closest distance to " NE2 GLN A  11 " =    1.107
peak=    4.131 closest distance to " CB  PRO A 213 " =    1.282
peak=    4.117 closest distance to " O   HOH Z 389 " =    1.876
peak=    4.107 closest distance to " ND2 ASN A 187 " =    1.577
peak=    4.105 closest distance to " CA  ALA A  51 " =    0.962
peak=    4.102 closest distance to " CB  GLU A 152 " =    1.211
peak=    4.099 closest distance to " O   HOH Z 346 " =    1.678
peak=    4.076 closest distance to " O   HOH Z 287 " =    1.814
peak=    4.057 closest distance to " O   HOH Z  80 " =    1.804
peak=    4.001 closest distance to " O   HOH Z 248 " =    1.416
peak=    3.987 closest distance to " O   HOH Z 173 " =    2.176
peak=    3.985 closest distance to " CA  ARG A 195 " =    1.264
peak=    3.983 closest distance to " O   HOH Z 130 " =    2.711
peak=    3.982 closest distance to " O   HOH Z  15 " =    2.117
peak=    3.959 closest distance to " O   HOH Z 188 " =    1.432
peak=    3.936 closest distance to " O   HOH Z 250 " =    1.412
peak=    3.921 closest distance to " O   HOH Z 203 " =    1.766
peak=    3.920 closest distance to " O   HOH Z  85 " =    1.482
peak=    3.915 closest distance to " OG BSER A 212 " =    2.524
peak=    3.914 closest distance to " O   HOH Z 421 " =    2.018
peak=    3.902 closest distance to " O   HOH Z 423 " =    1.883
peak=    3.897 closest distance to " O   HOH Z 327 " =    1.720
peak=    3.897 closest distance to " O   HOH Z 247 " =    1.357
peak=    3.887 closest distance to " O   HOH Z 117 " =    2.018
peak=    3.882 closest distance to " O   HOH Z 368 " =    2.142
peak=    3.874 closest distance to " O   HOH Z  63 " =    2.381
peak=    3.861 closest distance to " O   HOH Z  21 " =    1.864
peak=    3.859 closest distance to " CB  VAL A 202 " =    1.476
peak=    3.856 closest distance to " O   HOH Z 126 " =    1.954
peak=    3.852 closest distance to " O   HOH Z 227 " =    1.817
peak=    3.850 closest distance to " O   HOH Z 128 " =    1.988
peak=    3.845 closest distance to " O   HOH Z  40 " =    2.207
peak=    3.833 closest distance to " N   ASN A  39 " =    1.242
peak=    3.832 closest distance to " CD2 LEU A 297 " =    0.905
peak=    3.823 closest distance to " CG2BVAL A  41 " =    0.833
peak=    3.804 closest distance to " O   HOH Z  78 " =    1.677
peak=    3.798 closest distance to " CG  PRO A 243 " =    1.080
peak=    3.790 closest distance to " CB  TRP A 266 " =    1.127
peak=    3.790 closest distance to " O   HOH Z 359 " =    1.645
peak=    3.786 closest distance to " O   HOH Z 406 " =    1.483
peak=    3.784 closest distance to " NE2 GLN A  77 " =    3.133
peak=    3.775 closest distance to " CB  GLU A 277 " =    3.634
peak=    3.774 closest distance to " CE  LYS A 119 " =    1.116
peak=    3.763 closest distance to " CG2 ILE A 120 " =    1.249
peak=    3.763 closest distance to " O   HOH Z 132 " =    2.269
peak=    3.757 closest distance to " CB  THR A  31 " =    1.676
peak=    3.750 closest distance to " CB  SER A  26 " =    1.812
peak=    3.741 closest distance to " O   HOH Z  44 " =    2.158
peak=    3.737 closest distance to " CG AARG A 275 " =    1.167
peak=    3.729 closest distance to " N   CYS A 260 " =    0.970
peak=    3.728 closest distance to " CD  LYS A  76 " =    1.820
peak=    3.725 closest distance to " O   HOH Z  97 " =    1.962
peak=    3.721 closest distance to " O   HOH Z 394 " =    1.494
peak=    3.720 closest distance to " O   HOH Z 345 " =    1.716
peak=    3.716 closest distance to " O   HOH Z 427 " =    3.065
peak=    3.711 closest distance to " CD  PRO A  54 " =    1.069
peak=    3.711 closest distance to " O   HOH Z  59 " =    2.128
peak=    3.709 closest distance to " CD  ARG A 159 " =    0.818
peak=    3.701 closest distance to " O   ALA A 165 " =    1.501
peak=    3.693 closest distance to " CB  GLU A 128 " =    1.059
peak=    3.689 closest distance to " O   THR A 182 " =    1.456
peak=    3.686 closest distance to " CD  LYS A 166 " =    1.362
peak=    3.678 closest distance to " O   HOH Z  65 " =    0.977
peak=    3.677 closest distance to " CB  SER A  62 " =    0.989
peak=    3.661 closest distance to " CB  SER A   3 " =    1.159
peak=    3.650 closest distance to " O   HOH Z 298 " =    2.349
peak=    3.648 closest distance to " CB  ASN A  39 " =    0.803
peak=    3.648 closest distance to " O   HOH Z 134 " =    1.356
peak=    3.644 closest distance to " CG2 ILE A  20 " =    1.420
peak=    3.632 closest distance to " O   HOH Z 371 " =    3.210
peak=    3.628 closest distance to " CB  TRP A 179 " =    1.264
peak=    3.618 closest distance to " CA  ALA A  84 " =    1.157
peak=    3.611 closest distance to " NH1AARG A 145 " =    1.395
peak=    3.610 closest distance to " O   HOH Z 316 " =    3.011
peak=    3.610 closest distance to " O   HOH Z 422 " =    2.664
peak=    3.610 closest distance to " O   HOH Z 361 " =    3.470
peak=    3.610 closest distance to " NH1AARG A 275 " =    0.952
peak=    3.599 closest distance to " O   HOH Z 245 " =    1.350
peak=    3.596 closest distance to " CG2 VAL A 257 " =    0.799
peak=    3.592 closest distance to " CG  GLN A  11 " =    1.457
peak=    3.592 closest distance to " O   THR A 220 " =    1.133
peak=    3.591 closest distance to " O   HOH Z 117 " =    1.069
peak=    3.590 closest distance to " CA  ASN A 176 " =    1.490
peak=    3.589 closest distance to " CB  TYR A 169 " =    0.728
peak=    3.589 closest distance to " CE  LYS A  76 " =    0.874
peak=    3.586 closest distance to " ND2 ASN A 249 " =    0.928
peak=    3.586 closest distance to " O   HOH Z 279 " =    2.131
peak=    3.584 closest distance to " O   HOH Z 128 " =    2.494
peak=    3.580 closest distance to " CB  VAL A 265 " =    1.253
peak=    3.569 closest distance to " CB  ASN A 110 " =    1.090
peak=    3.567 closest distance to " CZ  PHE A  38 " =    1.200
peak=    3.564 closest distance to " O   HOH Z 380 " =    1.873
peak=    3.563 closest distance to " O   HOH Z 337 " =    3.638
peak=    3.560 closest distance to " O   HOH Z 284 " =    2.989
peak=    3.553 closest distance to " CG1 ILE A  33 " =    1.164
peak=    3.548 closest distance to " O   HOH Z 261 " =    2.095
peak=    3.546 closest distance to " O   HOH Z 303 " =    2.202
peak=    3.544 closest distance to " O   ASN A  74 " =    1.562
peak=    3.538 closest distance to " O   HOH Z 357 " =    2.098
peak=    3.537 closest distance to " O   HOH Z 392 " =    2.338
peak=    3.536 closest distance to " O   HOH Z 418 " =    3.415
peak=    3.536 closest distance to " O   HOH Z 124 " =    1.229
peak=    3.532 closest distance to " O   ARG A  56 " =    2.820
peak=    3.529 closest distance to " CA  ALA A 295 " =    1.017
peak=    3.528 closest distance to " O   HOH Z 336 " =    1.884
peak=    3.527 closest distance to " O   HOH Z 285 " =    2.737
peak=    3.520 closest distance to " CD1 LEU A  96 " =    0.737
peak=    3.515 closest distance to " CB  GLU A 175 " =    1.362
peak=    3.513 closest distance to " OH  TYR A 116 " =    1.114
peak=    3.490 closest distance to " CB  ASN A 148 " =    1.973
peak=    3.486 closest distance to " O   HOH Z 426 " =    1.477
peak=    3.485 closest distance to " O   HOH Z 265 " =    2.053
peak=    3.481 closest distance to " O   HOH Z 126 " =    1.529
peak=    3.481 closest distance to " O   HOH Z 291 " =    1.391
peak=    3.480 closest distance to " O   HOH Z 158 " =    3.033
peak=    3.477 closest distance to " CG  MET A 185 " =    1.149
peak=    3.470 closest distance to " O   HOH Z 132 " =    1.057
peak=    3.467 closest distance to " CB  ALA A 248 " =    1.336
peak=    3.466 closest distance to " N   ARG A 156 " =    1.447
peak=    3.463 closest distance to " CB  GLN A  88 " =    1.149
peak=    3.462 closest distance to " O   HOH Z 353 " =    2.674
peak=    3.453 closest distance to " O   HOH Z 258 " =    2.198
peak=    3.449 closest distance to " O   HOH Z  61 " =    1.629
peak=    3.449 closest distance to " O   HOH Z 180 " =    2.275
peak=    3.446 closest distance to " O   HOH Z 419 " =    1.671
peak=    3.433 closest distance to " CD  LYS A 119 " =    1.905
peak=    3.424 closest distance to " O  BHOH Z 338 " =    2.233
peak=    3.424 closest distance to " O   HOH Z  63 " =    2.201
peak=    3.418 closest distance to " O   HOH Z 325 " =    2.098
peak=    3.415 closest distance to " O   HOH Z 299 " =    4.323
peak=    3.413 closest distance to " CA  THR A  82 " =    1.853
peak=    3.407 closest distance to " CA  ASP A 162 " =    1.160
peak=    3.406 closest distance to " O   HOH Z 298 " =    4.178
peak=    3.403 closest distance to " O   HOH Z   1 " =    2.251
peak=    3.398 closest distance to " O   HOH Z 148 " =    3.288
peak=    3.394 closest distance to " CB  ASN A 215 " =    1.180
peak=    3.394 closest distance to " CA  ASN A 215 " =    1.031
peak=    3.393 closest distance to " CB  PRO A 198 " =    1.189
peak=    3.390 closest distance to " CB  PRO A  90 " =    0.888
peak=    3.385 closest distance to " O   HOH Z 412 " =    3.772
peak=    3.384 closest distance to " O   HOH Z 404 " =    2.273
peak=    3.381 closest distance to " O   HOH Z 108 " =    2.774
peak=    3.378 closest distance to " CA  ALA A 160 " =    0.881
peak=    3.367 closest distance to " CD  GLN A 194 " =    1.601
peak=    3.363 closest distance to " O   HOH Z  35 " =    2.362
peak=    3.358 closest distance to " CB  SER A 141 " =    1.049
peak=    3.358 closest distance to " O   HOH Z 344 " =    3.035
peak=    3.357 closest distance to " NZ  LYS A  48 " =    1.206
peak=    3.356 closest distance to " CG2AVAL A 121 " =    2.172
peak=    3.355 closest distance to " O   HOH Z 361 " =    2.555
peak=    3.354 closest distance to " CB  ALA A 114 " =    0.898
peak=    3.353 closest distance to " O   HOH Z 313 " =    1.922
peak=    3.353 closest distance to " CB  ASN A 285 " =    0.966
peak=    3.352 closest distance to " O   HOH Z 214 " =    2.440
peak=    3.351 closest distance to " O   HOH Z 282 " =    1.978
peak=    3.347 closest distance to " N   TRP A 150 " =    1.237
peak=    3.339 closest distance to " CG  LEU A 167 " =    1.241
peak=    3.335 closest distance to " O   HOH Z 163 " =    1.497
peak=    3.333 closest distance to " CG  GLN A  58 " =    0.805
peak=    3.333 closest distance to " N   TYR A 116 " =    1.671
peak=    3.332 closest distance to " O   HOH Z 366 " =    2.418
peak=    3.332 closest distance to " OG BSER A 164 " =    2.180
peak=    3.322 closest distance to " O   HOH Z  68 " =    1.799
peak=    3.316 closest distance to " CB  TYR A 247 " =    0.994
peak=    3.315 closest distance to " O   HOH Z 433 " =    1.435
peak=    3.313 closest distance to " O   HOH Z  88 " =    3.153
peak=    3.310 closest distance to " O   HOH Z 375 " =    2.100
peak=    3.307 closest distance to " CG2AVAL A  72 " =    1.822
peak=    3.304 closest distance to " N   ASP A 162 " =    1.178
peak=    3.304 closest distance to " CB  LYS A 289 " =    1.097
peak=    3.300 closest distance to " O   HOH Z 425 " =    1.951
peak=    3.300 closest distance to " CB  ASP A 191 " =    1.206
peak=    3.299 closest distance to " CB  TYR A 169 " =    0.793
peak=    3.299 closest distance to " CB  THR A  52 " =    0.702
peak=    3.293 closest distance to " CZ3 TRP A 266 " =    1.053
peak=    3.285 closest distance to " O   HOH Z  94 " =    2.608
peak=    3.284 closest distance to " O   HOH Z 251 " =    1.646
peak=    3.284 closest distance to " CB  HIS A 108 " =    0.850
peak=    3.282 closest distance to " O   HOH Z 132 " =    2.487
peak=    3.277 closest distance to " CA  THR A  42 " =    0.959
peak=    3.275 closest distance to " OD1 ASN A 301 " =    1.613
peak=    3.273 closest distance to " O   HOH Z  54 " =    1.624
peak=    3.269 closest distance to " CB  MET A  47 " =    1.109
peak=    3.261 closest distance to " OE1 GLU A   2 " =    2.264
peak=    3.260 closest distance to " O   HOH Z 383 " =    2.013
peak=    3.257 closest distance to " NH2BARG A 190 " =    1.736
peak=    3.257 closest distance to " O   HOH Z 345 " =    2.618
peak=    3.255 closest distance to " CB  ILE A 120 " =    1.309
peak=    3.253 closest distance to " O   HOH Z  48 " =    1.622
peak=    3.252 closest distance to " CA  SER A  32 " =    1.705
peak=    3.251 closest distance to " CZ3 TRP A  85 " =    0.959
peak=    3.249 closest distance to " O   HOH Z 250 " =    1.815
peak=    3.237 closest distance to " O   HOH Z 416 " =    2.957
peak=    3.237 closest distance to " CB  GLU A  46 " =    1.095
peak=    3.228 closest distance to " O   HOH Z 128 " =    1.489
peak=    3.228 closest distance to " O   HOH Z 343 " =    2.092
peak=    3.224 closest distance to " O   HOH Z 233 " =    1.704
peak=    3.223 closest distance to " O   HOH Z 334 " =    1.432
peak=    3.223 closest distance to " CA  ASN A 127 " =    1.132
peak=    3.221 closest distance to " O   HOH Z  30 " =    2.171
peak=    3.220 closest distance to " O   HOH Z 183 " =    1.948
peak=    3.218 closest distance to " O   HOH Z 305 " =    3.609
peak=    3.216 closest distance to " OG  SER A 245 " =    1.513
peak=    3.216 closest distance to " CE1 TYR A 186 " =    1.274
peak=    3.209 closest distance to " OD2 ASP A 286 " =    3.168
peak=    3.209 closest distance to " O   HOH Z 185 " =    1.769
peak=    3.198 closest distance to " CG  ARG A 269 " =    1.312
peak=    3.195 closest distance to " N   PHE A 130 " =    1.402
peak=    3.193 closest distance to " CB  PHE A  16 " =    1.102
peak=    3.189 closest distance to " CA  ALA A 129 " =    1.309
peak=    3.187 closest distance to " CG  GLU A  37 " =    0.867
peak=    3.185 closest distance to " CA  ALA A 100 " =    1.098
peak=    3.183 closest distance to " O   HOH Z 162 " =    1.882
peak=    3.178 closest distance to " O   HOH Z 423 " =    3.329
peak=    3.176 closest distance to " CA  VAL A 125 " =    1.153
peak=    3.174 closest distance to " O   HOH Z  46 " =    1.362
peak=    3.166 closest distance to " O   HOH Z 425 " =    1.275
peak=    3.163 closest distance to " O   HOH Z  22 " =    2.870
peak=    3.162 closest distance to " CD  GLN A 240 " =    1.502
peak=    3.162 closest distance to " O   HOH Z 244 " =    1.714
peak=    3.161 closest distance to " CB  ASP A 140 " =    1.117
peak=    3.160 closest distance to " CA  LYS A 117 " =    1.228
peak=    3.154 closest distance to " OD2 ASP A 298 " =    3.896
peak=    3.151 closest distance to " CG2 VAL A 197 " =    1.138
peak=    3.147 closest distance to " O   HOH Z 293 " =    1.824
peak=    3.146 closest distance to " O   HOH Z  19 " =    1.396
peak=    3.142 closest distance to " CA  SER A 146 " =    1.944
peak=    3.140 closest distance to " O   HOH Z  10 " =    1.758
peak=    3.140 closest distance to " OE1 GLN A 223 " =    2.289
peak=    3.138 closest distance to " OG1 THR A 294 " =    1.640
peak=    3.138 closest distance to " O   HOH Z 417 " =    2.142
peak=    3.134 closest distance to " CB  PRO A 243 " =    1.396
peak=    3.133 closest distance to " O   HOH Z 147 " =    1.833
peak=    3.130 closest distance to " CA  GLY A 241 " =    0.955
peak=    3.127 closest distance to " O   HOH Z 299 " =    4.343
peak=    3.125 closest distance to " CA  SER A  87 " =    1.032
peak=    3.124 closest distance to " CZ2 TRP A 179 " =    1.858
peak=    3.121 closest distance to " NE  ARG A  24 " =    0.917
peak=    3.119 closest distance to " O   HOH Z 420 " =    5.575
peak=    3.118 closest distance to " CB  LEU A  83 " =    0.783
peak=    3.116 closest distance to " CA  TYR A 116 " =    1.445
peak=    3.113 closest distance to " CG2 VAL A 202 " =    1.193
peak=    3.109 closest distance to " O   HOH Z 358 " =    2.244
peak=    3.109 closest distance to " O   HOH Z 298 " =    2.111
peak=    3.105 closest distance to " O   TYR A 116 " =    1.400
peak=    3.098 closest distance to " O   HOH Z 391 " =    2.956
peak=    3.093 closest distance to " O   TRP A 274 " =    1.669
peak=    3.083 closest distance to " CB  ALA A 100 " =    1.178
peak=    3.073 closest distance to " O   HOH Z 394 " =    3.711
peak=    3.062 closest distance to " O   HOH Z  63 " =    2.321
peak=    3.055 closest distance to " CA  ASP A 191 " =    0.963
peak=    3.003 closest distance to " OD1 ASN A 301 " =    1.051

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.767 - 5.952
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 207
   mapped sites are within: 0.767 - 5.952

peak=   -4.546 closest distance to " O   HOH Z 266 " =    5.173
peak=   -4.398 closest distance to " C   HIS A 108 " =    1.096
peak=   -4.354 closest distance to " OG BSER A 134 " =    1.419
peak=   -4.309 closest distance to " CD  ARG A  14 " =    3.457
peak=   -4.254 closest distance to " O   HOH Z 210 " =    0.847
peak=   -4.206 closest distance to " CD1 LEU A 101 " =    2.431
peak=   -4.179 closest distance to " CD  GLN A  58 " =    1.087
peak=   -4.167 closest distance to " O   HOH Z  13 " =    1.768
peak=   -4.111 closest distance to " OXT GLY A 302 " =    2.958
peak=   -4.033 closest distance to " CG2 ILE A  49 " =    2.716
peak=   -4.011 closest distance to " CG1AVAL A  41 " =    2.633
peak=   -4.011 closest distance to " CH2 TRP A 179 " =    1.318
peak=   -3.982 closest distance to " O   PRO A 163 " =    2.157
peak=   -3.924 closest distance to " O   HOH Z 165 " =    1.873
peak=   -3.923 closest distance to " O   PHE A 218 " =    1.557
peak=   -3.914 closest distance to " OE1 GLN A 223 " =    2.084
peak=   -3.890 closest distance to " C   THR A 279 " =    1.142
peak=   -3.867 closest distance to " CA  VAL A  67 " =    3.009
peak=   -3.863 closest distance to " O   PRO A 198 " =    1.330
peak=   -3.856 closest distance to " CD  GLN A  58 " =    1.177
peak=   -3.841 closest distance to " CD  ARG A 156 " =    2.036
peak=   -3.839 closest distance to " CZ  TYR A 169 " =    1.834
peak=   -3.816 closest distance to " O   HOH Z 377 " =    2.219
peak=   -3.789 closest distance to " O   HOH Z 348 " =    2.223
peak=   -3.788 closest distance to " O   HOH Z 374 " =    1.896
peak=   -3.781 closest distance to " O   GLY A 241 " =    2.304
peak=   -3.778 closest distance to " CD2 LEU A 237 " =    2.417
peak=   -3.770 closest distance to " CE2 TYR A  30 " =    2.831
peak=   -3.769 closest distance to " O   VAL A  67 " =    2.717
peak=   -3.767 closest distance to " CB  PRO A 243 " =    2.739
peak=   -3.739 closest distance to " CD2 TYR A 293 " =    1.916
peak=   -3.732 closest distance to " CG  ASP A 132 " =    2.291
peak=   -3.719 closest distance to " CB  ALA A 161 " =    2.573
peak=   -3.709 closest distance to " O   ALA A 256 " =    1.612
peak=   -3.703 closest distance to " O   HOH Z  81 " =    1.530
peak=   -3.702 closest distance to " CG  GLU A  53 " =    1.450
peak=   -3.699 closest distance to " O   HOH Z 102 " =    1.550
peak=   -3.692 closest distance to " O   HOH Z 183 " =    1.548
peak=   -3.691 closest distance to " O   HOH Z 290 " =    0.985
peak=   -3.670 closest distance to " O   SER A 210 " =    1.873
peak=   -3.668 closest distance to " O   HOH Z 174 " =    3.494
peak=   -3.667 closest distance to " ND2 ASN A  69 " =    1.792
peak=   -3.662 closest distance to " CZ  ARG A  66 " =    1.039
peak=   -3.650 closest distance to " O   VAL A 174 " =    2.160
peak=   -3.635 closest distance to " CG1 VAL A 112 " =    2.732
peak=   -3.626 closest distance to " CZ  TYR A 172 " =    1.837
peak=   -3.612 closest distance to " OG  SER A  97 " =    2.188
peak=   -3.609 closest distance to " NE2 GLN A  88 " =    1.619
peak=   -3.600 closest distance to " CB  PHE A 192 " =    2.047
peak=   -3.600 closest distance to " CD1 PHE A 130 " =    2.357
peak=   -3.594 closest distance to " O   HOH Z 252 " =    4.162
peak=   -3.588 closest distance to " CD  GLN A 223 " =    1.669
peak=   -3.582 closest distance to " O   HOH Z 166 " =    1.805
peak=   -3.579 closest distance to " CD1 LEU A  25 " =    2.515
peak=   -3.560 closest distance to " NE  ARG A  66 " =    4.449
peak=   -3.560 closest distance to " O   HOH Z 366 " =    1.549
peak=   -3.558 closest distance to " CD1 PHE A  59 " =    1.983
peak=   -3.552 closest distance to " O   HOH Z 171 " =    2.402
peak=   -3.552 closest distance to " CD  GLN A 223 " =    1.467
peak=   -3.541 closest distance to " CB  ALA A  43 " =    2.459
peak=   -3.540 closest distance to " O   ALA A   1 " =    1.901
peak=   -3.540 closest distance to " O   HOH Z 351 " =    1.464
peak=   -3.540 closest distance to " O   ALA A  34 " =    2.240
peak=   -3.533 closest distance to " CE BMET A  47 " =    1.507
peak=   -3.524 closest distance to " O   HOH Z 198 " =    1.444
peak=   -3.523 closest distance to " ND2 ASN A  45 " =    1.111
peak=   -3.517 closest distance to " O   HOH Z  71 " =    2.192
peak=   -3.516 closest distance to " NE2 GLN A  88 " =    1.087
peak=   -3.511 closest distance to " CB  ALA A  10 " =    2.343
peak=   -3.511 closest distance to " OE1 GLN A 183 " =    1.452
peak=   -3.510 closest distance to " OD2 ASP A 191 " =    1.441
peak=   -3.504 closest distance to " CB  ALA A 248 " =    2.279
peak=   -3.497 closest distance to " CA  GLY A 241 " =    3.103
peak=   -3.493 closest distance to " N   THR A  52 " =    1.715
peak=   -3.493 closest distance to " O   HOH Z  15 " =    1.521
peak=   -3.492 closest distance to " OD2 ASP A 171 " =    2.344
peak=   -3.491 closest distance to " N   ALA A 248 " =    1.739
peak=   -3.491 closest distance to " CE  MET A 105 " =    2.359
peak=   -3.490 closest distance to " O   HOH Z  59 " =    3.958
peak=   -3.487 closest distance to " CD2 TYR A 247 " =    2.385
peak=   -3.476 closest distance to " CD1 ILE A 106 " =    2.172
peak=   -3.475 closest distance to " OH  TYR A 169 " =    0.960
peak=   -3.474 closest distance to " CA  ASP A 298 " =    1.055
peak=   -3.474 closest distance to " CD2 HIS A 207 " =    2.321
peak=   -3.474 closest distance to " N   ALA A  43 " =    2.608
peak=   -3.472 closest distance to " O   GLY A  80 " =    2.551
peak=   -3.472 closest distance to " CD2 LEU A 237 " =    2.330
peak=   -3.470 closest distance to " O   HOH Z  81 " =    0.944
peak=   -3.465 closest distance to " CH2 TRP A 150 " =    1.113
peak=   -3.462 closest distance to " CG1 VAL A  78 " =    2.628
peak=   -3.458 closest distance to " O   HOH Z 377 " =    1.627
peak=   -3.456 closest distance to " CG2 VAL A 189 " =    2.196
peak=   -3.454 closest distance to " O   HOH Z 150 " =    2.151
peak=   -3.449 closest distance to " OD1 ASN A 148 " =    1.435
peak=   -3.440 closest distance to " O   HOH Z  11 " =    2.026
peak=   -3.432 closest distance to " N   ALA A 226 " =    1.881
peak=   -3.420 closest distance to " O  BHOH Z 338 " =    1.265
peak=   -3.419 closest distance to " O   HOH Z 126 " =    1.899
peak=   -3.410 closest distance to " CG  PHE A 283 " =    2.481
peak=   -3.409 closest distance to " OG BSER A 210 " =    1.374
peak=   -3.400 closest distance to " O   HOH Z  10 " =    1.625
peak=   -3.392 closest distance to " O   HOH Z 208 " =    1.816
peak=   -3.384 closest distance to " O   HOH Z  65 " =    0.767
peak=   -3.379 closest distance to " O   SER A 146 " =    1.084
peak=   -3.377 closest distance to " OD1 ASN A 301 " =    1.883
peak=   -3.372 closest distance to " CB  TRP A  85 " =    2.452
peak=   -3.372 closest distance to " O   HOH Z 198 " =    1.566
peak=   -3.368 closest distance to " O   TRP A  92 " =    2.009
peak=   -3.361 closest distance to " NH2 ARG A  66 " =    5.919
peak=   -3.357 closest distance to " CB  ALA A 291 " =    2.167
peak=   -3.349 closest distance to " NH2 ARG A  56 " =    2.119
peak=   -3.349 closest distance to " O   ALA A  10 " =    1.908
peak=   -3.341 closest distance to " CA  GLY A 133 " =    1.955
peak=   -3.340 closest distance to " O   HOH Z  38 " =    1.585
peak=   -3.340 closest distance to " O   HOH Z 166 " =    1.635
peak=   -3.339 closest distance to " O   HOH Z 111 " =    2.005
peak=   -3.336 closest distance to " O   HOH Z 234 " =    3.855
peak=   -3.335 closest distance to " O   HOH Z 301 " =    2.408
peak=   -3.332 closest distance to " OE2 GLU A   2 " =    1.758
peak=   -3.332 closest distance to " CG  MET A 105 " =    0.969
peak=   -3.329 closest distance to " O   HOH Z 193 " =    1.372
peak=   -3.324 closest distance to " CE3 TRP A 150 " =    2.119
peak=   -3.324 closest distance to " CZ  PHE A  38 " =    2.241
peak=   -3.321 closest distance to " N   SER A 276 " =    1.354
peak=   -3.317 closest distance to " CG  PRO A 243 " =    1.697
peak=   -3.316 closest distance to " NE2 GLN A  11 " =    1.750
peak=   -3.315 closest distance to " O   SER A  95 " =    1.681
peak=   -3.305 closest distance to " O   HOH Z 395 " =    5.089
peak=   -3.305 closest distance to " O   GLN A  11 " =    1.246
peak=   -3.299 closest distance to " CD2 PHE A  61 " =    2.144
peak=   -3.298 closest distance to " OD1 ASP A 171 " =    1.408
peak=   -3.297 closest distance to " ND2 ASN A  45 " =    1.661
peak=   -3.285 closest distance to " O   HOH Z 193 " =    2.041
peak=   -3.285 closest distance to " O   HOH Z 172 " =    5.407
peak=   -3.285 closest distance to " CD  ARG A  79 " =    1.274
peak=   -3.275 closest distance to " OG BSER A 134 " =    1.877
peak=   -3.275 closest distance to " O   GLN A  94 " =    2.160
peak=   -3.273 closest distance to " O   GLU A 152 " =    1.440
peak=   -3.270 closest distance to " O   HOH Z 244 " =    1.337
peak=   -3.268 closest distance to " O   HOH Z 422 " =    1.563
peak=   -3.268 closest distance to " C   GLN A 144 " =    0.921
peak=   -3.259 closest distance to " CD  ARG A 139 " =    1.584
peak=   -3.257 closest distance to " O   HOH Z 281 " =    2.486
peak=   -3.257 closest distance to " CG1 VAL A  67 " =    3.006
peak=   -3.257 closest distance to " O   HOH Z 211 " =    1.623
peak=   -3.257 closest distance to " O   HOH Z 174 " =    2.340
peak=   -3.254 closest distance to " ND2 ASN A 187 " =    1.563
peak=   -3.251 closest distance to " CE2 PHE A  61 " =    2.684
peak=   -3.249 closest distance to " O   HOH Z 418 " =    1.333
peak=   -3.248 closest distance to " O   HOH Z 313 " =    2.109
peak=   -3.243 closest distance to " ND2 ASN A  39 " =    1.133
peak=   -3.241 closest distance to " O   HOH Z 103 " =    1.841
peak=   -3.241 closest distance to " OE2 GLU A 152 " =    1.380
peak=   -3.236 closest distance to " O   HOH Z  88 " =    4.388
peak=   -3.229 closest distance to " CB  ALA A 291 " =    2.315
peak=   -3.227 closest distance to " NE2 GLN A  55 " =    1.754
peak=   -3.220 closest distance to " ND2BASN A 224 " =    1.810
peak=   -3.213 closest distance to " O   HOH Z 215 " =    3.991
peak=   -3.212 closest distance to " OG  SER A  26 " =    1.149
peak=   -3.209 closest distance to " NE2 GLN A 223 " =    1.172
peak=   -3.203 closest distance to " O   HOH Z 252 " =    3.359
peak=   -3.198 closest distance to " O   HOH Z  43 " =    4.758
peak=   -3.198 closest distance to " O   HOH Z 431 " =    4.196
peak=   -3.197 closest distance to " NH1 ARG A 195 " =    2.667
peak=   -3.195 closest distance to " O   HOH Z  53 " =    1.797
peak=   -3.194 closest distance to " O   ARG A  24 " =    1.887
peak=   -3.191 closest distance to " CD2 LEU A 282 " =    2.042
peak=   -3.190 closest distance to " CG  GLN A 103 " =    2.481
peak=   -3.189 closest distance to " O   HOH Z 362 " =    5.952
peak=   -3.189 closest distance to " O   HOH Z 433 " =    2.740
peak=   -3.187 closest distance to " CA  GLY A 203 " =    2.364
peak=   -3.186 closest distance to " O   HOH Z 396 " =    1.664
peak=   -3.181 closest distance to " O   HOH Z 109 " =    2.181
peak=   -3.180 closest distance to " C   GLY A  91 " =    1.329
peak=   -3.179 closest distance to " O   HOH Z 364 " =    5.080
peak=   -3.173 closest distance to " O   HOH Z 251 " =    1.587
peak=   -3.171 closest distance to " O   HOH Z 148 " =    3.832
peak=   -3.169 closest distance to " O   HOH Z 427 " =    1.513
peak=   -3.167 closest distance to " O   HOH Z 389 " =    1.731
peak=   -3.164 closest distance to " O   HOH Z 426 " =    1.732
peak=   -3.158 closest distance to " CD  LYS A 289 " =    2.308
peak=   -3.157 closest distance to " O   GLY A  80 " =    2.283
peak=   -3.153 closest distance to " NH2AARG A 275 " =    4.895
peak=   -3.148 closest distance to " CG1 VAL A 265 " =    2.677
peak=   -3.148 closest distance to " O   HOH Z 423 " =    2.284
peak=   -3.143 closest distance to " O   HOH Z 135 " =    1.386
peak=   -3.132 closest distance to " CZ3 TRP A 274 " =    2.169
peak=   -3.127 closest distance to " O   HOH Z 362 " =    4.249
peak=   -3.123 closest distance to " O   SER A  26 " =    1.367
peak=   -3.115 closest distance to " O   HOH Z 288 " =    1.322
peak=   -3.115 closest distance to " CA  GLY A 111 " =    2.522
peak=   -3.102 closest distance to " OXT GLY A 302 " =    3.172
peak=   -3.100 closest distance to " O   ASN A 301 " =    1.392
peak=   -3.094 closest distance to " CG  GLU A  46 " =    2.395
peak=   -3.091 closest distance to " C   SER A 206 " =    1.510
peak=   -3.088 closest distance to " O   HOH Z 283 " =    2.261
peak=   -3.078 closest distance to " O   HOH Z 156 " =    3.460
peak=   -3.076 closest distance to " OD1 ASN A  39 " =    2.259
peak=   -3.067 closest distance to " CB  ALA A   9 " =    2.438
peak=   -3.065 closest distance to " CD2 LEU A 300 " =    2.708
peak=   -3.053 closest distance to " O   HOH Z  52 " =    1.558
peak=   -3.041 closest distance to " NH2 ARG A  66 " =    5.134
peak=   -3.031 closest distance to " N   GLN A  58 " =    2.081
peak=   -3.002 closest distance to " O   HOH Z 414 " =    1.681
peak=   -3.002 closest distance to " CA  GLY A 241 " =    2.881

================= 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    :  0.4432 0.4366   6.249096e+00   6.242305e+00
   1_bss:  0.4362 0.4282   6.241709e+00   6.234350e+00
   1_xyz:  0.2917 0.3224   5.940970e+00   6.014276e+00
   1_adp:  0.2605 0.3283   5.880964e+00   6.032264e+00
   1_occ:  0.2604 0.3281   5.880627e+00   6.032364e+00
   2_bss:  0.2568 0.3226   5.872039e+00   6.024987e+00
   2_xyz:  0.1857 0.2347   5.573973e+00   5.761457e+00
   2_adp:  0.1674 0.2144   5.486062e+00   5.679173e+00
   2_occ:  0.1672 0.2142   5.485255e+00   5.678190e+00
   3_bss:  0.1669 0.2134   5.483253e+00   5.674759e+00
   3_xyz:  0.1411 0.1833   5.336093e+00   5.538054e+00
   3_adp:  0.1353 0.1790   5.304802e+00   5.512123e+00
   3_occ:  0.1352 0.1789   5.304548e+00   5.511911e+00
   4_bss:  0.1354 0.1788   5.305286e+00   5.511092e+00
   4_xyz:  0.1240 0.1662   5.225382e+00   5.442316e+00
   4_adp:  0.1221 0.1652   5.214988e+00   5.434384e+00
   4_occ:  0.1221 0.1652   5.214809e+00   5.434186e+00
   5_bss:  0.1221 0.1652   5.214888e+00   5.434281e+00
   5_xyz:  0.1155 0.1597   5.176688e+00   5.405904e+00
   5_adp:  0.1145 0.1595   5.171665e+00   5.403956e+00
   5_occ:  0.1144 0.1594   5.171292e+00   5.404007e+00
   5_bss:  0.1144 0.1594   5.171401e+00   5.404100e+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:  0.296  29.138   0.122   1.859  -0.040   0.000  -0.000  -0.000
   1_xyz:  0.296  29.138   0.122   1.859  -0.040   0.000  -0.000  -0.000
   1_adp:  0.296  29.138   0.122   1.859  -0.040   0.000  -0.000  -0.000
   1_occ:  0.296  29.138   0.122   1.859  -0.040   0.000  -0.000  -0.000
   2_bss:  0.323  56.592  -1.970  -0.194  -0.658  -0.000  -0.000  -0.000
   2_xyz:  0.323  56.592  -1.970  -0.194  -0.658  -0.000  -0.000  -0.000
   2_adp:  0.323  56.592  -1.970  -0.194  -0.658  -0.000  -0.000  -0.000
   2_occ:  0.323  56.592  -1.970  -0.194  -0.658  -0.000  -0.000  -0.000
   3_bss:  0.326  56.592  -3.065  -1.325  -1.007  -0.000  -0.000  -0.000
   3_xyz:  0.326  56.592  -3.065  -1.325  -1.007  -0.000  -0.000  -0.000
   3_adp:  0.326  56.592  -3.065  -1.325  -1.007  -0.000  -0.000  -0.000
   3_occ:  0.326  56.592  -3.065  -1.325  -1.007  -0.000  -0.000  -0.000
   4_bss:  0.326  56.592  -3.452  -1.819  -1.194  -0.000  -0.000  -0.000
   4_xyz:  0.326  56.592  -3.452  -1.819  -1.194  -0.000  -0.000  -0.000
   4_adp:  0.326  56.592  -3.452  -1.819  -1.194  -0.000  -0.000  -0.000
   4_occ:  0.326  56.592  -3.452  -1.819  -1.194  -0.000  -0.000  -0.000
   5_bss:  0.326  56.592  -3.380  -1.867  -1.110  -0.000  -0.000  -0.000
   5_xyz:  0.326  56.592  -3.380  -1.867  -1.110  -0.000  -0.000  -0.000
   5_adp:  0.326  56.592  -3.380  -1.867  -1.110  -0.000  -0.000  -0.000
   5_occ:  0.326  56.592  -3.380  -1.867  -1.110  -0.000  -0.000  -0.000
   5_bss:  0.325  56.595  -3.229  -1.784  -0.945  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.424 0.5037  0.6778    60289.624
   1_bss:  50.581 0.5127  0.7106    57469.636
   1_xyz:  33.381 0.7209  0.9434    27980.320
   1_adp:  34.426 0.7079  0.9341    29163.562
   1_occ:  34.460 0.7075  0.9331    29168.290
   2_bss:  33.955 0.7129  0.8899    28286.030
   2_xyz:  23.530 0.8251  0.9862    14098.231
   2_adp:  20.914 0.8527  0.9983    11994.210
   2_occ:  20.887 0.8530  0.9985    11971.481
   3_bss:  20.770 0.8539  0.9682    11808.151
   3_xyz:  17.374 0.8859  0.9857     8617.768
   3_adp:  16.799 0.8913  0.9847     8276.896
   3_occ:  16.792 0.8914  0.9847     8272.156
   4_bss:  16.782 0.8915  0.9725     8268.052
   4_xyz:  15.371 0.9034  0.9766     7128.894
   4_adp:  15.173 0.9053  0.9721     7034.686
   4_occ:  15.170 0.9053  0.9720     7030.986
   5_bss:  15.171 0.9053  0.9734     7032.476
   5_xyz:  14.613 0.9100  0.9767     6700.272
   5_adp:  14.543 0.9107  0.9720     6681.723
   5_occ:  14.543 0.9108  0.9717     6680.559
   5_bss:  14.547 0.9107  0.9764     6681.826
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   2.1973e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   2.1973e-01
   1_xyz:   1.465  0.012  0.089 15.395  0.005  4.104   1.1808e-01
   1_adp:   1.465  0.012  0.089 15.395  0.005  4.104   1.1808e-01
   1_occ:   1.465  0.012  0.089 15.395  0.005  4.104   1.1808e-01
   2_bss:   1.465  0.012  0.089 15.395  0.005  4.104   1.1808e-01
   2_xyz:   1.165  0.008  0.077 14.655  0.005  4.129   7.2118e-02
   2_adp:   1.165  0.008  0.077 14.655  0.005  4.129   7.2118e-02
   2_occ:   1.165  0.008  0.077 14.655  0.005  4.129   7.2118e-02
   3_bss:   1.165  0.008  0.077 14.655  0.005  4.129   7.2118e-02
   3_xyz:   0.923  0.006  0.064 14.359  0.004  4.118   5.1631e-02
   3_adp:   0.923  0.006  0.064 14.359  0.004  4.118   5.1631e-02
   3_occ:   0.923  0.006  0.064 14.359  0.004  4.118   5.1631e-02
   4_bss:   0.923  0.006  0.064 14.359  0.004  4.118   5.1631e-02
   4_xyz:   0.975  0.006  0.071 14.410  0.004  4.124   5.4132e-02
   4_adp:   0.975  0.006  0.071 14.410  0.004  4.124   5.4132e-02
   4_occ:   0.975  0.006  0.071 14.410  0.004  4.124   5.4132e-02
   5_bss:   0.975  0.006  0.071 14.410  0.004  4.124   5.4132e-02
   5_xyz:   1.019  0.007  0.076 14.507  0.004  4.112   6.0251e-02
   5_adp:   1.019  0.007  0.076 14.507  0.004  4.112   6.0251e-02
   5_occ:   1.019  0.007  0.076 14.507  0.004  4.112   6.0251e-02
   5_bss:   1.019  0.007  0.076 14.507  0.004  4.112   6.0251e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.014   2.4446e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.014   2.4446e-01
   1_xyz:   9.122  0.120  0.286 83.936  0.017  2.024   1.0345e-01
   1_adp:   9.122  0.120  0.286 83.936  0.017  2.024   1.0345e-01
   1_occ:   9.122  0.120  0.286 83.936  0.017  2.024   1.0345e-01
   2_bss:   9.122  0.120  0.286 83.936  0.017  2.024   1.0345e-01
   2_xyz:   7.870  0.055  0.246 80.793  0.043  2.136   6.2667e-02
   2_adp:   7.870  0.055  0.246 80.793  0.043  2.136   6.2667e-02
   2_occ:   7.870  0.055  0.246 80.793  0.043  2.136   6.2667e-02
   3_bss:   7.870  0.055  0.246 80.793  0.043  2.136   6.2667e-02
   3_xyz:   6.432  0.038  0.213 77.331  0.040  2.205   3.4094e-02
   3_adp:   6.432  0.038  0.213 77.331  0.040  2.205   3.4094e-02
   3_occ:   6.432  0.038  0.213 77.331  0.040  2.205   3.4094e-02
   4_bss:   6.432  0.038  0.213 77.331  0.040  2.205   3.4094e-02
   4_xyz:   6.807  0.041  0.224 82.863  0.037  2.324   3.7287e-02
   4_adp:   6.807  0.041  0.224 82.863  0.037  2.324   3.7287e-02
   4_occ:   6.807  0.041  0.224 82.863  0.037  2.324   3.7287e-02
   5_bss:   6.807  0.041  0.224 82.863  0.037  2.324   3.7287e-02
   5_xyz:   7.227  0.043  0.251 82.325  0.035  2.362   5.0955e-02
   5_adp:   7.227  0.043  0.251 82.325  0.035  2.362   5.0955e-02
   5_occ:   7.227  0.043  0.251 82.325  0.035  2.362   5.0955e-02
   5_bss:   7.227  0.043  0.251 82.325  0.035  2.362   5.0955e-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:  99.68   0.00  18.74  85.09   0.00  14.62  99.68   2.95  41.18
   1_occ:  99.68   0.00  18.74  85.09   0.00  14.62  99.68   2.95  41.18
   2_bss:  99.68   0.00  18.74  85.09   0.00  14.62  99.68   2.95  41.18
   2_xyz:  99.68   0.00  18.74  85.09   0.00  14.62  99.68   2.95  41.18
   2_adp:  95.51   0.00  18.16  88.47   0.00  13.82  95.51   5.55  41.80
   2_occ:  95.51   0.00  18.16  88.47   0.00  13.82  95.51   5.55  41.80
   3_bss:  95.51   0.00  18.16  88.47   0.00  13.82  95.51   5.55  41.80
   3_xyz:  95.51   0.00  18.16  88.47   0.00  13.82  95.51   5.55  41.80
   3_adp:  95.07   1.18  17.96  90.64   1.18  13.51  95.07   6.23  42.17
   3_occ:  95.07   1.18  17.96  90.64   1.18  13.51  95.07   6.23  42.17
   4_bss:  95.07   1.18  17.96  90.64   1.18  13.51  95.07   6.23  42.17
   4_xyz:  95.07   1.18  17.96  90.64   1.18  13.51  95.07   6.23  42.17
   4_adp:  94.55   1.27  17.74  92.27   1.27  13.31  94.55   5.99  41.83
   4_occ:  94.55   1.27  17.74  92.27   1.27  13.31  94.55   5.99  41.83
   5_bss:  94.55   1.27  17.74  92.27   1.27  13.31  94.55   5.99  41.83
   5_xyz:  94.55   1.27  17.74  92.27   1.27  13.31  94.55   5.99  41.83
   5_adp:  96.37   0.00  17.60  96.37   0.91  13.17  93.81   0.00  41.72
   5_occ:  96.37   0.00  17.60  96.37   0.91  13.17  93.81   0.00  41.72
   5_bss:  96.37   0.00  17.60  96.37   0.92  13.18  93.82   0.00  41.72
------------------------------------------------------------------------
 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:    3.414    0.011    0.440
   1_adp:    3.414    0.011    0.440
   1_occ:    3.414    0.011    0.440
   2_bss:    3.414    0.011    0.440
   2_xyz:    3.487    0.042    0.568
   2_adp:    3.487    0.042    0.568
   2_occ:    3.487    0.042    0.568
   3_bss:    3.487    0.042    0.568
   3_xyz:    3.546    0.051    0.637
   3_adp:    3.546    0.051    0.637
   3_occ:    3.546    0.051    0.637
   4_bss:    3.546    0.051    0.637
   4_xyz:    3.606    0.061    0.665
   4_adp:    3.606    0.061    0.665
   4_occ:    3.606    0.061    0.665
   5_bss:    3.606    0.061    0.665
   5_xyz:    3.709    0.071    0.685
   5_adp:    3.709    0.071    0.685
   5_occ:    3.709    0.071    0.685
   5_bss:    3.709    0.071    0.685
------------------------------------------------------------------------

CPU time actual refinement: 349.60


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_95/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_95/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_95/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_95/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_95/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 349.46 
  Macro-tasks:
    bulk solvent and scale       = 39.36  
    individual site refinement   = 151.07 
    weights calculation          = 30.61  
    collect and process          = 6.76   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 227.88 
  Micro-tasks:
    mask                            = 1.69   
    f_calc                          = 114.43 
    alpha_beta                      = 8.47   
    target                          = 1.24   
    gradients_wrt_atomic_parameters = 119.14 
    fmodel                         = 6.82   
    r_factors                      = 0.21   
    phase_errors                   = 11.77  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 264.01 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.871 micro seconds
Total CPU time: 6.04 minutes
from_scatterers_fft:    659 calls, 113.89 s
gradients_fft:          604 calls, 106.95 s

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

# Date 2008-01-16 Time 04:00:23 PST -0800 (1200484823.35 s)
Start R-work = 0.4432, R-free = 0.4366 (no bulk solvent and anisotropic scale)
Final R-work = 0.1394, R-free = 0.1792 (no bulk solvent and anisotropic scale)

Start R-work = 0.4362, R-free = 0.4282
Final R-work = 0.1144, R-free = 0.1594