# Date 2008-01-16 Time 03:44:15 PST -0800 (1200483855.52 s)
#phil __OFF__

Command line arguments: "../26.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 12424
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 26

-------------------------------------------------------------------------------
  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, 46.2261, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 46.2261, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6986 1.95068
Completeness in resolution range: 0.95757
Completeness with d_max=infinity: 0.954583

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.6986
                             d_min =   1.9507

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, 46.2261, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6986 1.95068
Completeness in resolution range: 0.95757
Completeness with d_max=infinity: 0.954583

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.6990 -  4.1735 [2157/2184]  1939   218  10.1%
  bin  2:  4.1735 -  3.3253 [2055/2071]  1853   202   9.8%
  bin  3:  3.3253 -  2.9086 [2043/2062]  1838   205  10.0%
  bin  4:  2.9086 -  2.6444 [2012/2042]  1810   202  10.0%
  bin  5:  2.6444 -  2.4558 [2005/2024]  1801   204  10.2%
  bin  6:  2.4558 -  2.3116 [1991/2016]  1794   197   9.9%
  bin  7:  2.3116 -  2.1962 [1992/2026]  1798   194   9.7%
  bin  8:  2.1962 -  2.1009 [1975/2006]  1775   200  10.1%
  bin  9:  2.1009 -  2.0202 [1972/2013]  1775   197  10.0%
  bin 10:  2.0202 -  1.9507 [1387/2013]  1247   140  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_26/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.12 -     1.88: 15
        1.88 -     2.63: 123
        2.63 -     3.39: 4409
        3.39 -     4.14: 9640
        4.14 -     4.90: 14890
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.119 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.310 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.467 3.040 -x+1,y+1/2,-z+1/2
  " NE2 GLN A  55 " - " O   ASN A 285 "  1.516 3.120 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.736 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 29072 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_26/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_26/model_refine_001.geo

CPU time processing inputs: 9.21


============================ 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 46.22605 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4368   r_free= 0.4308   ksol= 0.00   Bsol= 0.00   scale= 0.932    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.240689                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6990 -  4.6547 0.99   1398  154 0.3483 0.3400      6.4991         6.5|
|  2:  4.6547 -  3.7142 0.99   1336  153 0.3621 0.3405       6.711      6.6884|
|  3:  3.7142 -  3.2505 0.99   1321  145 0.4081 0.4074      6.6198      6.6883|
|  4:  3.2505 -  2.9560 0.99   1306  138 0.4119 0.4283      6.4738      6.5273|
|  5:  2.9560 -  2.7456 0.99   1305  148 0.4545 0.4096      6.3152      6.2951|
|  6:  2.7456 -  2.5846 0.99   1286  148 0.4694 0.4909      6.2428      6.1984|
|  7:  2.5846 -  2.4558 0.99   1289  145 0.4744 0.4466      6.2181      6.1278|
|  8:  2.4558 -  2.3493 0.98   1295  135 0.4846 0.5014      6.1648      6.2019|
|  9:  2.3493 -  2.2592 0.98   1274  148 0.4884 0.4865      6.0913      6.1247|
| 10:  2.2592 -  2.1815 0.98   1271  139 0.4923 0.4786      6.0943      6.0609|
| 11:  2.1815 -  2.1135 0.99   1281  142 0.4847 0.5097      6.0106      6.0315|
| 12:  2.1135 -  2.0533 0.97   1262  140 0.4888 0.4794      5.9557      6.0256|
| 13:  2.0533 -  1.9993 0.99   1256  140 0.4986 0.4465      5.8748      5.8028|
| 14:  1.9993 -  1.9507 0.58    750   84 0.5083 0.5173       5.871      5.7608|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6990 -  4.6547  1398   154  0.72  32.36   0.84     0.76      64067.24|
|  2:  4.6547 -  3.7142  1336   153  0.73  32.32   0.94     0.85      92651.49|
|  3:  3.7142 -  3.2505  1321   145  0.64  40.76   0.96     0.83     100156.59|
|  4:  3.2505 -  2.9560  1306   138  0.57  46.41   0.97     0.77      89912.23|
|  5:  2.9560 -  2.7456  1305   148  0.51  51.40   0.93     0.72      69294.01|
|  6:  2.7456 -  2.5846  1286   148  0.51  51.34   0.90     0.71      58175.49|
|  7:  2.5846 -  2.4558  1289   145  0.49  52.90   0.95     0.69      54022.27|
|  8:  2.4558 -  2.3493  1295   135  0.45  55.81   0.95     0.66      51580.91|
|  9:  2.3493 -  2.2592  1274   148  0.44  56.89   0.94     0.65      48615.08|
| 10:  2.2592 -  2.1815  1271   139  0.45  56.01   0.98     0.67      42784.07|
| 11:  2.1815 -  2.1135  1281   142  0.44  56.53   0.97     0.69      39770.88|
| 12:  2.1135 -  2.0533  1262   140  0.43  57.84   1.00     0.66      36700.62|
| 13:  2.0533 -  1.9993  1256   140  0.37  62.33   1.00     0.58      33916.14|
| 14:  1.9993 -  1.9507   750    84  0.34  64.73   0.98     0.45      28840.57|
|alpha:            min =        0.45 max =            0.85 mean =         0.70|
|beta:             min =    28840.57 max =       100156.59 mean =     59135.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.51|
|phase err.(work): min =        0.00 max =           90.00 mean =        50.62|
|phase err.(test): min =        0.00 max =           89.96 mean =        50.41|
|-----------------------------------------------------------------------------|

============================== 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 = 9.328702              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.090   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.706075              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.821   (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 |  1.119 -  1.497:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.497 -  1.875:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.875 -  2.254:       37 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.254 -  2.632:       86 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.632 -  3.010:     1986 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.010 -  3.388:     2423 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.388 -  3.766:     4072 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.766 -  4.144:     5568 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.144 -  4.522:     6627 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.522 -  4.900:     8263 |
|-----------------------------------------------------------------------------|
|-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 |        0.225 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.106    4.900  1.119 |       1.161 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.300)------------------------------------------|
|    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 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4368   r_free= 0.4308   ksol= 0.00   Bsol= 0.00   scale= 0.932    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.240689                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4266   r_free= 0.4212   ksol= 0.33   Bsol= 20.00   scale= 0.960   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.67,1.28,-1.58,0.00,-0.00,-0.00); trace/3= 0.12                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.230350                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.777283              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.921   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.927015              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.557   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4266      final r-factor (work) = 0.2846          |
| start r-factor (free) = 0.4212      final r-factor (free) = 0.3180          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.4541 = 7.78 * 0.50 * 6.2308 + 1.00 * 0.2247                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.6820 = 7.78 * 0.50 * 6.0585 + 1.00 * 0.1225                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2846      final r-factor (work) = 0.2565          |
| start r-factor (free) = 0.3180      final r-factor (free) = 0.3273          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6226 = 0.93 * 1.00 * 6.0585 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4444 = 0.93 * 1.00 * 5.8557 + 1.00 * 0.0161                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.300)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.77  18.59    None  None   None       |
|    all(noH): 2823   0      0.00    100.77  18.59    None  None   None       |
|    Sol.    : 438    0      2.61    100.77  41.20    None  None   None       |
|    Mac.    : 2385   0      0.00    85.02   14.44    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.077:  956   |   5:    50.385 -  60.462:   95        |
|      1:    10.077 -  20.154:  978   |   6:    60.462 -  70.539:   52        |
|      2:    20.154 -  30.231:  392   |   7:    70.539 -  80.616:   24        |
|      3:    30.231 -  40.308:  202   |   8:    80.616 -  90.693:    1        |
|      4:    40.308 -  50.385:  121   |   9:    90.693 - 100.770:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2565 r_free = 0.3273             target_work(ml) = 5.870         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2563 r_free = 0.3280             target_work(ml) = 5.870         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2563   r_free= 0.3280   ksol= 0.33   Bsol= 20.00   scale= 1.043   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.67,1.28,-1.58,0.00,-0.00,-0.00); trace/3= 0.12                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.870028                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2523   r_free= 0.3240   ksol= 0.33   Bsol= 34.48   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.70,-0.76,-1.05,-0.00,-0.00,-0.00); trace/3= -1.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.856829                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.423165              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.268   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.322246              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.969   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2523      final r-factor (work) = 0.1862          |
| start r-factor (free) = 0.3240      final r-factor (free) = 0.2448          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.0666 = 4.42 * 0.50 * 5.8527 + 1.00 * 0.1228                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7619 = 4.42 * 0.50 * 5.7423 + 1.00 * 0.0623                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1862      final r-factor (work) = 0.1708          |
| start r-factor (free) = 0.2448      final r-factor (free) = 0.2248          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8661 = 0.32 * 1.00 * 5.7423 + 1.00 * 0.0157                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7971 = 0.32 * 1.00 * 5.5457 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.300)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.03   17.73    None  None   None       |
|    all(noH): 2823   0      0.00    89.03   17.73    None  None   None       |
|    Sol.    : 438    0      5.59    86.18   40.66    None  None   None       |
|    Mac.    : 2385   0      0.00    89.03   13.52    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.903:  772   |   5:    44.514 -  53.417:  103        |
|      1:     8.903 -  17.806: 1205   |   6:    53.417 -  62.320:   85        |
|      2:    17.806 -  26.708:  320   |   7:    62.320 -  71.223:   20        |
|      3:    26.708 -  35.611:  168   |   8:    71.223 -  80.125:   11        |
|      4:    35.611 -  44.514:  136   |   9:    80.125 -  89.028:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1708 r_free = 0.2248             target_work(ml) = 5.508         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1706 r_free = 0.2243             target_work(ml) = 5.507         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1706   r_free= 0.2243   ksol= 0.33   Bsol= 34.48   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.70,-0.76,-1.05,-0.00,-0.00,-0.00); trace/3= -1.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.506859                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1705   r_free= 0.2239   ksol= 0.31   Bsol= 35.40   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-1.69,-1.07,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.504192                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.578739              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.204  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.198211              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.246  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1705      final r-factor (work) = 0.1358          |
| start r-factor (free) = 0.2239      final r-factor (free) = 0.1825          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2143 = 2.58 * 0.50 * 5.5470 + 1.00 * 0.0623                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0246 = 2.58 * 0.50 * 5.4052 + 1.00 * 0.0552                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1358      final r-factor (work) = 0.1288          |
| start r-factor (free) = 0.1825      final r-factor (free) = 0.1737          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0809 = 0.20 * 1.00 * 5.4052 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0537 = 0.20 * 1.00 * 5.2769 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.300)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.07    89.11   17.26    None  None   None       |
|    all(noH): 2823   0      1.07    89.11   17.26    None  None   None       |
|    Sol.    : 438    0      4.57    84.46   40.16    None  None   None       |
|    Mac.    : 2385   0      1.07    89.11   13.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.071 -   9.875:  965   |   5:    45.089 -  53.893:  104        |
|      1:     9.875 -  18.678: 1149   |   6:    53.893 -  62.697:   72        |
|      2:    18.678 -  27.482:  242   |   7:    62.697 -  71.500:   22        |
|      3:    27.482 -  36.286:  128   |   8:    71.500 -  80.304:    7        |
|      4:    36.286 -  45.089:  130   |   9:    80.304 -  89.108:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1288 r_free = 0.1737             target_work(ml) = 5.250         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1286 r_free = 0.1737             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1286   r_free= 0.1737   ksol= 0.31   Bsol= 35.40   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-1.69,-1.07,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.249136                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1284   r_free= 0.1730   ksol= 0.31   Bsol= 35.40   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.02,-2.30,-1.30,-0.00,-0.00,-0.00); trace/3= -2.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.247719                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.229904              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 127.371  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.374719              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.546  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1284      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1730      final r-factor (free) = 0.1610          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5799 = 3.23 * 0.50 * 5.2786 + 1.00 * 0.0552                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4555 = 3.23 * 0.50 * 5.1949 + 1.00 * 0.0661                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1111          |
| start r-factor (free) = 0.1610      final r-factor (free) = 0.1582          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9544 = 0.37 * 1.00 * 5.1949 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9357 = 0.37 * 1.00 * 5.1443 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.300)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.76    90.06   17.11    None  None   None       |
|    all(noH): 2823   0      0.76    90.06   17.11    None  None   None       |
|    Sol.    : 438    0      4.84    84.93   40.08    None  None   None       |
|    Mac.    : 2385   0      0.76    90.06   12.89    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:     0.764 -   9.694:  959   |   5:    45.413 -  54.343:  103        |
|      1:     9.694 -  18.624: 1174   |   6:    54.343 -  63.272:   67        |
|      2:    18.624 -  27.553:  238   |   7:    63.272 -  72.202:   25        |
|      3:    27.553 -  36.483:  118   |   8:    72.202 -  81.132:    6        |
|      4:    36.483 -  45.413:  129   |   9:    81.132 -  90.062:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1111 r_free = 0.1582             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1110 r_free = 0.1584             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1110   r_free= 0.1584   ksol= 0.31   Bsol= 35.40   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.02,-2.30,-1.30,-0.00,-0.00,-0.00); trace/3= -2.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.136858                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1109   r_free= 0.1584   ksol= 0.32   Bsol= 37.49   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.99,-2.33,-1.19,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.136447                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.141140              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 138.016  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 7.439516              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 104.222  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1109      final r-factor (work) = 0.1076          |
| start r-factor (free) = 0.1584      final r-factor (free) = 0.1568          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1453 = 3.14 * 0.50 * 5.1441 + 1.00 * 0.0661                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1145 = 3.14 * 0.50 * 5.1241 + 1.00 * 0.0667                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1076      final r-factor (work) = 0.1064          |
| start r-factor (free) = 0.1568      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 38.1289 = 7.44 * 1.00 * 5.1241 + 1.00 * 0.0080                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 38.0368 = 7.44 * 1.00 * 5.1115 + 1.00 * 0.0096                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.300)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.94   17.21    None  None   None       |
|    all(noH): 2823   0      0.00    97.94   17.21    None  None   None       |
|    Sol.    : 438    0      6.04    90.61   41.05    None  None   None       |
|    Mac.    : 2385   0      0.00    97.94   12.83    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 -   9.794: 1039   |   5:    48.970 -  58.764:   95        |
|      1:     9.794 -  19.588: 1137   |   6:    58.764 -  68.558:   52        |
|      2:    19.588 -  29.382:  218   |   7:    68.558 -  78.352:   24        |
|      3:    29.382 -  39.176:  127   |   8:    78.352 -  88.146:    6        |
|      4:    39.176 -  48.970:  121   |   9:    88.146 -  97.940:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1064 r_free = 0.1572             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1064 r_free = 0.1574             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1064   r_free= 0.1574   ksol= 0.32   Bsol= 37.49   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.99,-2.33,-1.19,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.115659                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6990 -  4.6547 0.99   1398  154 0.0973 0.1266      5.3694      5.5434|
|  2:  4.6547 -  3.7142 0.99   1336  153 0.0812 0.1144      5.4142      5.6182|
|  3:  3.7142 -  3.2505 0.99   1321  145 0.1021 0.1525      5.4484      5.8411|
|  4:  3.2505 -  2.9560 0.99   1306  138 0.1136 0.1553      5.4052      5.5679|
|  5:  2.9560 -  2.7456 0.99   1305  148 0.1212 0.1684      5.2699       5.515|
|  6:  2.7456 -  2.5846 0.99   1286  148 0.1158 0.1888      5.1639      5.4414|
|  7:  2.5846 -  2.4558 0.99   1289  145 0.1156 0.1542      5.1232       5.302|
|  8:  2.4558 -  2.3493 0.98   1295  135 0.1089 0.1639      5.0365      5.3077|
|  9:  2.3493 -  2.2592 0.98   1274  148 0.1144 0.1847      5.0077      5.3272|
| 10:  2.2592 -  2.1815 0.98   1271  139 0.1044 0.1658      4.9286      5.1538|
| 11:  2.1815 -  2.1135 0.99   1281  142 0.1069 0.1860       4.909      5.3041|
| 12:  2.1135 -  2.0533 0.97   1262  140 0.1055 0.1571       4.857       5.135|
| 13:  2.0533 -  1.9993 0.99   1256  140 0.1046 0.1801       4.765      5.0321|
| 14:  1.9993 -  1.9507 0.58    750   84 0.0997 0.1910      4.6691      4.9882|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6990 -  4.6547  1398   154  0.94   9.06   0.99     0.96       7078.52|
|  2:  4.6547 -  3.7142  1336   153  0.95   7.85   1.03     1.02       9036.99|
|  3:  3.7142 -  3.2505  1321   145  0.93  11.21   1.04     1.03      10135.05|
|  4:  3.2505 -  2.9560  1306   138  0.93  12.80   1.02     1.01       9592.75|
|  5:  2.9560 -  2.7456  1305   148  0.91  15.22   1.01     0.98       7768.39|
|  6:  2.7456 -  2.5846  1286   148  0.90  15.52   0.99     0.96       6578.41|
|  7:  2.5846 -  2.4558  1289   145  0.91  15.30   0.99     0.95       5881.35|
|  8:  2.4558 -  2.3493  1295   135  0.91  14.71   1.00     0.98       5127.49|
|  9:  2.3493 -  2.2592  1274   148  0.91  15.18   1.01     0.98       4885.96|
| 10:  2.2592 -  2.1815  1271   139  0.90  15.74   1.00     0.96       4334.32|
| 11:  2.1815 -  2.1135  1281   142  0.90  16.15   1.00     0.97       4306.73|
| 12:  2.1135 -  2.0533  1262   140  0.91  15.46   1.02     1.02       3968.17|
| 13:  2.0533 -  1.9993  1256   140  0.90  15.92   1.01     0.99       3315.72|
| 14:  1.9993 -  1.9507   750    84  0.91  14.78   0.99     0.96       2657.10|
|alpha:            min =        0.95 max =            1.03 mean =         0.99|
|beta:             min =     2657.10 max =        10135.05 mean =      6189.46|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.81 mean =        13.83|
|phase err.(test): min =        0.00 max =           88.61 mean =        13.46|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1063   r_free= 0.1573   ksol= 0.32   Bsol= 41.55   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-2.21,-1.01,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.115127                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1063   r_free= 0.1573   ksol= 0.32   Bsol= 41.55   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-2.21,-1.01,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.115127                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6990 -  4.6547 0.99   1398  154 0.0974 0.1265      5.3698      5.5441|
|  2:  4.6547 -  3.7142 0.99   1336  153 0.0815 0.1147      5.4165      5.6202|
|  3:  3.7142 -  3.2505 0.99   1321  145 0.1023 0.1526        5.45      5.8429|
|  4:  3.2505 -  2.9560 0.99   1306  138 0.1136 0.1550      5.4047      5.5664|
|  5:  2.9560 -  2.7456 0.99   1305  148 0.1210 0.1680      5.2684      5.5132|
|  6:  2.7456 -  2.5846 0.99   1286  148 0.1156 0.1883      5.1624      5.4388|
|  7:  2.5846 -  2.4558 0.99   1289  145 0.1155 0.1540      5.1214      5.3005|
|  8:  2.4558 -  2.3493 0.98   1295  135 0.1087 0.1636       5.035      5.3055|
|  9:  2.3493 -  2.2592 0.98   1274  148 0.1144 0.1849      5.0071      5.3277|
| 10:  2.2592 -  2.1815 0.98   1271  139 0.1042 0.1656      4.9281      5.1531|
| 11:  2.1815 -  2.1135 0.99   1281  142 0.1068 0.1858       4.908      5.3027|
| 12:  2.1135 -  2.0533 0.97   1262  140 0.1054 0.1572      4.8563      5.1344|
| 13:  2.0533 -  1.9993 0.99   1256  140 0.1046 0.1800      4.7641      5.0313|
| 14:  1.9993 -  1.9507 0.58    750   84 0.0995 0.1905      4.6671      4.9857|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6990 -  4.6547  1398   154  0.94   9.07   0.99     0.96       7090.53|
|  2:  4.6547 -  3.7142  1336   153  0.95   7.86   1.04     1.02       9061.94|
|  3:  3.7142 -  3.2505  1321   145  0.93  11.23   1.05     1.04      10160.73|
|  4:  3.2505 -  2.9560  1306   138  0.93  12.79   1.03     1.02       9579.03|
|  5:  2.9560 -  2.7456  1305   148  0.91  15.20   1.01     0.99       7745.24|
|  6:  2.7456 -  2.5846  1286   148  0.90  15.49   0.99     0.97       6556.69|
|  7:  2.5846 -  2.4558  1289   145  0.91  15.27   1.00     0.96       5855.36|
|  8:  2.4558 -  2.3493  1295   135  0.91  14.68   1.01     0.99       5109.99|
|  9:  2.3493 -  2.2592  1274   148  0.91  15.17   1.02     0.99       4876.82|
| 10:  2.2592 -  2.1815  1271   139  0.90  15.73   1.01     0.97       4329.93|
| 11:  2.1815 -  2.1135  1281   142  0.90  16.13   1.01     0.98       4295.78|
| 12:  2.1135 -  2.0533  1262   140  0.91  15.44   1.03     1.03       3961.11|
| 13:  2.0533 -  1.9993  1256   140  0.90  15.89   1.02     0.99       3306.97|
| 14:  1.9993 -  1.9507   750    84  0.91  14.73   1.00     0.96       2644.95|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2644.95 max =        10160.73 mean =      6183.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.82|
|phase err.(test): min =        0.00 max =           88.35 mean =        13.45|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.300)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.94   17.21    None  None   None       |
|    all(noH): 2823   0      0.00    97.94   17.21    None  None   None       |
|    Sol.    : 438    0      6.05    90.61   41.05    None  None   None       |
|    Mac.    : 2385   0      0.00    97.94   12.84    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 -   9.797: 1039   |   5:    48.973 -  58.767:   95        |
|      1:     9.797 -  19.591: 1137   |   6:    58.767 -  68.561:   52        |
|      2:    19.591 -  29.385:  218   |   7:    68.561 -  78.355:   24        |
|      3:    29.385 -  39.179:  127   |   8:    78.355 -  88.149:    6        |
|      4:    39.179 -  48.973:  121   |   9:    88.149 -  97.943:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 279         
Filter by distance & map next to the model:
   mapped sites are within: 0.495 - 4.370
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 276 from: 279
   mapped sites are within: 0.723 - 4.370

peak=    6.651 closest distance to " O   HOH Z 142 " =    1.895
peak=    6.291 closest distance to " NE2 GLN A  11 " =    1.179
peak=    6.024 closest distance to " O   HOH Z 375 " =    1.281
peak=    5.975 closest distance to " O   HOH Z 126 " =    1.941
peak=    5.707 closest distance to " O   HOH Z 236 " =    1.508
peak=    5.518 closest distance to " CB  ARG A 275 " =    0.948
peak=    5.393 closest distance to " NH2 ARG A  56 " =    2.107
peak=    5.278 closest distance to " O   HOH Z 417 " =    1.525
peak=    5.072 closest distance to " CG  PRO A  54 " =    1.181
peak=    4.847 closest distance to " O   HOH Z 427 " =    2.720
peak=    4.716 closest distance to " CG  PRO A 213 " =    1.239
peak=    4.709 closest distance to " O   HOH Z 371 " =    1.928
peak=    4.707 closest distance to " O   HOH Z 193 " =    1.642
peak=    4.642 closest distance to " O   HOH Z 287 " =    1.732
peak=    4.639 closest distance to " O   HOH Z  78 " =    1.709
peak=    4.617 closest distance to " O   HOH Z 403 " =    1.795
peak=    4.609 closest distance to " O   HOH Z 209 " =    2.222
peak=    4.597 closest distance to " O   HOH Z 272 " =    1.802
peak=    4.564 closest distance to " OG BSER A 164 " =    2.130
peak=    4.558 closest distance to " NZ  LYS A 117 " =    2.947
peak=    4.552 closest distance to " O   HOH Z 316 " =    2.958
peak=    4.551 closest distance to " CB  GLN A 183 " =    1.216
peak=    4.537 closest distance to " O   HOH Z 250 " =    2.402
peak=    4.536 closest distance to " O   HOH Z 369 " =    2.235
peak=    4.529 closest distance to " CB  SER A  63 " =    1.183
peak=    4.528 closest distance to " O   HOH Z 112 " =    1.295
peak=    4.528 closest distance to " C   PRO A 198 " =    1.470
peak=    4.518 closest distance to " O   HOH Z 416 " =    2.299
peak=    4.503 closest distance to " O   HOH Z 327 " =    1.702
peak=    4.482 closest distance to " CG  ARG A  66 " =    2.673
peak=    4.470 closest distance to " CA  TYR A  30 " =    0.932
peak=    4.462 closest distance to " CB  GLN A 223 " =    1.548
peak=    4.419 closest distance to " O   SER A  87 " =    2.237
peak=    4.396 closest distance to " CB  GLU A 152 " =    1.274
peak=    4.386 closest distance to " CB  ARG A  79 " =    1.406
peak=    4.362 closest distance to " O   HOH Z  44 " =    1.812
peak=    4.269 closest distance to " O   HOH Z 298 " =    1.865
peak=    4.265 closest distance to " O   HOH Z   9 " =    2.344
peak=    4.225 closest distance to " O   HOH Z 203 " =    1.739
peak=    4.218 closest distance to " O   HOH Z 128 " =    2.049
peak=    4.206 closest distance to " O   HOH Z 189 " =    1.906
peak=    4.177 closest distance to " CB  ASN A 148 " =    1.430
peak=    4.158 closest distance to " O   HOH Z  93 " =    2.259
peak=    4.132 closest distance to " O   HOH Z 425 " =    2.122
peak=    4.116 closest distance to " O   HOH Z 402 " =    1.416
peak=    4.082 closest distance to " CD2 TRP A 179 " =    1.382
peak=    4.068 closest distance to " O   HOH Z 245 " =    1.326
peak=    4.064 closest distance to " CB  SER A  26 " =    1.711
peak=    4.040 closest distance to " CB  ARG A 190 " =    1.676
peak=    4.029 closest distance to " CG  TRP A 179 " =    2.196
peak=    4.020 closest distance to " ND2 ASN A 187 " =    1.264
peak=    4.019 closest distance to " O   HOH Z 419 " =    2.114
peak=    4.013 closest distance to " O   HOH Z  61 " =    1.627
peak=    3.965 closest distance to " O   HOH Z 250 " =    1.462
peak=    3.961 closest distance to " O   HOH Z 368 " =    3.578
peak=    3.954 closest distance to " O   HOH Z 423 " =    2.490
peak=    3.951 closest distance to " O   HOH Z 289 " =    1.672
peak=    3.951 closest distance to " CB  PRO A  54 " =    0.925
peak=    3.931 closest distance to " O   HOH Z 132 " =    1.973
peak=    3.919 closest distance to " O   HOH Z 344 " =    3.190
peak=    3.910 closest distance to " NZ  LYS A 119 " =    2.765
peak=    3.896 closest distance to " O   HOH Z   1 " =    1.968
peak=    3.877 closest distance to " O   HOH Z 234 " =    3.454
peak=    3.870 closest distance to " O   HOH Z  97 " =    1.926
peak=    3.869 closest distance to " O   HOH Z 257 " =    2.058
peak=    3.863 closest distance to " CG2 VAL A 257 " =    0.838
peak=    3.842 closest distance to " CB  ARG A 139 " =    1.127
peak=    3.834 closest distance to " O   HOH Z 368 " =    2.018
peak=    3.833 closest distance to " CG  MET A 185 " =    1.248
peak=    3.831 closest distance to " CG2 ILE A 120 " =    1.098
peak=    3.830 closest distance to " O   HOH Z 371 " =    3.072
peak=    3.828 closest distance to " CB  VAL A 202 " =    1.595
peak=    3.818 closest distance to " CD2 LEU A 297 " =    1.008
peak=    3.813 closest distance to " CB  THR A  31 " =    1.719
peak=    3.813 closest distance to " OG BSER A  99 " =    2.352
peak=    3.811 closest distance to " O   HOH Z 416 " =    1.035
peak=    3.802 closest distance to " O   HOH Z  88 " =    2.426
peak=    3.786 closest distance to " NH1AARG A 145 " =    1.230
peak=    3.785 closest distance to " O   HOH Z 375 " =    2.129
peak=    3.770 closest distance to " CB  VAL A 265 " =    1.287
peak=    3.761 closest distance to " CG1 ILE A  33 " =    1.193
peak=    3.761 closest distance to " CB  SER A   3 " =    1.288
peak=    3.756 closest distance to " O   HOH Z 336 " =    1.808
peak=    3.739 closest distance to " O   HOH Z 365 " =    2.646
peak=    3.736 closest distance to " O   HOH Z 128 " =    1.985
peak=    3.735 closest distance to " O   HOH Z 380 " =    1.677
peak=    3.735 closest distance to " O   HOH Z 415 " =    3.467
peak=    3.725 closest distance to " CA  ASN A 215 " =    1.041
peak=    3.719 closest distance to " CB  GLU A 128 " =    1.071
peak=    3.714 closest distance to " O   HOH Z 305 " =    3.383
peak=    3.708 closest distance to " O   HOH Z 286 " =    2.322
peak=    3.703 closest distance to " O   HOH Z   6 " =    2.239
peak=    3.674 closest distance to " O   HOH Z 389 " =    1.601
peak=    3.659 closest distance to " CB  ALA A 114 " =    1.322
peak=    3.657 closest distance to " O   HOH Z  61 " =    1.477
peak=    3.652 closest distance to " O   HOH Z  66 " =    2.182
peak=    3.647 closest distance to " N   PHE A 130 " =    1.222
peak=    3.643 closest distance to " O   HOH Z 193 " =    2.056
peak=    3.633 closest distance to " O   HOH Z  10 " =    1.835
peak=    3.627 closest distance to " O   HOH Z 213 " =    1.637
peak=    3.626 closest distance to " OD2 ASP A 286 " =    2.519
peak=    3.620 closest distance to " CG  PRO A 243 " =    1.101
peak=    3.603 closest distance to " O   HOH Z 411 " =    3.732
peak=    3.601 closest distance to " O   HOH Z 144 " =    1.996
peak=    3.598 closest distance to " O   HOH Z 109 " =    2.241
peak=    3.596 closest distance to " CB  GLN A  89 " =    1.450
peak=    3.589 closest distance to " O   HOH Z 353 " =    2.600
peak=    3.583 closest distance to " O   HOH Z  59 " =    1.469
peak=    3.579 closest distance to " CB  TRP A 266 " =    1.162
peak=    3.578 closest distance to " OD1 ASN A 148 " =    1.662
peak=    3.575 closest distance to " O   HOH Z 147 " =    1.756
peak=    3.571 closest distance to " O   HOH Z   3 " =    1.880
peak=    3.567 closest distance to " CA  ALA A  84 " =    1.298
peak=    3.561 closest distance to " O   HOH Z 234 " =    1.966
peak=    3.535 closest distance to " O   HOH Z 126 " =    1.454
peak=    3.534 closest distance to " O   HOH Z 357 " =    1.820
peak=    3.528 closest distance to " O   HOH Z   1 " =    1.495
peak=    3.526 closest distance to " O   HOH Z 158 " =    2.897
peak=    3.525 closest distance to " O   HOH Z 141 " =    1.715
peak=    3.525 closest distance to " CB  LYS A 117 " =    1.181
peak=    3.521 closest distance to " O   HOH Z 222 " =    2.345
peak=    3.516 closest distance to " O   HOH Z 153 " =    1.586
peak=    3.516 closest distance to " O   HOH Z 116 " =    2.642
peak=    3.512 closest distance to " CG1 ILE A 120 " =    1.441
peak=    3.507 closest distance to " O   HOH Z  40 " =    1.851
peak=    3.505 closest distance to " O   HOH Z 106 " =    2.790
peak=    3.504 closest distance to " CB  THR A 279 " =    1.679
peak=    3.502 closest distance to " CB  LEU A 228 " =    1.103
peak=    3.501 closest distance to " O   HOH Z 392 " =    2.746
peak=    3.496 closest distance to " O   HOH Z 426 " =    1.520
peak=    3.487 closest distance to " CB  GLU A 277 " =    3.463
peak=    3.479 closest distance to " O   HOH Z 146 " =    1.622
peak=    3.478 closest distance to " O   HOH Z  24 " =    1.680
peak=    3.476 closest distance to " CE  LYS A 119 " =    1.222
peak=    3.473 closest distance to " CA  ALA A 299 " =    0.965
peak=    3.470 closest distance to " O   HOH Z  10 " =    2.462
peak=    3.468 closest distance to " O   HOH Z 425 " =    1.250
peak=    3.467 closest distance to " O   HOH Z 244 " =    1.666
peak=    3.461 closest distance to " N   TYR A 116 " =    1.570
peak=    3.458 closest distance to " O   HOH Z 227 " =    1.870
peak=    3.455 closest distance to " CA  LEU A 300 " =    1.008
peak=    3.455 closest distance to " O   HOH Z 112 " =    2.256
peak=    3.454 closest distance to " O   HOH Z 180 " =    2.254
peak=    3.452 closest distance to " O   HOH Z 291 " =    1.423
peak=    3.447 closest distance to " NE2 GLN A  73 " =    3.682
peak=    3.434 closest distance to " O   HOH Z 128 " =    1.944
peak=    3.433 closest distance to " CB  LYS A 290 " =    1.031
peak=    3.429 closest distance to " O   HOH Z 345 " =    3.166
peak=    3.428 closest distance to " O   HOH Z 423 " =    1.845
peak=    3.428 closest distance to " O   HOH Z 437 " =    1.615
peak=    3.425 closest distance to " CB  THR A 157 " =    1.140
peak=    3.423 closest distance to " CE ALYS A 290 " =    1.270
peak=    3.419 closest distance to " OD1 ASN A  69 " =    2.424
peak=    3.412 closest distance to " O   HOH Z 394 " =    1.614
peak=    3.412 closest distance to " O   HOH Z  58 " =    1.317
peak=    3.409 closest distance to " O   HOH Z 284 " =    2.751
peak=    3.404 closest distance to " O   HOH Z 188 " =    2.324
peak=    3.401 closest distance to " O   HOH Z 435 " =    1.808
peak=    3.400 closest distance to " CB  TRP A 179 " =    1.207
peak=    3.399 closest distance to " OG  SER A  62 " =    2.776
peak=    3.396 closest distance to " O   HOH Z  63 " =    1.304
peak=    3.395 closest distance to " CE AMET A  47 " =    1.221
peak=    3.393 closest distance to " CE  LYS A  76 " =    0.865
peak=    3.393 closest distance to " NH2BARG A 145 " =    2.102
peak=    3.380 closest distance to " CB  GLN A  88 " =    1.276
peak=    3.378 closest distance to " CG  PRO A 198 " =    1.235
peak=    3.377 closest distance to " O   HOH Z 337 " =    3.355
peak=    3.376 closest distance to " CD  GLN A 194 " =    1.429
peak=    3.375 closest distance to " CA  ASN A 127 " =    1.060
peak=    3.374 closest distance to " O   HOH Z 145 " =    2.355
peak=    3.361 closest distance to " O   HOH Z 207 " =    1.711
peak=    3.358 closest distance to " N   ASN A  39 " =    1.217
peak=    3.357 closest distance to " CA  SER A 146 " =    1.823
peak=    3.357 closest distance to " O   HOH Z 194 " =    1.850
peak=    3.350 closest distance to " CB  ALA A  10 " =    1.325
peak=    3.342 closest distance to " O   HOH Z 298 " =    2.673
peak=    3.338 closest distance to " O   HOH Z 346 " =    1.419
peak=    3.336 closest distance to " O   HOH Z  43 " =    2.511
peak=    3.333 closest distance to " O   GLY A 147 " =    1.572
peak=    3.329 closest distance to " O   HOH Z  85 " =    1.561
peak=    3.328 closest distance to " O   HOH Z 302 " =    1.625
peak=    3.326 closest distance to " O   HOH Z 175 " =    2.026
peak=    3.325 closest distance to " O   HOH Z 272 " =    2.035
peak=    3.313 closest distance to " O   HOH Z 173 " =    2.072
peak=    3.312 closest distance to " O   HOH Z 406 " =    1.557
peak=    3.310 closest distance to " O   HOH Z  66 " =    2.143
peak=    3.304 closest distance to " CA  ALA A  21 " =    1.120
peak=    3.300 closest distance to " CA  PHE A 283 " =    1.256
peak=    3.300 closest distance to " O   HOH Z  88 " =    2.361
peak=    3.299 closest distance to " O   HOH Z  63 " =    1.831
peak=    3.296 closest distance to " CB  ASN A 110 " =    1.012
peak=    3.294 closest distance to " O   HOH Z 119 " =    4.370
peak=    3.294 closest distance to " NH2AARG A 190 " =    1.855
peak=    3.289 closest distance to " O   ASN A  74 " =    1.902
peak=    3.287 closest distance to " O   HOH Z 423 " =    1.371
peak=    3.286 closest distance to " N   GLU A   2 " =    1.438
peak=    3.285 closest distance to " NE  ARG A  14 " =    1.207
peak=    3.282 closest distance to " O   HOH Z 124 " =    1.192
peak=    3.279 closest distance to " N   HIS A  86 " =    1.840
peak=    3.279 closest distance to " CA  MET A  40 " =    1.180
peak=    3.268 closest distance to " CG  GLU A 277 " =    1.960
peak=    3.266 closest distance to " O   HOH Z 214 " =    2.459
peak=    3.265 closest distance to " O   HOH Z  88 " =    1.905
peak=    3.264 closest distance to " CG2 THR A 294 " =    1.616
peak=    3.262 closest distance to " CB  LEU A 300 " =    0.993
peak=    3.259 closest distance to " O   HOH Z   2 " =    1.367
peak=    3.259 closest distance to " CG AARG A 275 " =    1.122
peak=    3.253 closest distance to " NH1BARG A 145 " =    1.259
peak=    3.249 closest distance to " O   HOH Z  94 " =    1.928
peak=    3.248 closest distance to " O   HOH Z 251 " =    1.664
peak=    3.247 closest distance to " CB  PHE A 130 " =    1.021
peak=    3.245 closest distance to " O   HOH Z 422 " =    2.556
peak=    3.245 closest distance to " O   HOH Z 329 " =    3.832
peak=    3.245 closest distance to " OG BSER A 258 " =    3.058
peak=    3.243 closest distance to " CB  ALA A  34 " =    1.157
peak=    3.243 closest distance to " O   HOH Z 433 " =    1.838
peak=    3.239 closest distance to " N   TRP A 177 " =    1.559
peak=    3.236 closest distance to " O   HOH Z 408 " =    1.379
peak=    3.236 closest distance to " CG  MET A 113 " =    0.928
peak=    3.232 closest distance to " O   HOH Z  47 " =    1.481
peak=    3.230 closest distance to " O   HOH Z 132 " =    1.023
peak=    3.229 closest distance to " CG  LEU A 101 " =    1.089
peak=    3.229 closest distance to " O   HOH Z 421 " =    1.916
peak=    3.224 closest distance to " CB  TYR A 169 " =    1.257
peak=    3.222 closest distance to " N   ASN A 127 " =    1.367
peak=    3.221 closest distance to " CB  PRO A 163 " =    4.021
peak=    3.219 closest distance to " CB  ASN A  39 " =    0.836
peak=    3.218 closest distance to " CD2 LEU A 255 " =    1.278
peak=    3.217 closest distance to " C   PHE A  59 " =    0.723
peak=    3.217 closest distance to " O  BHOH Z 338 " =    2.334
peak=    3.214 closest distance to " CB  SER A  62 " =    1.399
peak=    3.213 closest distance to " OG ASER A  99 " =    1.463
peak=    3.213 closest distance to " CA  ALA A 233 " =    0.880
peak=    3.212 closest distance to " CG1BVAL A  72 " =    1.403
peak=    3.211 closest distance to " CA  ALA A 291 " =    0.773
peak=    3.207 closest distance to " OD1BASN A 224 " =    2.163
peak=    3.206 closest distance to " O   HOH Z  80 " =    1.980
peak=    3.202 closest distance to " O   HOH Z 281 " =    1.820
peak=    3.197 closest distance to " O   HOH Z 390 " =    2.181
peak=    3.196 closest distance to " O   HOH Z  44 " =    2.949
peak=    3.195 closest distance to " CA  ASP A 140 " =    1.190
peak=    3.193 closest distance to " CD1 ILE A 263 " =    1.493
peak=    3.190 closest distance to " CZ  PHE A 218 " =    0.996
peak=    3.186 closest distance to " NH1 ARG A  14 " =    1.255
peak=    3.186 closest distance to " O   HOH Z  85 " =    2.168
peak=    3.181 closest distance to " O   HOH Z  40 " =    2.100
peak=    3.173 closest distance to " O   HOH Z 248 " =    1.496
peak=    3.163 closest distance to " CA  ARG A 195 " =    1.272
peak=    3.162 closest distance to " O   HOH Z 305 " =    3.016
peak=    3.161 closest distance to " CA  ASP A 162 " =    1.021
peak=    3.159 closest distance to " CD1 ILE A  49 " =    1.450
peak=    3.154 closest distance to " CG2 VAL A 197 " =    1.115
peak=    3.146 closest distance to " CG  PRO A  90 " =    1.092
peak=    3.144 closest distance to " CB  ASP A 171 " =    1.418
peak=    3.141 closest distance to " OE2 GLU A  53 " =    2.091
peak=    3.139 closest distance to " CG2 THR A 221 " =    1.000
peak=    3.136 closest distance to " O   HOH Z 432 " =    1.678
peak=    3.129 closest distance to " O   HOH Z 267 " =    2.047
peak=    3.128 closest distance to " O   HOH Z  71 " =    1.943
peak=    3.128 closest distance to " O   HOH Z 373 " =    1.389
peak=    3.125 closest distance to " O   HOH Z 334 " =    2.151
peak=    3.124 closest distance to " O  BHOH Z  74 " =    1.357
peak=    3.120 closest distance to " O   HOH Z  59 " =    1.936
peak=    3.112 closest distance to " OG BSER A 134 " =    2.863
peak=    3.111 closest distance to " O   HOH Z 227 " =    1.999
peak=    3.106 closest distance to " NH1 ARG A 138 " =    1.195
peak=    3.101 closest distance to " O   HOH Z 189 " =    2.627
peak=    3.100 closest distance to " O   HOH Z 409 " =    2.434
peak=    3.093 closest distance to " O   HOH Z  43 " =    1.953
peak=    3.081 closest distance to " CA  THR A 264 " =    0.833
peak=    3.081 closest distance to " CB  VAL A 126 " =    1.231
peak=    3.069 closest distance to " O   HOH Z 409 " =    2.949
peak=    3.061 closest distance to " O   HOH Z 172 " =    3.045
peak=    3.043 closest distance to " O   HOH Z 184 " =    1.808
peak=    3.042 closest distance to " N   TRP A 150 " =    1.037
peak=    3.040 closest distance to " O   HOH Z 217 " =    2.156

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.721 - 5.833
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 210 from: 210
   mapped sites are within: 0.721 - 5.833

peak=   -4.536 closest distance to " CG2 ILE A  20 " =    2.893
peak=   -4.504 closest distance to " OG BSER A 134 " =    1.328
peak=   -4.354 closest distance to " C   ILE A 239 " =    2.141
peak=   -4.314 closest distance to " CD1 LEU A 255 " =    2.797
peak=   -4.298 closest distance to " O   HOH Z 372 " =    2.418
peak=   -4.217 closest distance to " C   HIS A 108 " =    1.159
peak=   -4.203 closest distance to " OD2 ASP A 191 " =    1.394
peak=   -4.191 closest distance to " O   HOH Z 266 " =    4.795
peak=   -4.180 closest distance to " O   PRO A 198 " =    1.300
peak=   -4.161 closest distance to " CD  ARG A 156 " =    2.071
peak=   -4.159 closest distance to " N   GLN A  58 " =    1.695
peak=   -4.133 closest distance to " CG  PHE A 283 " =    2.575
peak=   -4.117 closest distance to " CG1 VAL A 112 " =    2.828
peak=   -4.106 closest distance to " CD  ARG A  14 " =    3.264
peak=   -4.102 closest distance to " CG  GLN A 223 " =    1.924
peak=   -4.076 closest distance to " OXT GLY A 302 " =    2.828
peak=   -4.075 closest distance to " O   VAL A  67 " =    2.565
peak=   -4.071 closest distance to " OG  SER A   3 " =    1.661
peak=   -4.022 closest distance to " CB  PRO A 243 " =    2.630
peak=   -3.976 closest distance to " O   ALA A 161 " =    1.624
peak=   -3.957 closest distance to " CG  GLN A  58 " =    1.100
peak=   -3.918 closest distance to " O   HOH Z  13 " =    1.555
peak=   -3.880 closest distance to " O   HOH Z 198 " =    1.748
peak=   -3.867 closest distance to " O   HOH Z  52 " =    1.334
peak=   -3.834 closest distance to " CB  PHE A 192 " =    1.872
peak=   -3.818 closest distance to " N   HIS A 115 " =    2.099
peak=   -3.811 closest distance to " CE  MET A 105 " =    2.272
peak=   -3.790 closest distance to " ND2 ASN A  45 " =    1.265
peak=   -3.772 closest distance to " O   PRO A 198 " =    1.277
peak=   -3.771 closest distance to " CZ  TYR A 169 " =    1.839
peak=   -3.770 closest distance to " N   ALA A 248 " =    1.699
peak=   -3.762 closest distance to " CB  TRP A  85 " =    2.386
peak=   -3.747 closest distance to " O   PHE A 218 " =    1.481
peak=   -3.730 closest distance to " O   HOH Z 429 " =    1.981
peak=   -3.725 closest distance to " O   HOH Z 351 " =    1.557
peak=   -3.709 closest distance to " OD2 ASP A  50 " =    1.491
peak=   -3.696 closest distance to " O   HOH Z 185 " =    2.213
peak=   -3.684 closest distance to " CZ  PHE A  59 " =    1.407
peak=   -3.680 closest distance to " CD1 PHE A 130 " =    2.348
peak=   -3.667 closest distance to " O   HOH Z 407 " =    2.433
peak=   -3.656 closest distance to " O   SER A 135 " =    1.450
peak=   -3.653 closest distance to " OD1 ASP A 191 " =    1.453
peak=   -3.650 closest distance to " O   HOH Z 389 " =    1.911
peak=   -3.646 closest distance to " CG  GLN A  58 " =    1.374
peak=   -3.637 closest distance to " O   TRP A  70 " =    1.427
peak=   -3.634 closest distance to " O   PRO A 243 " =    2.546
peak=   -3.632 closest distance to " O   ALA A  34 " =    2.189
peak=   -3.621 closest distance to " OD2 ASP A 171 " =    2.132
peak=   -3.617 closest distance to " OD1 ASP A 171 " =    1.571
peak=   -3.603 closest distance to " O   HOH Z 290 " =    1.281
peak=   -3.601 closest distance to " O   HOH Z 102 " =    1.631
peak=   -3.595 closest distance to " CB  ASN A  39 " =    2.249
peak=   -3.590 closest distance to " CG  PRO A 243 " =    1.605
peak=   -3.589 closest distance to " O   VAL A 174 " =    2.222
peak=   -3.585 closest distance to " O   VAL A 189 " =    2.475
peak=   -3.584 closest distance to " NE  ARG A 156 " =    1.853
peak=   -3.580 closest distance to " ND2 ASN A  39 " =    1.321
peak=   -3.575 closest distance to " O   HOH Z 139 " =    5.053
peak=   -3.570 closest distance to " CB  ALA A 244 " =    1.997
peak=   -3.554 closest distance to " O   ALA A 292 " =    1.896
peak=   -3.550 closest distance to " O   HOH Z 131 " =    4.080
peak=   -3.547 closest distance to " CD  ARG A 139 " =    1.523
peak=   -3.545 closest distance to " OD1 ASP A 191 " =    1.854
peak=   -3.533 closest distance to " CB  PHE A 208 " =    2.167
peak=   -3.533 closest distance to " CB  ALA A 291 " =    2.318
peak=   -3.531 closest distance to " OE1 GLN A 183 " =    1.295
peak=   -3.529 closest distance to " CB  ASP A 286 " =    2.180
peak=   -3.527 closest distance to " CA  GLY A 133 " =    2.015
peak=   -3.524 closest distance to " OD1 ASN A  39 " =    2.133
peak=   -3.522 closest distance to " OD1 ASN A 148 " =    1.591
peak=   -3.521 closest distance to " O   HOH Z 165 " =    2.208
peak=   -3.517 closest distance to " O   SER A 146 " =    1.008
peak=   -3.513 closest distance to " CA  GLY A  98 " =    1.842
peak=   -3.501 closest distance to " CB  ALA A 131 " =    1.950
peak=   -3.498 closest distance to " CD2 PHE A 225 " =    1.198
peak=   -3.495 closest distance to " CB  PRO A 163 " =    2.535
peak=   -3.491 closest distance to " O   HOH Z 256 " =    1.402
peak=   -3.486 closest distance to " O   PRO A 163 " =    1.854
peak=   -3.484 closest distance to " O   HOH Z  90 " =    2.269
peak=   -3.480 closest distance to " CG1 VAL A 230 " =    1.879
peak=   -3.473 closest distance to " O   SER A  22 " =    2.253
peak=   -3.470 closest distance to " O   HOH Z 198 " =    1.536
peak=   -3.469 closest distance to " O   HOH Z 263 " =    2.981
peak=   -3.467 closest distance to " O   HOH Z 313 " =    1.748
peak=   -3.465 closest distance to " CD  LYS A 289 " =    2.379
peak=   -3.462 closest distance to " N   ALA A  43 " =    2.429
peak=   -3.458 closest distance to " CD1 LEU A 101 " =    2.283
peak=   -3.458 closest distance to " O   ALA A  51 " =    1.152
peak=   -3.457 closest distance to " O   HOH Z 298 " =    1.318
peak=   -3.452 closest distance to " O   HOH Z 362 " =    5.833
peak=   -3.452 closest distance to " O   HOH Z  11 " =    1.804
peak=   -3.443 closest distance to " CD1 PHE A  59 " =    2.041
peak=   -3.441 closest distance to " CB  ALA A 291 " =    2.122
peak=   -3.431 closest distance to " CD  ARG A  36 " =    1.865
peak=   -3.431 closest distance to " O   HOH Z 134 " =    3.112
peak=   -3.429 closest distance to " O   HOH Z  11 " =    1.999
peak=   -3.424 closest distance to " ND2 ASN A 187 " =    1.559
peak=   -3.423 closest distance to " O   HOH Z 250 " =    1.297
peak=   -3.421 closest distance to " CG2 ILE A 263 " =    2.240
peak=   -3.416 closest distance to " O   HOH Z  24 " =    1.264
peak=   -3.414 closest distance to " C   ALA A 158 " =    1.400
peak=   -3.411 closest distance to " O   HOH Z 137 " =    1.434
peak=   -3.408 closest distance to " O   HOH Z 166 " =    1.335
peak=   -3.403 closest distance to " O   HOH Z 423 " =    2.291
peak=   -3.401 closest distance to " CB  ASP A 132 " =    2.342
peak=   -3.401 closest distance to " O   HOH Z  44 " =    2.272
peak=   -3.399 closest distance to " O   SER A   3 " =    1.079
peak=   -3.392 closest distance to " CD2 PHE A  61 " =    2.299
peak=   -3.388 closest distance to " O   HOH Z 388 " =    2.000
peak=   -3.380 closest distance to " OG  SER A  87 " =    1.373
peak=   -3.379 closest distance to " O   HOH Z 213 " =    1.376
peak=   -3.378 closest distance to " CZ2 TRP A 274 " =    1.028
peak=   -3.377 closest distance to " O   SER A  95 " =    1.362
peak=   -3.370 closest distance to " OG1 THR A  82 " =    1.778
peak=   -3.367 closest distance to " OG1 THR A 178 " =    1.257
peak=   -3.367 closest distance to " O   SER A 210 " =    1.942
peak=   -3.360 closest distance to " O   ILE A 120 " =    1.575
peak=   -3.360 closest distance to " O   HOH Z 148 " =    1.815
peak=   -3.359 closest distance to " CB  GLN A  55 " =    1.399
peak=   -3.355 closest distance to " CE1 TYR A 169 " =    2.434
peak=   -3.351 closest distance to " N   PRO A 163 " =    1.568
peak=   -3.351 closest distance to " O   HOH Z 211 " =    1.650
peak=   -3.348 closest distance to " O   HOH Z 385 " =    1.723
peak=   -3.341 closest distance to " O   HOH Z  63 " =    1.694
peak=   -3.339 closest distance to " NH1 ARG A 195 " =    2.666
peak=   -3.335 closest distance to " CE2 TYR A  30 " =    2.726
peak=   -3.332 closest distance to " N   PHE A  59 " =    1.806
peak=   -3.329 closest distance to " O   HOH Z 114 " =    3.098
peak=   -3.326 closest distance to " CZ3 TRP A 179 " =    1.226
peak=   -3.322 closest distance to " O   HOH Z 103 " =    1.757
peak=   -3.318 closest distance to " CB  ALA A  43 " =    2.322
peak=   -3.317 closest distance to " C   GLN A 205 " =    1.717
peak=   -3.314 closest distance to " CE3 TRP A 274 " =    2.168
peak=   -3.310 closest distance to " O   HOH Z 345 " =    1.839
peak=   -3.307 closest distance to " O   GLN A 240 " =    1.614
peak=   -3.304 closest distance to " CB  ALA A  51 " =    1.891
peak=   -3.297 closest distance to " CA  GLY A 203 " =    2.333
peak=   -3.294 closest distance to " CG1 VAL A  78 " =    2.696
peak=   -3.293 closest distance to " O   HOH Z  60 " =    1.852
peak=   -3.290 closest distance to " O   HOH Z 147 " =    1.506
peak=   -3.289 closest distance to " O   ARG A 145 " =    1.583
peak=   -3.288 closest distance to " O   HOH Z 253 " =    3.488
peak=   -3.284 closest distance to " O   HOH Z 427 " =    1.464
peak=   -3.283 closest distance to " C   ASP A 231 " =    2.477
peak=   -3.279 closest distance to " O   HOH Z 298 " =    2.336
peak=   -3.276 closest distance to " OG  SER A  97 " =    2.145
peak=   -3.276 closest distance to " N   MET A 188 " =    1.929
peak=   -3.274 closest distance to " CG  GLU A   2 " =    2.048
peak=   -3.263 closest distance to " O   HOH Z 140 " =    1.915
peak=   -3.263 closest distance to " C   GLY A  91 " =    1.344
peak=   -3.260 closest distance to " OG BSER A 134 " =    1.471
peak=   -3.255 closest distance to " O   GLN A  89 " =    1.574
peak=   -3.252 closest distance to " OE2 GLU A 152 " =    1.239
peak=   -3.250 closest distance to " CA  GLY A  23 " =    1.948
peak=   -3.247 closest distance to " CG  GLN A  88 " =    0.869
peak=   -3.245 closest distance to " CG2 ILE A  49 " =    2.695
peak=   -3.243 closest distance to " CA  GLY A 241 " =    2.193
peak=   -3.240 closest distance to " O   HOH Z  38 " =    1.995
peak=   -3.240 closest distance to " O   HOH Z 385 " =    1.852
peak=   -3.229 closest distance to " O   GLY A  80 " =    2.144
peak=   -3.228 closest distance to " O   MET A  40 " =    2.706
peak=   -3.224 closest distance to " O   ASN A 187 " =    1.412
peak=   -3.222 closest distance to " CG  ASP A 231 " =    0.721
peak=   -3.221 closest distance to " O   TRP A 274 " =    1.441
peak=   -3.220 closest distance to " ND2 ASN A 209 " =    1.735
peak=   -3.211 closest distance to " O   HOH Z 383 " =    0.961
peak=   -3.206 closest distance to " OG  SER A  97 " =    1.537
peak=   -3.204 closest distance to " O   ILE A 106 " =    1.987
peak=   -3.202 closest distance to " O   HOH Z 218 " =    3.151
peak=   -3.199 closest distance to " O   HOH Z   6 " =    1.436
peak=   -3.197 closest distance to " CE1 HIS A  81 " =    1.722
peak=   -3.193 closest distance to " O   ASN A 285 " =    1.677
peak=   -3.190 closest distance to " CD2 LEU A 237 " =    2.504
peak=   -3.185 closest distance to " CB  SER A 210 " =    1.319
peak=   -3.184 closest distance to " O   VAL A 125 " =    2.104
peak=   -3.181 closest distance to " O   HOH Z  77 " =    2.218
peak=   -3.171 closest distance to " CB  ALA A 248 " =    2.195
peak=   -3.170 closest distance to " CD1 LEU A 228 " =    1.956
peak=   -3.168 closest distance to " CG2 VAL A 189 " =    2.044
peak=   -3.166 closest distance to " CA  GLY A  57 " =    2.201
peak=   -3.165 closest distance to " N   ASN A 127 " =    1.422
peak=   -3.165 closest distance to " CZ  ARG A 259 " =    0.879
peak=   -3.164 closest distance to " O   HOH Z 107 " =    1.512
peak=   -3.162 closest distance to " N   GLN A  77 " =    1.663
peak=   -3.157 closest distance to " O   HOH Z 250 " =    1.536
peak=   -3.148 closest distance to " NH2 ARG A  79 " =    2.047
peak=   -3.145 closest distance to " O   HOH Z 123 " =    2.279
peak=   -3.144 closest distance to " O   HOH Z 191 " =    5.642
peak=   -3.137 closest distance to " O   LYS A  76 " =    1.516
peak=   -3.133 closest distance to " O   HOH Z 421 " =    2.908
peak=   -3.129 closest distance to " O   HOH Z 389 " =    1.400
peak=   -3.125 closest distance to " NE2 GLN A  55 " =    0.868
peak=   -3.123 closest distance to " OG  SER A 245 " =    1.323
peak=   -3.122 closest distance to " ND2 ASN A 142 " =    2.013
peak=   -3.121 closest distance to " N   ASP A 286 " =    2.164
peak=   -3.120 closest distance to " O   HOH Z 193 " =    1.969
peak=   -3.114 closest distance to " O   HOH Z 281 " =    2.725
peak=   -3.114 closest distance to " CD2 TYR A 293 " =    1.920
peak=   -3.112 closest distance to " O   HOH Z 326 " =    1.587
peak=   -3.102 closest distance to " O   ASP A 298 " =    1.602
peak=   -3.101 closest distance to " O   ASN A 301 " =    1.375
peak=   -3.099 closest distance to " CG  GLU A 152 " =    1.098
peak=   -3.084 closest distance to " NH1BARG A 145 " =    3.680
peak=   -3.080 closest distance to " O   HOH Z  89 " =    2.772
peak=   -3.074 closest distance to " OD1 ASP A 238 " =    1.930
peak=   -3.057 closest distance to " CD1 ILE A 263 " =    2.444
peak=   -3.055 closest distance to " O   HOH Z 361 " =    3.284
peak=   -3.047 closest distance to " CB  ASP A 132 " =    2.237
peak=   -3.044 closest distance to " O   HOH Z 168 " =    1.584
peak=   -3.032 closest distance to " O   GLU A 152 " =    1.434

================= 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    :  0.4368 0.4308   6.240689e+00   6.235325e+00
   1_bss:  0.4266 0.4212   6.230350e+00   6.216737e+00
   1_xyz:  0.2846 0.3180   5.924189e+00   5.996403e+00
   1_adp:  0.2565 0.3273   5.869951e+00   6.025199e+00
   1_occ:  0.2563 0.3280   5.870028e+00   6.026044e+00
   2_bss:  0.2523 0.3240   5.856829e+00   6.016835e+00
   2_xyz:  0.1862 0.2448   5.582974e+00   5.786406e+00
   2_adp:  0.1708 0.2248   5.508145e+00   5.714272e+00
   2_occ:  0.1706 0.2243   5.506859e+00   5.712629e+00
   3_bss:  0.1705 0.2239   5.504192e+00   5.708827e+00
   3_xyz:  0.1358 0.1825   5.300225e+00   5.519767e+00
   3_adp:  0.1288 0.1737   5.250023e+00   5.468430e+00
   3_occ:  0.1286 0.1737   5.249136e+00   5.467507e+00
   4_bss:  0.1284 0.1730   5.247719e+00   5.465540e+00
   4_xyz:  0.1138 0.1610   5.155640e+00   5.395412e+00
   4_adp:  0.1111 0.1582   5.136947e+00   5.382310e+00
   4_occ:  0.1110 0.1584   5.136858e+00   5.382383e+00
   5_bss:  0.1109 0.1584   5.136447e+00   5.381898e+00
   5_xyz:  0.1076 0.1568   5.117670e+00   5.373181e+00
   5_adp:  0.1064 0.1572   5.115625e+00   5.378023e+00
   5_occ:  0.1064 0.1574   5.115659e+00   5.378190e+00
   5_bss:  0.1063 0.1573   5.115127e+00   5.377510e+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:  0.333  20.001   0.675   1.275  -1.576   0.000  -0.000  -0.000
   1_xyz:  0.333  20.001   0.675   1.275  -1.576   0.000  -0.000  -0.000
   1_adp:  0.333  20.001   0.675   1.275  -1.576   0.000  -0.000  -0.000
   1_occ:  0.333  20.001   0.675   1.275  -1.576   0.000  -0.000  -0.000
   2_bss:  0.331  34.475  -1.700  -0.765  -1.052  -0.000  -0.000  -0.000
   2_xyz:  0.331  34.475  -1.700  -0.765  -1.052  -0.000  -0.000  -0.000
   2_adp:  0.331  34.475  -1.700  -0.765  -1.052  -0.000  -0.000  -0.000
   2_occ:  0.331  34.475  -1.700  -0.765  -1.052  -0.000  -0.000  -0.000
   3_bss:  0.313  35.399  -2.492  -1.685  -1.074  -0.000  -0.000  -0.000
   3_xyz:  0.313  35.399  -2.492  -1.685  -1.074  -0.000  -0.000  -0.000
   3_adp:  0.313  35.399  -2.492  -1.685  -1.074  -0.000  -0.000  -0.000
   3_occ:  0.313  35.399  -2.492  -1.685  -1.074  -0.000  -0.000  -0.000
   4_bss:  0.314  35.399  -3.021  -2.304  -1.303  -0.000  -0.000  -0.000
   4_xyz:  0.314  35.399  -3.021  -2.304  -1.303  -0.000  -0.000  -0.000
   4_adp:  0.314  35.399  -3.021  -2.304  -1.303  -0.000  -0.000  -0.000
   4_occ:  0.314  35.399  -3.021  -2.304  -1.303  -0.000  -0.000  -0.000
   5_bss:  0.318  37.489  -2.990  -2.334  -1.188  -0.000  -0.000  -0.000
   5_xyz:  0.318  37.489  -2.990  -2.334  -1.188  -0.000  -0.000  -0.000
   5_adp:  0.318  37.489  -2.990  -2.334  -1.188  -0.000  -0.000  -0.000
   5_occ:  0.318  37.489  -2.990  -2.334  -1.188  -0.000  -0.000  -0.000
   5_bss:  0.322  41.549  -2.838  -2.215  -1.011  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.595 0.5145  0.7010    59129.825
   1_bss:  49.454 0.5270  0.7234    55530.880
   1_xyz:  32.138 0.7351  0.9575    26602.844
   1_adp:  33.740 0.7160  0.9383    28694.905
   1_occ:  33.793 0.7154  0.9371    28776.584
   2_bss:  33.179 0.7218  0.9038    27650.627
   2_xyz:  23.821 0.8230  0.9932    14981.807
   2_adp:  21.309 0.8494  1.0080    12727.853
   2_occ:  21.272 0.8497  1.0081    12674.409
   3_bss:  21.097 0.8512  0.9875    12477.595
   3_xyz:  16.981 0.8892  1.0048     8329.716
   3_adp:  15.746 0.9004  1.0054     7535.642
   3_occ:  15.729 0.9005  1.0053     7514.187
   4_bss:  15.670 0.9010  0.9885     7461.391
   4_xyz:  14.249 0.9127  0.9937     6418.188
   4_adp:  13.946 0.9153  0.9911     6269.131
   4_occ:  13.949 0.9152  0.9910     6268.249
   5_bss:  13.938 0.9153  0.9926     6264.000
   5_xyz:  13.705 0.9173  0.9923     6141.328
   5_adp:  13.794 0.9167  0.9855     6185.319
   5_occ:  13.796 0.9167  0.9854     6188.921
   5_bss:  13.782 0.9168  0.9912     6182.772
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.106   2.2471e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.106   2.2471e-01
   1_xyz:   1.451  0.012  0.095 15.282  0.007  4.103   1.2250e-01
   1_adp:   1.451  0.012  0.095 15.282  0.007  4.103   1.2250e-01
   1_occ:   1.451  0.012  0.095 15.282  0.007  4.103   1.2250e-01
   2_bss:   1.451  0.012  0.095 15.282  0.007  4.103   1.2250e-01
   2_xyz:   1.036  0.006  0.070 14.531  0.004  4.108   6.2272e-02
   2_adp:   1.036  0.006  0.070 14.531  0.004  4.108   6.2272e-02
   2_occ:   1.036  0.006  0.070 14.531  0.004  4.108   6.2272e-02
   3_bss:   1.036  0.006  0.070 14.531  0.004  4.108   6.2272e-02
   3_xyz:   0.961  0.006  0.067 14.604  0.004  4.110   5.5210e-02
   3_adp:   0.961  0.006  0.067 14.604  0.004  4.110   5.5210e-02
   3_occ:   0.961  0.006  0.067 14.604  0.004  4.110   5.5210e-02
   4_bss:   0.961  0.006  0.067 14.604  0.004  4.110   5.5210e-02
   4_xyz:   1.075  0.007  0.075 14.972  0.005  4.105   6.6060e-02
   4_adp:   1.075  0.007  0.075 14.972  0.005  4.105   6.6060e-02
   4_occ:   1.075  0.007  0.075 14.972  0.005  4.105   6.6060e-02
   5_bss:   1.075  0.007  0.075 14.972  0.005  4.105   6.6060e-02
   5_xyz:   1.082  0.007  0.076 14.970  0.005  4.106   6.6702e-02
   5_adp:   1.082  0.007  0.076 14.970  0.005  4.106   6.6702e-02
   5_occ:   1.082  0.007  0.076 14.970  0.005  4.106   6.6702e-02
   5_bss:   1.082  0.007  0.076 14.970  0.005  4.106   6.6702e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.119   2.4039e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.119   2.4039e-01
   1_xyz:   9.324  0.095  0.312 86.654  0.063  1.949   1.1443e-01
   1_adp:   9.324  0.095  0.312 86.654  0.063  1.949   1.1443e-01
   1_occ:   9.324  0.095  0.312 86.654  0.063  1.949   1.1443e-01
   2_bss:   9.324  0.095  0.312 86.654  0.063  1.949   1.1443e-01
   2_xyz:   7.362  0.034  0.228 78.342  0.035  2.319   6.3480e-02
   2_adp:   7.362  0.034  0.228 78.342  0.035  2.319   6.3480e-02
   2_occ:   7.362  0.034  0.228 78.342  0.035  2.319   6.3480e-02
   3_bss:   7.362  0.034  0.228 78.342  0.035  2.319   6.3480e-02
   3_xyz:   7.949  0.046  0.214 82.736  0.028  2.365   4.0042e-02
   3_adp:   7.949  0.046  0.214 82.736  0.028  2.365   4.0042e-02
   3_occ:   7.949  0.046  0.214 82.736  0.028  2.365   4.0042e-02
   4_bss:   7.949  0.046  0.214 82.736  0.028  2.365   4.0042e-02
   4_xyz:   7.828  0.049  0.237 85.075  0.045  2.261   6.0552e-02
   4_adp:   7.828  0.049  0.237 85.075  0.045  2.261   6.0552e-02
   4_occ:   7.828  0.049  0.237 85.075  0.045  2.261   6.0552e-02
   5_bss:   7.828  0.049  0.237 85.075  0.045  2.261   6.0552e-02
   5_xyz:   7.543  0.053  0.243 84.577  0.040  2.234   5.3250e-02
   5_adp:   7.543  0.053  0.243 84.577  0.040  2.234   5.3250e-02
   5_occ:   7.543  0.053  0.243 84.577  0.040  2.234   5.3250e-02
   5_bss:   7.543  0.053  0.243 84.577  0.040  2.234   5.3250e-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: 100.77   0.00  18.59  85.02   0.00  14.44 100.77   2.61  41.20
   1_occ: 100.77   0.00  18.59  85.02   0.00  14.44 100.77   2.61  41.20
   2_bss: 100.77   0.00  18.59  85.02   0.00  14.44 100.77   2.61  41.20
   2_xyz: 100.77   0.00  18.59  85.02   0.00  14.44 100.77   2.61  41.20
   2_adp:  89.03   0.00  17.73  89.03   0.00  13.52  86.18   5.59  40.66
   2_occ:  89.03   0.00  17.73  89.03   0.00  13.52  86.18   5.59  40.66
   3_bss:  89.03   0.00  17.73  89.03   0.00  13.52  86.18   5.59  40.66
   3_xyz:  89.03   0.00  17.73  89.03   0.00  13.52  86.18   5.59  40.66
   3_adp:  89.11   1.07  17.26  89.11   1.07  13.06  84.46   4.57  40.16
   3_occ:  89.11   1.07  17.26  89.11   1.07  13.06  84.46   4.57  40.16
   4_bss:  89.11   1.07  17.26  89.11   1.07  13.06  84.46   4.57  40.16
   4_xyz:  89.11   1.07  17.26  89.11   1.07  13.06  84.46   4.57  40.16
   4_adp:  90.06   0.76  17.11  90.06   0.76  12.89  84.93   4.84  40.08
   4_occ:  90.06   0.76  17.11  90.06   0.76  12.89  84.93   4.84  40.08
   5_bss:  90.06   0.76  17.11  90.06   0.76  12.89  84.93   4.84  40.08
   5_xyz:  90.06   0.76  17.11  90.06   0.76  12.89  84.93   4.84  40.08
   5_adp:  97.94   0.00  17.21  97.94   0.00  12.83  90.61   6.04  41.05
   5_occ:  97.94   0.00  17.21  97.94   0.00  12.83  90.61   6.04  41.05
   5_bss:  97.94   0.00  17.21  97.94   0.00  12.84  90.61   6.05  41.05
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    2.558    0.014    0.414
   1_adp:    2.558    0.014    0.414
   1_occ:    2.558    0.014    0.414
   2_bss:    2.558    0.014    0.414
   2_xyz:    2.315    0.062    0.526
   2_adp:    2.315    0.062    0.526
   2_occ:    2.315    0.062    0.526
   3_bss:    2.315    0.062    0.526
   3_xyz:    2.127    0.057    0.620
   3_adp:    2.127    0.057    0.620
   3_occ:    2.127    0.057    0.620
   4_bss:    2.127    0.057    0.620
   4_xyz:    1.796    0.078    0.656
   4_adp:    1.796    0.078    0.656
   4_occ:    1.796    0.078    0.656
   5_bss:    1.796    0.078    0.656
   5_xyz:    1.464    0.103    0.665
   5_adp:    1.464    0.103    0.665
   5_occ:    1.464    0.103    0.665
   5_bss:    1.464    0.103    0.665
------------------------------------------------------------------------

CPU time actual refinement: 335.93


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_26/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_26/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_26/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_26/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_26/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 335.78 
  Macro-tasks:
    bulk solvent and scale       = 41.92  
    individual site refinement   = 137.55 
    weights calculation          = 29.36  
    collect and process          = 6.55   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 215.50 
  Micro-tasks:
    mask                            = 1.75   
    f_calc                          = 106.68 
    alpha_beta                      = 8.22   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 115.33 
    fmodel                         = 7.18   
    r_factors                      = 0.26   
    phase_errors                   = 10.73  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 251.58 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.754 micro seconds
Total CPU time: 5.82 minutes
from_scatterers_fft:    646 calls, 106.29 s
gradients_fft:          591 calls, 101.93 s

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

# Date 2008-01-16 Time 03:50:04 PST -0800 (1200484204.52 s)
Start R-work = 0.4368, R-free = 0.4308 (no bulk solvent and anisotropic scale)
Final R-work = 0.1321, R-free = 0.1765 (no bulk solvent and anisotropic scale)

Start R-work = 0.4266, R-free = 0.4212
Final R-work = 0.1063, R-free = 0.1573