# Date 2008-01-16 Time 03:54:36 PST -0800 (1200484476.73 s)
#phil __OFF__

Command line arguments: "../96.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2009
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 96

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.4938, 47.6339, 87.6859, 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, 47.6339, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9291 1.95095
Completeness in resolution range: 0.912432
Completeness with d_max=infinity: 0.90972

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9291
                             d_min =   1.9510

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 47.6339, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9291 1.95095
Completeness in resolution range: 0.912432
Completeness with d_max=infinity: 0.90972

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9295 -  4.1754 [2247/2275]  2017   230  10.2%
  bin  2:  4.1754 -  3.3262 [2172/2195]  1954   218  10.0%
  bin  3:  3.3262 -  2.9093 [2135/2160]  1932   203   9.5%
  bin  4:  2.9093 -  2.6449 [2115/2133]  1896   219  10.4%
  bin  5:  2.6449 -  2.4562 [2091/2133]  1880   211  10.1%
  bin  6:  2.4562 -  2.3120 [2109/2137]  1903   206   9.8%
  bin  7:  2.3120 -  2.1966 [2066/2102]  1864   202   9.8%
  bin  8:  2.1966 -  2.1012 [2089/2131]  1879   210  10.1%
  bin  9:  2.1012 -  2.0205 [1983/2096]  1788   195   9.8%
  bin 10:  2.0205 -  1.9510 [ 582/2107]   517    65  11.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_96/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: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.01 -     1.78: 9
        1.78 -     2.56: 62
        2.56 -     3.34: 3987
        3.34 -     4.12: 9407
        4.12 -     4.90: 14919
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.006 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.279 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.283 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.368 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.402 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28379 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_96/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_96/model_refine_001.geo

CPU time processing inputs: 9.63


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.49375 47.63395 87.68585 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 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4601   r_free= 0.4569   ksol= 0.00   Bsol= 0.00   scale= 0.898    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.265315                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9295 -  4.6575 0.99   1462  161 0.3528 0.3755      6.5276      6.5733|
|  2:  4.6575 -  3.7155 0.99   1416  156 0.3892 0.3887      6.7564      6.7714|
|  3:  3.7155 -  3.2514 0.99   1371  157 0.4340 0.4301      6.6341      6.6555|
|  4:  3.2514 -  2.9566 0.99   1381  146 0.4548 0.4384      6.4727      6.4701|
|  5:  2.9566 -  2.7461 0.99   1355  153 0.4860 0.4568       6.335      6.3451|
|  6:  2.7461 -  2.5851 0.99   1369  153 0.4860 0.5366      6.2498      6.1825|
|  7:  2.5851 -  2.4562 0.98   1325  155 0.4967 0.4209      6.2012       6.117|
|  8:  2.4562 -  2.3497 0.98   1360  144 0.5239 0.5069       6.165      6.1815|
|  9:  2.3497 -  2.2596 0.99   1342  147 0.5238 0.4922      6.1055      6.1568|
| 10:  2.2596 -  2.1819 0.98   1344  145 0.5184 0.5008      6.0882      6.0868|
| 11:  2.1819 -  2.1138 0.97   1322  156 0.5269 0.5447      5.9934      6.0298|
| 12:  2.1138 -  2.0536 0.98   1333  150 0.5252 0.5198      5.9527      5.9319|
| 13:  2.0536 -  1.9996 0.75   1020  107 0.5025 0.5599      5.8587      5.8143|
| 14:  1.9996 -  1.9510 0.17    230   29 0.4939 0.5048      5.9212      5.6949|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9295 -  4.6575  1462   161  0.70  34.13   0.83     0.71      69300.14|
|  2:  4.6575 -  3.7155  1416   156  0.71  34.16   0.93     0.80     100430.08|
|  3:  3.7155 -  3.2514  1371   157  0.61  43.14   0.91     0.79     106175.09|
|  4:  3.2514 -  2.9566  1381   146  0.52  50.22   0.91     0.71      92397.32|
|  5:  2.9566 -  2.7461  1355   153  0.45  55.53   0.89     0.64      75272.79|
|  6:  2.7461 -  2.5851  1369   153  0.44  56.96   0.90     0.61      64736.39|
|  7:  2.5851 -  2.4562  1325   155  0.43  57.43   0.90     0.61      59202.69|
|  8:  2.4562 -  2.3497  1360   144  0.41  58.91   0.92     0.60      52700.75|
|  9:  2.3497 -  2.2596  1342   147  0.41  59.07   0.90     0.62      50001.51|
| 10:  2.2596 -  2.1819  1344   145  0.40  59.66   0.92     0.59      44940.93|
| 11:  2.1819 -  2.1138  1322   156  0.33  65.22   0.91     0.53      46537.21|
| 12:  2.1138 -  2.0536  1333   150  0.27  69.56   0.94     0.45      45558.24|
| 13:  2.0536 -  1.9996  1020   107  0.25  71.67   0.94     0.42      41032.86|
| 14:  1.9996 -  1.9510   230    29  0.34  64.45   0.99     0.42      29157.02|
|alpha:            min =        0.42 max =            0.80 mean =         0.63|
|beta:             min =    29157.02 max =       106175.09 mean =     65555.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.46|
|phase err.(work): min =        0.00 max =           90.00 mean =        54.60|
|phase err.(test): min =        0.00 max =           89.94 mean =        54.77|
|-----------------------------------------------------------------------------|

============================== 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 = 9.445533              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.270   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.136665              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.538   (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 |  1.006 -  1.395:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.395 -  1.785:        5 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.785 -  2.174:       18 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.174 -  2.564:       44 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.564 -  2.953:     1650 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.953 -  3.342:     2337 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.342 -  3.732:     3832 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.732 -  4.121:     5575 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.121 -  4.511:     6570 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.511 -  4.900:     8349 |
|-----------------------------------------------------------------------------|
|-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 |        0.223 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.006 |       1.071 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.784)------------------------------------------|
|    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 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4601   r_free= 0.4569   ksol= 0.00   Bsol= 0.00   scale= 0.898    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.265315                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4534   r_free= 0.4483   ksol= 0.28   Bsol= 20.00   scale= 0.942   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.24,1.54,1.27,0.00,0.00,0.00); trace/3= 0.86                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.259308                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.090577              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.867   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.180310              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.135   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4534      final r-factor (work) = 0.3267          |
| start r-factor (free) = 0.4483      final r-factor (free) = 0.3580          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.5469 = 8.09 * 0.50 * 6.2601 + 1.00 * 0.2229                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.8998 = 8.09 * 0.50 * 6.1228 + 1.00 * 0.1314                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3267      final r-factor (work) = 0.2902          |
| start r-factor (free) = 0.3580      final r-factor (free) = 0.3621          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2327 = 1.18 * 1.00 * 6.1228 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0581 = 1.18 * 1.00 * 5.9634 + 1.00 * 0.0194                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.784)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.44  19.40    None  None   None       |
|    all(noH): 2823   0      0.00    102.44  19.40    None  None   None       |
|    Sol.    : 438    0      0.00    102.44  41.30    None  None   None       |
|    Mac.    : 2385   0      0.00    95.51   15.38    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 -  10.244:  964   |   5:    51.219 -  61.463:   90        |
|      1:    10.244 -  20.488:  889   |   6:    61.463 -  71.707:   41        |
|      2:    20.488 -  30.731:  432   |   7:    71.707 -  81.950:   29        |
|      3:    30.731 -  40.975:  239   |   8:    81.950 -  92.194:   11        |
|      4:    40.975 -  51.219:  124   |   9:    92.194 - 102.438:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2902 r_free = 0.3621             target_work(ml) = 5.971         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2901 r_free = 0.3627             target_work(ml) = 5.971         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2901   r_free= 0.3627   ksol= 0.28   Bsol= 20.00   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.24,1.54,1.27,0.00,0.00,0.00); trace/3= 0.86                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.970993                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2873   r_free= 0.3586   ksol= 0.32   Bsol= 52.75   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.82,0.01,0.08,0.00,0.00,0.00); trace/3= -0.58                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.964118                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.714255              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.170   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.334852              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.511  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2873      final r-factor (work) = 0.2073          |
| start r-factor (free) = 0.3586      final r-factor (free) = 0.2608          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.1337 = 7.71 * 0.50 * 5.9636 + 1.00 * 0.1314                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.6519 = 7.71 * 0.50 * 5.8506 + 1.00 * 0.0852                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2073      final r-factor (work) = 0.1852          |
| start r-factor (free) = 0.2608      final r-factor (free) = 0.2362          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9785 = 0.33 * 1.00 * 5.8506 + 1.00 * 0.0194                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8924 = 0.33 * 1.00 * 5.6208 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.784)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.44   18.52    None  None   None       |
|    all(noH): 2823   0      0.00    98.44   18.52    None  None   None       |
|    Sol.    : 438    0      5.76    98.44   41.85    None  None   None       |
|    Mac.    : 2385   0      0.00    90.88   14.23    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 -   9.844:  928   |   5:    49.221 -  59.066:  100        |
|      1:     9.844 -  19.689: 1097   |   6:    59.066 -  68.910:   44        |
|      2:    19.689 -  29.533:  304   |   7:    68.910 -  78.754:   25        |
|      3:    29.533 -  39.377:  165   |   8:    78.754 -  88.598:    7        |
|      4:    39.377 -  49.221:  148   |   9:    88.598 -  98.443:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1852 r_free = 0.2362             target_work(ml) = 5.573         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1849 r_free = 0.2356             target_work(ml) = 5.571         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1849   r_free= 0.2356   ksol= 0.32   Bsol= 52.75   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.82,0.01,0.08,0.00,0.00,0.00); trace/3= -0.58                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.571480                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1845   r_free= 0.2345   ksol= 0.33   Bsol= 55.88   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-1.31,-0.64,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.569295                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.215182              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.821  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.558199              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.776  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1845      final r-factor (work) = 0.1401          |
| start r-factor (free) = 0.2345      final r-factor (free) = 0.1859          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.7550 = 5.22 * 0.50 * 5.6258 + 1.00 * 0.0852                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.3139 = 5.22 * 0.50 * 5.4599 + 1.00 * 0.0768                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1401      final r-factor (work) = 0.1290          |
| start r-factor (free) = 0.1859      final r-factor (free) = 0.1770          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0579 = 0.56 * 1.00 * 5.4599 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9669 = 0.56 * 1.00 * 5.2968 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.784)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.19    98.42   18.19    None  None   None       |
|    all(noH): 2823   0      1.19    98.42   18.19    None  None   None       |
|    Sol.    : 438    0      6.75    98.42   43.10    None  None   None       |
|    Mac.    : 2385   0      1.19    90.09   13.61    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.187 -  10.911: 1145   |   5:    49.805 -  59.528:  106        |
|      1:    10.911 -  20.634: 1026   |   6:    59.528 -  69.252:   60        |
|      2:    20.634 -  30.358:  204   |   7:    69.252 -  78.975:   17        |
|      3:    30.358 -  40.081:  122   |   8:    78.975 -  88.699:    9        |
|      4:    40.081 -  49.805:  130   |   9:    88.699 -  98.422:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1290 r_free = 0.1770             target_work(ml) = 5.273         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1290 r_free = 0.1769             target_work(ml) = 5.272         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1290   r_free= 0.1769   ksol= 0.33   Bsol= 55.88   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-1.31,-0.64,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.272484                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1293   r_free= 0.1770   ksol= 0.33   Bsol= 55.88   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.49,-1.92,-1.04,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.273041                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.171156              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 127.140  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.065532              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.366  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1293      final r-factor (work) = 0.1235          |
| start r-factor (free) = 0.1770      final r-factor (free) = 0.1676          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8311 = 2.17 * 0.50 * 5.3007 + 1.00 * 0.0768                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7634 = 2.17 * 0.50 * 5.2553 + 1.00 * 0.0583                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1235      final r-factor (work) = 0.1210          |
| start r-factor (free) = 0.1676      final r-factor (free) = 0.1672          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6099 = 1.07 * 1.00 * 5.2553 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5731 = 1.07 * 1.00 * 5.2202 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.784)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.76    100.25  18.09    None  None   None       |
|    all(noH): 2823   0      0.76    100.25  18.09    None  None   None       |
|    Sol.    : 438    0      5.10    100.25  43.30    None  None   None       |
|    Mac.    : 2385   0      0.76    93.01   13.46    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:     0.763 -  10.713: 1119   |   5:    50.509 -  60.458:   92        |
|      1:    10.713 -  20.662: 1064   |   6:    60.458 -  70.407:   63        |
|      2:    20.662 -  30.611:  202   |   7:    70.407 -  80.356:   30        |
|      3:    30.611 -  40.560:  127   |   8:    80.356 -  90.305:    7        |
|      4:    40.560 -  50.509:  113   |   9:    90.305 - 100.254:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1210 r_free = 0.1672             target_work(ml) = 5.219         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1209 r_free = 0.1672             target_work(ml) = 5.219         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1209   r_free= 0.1672   ksol= 0.33   Bsol= 55.88   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.49,-1.92,-1.04,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.218706                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1209   r_free= 0.1672   ksol= 0.32   Bsol= 55.88   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.45,-1.93,-0.97,-0.00,-0.00,-0.00); trace/3= -2.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.218676                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.061692              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.910  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.062736              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.166  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1209      final r-factor (work) = 0.1165          |
| start r-factor (free) = 0.1672      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4393 = 2.06 * 0.50 * 5.2200 + 1.00 * 0.0583                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4239 = 2.06 * 0.50 * 5.2030 + 1.00 * 0.0604                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1165      final r-factor (work) = 0.1157          |
| start r-factor (free) = 0.1637      final r-factor (free) = 0.1626          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5402 = 1.06 * 1.00 * 5.2030 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5234 = 1.06 * 1.00 * 5.1873 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.784)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.31   17.86    None  None   None       |
|    all(noH): 2823   0      0.00    99.31   17.86    None  None   None       |
|    Sol.    : 438    0      0.00    99.31   42.70    None  None   None       |
|    Mac.    : 2385   0      0.61    96.29   13.29    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 -   9.931:  973   |   5:    49.655 -  59.586:  100        |
|      1:     9.931 -  19.862: 1183   |   6:    59.586 -  69.517:   58        |
|      2:    19.862 -  29.793:  227   |   7:    69.517 -  79.448:   32        |
|      3:    29.793 -  39.724:  125   |   8:    79.448 -  89.379:    8        |
|      4:    39.724 -  49.655:  111   |   9:    89.379 -  99.310:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1157 r_free = 0.1626             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1155 r_free = 0.1627             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1627   ksol= 0.32   Bsol= 55.88   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.45,-1.93,-0.97,-0.00,-0.00,-0.00); trace/3= -2.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.185120                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9295 -  4.6575 0.99   1462  161 0.0974 0.1300      5.3818      5.5739|
|  2:  4.6575 -  3.7155 0.99   1416  156 0.0818 0.1053      5.4039       5.589|
|  3:  3.7155 -  3.2514 0.99   1371  157 0.1093 0.1517      5.4729      5.8156|
|  4:  3.2514 -  2.9566 0.99   1381  146 0.1284 0.1694       5.465      5.6541|
|  5:  2.9566 -  2.7461 0.99   1355  153 0.1371 0.1738       5.363      5.5449|
|  6:  2.7461 -  2.5851 0.99   1369  153 0.1301 0.2153       5.247      5.5213|
|  7:  2.5851 -  2.4562 0.98   1325  155 0.1314 0.1725      5.2043      5.3925|
|  8:  2.4562 -  2.3497 0.98   1360  144 0.1233 0.1773      5.1243      5.3204|
|  9:  2.3497 -  2.2596 0.99   1342  147 0.1193 0.1842      5.0448      5.3305|
| 10:  2.2596 -  2.1819 0.98   1344  145 0.1215 0.1905      4.9979      5.2384|
| 11:  2.1819 -  2.1138 0.97   1322  156 0.1219 0.1842      4.9389      5.2614|
| 12:  2.1138 -  2.0536 0.98   1333  150 0.1188 0.1574      4.8886      5.0952|
| 13:  2.0536 -  1.9996 0.75   1020  107 0.1142 0.2063      4.7956      5.0886|
| 14:  1.9996 -  1.9510 0.17    230   29 0.1118 0.1671      4.7998      4.8986|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9295 -  4.6575  1462   161  0.94   9.24   0.97     0.94       7353.58|
|  2:  4.6575 -  3.7155  1416   156  0.95   8.01   1.01     1.00       8852.88|
|  3:  3.7155 -  3.2514  1371   157  0.93  11.57   1.03     1.02      10382.63|
|  4:  3.2514 -  2.9566  1381   146  0.91  14.85   1.01     1.00      10704.96|
|  5:  2.9566 -  2.7461  1355   153  0.89  16.86   1.00     0.98       9221.57|
|  6:  2.7461 -  2.5851  1369   153  0.89  17.42   0.98     0.95       7730.40|
|  7:  2.5851 -  2.4562  1325   155  0.90  16.84   0.99     0.96       6864.86|
|  8:  2.4562 -  2.3497  1360   144  0.89  17.00   1.00     0.96       6139.20|
|  9:  2.3497 -  2.2596  1342   147  0.90  16.63   0.99     0.94       5293.80|
| 10:  2.2596 -  2.1819  1344   145  0.89  16.91   0.99     0.95       4850.01|
| 11:  2.1819 -  2.1138  1322   156  0.89  17.14   0.98     0.94       4442.49|
| 12:  2.1138 -  2.0536  1333   150  0.90  16.58   0.99     0.99       4058.55|
| 13:  2.0536 -  1.9996  1020   107  0.89  17.36   0.98     0.96       3543.91|
| 14:  1.9996 -  1.9510   230    29  0.91  14.92   0.96     0.91       3125.16|
|alpha:            min =        0.91 max =            1.02 mean =         0.97|
|beta:             min =     3125.16 max =        10704.96 mean =      6923.85|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.99|
|phase err.(test): min =        0.00 max =           87.98 mean =        14.53|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1627   ksol= 0.32   Bsol= 55.19   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.27,-1.81,-0.80,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.185320                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1627   ksol= 0.32   Bsol= 55.19   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.27,-1.81,-0.80,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.185320                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9295 -  4.6575 0.99   1462  161 0.0974 0.1302      5.3824      5.5753|
|  2:  4.6575 -  3.7155 0.99   1416  156 0.0818 0.1052      5.4042      5.5888|
|  3:  3.7155 -  3.2514 0.99   1371  157 0.1093 0.1518      5.4729      5.8159|
|  4:  3.2514 -  2.9566 0.99   1381  146 0.1284 0.1695      5.4651      5.6542|
|  5:  2.9566 -  2.7461 0.99   1355  153 0.1371 0.1737       5.363      5.5444|
|  6:  2.7461 -  2.5851 0.99   1369  153 0.1301 0.2153       5.247      5.5216|
|  7:  2.5851 -  2.4562 0.98   1325  155 0.1315 0.1726      5.2045      5.3925|
|  8:  2.4562 -  2.3497 0.98   1360  144 0.1233 0.1773      5.1245      5.3205|
|  9:  2.3497 -  2.2596 0.99   1342  147 0.1193 0.1843      5.0451      5.3312|
| 10:  2.2596 -  2.1819 0.98   1344  145 0.1215 0.1905      4.9981      5.2384|
| 11:  2.1819 -  2.1138 0.97   1322  156 0.1219 0.1842      4.9392      5.2617|
| 12:  2.1138 -  2.0536 0.98   1333  150 0.1189 0.1575      4.8886      5.0951|
| 13:  2.0536 -  1.9996 0.75   1020  107 0.1142 0.2063      4.7957      5.0876|
| 14:  1.9996 -  1.9510 0.17    230   29 0.1118 0.1671      4.8005      4.8996|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9295 -  4.6575  1462   161  0.94   9.25   0.97     0.95       7363.95|
|  2:  4.6575 -  3.7155  1416   156  0.95   8.02   1.02     1.00       8858.16|
|  3:  3.7155 -  3.2514  1371   157  0.93  11.58   1.03     1.02      10384.94|
|  4:  3.2514 -  2.9566  1381   146  0.91  14.86   1.02     1.01      10708.80|
|  5:  2.9566 -  2.7461  1355   153  0.89  16.86   1.01     0.99       9222.17|
|  6:  2.7461 -  2.5851  1369   153  0.89  17.43   0.98     0.96       7730.77|
|  7:  2.5851 -  2.4562  1325   155  0.89  16.85   0.99     0.96       6866.75|
|  8:  2.4562 -  2.3497  1360   144  0.89  17.01   1.00     0.96       6141.24|
|  9:  2.3497 -  2.2596  1342   147  0.90  16.63   0.99     0.95       5296.93|
| 10:  2.2596 -  2.1819  1344   145  0.89  16.92   1.00     0.96       4851.43|
| 11:  2.1819 -  2.1138  1322   156  0.89  17.15   0.99     0.95       4443.51|
| 12:  2.1138 -  2.0536  1333   150  0.90  16.59   1.00     1.00       4059.74|
| 13:  2.0536 -  1.9996  1020   107  0.89  17.36   0.99     0.97       3543.55|
| 14:  1.9996 -  1.9510   230    29  0.91  14.93   0.97     0.92       3124.70|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     3124.70 max =        10708.80 mean =      6926.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        15.00|
|phase err.(test): min =        0.00 max =           88.00 mean =        14.53|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.784)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.31   17.86    None  None   None       |
|    all(noH): 2823   0      0.00    99.31   17.86    None  None   None       |
|    Sol.    : 438    0      0.00    99.31   42.70    None  None   None       |
|    Mac.    : 2385   0      0.62    96.29   13.30    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 -   9.934:  973   |   5:    49.658 -  59.589:  100        |
|      1:     9.934 -  19.865: 1183   |   6:    59.589 -  69.520:   58        |
|      2:    19.865 -  29.796:  227   |   7:    69.520 -  79.451:   32        |
|      3:    29.796 -  39.727:  125   |   8:    79.451 -  89.382:    8        |
|      4:    39.727 -  49.658:  111   |   9:    89.382 -  99.313:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 309         
Filter by distance & map next to the model:
   mapped sites are within: 0.504 - 4.766
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 306 from: 309
   mapped sites are within: 0.709 - 4.766

peak=    6.719 closest distance to " O  BHOH Z  74 " =    1.151
peak=    5.743 closest distance to " O   HOH Z 113 " =    2.161
peak=    5.001 closest distance to " CB  ARG A 275 " =    0.995
peak=    4.958 closest distance to " O   HOH Z 417 " =    2.714
peak=    4.943 closest distance to " O   HOH Z  49 " =    1.193
peak=    4.910 closest distance to " CG  PRO A  54 " =    1.339
peak=    4.780 closest distance to " O   HOH Z  43 " =    2.173
peak=    4.773 closest distance to " O   HOH Z  65 " =    0.952
peak=    4.727 closest distance to " CA  TYR A  30 " =    0.907
peak=    4.703 closest distance to " CB  GLN A 223 " =    1.442
peak=    4.699 closest distance to " CG  PRO A  90 " =    1.195
peak=    4.570 closest distance to " CA  ARG A  36 " =    1.078
peak=    4.525 closest distance to " O   HOH Z 403 " =    1.791
peak=    4.502 closest distance to " O   HOH Z 234 " =    3.584
peak=    4.486 closest distance to " CG  PRO A 198 " =    1.222
peak=    4.443 closest distance to " O   HOH Z 142 " =    1.484
peak=    4.433 closest distance to " CB  GLN A 183 " =    1.253
peak=    4.424 closest distance to " CB  PRO A  54 " =    1.032
peak=    4.420 closest distance to " O   HOH Z 186 " =    2.275
peak=    4.417 closest distance to " O   HOH Z  63 " =    1.944
peak=    4.403 closest distance to " O   HOH Z 210 " =    0.919
peak=    4.397 closest distance to " O   GLY A  23 " =    2.450
peak=    4.391 closest distance to " NZ  LYS A 117 " =    3.051
peak=    4.380 closest distance to " CD2 TRP A 179 " =    1.327
peak=    4.346 closest distance to " O   HOH Z 188 " =    1.490
peak=    4.337 closest distance to " CD  ARG A 269 " =    1.012
peak=    4.326 closest distance to " CB  ARG A 190 " =    1.734
peak=    4.305 closest distance to " O   HOH Z 232 " =    2.276
peak=    4.301 closest distance to " CZ  PHE A 218 " =    1.198
peak=    4.298 closest distance to " CB  GLU A 152 " =    1.163
peak=    4.291 closest distance to " NH2BARG A 145 " =    2.176
peak=    4.272 closest distance to " O   HOH Z 369 " =    2.547
peak=    4.266 closest distance to " C   PRO A 198 " =    1.540
peak=    4.261 closest distance to " O   HOH Z 193 " =    1.735
peak=    4.250 closest distance to " O   HOH Z 117 " =    1.096
peak=    4.243 closest distance to " CB  SER A  63 " =    1.060
peak=    4.181 closest distance to " NE2 GLN A  11 " =    1.099
peak=    4.181 closest distance to " O   HOH Z 188 " =    2.670
peak=    4.176 closest distance to " CB  ARG A  79 " =    1.456
peak=    4.174 closest distance to " O   HOH Z 423 " =    1.897
peak=    4.173 closest distance to " O   HOH Z 248 " =    1.311
peak=    4.166 closest distance to " CB  PRO A 213 " =    1.256
peak=    4.148 closest distance to " CG  ARG A  66 " =    2.646
peak=    4.133 closest distance to " O   HOH Z 209 " =    2.267
peak=    4.120 closest distance to " O   HOH Z 298 " =    1.747
peak=    4.099 closest distance to " CA  ALA A  51 " =    0.944
peak=    4.097 closest distance to " O   HOH Z 287 " =    1.750
peak=    4.066 closest distance to " O   SER A  87 " =    2.238
peak=    4.062 closest distance to " ND2 ASN A 187 " =    1.625
peak=    4.061 closest distance to " O   HOH Z 365 " =    2.504
peak=    4.044 closest distance to " O   HOH Z 346 " =    1.671
peak=    4.013 closest distance to " O   HOH Z 203 " =    1.751
peak=    4.004 closest distance to " CB  ASN A 148 " =    1.445
peak=    4.001 closest distance to " O   HOH Z 327 " =    1.723
peak=    3.999 closest distance to " CD2 LEU A 297 " =    0.935
peak=    3.992 closest distance to " O   HOH Z 126 " =    1.784
peak=    3.981 closest distance to " O   HOH Z 132 " =    1.108
peak=    3.944 closest distance to " CA  ARG A 195 " =    1.253
peak=    3.938 closest distance to " O   HOH Z 394 " =    1.510
peak=    3.937 closest distance to " O   HOH Z 389 " =    1.864
peak=    3.934 closest distance to " O   HOH Z  97 " =    1.740
peak=    3.920 closest distance to " O   HOH Z 369 " =    1.887
peak=    3.905 closest distance to " O   HOH Z 134 " =    1.438
peak=    3.900 closest distance to " O   HOH Z  80 " =    1.861
peak=    3.900 closest distance to " CG  PRO A 243 " =    1.082
peak=    3.888 closest distance to " CB  THR A  31 " =    1.718
peak=    3.885 closest distance to " O   HOH Z 368 " =    2.118
peak=    3.872 closest distance to " O   THR A 182 " =    1.447
peak=    3.864 closest distance to " CG  GLN A  58 " =    0.800
peak=    3.863 closest distance to " CD  PRO A  54 " =    1.009
peak=    3.854 closest distance to " O   HOH Z  78 " =    1.638
peak=    3.842 closest distance to " O   HOH Z  97 " =    1.999
peak=    3.836 closest distance to " O   HOH Z 279 " =    2.101
peak=    3.829 closest distance to " O   HOH Z  40 " =    2.135
peak=    3.823 closest distance to " O   HOH Z 272 " =    1.860
peak=    3.821 closest distance to " O   HOH Z 173 " =    2.170
peak=    3.820 closest distance to " CB  SER A  62 " =    0.976
peak=    3.819 closest distance to " CE  LYS A 119 " =    1.088
peak=    3.813 closest distance to " CG2BVAL A  41 " =    0.816
peak=    3.811 closest distance to " O   HOH Z 426 " =    1.448
peak=    3.808 closest distance to " O   HOH Z 359 " =    1.657
peak=    3.805 closest distance to " CB  TRP A 266 " =    1.117
peak=    3.799 closest distance to " O   HOH Z 102 " =    1.299
peak=    3.797 closest distance to " N   ASN A  39 " =    1.317
peak=    3.786 closest distance to " O   HOH Z 180 " =    2.278
peak=    3.771 closest distance to " O   HOH Z  44 " =    2.328
peak=    3.770 closest distance to " O   HOH Z 132 " =    2.247
peak=    3.765 closest distance to " CB  SER A  26 " =    1.854
peak=    3.762 closest distance to " O   HOH Z  85 " =    1.544
peak=    3.761 closest distance to " CD  LYS A  76 " =    1.750
peak=    3.751 closest distance to " CB  PRO A  90 " =    1.076
peak=    3.749 closest distance to " CG2 ILE A 120 " =    1.239
peak=    3.748 closest distance to " CD  LYS A 166 " =    1.366
peak=    3.743 closest distance to " O   HOH Z 421 " =    2.016
peak=    3.734 closest distance to " O   HOH Z  59 " =    2.077
peak=    3.732 closest distance to " O   HOH Z 345 " =    1.731
peak=    3.729 closest distance to " O   HOH Z  15 " =    2.196
peak=    3.728 closest distance to " O   HOH Z 227 " =    1.681
peak=    3.727 closest distance to " CB  ALA A 248 " =    1.352
peak=    3.724 closest distance to " CE  LYS A  76 " =    0.852
peak=    3.721 closest distance to " CA  ALA A 295 " =    0.998
peak=    3.721 closest distance to " ND2 ASN A 249 " =    0.902
peak=    3.699 closest distance to " CB  VAL A 202 " =    1.482
peak=    3.698 closest distance to " CZ3 TRP A 266 " =    1.035
peak=    3.696 closest distance to " O   HOH Z 427 " =    3.029
peak=    3.693 closest distance to " O   HOH Z 316 " =    3.032
peak=    3.685 closest distance to " O   HOH Z 126 " =    1.833
peak=    3.681 closest distance to " O   HOH Z 402 " =    1.418
peak=    3.678 closest distance to " O   HOH Z 146 " =    2.316
peak=    3.678 closest distance to " NH1AARG A 145 " =    1.375
peak=    3.672 closest distance to " CA  ALA A 160 " =    0.911
peak=    3.671 closest distance to " CG2 ILE A  20 " =    1.385
peak=    3.667 closest distance to " CZ  PHE A  38 " =    1.185
peak=    3.665 closest distance to " O   HOH Z 412 " =    3.777
peak=    3.665 closest distance to " CB  GLU A 277 " =    3.633
peak=    3.649 closest distance to " OG BSER A 212 " =    2.563
peak=    3.643 closest distance to " O   HOH Z 298 " =    2.362
peak=    3.639 closest distance to " O   HOH Z 247 " =    1.349
peak=    3.631 closest distance to " O   HOH Z 361 " =    2.612
peak=    3.627 closest distance to " O   HOH Z 380 " =    1.921
peak=    3.615 closest distance to " O   HOH Z  21 " =    1.861
peak=    3.614 closest distance to " CD  ARG A 159 " =    0.804
peak=    3.609 closest distance to " O   HOH Z 371 " =    3.219
peak=    3.608 closest distance to " O   ALA A 165 " =    1.458
peak=    3.607 closest distance to " O   HOH Z 126 " =    1.499
peak=    3.606 closest distance to " NE2 GLN A  77 " =    3.137
peak=    3.599 closest distance to " CB  ASN A  39 " =    0.793
peak=    3.599 closest distance to " CB  TRP A 179 " =    1.257
peak=    3.597 closest distance to " O   HOH Z 357 " =    2.055
peak=    3.593 closest distance to " CG AARG A 275 " =    1.138
peak=    3.586 closest distance to " O   HOH Z 406 " =    1.483
peak=    3.584 closest distance to " CA  ASN A 176 " =    1.663
peak=    3.583 closest distance to " CB  ARG A 190 " =    1.150
peak=    3.570 closest distance to " OH  TYR A 116 " =    1.125
peak=    3.570 closest distance to " CB  VAL A 265 " =    1.176
peak=    3.568 closest distance to " O   HOH Z 128 " =    2.573
peak=    3.566 closest distance to " CB  ALA A 114 " =    0.886
peak=    3.566 closest distance to " O   HOH Z 361 " =    3.424
peak=    3.565 closest distance to " CB  TYR A 169 " =    0.770
peak=    3.555 closest distance to " CG  LEU A 167 " =    1.205
peak=    3.551 closest distance to " CA  ALA A  84 " =    1.204
peak=    3.550 closest distance to " O  BHOH Z 338 " =    2.148
peak=    3.549 closest distance to " CB  SER A   3 " =    1.260
peak=    3.540 closest distance to " O   ASN A  74 " =    1.462
peak=    3.531 closest distance to " O   HOH Z 284 " =    2.951
peak=    3.527 closest distance to " N   CYS A 260 " =    0.987
peak=    3.524 closest distance to " O   HOH Z 146 " =    2.361
peak=    3.522 closest distance to " O   HOH Z 250 " =    1.349
peak=    3.521 closest distance to " O   HOH Z 336 " =    1.952
peak=    3.518 closest distance to " CG1 ILE A  33 " =    1.162
peak=    3.516 closest distance to " CB  ASP A 191 " =    1.184
peak=    3.508 closest distance to " CB  THR A  52 " =    0.746
peak=    3.505 closest distance to " CD1 ILE A 199 " =    1.221
peak=    3.499 closest distance to " O   HOH Z 250 " =    1.594
peak=    3.497 closest distance to " CB  ASN A 285 " =    0.951
peak=    3.496 closest distance to " O   HOH Z  63 " =    2.203
peak=    3.488 closest distance to " CD1 LEU A  96 " =    0.723
peak=    3.488 closest distance to " O   HOH Z 214 " =    2.682
peak=    3.484 closest distance to " NH2AARG A 275 " =    3.577
peak=    3.481 closest distance to " CA  THR A  42 " =    0.991
peak=    3.480 closest distance to " O   HOH Z 299 " =    4.259
peak=    3.463 closest distance to " CA  ASP A 162 " =    1.183
peak=    3.462 closest distance to " O   HOH Z 414 " =    1.409
peak=    3.461 closest distance to " CG  GLN A  11 " =    1.567
peak=    3.460 closest distance to " O   HOH Z   1 " =    2.326
peak=    3.459 closest distance to " CB  PHE A  16 " =    1.087
peak=    3.457 closest distance to " CD  LYS A 119 " =    1.813
peak=    3.447 closest distance to " O   HOH Z 251 " =    1.607
peak=    3.447 closest distance to " O   HOH Z 124 " =    1.175
peak=    3.444 closest distance to " O   TYR A 116 " =    1.419
peak=    3.440 closest distance to " O   HOH Z 422 " =    2.669
peak=    3.440 closest distance to " OG  SER A 245 " =    1.496
peak=    3.440 closest distance to " N   ARG A 156 " =    1.427
peak=    3.439 closest distance to " O   HOH Z 298 " =    4.195
peak=    3.439 closest distance to " CB  SER A 141 " =    1.133
peak=    3.438 closest distance to " O   HOH Z 258 " =    2.133
peak=    3.437 closest distance to " OG BSER A 164 " =    2.149
peak=    3.437 closest distance to " O   HOH Z 313 " =    2.002
peak=    3.436 closest distance to " CB  ASN A 110 " =    1.051
peak=    3.432 closest distance to " O   HOH Z 285 " =    2.600
peak=    3.430 closest distance to " O   HOH Z 128 " =    2.025
peak=    3.429 closest distance to " CB  GLU A 128 " =    1.123
peak=    3.428 closest distance to " O   HOH Z 325 " =    2.103
peak=    3.424 closest distance to " CA  ILE A 106 " =    0.870
peak=    3.423 closest distance to " O   THR A 220 " =    1.131
peak=    3.421 closest distance to " O   GLY A  91 " =    1.352
peak=    3.419 closest distance to " O   HOH Z 158 " =    3.040
peak=    3.418 closest distance to " O   HOH Z 353 " =    2.719
peak=    3.417 closest distance to " CB  PHE A 204 " =    0.769
peak=    3.415 closest distance to " NH1AARG A 275 " =    0.929
peak=    3.413 closest distance to " O   ARG A  56 " =    2.852
peak=    3.413 closest distance to " CA  ALA A 100 " =    1.161
peak=    3.411 closest distance to " O   HOH Z 245 " =    1.325
peak=    3.404 closest distance to " CG2 VAL A 257 " =    0.776
peak=    3.403 closest distance to " O   HOH Z 375 " =    2.094
peak=    3.396 closest distance to " CB  GLN A  88 " =    1.120
peak=    3.392 closest distance to " O   HOH Z 261 " =    2.246
peak=    3.388 closest distance to " N   TYR A 116 " =    1.644
peak=    3.377 closest distance to " O   HOH Z 108 " =    2.707
peak=    3.374 closest distance to " O   HOH Z  20 " =    1.020
peak=    3.364 closest distance to " O   HOH Z 344 " =    3.041
peak=    3.359 closest distance to " O   HOH Z 282 " =    1.961
peak=    3.358 closest distance to " CG  MET A 185 " =    1.167
peak=    3.351 closest distance to " CB  ASN A 215 " =    1.180
peak=    3.345 closest distance to " O   HOH Z 305 " =    3.485
peak=    3.333 closest distance to " CG2AVAL A 121 " =    2.180
peak=    3.332 closest distance to " O   HOH Z 392 " =    2.282
peak=    3.331 closest distance to " CE1 TYR A 186 " =    1.257
peak=    3.330 closest distance to " O   HOH Z 291 " =    1.353
peak=    3.329 closest distance to " CA  THR A  82 " =    1.749
peak=    3.316 closest distance to " O   HOH Z  85 " =    1.909
peak=    3.315 closest distance to " O   HOH Z  35 " =    2.389
peak=    3.313 closest distance to " CB  PRO A 198 " =    1.204
peak=    3.313 closest distance to " O   HOH Z 139 " =    4.766
peak=    3.311 closest distance to " O   HOH Z 148 " =    3.369
peak=    3.310 closest distance to " O   HOH Z 350 " =    2.068
peak=    3.304 closest distance to " O   HOH Z 433 " =    1.419
peak=    3.303 closest distance to " CG1 ILE A  20 " =    1.263
peak=    3.301 closest distance to " O   HOH Z 419 " =    1.685
peak=    3.301 closest distance to " CA  ASN A 217 " =    1.197
peak=    3.295 closest distance to " O   HOH Z  68 " =    1.646
peak=    3.292 closest distance to " CB  ASN A 142 " =    1.192
peak=    3.289 closest distance to " O   HOH Z  88 " =    3.151
peak=    3.285 closest distance to " CG  GLU A  37 " =    0.944
peak=    3.285 closest distance to " CA  ALA A 158 " =    1.415
peak=    3.283 closest distance to " O   HOH Z 299 " =    4.350
peak=    3.282 closest distance to " O   HOH Z 366 " =    2.389
peak=    3.275 closest distance to " O   HOH Z 383 " =    2.035
peak=    3.275 closest distance to " CA  ASN A 215 " =    1.029
peak=    3.272 closest distance to " CB  ASP A 124 " =    0.709
peak=    3.271 closest distance to " O   HOH Z 265 " =    1.959
peak=    3.266 closest distance to " O   HOH Z 421 " =    2.678
peak=    3.262 closest distance to " O   HOH Z 303 " =    2.086
peak=    3.255 closest distance to " O   HOH Z 234 " =    2.005
peak=    3.255 closest distance to " OG1 THR A 221 " =    1.105
peak=    3.251 closest distance to " NZ  LYS A  48 " =    1.098
peak=    3.249 closest distance to " O   ASN A 284 " =    1.636
peak=    3.243 closest distance to " CB  LEU A  83 " =    0.764
peak=    3.242 closest distance to " CB  LYS A 289 " =    1.125
peak=    3.228 closest distance to " O   HOH Z 404 " =    2.315
peak=    3.223 closest distance to " OD1 ASN A 301 " =    1.557
peak=    3.217 closest distance to " O   HOH Z  61 " =    1.583
peak=    3.216 closest distance to " OD2 ASP A 298 " =    3.849
peak=    3.216 closest distance to " O   HOH Z 415 " =    3.484
peak=    3.215 closest distance to " O   HOH Z 200 " =    2.639
peak=    3.215 closest distance to " O   HOH Z 425 " =    2.004
peak=    3.209 closest distance to " CB  PRO A 243 " =    1.223
peak=    3.205 closest distance to " O   HOH Z 411 " =    1.662
peak=    3.204 closest distance to " O   HOH Z 403 " =    1.479
peak=    3.198 closest distance to " N   HIS A 108 " =    1.781
peak=    3.198 closest distance to " CA  SER A  32 " =    1.685
peak=    3.197 closest distance to " C   SER A  32 " =    1.775
peak=    3.196 closest distance to " CB  GLU A  46 " =    1.085
peak=    3.192 closest distance to " CB  ASP A 140 " =    1.165
peak=    3.192 closest distance to " CB  ARG A 269 " =    0.737
peak=    3.192 closest distance to " O   HOH Z 182 " =    2.032
peak=    3.187 closest distance to " CA  ALA A 129 " =    1.429
peak=    3.179 closest distance to " O   HOH Z 132 " =    2.480
peak=    3.175 closest distance to " OE1 GLU A   2 " =    2.116
peak=    3.170 closest distance to " O   HOH Z 116 " =    1.137
peak=    3.170 closest distance to " O   HOH Z 345 " =    2.685
peak=    3.168 closest distance to " CG1 ILE A  49 " =    1.603
peak=    3.165 closest distance to " CA  TYR A 116 " =    1.334
peak=    3.163 closest distance to " O   HOH Z  94 " =    2.583
peak=    3.160 closest distance to " O   HOH Z  63 " =    2.320
peak=    3.160 closest distance to " NE  ARG A  24 " =    0.936
peak=    3.159 closest distance to " O   HOH Z 163 " =    1.462
peak=    3.158 closest distance to " CD  GLN A 194 " =    1.616
peak=    3.156 closest distance to " CB  MET A  47 " =    1.087
peak=    3.153 closest distance to " CA  SER A  87 " =    1.039
peak=    3.151 closest distance to " CA  VAL A 125 " =    1.134
peak=    3.151 closest distance to " O   HOH Z 185 " =    1.759
peak=    3.151 closest distance to " CG1BVAL A  72 " =    1.814
peak=    3.149 closest distance to " CB  LEU A 228 " =    1.108
peak=    3.142 closest distance to " CA  ALA A 248 " =    1.305
peak=    3.141 closest distance to " CB  ARG A  79 " =    0.835
peak=    3.139 closest distance to " CA  ASP A 191 " =    0.902
peak=    3.134 closest distance to " O   HOH Z 147 " =    1.828
peak=    3.129 closest distance to " N   PHE A 130 " =    1.407
peak=    3.126 closest distance to " OG1 THR A 294 " =    1.566
peak=    3.125 closest distance to " O   HOH Z 193 " =    1.891
peak=    3.124 closest distance to " O   HOH Z 199 " =    1.643
peak=    3.119 closest distance to " CA  LEU A  83 " =    1.347
peak=    3.118 closest distance to " O   HOH Z 194 " =    1.903
peak=    3.107 closest distance to " CA  ALA A 299 " =    0.965
peak=    3.107 closest distance to " CB  ALA A  10 " =    1.203
peak=    3.106 closest distance to " O   HOH Z 293 " =    1.890
peak=    3.104 closest distance to " O   HOH Z 298 " =    2.093
peak=    3.102 closest distance to " CD  ARG A  66 " =    2.759
peak=    3.101 closest distance to " O   HOH Z 183 " =    1.811
peak=    3.098 closest distance to " O   HOH Z 281 " =    2.931
peak=    3.098 closest distance to " O   HOH Z 358 " =    2.178
peak=    3.096 closest distance to " CG1AVAL A 121 " =    0.835
peak=    3.096 closest distance to " CA  SER A 146 " =    1.993
peak=    3.089 closest distance to " CA  LYS A 117 " =    1.199
peak=    3.086 closest distance to " O   HOH Z  85 " =    1.461
peak=    3.083 closest distance to " CG  ARG A 269 " =    1.404
peak=    3.081 closest distance to " CA  GLY A 241 " =    0.974
peak=    3.077 closest distance to " O   HOH Z  54 " =    1.639
peak=    3.076 closest distance to " CB  HIS A 108 " =    0.850
peak=    3.067 closest distance to " O   HOH Z  19 " =    1.240
peak=    3.066 closest distance to " OG1 THR A 264 " =    0.815
peak=    3.064 closest distance to " CB  GLN A 240 " =    1.403
peak=    3.031 closest distance to " N   CYS A 260 " =    0.879
peak=    3.023 closest distance to " OG1 THR A 294 " =    3.979
peak=    3.016 closest distance to " CE1 PHE A 218 " =    1.139

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.877 - 5.976
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 212
   mapped sites are within: 0.877 - 5.976

peak=   -4.518 closest distance to " CD  ARG A  14 " =    3.401
peak=   -4.478 closest distance to " O   HOH Z 266 " =    5.220
peak=   -4.465 closest distance to " CG2 ILE A  49 " =    2.770
peak=   -4.280 closest distance to " O   HOH Z  13 " =    1.766
peak=   -4.206 closest distance to " OXT GLY A 302 " =    2.928
peak=   -4.189 closest distance to " CG  GLN A  58 " =    1.092
peak=   -4.135 closest distance to " OG BSER A 134 " =    1.444
peak=   -4.133 closest distance to " CD1 LEU A 101 " =    2.418
peak=   -4.123 closest distance to " O   VAL A  67 " =    2.793
peak=   -4.109 closest distance to " C   HIS A 108 " =    1.150
peak=   -4.030 closest distance to " CD2 LEU A 237 " =    2.537
peak=   -4.020 closest distance to " O   HOH Z 377 " =    2.148
peak=   -3.992 closest distance to " CD2 TYR A 293 " =    1.787
peak=   -3.988 closest distance to " CE2 TYR A  30 " =    2.768
peak=   -3.962 closest distance to " CH2 TRP A 179 " =    1.302
peak=   -3.933 closest distance to " O   HOH Z 374 " =    1.926
peak=   -3.919 closest distance to " O   GLY A 241 " =    2.300
peak=   -3.904 closest distance to " O   PRO A 198 " =    1.366
peak=   -3.903 closest distance to " O   PRO A 163 " =    2.146
peak=   -3.894 closest distance to " O   PHE A 218 " =    1.514
peak=   -3.890 closest distance to " CD  GLN A  58 " =    1.190
peak=   -3.879 closest distance to " O   ALA A  34 " =    2.388
peak=   -3.877 closest distance to " O   HOH Z 198 " =    1.507
peak=   -3.852 closest distance to " O   HOH Z 165 " =    1.846
peak=   -3.845 closest distance to " CD  ARG A 156 " =    2.059
peak=   -3.826 closest distance to " CB  PRO A 243 " =    2.728
peak=   -3.790 closest distance to " CG2 ILE A  20 " =    3.020
peak=   -3.767 closest distance to " O   HOH Z 166 " =    1.825
peak=   -3.757 closest distance to " CZ  TYR A 169 " =    1.824
peak=   -3.750 closest distance to " CD  GLN A 223 " =    1.551
peak=   -3.722 closest distance to " NE2 GLN A  88 " =    1.643
peak=   -3.704 closest distance to " CD1 LEU A  25 " =    2.531
peak=   -3.697 closest distance to " O   HOH Z 210 " =    1.028
peak=   -3.689 closest distance to " O   VAL A 174 " =    2.161
peak=   -3.683 closest distance to " O   ALA A 256 " =    1.628
peak=   -3.670 closest distance to " CD1 ILE A 106 " =    2.208
peak=   -3.660 closest distance to " CE  MET A 105 " =    2.483
peak=   -3.649 closest distance to " O   HOH Z  10 " =    1.598
peak=   -3.647 closest distance to " CE BMET A  47 " =    1.464
peak=   -3.644 closest distance to " O   HOH Z 150 " =    2.151
peak=   -3.638 closest distance to " CG  ASP A 132 " =    2.346
peak=   -3.637 closest distance to " CH2 TRP A 150 " =    1.107
peak=   -3.637 closest distance to " CB  ALA A 184 " =    2.306
peak=   -3.625 closest distance to " O   HOH Z 348 " =    2.206
peak=   -3.622 closest distance to " CA  ASP A 298 " =    1.049
peak=   -3.621 closest distance to " CG  GLU A  53 " =    1.469
peak=   -3.621 closest distance to " CG1AVAL A  41 " =    2.599
peak=   -3.618 closest distance to " CG  PRO A 243 " =    1.686
peak=   -3.611 closest distance to " CZ  ARG A  66 " =    1.096
peak=   -3.608 closest distance to " O   SER A 210 " =    1.860
peak=   -3.600 closest distance to " CD1 PHE A  59 " =    1.971
peak=   -3.599 closest distance to " O   GLY A  80 " =    2.594
peak=   -3.593 closest distance to " CD2 TYR A 247 " =    2.404
peak=   -3.576 closest distance to " CA  GLY A 133 " =    2.013
peak=   -3.571 closest distance to " OG  SER A  97 " =    2.201
peak=   -3.570 closest distance to " O   ILE A  49 " =    1.760
peak=   -3.567 closest distance to " CE3 TRP A 150 " =    2.158
peak=   -3.565 closest distance to " O   HOH Z 208 " =    1.917
peak=   -3.562 closest distance to " O   HOH Z 174 " =    3.697
peak=   -3.562 closest distance to " C   THR A 279 " =    1.180
peak=   -3.561 closest distance to " CD2 HIS A 207 " =    2.188
peak=   -3.556 closest distance to " CG  MET A 105 " =    0.963
peak=   -3.551 closest distance to " N   ALA A  43 " =    2.649
peak=   -3.545 closest distance to " CG1 VAL A 112 " =    2.660
peak=   -3.541 closest distance to " CZ  TYR A 172 " =    1.833
peak=   -3.538 closest distance to " CD  GLN A 223 " =    1.548
peak=   -3.534 closest distance to " CB  ALA A 248 " =    2.270
peak=   -3.531 closest distance to " CG1 VAL A  78 " =    2.697
peak=   -3.530 closest distance to " CB  ALA A 161 " =    2.545
peak=   -3.527 closest distance to " CA  GLY A 241 " =    3.110
peak=   -3.526 closest distance to " NH2 ARG A  66 " =    5.976
peak=   -3.522 closest distance to " CB  PHE A 192 " =    2.086
peak=   -3.522 closest distance to " O   HOH Z  71 " =    2.335
peak=   -3.520 closest distance to " NE2 GLN A  88 " =    1.112
peak=   -3.504 closest distance to " O   HOH Z 183 " =    1.627
peak=   -3.504 closest distance to " O   HOH Z 102 " =    1.715
peak=   -3.499 closest distance to " O   HOH Z 166 " =    1.578
peak=   -3.491 closest distance to " CB  ALA A  43 " =    2.434
peak=   -3.479 closest distance to " O   HOH Z 113 " =    2.007
peak=   -3.470 closest distance to " O   GLU A 152 " =    1.425
peak=   -3.465 closest distance to " ND2 ASN A  69 " =    1.819
peak=   -3.460 closest distance to " O   HOH Z 252 " =    4.019
peak=   -3.459 closest distance to " C   GLN A 144 " =    0.914
peak=   -3.457 closest distance to " CB  TRP A  85 " =    2.466
peak=   -3.456 closest distance to " O   HOH Z 171 " =    2.416
peak=   -3.454 closest distance to " O   HOH Z 191 " =    5.947
peak=   -3.453 closest distance to " OD1 ASN A 148 " =    1.448
peak=   -3.449 closest distance to " NE  ARG A  79 " =    1.287
peak=   -3.447 closest distance to " CG2 VAL A 189 " =    2.214
peak=   -3.444 closest distance to " O   TRP A  92 " =    2.015
peak=   -3.443 closest distance to " CZ  PHE A  38 " =    2.205
peak=   -3.443 closest distance to " O   HOH Z 211 " =    1.530
peak=   -3.435 closest distance to " O   HOH Z  59 " =    4.031
peak=   -3.434 closest distance to " O   SER A 146 " =    1.103
peak=   -3.429 closest distance to " CB  ALA A 291 " =    2.401
peak=   -3.428 closest distance to " N   SER A 276 " =    1.333
peak=   -3.425 closest distance to " CB  ALA A  10 " =    2.326
peak=   -3.417 closest distance to " OG BSER A 210 " =    1.389
peak=   -3.415 closest distance to " O   HOH Z 366 " =    1.559
peak=   -3.404 closest distance to " OD1 ASP A 171 " =    1.462
peak=   -3.400 closest distance to " O   HOH Z  81 " =    2.021
peak=   -3.394 closest distance to " ND2 ASN A 249 " =    2.292
peak=   -3.394 closest distance to " CD2 PHE A  61 " =    2.124
peak=   -3.394 closest distance to " OD2 ASP A 191 " =    1.546
peak=   -3.392 closest distance to " O   HOH Z 264 " =    1.787
peak=   -3.391 closest distance to " O   ALA A   1 " =    1.917
peak=   -3.391 closest distance to " CG1 VAL A  67 " =    2.964
peak=   -3.372 closest distance to " N   ALA A 226 " =    1.876
peak=   -3.369 closest distance to " O   HOH Z  11 " =    2.095
peak=   -3.361 closest distance to " OD2 ASP A 171 " =    2.334
peak=   -3.356 closest distance to " O   HOH Z 240 " =    4.068
peak=   -3.355 closest distance to " NE2 GLN A 223 " =    1.243
peak=   -3.350 closest distance to " CG  PHE A 283 " =    2.492
peak=   -3.348 closest distance to " O   HOH Z  53 " =    1.786
peak=   -3.345 closest distance to " O   HOH Z 174 " =    2.326
peak=   -3.342 closest distance to " CD  PRO A 243 " =    2.011
peak=   -3.340 closest distance to " O   HOH Z  38 " =    1.654
peak=   -3.339 closest distance to " ND2BASN A 224 " =    1.792
peak=   -3.338 closest distance to " ND2 ASN A  39 " =    1.138
peak=   -3.337 closest distance to " N   SER A  12 " =    1.299
peak=   -3.334 closest distance to " CE2 PHE A  61 " =    2.718
peak=   -3.327 closest distance to " OD1 ASN A 301 " =    1.937
peak=   -3.323 closest distance to " O   HOH Z 111 " =    1.954
peak=   -3.318 closest distance to " OE1 GLN A 183 " =    1.339
peak=   -3.317 closest distance to " O   HOH Z 313 " =    2.130
peak=   -3.316 closest distance to " O   HOH Z 109 " =    1.804
peak=   -3.314 closest distance to " O   HOH Z 193 " =    1.300
peak=   -3.313 closest distance to " CG1 VAL A 265 " =    2.597
peak=   -3.308 closest distance to " O   SER A  26 " =    1.386
peak=   -3.307 closest distance to " CA  GLY A 203 " =    2.371
peak=   -3.306 closest distance to " O   HOH Z 196 " =    1.859
peak=   -3.304 closest distance to " N   ALA A 248 " =    1.796
peak=   -3.299 closest distance to " OG  SER A  26 " =    1.186
peak=   -3.298 closest distance to " O   ALA A  10 " =    1.961
peak=   -3.297 closest distance to " NE  ARG A  66 " =    4.418
peak=   -3.296 closest distance to " ND2 ASN A  45 " =    1.896
peak=   -3.296 closest distance to " N   PHE A  59 " =    1.799
peak=   -3.293 closest distance to " O   HOH Z 110 " =    1.392
peak=   -3.291 closest distance to " O   HOH Z 290 " =    0.973
peak=   -3.289 closest distance to " O   GLN A  94 " =    2.249
peak=   -3.287 closest distance to " O   SER A  95 " =    1.705
peak=   -3.285 closest distance to " O   HOH Z 357 " =    2.146
peak=   -3.283 closest distance to " O   HOH Z 426 " =    1.725
peak=   -3.282 closest distance to " O   HOH Z 427 " =    1.516
peak=   -3.282 closest distance to " O   HOH Z 433 " =    2.721
peak=   -3.280 closest distance to " O   HOH Z 198 " =    1.559
peak=   -3.278 closest distance to " O   HOH Z 126 " =    1.953
peak=   -3.278 closest distance to " O   HOH Z 418 " =    1.411
peak=   -3.268 closest distance to " O   HOH Z 103 " =    1.792
peak=   -3.268 closest distance to " CE1 PHE A 218 " =    2.624
peak=   -3.258 closest distance to " O   HOH Z 351 " =    1.417
peak=   -3.258 closest distance to " O   HOH Z 234 " =    3.843
peak=   -3.255 closest distance to " NE2 GLN A  11 " =    1.675
peak=   -3.254 closest distance to " ND2 ASN A  45 " =    1.046
peak=   -3.251 closest distance to " ND2 ASN A 187 " =    1.593
peak=   -3.249 closest distance to " O   HOH Z 377 " =    1.634
peak=   -3.247 closest distance to " O   HOH Z 431 " =    4.185
peak=   -3.245 closest distance to " O   HOH Z 111 " =    3.787
peak=   -3.240 closest distance to " O   HOH Z 252 " =    3.517
peak=   -3.238 closest distance to " CB  ALA A 291 " =    2.269
peak=   -3.237 closest distance to " CZ  PHE A  38 " =    2.068
peak=   -3.235 closest distance to " CG1 VAL A 112 " =    2.621
peak=   -3.234 closest distance to " O   ASN A 252 " =    1.427
peak=   -3.222 closest distance to " OD1 ASP A 191 " =    1.437
peak=   -3.220 closest distance to " O   HOH Z 244 " =    1.358
peak=   -3.216 closest distance to " O   HOH Z  41 " =    2.086
peak=   -3.210 closest distance to " CD1 ILE A 151 " =    2.414
peak=   -3.209 closest distance to " O   HOH Z 156 " =    3.456
peak=   -3.208 closest distance to " O   HOH Z  43 " =    4.493
peak=   -3.208 closest distance to " O   HOH Z 283 " =    2.365
peak=   -3.207 closest distance to " O   HOH Z 364 " =    5.018
peak=   -3.206 closest distance to " CD  ARG A 139 " =    1.529
peak=   -3.204 closest distance to " CG  HIS A  86 " =    1.193
peak=   -3.204 closest distance to " CD2 LEU A 282 " =    2.054
peak=   -3.191 closest distance to " CA  GLY A  57 " =    2.190
peak=   -3.189 closest distance to " O   HOH Z 281 " =    2.508
peak=   -3.188 closest distance to " O   HOH Z 139 " =    3.260
peak=   -3.187 closest distance to " O   HOH Z 265 " =    2.464
peak=   -3.186 closest distance to " O   HOH Z 215 " =    2.226
peak=   -3.184 closest distance to " OE2 GLU A   2 " =    1.870
peak=   -3.181 closest distance to " CA  GLY A 241 " =    2.889
peak=   -3.181 closest distance to " O   HOH Z 396 " =    1.776
peak=   -3.181 closest distance to " O   HOH Z 297 " =    2.757
peak=   -3.180 closest distance to " O   HOH Z 185 " =    2.406
peak=   -3.176 closest distance to " OH  TYR A 169 " =    0.979
peak=   -3.176 closest distance to " O   HOH Z 423 " =    2.295
peak=   -3.169 closest distance to " O   HOH Z 395 " =    5.081
peak=   -3.168 closest distance to " CD  LYS A 289 " =    2.336
peak=   -3.160 closest distance to " O   HOH Z 197 " =    5.373
peak=   -3.150 closest distance to " O   HOH Z  64 " =    2.386
peak=   -3.149 closest distance to " O   ASN A  45 " =    1.851
peak=   -3.149 closest distance to " O   THR A   4 " =    1.213
peak=   -3.142 closest distance to " O   HOH Z 251 " =    1.691
peak=   -3.132 closest distance to " O   ARG A  24 " =    1.904
peak=   -3.125 closest distance to " OG BSER A 134 " =    1.934
peak=   -3.120 closest distance to " O   HOH Z  78 " =    1.871
peak=   -3.119 closest distance to " ND2 ASN A 215 " =    2.245
peak=   -3.114 closest distance to " CG2 THR A  18 " =    2.944
peak=   -3.113 closest distance to " O   SER A   3 " =    1.018
peak=   -3.113 closest distance to " O   SER A 276 " =    1.639
peak=   -3.112 closest distance to " OD1 ASN A  39 " =    2.263
peak=   -3.105 closest distance to " ND2 ASN A  60 " =    1.294
peak=   -3.099 closest distance to " C   SER A 206 " =    1.528
peak=   -3.098 closest distance to " O   ASN A 301 " =    1.323
peak=   -3.068 closest distance to " O   ASP A 132 " =    2.441
peak=   -3.059 closest distance to " CB  ALA A   9 " =    2.466
peak=   -3.057 closest distance to " C   GLY A  17 " =    0.877
peak=   -3.053 closest distance to " CA  GLY A 111 " =    2.525
peak=   -3.050 closest distance to " CD2 LEU A 300 " =    2.758
peak=   -3.047 closest distance to " OXT GLY A 302 " =    3.184
peak=   -3.013 closest distance to " O   GLY A  17 " =    2.259

================= 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    :  0.4601 0.4569   6.265315e+00   6.260609e+00
   1_bss:  0.4534 0.4483   6.259308e+00   6.254287e+00
   1_xyz:  0.3267 0.3580   6.029138e+00   6.094577e+00
   1_adp:  0.2902 0.3621   5.971423e+00   6.109683e+00
   1_occ:  0.2901 0.3627   5.970993e+00   6.110061e+00
   2_bss:  0.2873 0.3586   5.964118e+00   6.104179e+00
   2_xyz:  0.2073 0.2608   5.669061e+00   5.851504e+00
   2_adp:  0.1852 0.2362   5.572710e+00   5.766756e+00
   2_occ:  0.1849 0.2356   5.571480e+00   5.764837e+00
   3_bss:  0.1845 0.2345   5.569295e+00   5.761605e+00
   3_xyz:  0.1401 0.1859   5.333745e+00   5.549820e+00
   3_adp:  0.1290 0.1770   5.272596e+00   5.500122e+00
   3_occ:  0.1290 0.1769   5.272484e+00   5.500189e+00
   4_bss:  0.1293 0.1770   5.273041e+00   5.498563e+00
   4_xyz:  0.1235 0.1676   5.229567e+00   5.452071e+00
   4_adp:  0.1210 0.1672   5.218792e+00   5.446316e+00
   4_occ:  0.1209 0.1672   5.218706e+00   5.446296e+00
   5_bss:  0.1209 0.1672   5.218676e+00   5.446340e+00
   5_xyz:  0.1165 0.1637   5.190632e+00   5.423668e+00
   5_adp:  0.1157 0.1626   5.185504e+00   5.419745e+00
   5_occ:  0.1155 0.1627   5.185120e+00   5.419948e+00
   5_bss:  0.1154 0.1627   5.185320e+00   5.420090e+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:  0.282  20.001  -0.236   1.540   1.270   0.000   0.000   0.000
   1_xyz:  0.282  20.001  -0.236   1.540   1.270   0.000   0.000   0.000
   1_adp:  0.282  20.001  -0.236   1.540   1.270   0.000   0.000   0.000
   1_occ:  0.282  20.001  -0.236   1.540   1.270   0.000   0.000   0.000
   2_bss:  0.319  52.752  -1.816   0.006   0.079   0.000   0.000   0.000
   2_xyz:  0.319  52.752  -1.816   0.006   0.079   0.000   0.000   0.000
   2_adp:  0.319  52.752  -1.816   0.006   0.079   0.000   0.000   0.000
   2_occ:  0.319  52.752  -1.816   0.006   0.079   0.000   0.000   0.000
   3_bss:  0.326  55.880  -3.065  -1.309  -0.643  -0.000  -0.000  -0.000
   3_xyz:  0.326  55.880  -3.065  -1.309  -0.643  -0.000  -0.000  -0.000
   3_adp:  0.326  55.880  -3.065  -1.309  -0.643  -0.000  -0.000  -0.000
   3_occ:  0.326  55.880  -3.065  -1.309  -0.643  -0.000  -0.000  -0.000
   4_bss:  0.326  55.880  -3.495  -1.917  -1.045  -0.000  -0.000  -0.000
   4_xyz:  0.326  55.880  -3.495  -1.917  -1.045  -0.000  -0.000  -0.000
   4_adp:  0.326  55.880  -3.495  -1.917  -1.045  -0.000  -0.000  -0.000
   4_occ:  0.326  55.880  -3.495  -1.917  -1.045  -0.000  -0.000  -0.000
   5_bss:  0.323  55.880  -3.449  -1.932  -0.967  -0.000  -0.000  -0.000
   5_xyz:  0.323  55.880  -3.449  -1.932  -0.967  -0.000  -0.000  -0.000
   5_adp:  0.323  55.880  -3.449  -1.932  -0.967  -0.000  -0.000  -0.000
   5_occ:  0.323  55.880  -3.449  -1.932  -0.967  -0.000  -0.000  -0.000
   5_bss:  0.321  55.185  -3.266  -1.812  -0.795  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.613 0.4629  0.6254    65552.523
   1_bss:  53.908 0.4703  0.6593    63177.651
   1_xyz:  37.855 0.6688  0.8973    35153.706
   1_adp:  39.044 0.6539  0.8863    36964.110
   1_occ:  39.060 0.6537  0.8851    36977.275
   2_bss:  38.588 0.6590  0.8501    36009.614
   2_xyz:  26.790 0.7910  0.9820    17824.243
   2_adp:  23.426 0.8275  1.0027    14677.790
   2_occ:  23.373 0.8281  1.0031    14605.470
   3_bss:  23.229 0.8292  0.9652    14402.571
   3_xyz:  17.806 0.8816  0.9922     8945.608
   3_adp:  16.718 0.8917  0.9900     8163.599
   3_occ:  16.719 0.8917  0.9900     8163.676
   4_bss:  16.686 0.8919  0.9737     8136.294
   4_xyz:  15.563 0.9019  0.9774     7304.361
   4_adp:  15.451 0.9030  0.9715     7250.448
   4_occ:  15.450 0.9030  0.9714     7247.182
   5_bss:  15.451 0.9030  0.9726     7246.883
   5_xyz:  15.033 0.9064  0.9748     6970.153
   5_adp:  14.942 0.9073  0.9687     6925.586
   5_occ:  14.945 0.9073  0.9685     6923.285
   5_bss:  14.952 0.9072  0.9739     6925.907
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   2.2295e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   2.2295e-01
   1_xyz:   1.569  0.012  0.090 15.331  0.006  4.105   1.3142e-01
   1_adp:   1.569  0.012  0.090 15.331  0.006  4.105   1.3142e-01
   1_occ:   1.569  0.012  0.090 15.331  0.006  4.105   1.3142e-01
   2_bss:   1.569  0.012  0.090 15.331  0.006  4.105   1.3142e-01
   2_xyz:   1.259  0.009  0.086 14.961  0.005  4.110   8.5231e-02
   2_adp:   1.259  0.009  0.086 14.961  0.005  4.110   8.5231e-02
   2_occ:   1.259  0.009  0.086 14.961  0.005  4.110   8.5231e-02
   3_bss:   1.259  0.009  0.086 14.961  0.005  4.110   8.5231e-02
   3_xyz:   1.185  0.009  0.079 14.816  0.005  4.121   7.6781e-02
   3_adp:   1.185  0.009  0.079 14.816  0.005  4.121   7.6781e-02
   3_occ:   1.185  0.009  0.079 14.816  0.005  4.121   7.6781e-02
   4_bss:   1.185  0.009  0.079 14.816  0.005  4.121   7.6781e-02
   4_xyz:   1.010  0.007  0.074 14.550  0.004  4.127   5.8345e-02
   4_adp:   1.010  0.007  0.074 14.550  0.004  4.127   5.8345e-02
   4_occ:   1.010  0.007  0.074 14.550  0.004  4.127   5.8345e-02
   5_bss:   1.010  0.007  0.074 14.550  0.004  4.127   5.8345e-02
   5_xyz:   1.034  0.007  0.076 14.491  0.004  4.113   6.0422e-02
   5_adp:   1.034  0.007  0.076 14.491  0.004  4.113   6.0422e-02
   5_occ:   1.034  0.007  0.076 14.491  0.004  4.113   6.0422e-02
   5_bss:   1.034  0.007  0.076 14.491  0.004  4.113   6.0422e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.006   2.4510e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.006   2.4510e-01
   1_xyz:   9.935  0.075  0.326 82.863  0.022  1.872   1.5760e-01
   1_adp:   9.935  0.075  0.326 82.863  0.022  1.872   1.5760e-01
   1_occ:   9.935  0.075  0.326 82.863  0.022  1.872   1.5760e-01
   2_bss:   9.935  0.075  0.326 82.863  0.022  1.872   1.5760e-01
   2_xyz:   7.649  0.045  0.298 79.941  0.036  2.114   8.0432e-02
   2_adp:   7.649  0.045  0.298 79.941  0.036  2.114   8.0432e-02
   2_occ:   7.649  0.045  0.298 79.941  0.036  2.114   8.0432e-02
   3_bss:   7.649  0.045  0.298 79.941  0.036  2.114   8.0432e-02
   3_xyz:   8.554  0.055  0.262 80.901  0.046  2.192   6.2230e-02
   3_adp:   8.554  0.055  0.262 80.901  0.046  2.192   6.2230e-02
   3_occ:   8.554  0.055  0.262 80.901  0.046  2.192   6.2230e-02
   4_bss:   8.554  0.055  0.262 80.901  0.046  2.192   6.2230e-02
   4_xyz:   6.936  0.042  0.240 81.825  0.038  2.332   3.8173e-02
   4_adp:   6.936  0.042  0.240 81.825  0.038  2.332   3.8173e-02
   4_occ:   6.936  0.042  0.240 81.825  0.038  2.332   3.8173e-02
   5_bss:   6.936  0.042  0.240 81.825  0.038  2.332   3.8173e-02
   5_xyz:   7.488  0.054  0.258 82.655  0.035  2.339   3.8342e-02
   5_adp:   7.488  0.054  0.258 82.655  0.035  2.339   3.8342e-02
   5_occ:   7.488  0.054  0.258 82.655  0.035  2.339   3.8342e-02
   5_bss:   7.488  0.054  0.258 82.655  0.035  2.339   3.8342e-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: 102.44   0.00  19.40  95.51   0.00  15.38 102.44   0.00  41.30
   1_occ: 102.44   0.00  19.40  95.51   0.00  15.38 102.44   0.00  41.30
   2_bss: 102.44   0.00  19.40  95.51   0.00  15.38 102.44   0.00  41.30
   2_xyz: 102.44   0.00  19.40  95.51   0.00  15.38 102.44   0.00  41.30
   2_adp:  98.44   0.00  18.52  90.88   0.00  14.23  98.44   5.76  41.85
   2_occ:  98.44   0.00  18.52  90.88   0.00  14.23  98.44   5.76  41.85
   3_bss:  98.44   0.00  18.52  90.88   0.00  14.23  98.44   5.76  41.85
   3_xyz:  98.44   0.00  18.52  90.88   0.00  14.23  98.44   5.76  41.85
   3_adp:  98.42   1.19  18.19  90.09   1.19  13.61  98.42   6.75  43.10
   3_occ:  98.42   1.19  18.19  90.09   1.19  13.61  98.42   6.75  43.10
   4_bss:  98.42   1.19  18.19  90.09   1.19  13.61  98.42   6.75  43.10
   4_xyz:  98.42   1.19  18.19  90.09   1.19  13.61  98.42   6.75  43.10
   4_adp: 100.25   0.76  18.09  93.01   0.76  13.46 100.25   5.10  43.30
   4_occ: 100.25   0.76  18.09  93.01   0.76  13.46 100.25   5.10  43.30
   5_bss: 100.25   0.76  18.09  93.01   0.76  13.46 100.25   5.10  43.30
   5_xyz: 100.25   0.76  18.09  93.01   0.76  13.46 100.25   5.10  43.30
   5_adp:  99.31   0.00  17.86  96.29   0.61  13.29  99.31   0.00  42.70
   5_occ:  99.31   0.00  17.86  96.29   0.61  13.29  99.31   0.00  42.70
   5_bss:  99.31   0.00  17.86  96.29   0.62  13.30  99.31   0.00  42.70
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    3.353    0.009    0.404
   1_adp:    3.353    0.009    0.404
   1_occ:    3.353    0.009    0.404
   2_bss:    3.353    0.009    0.404
   2_xyz:    3.454    0.026    0.589
   2_adp:    3.454    0.026    0.589
   2_occ:    3.454    0.026    0.589
   3_bss:    3.454    0.026    0.589
   3_xyz:    3.586    0.031    0.690
   3_adp:    3.586    0.031    0.690
   3_occ:    3.586    0.031    0.690
   4_bss:    3.586    0.031    0.690
   4_xyz:    3.666    0.065    0.710
   4_adp:    3.666    0.065    0.710
   4_occ:    3.666    0.065    0.710
   5_bss:    3.666    0.065    0.710
   5_xyz:    3.744    0.025    0.729
   5_adp:    3.744    0.025    0.729
   5_occ:    3.744    0.025    0.729
   5_bss:    3.744    0.025    0.729
------------------------------------------------------------------------

CPU time actual refinement: 355.58


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_96/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_96/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_96/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_96/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_96/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 355.44 
  Macro-tasks:
    bulk solvent and scale       = 44.90  
    individual site refinement   = 149.56 
    weights calculation          = 30.39  
    collect and process          = 6.64   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 231.60 
  Micro-tasks:
    mask                            = 1.95   
    f_calc                          = 113.36 
    alpha_beta                      = 8.65   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 122.27 
    fmodel                         = 7.09   
    r_factors                      = 0.27   
    phase_errors                   = 10.36  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 265.46 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.994 micro seconds
Total CPU time: 6.16 minutes
from_scatterers_fft:    650 calls, 113.05 s
gradients_fft:          595 calls, 108.43 s

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

# Date 2008-01-16 Time 04:00:45 PST -0800 (1200484845.59 s)
Start R-work = 0.4601, R-free = 0.4569 (no bulk solvent and anisotropic scale)
Final R-work = 0.1403, R-free = 0.1816 (no bulk solvent and anisotropic scale)

Start R-work = 0.4534, R-free = 0.4483
Final R-work = 0.1154, R-free = 0.1627