# Date 2008-01-16 Time 04:00:29 PST -0800 (1200484829.33 s)
#phil __OFF__

Command line arguments: "../135.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31879
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 135

-------------------------------------------------------------------------------
  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: (68.845, 45.9914, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 45.9914, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7343 1.96017
Completeness in resolution range: 0.976764
Completeness with d_max=infinity: 0.973657

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7343
                             d_min =   1.9602

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: (68.845, 45.9914, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7343 1.96017
Completeness in resolution range: 0.976764
Completeness with d_max=infinity: 0.973657

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7347 -  4.1936 [2110/2133]  1897   213  10.1%
  bin  2:  4.1936 -  3.3414 [2029/2049]  1828   201   9.9%
  bin  3:  3.3414 -  2.9228 [2001/2020]  1803   198   9.9%
  bin  4:  2.9228 -  2.6572 [1966/1996]  1766   200  10.2%
  bin  5:  2.6572 -  2.4677 [1979/1998]  1780   199  10.1%
  bin  6:  2.4677 -  2.3228 [1955/1980]  1759   196  10.0%
  bin  7:  2.3228 -  2.2069 [1939/1967]  1748   191   9.9%
  bin  8:  2.2069 -  2.1111 [1937/1973]  1744   193  10.0%
  bin  9:  2.1111 -  2.0301 [1941/1983]  1744   197  10.1%
  bin 10:  2.0301 -  1.9602 [1732/1956]  1561   171   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_135/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.19 -     1.93: 13
        1.93 -     2.67: 157
        2.67 -     3.41: 4587
        3.41 -     4.16: 9644
        4.16 -     4.90: 14702
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.187 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.269 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 112 " - " O   HOH Z 408 "  1.665 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.669 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.715 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 29098 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_135/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_135/model_refine_001.geo

CPU time processing inputs: 9.02


============================ 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 = 68.845 45.9914 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4592   r_free= 0.4598   ksol= 0.00   Bsol= 0.00   scale= 0.918    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.264369                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7347 -  4.6770 0.99   1376  152 0.3722 0.3643      6.5428      6.5336|
|  2:  4.6770 -  3.7322 0.99   1309  149 0.3914 0.3658      6.7705      6.7453|
|  3:  3.7322 -  3.2663 0.99   1292  142 0.4369 0.4118      6.6873      6.7352|
|  4:  3.2663 -  2.9703 0.99   1287  139 0.4392 0.4525      6.5174      6.5151|
|  5:  2.9703 -  2.7589 0.99   1265  145 0.4899 0.4463      6.3622      6.3441|
|  6:  2.7589 -  2.5972 0.99   1278  138 0.4897 0.5077      6.2788      6.2197|
|  7:  2.5972 -  2.4677 0.99   1267  146 0.4873 0.5078      6.2338      6.1751|
|  8:  2.4677 -  2.3608 0.98   1258  134 0.5094 0.5060      6.1917       6.207|
|  9:  2.3608 -  2.2702 0.98   1245  144 0.5078 0.5283      6.1156      6.1609|
| 10:  2.2702 -  2.1921 1.00   1251  139 0.5022 0.5172       6.109      6.1074|
| 11:  2.1921 -  2.1238 0.97   1264  138 0.4969 0.5533      6.0254      6.0759|
| 12:  2.1238 -  2.0633 0.98   1231  138 0.5025 0.5166      5.9767      6.0192|
| 13:  2.0633 -  2.0091 1.00   1260  138 0.4941 0.4816      5.8942      5.8603|
| 14:  2.0091 -  1.9602 0.84   1047  117 0.5176 0.4979      5.8561      5.7711|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7347 -  4.6770  1376   152  0.69  34.74   0.83     0.75      72393.65|
|  2:  4.6770 -  3.7322  1309   149  0.71  34.51   0.93     0.83     103721.62|
|  3:  3.7322 -  3.2663  1292   142  0.61  43.02   0.94     0.80     111770.63|
|  4:  3.2663 -  2.9703  1287   139  0.52  49.93   0.95     0.71     101895.29|
|  5:  2.9703 -  2.7589  1265   145  0.44  56.86   0.91     0.63      80711.21|
|  6:  2.7589 -  2.5972  1278   138  0.43  57.70   0.90     0.60      69150.79|
|  7:  2.5972 -  2.4677  1267   146  0.39  60.33   0.93     0.56      64834.78|
|  8:  2.4677 -  2.3608  1258   134  0.37  62.51   0.95     0.53      60066.51|
|  9:  2.3608 -  2.2702  1245   144  0.34  64.24   0.91     0.51      56656.85|
| 10:  2.2702 -  2.1921  1251   139  0.36  63.05   0.98     0.53      49558.57|
| 11:  2.1921 -  2.1238  1264   138  0.35  63.81   0.98     0.54      46504.37|
| 12:  2.1238 -  2.0633  1231   138  0.37  62.51   1.00     0.57      40800.47|
| 13:  2.0633 -  2.0091  1260   138  0.38  61.50   1.00     0.59      34480.52|
| 14:  2.0091 -  1.9602  1047   117  0.44  56.66   0.97     0.63      26063.82|
|alpha:            min =        0.51 max =            0.83 mean =         0.63|
|beta:             min =    26063.82 max =       111770.63 mean =     66443.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.46|
|phase err.(work): min =        0.00 max =           89.99 mean =        54.84|
|phase err.(test): min =        0.00 max =           89.88 mean =        54.96|
|-----------------------------------------------------------------------------|

============================== 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 = 18.792654             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.043   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.285989              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.767   (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 |  1.187 -  1.558:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.558 -  1.930:       11 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.930 -  2.301:       44 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.301 -  2.672:      113 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.672 -  3.043:     2187 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.043 -  3.415:     2400 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.415 -  3.786:     4114 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.786 -  4.157:     5530 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.157 -  4.529:     6584 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.529 -  4.900:     8118 |
|-----------------------------------------------------------------------------|
|-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 |        0.208 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.106    4.900  1.187 |       0.912 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.283)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4592   r_free= 0.4598   ksol= 0.00   Bsol= 0.00   scale= 0.918    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.264369                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4498   r_free= 0.4485   ksol= 0.34   Bsol= 11.33   scale= 0.944   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.90,2.04,-0.87,0.00,-0.00,-0.00); trace/3= 0.09                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.257257                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.916284             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.907   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.210600              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.498   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4498      final r-factor (work) = 0.2939          |
| start r-factor (free) = 0.4485      final r-factor (free) = 0.3288          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.8623 = 14.92 * 0.50 * 6.2555 + 1.00 * 0.2079                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 45.6839 = 14.92 * 0.50 * 6.0981 + 1.00 * 0.2032                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2939      final r-factor (work) = 0.2660          |
| start r-factor (free) = 0.3288      final r-factor (free) = 0.3434          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3894 = 1.21 * 1.00 * 6.0981 + 1.00 * 0.0070                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1907 = 1.21 * 1.00 * 5.8892 + 1.00 * 0.0613                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.283)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    117.19  18.71    None  None   None       |
|    all(noH): 2823   0      0.00    117.19  18.71    None  None   None       |
|    Sol.    : 438    0      3.50    103.52  41.30    None  None   None       |
|    Mac.    : 2385   0      0.00    117.19  14.57    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 -  11.719: 1162   |   5:    58.593 -  70.311:   63        |
|      1:    11.719 -  23.437:  929   |   6:    70.311 -  82.030:   27        |
|      2:    23.437 -  35.156:  319   |   7:    82.030 -  93.748:    1        |
|      3:    35.156 -  46.874:  200   |   8:    93.748 - 105.467:    1        |
|      4:    46.874 -  58.593:  120   |   9:   105.467 - 117.186:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2660 r_free = 0.3434             target_work(ml) = 5.911         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2657 r_free = 0.3439             target_work(ml) = 5.911         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2657   r_free= 0.3439   ksol= 0.34   Bsol= 11.33   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.90,2.04,-0.87,0.00,-0.00,-0.00); trace/3= 0.09                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.910673                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2632   r_free= 0.3402   ksol= 0.32   Bsol= 33.54   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.66,-0.20,-0.71,-0.00,-0.00,-0.00); trace/3= -0.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.897779                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.047046              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.367   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.838465              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.957   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2632      final r-factor (work) = 0.2027          |
| start r-factor (free) = 0.3402      final r-factor (free) = 0.2600          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.0568 = 5.05 * 0.50 * 5.8860 + 1.00 * 0.2032                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.7133 = 5.05 * 0.50 * 5.8050 + 1.00 * 0.0642                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2027      final r-factor (work) = 0.1834          |
| start r-factor (free) = 0.2600      final r-factor (free) = 0.2434          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8894 = 0.84 * 1.00 * 5.8050 + 1.00 * 0.0221                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7201 = 0.84 * 1.00 * 5.6136 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.283)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.89  18.22    None  None   None       |
|    all(noH): 2823   0      0.00    106.89  18.22    None  None   None       |
|    Sol.    : 438    0      5.22    106.89  43.73    None  None   None       |
|    Mac.    : 2385   0      0.00    95.72   13.54    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 -  10.689: 1171   |   5:    53.444 -  64.133:  105        |
|      1:    10.689 -  21.378:  950   |   6:    64.133 -  74.822:   50        |
|      2:    21.378 -  32.066:  249   |   7:    74.822 -  85.510:   15        |
|      3:    32.066 -  42.755:  160   |   8:    85.510 -  96.199:    1        |
|      4:    42.755 -  53.444:  121   |   9:    96.199 - 106.888:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1834 r_free = 0.2434             target_work(ml) = 5.580         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1833 r_free = 0.2433             target_work(ml) = 5.579         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1833   r_free= 0.2433   ksol= 0.32   Bsol= 33.54   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.66,-0.20,-0.71,-0.00,-0.00,-0.00); trace/3= -0.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.579222                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1834   r_free= 0.2430   ksol= 0.32   Bsol= 38.02   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.87,-1.02,-0.55,-0.00,-0.00,-0.00); trace/3= -1.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.575880                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.504752              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.361  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.321491              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.246  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1834      final r-factor (work) = 0.1418          |
| start r-factor (free) = 0.2430      final r-factor (free) = 0.1937          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7068 = 4.50 * 0.50 * 5.6131 + 1.00 * 0.0641                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.3765 = 4.50 * 0.50 * 5.4663 + 1.00 * 0.0642                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1418      final r-factor (work) = 0.1307          |
| start r-factor (free) = 0.1937      final r-factor (free) = 0.1792          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7707 = 0.32 * 1.00 * 5.4663 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7181 = 0.32 * 1.00 * 5.3106 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.283)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.68  17.33    None  None   None       |
|    all(noH): 2823   0      0.00    101.68  17.33    None  None   None       |
|    Sol.    : 438    0      4.83    101.68  42.45    None  None   None       |
|    Mac.    : 2385   0      0.00    94.98   12.71    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 -  10.168: 1158   |   5:    50.842 -  61.010:  104        |
|      1:    10.168 -  20.337: 1025   |   6:    61.010 -  71.179:   60        |
|      2:    20.337 -  30.505:  213   |   7:    71.179 -  81.347:   14        |
|      3:    30.505 -  40.674:  131   |   8:    81.347 -  91.516:    1        |
|      4:    40.674 -  50.842:  115   |   9:    91.516 - 101.684:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1307 r_free = 0.1792             target_work(ml) = 5.263         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1305 r_free = 0.1790             target_work(ml) = 5.262         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1305   r_free= 0.1790   ksol= 0.32   Bsol= 38.02   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.87,-1.02,-0.55,-0.00,-0.00,-0.00); trace/3= -1.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.262495                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1307   r_free= 0.1783   ksol= 0.32   Bsol= 37.81   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-1.85,-0.90,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.260872                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.535962              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 120.367  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.358015              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.419   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1307      final r-factor (work) = 0.1181          |
| start r-factor (free) = 0.1783      final r-factor (free) = 0.1671          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8025 = 2.54 * 0.50 * 5.3142 + 1.00 * 0.0642                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6769 = 2.54 * 0.50 * 5.2204 + 1.00 * 0.0576                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1181      final r-factor (work) = 0.1167          |
| start r-factor (free) = 0.1671      final r-factor (free) = 0.1655          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8790 = 0.36 * 1.00 * 5.2204 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8675 = 0.36 * 1.00 * 5.1800 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.283)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.52  17.27    None  None   None       |
|    all(noH): 2823   0      0.00    101.52  17.27    None  None   None       |
|    Sol.    : 438    0      5.40    101.52  42.34    None  None   None       |
|    Mac.    : 2385   0      0.00    95.00   12.66    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 -  10.152: 1176   |   5:    50.760 -  60.911:  104        |
|      1:    10.152 -  20.304: 1012   |   6:    60.911 -  71.063:   59        |
|      2:    20.304 -  30.456:  212   |   7:    71.063 -  81.215:   12        |
|      3:    30.456 -  40.608:  125   |   8:    81.215 -  91.367:    3        |
|      4:    40.608 -  50.760:  118   |   9:    91.367 - 101.519:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1167 r_free = 0.1655             target_work(ml) = 5.173         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1165 r_free = 0.1653             target_work(ml) = 5.172         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1165   r_free= 0.1653   ksol= 0.32   Bsol= 37.81   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-1.85,-0.90,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.172248                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1165   r_free= 0.1652   ksol= 0.31   Bsol= 39.01   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-1.85,-0.90,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.171704                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.370562              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.711  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.618922              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.462   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1165      final r-factor (work) = 0.1169          |
| start r-factor (free) = 0.1652      final r-factor (free) = 0.1636          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6070 = 1.37 * 0.50 * 5.1795 + 1.00 * 0.0576                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5921 = 1.37 * 0.50 * 5.1749 + 1.00 * 0.0458                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1169      final r-factor (work) = 0.1147          |
| start r-factor (free) = 0.1636      final r-factor (free) = 0.1632          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4033 = 1.62 * 1.00 * 5.1749 + 1.00 * 0.0256                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.3700 = 1.62 * 1.00 * 5.1639 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.283)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.25  17.20    None  None   None       |
|    all(noH): 2823   0      0.00    101.25  17.20    None  None   None       |
|    Sol.    : 438    0      6.15    101.25  42.55    None  None   None       |
|    Mac.    : 2385   0      0.00    98.57   12.54    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 -  10.125: 1184   |   5:    50.626 -  60.751:   93        |
|      1:    10.125 -  20.250: 1015   |   6:    60.751 -  70.876:   56        |
|      2:    20.250 -  30.375:  208   |   7:    70.876 -  81.001:   20        |
|      3:    30.375 -  40.501:  114   |   8:    81.001 -  91.126:    7        |
|      4:    40.501 -  50.626:  124   |   9:    91.126 - 101.251:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1147 r_free = 0.1632             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1147 r_free = 0.1632             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1632   ksol= 0.31   Bsol= 39.01   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-1.85,-0.90,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.164240                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7347 -  4.6770 0.99   1376  152 0.0997 0.1305      5.3886      5.5446|
|  2:  4.6770 -  3.7322 0.99   1309  149 0.0852 0.1156      5.4492       5.655|
|  3:  3.7322 -  3.2663 0.99   1292  142 0.1093 0.1508      5.5129       5.858|
|  4:  3.2663 -  2.9703 0.99   1287  139 0.1240 0.1702      5.4739      5.6467|
|  5:  2.9703 -  2.7589 0.99   1265  145 0.1370 0.1808      5.3525      5.5355|
|  6:  2.7589 -  2.5972 0.99   1278  138 0.1233 0.1749      5.2195      5.4185|
|  7:  2.5972 -  2.4677 0.99   1267  146 0.1264 0.1730      5.1596      5.4079|
|  8:  2.4677 -  2.3608 0.98   1258  134 0.1240 0.1736      5.1188      5.3631|
|  9:  2.3608 -  2.2702 0.98   1245  144 0.1186 0.1767      5.0499      5.2896|
| 10:  2.2702 -  2.1921 1.00   1251  139 0.1153 0.1868       4.995      5.2444|
| 11:  2.1921 -  2.1238 0.97   1264  138 0.1173 0.1838      4.9746      5.2846|
| 12:  2.1238 -  2.0633 0.98   1231  138 0.1202 0.1758      4.9264      5.2301|
| 13:  2.0633 -  2.0091 1.00   1260  138 0.1160 0.1858      4.8375      5.1206|
| 14:  2.0091 -  1.9602 0.84   1047  117 0.1053 0.1869      4.7076      4.9852|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7347 -  4.6770  1376   152  0.94   9.36   0.99     0.96       7324.91|
|  2:  4.6770 -  3.7322  1309   149  0.95   8.06   1.04     1.02       9251.18|
|  3:  3.7322 -  3.2663  1292   142  0.93  11.60   1.05     1.04      11029.93|
|  4:  3.2663 -  2.9703  1287   139  0.92  13.87   1.03     1.01      10645.17|
|  5:  2.9703 -  2.7589  1265   145  0.90  15.52   1.02     0.99       8403.89|
|  6:  2.7589 -  2.5972  1278   138  0.90  15.65   1.00     0.97       7024.81|
|  7:  2.5972 -  2.4677  1267   146  0.90  15.77   1.00     0.97       6133.54|
|  8:  2.4677 -  2.3608  1258   134  0.91  15.38   1.01     0.99       5586.73|
|  9:  2.3608 -  2.2702  1245   144  0.91  15.56   1.02     1.00       5209.19|
| 10:  2.2702 -  2.1921  1251   139  0.90  15.95   1.01     0.97       4647.92|
| 11:  2.1921 -  2.1238  1264   138  0.90  16.59   1.01     0.98       4731.55|
| 12:  2.1238 -  2.0633  1231   138  0.90  16.35   1.02     1.01       4304.58|
| 13:  2.0633 -  2.0091  1260   138  0.90  16.49   1.02     1.01       3690.92|
| 14:  2.0091 -  1.9602  1047   117  0.91  14.95   1.00     0.97       2840.20|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2840.20 max =        11029.93 mean =      6565.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.30|
|phase err.(test): min =        0.00 max =           88.15 mean =        14.08|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1632   ksol= 0.31   Bsol= 40.22   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-1.91,-0.82,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.163998                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1632   ksol= 0.31   Bsol= 40.22   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-1.91,-0.82,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.163998                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7347 -  4.6770 0.99   1376  152 0.0998 0.1308      5.3902      5.5466|
|  2:  4.6770 -  3.7322 0.99   1309  149 0.0853 0.1156        5.45      5.6552|
|  3:  3.7322 -  3.2663 0.99   1292  142 0.1094 0.1510      5.5134      5.8587|
|  4:  3.2663 -  2.9703 0.99   1287  139 0.1240 0.1703      5.4738      5.6468|
|  5:  2.9703 -  2.7589 0.99   1265  145 0.1370 0.1806       5.352      5.5347|
|  6:  2.7589 -  2.5972 0.99   1278  138 0.1232 0.1745      5.2186      5.4167|
|  7:  2.5972 -  2.4677 0.99   1267  146 0.1264 0.1731      5.1589      5.4078|
|  8:  2.4677 -  2.3608 0.98   1258  134 0.1240 0.1734      5.1184      5.3626|
|  9:  2.3608 -  2.2702 0.98   1245  144 0.1185 0.1766      5.0496      5.2889|
| 10:  2.2702 -  2.1921 1.00   1251  139 0.1153 0.1869      4.9945      5.2454|
| 11:  2.1921 -  2.1238 0.97   1264  138 0.1172 0.1837      4.9746      5.2846|
| 12:  2.1238 -  2.0633 0.98   1231  138 0.1201 0.1759      4.9255      5.2298|
| 13:  2.0633 -  2.0091 1.00   1260  138 0.1160 0.1857      4.8367      5.1191|
| 14:  2.0091 -  1.9602 0.84   1047  117 0.1052 0.1864      4.7059      4.9827|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7347 -  4.6770  1376   152  0.94   9.39   0.99     0.96       7358.83|
|  2:  4.6770 -  3.7322  1309   149  0.95   8.07   1.04     1.02       9270.86|
|  3:  3.7322 -  3.2663  1292   142  0.93  11.61   1.05     1.04      11039.56|
|  4:  3.2663 -  2.9703  1287   139  0.92  13.86   1.03     1.01      10639.66|
|  5:  2.9703 -  2.7589  1265   145  0.90  15.51   1.02     0.99       8386.50|
|  6:  2.7589 -  2.5972  1278   138  0.90  15.63   1.00     0.97       7010.19|
|  7:  2.5972 -  2.4677  1267   146  0.90  15.75   1.00     0.97       6121.60|
|  8:  2.4677 -  2.3608  1258   134  0.91  15.37   1.01     0.99       5578.27|
|  9:  2.3608 -  2.2702  1245   144  0.91  15.56   1.02     1.00       5207.22|
| 10:  2.2702 -  2.1921  1251   139  0.90  15.94   1.02     0.97       4645.60|
| 11:  2.1921 -  2.1238  1264   138  0.90  16.59   1.01     0.98       4734.05|
| 12:  2.1238 -  2.0633  1231   138  0.90  16.32   1.03     1.01       4296.98|
| 13:  2.0633 -  2.0091  1260   138  0.90  16.46   1.02     1.01       3680.40|
| 14:  2.0091 -  1.9602  1047   117  0.91  14.90   1.01     0.97       2826.81|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2826.81 max =        11039.56 mean =      6564.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.29|
|phase err.(test): min =        0.00 max =           88.16 mean =        14.08|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.283)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.25  17.20    None  None   None       |
|    all(noH): 2823   0      0.00    101.25  17.20    None  None   None       |
|    Sol.    : 438    0      6.15    101.25  42.55    None  None   None       |
|    Mac.    : 2385   0      0.00    98.57   12.54    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 -  10.128: 1184   |   5:    50.629 -  60.754:   93        |
|      1:    10.128 -  20.253: 1015   |   6:    60.754 -  70.879:   56        |
|      2:    20.253 -  30.378:  208   |   7:    70.879 -  81.004:   20        |
|      3:    30.378 -  40.504:  114   |   8:    81.004 -  91.129:    7        |
|      4:    40.504 -  50.629:  124   |   9:    91.129 - 101.254:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 306         
Filter by distance & map next to the model:
   mapped sites are within: 0.692 - 5.154
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 304 from: 306
   mapped sites are within: 0.703 - 5.154

peak=    6.916 closest distance to " O   HOH Z 385 " =    1.161
peak=    6.447 closest distance to " O   HOH Z 142 " =    1.987
peak=    6.352 closest distance to " O   HOH Z 375 " =    1.583
peak=    6.198 closest distance to " O   HOH Z 236 " =    1.645
peak=    6.176 closest distance to " NE2 GLN A  11 " =    1.296
peak=    5.997 closest distance to " O   HOH Z  65 " =    1.179
peak=    5.696 closest distance to " O   HOH Z 126 " =    2.103
peak=    5.679 closest distance to " O   HOH Z 130 " =    1.136
peak=    5.675 closest distance to " CG  PRO A  54 " =    1.324
peak=    5.473 closest distance to " CG  PRO A 213 " =    1.304
peak=    5.380 closest distance to " CB  ARG A 275 " =    1.014
peak=    5.356 closest distance to " O   HOH Z 427 " =    1.239
peak=    5.346 closest distance to " NH2 ARG A  56 " =    2.023
peak=    5.267 closest distance to " O   HOH Z 112 " =    1.433
peak=    5.242 closest distance to " O   HOH Z 417 " =    1.639
peak=    5.141 closest distance to " CG  PRO A  90 " =    1.166
peak=    5.033 closest distance to " O   HOH Z 427 " =    1.968
peak=    5.023 closest distance to " O   HOH Z 423 " =    1.591
peak=    5.006 closest distance to " O   HOH Z 287 " =    1.689
peak=    4.876 closest distance to " CG  PRO A 280 " =    0.858
peak=    4.858 closest distance to " O   HOH Z 380 " =    1.710
peak=    4.857 closest distance to " O   HOH Z 193 " =    1.714
peak=    4.784 closest distance to " CA  TYR A  30 " =    0.974
peak=    4.737 closest distance to " O   HOH Z  92 " =    1.335
peak=    4.655 closest distance to " CB  PRO A  54 " =    1.047
peak=    4.651 closest distance to " O   HOH Z 272 " =    1.861
peak=    4.648 closest distance to " CG2 VAL A 257 " =    0.948
peak=    4.626 closest distance to " O   HOH Z  24 " =    1.560
peak=    4.615 closest distance to " O   HOH Z 403 " =    1.334
peak=    4.611 closest distance to " O   HOH Z 232 " =    2.320
peak=    4.598 closest distance to " O   HOH Z 431 " =    1.117
peak=    4.582 closest distance to " CB  ASN A 148 " =    1.279
peak=    4.534 closest distance to " O   HOH Z  78 " =    1.614
peak=    4.505 closest distance to " O   HOH Z 209 " =    2.243
peak=    4.491 closest distance to " O   HOH Z 371 " =    2.096
peak=    4.470 closest distance to " O   HOH Z 130 " =    2.384
peak=    4.466 closest distance to " NZ  LYS A 117 " =    2.979
peak=    4.463 closest distance to " O   HOH Z  63 " =    1.659
peak=    4.454 closest distance to " O   HOH Z 124 " =    1.458
peak=    4.400 closest distance to " CB  SER A  63 " =    1.264
peak=    4.360 closest distance to " CB  GLU A 128 " =    1.051
peak=    4.339 closest distance to " CB  SER A   3 " =    1.234
peak=    4.297 closest distance to " OG BSER A 164 " =    2.082
peak=    4.292 closest distance to " CG  PRO A 198 " =    1.289
peak=    4.271 closest distance to " O   SER A  87 " =    2.328
peak=    4.256 closest distance to " O   HOH Z 371 " =    2.031
peak=    4.229 closest distance to " O   HOH Z 298 " =    1.836
peak=    4.212 closest distance to " O  BHOH Z  74 " =    1.346
peak=    4.195 closest distance to " O   HOH Z 316 " =    2.881
peak=    4.193 closest distance to " O   HOH Z   1 " =    1.573
peak=    4.183 closest distance to " CB  GLN A 223 " =    1.569
peak=    4.165 closest distance to " O   HOH Z 368 " =    3.564
peak=    4.066 closest distance to " O   HOH Z 117 " =    1.171
peak=    4.059 closest distance to " CG  PRO A 243 " =    1.163
peak=    4.039 closest distance to " O   HOH Z  52 " =    1.162
peak=    4.036 closest distance to " O   HOH Z 234 " =    3.499
peak=    4.020 closest distance to " O   HOH Z 425 " =    1.961
peak=    4.017 closest distance to " CG  TRP A 179 " =    2.261
peak=    4.016 closest distance to " O   HOH Z  44 " =    1.822
peak=    4.011 closest distance to " O   HOH Z 245 " =    1.263
peak=    4.007 closest distance to " O   HOH Z 213 " =    1.597
peak=    3.980 closest distance to " O   HOH Z 327 " =    1.758
peak=    3.971 closest distance to " CB  GLU A 152 " =    1.247
peak=    3.969 closest distance to " NH1BARG A 145 " =    1.403
peak=    3.925 closest distance to " O   HOH Z 419 " =    2.210
peak=    3.922 closest distance to " O   HOH Z 394 " =    1.623
peak=    3.921 closest distance to " O   HOH Z 289 " =    1.578
peak=    3.918 closest distance to " O   HOH Z 425 " =    1.419
peak=    3.913 closest distance to " O   HOH Z 227 " =    1.906
peak=    3.909 closest distance to " C   ALA A 299 " =    1.007
peak=    3.898 closest distance to " O   HOH Z   6 " =    2.142
peak=    3.887 closest distance to " CB  THR A  31 " =    1.713
peak=    3.879 closest distance to " CE  LYS A 119 " =    1.236
peak=    3.875 closest distance to " O   HOH Z 352 " =    1.767
peak=    3.875 closest distance to " O   HOH Z  61 " =    1.515
peak=    3.870 closest distance to " CB  GLN A 183 " =    1.180
peak=    3.867 closest distance to " O   HOH Z 132 " =    1.116
peak=    3.865 closest distance to " N   GLU A   2 " =    1.373
peak=    3.861 closest distance to " O   HOH Z 247 " =    1.167
peak=    3.853 closest distance to " NZ  LYS A 119 " =    2.661
peak=    3.843 closest distance to " O   HOH Z 106 " =    2.641
peak=    3.835 closest distance to " O   HOH Z 414 " =    1.297
peak=    3.830 closest distance to " O   HOH Z   3 " =    1.967
peak=    3.827 closest distance to " O   HOH Z  32 " =    1.901
peak=    3.815 closest distance to " O   HOH Z 419 " =    1.806
peak=    3.814 closest distance to " O   HOH Z  93 " =    1.996
peak=    3.800 closest distance to " O   HOH Z 286 " =    2.277
peak=    3.791 closest distance to " CB  SER A 216 " =    0.828
peak=    3.791 closest distance to " O   HOH Z 389 " =    1.573
peak=    3.786 closest distance to " O   HOH Z  97 " =    1.899
peak=    3.785 closest distance to " O   HOH Z 366 " =    2.623
peak=    3.777 closest distance to " OG  SER A  62 " =    2.840
peak=    3.775 closest distance to " O   HOH Z  68 " =    2.143
peak=    3.771 closest distance to " O   HOH Z 128 " =    2.005
peak=    3.760 closest distance to " O   HOH Z 290 " =    1.036
peak=    3.755 closest distance to " O   HOH Z  11 " =    1.501
peak=    3.736 closest distance to " OG BSER A  99 " =    2.313
peak=    3.720 closest distance to " CG1 ILE A  33 " =    1.286
peak=    3.718 closest distance to " CG AARG A 275 " =    0.994
peak=    3.716 closest distance to " O   HOH Z 258 " =    2.045
peak=    3.715 closest distance to " O   HOH Z 146 " =    1.600
peak=    3.698 closest distance to " CB  TYR A 169 " =    0.757
peak=    3.694 closest distance to " ND2 ASN A 187 " =    1.557
peak=    3.682 closest distance to " O   HOH Z  61 " =    1.689
peak=    3.682 closest distance to " CB  GLU A 277 " =    3.429
peak=    3.678 closest distance to " C   PRO A 198 " =    1.555
peak=    3.674 closest distance to " O   HOH Z   9 " =    2.106
peak=    3.669 closest distance to " CB  SER A  26 " =    1.616
peak=    3.667 closest distance to " CB  SER A 276 " =    1.266
peak=    3.666 closest distance to " O   HOH Z 139 " =    1.197
peak=    3.665 closest distance to " O   HOH Z 344 " =    3.117
peak=    3.662 closest distance to " O   HOH Z  88 " =    2.620
peak=    3.656 closest distance to " NH1AARG A 145 " =    1.150
peak=    3.652 closest distance to " O   HOH Z 212 " =    1.640
peak=    3.651 closest distance to " O   HOH Z 222 " =    2.142
peak=    3.644 closest distance to " O   HOH Z 189 " =    1.768
peak=    3.640 closest distance to " CB  TRP A 179 " =    1.163
peak=    3.636 closest distance to " O   HOH Z 305 " =    3.414
peak=    3.628 closest distance to " O   HOH Z 144 " =    2.126
peak=    3.627 closest distance to " O   HOH Z 250 " =    1.413
peak=    3.626 closest distance to " O   HOH Z 132 " =    1.941
peak=    3.625 closest distance to " NE2 GLN A  58 " =    3.829
peak=    3.622 closest distance to " O   HOH Z 244 " =    1.700
peak=    3.618 closest distance to " O   HOH Z 166 " =    1.423
peak=    3.616 closest distance to " O   HOH Z 434 " =    1.205
peak=    3.611 closest distance to " O   HOH Z 357 " =    1.818
peak=    3.606 closest distance to " O   HOH Z  80 " =    1.936
peak=    3.592 closest distance to " O   HOH Z 194 " =    1.860
peak=    3.588 closest distance to " CG2 THR A 221 " =    1.242
peak=    3.585 closest distance to " O   HOH Z 222 " =    1.172
peak=    3.581 closest distance to " O   HOH Z 156 " =    3.116
peak=    3.580 closest distance to " O   HOH Z  59 " =    2.180
peak=    3.572 closest distance to " O   HOH Z 423 " =    1.674
peak=    3.572 closest distance to " O   HOH Z 302 " =    1.362
peak=    3.569 closest distance to " CA  ASN A 215 " =    1.094
peak=    3.566 closest distance to " CA  PRO A  54 " =    1.248
peak=    3.560 closest distance to " O   HOH Z 126 " =    1.397
peak=    3.559 closest distance to " CB  LYS A 117 " =    1.185
peak=    3.555 closest distance to " CB  PHE A 130 " =    0.996
peak=    3.550 closest distance to " CD BLYS A 290 " =    1.115
peak=    3.541 closest distance to " O   HOH Z 423 " =    1.926
peak=    3.527 closest distance to " CA  ALA A  21 " =    1.149
peak=    3.525 closest distance to " CE  LYS A  76 " =    0.832
peak=    3.522 closest distance to " CA  PHE A 283 " =    1.352
peak=    3.518 closest distance to " N   ALA A   1 " =    2.928
peak=    3.512 closest distance to " O   HOH Z 368 " =    1.952
peak=    3.507 closest distance to " CG2 ILE A 120 " =    1.147
peak=    3.506 closest distance to " O   HOH Z 175 " =    1.999
peak=    3.501 closest distance to " O   HOH Z 383 " =    2.026
peak=    3.492 closest distance to " CB  VAL A 202 " =    1.616
peak=    3.489 closest distance to " CB  VAL A 265 " =    1.302
peak=    3.480 closest distance to " CG2 THR A 294 " =    1.642
peak=    3.474 closest distance to " O   HOH Z 437 " =    1.832
peak=    3.473 closest distance to " CB  ALA A 114 " =    1.312
peak=    3.472 closest distance to " O   HOH Z 214 " =    2.307
peak=    3.470 closest distance to " CG1 ILE A 120 " =    1.396
peak=    3.469 closest distance to " O   HOH Z   9 " =    0.922
peak=    3.463 closest distance to " O   HOH Z 385 " =    3.557
peak=    3.458 closest distance to " CB  ARG A 190 " =    1.764
peak=    3.456 closest distance to " O   HOH Z 119 " =    4.316
peak=    3.441 closest distance to " CD  LYS A 166 " =    1.411
peak=    3.441 closest distance to " O   HOH Z 407 " =    2.399
peak=    3.439 closest distance to " O   HOH Z 405 " =    1.330
peak=    3.437 closest distance to " CB  ARG A  79 " =    1.099
peak=    3.435 closest distance to " O   HOH Z 365 " =    5.154
peak=    3.434 closest distance to " O   HOH Z   1 " =    1.668
peak=    3.427 closest distance to " NZ  LYS A 117 " =    1.296
peak=    3.426 closest distance to " O   HOH Z 419 " =    1.415
peak=    3.424 closest distance to " O   HOH Z 352 " =    1.294
peak=    3.414 closest distance to " N   GLN A 278 " =    1.057
peak=    3.413 closest distance to " O   HOH Z 207 " =    1.635
peak=    3.410 closest distance to " CA  ALA A  84 " =    1.141
peak=    3.403 closest distance to " OD1BASN A 224 " =    2.114
peak=    3.400 closest distance to " CB  THR A 157 " =    1.034
peak=    3.398 closest distance to " O   GLY A 147 " =    1.541
peak=    3.396 closest distance to " O   HOH Z 189 " =    2.727
peak=    3.394 closest distance to " CB  TRP A 266 " =    1.119
peak=    3.389 closest distance to " O   HOH Z  44 " =    3.146
peak=    3.388 closest distance to " OD1 ASN A  69 " =    2.448
peak=    3.387 closest distance to " O   HOH Z 109 " =    2.456
peak=    3.386 closest distance to " O   HOH Z 346 " =    1.489
peak=    3.381 closest distance to " O   HOH Z 422 " =    2.522
peak=    3.370 closest distance to " O   HOH Z 153 " =    3.499
peak=    3.366 closest distance to " O   HOH Z 112 " =    1.994
peak=    3.363 closest distance to " O   HOH Z 416 " =    1.057
peak=    3.361 closest distance to " O   HOH Z 365 " =    1.590
peak=    3.360 closest distance to " O   HOH Z 426 " =    1.769
peak=    3.354 closest distance to " O   HOH Z 362 " =    1.915
peak=    3.351 closest distance to " CB  LEU A 300 " =    1.012
peak=    3.349 closest distance to " O   ALA A   1 " =    1.494
peak=    3.339 closest distance to " O   HOH Z   7 " =    1.296
peak=    3.338 closest distance to " CD2 LEU A 297 " =    0.989
peak=    3.337 closest distance to " CB  LEU A 228 " =    1.079
peak=    3.336 closest distance to " CG  GLU A 277 " =    1.977
peak=    3.335 closest distance to " CB  HIS A 108 " =    0.830
peak=    3.335 closest distance to " O   HOH Z  10 " =    1.717
peak=    3.335 closest distance to " CB  ALA A  21 " =    1.902
peak=    3.329 closest distance to " O   HOH Z 378 " =    0.885
peak=    3.328 closest distance to " N   TYR A  15 " =    1.120
peak=    3.327 closest distance to " O   HOH Z 411 " =    3.608
peak=    3.326 closest distance to " O   HOH Z 207 " =    2.040
peak=    3.325 closest distance to " O   HOH Z 173 " =    2.188
peak=    3.324 closest distance to " CZ  PHE A  38 " =    1.202
peak=    3.323 closest distance to " O   HOH Z 344 " =    1.112
peak=    3.321 closest distance to " O   HOH Z 373 " =    1.452
peak=    3.313 closest distance to " O   HOH Z 284 " =    1.430
peak=    3.313 closest distance to " O   HOH Z  59 " =    1.321
peak=    3.312 closest distance to " CE1 HIS A 108 " =    1.379
peak=    3.306 closest distance to " O   HOH Z 145 " =    2.348
peak=    3.304 closest distance to " CB  ALA A  34 " =    1.170
peak=    3.301 closest distance to " CB  GLU A 277 " =    1.049
peak=    3.292 closest distance to " CA  ARG A  36 " =    0.994
peak=    3.290 closest distance to " O   HOH Z 298 " =    2.567
peak=    3.288 closest distance to " O   HOH Z 337 " =    3.443
peak=    3.287 closest distance to " CB  ARG A 139 " =    1.075
peak=    3.282 closest distance to " CD  ARG A 138 " =    0.742
peak=    3.282 closest distance to " O   HOH Z 125 " =    2.269
peak=    3.281 closest distance to " CG  MET A 185 " =    1.472
peak=    3.279 closest distance to " O   HOH Z 234 " =    2.003
peak=    3.277 closest distance to " N   HIS A  86 " =    1.813
peak=    3.268 closest distance to " CE AMET A  47 " =    1.219
peak=    3.267 closest distance to " O   HOH Z 130 " =    2.678
peak=    3.265 closest distance to " O   HOH Z 392 " =    1.071
peak=    3.260 closest distance to " CG  LEU A 167 " =    1.197
peak=    3.260 closest distance to " CA  ILE A 234 " =    1.025
peak=    3.259 closest distance to " CG  GLN A  89 " =    1.422
peak=    3.258 closest distance to " O   HOH Z 193 " =    2.031
peak=    3.258 closest distance to " O   HOH Z 151 " =    1.473
peak=    3.257 closest distance to " N   ALA A   1 " =    1.000
peak=    3.257 closest distance to " O   HOH Z 272 " =    1.976
peak=    3.254 closest distance to " CA  ASN A 127 " =    0.971
peak=    3.253 closest distance to " O   HOH Z 329 " =    3.598
peak=    3.253 closest distance to " O   HOH Z 181 " =    2.174
peak=    3.248 closest distance to " O   HOH Z  47 " =    1.551
peak=    3.248 closest distance to " CB  SER A  99 " =    0.948
peak=    3.243 closest distance to " CB  ALA A 114 " =    0.837
peak=    3.241 closest distance to " CB  ASP A 200 " =    0.939
peak=    3.238 closest distance to " O   HOH Z  50 " =    1.528
peak=    3.235 closest distance to " NH1 ARG A  14 " =    1.110
peak=    3.232 closest distance to " O   HOH Z   1 " =    1.474
peak=    3.229 closest distance to " O   HOH Z 381 " =    1.917
peak=    3.224 closest distance to " O   PRO A 198 " =    1.228
peak=    3.221 closest distance to " NE1 TRP A 274 " =    0.965
peak=    3.218 closest distance to " SD AMET A  47 " =    1.097
peak=    3.218 closest distance to " CB  GLU A 175 " =    0.927
peak=    3.214 closest distance to " O   HOH Z 214 " =    3.626
peak=    3.214 closest distance to " CB  MET A 188 " =    1.554
peak=    3.211 closest distance to " CG  ARG A 269 " =    1.335
peak=    3.210 closest distance to " O   HOH Z 291 " =    1.503
peak=    3.205 closest distance to " N   PHE A 130 " =    1.158
peak=    3.200 closest distance to " O   HOH Z 406 " =    1.480
peak=    3.200 closest distance to " O   HOH Z 326 " =    1.828
peak=    3.198 closest distance to " O   HOH Z 336 " =    1.832
peak=    3.197 closest distance to " O   HOH Z 211 " =    0.950
peak=    3.193 closest distance to " CB  ARG A 219 " =    0.820
peak=    3.190 closest distance to " CB  TYR A 116 " =    0.984
peak=    3.189 closest distance to " O   HOH Z 345 " =    3.167
peak=    3.188 closest distance to " CH2 TRP A  92 " =    2.043
peak=    3.187 closest distance to " CB  GLU A 152 " =    1.393
peak=    3.186 closest distance to " CG  MET A 113 " =    0.964
peak=    3.185 closest distance to " CA  ASN A 176 " =    1.386
peak=    3.185 closest distance to " CD2 TRP A 179 " =    1.370
peak=    3.183 closest distance to " OH  TYR A 116 " =    1.044
peak=    3.181 closest distance to " CB  ASN A 215 " =    1.040
peak=    3.181 closest distance to " N   ASN A 127 " =    1.378
peak=    3.178 closest distance to " CB  ALA A 291 " =    1.372
peak=    3.174 closest distance to " CG AARG A 275 " =    1.120
peak=    3.172 closest distance to " CB  ARG A 156 " =    1.087
peak=    3.170 closest distance to " NZ  LYS A  76 " =    1.556
peak=    3.166 closest distance to " CE3 TRP A  85 " =    0.999
peak=    3.164 closest distance to " O   HOH Z 423 " =    1.336
peak=    3.162 closest distance to " O   HOH Z 218 " =    1.821
peak=    3.160 closest distance to " CG2 ILE A  20 " =    1.107
peak=    3.155 closest distance to " CB  ARG A 138 " =    0.703
peak=    3.152 closest distance to " CB  SER A 273 " =    0.791
peak=    3.148 closest distance to " O   HOH Z  88 " =    2.401
peak=    3.147 closest distance to " O   HOH Z 171 " =    2.672
peak=    3.146 closest distance to " O   HOH Z 172 " =    2.607
peak=    3.146 closest distance to " O   HOH Z 251 " =    1.771
peak=    3.144 closest distance to " O   HOH Z 158 " =    2.599
peak=    3.141 closest distance to " O   HOH Z 189 " =    2.308
peak=    3.138 closest distance to " CA  LYS A 290 " =    1.275
peak=    3.134 closest distance to " O   HOH Z 291 " =    1.926
peak=    3.132 closest distance to " CB  GLN A 278 " =    0.798
peak=    3.130 closest distance to " O  BHOH Z 338 " =    2.334
peak=    3.126 closest distance to " NH2BARG A 145 " =    2.114
peak=    3.113 closest distance to " CG  GLN A 240 " =    3.488
peak=    3.113 closest distance to " O   HOH Z 155 " =    1.636
peak=    3.111 closest distance to " CB  VAL A 126 " =    1.211
peak=    3.111 closest distance to " O   HOH Z  80 " =    2.294
peak=    3.107 closest distance to " NE2 GLN A 278 " =    3.396
peak=    3.102 closest distance to " CA  MET A 105 " =    0.795
peak=    3.100 closest distance to " O   HOH Z 426 " =    1.019
peak=    3.097 closest distance to " O   ARG A 145 " =    1.914
peak=    3.096 closest distance to " O   HOH Z 128 " =    1.971
peak=    3.093 closest distance to " CD1 ILE A 263 " =    1.443
peak=    3.089 closest distance to " O   HOH Z 189 " =    3.726
peak=    3.071 closest distance to " CG2 VAL A 197 " =    1.047
peak=    3.070 closest distance to " CB  SER A  62 " =    1.257
peak=    3.067 closest distance to " O   HOH Z  94 " =    1.908
peak=    3.061 closest distance to " CD  ARG A  79 " =    1.083
peak=    3.013 closest distance to " O   HOH Z 241 " =    2.472
peak=    3.013 closest distance to " O   HOH Z   9 " =    1.889
peak=    3.012 closest distance to " O   HOH Z 158 " =    3.271

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.777 - 5.607
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 207
   mapped sites are within: 0.777 - 5.607

peak=   -4.550 closest distance to " O   HOH Z 385 " =    1.120
peak=   -4.461 closest distance to " OG BSER A 134 " =    1.424
peak=   -4.430 closest distance to " OD2 ASP A 191 " =    1.404
peak=   -4.332 closest distance to " CD  ARG A 156 " =    2.003
peak=   -4.258 closest distance to " O   PRO A 198 " =    1.266
peak=   -4.254 closest distance to " CG2 ILE A  20 " =    2.784
peak=   -4.171 closest distance to " O   HOH Z 198 " =    1.682
peak=   -4.129 closest distance to " C   HIS A 108 " =    1.126
peak=   -4.081 closest distance to " OD2 ASP A 171 " =    1.994
peak=   -4.057 closest distance to " O   HOH Z 372 " =    2.551
peak=   -4.054 closest distance to " O   HOH Z 290 " =    1.035
peak=   -4.036 closest distance to " CD1 LEU A 255 " =    2.838
peak=   -4.010 closest distance to " N   GLN A  58 " =    1.598
peak=   -4.008 closest distance to " CB  TYR A  15 " =    2.134
peak=   -4.005 closest distance to " CA  GLY A  98 " =    1.781
peak=   -4.005 closest distance to " O   SER A 135 " =    1.494
peak=   -3.956 closest distance to " CD  ARG A  14 " =    3.204
peak=   -3.949 closest distance to " CZ  PHE A  59 " =    1.342
peak=   -3.930 closest distance to " O   SER A  95 " =    1.361
peak=   -3.912 closest distance to " O   HOH Z 351 " =    1.534
peak=   -3.883 closest distance to " O   ALA A 161 " =    1.656
peak=   -3.867 closest distance to " O   HOH Z 185 " =    1.960
peak=   -3.865 closest distance to " O   HOH Z  65 " =    0.876
peak=   -3.864 closest distance to " O   HOH Z 388 " =    2.064
peak=   -3.859 closest distance to " CD1 ILE A 239 " =    2.262
peak=   -3.850 closest distance to " OG  SER A   3 " =    1.510
peak=   -3.848 closest distance to " CG  PHE A 283 " =    2.563
peak=   -3.825 closest distance to " O   PHE A 218 " =    1.367
peak=   -3.806 closest distance to " CG  GLN A  58 " =    1.050
peak=   -3.802 closest distance to " CA  GLY A 133 " =    1.887
peak=   -3.797 closest distance to " O   HOH Z 266 " =    4.588
peak=   -3.797 closest distance to " CG  PRO A 243 " =    1.537
peak=   -3.779 closest distance to " CB  ALA A 248 " =    2.061
peak=   -3.776 closest distance to " O   HOH Z 407 " =    2.757
peak=   -3.767 closest distance to " O   VAL A  67 " =    2.680
peak=   -3.764 closest distance to " O   ALA A  34 " =    2.875
peak=   -3.762 closest distance to " O   HOH Z 256 " =    1.370
peak=   -3.746 closest distance to " O   HOH Z 427 " =    1.768
peak=   -3.743 closest distance to " OE1 GLU A 277 " =    2.022
peak=   -3.742 closest distance to " CB  ALA A 291 " =    2.071
peak=   -3.700 closest distance to " O   HOH Z  13 " =    1.539
peak=   -3.698 closest distance to " N   GLN A 122 " =    1.432
peak=   -3.698 closest distance to " O   HOH Z  60 " =    1.824
peak=   -3.693 closest distance to " O   HOH Z 377 " =    1.997
peak=   -3.690 closest distance to " O   HOH Z 412 " =    5.456
peak=   -3.684 closest distance to " OD1 ASP A 191 " =    1.340
peak=   -3.680 closest distance to " O   HOH Z 102 " =    1.650
peak=   -3.675 closest distance to " O   HOH Z 250 " =    1.282
peak=   -3.670 closest distance to " CD1 LEU A 101 " =    2.211
peak=   -3.662 closest distance to " CB  ASN A  39 " =    2.289
peak=   -3.654 closest distance to " O   MET A  40 " =    2.716
peak=   -3.620 closest distance to " CG1 VAL A 112 " =    2.978
peak=   -3.616 closest distance to " ND2 ASN A  45 " =    1.007
peak=   -3.615 closest distance to " CB  PRO A 243 " =    2.574
peak=   -3.607 closest distance to " OXT GLY A 302 " =    2.780
peak=   -3.600 closest distance to " O   HOH Z  37 " =    1.396
peak=   -3.599 closest distance to " O   HOH Z 211 " =    1.705
peak=   -3.598 closest distance to " CZ2 TRP A 274 " =    0.970
peak=   -3.574 closest distance to " O   HOH Z 263 " =    3.034
peak=   -3.561 closest distance to " N   THR A 157 " =    1.443
peak=   -3.559 closest distance to " O   HOH Z 423 " =    2.557
peak=   -3.557 closest distance to " O   PRO A 198 " =    1.266
peak=   -3.552 closest distance to " O   SER A  22 " =    2.411
peak=   -3.550 closest distance to " CD2 TYR A 293 " =    1.869
peak=   -3.548 closest distance to " OG  SER A  63 " =    1.194
peak=   -3.548 closest distance to " CZ3 TRP A 123 " =    1.620
peak=   -3.523 closest distance to " NH2 ARG A  79 " =    2.124
peak=   -3.522 closest distance to " O   TRP A  70 " =    1.405
peak=   -3.520 closest distance to " NE  ARG A  36 " =    1.913
peak=   -3.518 closest distance to " O   HOH Z 369 " =    2.152
peak=   -3.518 closest distance to " OD1 ASP A 191 " =    1.820
peak=   -3.516 closest distance to " O   ALA A  51 " =    1.169
peak=   -3.505 closest distance to " CB  PHE A 208 " =    2.236
peak=   -3.505 closest distance to " O   ARG A 145 " =    1.558
peak=   -3.501 closest distance to " O   HOH Z  90 " =    2.231
peak=   -3.499 closest distance to " CB  ALA A   7 " =    1.920
peak=   -3.499 closest distance to " O   ASN A 187 " =    1.371
peak=   -3.493 closest distance to " ND2 ASN A 187 " =    1.520
peak=   -3.474 closest distance to " CD2 PHE A 225 " =    1.122
peak=   -3.473 closest distance to " O   TYR A 186 " =    1.461
peak=   -3.455 closest distance to " O   GLN A 183 " =    1.227
peak=   -3.452 closest distance to " O   HOH Z 385 " =    2.167
peak=   -3.448 closest distance to " O   HOH Z 147 " =    1.384
peak=   -3.446 closest distance to " OG  SER A  97 " =    1.913
peak=   -3.441 closest distance to " CD2 LEU A 237 " =    2.413
peak=   -3.438 closest distance to " CB  ILE A  33 " =    2.854
peak=   -3.437 closest distance to " O   HOH Z 131 " =    4.083
peak=   -3.433 closest distance to " CA  GLY A  57 " =    2.016
peak=   -3.433 closest distance to " O   PRO A 163 " =    1.070
peak=   -3.428 closest distance to " OG  SER A  97 " =    1.606
peak=   -3.426 closest distance to " O   HOH Z  24 " =    1.303
peak=   -3.423 closest distance to " NE2 GLN A 278 " =    1.624
peak=   -3.423 closest distance to " CA  GLY A  23 " =    1.926
peak=   -3.421 closest distance to " O   HOH Z 313 " =    1.659
peak=   -3.417 closest distance to " CB  PHE A 192 " =    1.804
peak=   -3.415 closest distance to " C   ALA A 158 " =    1.433
peak=   -3.411 closest distance to " OE1 GLN A  88 " =    1.039
peak=   -3.410 closest distance to " O   HOH Z 213 " =    1.328
peak=   -3.410 closest distance to " O   HOH Z 298 " =    2.407
peak=   -3.410 closest distance to " ND2 ASN A  69 " =    1.539
peak=   -3.405 closest distance to " O   VAL A 189 " =    2.372
peak=   -3.404 closest distance to " CD  LYS A 289 " =    2.410
peak=   -3.395 closest distance to " O   ALA A  10 " =    1.709
peak=   -3.391 closest distance to " OG  SER A  87 " =    1.532
peak=   -3.389 closest distance to " O   HOH Z 438 " =    0.971
peak=   -3.385 closest distance to " NH1AARG A 275 " =    1.847
peak=   -3.383 closest distance to " O   HOH Z 231 " =    2.126
peak=   -3.382 closest distance to " ND2 ASN A  39 " =    1.331
peak=   -3.380 closest distance to " CG1 VAL A 230 " =    1.944
peak=   -3.377 closest distance to " O   ILE A 120 " =    1.744
peak=   -3.371 closest distance to " O   HOH Z 435 " =    3.003
peak=   -3.361 closest distance to " CG  MET A 105 " =    0.881
peak=   -3.359 closest distance to " OE1 GLN A 183 " =    1.377
peak=   -3.358 closest distance to " ND2 ASN A  45 " =    1.093
peak=   -3.348 closest distance to " CA  GLY A 203 " =    2.301
peak=   -3.345 closest distance to " O   ILE A  49 " =    1.596
peak=   -3.344 closest distance to " OE1 GLN A 205 " =    1.220
peak=   -3.342 closest distance to " CE  MET A 105 " =    2.250
peak=   -3.340 closest distance to " O   HOH Z  39 " =    1.632
peak=   -3.335 closest distance to " CZ  TYR A 169 " =    1.789
peak=   -3.332 closest distance to " N   ALA A 248 " =    1.638
peak=   -3.329 closest distance to " O   HOH Z  52 " =    2.024
peak=   -3.327 closest distance to " OE1 GLU A  44 " =    1.890
peak=   -3.303 closest distance to " OD1 ASN A 148 " =    1.646
peak=   -3.300 closest distance to " N   MET A 188 " =    1.972
peak=   -3.298 closest distance to " O   HOH Z 134 " =    3.062
peak=   -3.296 closest distance to " CB  SER A 210 " =    1.235
peak=   -3.293 closest distance to " CB  ASP A 132 " =    2.330
peak=   -3.285 closest distance to " CB  ALA A 244 " =    2.006
peak=   -3.283 closest distance to " CG2 VAL A  78 " =    1.467
peak=   -3.280 closest distance to " OG BSER A 134 " =    1.541
peak=   -3.280 closest distance to " N   GLN A  58 " =    1.218
peak=   -3.280 closest distance to " O   HOH Z 392 " =    1.207
peak=   -3.279 closest distance to " CG2 VAL A 296 " =    1.844
peak=   -3.278 closest distance to " O   HOH Z  63 " =    2.373
peak=   -3.277 closest distance to " CG  GLN A  88 " =    0.931
peak=   -3.277 closest distance to " N   ASN A 127 " =    1.400
peak=   -3.268 closest distance to " OD1 ASP A 200 " =    1.280
peak=   -3.261 closest distance to " OG  SER A  63 " =    1.442
peak=   -3.260 closest distance to " CB  ALA A  43 " =    2.209
peak=   -3.250 closest distance to " O   SER A   3 " =    1.152
peak=   -3.248 closest distance to " ND2 ASN A  45 " =    1.633
peak=   -3.246 closest distance to " O   HOH Z 191 " =    5.607
peak=   -3.242 closest distance to " O   HOH Z 166 " =    1.349
peak=   -3.232 closest distance to " CE2 TYR A  30 " =    2.734
peak=   -3.228 closest distance to " O   HOH Z 148 " =    1.753
peak=   -3.228 closest distance to " CB  CYS A 201 " =    2.359
peak=   -3.224 closest distance to " O   VAL A 174 " =    2.098
peak=   -3.220 closest distance to " C   LEU A 143 " =    1.042
peak=   -3.219 closest distance to " CE3 TRP A 274 " =    2.233
peak=   -3.219 closest distance to " O   HOH Z 243 " =    1.958
peak=   -3.216 closest distance to " O   GLN A 194 " =    1.412
peak=   -3.216 closest distance to " O   HOH Z 288 " =    1.341
peak=   -3.214 closest distance to " O   HOH Z 326 " =    1.516
peak=   -3.212 closest distance to " N   ARG A 159 " =    1.976
peak=   -3.212 closest distance to " O   HOH Z  93 " =    1.771
peak=   -3.211 closest distance to " OG  SER A 245 " =    1.364
peak=   -3.210 closest distance to " O   HOH Z  11 " =    1.775
peak=   -3.207 closest distance to " O   HOH Z  52 " =    1.489
peak=   -3.207 closest distance to " O   HOH Z 119 " =    2.286
peak=   -3.207 closest distance to " O   HOH Z 377 " =    1.042
peak=   -3.206 closest distance to " O   ASP A 162 " =    2.109
peak=   -3.206 closest distance to " OG  SER A  87 " =    1.823
peak=   -3.204 closest distance to " O   HOH Z 165 " =    2.204
peak=   -3.204 closest distance to " C   ALA A 114 " =    1.984
peak=   -3.203 closest distance to " CG  GLN A 223 " =    2.092
peak=   -3.203 closest distance to " O   HOH Z 374 " =    2.657
peak=   -3.199 closest distance to " CD2 PHE A  61 " =    2.035
peak=   -3.197 closest distance to " O   ALA A 180 " =    1.063
peak=   -3.196 closest distance to " O   HOH Z 234 " =    3.760
peak=   -3.195 closest distance to " O   HOH Z  28 " =    2.118
peak=   -3.194 closest distance to " OD2 ASP A  50 " =    1.469
peak=   -3.193 closest distance to " C   ASN A 285 " =    2.142
peak=   -3.190 closest distance to " O   ASP A 270 " =    1.888
peak=   -3.189 closest distance to " O   VAL A 197 " =    1.469
peak=   -3.188 closest distance to " CD  PRO A 198 " =    1.455
peak=   -3.184 closest distance to " O   HOH Z 416 " =    0.777
peak=   -3.180 closest distance to " NH1BARG A 145 " =    3.520
peak=   -3.178 closest distance to " CZ  PHE A 130 " =    0.899
peak=   -3.178 closest distance to " O   ALA A   1 " =    1.658
peak=   -3.177 closest distance to " C   ASP A 124 " =    1.999
peak=   -3.169 closest distance to " OD2 ASP A  27 " =    1.359
peak=   -3.169 closest distance to " CD1 PHE A  59 " =    2.057
peak=   -3.166 closest distance to " CB  ALA A 291 " =    2.255
peak=   -3.166 closest distance to " O   HOH Z 193 " =    1.474
peak=   -3.162 closest distance to " CG  LEU A  83 " =    2.004
peak=   -3.154 closest distance to " O   GLN A 278 " =    1.296
peak=   -3.139 closest distance to " O   HOH Z 187 " =    1.948
peak=   -3.131 closest distance to " CB  PRO A 163 " =    2.551
peak=   -3.127 closest distance to " CG  GLN A 240 " =    2.391
peak=   -3.124 closest distance to " CE  LYS A 166 " =    1.184
peak=   -3.123 closest distance to " O   HOH Z 389 " =    1.366
peak=   -3.123 closest distance to " OG1 THR A  82 " =    1.719
peak=   -3.119 closest distance to " O   HOH Z 236 " =    2.156
peak=   -3.114 closest distance to " O   HOH Z 416 " =    1.105
peak=   -3.114 closest distance to " CB  GLN A  55 " =    1.332
peak=   -3.100 closest distance to " O   HOH Z  52 " =    1.176
peak=   -3.092 closest distance to " NH2 ARG A 219 " =    1.762
peak=   -3.091 closest distance to " O   ILE A 106 " =    2.092
peak=   -3.087 closest distance to " O   HOH Z 234 " =    1.399
peak=   -3.073 closest distance to " CG  GLN A  11 " =    2.069
peak=   -3.073 closest distance to " CB  ALA A 114 " =    2.497
peak=   -3.069 closest distance to " O   HOH Z 158 " =    1.993
peak=   -3.064 closest distance to " O   HOH Z   1 " =    3.617
peak=   -3.050 closest distance to " CA  GLY A  57 " =    2.071
peak=   -3.031 closest distance to " CD1 TRP A 179 " =    1.354
peak=   -3.020 closest distance to " N   ASN A 127 " =    1.746

================= 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    :  0.4592 0.4598   6.264369e+00   6.258725e+00
   1_bss:  0.4498 0.4485   6.257257e+00   6.241597e+00
   1_xyz:  0.2939 0.3288   5.955773e+00   6.034803e+00
   1_adp:  0.2660 0.3434   5.910891e+00   6.068958e+00
   1_occ:  0.2657 0.3439   5.910673e+00   6.069205e+00
   2_bss:  0.2632 0.3402   5.897779e+00   6.058076e+00
   2_xyz:  0.2027 0.2600   5.660209e+00   5.851874e+00
   2_adp:  0.1834 0.2434   5.579773e+00   5.788130e+00
   2_occ:  0.1833 0.2433   5.579222e+00   5.787628e+00
   3_bss:  0.1834 0.2430   5.575880e+00   5.783883e+00
   3_xyz:  0.1418 0.1937   5.344748e+00   5.579654e+00
   3_adp:  0.1307 0.1792   5.263412e+00   5.497919e+00
   3_occ:  0.1305 0.1790   5.262495e+00   5.496732e+00
   4_bss:  0.1307 0.1783   5.260872e+00   5.493349e+00
   4_xyz:  0.1181 0.1671   5.185194e+00   5.429019e+00
   4_adp:  0.1167 0.1655   5.173007e+00   5.417594e+00
   4_occ:  0.1165 0.1653   5.172248e+00   5.416741e+00
   5_bss:  0.1165 0.1652   5.171704e+00   5.416240e+00
   5_xyz:  0.1169 0.1636   5.172274e+00   5.409007e+00
   5_adp:  0.1147 0.1632   5.164318e+00   5.407129e+00
   5_occ:  0.1147 0.1632   5.164240e+00   5.407017e+00
   5_bss:  0.1147 0.1632   5.163998e+00   5.406741e+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:  0.340  11.326  -0.899   2.039  -0.873   0.000  -0.000  -0.000
   1_xyz:  0.340  11.326  -0.899   2.039  -0.873   0.000  -0.000  -0.000
   1_adp:  0.340  11.326  -0.899   2.039  -0.873   0.000  -0.000  -0.000
   1_occ:  0.340  11.326  -0.899   2.039  -0.873   0.000  -0.000  -0.000
   2_bss:  0.324  33.541  -1.659  -0.200  -0.707  -0.000  -0.000  -0.000
   2_xyz:  0.324  33.541  -1.659  -0.200  -0.707  -0.000  -0.000  -0.000
   2_adp:  0.324  33.541  -1.659  -0.200  -0.707  -0.000  -0.000  -0.000
   2_occ:  0.324  33.541  -1.659  -0.200  -0.707  -0.000  -0.000  -0.000
   3_bss:  0.323  38.015  -1.872  -1.017  -0.547  -0.000  -0.000  -0.000
   3_xyz:  0.323  38.015  -1.872  -1.017  -0.547  -0.000  -0.000  -0.000
   3_adp:  0.323  38.015  -1.872  -1.017  -0.547  -0.000  -0.000  -0.000
   3_occ:  0.323  38.015  -1.872  -1.017  -0.547  -0.000  -0.000  -0.000
   4_bss:  0.317  37.807  -2.381  -1.847  -0.896  -0.000  -0.000  -0.000
   4_xyz:  0.317  37.807  -2.381  -1.847  -0.896  -0.000  -0.000  -0.000
   4_adp:  0.317  37.807  -2.381  -1.847  -0.896  -0.000  -0.000  -0.000
   4_occ:  0.317  37.807  -2.381  -1.847  -0.896  -0.000  -0.000  -0.000
   5_bss:  0.308  39.008  -2.381  -1.847  -0.896  -0.000  -0.000  -0.000
   5_xyz:  0.308  39.008  -2.381  -1.847  -0.896  -0.000  -0.000  -0.000
   5_adp:  0.308  39.008  -2.381  -1.847  -0.896  -0.000  -0.000  -0.000
   5_occ:  0.308  39.008  -2.381  -1.847  -0.896  -0.000  -0.000  -0.000
   5_bss:  0.313  40.218  -2.315  -1.908  -0.818  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.853 0.4604  0.6287    66442.883
   1_bss:  53.584 0.4747  0.6489    62226.148
   1_xyz:  33.861 0.7160  0.9316    29540.676
   1_adp:  36.247 0.6873  0.8951    32772.618
   1_occ:  36.308 0.6865  0.8932    32815.109
   2_bss:  35.578 0.6943  0.8772    31400.957
   2_xyz:  25.861 0.8022  0.9817    17506.725
   2_adp:  23.419 0.8284  0.9929    15079.613
   2_occ:  23.402 0.8285  0.9928    15053.139
   3_bss:  23.254 0.8298  0.9838    14843.617
   3_xyz:  18.394 0.8761  1.0107     9361.336
   3_adp:  16.358 0.8949  1.0142     7988.811
   3_occ:  16.334 0.8951  1.0140     7950.488
   4_bss:  16.260 0.8956  0.9931     7867.375
   4_xyz:  14.828 0.9079  0.9981     6861.165
   4_adp:  14.515 0.9107  0.9980     6722.661
   4_occ:  14.505 0.9108  0.9981     6707.421
   5_bss:  14.492 0.9109  0.9981     6694.695
   5_xyz:  14.337 0.9124  0.9979     6578.138
   5_adp:  14.278 0.9130  0.9927     6567.358
   5_occ:  14.277 0.9130  0.9927     6565.231
   5_bss:  14.269 0.9131  0.9940     6563.673
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.106   2.0795e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.106   2.0795e-01
   1_xyz:   1.815  0.017  0.117 15.781  0.008  4.101   2.0323e-01
   1_adp:   1.815  0.017  0.117 15.781  0.008  4.101   2.0323e-01
   1_occ:   1.815  0.017  0.117 15.781  0.008  4.101   2.0323e-01
   2_bss:   1.815  0.017  0.117 15.781  0.008  4.101   2.0323e-01
   2_xyz:   1.051  0.007  0.077 14.424  0.004  4.122   6.4155e-02
   2_adp:   1.051  0.007  0.077 14.424  0.004  4.122   6.4155e-02
   2_occ:   1.051  0.007  0.077 14.424  0.004  4.122   6.4155e-02
   3_bss:   1.051  0.007  0.077 14.424  0.004  4.122   6.4155e-02
   3_xyz:   1.069  0.007  0.072 14.683  0.004  4.108   6.4233e-02
   3_adp:   1.069  0.007  0.072 14.683  0.004  4.108   6.4233e-02
   3_occ:   1.069  0.007  0.072 14.683  0.004  4.108   6.4233e-02
   4_bss:   1.069  0.007  0.072 14.683  0.004  4.108   6.4233e-02
   4_xyz:   0.993  0.006  0.070 14.601  0.004  4.110   5.7565e-02
   4_adp:   0.993  0.006  0.070 14.601  0.004  4.110   5.7565e-02
   4_occ:   0.993  0.006  0.070 14.601  0.004  4.110   5.7565e-02
   5_bss:   0.993  0.006  0.070 14.601  0.004  4.110   5.7565e-02
   5_xyz:   0.857  0.004  0.061 14.115  0.003  4.107   4.5839e-02
   5_adp:   0.857  0.004  0.061 14.115  0.003  4.107   4.5839e-02
   5_occ:   0.857  0.004  0.061 14.115  0.003  4.107   4.5839e-02
   5_bss:   0.857  0.004  0.061 14.115  0.003  4.107   4.5839e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.187   2.3818e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.187   2.3818e-01
   1_xyz:   9.339  0.109  0.492 83.630  0.055  2.012   3.5758e-01
   1_adp:   9.339  0.109  0.492 83.630  0.055  2.012   3.5758e-01
   1_occ:   9.339  0.109  0.492 83.630  0.055  2.012   3.5758e-01
   2_bss:   9.339  0.109  0.492 83.630  0.055  2.012   3.5758e-01
   2_xyz:   7.095  0.036  0.289 80.928  0.025  2.296   5.8708e-02
   2_adp:   7.095  0.036  0.289 80.928  0.025  2.296   5.8708e-02
   2_occ:   7.095  0.036  0.289 80.928  0.025  2.296   5.8708e-02
   3_bss:   7.095  0.036  0.289 80.928  0.025  2.296   5.8708e-02
   3_xyz:   7.874  0.045  0.231 82.005  0.025  2.262   5.4498e-02
   3_adp:   7.874  0.045  0.231 82.005  0.025  2.262   5.4498e-02
   3_occ:   7.874  0.045  0.231 82.005  0.025  2.262   5.4498e-02
   4_bss:   7.874  0.045  0.231 82.005  0.025  2.262   5.4498e-02
   4_xyz:   7.174  0.032  0.217 82.950  0.037  2.305   4.1218e-02
   4_adp:   7.174  0.032  0.217 82.950  0.037  2.305   4.1218e-02
   4_occ:   7.174  0.032  0.217 82.950  0.037  2.305   4.1218e-02
   5_bss:   7.174  0.032  0.217 82.950  0.037  2.305   4.1218e-02
   5_xyz:   6.970  0.038  0.184 84.631  0.036  2.359   2.6280e-02
   5_adp:   6.970  0.038  0.184 84.631  0.036  2.359   2.6280e-02
   5_occ:   6.970  0.038  0.184 84.631  0.036  2.359   2.6280e-02
   5_bss:   6.970  0.038  0.184 84.631  0.036  2.359   2.6280e-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: 117.19   0.00  18.71 117.19   0.00  14.57 103.52   3.50  41.30
   1_occ: 117.19   0.00  18.71 117.19   0.00  14.57 103.52   3.50  41.30
   2_bss: 117.19   0.00  18.71 117.19   0.00  14.57 103.52   3.50  41.30
   2_xyz: 117.19   0.00  18.71 117.19   0.00  14.57 103.52   3.50  41.30
   2_adp: 106.89   0.00  18.22  95.72   0.00  13.54 106.89   5.22  43.73
   2_occ: 106.89   0.00  18.22  95.72   0.00  13.54 106.89   5.22  43.73
   3_bss: 106.89   0.00  18.22  95.72   0.00  13.54 106.89   5.22  43.73
   3_xyz: 106.89   0.00  18.22  95.72   0.00  13.54 106.89   5.22  43.73
   3_adp: 101.68   0.00  17.33  94.98   0.00  12.71 101.68   4.83  42.45
   3_occ: 101.68   0.00  17.33  94.98   0.00  12.71 101.68   4.83  42.45
   4_bss: 101.68   0.00  17.33  94.98   0.00  12.71 101.68   4.83  42.45
   4_xyz: 101.68   0.00  17.33  94.98   0.00  12.71 101.68   4.83  42.45
   4_adp: 101.52   0.00  17.27  95.00   0.00  12.66 101.52   5.40  42.34
   4_occ: 101.52   0.00  17.27  95.00   0.00  12.66 101.52   5.40  42.34
   5_bss: 101.52   0.00  17.27  95.00   0.00  12.66 101.52   5.40  42.34
   5_xyz: 101.52   0.00  17.27  95.00   0.00  12.66 101.52   5.40  42.34
   5_adp: 101.25   0.00  17.20  98.57   0.00  12.54 101.25   6.15  42.55
   5_occ: 101.25   0.00  17.20  98.57   0.00  12.54 101.25   6.15  42.55
   5_bss: 101.25   0.00  17.20  98.57   0.00  12.54 101.25   6.15  42.55
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    2.151    0.041    0.506
   1_adp:    2.151    0.041    0.506
   1_occ:    2.151    0.041    0.506
   2_bss:    2.151    0.041    0.506
   2_xyz:    1.795    0.051    0.594
   2_adp:    1.795    0.051    0.594
   2_occ:    1.795    0.051    0.594
   3_bss:    1.795    0.051    0.594
   3_xyz:    1.565    0.033    0.706
   3_adp:    1.565    0.033    0.706
   3_occ:    1.565    0.033    0.706
   4_bss:    1.565    0.033    0.706
   4_xyz:    1.390    0.098    0.731
   4_adp:    1.390    0.098    0.731
   4_occ:    1.390    0.098    0.731
   5_bss:    1.390    0.098    0.731
   5_xyz:    1.447    0.090    0.743
   5_adp:    1.447    0.090    0.743
   5_occ:    1.447    0.090    0.743
   5_bss:    1.447    0.090    0.743
------------------------------------------------------------------------

CPU time actual refinement: 347.16


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_135/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_135/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_135/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_135/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_135/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 347.03 
  Macro-tasks:
    bulk solvent and scale       = 47.03  
    individual site refinement   = 137.73 
    weights calculation          = 30.33  
    collect and process          = 6.72   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 221.90 
  Micro-tasks:
    mask                            = 1.67   
    f_calc                          = 111.43 
    alpha_beta                      = 8.76   
    target                          = 1.23   
    gradients_wrt_atomic_parameters = 113.75 
    fmodel                         = 7.47   
    r_factors                      = 0.22   
    phase_errors                   = 11.60  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 256.39 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.917 micro seconds
Total CPU time: 6.01 minutes
from_scatterers_fft:    652 calls, 110.95 s
gradients_fft:          597 calls, 102.32 s

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

# Date 2008-01-16 Time 04:06:29 PST -0800 (1200485189.85 s)
Start R-work = 0.4592, R-free = 0.4598 (no bulk solvent and anisotropic scale)
Final R-work = 0.1372, R-free = 0.1799 (no bulk solvent and anisotropic scale)

Start R-work = 0.4498, R-free = 0.4485
Final R-work = 0.1147, R-free = 0.1632