# Date 2008-01-16 Time 04:19:14 PST -0800 (1200485954.94 s)
#phil __OFF__

Command line arguments: "../262.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28246
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 262

-------------------------------------------------------------------------------
  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: (69.1963, 45.9914, 88.1178, 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: 2.75, per 1000 atoms: 0.97


================================== 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: (69.1963, 45.9914, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.906 1.9624
Completeness in resolution range: 0.945963
Completeness with d_max=infinity: 0.943094

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9060
                             d_min =   1.9624

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: (69.1963, 45.9914, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.906 1.9624
Completeness in resolution range: 0.945963
Completeness with d_max=infinity: 0.943094

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9064 -  4.1993 [2176/2200]  1956   220  10.1%
  bin  2:  4.1993 -  3.3455 [2092/2112]  1884   208   9.9%
  bin  3:  3.3455 -  2.9262 [2063/2082]  1860   203   9.8%
  bin  4:  2.9262 -  2.6603 [2031/2061]  1821   210  10.3%
  bin  5:  2.6603 -  2.4706 [2033/2052]  1832   201   9.9%
  bin  6:  2.4706 -  2.3255 [2033/2058]  1827   206  10.1%
  bin  7:  2.3255 -  2.2094 [1999/2027]  1804   195   9.8%
  bin  8:  2.2094 -  2.1135 [2002/2038]  1801   201  10.0%
  bin  9:  2.1135 -  2.0324 [1990/2038]  1795   195   9.8%
  bin 10:  2.0324 -  1.9624 [1170/2040]  1050   120  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_262/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:
        1.14 -     1.89: 10
        1.89 -     2.65: 111
        2.65 -     3.40: 4410
        3.40 -     4.15: 9475
        4.15 -     4.90: 14586
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.143 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.589 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.602 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.729 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  53 " - " O   HOH Z 102 "  1.782 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28587 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_262/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_262/model_refine_001.geo

CPU time processing inputs: 7.87


============================ 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 = 69.19625 45.9914 88.1178 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 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4715   r_free= 0.4726   ksol= 0.00   Bsol= 0.00   scale= 0.895    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.279624                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9064 -  4.6838 0.99   1413  154 0.3704 0.3538      6.5667      6.5091|
|  2:  4.6838 -  3.7370 0.99   1358  154 0.4004 0.4163      6.7812      6.7935|
|  3:  3.7370 -  3.2703 0.99   1326  149 0.4448 0.4214      6.6847      6.6828|
|  4:  3.2703 -  2.9739 0.99   1335  147 0.4696 0.4976      6.5361      6.5513|
|  5:  2.9739 -  2.7621 0.99   1305  146 0.5048 0.4516      6.3586      6.3677|
|  6:  2.7621 -  2.6002 0.99   1316  147 0.5027 0.5242      6.2768      6.1937|
|  7:  2.6002 -  2.4706 0.99   1300  145 0.5141 0.5171      6.2293      6.1471|
|  8:  2.4706 -  2.3635 0.98   1307  141 0.5309 0.5210       6.191      6.2069|
|  9:  2.3635 -  2.2728 0.98   1291  143 0.5117 0.5419      6.1117      6.1882|
| 10:  2.2728 -  2.1946 1.00   1293  144 0.5198 0.5341      6.1003      6.0881|
| 11:  2.1946 -  2.1262 0.98   1276  148 0.5200 0.5026        6.02      6.0335|
| 12:  2.1262 -  2.0656 0.98   1305  137 0.5247 0.4990      5.9711      5.9763|
| 13:  2.0656 -  2.0114 0.93   1215  136 0.5108 0.5200      5.8829      5.8222|
| 14:  2.0114 -  1.9624 0.46    590   68 0.5351 0.5162      5.9071      5.8113|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9064 -  4.6838  1413   154  0.72  32.43   0.82     0.79      67044.72|
|  2:  4.6838 -  3.7370  1358   154  0.69  36.06   0.91     0.80     111052.72|
|  3:  3.7370 -  3.2703  1326   149  0.58  45.87   0.92     0.76     120474.86|
|  4:  3.2703 -  2.9739  1335   147  0.47  54.05   0.90     0.66     113397.50|
|  5:  2.9739 -  2.7621  1305   146  0.42  57.98   0.89     0.61      80191.04|
|  6:  2.7621 -  2.6002  1316   147  0.41  59.39   0.89     0.57      69592.85|
|  7:  2.6002 -  2.4706  1300   145  0.39  60.47   0.91     0.54      60938.68|
|  8:  2.4706 -  2.3635  1307   141  0.35  63.56   0.90     0.51      58805.91|
|  9:  2.3635 -  2.2728  1291   143  0.35  63.82   0.93     0.51      54363.51|
| 10:  2.2728 -  2.1946  1293   144  0.35  63.62   0.93     0.52      48902.54|
| 11:  2.1946 -  2.1262  1276   148  0.34  64.46   0.93     0.54      48084.99|
| 12:  2.1262 -  2.0656  1305   137  0.33  65.11   0.94     0.54      43276.41|
| 13:  2.0656 -  2.0114  1215   136  0.32  65.89   0.94     0.52      37601.88|
| 14:  2.0114 -  1.9624   590    68  0.37  62.36   1.00     0.51      28916.17|
|alpha:            min =        0.51 max =            0.80 mean =         0.60|
|beta:             min =    28916.17 max =       120474.86 mean =     69369.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.99 mean =        56.27|
|phase err.(test): min =        0.00 max =           89.78 mean =        56.59|
|-----------------------------------------------------------------------------|

============================== 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 = 19.442990             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.767   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.731473              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.572   (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 |  1.143 -  1.518:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.518 -  1.894:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.894 -  2.270:       30 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.270 -  2.646:       81 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.646 -  3.021:     2022 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.021 -  3.397:     2388 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.397 -  3.773:     4002 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.773 -  4.148:     5473 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.148 -  4.524:     6532 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.524 -  4.900:     8054 |
|-----------------------------------------------------------------------------|
|-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 |        0.194 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.107    4.900  1.143 |       0.656 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.590)------------------------------------------|
|    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 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4715   r_free= 0.4726   ksol= 0.00   Bsol= 0.00   scale= 0.895    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.279624                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4627   r_free= 0.4638   ksol= 0.33   Bsol= 24.03   scale= 0.937   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,1.52,2.62,0.00,0.00,0.00); trace/3= 0.69                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.274442                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.834899             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.541   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.261460              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.226   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4627      final r-factor (work) = 0.3210          |
| start r-factor (free) = 0.4638      final r-factor (free) = 0.3620          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.6895 = 14.83 * 0.50 * 6.2685 + 1.00 * 0.1935                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 45.6492 = 14.83 * 0.50 * 6.1281 + 1.00 * 0.1946                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3210      final r-factor (work) = 0.2900          |
| start r-factor (free) = 0.3620      final r-factor (free) = 0.3769          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7368 = 1.26 * 1.00 * 6.1281 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5524 = 1.26 * 1.00 * 5.9671 + 1.00 * 0.0251                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.590)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.44  18.58    None  None   None       |
|    all(noH): 2823   0      0.00    103.44  18.58    None  None   None       |
|    Sol.    : 438    0      0.00    103.44  40.37    None  None   None       |
|    Mac.    : 2385   0      0.00    76.93   14.58    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 -  10.344:  960   |   5:    51.720 -  62.064:   60        |
|      1:    10.344 -  20.688:  972   |   6:    62.064 -  72.408:   49        |
|      2:    20.688 -  31.032:  434   |   7:    72.408 -  82.752:   15        |
|      3:    31.032 -  41.376:  201   |   8:    82.752 -  93.096:    6        |
|      4:    41.376 -  51.720:  125   |   9:    93.096 - 103.440:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2900 r_free = 0.3769             target_work(ml) = 5.984         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2895 r_free = 0.3773             target_work(ml) = 5.985         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2895   r_free= 0.3773   ksol= 0.33   Bsol= 24.03   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,1.52,2.62,0.00,0.00,0.00); trace/3= 0.69                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 5.985131                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2882   r_free= 0.3763   ksol= 0.34   Bsol= 59.69   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,-0.17,1.24,-0.00,0.00,0.00); trace/3= -0.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 5.982497                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.753502              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.926   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.707414              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 100.108  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2882      final r-factor (work) = 0.2300          |
| start r-factor (free) = 0.3763      final r-factor (free) = 0.2974          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.3423 = 6.75 * 0.50 * 5.9667 + 1.00 * 0.1941                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.0262 = 6.75 * 0.50 * 5.9089 + 1.00 * 0.0732                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2300      final r-factor (work) = 0.2123          |
| start r-factor (free) = 0.2974      final r-factor (free) = 0.2800          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2041 = 0.71 * 1.00 * 5.9089 + 1.00 * 0.0240                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0767 = 0.71 * 1.00 * 5.7429 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.590)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.55  18.28    None  None   None       |
|    all(noH): 2823   0      0.00    104.55  18.28    None  None   None       |
|    Sol.    : 438    0      3.01    104.55  42.75    None  None   None       |
|    Mac.    : 2385   0      0.00    87.81   13.79    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 -  10.455: 1092   |   5:    52.275 -  62.730:   92        |
|      1:    10.455 -  20.910:  954   |   6:    62.730 -  73.185:   51        |
|      2:    20.910 -  31.365:  308   |   7:    73.185 -  83.641:   16        |
|      3:    31.365 -  41.820:  189   |   8:    83.641 -  94.096:    4        |
|      4:    41.820 -  52.275:  116   |   9:    94.096 - 104.551:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2123 r_free = 0.2800             target_work(ml) = 5.714         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2121 r_free = 0.2795             target_work(ml) = 5.713         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2121   r_free= 0.2795   ksol= 0.34   Bsol= 59.69   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,-0.17,1.24,-0.00,0.00,0.00); trace/3= -0.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.712962                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2122   r_free= 0.2789   ksol= 0.33   Bsol= 57.85   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-0.72,0.79,-0.00,0.00,0.00); trace/3= -0.61                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.710782                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.970222              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.537  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.584369              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.943  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2122      final r-factor (work) = 0.1642          |
| start r-factor (free) = 0.2789      final r-factor (free) = 0.2218          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4730 = 3.97 * 0.50 * 5.7426 + 1.00 * 0.0732                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1919 = 3.97 * 0.50 * 5.6066 + 1.00 * 0.0621                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1642      final r-factor (work) = 0.1505          |
| start r-factor (free) = 0.2218      final r-factor (free) = 0.2044          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2904 = 0.58 * 1.00 * 5.6066 + 1.00 * 0.0140                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1907 = 0.58 * 1.00 * 5.4399 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.590)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.97  17.61    None  None   None       |
|    all(noH): 2823   0      0.00    101.97  17.61    None  None   None       |
|    Sol.    : 438    0      4.82    101.97  44.33    None  None   None       |
|    Mac.    : 2385   0      0.00    91.13   12.70    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 -  10.197: 1198   |   5:    50.986 -  61.184:  102        |
|      1:    10.197 -  20.395:  965   |   6:    61.184 -  71.381:   68        |
|      2:    20.395 -  30.592:  211   |   7:    71.381 -  81.578:   21        |
|      3:    30.592 -  40.789:  131   |   8:    81.578 -  91.775:    6        |
|      4:    40.789 -  50.986:  119   |   9:    91.775 - 101.973:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1505 r_free = 0.2044             target_work(ml) = 5.401         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1504 r_free = 0.2043             target_work(ml) = 5.401         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1504   r_free= 0.2043   ksol= 0.33   Bsol= 57.85   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-0.72,0.79,-0.00,0.00,0.00); trace/3= -0.61                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.400607                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1508   r_free= 0.2042   ksol= 0.32   Bsol= 55.47   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-1.50,0.41,-0.00,0.00,0.00); trace/3= -1.07                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.399294                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.054123              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.487  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.295162              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.199  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1508      final r-factor (work) = 0.1335          |
| start r-factor (free) = 0.2042      final r-factor (free) = 0.1831          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6514 = 2.05 * 0.50 * 5.4421 + 1.00 * 0.0621                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5502 = 2.05 * 0.50 * 5.3529 + 1.00 * 0.0524                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1335      final r-factor (work) = 0.1302          |
| start r-factor (free) = 0.1831      final r-factor (free) = 0.1776          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5917 = 0.30 * 1.00 * 5.3529 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5690 = 0.30 * 1.00 * 5.2815 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.590)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.71    99.16   17.04    None  None   None       |
|    all(noH): 2823   0      0.71    99.16   17.04    None  None   None       |
|    Sol.    : 438    0      4.61    99.16   42.89    None  None   None       |
|    Mac.    : 2385   0      0.71    92.73   12.29    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.706 -  10.552: 1324   |   5:    49.932 -  59.777:  102        |
|      1:    10.552 -  20.397:  876   |   6:    59.777 -  69.622:   64        |
|      2:    20.397 -  30.242:  207   |   7:    69.622 -  79.467:   25        |
|      3:    30.242 -  40.087:  118   |   8:    79.467 -  89.312:    7        |
|      4:    40.087 -  49.932:   97   |   9:    89.312 -  99.157:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1302 r_free = 0.1776             target_work(ml) = 5.265         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1301 r_free = 0.1776             target_work(ml) = 5.265         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1301   r_free= 0.1776   ksol= 0.32   Bsol= 55.47   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-1.50,0.41,-0.00,0.00,0.00); trace/3= -1.07                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.264742                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1301   r_free= 0.1776   ksol= 0.32   Bsol= 55.47   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-1.67,0.38,-0.00,0.00,0.00); trace/3= -1.14                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.264472                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.440299              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.146  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.052094              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.883  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1301      final r-factor (work) = 0.1245          |
| start r-factor (free) = 0.1776      final r-factor (free) = 0.1699          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8556 = 1.44 * 0.50 * 5.2811 + 1.00 * 0.0524                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8267 = 1.44 * 0.50 * 5.2458 + 1.00 * 0.0489                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1245      final r-factor (work) = 0.1225          |
| start r-factor (free) = 0.1699      final r-factor (free) = 0.1703          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5292 = 1.05 * 1.00 * 5.2458 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4995 = 1.05 * 1.00 * 5.2163 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.590)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.22    100.69  17.10    None  None   None       |
|    all(noH): 2823   0      0.22    100.69  17.10    None  None   None       |
|    Sol.    : 438    0      4.54    99.23   43.77    None  None   None       |
|    Mac.    : 2385   0      0.22    100.69  12.20    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:     0.217 -  10.265: 1308   |   5:    50.454 -  60.501:   86        |
|      1:    10.265 -  20.312:  912   |   6:    60.501 -  70.548:   68        |
|      2:    20.312 -  30.359:  188   |   7:    70.548 -  80.596:   33        |
|      3:    30.359 -  40.407:  111   |   8:    80.596 -  90.643:    9        |
|      4:    40.407 -  50.454:  102   |   9:    90.643 - 100.690:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1225 r_free = 0.1703             target_work(ml) = 5.218         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1224 r_free = 0.1704             target_work(ml) = 5.217         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1224   r_free= 0.1704   ksol= 0.32   Bsol= 55.47   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-1.67,0.38,-0.00,0.00,0.00); trace/3= -1.14                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.217448                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9064 -  4.6838 0.99   1413  154 0.1027 0.1308      5.4108      5.5735|
|  2:  4.6838 -  3.7370 0.99   1358  154 0.0884 0.1170      5.4686      5.6828|
|  3:  3.7370 -  3.2703 0.99   1326  149 0.1170 0.1528      5.5502      5.8413|
|  4:  3.2703 -  2.9739 0.99   1335  147 0.1378 0.1895      5.5358      5.6935|
|  5:  2.9739 -  2.7621 0.99   1305  146 0.1503 0.1748      5.4322      5.6046|
|  6:  2.7621 -  2.6002 0.99   1316  147 0.1379 0.2263       5.299      5.5652|
|  7:  2.6002 -  2.4706 0.99   1300  145 0.1454 0.1752      5.2736      5.4077|
|  8:  2.4706 -  2.3635 0.98   1307  141 0.1340 0.1925      5.1833      5.4433|
|  9:  2.3635 -  2.2728 0.98   1291  143 0.1265 0.1927      5.0983      5.4019|
| 10:  2.2728 -  2.1946 1.00   1293  144 0.1211 0.1836      5.0222        5.23|
| 11:  2.1946 -  2.1262 0.98   1276  148 0.1223 0.1932      4.9907      5.2962|
| 12:  2.1262 -  2.0656 0.98   1305  137 0.1302 0.1878      4.9666      5.2733|
| 13:  2.0656 -  2.0114 0.93   1215  136 0.1108 0.1780       4.788      5.0165|
| 14:  2.0114 -  1.9624 0.46    590   68 0.0936 0.1605       4.621      4.9164|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9064 -  4.6838  1413   154  0.93   9.80   0.98     0.95       7782.34|
|  2:  4.6838 -  3.7370  1358   154  0.95   8.24   1.02     1.01       9584.49|
|  3:  3.7370 -  3.2703  1326   149  0.93  12.10   1.04     1.04      11533.83|
|  4:  3.2703 -  2.9739  1335   147  0.91  15.05   1.02     1.00      11633.14|
|  5:  2.9739 -  2.7621  1305   146  0.89  17.62   1.01     0.98      10170.19|
|  6:  2.7621 -  2.6002  1316   147  0.88  17.78   0.97     0.94       8211.56|
|  7:  2.6002 -  2.4706  1300   145  0.89  17.77   0.99     0.96       7542.68|
|  8:  2.4706 -  2.3635  1307   141  0.89  17.51   1.00     0.97       6647.55|
|  9:  2.3635 -  2.2728  1291   143  0.90  16.73   1.00     0.95       5745.66|
| 10:  2.2728 -  2.1946  1293   144  0.89  17.11   1.00     0.97       5092.98|
| 11:  2.1946 -  2.1262  1276   148  0.89  17.65   0.99     0.95       4954.44|
| 12:  2.1262 -  2.0656  1305   137  0.89  17.66   1.01     1.00       4663.04|
| 13:  2.0656 -  2.0114  1215   136  0.90  16.56   1.00     0.97       3439.69|
| 14:  2.0114 -  1.9624   590    68  0.94  11.99   0.99     0.96       2307.02|
|alpha:            min =        0.94 max =            1.04 mean =         0.98|
|beta:             min =     2307.02 max =        11633.14 mean =      7337.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.90 mean =        15.32|
|phase err.(test): min =        0.00 max =           88.66 mean =        14.88|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1226   r_free= 0.1706   ksol= 0.32   Bsol= 55.47   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-1.67,0.46,-0.00,0.00,0.00); trace/3= -1.07                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.217356                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1226   r_free= 0.1706   ksol= 0.32   Bsol= 55.47   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-1.67,0.46,-0.00,0.00,0.00); trace/3= -1.07                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.217356                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9064 -  4.6838 0.99   1413  154 0.1035 0.1303      5.4065      5.5629|
|  2:  4.6838 -  3.7370 0.99   1358  154 0.0890 0.1177       5.472      5.6889|
|  3:  3.7370 -  3.2703 0.99   1326  149 0.1181 0.1516      5.5557      5.8346|
|  4:  3.2703 -  2.9739 0.99   1335  147 0.1380 0.1913      5.5373      5.6993|
|  5:  2.9739 -  2.7621 0.99   1305  146 0.1503 0.1740      5.4325      5.6015|
|  6:  2.7621 -  2.6002 0.99   1316  147 0.1376 0.2256       5.298      5.5636|
|  7:  2.6002 -  2.4706 0.99   1300  145 0.1454 0.1758      5.2735      5.4093|
|  8:  2.4706 -  2.3635 0.98   1307  141 0.1341 0.1922      5.1825      5.4412|
|  9:  2.3635 -  2.2728 0.98   1291  143 0.1264 0.1925      5.0977      5.4023|
| 10:  2.2728 -  2.1946 1.00   1293  144 0.1210 0.1838      5.0215      5.2305|
| 11:  2.1946 -  2.1262 0.98   1276  148 0.1222 0.1927      4.9901      5.2948|
| 12:  2.1262 -  2.0656 0.98   1305  137 0.1301 0.1875       4.966      5.2724|
| 13:  2.0656 -  2.0114 0.93   1215  136 0.1107 0.1776      4.7862      5.0155|
| 14:  2.0114 -  1.9624 0.46    590   68 0.0935 0.1600      4.6182      4.9122|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9064 -  4.6838  1413   154  0.94   9.69   0.97     0.95       7707.56|
|  2:  4.6838 -  3.7370  1358   154  0.95   8.21   1.02     1.01       9526.25|
|  3:  3.7370 -  3.2703  1326   149  0.93  12.11   1.04     1.04      11563.86|
|  4:  3.2703 -  2.9739  1335   147  0.91  15.09   1.02     1.01      11679.93|
|  5:  2.9739 -  2.7621  1305   146  0.89  17.62   1.01     0.99      10168.98|
|  6:  2.7621 -  2.6002  1316   147  0.88  17.76   0.98     0.94       8201.33|
|  7:  2.6002 -  2.4706  1300   145  0.89  17.75   1.00     0.96       7526.78|
|  8:  2.4706 -  2.3635  1307   141  0.89  17.52   1.00     0.97       6642.79|
|  9:  2.3635 -  2.2728  1291   143  0.90  16.72   1.00     0.95       5744.89|
| 10:  2.2728 -  2.1946  1293   144  0.89  17.12   1.00     0.97       5092.73|
| 11:  2.1946 -  2.1262  1276   148  0.89  17.64   1.00     0.95       4949.43|
| 12:  2.1262 -  2.0656  1305   137  0.89  17.65   1.01     1.00       4657.33|
| 13:  2.0656 -  2.0114  1215   136  0.90  16.51   1.00     0.98       3421.84|
| 14:  2.0114 -  1.9624   590    68  0.94  11.92   0.99     0.97       2285.95|
|alpha:            min =        0.94 max =            1.04 mean =         0.98|
|beta:             min =     2285.95 max =        11679.93 mean =      7327.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.90 mean =        15.30|
|phase err.(test): min =        0.00 max =           87.21 mean =        14.88|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.590)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.21    100.69  17.09    None  None   None       |
|    all(noH): 2823   0      0.21    100.69  17.09    None  None   None       |
|    Sol.    : 438    0      4.53    99.22   43.76    None  None   None       |
|    Mac.    : 2385   0      0.21    100.69  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:     0.212 -  10.259: 1308   |   5:    50.449 -  60.496:   86        |
|      1:    10.259 -  20.307:  912   |   6:    60.496 -  70.543:   68        |
|      2:    20.307 -  30.354:  188   |   7:    70.543 -  80.591:   33        |
|      3:    30.354 -  40.401:  111   |   8:    80.591 -  90.638:    9        |
|      4:    40.401 -  50.449:  102   |   9:    90.638 - 100.685:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 307         
Filter by distance & map next to the model:
   mapped sites are within: 0.602 - 4.366
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 303 from: 307
   mapped sites are within: 0.728 - 4.366

peak=    7.353 closest distance to " O   HOH Z 403 " =    1.273
peak=    6.293 closest distance to " O   HOH Z 385 " =    1.155
peak=    6.187 closest distance to " O   HOH Z 117 " =    1.571
peak=    5.897 closest distance to " O   HOH Z 375 " =    1.566
peak=    5.713 closest distance to " O   HOH Z 142 " =    1.887
peak=    5.563 closest distance to " O   HOH Z 245 " =    1.119
peak=    5.474 closest distance to " O   HOH Z 287 " =    2.023
peak=    5.418 closest distance to " NE2 GLN A  11 " =    1.210
peak=    5.377 closest distance to " O   HOH Z 417 " =    2.478
peak=    5.375 closest distance to " O   HOH Z  65 " =    1.263
peak=    5.355 closest distance to " O   HOH Z 423 " =    1.865
peak=    5.334 closest distance to " CG  PRO A  54 " =    1.423
peak=    5.250 closest distance to " O   HOH Z  69 " =    1.417
peak=    5.242 closest distance to " O   HOH Z 403 " =    2.023
peak=    5.218 closest distance to " O   HOH Z 222 " =    1.268
peak=    5.066 closest distance to " O   HOH Z  63 " =    1.719
peak=    5.061 closest distance to " O   HOH Z  49 " =    1.276
peak=    5.011 closest distance to " O   HOH Z 105 " =    1.097
peak=    4.953 closest distance to " O   HOH Z   9 " =    1.963
peak=    4.922 closest distance to " O   HOH Z 126 " =    2.118
peak=    4.898 closest distance to " O   HOH Z  39 " =    1.292
peak=    4.890 closest distance to " CB  ARG A 275 " =    0.971
peak=    4.829 closest distance to " O   HOH Z  57 " =    2.435
peak=    4.825 closest distance to " CB  PRO A  54 " =    1.098
peak=    4.805 closest distance to " O   HOH Z 427 " =    2.358
peak=    4.784 closest distance to " O   HOH Z 425 " =    1.470
peak=    4.701 closest distance to " CG  PRO A  90 " =    1.101
peak=    4.699 closest distance to " O   HOH Z   7 " =    1.495
peak=    4.675 closest distance to " O   HOH Z 422 " =    0.977
peak=    4.665 closest distance to " O   HOH Z 236 " =    1.561
peak=    4.614 closest distance to " O   HOH Z 380 " =    1.871
peak=    4.547 closest distance to " CG2 VAL A 257 " =    0.921
peak=    4.493 closest distance to " O   HOH Z 371 " =    2.025
peak=    4.455 closest distance to " CE  LYS A 119 " =    1.294
peak=    4.427 closest distance to " CG  PRO A 198 " =    1.263
peak=    4.407 closest distance to " CB  GLN A 223 " =    1.495
peak=    4.403 closest distance to " O   HOH Z 427 " =    1.183
peak=    4.402 closest distance to " O   HOH Z  24 " =    2.043
peak=    4.387 closest distance to " CA  TYR A  30 " =    1.049
peak=    4.382 closest distance to " CG  PRO A 213 " =    1.250
peak=    4.352 closest distance to " O   HOH Z 403 " =    1.910
peak=    4.346 closest distance to " NH2 ARG A  56 " =    2.075
peak=    4.320 closest distance to " O   HOH Z 232 " =    2.205
peak=    4.320 closest distance to " O   HOH Z 112 " =    1.207
peak=    4.278 closest distance to " CG  GLN A  58 " =    0.959
peak=    4.270 closest distance to " NH1AARG A 145 " =    1.212
peak=    4.267 closest distance to " NZ  LYS A 119 " =    2.363
peak=    4.256 closest distance to " O   HOH Z 124 " =    1.377
peak=    4.249 closest distance to " O   HOH Z 298 " =    1.867
peak=    4.247 closest distance to " O   HOH Z  78 " =    1.610
peak=    4.241 closest distance to " CB  ASN A 148 " =    1.426
peak=    4.227 closest distance to " CB  THR A  31 " =    1.618
peak=    4.193 closest distance to " O   HOH Z 394 " =    1.847
peak=    4.188 closest distance to " O   SER A  87 " =    2.443
peak=    4.172 closest distance to " CB  ASN A 142 " =    1.023
peak=    4.141 closest distance to " CB  SER A 216 " =    0.957
peak=    4.134 closest distance to " O   HOH Z 402 " =    1.528
peak=    4.120 closest distance to " CB  GLU A 277 " =    3.554
peak=    4.111 closest distance to " CG  TRP A 179 " =    2.154
peak=    4.109 closest distance to " CB  ARG A  79 " =    1.232
peak=    4.108 closest distance to " O  BHOH Z  74 " =    1.289
peak=    4.107 closest distance to " CB  ARG A 190 " =    1.636
peak=    4.106 closest distance to " O   HOH Z 327 " =    1.695
peak=    4.101 closest distance to " O   HOH Z  40 " =    1.524
peak=    4.087 closest distance to " O   HOH Z   1 " =    1.752
peak=    4.071 closest distance to " O   HOH Z 272 " =    1.827
peak=    4.055 closest distance to " CB  SER A  63 " =    1.207
peak=    4.026 closest distance to " O   HOH Z 278 " =    1.097
peak=    4.016 closest distance to " CB  ASP A 191 " =    1.239
peak=    4.016 closest distance to " CB  ASN A  39 " =    0.980
peak=    3.985 closest distance to " N   GLN A 278 " =    1.463
peak=    3.975 closest distance to " O   HOH Z 365 " =    2.527
peak=    3.963 closest distance to " O   HOH Z 406 " =    1.630
peak=    3.944 closest distance to " CA  ARG A 195 " =    1.295
peak=    3.943 closest distance to " O   HOH Z 362 " =    1.977
peak=    3.935 closest distance to " CG  PRO A 243 " =    1.107
peak=    3.929 closest distance to " CB  VAL A 265 " =    1.307
peak=    3.929 closest distance to " CB  PHE A 130 " =    0.947
peak=    3.924 closest distance to " O   HOH Z  26 " =    1.380
peak=    3.901 closest distance to " O   HOH Z 215 " =    1.470
peak=    3.894 closest distance to " O   HOH Z  71 " =    1.504
peak=    3.887 closest distance to " CA  VAL A 125 " =    1.153
peak=    3.883 closest distance to " NZ  LYS A 117 " =    2.838
peak=    3.883 closest distance to " O   PRO A 198 " =    1.293
peak=    3.879 closest distance to " NH2AARG A 190 " =    1.946
peak=    3.871 closest distance to " O   HOH Z 130 " =    2.629
peak=    3.869 closest distance to " CB  PRO A  90 " =    1.029
peak=    3.859 closest distance to " CZ3 TRP A 266 " =    1.143
peak=    3.859 closest distance to " O   HOH Z 143 " =    1.367
peak=    3.852 closest distance to " CB  ALA A 114 " =    0.834
peak=    3.851 closest distance to " CB  GLU A  46 " =    1.122
peak=    3.823 closest distance to " O   HOH Z 132 " =    1.007
peak=    3.799 closest distance to " CG  GLN A  11 " =    2.162
peak=    3.793 closest distance to " OG ASER A 258 " =    3.072
peak=    3.783 closest distance to " ND2 ASN A 249 " =    0.830
peak=    3.775 closest distance to " O   HOH Z 203 " =    1.584
peak=    3.774 closest distance to " O   HOH Z 368 " =    3.566
peak=    3.772 closest distance to " O   HOH Z 218 " =    1.705
peak=    3.764 closest distance to " CZ  PHE A 218 " =    1.178
peak=    3.743 closest distance to " O   HOH Z 411 " =    3.874
peak=    3.739 closest distance to " O   HOH Z  61 " =    1.554
peak=    3.735 closest distance to " O   HOH Z 357 " =    1.933
peak=    3.730 closest distance to " CB  ARG A  79 " =    0.897
peak=    3.721 closest distance to " CB  SER A 210 " =    0.831
peak=    3.717 closest distance to " O   HOH Z 405 " =    1.553
peak=    3.715 closest distance to " CB  TRP A 266 " =    1.160
peak=    3.712 closest distance to " CA  ASN A 127 " =    1.050
peak=    3.708 closest distance to " O   HOH Z 153 " =    3.687
peak=    3.707 closest distance to " CD  ARG A 259 " =    1.666
peak=    3.698 closest distance to " O   HOH Z 286 " =    2.300
peak=    3.695 closest distance to " O   HOH Z  43 " =    1.459
peak=    3.694 closest distance to " CD2 TRP A 179 " =    1.302
peak=    3.693 closest distance to " CZ  PHE A  38 " =    1.272
peak=    3.691 closest distance to " CA  ALA A  51 " =    1.038
peak=    3.680 closest distance to " CB  ASN A 215 " =    1.057
peak=    3.680 closest distance to " O   HOH Z  59 " =    1.666
peak=    3.665 closest distance to " O   HOH Z 258 " =    2.174
peak=    3.662 closest distance to " O   HOH Z  68 " =    2.100
peak=    3.658 closest distance to " NZ  LYS A 166 " =    1.098
peak=    3.653 closest distance to " NH1 ARG A  14 " =    1.020
peak=    3.648 closest distance to " CB  LEU A 300 " =    0.943
peak=    3.648 closest distance to " CB  SER A  62 " =    0.891
peak=    3.639 closest distance to " O   HOH Z 346 " =    1.648
peak=    3.634 closest distance to " O   HOH Z 352 " =    1.472
peak=    3.624 closest distance to " O   HOH Z 214 " =    2.455
peak=    3.619 closest distance to " O   HOH Z 437 " =    1.712
peak=    3.613 closest distance to " CG  LYS A  76 " =    1.732
peak=    3.610 closest distance to " O   HOH Z 234 " =    3.492
peak=    3.607 closest distance to " OE1 GLN A  77 " =    1.275
peak=    3.602 closest distance to " CG  LEU A 167 " =    1.274
peak=    3.600 closest distance to " OG BSER A 164 " =    2.238
peak=    3.594 closest distance to " ND2 ASN A 187 " =    1.523
peak=    3.592 closest distance to " CB  ASP A 107 " =    1.082
peak=    3.592 closest distance to " CA  ALA A 160 " =    1.145
peak=    3.588 closest distance to " CE3 TRP A 150 " =    1.102
peak=    3.580 closest distance to " CG2 VAL A 197 " =    1.064
peak=    3.574 closest distance to " N   GLU A   2 " =    1.420
peak=    3.567 closest distance to " O   HOH Z 365 " =    1.428
peak=    3.561 closest distance to " CB  ALA A 114 " =    0.987
peak=    3.558 closest distance to " O   HOH Z 193 " =    1.415
peak=    3.555 closest distance to " O   HOH Z 132 " =    2.097
peak=    3.553 closest distance to " CB  LYS A 117 " =    1.256
peak=    3.548 closest distance to " N   TYR A  15 " =    1.198
peak=    3.548 closest distance to " N   PHE A 130 " =    1.272
peak=    3.546 closest distance to " CG1 ILE A 120 " =    1.404
peak=    3.539 closest distance to " O   HOH Z 434 " =    1.614
peak=    3.538 closest distance to " O   HOH Z 425 " =    1.954
peak=    3.530 closest distance to " OG  SER A  62 " =    2.940
peak=    3.521 closest distance to " CA  ASN A 215 " =    1.058
peak=    3.518 closest distance to " CB  GLN A 183 " =    1.227
peak=    3.517 closest distance to " CB  VAL A 202 " =    1.727
peak=    3.513 closest distance to " O   HOH Z 368 " =    1.851
peak=    3.510 closest distance to " CB  ASN A 110 " =    1.017
peak=    3.505 closest distance to " CG2 THR A 221 " =    1.161
peak=    3.498 closest distance to " N   SER A  97 " =    0.799
peak=    3.498 closest distance to " O   HOH Z 188 " =    2.695
peak=    3.492 closest distance to " O   HOH Z 145 " =    1.187
peak=    3.492 closest distance to " CB  GLN A  88 " =    1.298
peak=    3.488 closest distance to " CB  ARG A 156 " =    1.256
peak=    3.488 closest distance to " O   HOH Z 227 " =    1.942
peak=    3.484 closest distance to " CB  TRP A 179 " =    1.298
peak=    3.482 closest distance to " O   HOH Z 290 " =    1.070
peak=    3.470 closest distance to " O   HOH Z 193 " =    1.453
peak=    3.468 closest distance to " O   HOH Z  83 " =    1.268
peak=    3.468 closest distance to " CG2 ILE A  20 " =    1.730
peak=    3.463 closest distance to " O   HOH Z 359 " =    1.528
peak=    3.462 closest distance to " NH2BARG A 145 " =    1.739
peak=    3.460 closest distance to " CE BMET A  47 " =    1.131
peak=    3.460 closest distance to " CB  SER A 273 " =    0.949
peak=    3.455 closest distance to " CG1 ILE A  33 " =    1.221
peak=    3.454 closest distance to " CB  HIS A 108 " =    0.896
peak=    3.446 closest distance to " CB  SER A   3 " =    1.223
peak=    3.446 closest distance to " O   HOH Z 244 " =    1.645
peak=    3.439 closest distance to " CG  MET A 113 " =    1.010
peak=    3.436 closest distance to " O   HOH Z  88 " =    2.931
peak=    3.436 closest distance to " CB  SER A 212 " =    1.313
peak=    3.434 closest distance to " CG AARG A 275 " =    1.178
peak=    3.427 closest distance to " N   CYS A 260 " =    0.954
peak=    3.425 closest distance to " O   HOH Z 201 " =    1.440
peak=    3.423 closest distance to " O   HOH Z 414 " =    1.302
peak=    3.423 closest distance to " O   THR A 220 " =    1.220
peak=    3.421 closest distance to " O   HOH Z 216 " =    4.008
peak=    3.420 closest distance to " O   HOH Z   1 " =    1.693
peak=    3.417 closest distance to " CB  ASN A 187 " =    1.073
peak=    3.414 closest distance to " O   HOH Z 116 " =    2.843
peak=    3.413 closest distance to " O   HOH Z 128 " =    2.846
peak=    3.411 closest distance to " O   HOH Z 158 " =    3.099
peak=    3.402 closest distance to " O   HOH Z 392 " =    1.178
peak=    3.397 closest distance to " O   HOH Z 172 " =    2.367
peak=    3.393 closest distance to " N   TYR A 116 " =    1.344
peak=    3.388 closest distance to " NE2 GLN A  58 " =    4.366
peak=    3.384 closest distance to " O   HOH Z 371 " =    1.775
peak=    3.382 closest distance to " CB  ASP A 124 " =    0.882
peak=    3.380 closest distance to " CG2 ILE A 239 " =    0.761
peak=    3.378 closest distance to " CB  ALA A   1 " =    1.084
peak=    3.373 closest distance to " O   HOH Z 368 " =    4.278
peak=    3.372 closest distance to " CB  SER A 276 " =    1.313
peak=    3.361 closest distance to " O   HOH Z 389 " =    1.136
peak=    3.357 closest distance to " CA  TYR A 116 " =    1.427
peak=    3.356 closest distance to " CD  ARG A  66 " =    2.321
peak=    3.354 closest distance to " O   HOH Z   6 " =    1.539
peak=    3.352 closest distance to " CD  ARG A 159 " =    0.828
peak=    3.352 closest distance to " CA  ARG A  36 " =    1.005
peak=    3.348 closest distance to " O   HOH Z 305 " =    3.614
peak=    3.346 closest distance to " ND1 HIS A  86 " =    1.841
peak=    3.346 closest distance to " CG  GLN A  89 " =    1.516
peak=    3.344 closest distance to " CA  PHE A 283 " =    1.185
peak=    3.342 closest distance to " O   HOH Z 251 " =    1.398
peak=    3.340 closest distance to " O   HOH Z 185 " =    1.405
peak=    3.337 closest distance to " O   HOH Z  12 " =    1.271
peak=    3.336 closest distance to " CB  LYS A  76 " =    0.924
peak=    3.335 closest distance to " O   HOH Z  44 " =    1.673
peak=    3.333 closest distance to " NH1BARG A 145 " =    1.402
peak=    3.330 closest distance to " CB  ARG A 156 " =    1.207
peak=    3.328 closest distance to " ND2BASN A 224 " =    0.814
peak=    3.328 closest distance to " NE2 HIS A 207 " =    1.071
peak=    3.324 closest distance to " CB  GLU A 128 " =    0.961
peak=    3.319 closest distance to " CB  TYR A  30 " =    1.498
peak=    3.307 closest distance to " O   HOH Z  97 " =    1.903
peak=    3.306 closest distance to " O   HOH Z 378 " =    0.924
peak=    3.298 closest distance to " OE2 GLU A  53 " =    1.928
peak=    3.297 closest distance to " CA  ARG A 139 " =    0.961
peak=    3.293 closest distance to " CB  SER A  26 " =    1.764
peak=    3.288 closest distance to " CA  SER A  87 " =    1.026
peak=    3.288 closest distance to " CA  ILE A 234 " =    1.048
peak=    3.287 closest distance to " CB  ALA A 291 " =    0.942
peak=    3.284 closest distance to " O   HOH Z 128 " =    2.027
peak=    3.283 closest distance to " O   HOH Z  28 " =    1.908
peak=    3.281 closest distance to " O   HOH Z  48 " =    1.656
peak=    3.275 closest distance to " CG2BVAL A  41 " =    0.876
peak=    3.265 closest distance to " CB  ASP A 140 " =    0.987
peak=    3.260 closest distance to " N   ASN A  39 " =    1.142
peak=    3.260 closest distance to " O   HOH Z 207 " =    2.370
peak=    3.255 closest distance to " O   HOH Z 156 " =    2.542
peak=    3.250 closest distance to " O   HOH Z  61 " =    1.638
peak=    3.247 closest distance to " N   ARG A 156 " =    1.226
peak=    3.245 closest distance to " O   HOH Z 188 " =    1.505
peak=    3.244 closest distance to " O   HOH Z  10 " =    1.715
peak=    3.243 closest distance to " O   HOH Z 248 " =    1.582
peak=    3.238 closest distance to " O   HOH Z 126 " =    1.454
peak=    3.237 closest distance to " O   HOH Z  88 " =    2.552
peak=    3.232 closest distance to " CD1 ILE A 199 " =    1.314
peak=    3.229 closest distance to " O   THR A 182 " =    1.527
peak=    3.224 closest distance to " O   HOH Z 422 " =    2.248
peak=    3.220 closest distance to " O   HOH Z  77 " =    1.279
peak=    3.219 closest distance to " CB  THR A 157 " =    1.133
peak=    3.215 closest distance to " CA  VAL A 153 " =    1.130
peak=    3.215 closest distance to " CD1AILE A 234 " =    0.948
peak=    3.215 closest distance to " O   HOH Z 394 " =    3.716
peak=    3.213 closest distance to " O   HOH Z  90 " =    4.051
peak=    3.213 closest distance to " CG  LEU A 101 " =    1.100
peak=    3.212 closest distance to " CA  ASP A 124 " =    0.904
peak=    3.209 closest distance to " O   HOH Z 146 " =    1.477
peak=    3.209 closest distance to " CA  ALA A 100 " =    1.056
peak=    3.208 closest distance to " OD1 ASN A  69 " =    2.579
peak=    3.206 closest distance to " CB  ASN A 285 " =    1.004
peak=    3.206 closest distance to " O   HOH Z 285 " =    2.510
peak=    3.205 closest distance to " O   HOH Z 213 " =    2.076
peak=    3.204 closest distance to " O   HOH Z   2 " =    1.681
peak=    3.198 closest distance to " CB  ARG A 219 " =    0.878
peak=    3.196 closest distance to " O   GLN A 194 " =    1.666
peak=    3.193 closest distance to " O   HOH Z 261 " =    1.779
peak=    3.190 closest distance to " CB  TYR A 169 " =    0.728
peak=    3.190 closest distance to " OG BSER A  99 " =    2.394
peak=    3.187 closest distance to " O   HOH Z 193 " =    1.910
peak=    3.186 closest distance to " O   HOH Z 180 " =    2.353
peak=    3.184 closest distance to " CA  ALA A 291 " =    0.826
peak=    3.184 closest distance to " CB  PRO A 243 " =    1.203
peak=    3.182 closest distance to " O   HOH Z 111 " =    1.462
peak=    3.181 closest distance to " O   HOH Z 128 " =    1.925
peak=    3.176 closest distance to " CG1BVAL A  72 " =    1.065
peak=    3.176 closest distance to " O   HOH Z  44 " =    2.803
peak=    3.175 closest distance to " O   HOH Z  47 " =    1.864
peak=    3.173 closest distance to " CB  VAL A 268 " =    0.919
peak=    3.172 closest distance to " CB  ASN A 176 " =    1.113
peak=    3.170 closest distance to " O   HOH Z 181 " =    2.153
peak=    3.168 closest distance to " CA  MET A 105 " =    0.969
peak=    3.168 closest distance to " O   HOH Z 280 " =    1.464
peak=    3.164 closest distance to " CG2 ILE A  20 " =    1.196
peak=    3.163 closest distance to " O   HOH Z 343 " =    2.932
peak=    3.163 closest distance to " O   HOH Z 344 " =    3.141
peak=    3.157 closest distance to " CA  ASN A 217 " =    1.215
peak=    3.155 closest distance to " O   HOH Z 109 " =    1.114
peak=    3.152 closest distance to " N   GLU A  44 " =    1.095
peak=    3.143 closest distance to " CG2 ILE A 120 " =    1.165
peak=    3.136 closest distance to " N   ASP A 162 " =    0.987
peak=    3.131 closest distance to " O   HOH Z 435 " =    1.736
peak=    3.120 closest distance to " O   HOH Z 272 " =    2.015
peak=    3.109 closest distance to " O   HOH Z 303 " =    2.155
peak=    3.106 closest distance to " CZ3 TRP A 274 " =    1.368
peak=    3.105 closest distance to " NE1 TRP A  85 " =    1.010
peak=    3.099 closest distance to " CD  ARG A  79 " =    0.912
peak=    3.083 closest distance to " CB  ARG A 156 " =    0.892
peak=    3.082 closest distance to " OG BSER A 134 " =    2.666
peak=    3.077 closest distance to " CA  ALA A 129 " =    1.254
peak=    3.075 closest distance to " CG  LYS A 119 " =    1.050
peak=    3.072 closest distance to " N   GLY A 133 " =    3.778
peak=    3.070 closest distance to " O   ALA A  71 " =    1.325
peak=    3.070 closest distance to " O   HOH Z 106 " =    4.099
peak=    3.060 closest distance to " CD  LYS A  76 " =    1.236
peak=    3.052 closest distance to " O   HOH Z 184 " =    1.487
peak=    3.043 closest distance to " O   HOH Z 193 " =    0.956
peak=    3.029 closest distance to " NH1 ARG A 138 " =    1.053

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 193         
Filter by distance & map next to the model:
   mapped sites are within: 0.827 - 5.720
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 193
   mapped sites are within: 0.827 - 5.720

peak=   -4.419 closest distance to " O   HOH Z 385 " =    1.415
peak=   -4.416 closest distance to " O   PRO A 198 " =    1.146
peak=   -4.385 closest distance to " O   HOH Z  69 " =    1.633
peak=   -4.250 closest distance to " O   HOH Z 276 " =    1.238
peak=   -4.237 closest distance to " CD  ARG A 156 " =    2.004
peak=   -4.219 closest distance to " O   HOH Z 131 " =    3.941
peak=   -4.149 closest distance to " O   GLU A 152 " =    1.329
peak=   -4.105 closest distance to " CD  ARG A  14 " =    3.277
peak=   -4.092 closest distance to " CB  PRO A 243 " =    2.544
peak=   -4.071 closest distance to " CA  GLY A 241 " =    2.265
peak=   -4.062 closest distance to " OG BSER A 134 " =    1.380
peak=   -4.026 closest distance to " C   HIS A 108 " =    1.159
peak=   -4.011 closest distance to " O   ALA A  10 " =    1.595
peak=   -4.011 closest distance to " O   SER A  22 " =    2.640
peak=   -4.010 closest distance to " O   HOH Z  24 " =    1.046
peak=   -4.004 closest distance to " O   HOH Z 377 " =    1.950
peak=   -3.981 closest distance to " CZ2 TRP A  92 " =    2.817
peak=   -3.977 closest distance to " O   HOH Z 231 " =    2.054
peak=   -3.964 closest distance to " CD2 TYR A 293 " =    1.796
peak=   -3.936 closest distance to " O   HOH Z 351 " =    1.569
peak=   -3.931 closest distance to " CB  ALA A  43 " =    2.425
peak=   -3.926 closest distance to " O   HOH Z 185 " =    2.053
peak=   -3.910 closest distance to " CB  GLN A  55 " =    1.155
peak=   -3.860 closest distance to " O   HOH Z  60 " =    1.702
peak=   -3.845 closest distance to " CE BMET A  47 " =    1.048
peak=   -3.826 closest distance to " CB  ASN A  45 " =    2.014
peak=   -3.809 closest distance to " N   THR A 157 " =    1.489
peak=   -3.807 closest distance to " O   PRO A 163 " =    1.098
peak=   -3.804 closest distance to " CG2 ILE A  20 " =    2.958
peak=   -3.786 closest distance to " OD1 ASP A 171 " =    1.523
peak=   -3.783 closest distance to " CG  GLN A  58 " =    1.056
peak=   -3.769 closest distance to " CZ2 TRP A 274 " =    0.903
peak=   -3.765 closest distance to " O   HOH Z 298 " =    2.513
peak=   -3.747 closest distance to " O   HOH Z 105 " =    1.203
peak=   -3.731 closest distance to " CG1 VAL A 112 " =    2.673
peak=   -3.725 closest distance to " O   SER A 135 " =    1.459
peak=   -3.717 closest distance to " O   HOH Z 123 " =    2.495
peak=   -3.702 closest distance to " CE1 TYR A 247 " =    2.703
peak=   -3.699 closest distance to " CA  GLY A  98 " =    1.777
peak=   -3.680 closest distance to " O   HOH Z 211 " =    1.130
peak=   -3.676 closest distance to " OD2 ASP A 191 " =    1.353
peak=   -3.676 closest distance to " O   HOH Z 286 " =    1.570
peak=   -3.670 closest distance to " CZ  PHE A  59 " =    1.421
peak=   -3.669 closest distance to " O   HOH Z 100 " =    1.068
peak=   -3.668 closest distance to " CD1 LEU A 255 " =    2.822
peak=   -3.661 closest distance to " O   HOH Z  28 " =    1.379
peak=   -3.659 closest distance to " CD1 LEU A 101 " =    2.250
peak=   -3.653 closest distance to " O   VAL A  67 " =    2.572
peak=   -3.629 closest distance to " CB  ALA A 291 " =    2.214
peak=   -3.629 closest distance to " O   HOH Z 372 " =    2.337
peak=   -3.620 closest distance to " CA  HIS A 207 " =    1.215
peak=   -3.618 closest distance to " CA  GLY A 133 " =    1.924
peak=   -3.615 closest distance to " O   PRO A 243 " =    2.470
peak=   -3.608 closest distance to " OG  SER A  97 " =    2.085
peak=   -3.604 closest distance to " O   PHE A 218 " =    1.340
peak=   -3.601 closest distance to " CB  PHE A 192 " =    1.943
peak=   -3.591 closest distance to " O   HOH Z  39 " =    1.168
peak=   -3.577 closest distance to " NE2 GLN A  55 " =    1.212
peak=   -3.573 closest distance to " O   HOH Z 427 " =    1.882
peak=   -3.564 closest distance to " O   PRO A 198 " =    1.329
peak=   -3.551 closest distance to " O   HOH Z 201 " =    1.799
peak=   -3.544 closest distance to " CB  ALA A 158 " =    1.657
peak=   -3.544 closest distance to " CD  GLN A  77 " =    1.266
peak=   -3.542 closest distance to " O   HOH Z 348 " =    1.990
peak=   -3.541 closest distance to " O   HOH Z 389 " =    1.269
peak=   -3.535 closest distance to " CD2 LEU A 237 " =    2.858
peak=   -3.534 closest distance to " O   TRP A  70 " =    1.339
peak=   -3.506 closest distance to " ND2 ASN A 285 " =    2.041
peak=   -3.490 closest distance to " CB  ASP A  27 " =    2.317
peak=   -3.480 closest distance to " CB  GLN A  11 " =    1.759
peak=   -3.474 closest distance to " O   ILE A  49 " =    1.648
peak=   -3.473 closest distance to " O   HOH Z 429 " =    1.935
peak=   -3.467 closest distance to " O   HOH Z  26 " =    0.904
peak=   -3.460 closest distance to " O   HOH Z 278 " =    1.224
peak=   -3.459 closest distance to " CG  MET A 105 " =    1.046
peak=   -3.447 closest distance to " CD  GLU A 277 " =    1.373
peak=   -3.444 closest distance to " O   HOH Z 412 " =    3.541
peak=   -3.444 closest distance to " CG2 THR A  18 " =    2.807
peak=   -3.442 closest distance to " CG1BVAL A  72 " =    2.164
peak=   -3.439 closest distance to " O   HOH Z 313 " =    1.623
peak=   -3.435 closest distance to " OE1 GLN A  88 " =    1.106
peak=   -3.430 closest distance to " N   ALA A 242 " =    2.091
peak=   -3.411 closest distance to " OE2 GLU A 152 " =    1.207
peak=   -3.410 closest distance to " CD2 PHE A  61 " =    2.039
peak=   -3.406 closest distance to " O   HOH Z 359 " =    3.140
peak=   -3.406 closest distance to " CB  ASP A 132 " =    2.439
peak=   -3.403 closest distance to " OD2 ASP A 171 " =    1.470
peak=   -3.402 closest distance to " CB  SER A 210 " =    1.032
peak=   -3.402 closest distance to " CG  LEU A  83 " =    2.280
peak=   -3.395 closest distance to " O   HOH Z 290 " =    0.990
peak=   -3.387 closest distance to " CZ  PHE A 155 " =    1.115
peak=   -3.384 closest distance to " CE  MET A 105 " =    2.563
peak=   -3.382 closest distance to " CA  ASN A 127 " =    1.314
peak=   -3.381 closest distance to " O   HOH Z 219 " =    4.788
peak=   -3.376 closest distance to " CB  ASN A  39 " =    2.376
peak=   -3.375 closest distance to " O   HOH Z 165 " =    2.245
peak=   -3.374 closest distance to " O   HOH Z 266 " =    5.175
peak=   -3.372 closest distance to " N   ALA A  43 " =    2.532
peak=   -3.362 closest distance to " ND2 ASN A 249 " =    2.177
peak=   -3.354 closest distance to " CZ  PHE A  38 " =    2.542
peak=   -3.350 closest distance to " O   HOH Z 103 " =    1.547
peak=   -3.332 closest distance to " NE2 GLN A 278 " =    1.418
peak=   -3.322 closest distance to " OD1 ASN A 148 " =    1.399
peak=   -3.316 closest distance to " OXT GLY A 302 " =    3.159
peak=   -3.315 closest distance to " O   HOH Z 198 " =    1.348
peak=   -3.310 closest distance to " O   HOH Z 126 " =    1.548
peak=   -3.305 closest distance to " C   GLN A  58 " =    2.044
peak=   -3.300 closest distance to " OD1 ASP A 191 " =    1.742
peak=   -3.297 closest distance to " O   HOH Z 166 " =    1.706
peak=   -3.291 closest distance to " CB  ASP A 132 " =    2.392
peak=   -3.291 closest distance to " O   HOH Z 412 " =    5.720
peak=   -3.288 closest distance to " O   HOH Z 421 " =    2.804
peak=   -3.281 closest distance to " O   HOH Z 283 " =    2.494
peak=   -3.278 closest distance to " OG  SER A  87 " =    1.708
peak=   -3.276 closest distance to " CG2BVAL A  72 " =    1.930
peak=   -3.273 closest distance to " OE1 GLN A 183 " =    1.575
peak=   -3.272 closest distance to " O   PRO A 163 " =    1.758
peak=   -3.270 closest distance to " O   HOH Z  11 " =    1.468
peak=   -3.269 closest distance to " O   HOH Z 102 " =    1.444
peak=   -3.266 closest distance to " O   HOH Z 415 " =    1.605
peak=   -3.266 closest distance to " NE  ARG A  36 " =    1.973
peak=   -3.262 closest distance to " O   HOH Z 340 " =    2.001
peak=   -3.262 closest distance to " O   HOH Z  71 " =    1.254
peak=   -3.259 closest distance to " CD  PRO A 213 " =    2.031
peak=   -3.257 closest distance to " O   HOH Z  49 " =    1.037
peak=   -3.256 closest distance to " NZ  LYS A 166 " =    1.150
peak=   -3.249 closest distance to " O   HOH Z 129 " =    3.548
peak=   -3.247 closest distance to " N   GLN A  58 " =    1.193
peak=   -3.247 closest distance to " O   SER A  95 " =    1.485
peak=   -3.244 closest distance to " CG  GLU A 128 " =    1.658
peak=   -3.243 closest distance to " O   HOH Z 374 " =    1.889
peak=   -3.242 closest distance to " N   GLN A 122 " =    1.245
peak=   -3.238 closest distance to " O   HOH Z 105 " =    0.827
peak=   -3.235 closest distance to " OD2 ASP A 171 " =    2.173
peak=   -3.232 closest distance to " OE1 GLN A 223 " =    2.336
peak=   -3.230 closest distance to " O   SER A 210 " =    1.903
peak=   -3.228 closest distance to " O   ALA A   9 " =    1.104
peak=   -3.227 closest distance to " O   ARG A 219 " =    1.829
peak=   -3.225 closest distance to " CG  GLN A  88 " =    0.839
peak=   -3.219 closest distance to " OG  SER A  63 " =    1.185
peak=   -3.217 closest distance to " CA  ASP A 298 " =    1.095
peak=   -3.214 closest distance to " O   HOH Z 393 " =    4.982
peak=   -3.211 closest distance to " O   HOH Z 263 " =    3.071
peak=   -3.210 closest distance to " O   HOH Z 298 " =    1.196
peak=   -3.204 closest distance to " O   GLY A  80 " =    2.384
peak=   -3.203 closest distance to " O   HOH Z  97 " =    1.142
peak=   -3.202 closest distance to " O   HOH Z 369 " =    2.279
peak=   -3.201 closest distance to " O   HOH Z 384 " =    1.499
peak=   -3.196 closest distance to " O   HOH Z 357 " =    1.884
peak=   -3.195 closest distance to " O   HOH Z 406 " =    1.445
peak=   -3.194 closest distance to " OG  SER A   3 " =    1.668
peak=   -3.193 closest distance to " O   HOH Z 404 " =    1.357
peak=   -3.192 closest distance to " O   HOH Z 231 " =    1.151
peak=   -3.185 closest distance to " CZ3 TRP A 179 " =    1.332
peak=   -3.184 closest distance to " OG BSER A 210 " =    2.484
peak=   -3.171 closest distance to " O   ALA A 161 " =    1.705
peak=   -3.169 closest distance to " N   PHE A  59 " =    1.921
peak=   -3.169 closest distance to " O   HOH Z 407 " =    2.773
peak=   -3.167 closest distance to " CE2 TYR A  30 " =    2.768
peak=   -3.164 closest distance to " O   HOH Z  64 " =    1.440
peak=   -3.164 closest distance to " OG  SER A 245 " =    1.513
peak=   -3.163 closest distance to " CD  ARG A  79 " =    1.107
peak=   -3.159 closest distance to " NH2 ARG A 219 " =    1.725
peak=   -3.155 closest distance to " CZ3 TRP A 123 " =    1.719
peak=   -3.154 closest distance to " O   HOH Z 134 " =    4.031
peak=   -3.151 closest distance to " OD1 ASP A 200 " =    1.467
peak=   -3.149 closest distance to " O   HOH Z 397 " =    1.167
peak=   -3.148 closest distance to " CD1 TRP A  70 " =    1.043
peak=   -3.145 closest distance to " O   HOH Z 265 " =    2.643
peak=   -3.145 closest distance to " O   HOH Z 216 " =    1.474
peak=   -3.138 closest distance to " O   HOH Z 253 " =    3.692
peak=   -3.136 closest distance to " C   ASP A 124 " =    2.057
peak=   -3.132 closest distance to " CZ  PHE A  16 " =    2.255
peak=   -3.115 closest distance to " O   GLN A 144 " =    1.388
peak=   -3.112 closest distance to " O   HOH Z 108 " =    1.358
peak=   -3.112 closest distance to " O   HOH Z 251 " =    1.056
peak=   -3.111 closest distance to " O   ILE A 106 " =    1.919
peak=   -3.106 closest distance to " O   HOH Z 111 " =    2.222
peak=   -3.105 closest distance to " O   HOH Z 105 " =    1.698
peak=   -3.104 closest distance to " OD1 ASN A 301 " =    1.783
peak=   -3.101 closest distance to " O   HOH Z 140 " =    1.217
peak=   -3.097 closest distance to " CG1 VAL A 126 " =    2.518
peak=   -3.095 closest distance to " O   HOH Z  35 " =    2.567
peak=   -3.092 closest distance to " OD2 ASP A 140 " =    1.099
peak=   -3.092 closest distance to " O   THR A 220 " =    1.794
peak=   -3.089 closest distance to " O   HOH Z 346 " =    1.731
peak=   -3.088 closest distance to " O   HOH Z 292 " =    1.465
peak=   -3.084 closest distance to " N   ALA A 226 " =    1.961
peak=   -3.070 closest distance to " OE1 GLN A 223 " =    1.854
peak=   -3.047 closest distance to " CA  GLY A  57 " =    2.113
peak=   -3.046 closest distance to " O   ALA A  34 " =    2.373
peak=   -3.030 closest distance to " O   ALA A 180 " =    1.160
peak=   -3.023 closest distance to " O   HOH Z   5 " =    1.097

================= 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    :  0.4715 0.4726   6.279624e+00   6.265606e+00
   1_bss:  0.4627 0.4638   6.274442e+00   6.255059e+00
   1_xyz:  0.3210 0.3620   6.025314e+00   6.104247e+00
   1_adp:  0.2900 0.3769   5.984357e+00   6.129514e+00
   1_occ:  0.2895 0.3773   5.985131e+00   6.130495e+00
   2_bss:  0.2882 0.3763   5.982497e+00   6.128990e+00
   2_xyz:  0.2300 0.2974   5.776729e+00   5.961520e+00
   2_adp:  0.2123 0.2800   5.713892e+00   5.907904e+00
   2_occ:  0.2121 0.2795   5.712962e+00   5.906849e+00
   3_bss:  0.2122 0.2789   5.710782e+00   5.905715e+00
   3_xyz:  0.1642 0.2218   5.479649e+00   5.697533e+00
   3_adp:  0.1505 0.2044   5.401199e+00   5.625378e+00
   3_occ:  0.1504 0.2043   5.400607e+00   5.624582e+00
   4_bss:  0.1508 0.2042   5.399294e+00   5.622113e+00
   4_xyz:  0.1335 0.1831   5.292101e+00   5.519814e+00
   4_adp:  0.1302 0.1776   5.265276e+00   5.489137e+00
   4_occ:  0.1301 0.1776   5.264742e+00   5.488445e+00
   5_bss:  0.1301 0.1776   5.264472e+00   5.488210e+00
   5_xyz:  0.1245 0.1699   5.224819e+00   5.448521e+00
   5_adp:  0.1225 0.1703   5.217533e+00   5.450251e+00
   5_occ:  0.1224 0.1704   5.217448e+00   5.450322e+00
   5_bss:  0.1226 0.1706   5.217356e+00   5.449206e+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:  0.328  24.032  -2.086   1.519   2.625   0.000   0.000   0.000
   1_xyz:  0.328  24.032  -2.086   1.519   2.625   0.000   0.000   0.000
   1_adp:  0.328  24.032  -2.086   1.519   2.625   0.000   0.000   0.000
   1_occ:  0.328  24.032  -2.086   1.519   2.625   0.000   0.000   0.000
   2_bss:  0.342  59.693  -1.855  -0.167   1.236  -0.000   0.000   0.000
   2_xyz:  0.342  59.693  -1.855  -0.167   1.236  -0.000   0.000   0.000
   2_adp:  0.342  59.693  -1.855  -0.167   1.236  -0.000   0.000   0.000
   2_occ:  0.342  59.693  -1.855  -0.167   1.236  -0.000   0.000   0.000
   3_bss:  0.331  57.854  -1.890  -0.723   0.794  -0.000   0.000   0.000
   3_xyz:  0.331  57.854  -1.890  -0.723   0.794  -0.000   0.000   0.000
   3_adp:  0.331  57.854  -1.890  -0.723   0.794  -0.000   0.000   0.000
   3_occ:  0.331  57.854  -1.890  -0.723   0.794  -0.000   0.000   0.000
   4_bss:  0.322  55.475  -2.124  -1.497   0.407  -0.000   0.000   0.000
   4_xyz:  0.322  55.475  -2.124  -1.497   0.407  -0.000   0.000   0.000
   4_adp:  0.322  55.475  -2.124  -1.497   0.407  -0.000   0.000   0.000
   4_occ:  0.322  55.475  -2.124  -1.497   0.407  -0.000   0.000   0.000
   5_bss:  0.322  55.475  -2.146  -1.667   0.383  -0.000   0.000   0.000
   5_xyz:  0.322  55.475  -2.146  -1.667   0.383  -0.000   0.000   0.000
   5_adp:  0.322  55.475  -2.146  -1.667   0.383  -0.000   0.000   0.000
   5_occ:  0.322  55.475  -2.146  -1.667   0.383  -0.000   0.000   0.000
   5_bss:  0.319  55.470  -2.011  -1.666   0.456  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.300 0.4417  0.6043    69377.711
   1_bss:  55.018 0.4566  0.6419    66129.334
   1_xyz:  38.908 0.6561  0.8833    37151.201
   1_adp:  41.105 0.6288  0.8496    40826.011
   1_occ:  41.254 0.6270  0.8463    40993.497
   2_bss:  40.930 0.6308  0.8251    40453.168
   2_xyz:  30.669 0.7494  0.9455    23732.830
   2_adp:  28.019 0.7794  0.9552    20744.396
   2_occ:  27.975 0.7799  0.9554    20673.707
   3_bss:  27.880 0.7807  0.9440    20513.715
   3_xyz:  21.642 0.8447  0.9887    12578.211
   3_adp:  19.632 0.8649  0.9888    10820.902
   3_occ:  19.613 0.8651  0.9886    10797.428
   4_bss:  19.533 0.8657  0.9728    10713.183
   4_xyz:  16.957 0.8897  0.9833     8523.500
   4_adp:  16.180 0.8969  0.9786     8080.206
   4_occ:  16.167 0.8970  0.9785     8063.434
   5_bss:  16.161 0.8971  0.9761     8060.919
   5_xyz:  15.332 0.9039  0.9814     7347.072
   5_adp:  15.273 0.9047  0.9758     7338.649
   5_occ:  15.273 0.9047  0.9757     7337.630
   5_bss:  15.257 0.9048  0.9782     7327.776
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.107   1.9353e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.107   1.9353e-01
   1_xyz:   1.815  0.016  0.125 16.659  0.008  4.104   1.9465e-01
   1_adp:   1.815  0.016  0.125 16.659  0.008  4.104   1.9465e-01
   1_occ:   1.815  0.016  0.125 16.659  0.008  4.104   1.9465e-01
   2_bss:   1.815  0.016  0.125 16.659  0.008  4.104   1.9465e-01
   2_xyz:   1.139  0.008  0.084 15.414  0.004  4.119   7.3195e-02
   2_adp:   1.139  0.008  0.084 15.414  0.004  4.119   7.3195e-02
   2_occ:   1.139  0.008  0.084 15.414  0.004  4.119   7.3195e-02
   3_bss:   1.139  0.008  0.084 15.414  0.004  4.119   7.3195e-02
   3_xyz:   1.025  0.007  0.072 15.059  0.004  4.127   6.2134e-02
   3_adp:   1.025  0.007  0.072 15.059  0.004  4.127   6.2134e-02
   3_occ:   1.025  0.007  0.072 15.059  0.004  4.127   6.2134e-02
   4_bss:   1.025  0.007  0.072 15.059  0.004  4.127   6.2134e-02
   4_xyz:   0.924  0.006  0.067 14.687  0.003  4.115   5.2384e-02
   4_adp:   0.924  0.006  0.067 14.687  0.003  4.115   5.2384e-02
   4_occ:   0.924  0.006  0.067 14.687  0.003  4.115   5.2384e-02
   5_bss:   0.924  0.006  0.067 14.687  0.003  4.115   5.2384e-02
   5_xyz:   0.885  0.005  0.066 14.478  0.003  4.117   4.8941e-02
   5_adp:   0.885  0.005  0.066 14.478  0.003  4.117   4.8941e-02
   5_occ:   0.885  0.005  0.066 14.478  0.003  4.117   4.8941e-02
   5_bss:   0.885  0.005  0.066 14.478  0.003  4.117   4.8941e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.143   2.4081e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.143   2.4081e-01
   1_xyz:  11.608  0.087  0.399 89.412  0.064  2.027   2.7402e-01
   1_adp:  11.608  0.087  0.399 89.412  0.064  2.027   2.7402e-01
   1_occ:  11.608  0.087  0.399 89.412  0.064  2.027   2.7402e-01
   2_bss:  11.608  0.087  0.399 89.412  0.064  2.027   2.7402e-01
   2_xyz:   8.033  0.054  0.295 83.378  0.034  2.261   5.2158e-02
   2_adp:   8.033  0.054  0.295 83.378  0.034  2.261   5.2158e-02
   2_occ:   8.033  0.054  0.295 83.378  0.034  2.261   5.2158e-02
   3_bss:   8.033  0.054  0.295 83.378  0.034  2.261   5.2158e-02
   3_xyz:   6.322  0.047  0.222 83.030  0.039  2.324   4.9033e-02
   3_adp:   6.322  0.047  0.222 83.030  0.039  2.324   4.9033e-02
   3_occ:   6.322  0.047  0.222 83.030  0.039  2.324   4.9033e-02
   4_bss:   6.322  0.047  0.222 83.030  0.039  2.324   4.9033e-02
   4_xyz:   6.637  0.044  0.206 81.227  0.030  2.260   3.3261e-02
   4_adp:   6.637  0.044  0.206 81.227  0.030  2.260   3.3261e-02
   4_occ:   6.637  0.044  0.206 81.227  0.030  2.260   3.3261e-02
   5_bss:   6.637  0.044  0.206 81.227  0.030  2.260   3.3261e-02
   5_xyz:   6.371  0.039  0.209 82.906  0.035  2.334   3.0758e-02
   5_adp:   6.371  0.039  0.209 82.906  0.035  2.334   3.0758e-02
   5_occ:   6.371  0.039  0.209 82.906  0.035  2.334   3.0758e-02
   5_bss:   6.371  0.039  0.209 82.906  0.035  2.334   3.0758e-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: 103.44   0.00  18.58  76.93   0.00  14.58 103.44   0.00  40.37
   1_occ: 103.44   0.00  18.58  76.93   0.00  14.58 103.44   0.00  40.37
   2_bss: 103.44   0.00  18.58  76.93   0.00  14.58 103.44   0.00  40.37
   2_xyz: 103.44   0.00  18.58  76.93   0.00  14.58 103.44   0.00  40.37
   2_adp: 104.55   0.00  18.28  87.81   0.00  13.79 104.55   3.01  42.75
   2_occ: 104.55   0.00  18.28  87.81   0.00  13.79 104.55   3.01  42.75
   3_bss: 104.55   0.00  18.28  87.81   0.00  13.79 104.55   3.01  42.75
   3_xyz: 104.55   0.00  18.28  87.81   0.00  13.79 104.55   3.01  42.75
   3_adp: 101.97   0.00  17.61  91.13   0.00  12.70 101.97   4.82  44.33
   3_occ: 101.97   0.00  17.61  91.13   0.00  12.70 101.97   4.82  44.33
   4_bss: 101.97   0.00  17.61  91.13   0.00  12.70 101.97   4.82  44.33
   4_xyz: 101.97   0.00  17.61  91.13   0.00  12.70 101.97   4.82  44.33
   4_adp:  99.16   0.71  17.04  92.73   0.71  12.29  99.16   4.61  42.89
   4_occ:  99.16   0.71  17.04  92.73   0.71  12.29  99.16   4.61  42.89
   5_bss:  99.16   0.71  17.04  92.73   0.71  12.29  99.16   4.61  42.89
   5_xyz:  99.16   0.71  17.04  92.73   0.71  12.29  99.16   4.61  42.89
   5_adp: 100.69   0.22  17.10 100.69   0.22  12.20  99.23   4.54  43.77
   5_occ: 100.69   0.22  17.10 100.69   0.22  12.20  99.23   4.54  43.77
   5_bss: 100.69   0.21  17.09 100.69   0.21  12.19  99.22   4.53  43.76
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    3.014    0.029    0.512
   1_adp:    3.014    0.029    0.512
   1_occ:    3.014    0.029    0.512
   2_bss:    3.014    0.029    0.512
   2_xyz:    2.513    0.042    0.602
   2_adp:    2.513    0.042    0.602
   2_occ:    2.513    0.042    0.602
   3_bss:    2.513    0.042    0.602
   3_xyz:    2.224    0.093    0.728
   3_adp:    2.224    0.093    0.728
   3_occ:    2.224    0.093    0.728
   4_bss:    2.224    0.093    0.728
   4_xyz:    2.174    0.050    0.763
   4_adp:    2.174    0.050    0.763
   4_occ:    2.174    0.050    0.763
   5_bss:    2.174    0.050    0.763
   5_xyz:    2.169    0.043    0.786
   5_adp:    2.169    0.043    0.786
   5_occ:    2.169    0.043    0.786
   5_bss:    2.169    0.043    0.786
------------------------------------------------------------------------

CPU time actual refinement: 280.83


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_262/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_262/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_262/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_262/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_262/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 280.70 
  Macro-tasks:
    bulk solvent and scale       = 37.61  
    individual site refinement   = 110.64 
    weights calculation          = 25.61  
    collect and process          = 5.53   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 179.49 
  Micro-tasks:
    mask                            = 1.93   
    f_calc                          = 87.44  
    alpha_beta                      = 7.06   
    target                          = 0.99   
    gradients_wrt_atomic_parameters = 94.32  
    fmodel                         = 6.08   
    r_factors                      = 0.22   
    phase_errors                   = 8.63   
    foms                           = 0.23   
    TOTAL for micro-tasks          = 206.90 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.018 micro seconds
Total CPU time: 4.87 minutes
from_scatterers_fft:    635 calls, 87.02 s
gradients_fft:          580 calls, 83.26 s

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

# Date 2008-01-16 Time 04:24:06 PST -0800 (1200486246.42 s)
Start R-work = 0.4715, R-free = 0.4726 (no bulk solvent and anisotropic scale)
Final R-work = 0.1421, R-free = 0.1852 (no bulk solvent and anisotropic scale)

Start R-work = 0.4627, R-free = 0.4638
Final R-work = 0.1226, R-free = 0.1706