# Date 2008-01-16 Time 05:55:07 PST -0800 (1200491707.20 s)
#phil __OFF__

Command line arguments: "../936.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18733
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 936

-------------------------------------------------------------------------------
  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: (70.9525, 47.6339, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.24, per 1000 atoms: 1.15


================================== 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: (70.9525, 47.6339, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.96145
Completeness in resolution range: 0.926019
Completeness with d_max=infinity: 0.923269

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0179
                             d_min =   1.9614

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: (70.9525, 47.6339, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.96145
Completeness in resolution range: 0.926019
Completeness with d_max=infinity: 0.923269

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0183 -  4.1979 [2218/2247]  1997   221  10.0%
  bin  2:  4.1979 -  3.3441 [2129/2152]  1918   211   9.9%
  bin  3:  3.3441 -  2.9249 [2100/2125]  1884   216  10.3%
  bin  4:  2.9249 -  2.6591 [2086/2102]  1887   199   9.5%
  bin  5:  2.6591 -  2.4694 [2074/2118]  1860   214  10.3%
  bin  6:  2.4694 -  2.3244 [2048/2076]  1849   199   9.7%
  bin  7:  2.3244 -  2.2084 [2052/2088]  1844   208  10.1%
  bin  8:  2.2084 -  2.1125 [2044/2086]  1837   207  10.1%
  bin  9:  2.1125 -  2.0314 [2020/2066]  1822   198   9.8%
  bin 10:  2.0314 -  1.9614 [ 818/2094]   732    86  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_936/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:
        1.68 -     2.32: 22
        2.32 -     2.97: 1752
        2.97 -     3.61: 4533
        3.61 -     4.26: 9156
        4.26 -     4.90: 12813
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.679 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.787 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.796 3.040 -x+1/2,-y+1,z-1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.801 3.120 -x+1/2,-y+1,z-1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.804 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28271 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_936/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_936/model_refine_001.geo

CPU time processing inputs: 9.02


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 47.63395 84.6622 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 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4272   r_free= 0.4240   ksol= 0.00   Bsol= 0.00   scale= 0.918    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.229521                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6826 0.99   1439  163 0.3305 0.3373      6.4666      6.4599|
|  2:  4.6826 -  3.7355 0.99   1382  146 0.3465 0.3508      6.7011      6.6707|
|  3:  3.7355 -  3.2689 0.99   1370  156 0.3852 0.3598      6.5684      6.6056|
|  4:  3.2689 -  2.9725 0.99   1341  148 0.4127 0.3989      6.4331      6.4181|
|  5:  2.9725 -  2.7609 0.98   1334  148 0.4294 0.4218      6.2875      6.2889|
|  6:  2.7609 -  2.5990 0.99   1346  152 0.4652 0.4615      6.2281      6.1423|
|  7:  2.5990 -  2.4694 0.98   1334  148 0.4586 0.4168       6.198      6.1332|
|  8:  2.4694 -  2.3624 0.99   1309  145 0.4891 0.4983      6.1312      6.1887|
|  9:  2.3624 -  2.2717 0.99   1327  149 0.5004 0.4789      6.1091      6.0856|
| 10:  2.2717 -  2.1936 0.98   1331  144 0.4912 0.5459      6.0616      6.1285|
| 11:  2.1936 -  2.1252 0.97   1290  141 0.4951 0.5353      6.0081      5.9887|
| 12:  2.1252 -  2.0646 0.99   1328  154 0.4936 0.5374      5.9283      5.9898|
| 13:  2.0646 -  2.0104 0.88   1175  132 0.4953 0.4256      5.8572      5.7972|
| 14:  2.0104 -  1.9614 0.24    324   33 0.5673 0.5093      5.8336      5.8144|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.6826  1439   163  0.75  30.19   0.85     0.77      56817.57|
|  2:  4.6826 -  3.7355  1382   146  0.76  29.73   0.94     0.84      76517.95|
|  3:  3.7355 -  3.2689  1370   156  0.68  36.83   0.93     0.85      82116.33|
|  4:  3.2689 -  2.9725  1341   148  0.61  43.08   0.95     0.81      74976.00|
|  5:  2.9725 -  2.7609  1334   148  0.55  47.97   0.91     0.75      62402.35|
|  6:  2.7609 -  2.5990  1346   152  0.51  50.87   0.93     0.71      54193.59|
|  7:  2.5990 -  2.4694  1334   148  0.51  51.08   0.94     0.69      49749.16|
|  8:  2.4694 -  2.3624  1309   145  0.46  55.41   0.90     0.66      49461.42|
|  9:  2.3624 -  2.2717  1327   149  0.43  57.96   0.93     0.62      47712.79|
| 10:  2.2717 -  2.1936  1331   144  0.38  61.71   0.97     0.56      48708.11|
| 11:  2.1936 -  2.1252  1290   141  0.34  64.57   0.94     0.51      45884.79|
| 12:  2.1252 -  2.0646  1328   154  0.31  67.11   0.94     0.50      43852.17|
| 13:  2.0646 -  2.0104  1175   132  0.33  65.41   0.95     0.51      36107.13|
| 14:  2.0104 -  1.9614   324    33  0.36  63.20   0.89     0.55      28971.53|
|alpha:            min =        0.50 max =            0.85 mean =         0.68|
|beta:             min =    28971.53 max =        82116.33 mean =     55884.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.51|
|phase err.(work): min =        0.00 max =           89.99 mean =        50.75|
|phase err.(test): min =        0.00 max =           89.84 mean =        50.87|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.997569              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.244   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.014290              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.376   (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 |  1.679 -  2.001:       10 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.001 -  2.323:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.323 -  2.645:       61 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.645 -  2.967:     1691 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.967 -  3.289:     1901 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.289 -  3.612:     2632 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.612 -  3.934:     4712 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.934 -  4.256:     4444 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.256 -  4.578:     5847 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.578 -  4.900:     6966 |
|-----------------------------------------------------------------------------|
|-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 |        0.176 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.679 |       0.377 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.949)------------------------------------------|
|    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 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4272   r_free= 0.4240   ksol= 0.00   Bsol= 0.00   scale= 0.918    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.229521                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4179   r_free= 0.4143   ksol= 0.30   Bsol= 37.34   scale= 0.956   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,2.30,1.47,0.00,0.00,0.00); trace/3= 0.59                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.221207                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.156304              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.208   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.907201              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.114   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4179      final r-factor (work) = 0.2753          |
| start r-factor (free) = 0.4143      final r-factor (free) = 0.3068          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.5397 = 8.16 * 0.50 * 6.2194 + 1.00 * 0.1761                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.7211 = 8.16 * 0.50 * 6.0342 + 1.00 * 0.1128                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2753      final r-factor (work) = 0.2506          |
| start r-factor (free) = 0.3068      final r-factor (free) = 0.3136          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4804 = 0.91 * 1.00 * 6.0342 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3054 = 0.91 * 1.00 * 5.8319 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.949)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.22   18.10    None  None   None       |
|    all(noH): 2823   0      0.00    88.22   18.10    None  None   None       |
|    Sol.    : 438    0      4.61    87.65   41.43    None  None   None       |
|    Mac.    : 2385   0      0.00    88.22   13.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.822:  825   |   5:    44.109 -  52.930:  104        |
|      1:     8.822 -  17.643: 1032   |   6:    52.930 -  61.752:   73        |
|      2:    17.643 -  26.465:  405   |   7:    61.752 -  70.574:   41        |
|      3:    26.465 -  35.287:  195   |   8:    70.574 -  79.395:   19        |
|      4:    35.287 -  44.109:  121   |   9:    79.395 -  88.217:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2506 r_free = 0.3136             target_work(ml) = 5.839         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2502 r_free = 0.3141             target_work(ml) = 5.838         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2502   r_free= 0.3141   ksol= 0.30   Bsol= 37.34   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,2.30,1.47,0.00,0.00,0.00); trace/3= 0.59                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.837748                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2470   r_free= 0.3110   ksol= 0.33   Bsol= 59.08   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-0.13,-0.77,-0.00,-0.00,-0.00); trace/3= -1.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.833762                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.267833              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.846   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.375968              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.591  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2470      final r-factor (work) = 0.1748          |
| start r-factor (free) = 0.3110      final r-factor (free) = 0.2185          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.4831 = 5.27 * 0.50 * 5.8355 + 1.00 * 0.1128                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.1079 = 5.27 * 0.50 * 5.7097 + 1.00 * 0.0690                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1748      final r-factor (work) = 0.1578          |
| start r-factor (free) = 0.2185      final r-factor (free) = 0.2015          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1612 = 0.38 * 1.00 * 5.7097 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0657 = 0.38 * 1.00 * 5.4676 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.949)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.16    84.40   17.81    None  None   None       |
|    all(noH): 2823   0      1.16    84.40   17.81    None  None   None       |
|    Sol.    : 438    0      5.50    84.03   42.26    None  None   None       |
|    Mac.    : 2385   0      1.16    84.40   13.32    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.158 -   9.482:  926   |   5:    42.779 -  51.103:  106        |
|      1:     9.482 -  17.806: 1078   |   6:    51.103 -  59.427:   83        |
|      2:    17.806 -  26.131:  298   |   7:    59.427 -  67.751:   50        |
|      3:    26.131 -  34.455:  128   |   8:    67.751 -  76.075:   22        |
|      4:    34.455 -  42.779:  121   |   9:    76.075 -  84.399:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1578 r_free = 0.2015             target_work(ml) = 5.429         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1576 r_free = 0.2016             target_work(ml) = 5.429         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1576   r_free= 0.2016   ksol= 0.33   Bsol= 59.08   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-0.13,-0.77,-0.00,-0.00,-0.00); trace/3= -1.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.428582                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1576   r_free= 0.2018   ksol= 0.32   Bsol= 53.72   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-1.15,-1.56,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.429120                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.740439              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.473  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.335217              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.797  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1576      final r-factor (work) = 0.1306          |
| start r-factor (free) = 0.2018      final r-factor (free) = 0.1729          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5649 = 2.74 * 0.50 * 5.4705 + 1.00 * 0.0690                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3885 = 2.74 * 0.50 * 5.3485 + 1.00 * 0.0599                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1306      final r-factor (work) = 0.1233          |
| start r-factor (free) = 0.1729      final r-factor (free) = 0.1686          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1515 = 1.34 * 1.00 * 5.3485 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0105 = 1.34 * 1.00 * 5.2421 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.949)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.35  17.91    None  None   None       |
|    all(noH): 2823   0      0.00    101.35  17.91    None  None   None       |
|    Sol.    : 438    0      5.49    89.74   43.84    None  None   None       |
|    Mac.    : 2385   0      0.00    101.35  13.15    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 -  10.135: 1072   |   5:    50.676 -  60.811:  100        |
|      1:    10.135 -  20.270: 1098   |   6:    60.811 -  70.947:   61        |
|      2:    20.270 -  30.406:  219   |   7:    70.947 -  81.082:   29        |
|      3:    30.406 -  40.541:  120   |   8:    81.082 -  91.217:   14        |
|      4:    40.541 -  50.676:  106   |   9:    91.217 - 101.352:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1233 r_free = 0.1686             target_work(ml) = 5.230         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1232 r_free = 0.1686             target_work(ml) = 5.230         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1232   r_free= 0.1686   ksol= 0.32   Bsol= 53.72   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-1.15,-1.56,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.230196                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1236   r_free= 0.1691   ksol= 0.32   Bsol= 56.45   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-1.58,-1.78,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.232308                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.880532              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 127.936  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.544652              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.208  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1236      final r-factor (work) = 0.1181          |
| start r-factor (free) = 0.1691      final r-factor (free) = 0.1642          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9899 = 1.88 * 0.50 * 5.2432 + 1.00 * 0.0599                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9567 = 1.88 * 0.50 * 5.2129 + 1.00 * 0.0552                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1181      final r-factor (work) = 0.1169          |
| start r-factor (free) = 0.1642      final r-factor (free) = 0.1636          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8503 = 0.54 * 1.00 * 5.2129 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8378 = 0.54 * 1.00 * 5.1916 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.949)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.62    107.16  17.50    None  None   None       |
|    all(noH): 2823   0      1.62    107.16  17.50    None  None   None       |
|    Sol.    : 438    0      5.28    88.93   42.31    None  None   None       |
|    Mac.    : 2385   0      1.62    107.16  12.94    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.623 -  12.177: 1521   |   5:    54.391 -  64.945:   83        |
|      1:    12.177 -  22.730:  750   |   6:    64.945 -  75.499:   37        |
|      2:    22.730 -  33.284:  177   |   7:    75.499 -  86.052:   13        |
|      3:    33.284 -  43.838:  123   |   8:    86.052 -  96.606:    6        |
|      4:    43.838 -  54.391:  110   |   9:    96.606 - 107.160:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1169 r_free = 0.1636             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1169 r_free = 0.1636             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1636   ksol= 0.32   Bsol= 56.45   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-1.58,-1.78,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.188288                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1636   ksol= 0.32   Bsol= 56.45   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-1.60,-1.71,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.188309                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.554224              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.894  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.687634              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.304  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1169      final r-factor (work) = 0.1094          |
| start r-factor (free) = 0.1636      final r-factor (free) = 0.1600          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2813 = 3.55 * 0.50 * 5.1916 + 1.00 * 0.0552                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2494 = 3.55 * 0.50 * 5.1608 + 1.00 * 0.0781                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1094      final r-factor (work) = 0.1087          |
| start r-factor (free) = 0.1600      final r-factor (free) = 0.1597          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5589 = 0.69 * 1.00 * 5.1608 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5473 = 0.69 * 1.00 * 5.1443 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.949)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.16    112.21  17.18    None  None   None       |
|    all(noH): 2823   0      1.16    112.21  17.18    None  None   None       |
|    Sol.    : 438    0      5.60    90.41   41.32    None  None   None       |
|    Mac.    : 2385   0      1.16    112.21  12.74    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.159 -  12.264: 1572   |   5:    56.683 -  67.787:   58        |
|      1:    12.264 -  23.368:  728   |   6:    67.787 -  78.892:   26        |
|      2:    23.368 -  34.473:  164   |   7:    78.892 -  89.997:    9        |
|      3:    34.473 -  45.578:  140   |   8:    89.997 - 101.101:    6        |
|      4:    45.578 -  56.683:  119   |   9:   101.101 - 112.206:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1087 r_free = 0.1597             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1087 r_free = 0.1597             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1597   ksol= 0.32   Bsol= 56.45   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-1.60,-1.71,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.143868                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6826 0.99   1439  163 0.0930 0.1262       5.334      5.5198|
|  2:  4.6826 -  3.7355 0.99   1382  146 0.0795 0.1040       5.377      5.5897|
|  3:  3.7355 -  3.2689 0.99   1370  156 0.1026 0.1612      5.4395      5.8856|
|  4:  3.2689 -  2.9725 0.99   1341  148 0.1247 0.1540      5.4588      5.5983|
|  5:  2.9725 -  2.7609 0.98   1334  148 0.1303 0.1827      5.3243       5.519|
|  6:  2.7609 -  2.5990 0.99   1346  152 0.1221 0.1833      5.2073      5.4384|
|  7:  2.5990 -  2.4694 0.98   1334  148 0.1189 0.1758      5.1458      5.3922|
|  8:  2.4694 -  2.3624 0.99   1309  145 0.1147 0.1668      5.0558      5.2797|
|  9:  2.3624 -  2.2717 0.99   1327  149 0.1138 0.1946      5.0238      5.3358|
| 10:  2.2717 -  2.1936 0.98   1331  144 0.1084 0.1762      4.9646      5.2623|
| 11:  2.1936 -  2.1252 0.97   1290  141 0.1116 0.1845      4.9244      5.2506|
| 12:  2.1252 -  2.0646 0.99   1328  154 0.1078 0.1712      4.8637      5.0871|
| 13:  2.0646 -  2.0104 0.88   1175  132 0.1137 0.1822       4.785      5.0316|
| 14:  2.0104 -  1.9614 0.24    324   33 0.1076 0.1646      4.6446      4.9279|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.6826  1439   163  0.94   8.68   0.97     0.95       6667.71|
|  2:  4.6826 -  3.7355  1382   146  0.96   7.53   1.01     0.99       8240.94|
|  3:  3.7355 -  3.2689  1370   156  0.93  11.21   1.02     1.02       9922.30|
|  4:  3.2689 -  2.9725  1341   148  0.91  14.72   1.00     0.98      10776.74|
|  5:  2.9725 -  2.7609  1334   148  0.89  16.67   0.99     0.96       8651.93|
|  6:  2.7609 -  2.5990  1346   152  0.90  16.45   0.99     0.96       7233.33|
|  7:  2.5990 -  2.4694  1334   148  0.91  15.37   0.99     0.96       6212.44|
|  8:  2.4694 -  2.3624  1309   145  0.90  16.12   0.99     0.96       5509.97|
|  9:  2.3624 -  2.2717  1327   149  0.90  16.41   0.99     0.94       5093.77|
| 10:  2.2717 -  2.1936  1331   144  0.91  15.56   0.99     0.95       4630.56|
| 11:  2.1936 -  2.1252  1290   141  0.89  16.86   0.98     0.95       4483.87|
| 12:  2.1252 -  2.0646  1328   154  0.91  15.86   0.99     0.97       4038.46|
| 13:  2.0646 -  2.0104  1175   132  0.90  16.65   0.98     0.97       3406.04|
| 14:  2.0104 -  1.9614   324    33  0.89  16.33   0.97     0.94       2595.37|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2595.37 max =        10776.74 mean =      6507.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.89 mean =        14.41|
|phase err.(test): min =        0.00 max =           87.87 mean =        13.82|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1596   ksol= 0.32   Bsol= 54.18   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-1.45,-1.50,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.144018                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1596   ksol= 0.32   Bsol= 54.18   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-1.45,-1.50,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.144018                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6826 0.99   1439  163 0.0930 0.1262      5.3347      5.5198|
|  2:  4.6826 -  3.7355 0.99   1382  146 0.0793 0.1038      5.3759      5.5878|
|  3:  3.7355 -  3.2689 0.99   1370  156 0.1026 0.1611      5.4386      5.8857|
|  4:  3.2689 -  2.9725 0.99   1341  148 0.1247 0.1541       5.459      5.5984|
|  5:  2.9725 -  2.7609 0.98   1334  148 0.1303 0.1828      5.3247      5.5192|
|  6:  2.7609 -  2.5990 0.99   1346  152 0.1222 0.1834      5.2076      5.4387|
|  7:  2.5990 -  2.4694 0.98   1334  148 0.1190 0.1760      5.1464      5.3928|
|  8:  2.4694 -  2.3624 0.99   1309  145 0.1147 0.1668      5.0564      5.2802|
|  9:  2.3624 -  2.2717 0.99   1327  149 0.1137 0.1947      5.0242      5.3366|
| 10:  2.2717 -  2.1936 0.98   1331  144 0.1085 0.1762      4.9652      5.2626|
| 11:  2.1936 -  2.1252 0.97   1290  141 0.1116 0.1842      4.9245      5.2502|
| 12:  2.1252 -  2.0646 0.99   1328  154 0.1079 0.1713      4.8638      5.0879|
| 13:  2.0646 -  2.0104 0.88   1175  132 0.1137 0.1821       4.785      5.0307|
| 14:  2.0104 -  1.9614 0.24    324   33 0.1076 0.1642      4.6445      4.9269|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.6826  1439   163  0.94   8.69   0.97     0.95       6673.34|
|  2:  4.6826 -  3.7355  1382   146  0.96   7.53   1.01     1.00       8225.84|
|  3:  3.7355 -  3.2689  1370   156  0.93  11.19   1.03     1.03       9897.93|
|  4:  3.2689 -  2.9725  1341   148  0.91  14.72   1.01     0.99      10774.75|
|  5:  2.9725 -  2.7609  1334   148  0.89  16.66   0.99     0.96       8650.74|
|  6:  2.7609 -  2.5990  1346   152  0.90  16.46   0.99     0.97       7237.30|
|  7:  2.5990 -  2.4694  1334   148  0.91  15.39   0.99     0.96       6219.21|
|  8:  2.4694 -  2.3624  1309   145  0.90  16.13   1.00     0.97       5517.19|
|  9:  2.3624 -  2.2717  1327   149  0.90  16.42   0.99     0.95       5100.08|
| 10:  2.2717 -  2.1936  1331   144  0.91  15.57   0.99     0.96       4634.80|
| 11:  2.1936 -  2.1252  1290   141  0.89  16.86   0.99     0.96       4485.19|
| 12:  2.1252 -  2.0646  1328   154  0.91  15.87   1.00     0.98       4040.62|
| 13:  2.0646 -  2.0104  1175   132  0.90  16.65   0.99     0.98       3404.67|
| 14:  2.0104 -  1.9614   324    33  0.89  16.32   0.98     0.95       2591.74|
|alpha:            min =        0.95 max =            1.03 mean =         0.97|
|beta:             min =     2591.74 max =        10774.75 mean =      6506.46|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.42|
|phase err.(test): min =        0.00 max =           87.80 mean =        13.82|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.949)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.12    112.17  17.14    None  None   None       |
|    all(noH): 2823   0      1.12    112.17  17.14    None  None   None       |
|    Sol.    : 438    0      5.56    90.37   41.28    None  None   None       |
|    Mac.    : 2385   0      1.12    112.17  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:     1.119 -  12.223: 1572   |   5:    56.642 -  67.747:   58        |
|      1:    12.223 -  23.328:  728   |   6:    67.747 -  78.851:   26        |
|      2:    23.328 -  34.433:  164   |   7:    78.851 -  89.956:    9        |
|      3:    34.433 -  45.537:  140   |   8:    89.956 - 101.061:    6        |
|      4:    45.537 -  56.642:  119   |   9:   101.061 - 112.166:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 320         
Filter by distance & map next to the model:
   mapped sites are within: 0.520 - 5.970
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 316 from: 320
   mapped sites are within: 0.709 - 5.970

peak=    5.920 closest distance to " NH2 ARG A  56 " =    2.273
peak=    5.569 closest distance to " CB  SER A  63 " =    1.204
peak=    5.535 closest distance to " CB  GLN A 223 " =    1.470
peak=    5.232 closest distance to " CG  PRO A  54 " =    1.138
peak=    4.880 closest distance to " CB  GLN A 183 " =    1.297
peak=    4.762 closest distance to " O   HOH Z  15 " =    2.082
peak=    4.709 closest distance to " O   HOH Z 403 " =    1.774
peak=    4.631 closest distance to " O   HOH Z 232 " =    2.266
peak=    4.586 closest distance to " CB  ARG A 275 " =    0.891
peak=    4.561 closest distance to " O   HOH Z 193 " =    1.871
peak=    4.523 closest distance to " OD1 ASN A  69 " =    2.506
peak=    4.482 closest distance to " CA  TYR A  30 " =    0.928
peak=    4.478 closest distance to " CB  GLU A 277 " =    3.609
peak=    4.443 closest distance to " O   HOH Z 234 " =    3.767
peak=    4.443 closest distance to " O   HOH Z 368 " =    2.146
peak=    4.414 closest distance to " O   HOH Z 298 " =    1.900
peak=    4.402 closest distance to " O   HOH Z  20 " =    1.829
peak=    4.392 closest distance to " C   PRO A 198 " =    1.499
peak=    4.368 closest distance to " CB  GLU A 152 " =    1.153
peak=    4.367 closest distance to " CB  TYR A 169 " =    0.889
peak=    4.353 closest distance to " OD2 ASP A 286 " =    2.881
peak=    4.321 closest distance to " O   SER A  87 " =    2.174
peak=    4.311 closest distance to " O   HOH Z 132 " =    2.156
peak=    4.303 closest distance to " CB  SER A   3 " =    1.338
peak=    4.284 closest distance to " CG  PRO A 213 " =    1.154
peak=    4.281 closest distance to " CB  ARG A  79 " =    1.415
peak=    4.256 closest distance to " O   HOH Z  80 " =    1.678
peak=    4.248 closest distance to " CA  ALA A  21 " =    1.315
peak=    4.245 closest distance to " O   HOH Z 180 " =    2.274
peak=    4.232 closest distance to " O   HOH Z 374 " =    2.681
peak=    4.209 closest distance to " NH2 ARG A 156 " =    1.202
peak=    4.206 closest distance to " NZ  LYS A 117 " =    3.231
peak=    4.204 closest distance to " CB  GLU A 128 " =    1.139
peak=    4.201 closest distance to " NE2 GLN A  11 " =    1.045
peak=    4.190 closest distance to " O   HOH Z  40 " =    1.807
peak=    4.176 closest distance to " O   HOH Z  97 " =    1.883
peak=    4.156 closest distance to " NH2BARG A 145 " =    2.128
peak=    4.153 closest distance to " O   HOH Z 203 " =    1.890
peak=    4.151 closest distance to " O   HOH Z 426 " =    1.523
peak=    4.145 closest distance to " O   HOH Z 369 " =    2.229
peak=    4.135 closest distance to " CG1 ILE A  33 " =    1.160
peak=    4.125 closest distance to " O   HOH Z 134 " =    1.467
peak=    4.123 closest distance to " CA  THR A 221 " =    0.913
peak=    4.105 closest distance to " CG2 THR A 221 " =    1.067
peak=    4.102 closest distance to " O   HOH Z 108 " =    2.181
peak=    4.096 closest distance to " CB  VAL A 202 " =    1.621
peak=    4.094 closest distance to " O   HOH Z 316 " =    2.956
peak=    4.049 closest distance to " O   HOH Z  67 " =    1.967
peak=    4.023 closest distance to " CB  LEU A 228 " =    1.143
peak=    4.016 closest distance to " O   HOH Z 132 " =    2.699
peak=    4.016 closest distance to " O   HOH Z 126 " =    1.594
peak=    4.007 closest distance to " O   HOH Z  59 " =    2.400
peak=    4.004 closest distance to " O   HOH Z 163 " =    1.558
peak=    3.995 closest distance to " CG  ARG A  66 " =    2.563
peak=    3.995 closest distance to " OG BSER A 164 " =    2.471
peak=    3.995 closest distance to " CB  PRO A  54 " =    0.754
peak=    3.995 closest distance to " O   HOH Z 261 " =    2.122
peak=    3.979 closest distance to " O   HOH Z 284 " =    2.892
peak=    3.974 closest distance to " O   HOH Z 279 " =    2.225
peak=    3.972 closest distance to " O   HOH Z 193 " =    2.250
peak=    3.958 closest distance to " O   HOH Z  49 " =    2.367
peak=    3.955 closest distance to " O   HOH Z 236 " =    1.911
peak=    3.952 closest distance to " O   MET A 105 " =    1.887
peak=    3.946 closest distance to " O   HOH Z 142 " =    1.547
peak=    3.940 closest distance to " CB  ARG A 190 " =    1.675
peak=    3.916 closest distance to " O   HOH Z 126 " =    1.842
peak=    3.916 closest distance to " O   HOH Z 124 " =    1.376
peak=    3.908 closest distance to " O   HOH Z 389 " =    1.869
peak=    3.908 closest distance to " O   HOH Z 371 " =    3.402
peak=    3.906 closest distance to " O   HOH Z 133 " =    1.656
peak=    3.885 closest distance to " CB  TRP A 179 " =    1.358
peak=    3.869 closest distance to " O   HOH Z  63 " =    1.892
peak=    3.864 closest distance to " O   HOH Z 423 " =    1.959
peak=    3.861 closest distance to " O   HOH Z 326 " =    1.512
peak=    3.855 closest distance to " O   HOH Z  78 " =    1.833
peak=    3.852 closest distance to " O   HOH Z 313 " =    1.826
peak=    3.849 closest distance to " CB  ASN A 148 " =    1.248
peak=    3.838 closest distance to " ND1 HIS A  81 " =    1.554
peak=    3.837 closest distance to " O   HOH Z 411 " =    3.503
peak=    3.803 closest distance to " CG  PRO A 198 " =    1.315
peak=    3.786 closest distance to " O   HOH Z 174 " =    2.570
peak=    3.776 closest distance to " O   ALA A 165 " =    1.362
peak=    3.766 closest distance to " O   HOH Z 406 " =    1.683
peak=    3.765 closest distance to " O   HOH Z 427 " =    2.837
peak=    3.762 closest distance to " CD1 LEU A 300 " =    1.208
peak=    3.758 closest distance to " O   HOH Z 135 " =    1.821
peak=    3.754 closest distance to " O   HOH Z  43 " =    2.204
peak=    3.753 closest distance to " O   HOH Z 344 " =    3.006
peak=    3.751 closest distance to " O   HOH Z 272 " =    1.893
peak=    3.749 closest distance to " O   HOH Z 102 " =    1.270
peak=    3.749 closest distance to " CA  ARG A 195 " =    1.291
peak=    3.734 closest distance to " CA  ALA A  51 " =    0.997
peak=    3.733 closest distance to " CB  SER A 141 " =    1.017
peak=    3.727 closest distance to " ND2 ASN A 187 " =    1.533
peak=    3.724 closest distance to " CA  ASN A 176 " =    1.544
peak=    3.721 closest distance to " OG  SER A  62 " =    3.010
peak=    3.720 closest distance to " O   HOH Z  88 " =    3.413
peak=    3.719 closest distance to " O   HOH Z 247 " =    1.350
peak=    3.710 closest distance to " O   HOH Z 425 " =    1.306
peak=    3.707 closest distance to " O   HOH Z  61 " =    1.607
peak=    3.699 closest distance to " O   HOH Z  93 " =    2.622
peak=    3.697 closest distance to " CB  ASN A 148 " =    1.790
peak=    3.697 closest distance to " O   HOH Z  54 " =    1.696
peak=    3.687 closest distance to " O   HOH Z 345 " =    3.170
peak=    3.675 closest distance to " O   HOH Z 189 " =    2.151
peak=    3.667 closest distance to " CA  MET A  40 " =    1.082
peak=    3.665 closest distance to " O   HOH Z 108 " =    1.234
peak=    3.643 closest distance to " CG  PRO A 280 " =    0.718
peak=    3.635 closest distance to " O   HOH Z 214 " =    2.111
peak=    3.634 closest distance to " O   HOH Z 209 " =    2.318
peak=    3.631 closest distance to " O   HOH Z   6 " =    2.185
peak=    3.629 closest distance to " O   HOH Z  44 " =    1.912
peak=    3.629 closest distance to " CB  ARG A 139 " =    0.932
peak=    3.620 closest distance to " ND2 ASN A 110 " =    1.658
peak=    3.619 closest distance to " O   HOH Z 132 " =    1.025
peak=    3.614 closest distance to " O   HOH Z 295 " =    1.468
peak=    3.608 closest distance to " O   HOH Z  19 " =    1.901
peak=    3.598 closest distance to " O   HOH Z  54 " =    2.275
peak=    3.594 closest distance to " CG  PRO A  90 " =    1.051
peak=    3.594 closest distance to " O   HOH Z 345 " =    1.668
peak=    3.590 closest distance to " CB  TRP A 266 " =    0.927
peak=    3.589 closest distance to " O   HOH Z  30 " =    1.331
peak=    3.580 closest distance to " CG  PRO A 243 " =    1.231
peak=    3.578 closest distance to " O   HOH Z 147 " =    1.773
peak=    3.576 closest distance to " O   HOH Z 118 " =    1.559
peak=    3.572 closest distance to " CG1BVAL A  72 " =    1.600
peak=    3.571 closest distance to " CB  VAL A 265 " =    1.242
peak=    3.570 closest distance to " CD  ARG A 269 " =    0.927
peak=    3.570 closest distance to " CD  PRO A  54 " =    1.219
peak=    3.565 closest distance to " O   HOH Z 303 " =    2.138
peak=    3.560 closest distance to " CB  ASP A 140 " =    0.903
peak=    3.554 closest distance to " OE1 GLN A  11 " =    1.903
peak=    3.553 closest distance to " O   HOH Z 365 " =    2.959
peak=    3.546 closest distance to " CG  GLN A  58 " =    2.612
peak=    3.541 closest distance to " CA  ARG A  36 " =    1.237
peak=    3.539 closest distance to " O   HOH Z  61 " =    1.533
peak=    3.539 closest distance to " O   HOH Z 214 " =    0.828
peak=    3.537 closest distance to " O   HOH Z 130 " =    2.250
peak=    3.535 closest distance to " CB  PRO A  54 " =    1.221
peak=    3.534 closest distance to " CA  ALA A 160 " =    0.840
peak=    3.533 closest distance to " O   HOH Z 250 " =    1.450
peak=    3.531 closest distance to " NH1AARG A 145 " =    1.062
peak=    3.525 closest distance to " O   HOH Z 197 " =    2.615
peak=    3.524 closest distance to " CG BARG A 102 " =    1.887
peak=    3.515 closest distance to " CB  ALA A 100 " =    1.242
peak=    3.514 closest distance to " O   HOH Z 286 " =    2.186
peak=    3.513 closest distance to " CA  ASP A 191 " =    0.795
peak=    3.513 closest distance to " O   HOH Z 357 " =    1.981
peak=    3.508 closest distance to " O   HOH Z 227 " =    1.683
peak=    3.503 closest distance to " O   HOH Z  64 " =    2.288
peak=    3.496 closest distance to " CD  LYS A 166 " =    1.384
peak=    3.494 closest distance to " O   HOH Z 427 " =    3.083
peak=    3.486 closest distance to " CA  LYS A 117 " =    1.251
peak=    3.482 closest distance to " CB  ASN A 187 " =    1.176
peak=    3.480 closest distance to " O   HOH Z 128 " =    2.142
peak=    3.476 closest distance to " CG2BVAL A  41 " =    0.803
peak=    3.472 closest distance to " OD2 ASP A 298 " =    4.090
peak=    3.467 closest distance to " O   HOH Z 346 " =    1.563
peak=    3.464 closest distance to " N   ASN A  39 " =    1.350
peak=    3.460 closest distance to " O   GLY A  57 " =    2.529
peak=    3.458 closest distance to " CA  ASP A 124 " =    0.709
peak=    3.457 closest distance to " O   HOH Z 183 " =    1.525
peak=    3.455 closest distance to " O   HOH Z  48 " =    1.438
peak=    3.440 closest distance to " O   HOH Z 425 " =    2.126
peak=    3.435 closest distance to " O   HOH Z  21 " =    1.737
peak=    3.435 closest distance to " CB  ASN A 285 " =    0.880
peak=    3.432 closest distance to " O   HOH Z 260 " =    1.253
peak=    3.427 closest distance to " CG AARG A 275 " =    1.129
peak=    3.426 closest distance to " CG2 VAL A 197 " =    1.159
peak=    3.424 closest distance to " O   HOH Z 207 " =    2.118
peak=    3.422 closest distance to " O   HOH Z  10 " =    1.815
peak=    3.420 closest distance to " CB  MET A  40 " =    0.914
peak=    3.419 closest distance to " CA  ASP A 140 " =    1.147
peak=    3.415 closest distance to " CD2 LEU A 297 " =    0.903
peak=    3.408 closest distance to " O   HOH Z 245 " =    1.339
peak=    3.398 closest distance to " O   HOH Z 327 " =    2.514
peak=    3.396 closest distance to " CD  ARG A 159 " =    0.827
peak=    3.395 closest distance to " O   HOH Z 185 " =    1.750
peak=    3.394 closest distance to " O   HOH Z 116 " =    1.801
peak=    3.391 closest distance to " O   HOH Z 437 " =    1.471
peak=    3.390 closest distance to " O   HOH Z 337 " =    3.855
peak=    3.386 closest distance to " O   HOH Z 411 " =    1.712
peak=    3.385 closest distance to " O   HOH Z 281 " =    4.225
peak=    3.384 closest distance to " O   ALA A 158 " =    1.253
peak=    3.383 closest distance to " O   HOH Z 368 " =    2.534
peak=    3.382 closest distance to " CD BLYS A 290 " =    1.088
peak=    3.381 closest distance to " CA  ASP A 162 " =    1.213
peak=    3.375 closest distance to " O   HOH Z 361 " =    3.342
peak=    3.374 closest distance to " CD2 LEU A 255 " =    1.350
peak=    3.370 closest distance to " CB  TYR A 116 " =    1.026
peak=    3.369 closest distance to " O   HOH Z 394 " =    1.687
peak=    3.365 closest distance to " CD2 TRP A 179 " =    1.368
peak=    3.361 closest distance to " O   HOH Z 358 " =    2.123
peak=    3.360 closest distance to " CB  ILE A 120 " =    1.341
peak=    3.352 closest distance to " NE2 GLN A  58 " =    4.452
peak=    3.352 closest distance to " O   HOH Z 383 " =    2.043
peak=    3.343 closest distance to " CB  SER A 216 " =    0.842
peak=    3.342 closest distance to " O   HOH Z 128 " =    2.296
peak=    3.336 closest distance to " O   HOH Z 158 " =    2.969
peak=    3.336 closest distance to " O   HOH Z 166 " =    1.547
peak=    3.335 closest distance to " O   HOH Z 438 " =    2.251
peak=    3.334 closest distance to " NZ  LYS A  76 " =    1.314
peak=    3.333 closest distance to " CB  ARG A 259 " =    1.861
peak=    3.331 closest distance to " O   TRP A 274 " =    1.858
peak=    3.323 closest distance to " O   HOH Z 292 " =    1.639
peak=    3.321 closest distance to " O   HOH Z 227 " =    1.695
peak=    3.318 closest distance to " CD  ARG A  66 " =    2.994
peak=    3.317 closest distance to " O   HOH Z 214 " =    2.202
peak=    3.316 closest distance to " NE2 HIS A 115 " =    1.006
peak=    3.316 closest distance to " NZ  LYS A 166 " =    2.985
peak=    3.312 closest distance to " CA  TYR A 116 " =    1.472
peak=    3.308 closest distance to " O   HOH Z 250 " =    1.724
peak=    3.307 closest distance to " CA  GLY A 267 " =    1.056
peak=    3.307 closest distance to " O   HOH Z 423 " =    3.322
peak=    3.305 closest distance to " CD1 ILE A 106 " =    0.994
peak=    3.304 closest distance to " OG BSER A 258 " =    3.490
peak=    3.302 closest distance to " O   HOH Z  11 " =    1.208
peak=    3.302 closest distance to " O   THR A 251 " =    1.234
peak=    3.296 closest distance to " CA  LEU A  83 " =    1.458
peak=    3.293 closest distance to " CB  ASN A  39 " =    0.800
peak=    3.289 closest distance to " NH2AARG A 190 " =    1.323
peak=    3.284 closest distance to " CG  ARG A 219 " =    1.262
peak=    3.284 closest distance to " CD1 TRP A 266 " =    1.162
peak=    3.279 closest distance to " O   HOH Z 334 " =    1.474
peak=    3.279 closest distance to " CG1 VAL A 202 " =    2.123
peak=    3.278 closest distance to " CA  ALA A 158 " =    1.087
peak=    3.277 closest distance to " O   HOH Z 173 " =    2.027
peak=    3.272 closest distance to " O   HOH Z 261 " =    2.089
peak=    3.269 closest distance to " CB  MET A  47 " =    0.984
peak=    3.265 closest distance to " CA  ASN A 215 " =    1.187
peak=    3.264 closest distance to " CA  ASN A  74 " =    1.235
peak=    3.262 closest distance to " CZ  PHE A 218 " =    1.076
peak=    3.257 closest distance to " OG  SER A  22 " =    2.869
peak=    3.255 closest distance to " O   HOH Z  63 " =    2.211
peak=    3.254 closest distance to " CE1 TYR A 186 " =    1.143
peak=    3.251 closest distance to " CA  GLU A 152 " =    0.852
peak=    3.250 closest distance to " O   HOH Z  85 " =    1.972
peak=    3.243 closest distance to " O   HOH Z 197 " =    2.099
peak=    3.241 closest distance to " O   HOH Z 327 " =    1.892
peak=    3.240 closest distance to " CB  LEU A 143 " =    1.100
peak=    3.236 closest distance to " O   HOH Z 387 " =    2.645
peak=    3.233 closest distance to " CG2 VAL A  78 " =    0.923
peak=    3.229 closest distance to " CG  MET A  93 " =    1.014
peak=    3.228 closest distance to " CB  MET A 105 " =    1.225
peak=    3.227 closest distance to " CG  MET A 185 " =    1.196
peak=    3.226 closest distance to " O   HOH Z 156 " =    2.554
peak=    3.225 closest distance to " O   ALA A   1 " =    1.482
peak=    3.214 closest distance to " CA  ALA A 291 " =    0.912
peak=    3.212 closest distance to " CB  ALA A 291 " =    1.371
peak=    3.210 closest distance to " O   HOH Z 217 " =    2.120
peak=    3.208 closest distance to " OG1 THR A 294 " =    2.429
peak=    3.204 closest distance to " O   HOH Z 163 " =    1.843
peak=    3.203 closest distance to " CB  SER A  62 " =    0.721
peak=    3.200 closest distance to " CB  TRP A 150 " =    1.522
peak=    3.200 closest distance to " O   HOH Z 112 " =    1.524
peak=    3.200 closest distance to " O   HOH Z 388 " =    1.779
peak=    3.200 closest distance to " O   GLN A 278 " =    1.287
peak=    3.199 closest distance to " CA  GLY A 196 " =    1.091
peak=    3.199 closest distance to " CA  ALA A 248 " =    1.169
peak=    3.196 closest distance to " CD2 HIS A  81 " =    1.118
peak=    3.196 closest distance to " O   HOH Z 421 " =    1.635
peak=    3.195 closest distance to " CB  TYR A  30 " =    1.395
peak=    3.195 closest distance to " CB  SER A 212 " =    1.137
peak=    3.192 closest distance to " O   HOH Z 258 " =    2.158
peak=    3.191 closest distance to " CG BARG A 275 " =    1.425
peak=    3.190 closest distance to " O   HOH Z 227 " =    2.250
peak=    3.187 closest distance to " O   HOH Z 211 " =    2.689
peak=    3.185 closest distance to " CB  ALA A 248 " =    0.953
peak=    3.182 closest distance to " O   HOH Z 416 " =    2.808
peak=    3.179 closest distance to " O   HOH Z 285 " =    1.973
peak=    3.179 closest distance to " O   HOH Z 422 " =    2.633
peak=    3.179 closest distance to " O   HOH Z  38 " =    1.822
peak=    3.177 closest distance to " CG1 ILE A 151 " =    0.871
peak=    3.177 closest distance to " CE  LYS A 193 " =    1.881
peak=    3.175 closest distance to " O   HOH Z 417 " =    3.292
peak=    3.174 closest distance to " CG  MET A 185 " =    1.074
peak=    3.171 closest distance to " O   HOH Z 420 " =    1.847
peak=    3.161 closest distance to " N   ASN A 127 " =    1.263
peak=    3.161 closest distance to " CG  GLN A  55 " =    2.193
peak=    3.160 closest distance to " OE1 GLN A  58 " =    5.970
peak=    3.156 closest distance to " O   HOH Z 341 " =    1.760
peak=    3.155 closest distance to " OD1 ASP A 286 " =    1.583
peak=    3.155 closest distance to " C   SER A  32 " =    1.013
peak=    3.153 closest distance to " O   HOH Z 299 " =    2.361
peak=    3.151 closest distance to " O   VAL A  72 " =    3.152
peak=    3.149 closest distance to " O   HOH Z 391 " =    2.985
peak=    3.148 closest distance to " CG1 VAL A 153 " =    1.042
peak=    3.147 closest distance to " O   HOH Z 189 " =    1.310
peak=    3.146 closest distance to " CA  ALA A 295 " =    1.079
peak=    3.145 closest distance to " O   HOH Z   1 " =    2.481
peak=    3.140 closest distance to " O   HOH Z 238 " =    5.320
peak=    3.140 closest distance to " O   HOH Z 150 " =    1.551
peak=    3.134 closest distance to " NH2 ARG A 219 " =    1.923
peak=    3.133 closest distance to " O   HOH Z 114 " =    1.348
peak=    3.133 closest distance to " O   HOH Z 123 " =    2.229
peak=    3.125 closest distance to " C   PRO A 163 " =    1.677
peak=    3.125 closest distance to " CZ2 TRP A 179 " =    1.748
peak=    3.125 closest distance to " O   HOH Z  87 " =    2.445
peak=    3.118 closest distance to " O   HOH Z  66 " =    2.142
peak=    3.115 closest distance to " O   HOH Z  47 " =    1.229
peak=    3.112 closest distance to " O   HOH Z 329 " =    3.507
peak=    3.110 closest distance to " CA  GLN A 223 " =    0.900
peak=    3.109 closest distance to " O   HOH Z 353 " =    2.804
peak=    3.106 closest distance to " CD  LYS A 119 " =    1.402
peak=    3.105 closest distance to " OG BSER A  99 " =    2.213
peak=    3.104 closest distance to " CB  ALA A  71 " =    1.248
peak=    3.089 closest distance to " C   GLY A  80 " =    1.124
peak=    3.086 closest distance to " CG2 ILE A 120 " =    1.052
peak=    3.085 closest distance to " CA  MET A 105 " =    1.095
peak=    3.075 closest distance to " O   HOH Z   4 " =    1.889
peak=    3.067 closest distance to " O   HOH Z 171 " =    3.870
peak=    3.062 closest distance to " CG2 THR A  29 " =    1.537
peak=    3.052 closest distance to " O   HOH Z 106 " =    2.284
peak=    3.040 closest distance to " O   PHE A 155 " =    1.896
peak=    3.035 closest distance to " O   HOH Z  20 " =    1.971
peak=    3.026 closest distance to " O   HOH Z 359 " =    1.510

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.916 - 5.966
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 203
   mapped sites are within: 0.916 - 5.966

peak=   -4.773 closest distance to " O   HOH Z 266 " =    4.244
peak=   -4.669 closest distance to " CD  ARG A 156 " =    1.978
peak=   -4.296 closest distance to " O   VAL A  67 " =    2.761
peak=   -4.196 closest distance to " O   HOH Z 377 " =    2.072
peak=   -4.176 closest distance to " O   HOH Z 292 " =    4.547
peak=   -4.145 closest distance to " OXT GLY A 302 " =    2.923
peak=   -4.125 closest distance to " O   HOH Z  10 " =    1.586
peak=   -4.058 closest distance to " O   HOH Z 353 " =    2.276
peak=   -4.033 closest distance to " O   HOH Z  52 " =    1.568
peak=   -4.033 closest distance to " N   ALA A  43 " =    2.608
peak=   -4.028 closest distance to " O   PRO A 163 " =    2.119
peak=   -4.027 closest distance to " O   HOH Z 407 " =    3.411
peak=   -3.980 closest distance to " CD1 LEU A 228 " =    2.327
peak=   -3.977 closest distance to " O   HOH Z  17 " =    1.320
peak=   -3.966 closest distance to " O   HOH Z  13 " =    1.563
peak=   -3.960 closest distance to " OG  SER A  97 " =    2.163
peak=   -3.929 closest distance to " O   HOH Z 283 " =    1.918
peak=   -3.910 closest distance to " O   SER A 210 " =    1.870
peak=   -3.906 closest distance to " O   HOH Z  11 " =    1.837
peak=   -3.899 closest distance to " O   ILE A 109 " =    2.671
peak=   -3.896 closest distance to " CD1 PHE A  59 " =    1.907
peak=   -3.883 closest distance to " CD2 LEU A 300 " =    2.906
peak=   -3.881 closest distance to " CD  ARG A 139 " =    1.689
peak=   -3.875 closest distance to " C   HIS A 108 " =    1.082
peak=   -3.865 closest distance to " NH2 ARG A  66 " =    1.746
peak=   -3.862 closest distance to " O   HOH Z  43 " =    1.601
peak=   -3.842 closest distance to " O   HOH Z 377 " =    1.194
peak=   -3.841 closest distance to " CG  MET A  93 " =    2.488
peak=   -3.819 closest distance to " CD2 LEU A 237 " =    2.648
peak=   -3.816 closest distance to " CG  GLU A  53 " =    1.433
peak=   -3.812 closest distance to " SG  CYS A 254 " =    3.434
peak=   -3.803 closest distance to " CB  TYR A  15 " =    2.238
peak=   -3.801 closest distance to " O   HOH Z 372 " =    2.560
peak=   -3.798 closest distance to " N   SER A 276 " =    1.415
peak=   -3.790 closest distance to " OG  SER A  62 " =    1.489
peak=   -3.786 closest distance to " CB  PRO A 243 " =    2.614
peak=   -3.780 closest distance to " CB  ALA A 291 " =    2.391
peak=   -3.776 closest distance to " O   HOH Z 234 " =    4.253
peak=   -3.772 closest distance to " OD1 ASN A 148 " =    1.671
peak=   -3.744 closest distance to " OG ASER A 134 " =    1.279
peak=   -3.743 closest distance to " O   HOH Z 290 " =    1.109
peak=   -3.737 closest distance to " O   HOH Z 231 " =    2.284
peak=   -3.731 closest distance to " OE1 GLN A 223 " =    2.046
peak=   -3.725 closest distance to " SG ACYS A 201 " =    2.193
peak=   -3.709 closest distance to " CE2 TYR A  30 " =    2.732
peak=   -3.708 closest distance to " O   PRO A 198 " =    1.366
peak=   -3.693 closest distance to " O   HOH Z 165 " =    2.050
peak=   -3.685 closest distance to " O   HOH Z 118 " =    3.029
peak=   -3.674 closest distance to " NH2 ARG A  66 " =    5.300
peak=   -3.668 closest distance to " CG1 VAL A 112 " =    2.592
peak=   -3.667 closest distance to " N   GLN A  58 " =    1.650
peak=   -3.666 closest distance to " O   VAL A 125 " =    2.138
peak=   -3.665 closest distance to " N   MET A 188 " =    1.882
peak=   -3.662 closest distance to " ND2 ASN A  45 " =    1.012
peak=   -3.659 closest distance to " OE2 GLU A   2 " =    1.646
peak=   -3.651 closest distance to " CA  ASP A 298 " =    1.054
peak=   -3.650 closest distance to " O   VAL A  67 " =    2.873
peak=   -3.646 closest distance to " O   HOH Z 388 " =    2.053
peak=   -3.627 closest distance to " O   HOH Z  19 " =    2.122
peak=   -3.624 closest distance to " CB  ASP A 132 " =    2.418
peak=   -3.623 closest distance to " CZ  PHE A  59 " =    1.851
peak=   -3.622 closest distance to " C   ALA A 158 " =    1.231
peak=   -3.622 closest distance to " O   ASN A 187 " =    1.485
peak=   -3.621 closest distance to " O   HOH Z 198 " =    2.535
peak=   -3.616 closest distance to " ND2 ASN A 187 " =    1.586
peak=   -3.615 closest distance to " CH2 TRP A 179 " =    1.205
peak=   -3.601 closest distance to " OG BSER A 134 " =    1.243
peak=   -3.597 closest distance to " O   HOH Z 196 " =    2.182
peak=   -3.596 closest distance to " O   LEU A 167 " =    1.589
peak=   -3.584 closest distance to " O   HOH Z  38 " =    1.372
peak=   -3.582 closest distance to " OG BSER A 134 " =    1.776
peak=   -3.581 closest distance to " O   ALA A 256 " =    1.526
peak=   -3.579 closest distance to " CG2 THR A   4 " =    1.934
peak=   -3.575 closest distance to " NH1 ARG A 195 " =    2.588
peak=   -3.566 closest distance to " CE  MET A  93 " =    1.258
peak=   -3.549 closest distance to " O   HOH Z  97 " =    1.711
peak=   -3.538 closest distance to " CB  ASN A  39 " =    2.276
peak=   -3.533 closest distance to " OD1 ASP A 191 " =    1.692
peak=   -3.530 closest distance to " CB  ALA A 248 " =    1.941
peak=   -3.525 closest distance to " O   HOH Z 242 " =    1.581
peak=   -3.514 closest distance to " CB  CYS A 254 " =    2.448
peak=   -3.511 closest distance to " CD2 PHE A  59 " =    2.463
peak=   -3.510 closest distance to " CD  LYS A 289 " =    2.427
peak=   -3.509 closest distance to " NE2 GLN A  88 " =    1.914
peak=   -3.502 closest distance to " C   ILE A 234 " =    1.364
peak=   -3.500 closest distance to " O   GLY A 196 " =    1.121
peak=   -3.493 closest distance to " O   HOH Z  93 " =    1.451
peak=   -3.472 closest distance to " CA  GLY A 133 " =    2.293
peak=   -3.470 closest distance to " ND2 ASN A 249 " =    2.148
peak=   -3.463 closest distance to " O   HOH Z 311 " =    3.586
peak=   -3.460 closest distance to " O   GLY A 118 " =    2.259
peak=   -3.456 closest distance to " CG  ASP A 231 " =    0.916
peak=   -3.445 closest distance to " O   HOH Z 399 " =    2.337
peak=   -3.437 closest distance to " C   ASN A 285 " =    2.502
peak=   -3.435 closest distance to " O   HOH Z 166 " =    1.598
peak=   -3.434 closest distance to " O   HOH Z 166 " =    1.690
peak=   -3.428 closest distance to " O   ALA A 160 " =    1.477
peak=   -3.428 closest distance to " O   HOH Z 275 " =    1.479
peak=   -3.420 closest distance to " O   TRP A  92 " =    1.810
peak=   -3.419 closest distance to " CE  MET A 105 " =    1.950
peak=   -3.407 closest distance to " O   HOH Z 385 " =    1.989
peak=   -3.398 closest distance to " CZ  TYR A 169 " =    1.809
peak=   -3.397 closest distance to " CB  PRO A 163 " =    2.727
peak=   -3.392 closest distance to " CB  ASP A 286 " =    2.157
peak=   -3.388 closest distance to " CA  GLY A 203 " =    2.168
peak=   -3.374 closest distance to " O   HOH Z  15 " =    1.530
peak=   -3.373 closest distance to " O   VAL A 174 " =    2.156
peak=   -3.370 closest distance to " CD2 TYR A 293 " =    2.048
peak=   -3.368 closest distance to " CD  ARG A 195 " =    5.121
peak=   -3.366 closest distance to " O   HOH Z 266 " =    4.822
peak=   -3.362 closest distance to " CG  ARG A  66 " =    2.365
peak=   -3.358 closest distance to " O   HOH Z 151 " =    1.464
peak=   -3.352 closest distance to " NH2 ARG A  79 " =    1.882
peak=   -3.350 closest distance to " O   HOH Z 361 " =    3.386
peak=   -3.345 closest distance to " CB  SER A 245 " =    2.413
peak=   -3.342 closest distance to " CG  ASP A  50 " =    2.339
peak=   -3.341 closest distance to " CG  LEU A  83 " =    2.030
peak=   -3.338 closest distance to " OH  TYR A 169 " =    1.082
peak=   -3.332 closest distance to " OD1 ASN A 187 " =    1.726
peak=   -3.320 closest distance to " N   THR A 157 " =    1.678
peak=   -3.319 closest distance to " CB  LEU A 167 " =    2.196
peak=   -3.316 closest distance to " CG  PRO A 163 " =    2.572
peak=   -3.311 closest distance to " O   ASN A 301 " =    1.417
peak=   -3.311 closest distance to " NH2 ARG A 159 " =    2.410
peak=   -3.310 closest distance to " O   HOH Z  98 " =    2.086
peak=   -3.309 closest distance to " O   PHE A 218 " =    1.524
peak=   -3.308 closest distance to " CG2 THR A 221 " =    2.317
peak=   -3.307 closest distance to " CA  VAL A 232 " =    2.416
peak=   -3.306 closest distance to " O   HOH Z 102 " =    1.682
peak=   -3.304 closest distance to " O   HOH Z  90 " =    3.151
peak=   -3.300 closest distance to " OD2 ASP A  65 " =    1.695
peak=   -3.299 closest distance to " CG  GLN A  58 " =    1.215
peak=   -3.291 closest distance to " OG  SER A  26 " =    1.361
peak=   -3.289 closest distance to " CG  LYS A 119 " =    2.929
peak=   -3.284 closest distance to " OG BSER A 210 " =    2.223
peak=   -3.279 closest distance to " O   HOH Z 385 " =    3.812
peak=   -3.273 closest distance to " O   VAL A 189 " =    2.548
peak=   -3.267 closest distance to " O   HOH Z 435 " =    2.577
peak=   -3.264 closest distance to " CB  ALA A 291 " =    2.263
peak=   -3.264 closest distance to " OG  SER A  87 " =    1.481
peak=   -3.263 closest distance to " CB  TRP A  85 " =    2.425
peak=   -3.262 closest distance to " O   HOH Z 283 " =    5.966
peak=   -3.261 closest distance to " O   HOH Z  37 " =    1.856
peak=   -3.254 closest distance to " CD1 PHE A  16 " =    2.721
peak=   -3.253 closest distance to " O   HOH Z 396 " =    1.656
peak=   -3.251 closest distance to " CA  VAL A 197 " =    1.007
peak=   -3.251 closest distance to " CD1 LEU A 101 " =    2.665
peak=   -3.249 closest distance to " OD1 ASP A 171 " =    1.558
peak=   -3.248 closest distance to " C   LEU A 143 " =    1.209
peak=   -3.245 closest distance to " O   HOH Z 426 " =    1.643
peak=   -3.242 closest distance to " O   HOH Z 111 " =    1.455
peak=   -3.239 closest distance to " O   HOH Z 185 " =    2.342
peak=   -3.231 closest distance to " O   PRO A 198 " =    1.357
peak=   -3.223 closest distance to " O   HOH Z 265 " =    2.017
peak=   -3.222 closest distance to " CG2 VAL A 189 " =    2.164
peak=   -3.220 closest distance to " O   HOH Z   6 " =    1.837
peak=   -3.215 closest distance to " N   ALA A 226 " =    2.092
peak=   -3.214 closest distance to " CD1 TYR A 247 " =    2.229
peak=   -3.213 closest distance to " O   HOH Z  90 " =    1.952
peak=   -3.213 closest distance to " CB  SER A 258 " =    2.057
peak=   -3.212 closest distance to " O   PRO A 198 " =    1.734
peak=   -3.210 closest distance to " N   GLN A 122 " =    1.562
peak=   -3.208 closest distance to " O   HOH Z 393 " =    1.566
peak=   -3.205 closest distance to " OD2 ASP A 171 " =    1.783
peak=   -3.202 closest distance to " NE2 GLN A  58 " =    1.000
peak=   -3.201 closest distance to " O   HOH Z 418 " =    1.464
peak=   -3.194 closest distance to " O   HOH Z 427 " =    1.339
peak=   -3.192 closest distance to " O   HOH Z  91 " =    1.996
peak=   -3.188 closest distance to " O   HOH Z  76 " =    2.000
peak=   -3.188 closest distance to " CG2 ILE A 263 " =    2.311
peak=   -3.181 closest distance to " O   ALA A  34 " =    2.466
peak=   -3.181 closest distance to " CE3 TRP A  70 " =    1.695
peak=   -3.176 closest distance to " CE1 TYR A 169 " =    2.401
peak=   -3.176 closest distance to " CB  PHE A 208 " =    2.201
peak=   -3.176 closest distance to " CA  GLY A  98 " =    2.156
peak=   -3.172 closest distance to " CD2 LEU A 167 " =    1.724
peak=   -3.172 closest distance to " OD2 ASP A 171 " =    2.397
peak=   -3.167 closest distance to " O   HOH Z 414 " =    1.423
peak=   -3.167 closest distance to " O   HOH Z 252 " =    3.647
peak=   -3.166 closest distance to " CD2 LEU A 237 " =    2.599
peak=   -3.165 closest distance to " CG  TRP A 266 " =    1.679
peak=   -3.162 closest distance to " O   HOH Z  71 " =    1.456
peak=   -3.159 closest distance to " O   HOH Z 236 " =    1.347
peak=   -3.143 closest distance to " O   HOH Z 417 " =    2.627
peak=   -3.124 closest distance to " O   HOH Z 389 " =    1.786
peak=   -3.111 closest distance to " O   HOH Z 241 " =    1.349
peak=   -3.109 closest distance to " CD  PRO A 198 " =    1.538
peak=   -3.099 closest distance to " O   HOH Z 280 " =    2.321
peak=   -3.098 closest distance to " N   VAL A 189 " =    1.706
peak=   -3.096 closest distance to " O   HOH Z 207 " =    2.116
peak=   -3.081 closest distance to " OE1 GLN A 223 " =    2.216
peak=   -3.079 closest distance to " O   HOH Z 244 " =    1.673
peak=   -3.078 closest distance to " N   LEU A 261 " =    1.257
peak=   -3.070 closest distance to " CG  PHE A 283 " =    2.776
peak=   -3.067 closest distance to " CB  PHE A 192 " =    1.904
peak=   -3.061 closest distance to " O   HOH Z 211 " =    1.675
peak=   -3.056 closest distance to " O   HOH Z 252 " =    3.886
peak=   -3.043 closest distance to " CB  ALA A 114 " =    2.336
peak=   -3.039 closest distance to " O   HOH Z   1 " =    3.883
peak=   -3.036 closest distance to " CG  ASN A 301 " =    1.972
peak=   -3.033 closest distance to " O   HOH Z 423 " =    2.329
peak=   -3.027 closest distance to " O   HOH Z  98 " =    1.519

================= 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    :  0.4272 0.4240   6.229521e+00   6.222518e+00
   1_bss:  0.4179 0.4143   6.221207e+00   6.207174e+00
   1_xyz:  0.2753 0.3068   5.891719e+00   5.976510e+00
   1_adp:  0.2506 0.3136   5.838995e+00   5.994247e+00
   1_occ:  0.2502 0.3141   5.837748e+00   5.993367e+00
   2_bss:  0.2470 0.3110   5.833762e+00   5.989810e+00
   2_xyz:  0.1748 0.2185   5.512738e+00   5.710689e+00
   2_adp:  0.1578 0.2015   5.429339e+00   5.628515e+00
   2_occ:  0.1576 0.2016   5.428582e+00   5.627768e+00
   3_bss:  0.1576 0.2018   5.429120e+00   5.626832e+00
   3_xyz:  0.1306 0.1729   5.267043e+00   5.482161e+00
   3_adp:  0.1233 0.1686   5.230440e+00   5.457868e+00
   3_occ:  0.1232 0.1686   5.230196e+00   5.457753e+00
   4_bss:  0.1236 0.1691   5.232308e+00   5.459628e+00
   4_xyz:  0.1181 0.1642   5.194704e+00   5.427745e+00
   4_adp:  0.1169 0.1636   5.188146e+00   5.421535e+00
   4_occ:  0.1169 0.1636   5.188288e+00   5.421988e+00
   5_bss:  0.1169 0.1636   5.188309e+00   5.421992e+00
   5_xyz:  0.1094 0.1600   5.146984e+00   5.398532e+00
   5_adp:  0.1087 0.1597   5.143697e+00   5.396626e+00
   5_occ:  0.1087 0.1597   5.143868e+00   5.397099e+00
   5_bss:  0.1087 0.1596   5.144018e+00   5.397137e+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:  0.304  37.343  -1.994   2.303   1.472   0.000   0.000   0.000
   1_xyz:  0.304  37.343  -1.994   2.303   1.472   0.000   0.000   0.000
   1_adp:  0.304  37.343  -1.994   2.303   1.472   0.000   0.000   0.000
   1_occ:  0.304  37.343  -1.994   2.303   1.472   0.000   0.000   0.000
   2_bss:  0.326  59.078  -2.130  -0.132  -0.770  -0.000  -0.000  -0.000
   2_xyz:  0.326  59.078  -2.130  -0.132  -0.770  -0.000  -0.000  -0.000
   2_adp:  0.326  59.078  -2.130  -0.132  -0.770  -0.000  -0.000  -0.000
   2_occ:  0.326  59.078  -2.130  -0.132  -0.770  -0.000  -0.000  -0.000
   3_bss:  0.322  53.716  -2.351  -1.154  -1.556  -0.000  -0.000  -0.000
   3_xyz:  0.322  53.716  -2.351  -1.154  -1.556  -0.000  -0.000  -0.000
   3_adp:  0.322  53.716  -2.351  -1.154  -1.556  -0.000  -0.000  -0.000
   3_occ:  0.322  53.716  -2.351  -1.154  -1.556  -0.000  -0.000  -0.000
   4_bss:  0.321  56.452  -2.319  -1.582  -1.780  -0.000  -0.000  -0.000
   4_xyz:  0.321  56.452  -2.319  -1.582  -1.780  -0.000  -0.000  -0.000
   4_adp:  0.321  56.452  -2.319  -1.582  -1.780  -0.000  -0.000  -0.000
   4_occ:  0.321  56.452  -2.319  -1.582  -1.780  -0.000  -0.000  -0.000
   5_bss:  0.321  56.452  -2.179  -1.595  -1.709  -0.000  -0.000  -0.000
   5_xyz:  0.321  56.452  -2.179  -1.595  -1.709  -0.000  -0.000  -0.000
   5_adp:  0.321  56.452  -2.179  -1.595  -1.709  -0.000  -0.000  -0.000
   5_occ:  0.321  56.452  -2.179  -1.595  -1.709  -0.000  -0.000  -0.000
   5_bss:  0.321  54.181  -1.939  -1.448  -1.498  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.760 0.5107  0.6751    55880.894
   1_bss:  49.407 0.5255  0.7102    52078.599
   1_xyz:  31.873 0.7376  0.9504    25277.323
   1_adp:  32.878 0.7252  0.9372    26532.473
   1_occ:  32.839 0.7256  0.9374    26457.613
   2_bss:  32.545 0.7288  0.8918    26136.359
   2_xyz:  21.854 0.8423  0.9817    12593.391
   2_adp:  19.518 0.8661  0.9901    10638.750
   2_occ:  19.508 0.8662  0.9900    10624.123
   3_bss:  19.483 0.8665  0.9668    10605.036
   3_xyz:  16.213 0.8960  0.9819     7709.054
   3_adp:  15.657 0.9012  0.9787     7386.586
   3_occ:  15.651 0.9012  0.9787     7385.974
   4_bss:  15.694 0.9009  0.9717     7455.230
   4_xyz:  15.011 0.9065  0.9737     6924.602
   4_adp:  14.843 0.9081  0.9690     6853.468
   4_occ:  14.849 0.9080  0.9688     6858.096
   5_bss:  14.850 0.9080  0.9711     6858.964
   5_xyz:  14.415 0.9114  0.9735     6533.401
   5_adp:  14.349 0.9121  0.9681     6501.598
   5_occ:  14.355 0.9121  0.9680     6507.017
   5_bss:  14.358 0.9121  0.9734     6506.411
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.7613e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.7613e-01
   1_xyz:   1.436  0.011  0.087 15.819  0.005  4.118   1.1283e-01
   1_adp:   1.436  0.011  0.087 15.819  0.005  4.118   1.1283e-01
   1_occ:   1.436  0.011  0.087 15.819  0.005  4.118   1.1283e-01
   2_bss:   1.436  0.011  0.087 15.819  0.005  4.118   1.1283e-01
   2_xyz:   1.124  0.008  0.076 14.489  0.005  4.112   6.9046e-02
   2_adp:   1.124  0.008  0.076 14.489  0.005  4.112   6.9046e-02
   2_occ:   1.124  0.008  0.076 14.489  0.005  4.112   6.9046e-02
   3_bss:   1.124  0.008  0.076 14.489  0.005  4.112   6.9046e-02
   3_xyz:   1.010  0.007  0.071 14.488  0.004  4.118   5.9898e-02
   3_adp:   1.010  0.007  0.071 14.488  0.004  4.118   5.9898e-02
   3_occ:   1.010  0.007  0.071 14.488  0.004  4.118   5.9898e-02
   4_bss:   1.010  0.007  0.071 14.488  0.004  4.118   5.9898e-02
   4_xyz:   0.973  0.006  0.070 14.398  0.004  4.120   5.5222e-02
   4_adp:   0.973  0.006  0.070 14.398  0.004  4.120   5.5222e-02
   4_occ:   0.973  0.006  0.070 14.398  0.004  4.120   5.5222e-02
   5_bss:   0.973  0.006  0.070 14.398  0.004  4.120   5.5222e-02
   5_xyz:   1.172  0.010  0.084 14.880  0.005  4.124   7.8115e-02
   5_adp:   1.172  0.010  0.084 14.880  0.005  4.124   7.8115e-02
   5_occ:   1.172  0.010  0.084 14.880  0.005  4.124   7.8115e-02
   5_bss:   1.172  0.010  0.084 14.880  0.005  4.124   7.8115e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.679   2.4175e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.679   2.4175e-01
   1_xyz:   9.067  0.092  0.360 86.350  0.031  2.051   1.0565e-01
   1_adp:   9.067  0.092  0.360 86.350  0.031  2.051   1.0565e-01
   1_occ:   9.067  0.092  0.360 86.350  0.031  2.051   1.0565e-01
   2_bss:   9.067  0.092  0.360 86.350  0.031  2.051   1.0565e-01
   2_xyz:   7.041  0.053  0.271 88.735  0.045  2.317   5.9808e-02
   2_adp:   7.041  0.053  0.271 88.735  0.045  2.317   5.9808e-02
   2_occ:   7.041  0.053  0.271 88.735  0.045  2.317   5.9808e-02
   3_bss:   7.041  0.053  0.271 88.735  0.045  2.317   5.9808e-02
   3_xyz:   7.077  0.048  0.239 80.527  0.035  2.309   4.7259e-02
   3_adp:   7.077  0.048  0.239 80.527  0.035  2.309   4.7259e-02
   3_occ:   7.077  0.048  0.239 80.527  0.035  2.309   4.7259e-02
   4_bss:   7.077  0.048  0.239 80.527  0.035  2.309   4.7259e-02
   4_xyz:   7.122  0.035  0.229 83.138  0.032  2.382   3.5914e-02
   4_adp:   7.122  0.035  0.229 83.138  0.032  2.382   3.5914e-02
   4_occ:   7.122  0.035  0.229 83.138  0.032  2.382   3.5914e-02
   5_bss:   7.122  0.035  0.229 83.138  0.032  2.382   3.5914e-02
   5_xyz:   8.015  0.052  0.261 81.337  0.035  2.240   6.1310e-02
   5_adp:   8.015  0.052  0.261 81.337  0.035  2.240   6.1310e-02
   5_occ:   8.015  0.052  0.261 81.337  0.035  2.240   6.1310e-02
   5_bss:   8.015  0.052  0.261 81.337  0.035  2.240   6.1310e-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:  88.22   0.00  18.10  88.22   0.00  13.81  87.65   4.61  41.43
   1_occ:  88.22   0.00  18.10  88.22   0.00  13.81  87.65   4.61  41.43
   2_bss:  88.22   0.00  18.10  88.22   0.00  13.81  87.65   4.61  41.43
   2_xyz:  88.22   0.00  18.10  88.22   0.00  13.81  87.65   4.61  41.43
   2_adp:  84.40   1.16  17.81  84.40   1.16  13.32  84.03   5.50  42.26
   2_occ:  84.40   1.16  17.81  84.40   1.16  13.32  84.03   5.50  42.26
   3_bss:  84.40   1.16  17.81  84.40   1.16  13.32  84.03   5.50  42.26
   3_xyz:  84.40   1.16  17.81  84.40   1.16  13.32  84.03   5.50  42.26
   3_adp: 101.35   0.00  17.91 101.35   0.00  13.15  89.74   5.49  43.84
   3_occ: 101.35   0.00  17.91 101.35   0.00  13.15  89.74   5.49  43.84
   4_bss: 101.35   0.00  17.91 101.35   0.00  13.15  89.74   5.49  43.84
   4_xyz: 101.35   0.00  17.91 101.35   0.00  13.15  89.74   5.49  43.84
   4_adp: 107.16   1.62  17.50 107.16   1.62  12.94  88.93   5.28  42.31
   4_occ: 107.16   1.62  17.50 107.16   1.62  12.94  88.93   5.28  42.31
   5_bss: 107.16   1.62  17.50 107.16   1.62  12.94  88.93   5.28  42.31
   5_xyz: 107.16   1.62  17.50 107.16   1.62  12.94  88.93   5.28  42.31
   5_adp: 112.21   1.16  17.18 112.21   1.16  12.74  90.41   5.60  41.32
   5_occ: 112.21   1.16  17.18 112.21   1.16  12.74  90.41   5.60  41.32
   5_bss: 112.17   1.12  17.14 112.17   1.12  12.70  90.37   5.56  41.28
------------------------------------------------------------------------
 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:    1.977    0.034    0.436
   1_adp:    1.977    0.034    0.436
   1_occ:    1.977    0.034    0.436
   2_bss:    1.977    0.034    0.436
   2_xyz:    1.243    0.019    0.548
   2_adp:    1.243    0.019    0.548
   2_occ:    1.243    0.019    0.548
   3_bss:    1.243    0.019    0.548
   3_xyz:    1.298    0.037    0.623
   3_adp:    1.298    0.037    0.623
   3_occ:    1.298    0.037    0.623
   4_bss:    1.298    0.037    0.623
   4_xyz:    1.351    0.054    0.641
   4_adp:    1.351    0.054    0.641
   4_occ:    1.351    0.054    0.641
   5_bss:    1.351    0.054    0.641
   5_xyz:    1.488    0.062    0.661
   5_adp:    1.488    0.062    0.661
   5_occ:    1.488    0.062    0.661
   5_bss:    1.488    0.062    0.661
------------------------------------------------------------------------

CPU time actual refinement: 369.50


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_936/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_936/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_936/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_936/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_936/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 369.34 
  Macro-tasks:
    bulk solvent and scale       = 38.78  
    individual site refinement   = 159.48 
    weights calculation          = 30.51  
    collect and process          = 6.63   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 235.50 
  Micro-tasks:
    mask                            = 1.85   
    f_calc                          = 125.18 
    alpha_beta                      = 8.64   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 132.18 
    fmodel                         = 6.56   
    r_factors                      = 0.17   
    phase_errors                   = 10.80  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 286.84 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 5.173 micro seconds
Total CPU time: 6.38 minutes
from_scatterers_fft:    651 calls, 124.81 s
gradients_fft:          596 calls, 118.38 s

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

# Date 2008-01-16 Time 06:01:30 PST -0800 (1200492090.29 s)
Start R-work = 0.4272, R-free = 0.4240 (no bulk solvent and anisotropic scale)
Final R-work = 0.1305, R-free = 0.1780 (no bulk solvent and anisotropic scale)

Start R-work = 0.4179, R-free = 0.4143
Final R-work = 0.1087, R-free = 0.1596