# Date 2008-01-16 Time 03:56:26 PST -0800 (1200484586.84 s)
#phil __OFF__

Command line arguments: "../109.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18207
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 109

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.4938, 47.8686, 88.5498, 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: 3.25, 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: (68.4938, 47.8686, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0111 1.95105
Completeness in resolution range: 0.898867
Completeness with d_max=infinity: 0.896235

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0111
                             d_min =   1.9511

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 47.8686, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0111 1.95105
Completeness in resolution range: 0.898867
Completeness with d_max=infinity: 0.896235

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0116 -  4.1761 [2289/2317]  2057   232  10.1%
  bin  2:  4.1761 -  3.3265 [2200/2223]  1978   222  10.1%
  bin  3:  3.3265 -  2.9095 [2163/2188]  1955   208   9.6%
  bin  4:  2.9095 -  2.6451 [2135/2162]  1918   217  10.2%
  bin  5:  2.6451 -  2.4564 [2123/2156]  1902   221  10.4%
  bin  6:  2.4564 -  2.3121 [2139/2167]  1934   205   9.6%
  bin  7:  2.3121 -  2.1967 [2098/2134]  1891   207   9.9%
  bin  8:  2.1967 -  2.1013 [2104/2146]  1892   212  10.1%
  bin  9:  2.1013 -  2.0206 [1878/2158]  1695   183   9.7%
  bin 10:  2.0206 -  1.9511 [ 460/2142]   408    52  11.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_109/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:
        1.01 -     1.79: 15
        1.79 -     2.57: 68
        2.57 -     3.34: 3979
        3.34 -     4.12: 9353
        4.12 -     4.90: 14793
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.011 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.046 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  57 " - " O   HOH Z 104 "  1.209 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.275 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.296 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28203 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_109/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_109/model_refine_001.geo

CPU time processing inputs: 9.29


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.49375 47.8686 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5048   r_free= 0.5119   ksol= 0.00   Bsol= 0.00   scale= 0.857    |
|                                                                             |
| 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:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.306450                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0116 -  4.6584 0.99   1483  162 0.4033 0.4201      6.6236      6.6412|
|  2:  4.6584 -  3.7160 0.99   1430  158 0.4552 0.4904      6.8633      6.9177|
|  3:  3.7160 -  3.2517 0.99   1401  163 0.4950 0.4845      6.7062      6.7095|
|  4:  3.2517 -  2.9569 0.98   1387  145 0.5074 0.4793       6.525      6.5126|
|  5:  2.9569 -  2.7463 0.99   1392  161 0.5316 0.5577       6.372      6.4046|
|  6:  2.7463 -  2.5853 0.99   1378  154 0.5390 0.5334      6.2799      6.1867|
|  7:  2.5853 -  2.4564 0.98   1339  157 0.5403 0.4881      6.2326       6.172|
|  8:  2.4564 -  2.3499 0.98   1388  150 0.5504 0.5636      6.1664      6.2184|
|  9:  2.3499 -  2.2597 0.99   1348  136 0.5623 0.5761      6.1233      6.1724|
| 10:  2.2597 -  2.1820 0.99   1378  152 0.5387 0.5456      6.0775      6.0937|
| 11:  2.1820 -  2.1139 0.97   1344  154 0.5491 0.5491      6.0017      6.0214|
| 12:  2.1139 -  2.0537 0.98   1346  156 0.5461 0.5779       5.946      5.9175|
| 13:  2.0537 -  1.9997 0.60    818   86 0.5254 0.5769      5.8733      5.8418|
| 14:  1.9997 -  1.9511 0.14    198   25 0.4864 0.4603      5.9046      5.7282|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0116 -  4.6584  1483   162  0.66  37.57   0.80     0.68      82708.13|
|  2:  4.6584 -  3.7160  1430   158  0.63  41.08   0.88     0.73     134927.55|
|  3:  3.7160 -  3.2517  1401   163  0.49  52.83   0.86     0.67     144776.11|
|  4:  3.2517 -  2.9569  1387   145  0.37  61.64   0.86     0.55     124985.24|
|  5:  2.9569 -  2.7463  1392   161  0.30  67.65   0.84     0.45      97198.19|
|  6:  2.7463 -  2.5853  1378   154  0.27  70.03   0.86     0.40      82593.75|
|  7:  2.5853 -  2.4564  1339   157  0.25  71.45   0.86     0.35      74696.63|
|  8:  2.4564 -  2.3499  1388   150  0.21  74.44   0.87     0.32      68215.85|
|  9:  2.3499 -  2.2597  1348   136  0.18  76.27   0.87     0.30      66647.12|
| 10:  2.2597 -  2.1820  1378   152  0.20  75.11   0.89     0.30      56991.51|
| 11:  2.1820 -  2.1139  1344   154  0.17  77.47   0.87     0.28      55050.45|
| 12:  2.1139 -  2.0537  1346   156  0.13  80.64   0.92     0.21      49922.38|
| 13:  2.0537 -  1.9997   818    86  0.06  85.28   0.92     0.11      46127.67|
| 14:  1.9997 -  1.9511   198    25  0.09  83.32   0.98     0.11      35223.50|
|alpha:            min =        0.11 max =            0.73 mean =         0.42|
|beta:             min =    35223.50 max =       144776.11 mean =     84507.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.31|
|phase err.(work): min =        0.00 max =           90.00 mean =        66.30|
|phase err.(test): min =        0.00 max =           89.98 mean =        66.37|
|-----------------------------------------------------------------------------|

============================== 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 = 26.325367             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.319   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.042499              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.905   (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 |  1.011 -  1.400:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.400 -  1.789:       10 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.789 -  2.178:       19 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.178 -  2.567:       49 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.567 -  2.956:     1640 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.956 -  3.345:     2339 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.345 -  3.733:     3808 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.733 -  4.122:     5545 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.122 -  4.511:     6511 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.511 -  4.900:     8282 |
|-----------------------------------------------------------------------------|
|-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 |        0.243 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.011 |       1.342 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5048   r_free= 0.5119   ksol= 0.00   Bsol= 0.00   scale= 0.857    |
|                                                                             |
| 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:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.306450                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4994   r_free= 0.5021   ksol= 0.30   Bsol= 28.17   scale= 0.901   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,1.77,2.76,0.00,0.00,0.00); trace/3= 0.95                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.238030                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 20.983677             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.874   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.333938              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.339   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4994      final r-factor (work) = 0.4027          |
| start r-factor (free) = 0.5021      final r-factor (free) = 0.4351          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 66.3672 = 20.98 * 0.50 * 6.3025 + 1.00 * 0.2426                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 64.7737 = 20.98 * 0.50 * 6.1558 + 1.00 * 0.1882                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4027      final r-factor (work) = 0.3562          |
| start r-factor (free) = 0.4351      final r-factor (free) = 0.4414          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.3733 = 2.33 * 1.00 * 6.1558 + 1.00 * 0.0061                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.3232 = 2.33 * 1.00 * 6.1244 + 1.00 * 0.0293                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    119.34  21.27    None  None   None       |
|    all(noH): 2823   0      0.00    119.34  21.27    None  None   None       |
|    Sol.    : 438    0      0.00    119.34  41.37    None  None   None       |
|    Mac.    : 2385   0      0.00    106.94  17.57    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.934: 1023   |   5:    59.669 -  71.603:   71        |
|      1:    11.934 -  23.868:  815   |   6:    71.603 -  83.536:   36        |
|      2:    23.868 -  35.801:  513   |   7:    83.536 -  95.470:   14        |
|      3:    35.801 -  47.735:  213   |   8:    95.470 - 107.404:    5        |
|      4:    47.735 -  59.669:  132   |   9:   107.404 - 119.338:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3562 r_free = 0.4414             target_work(ml) = 6.129         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3559 r_free = 0.4416             target_work(ml) = 6.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3559   r_free= 0.4416   ksol= 0.30   Bsol= 28.17   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,1.77,2.76,0.00,0.00,0.00); trace/3= 0.95                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.128807                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3551   r_free= 0.4399   ksol= 0.29   Bsol= 28.17   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.11,1.29,2.13,0.00,0.00,0.00); trace/3= 0.77                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.126376                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.819611             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.071   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.710070              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.479  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3551      final r-factor (work) = 0.2931          |
| start r-factor (free) = 0.4399      final r-factor (free) = 0.3612          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.3897 = 11.82 * 0.50 * 6.1256 + 1.00 * 0.1883                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.9542 = 11.82 * 0.50 * 6.0667 + 1.00 * 0.1014                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2931      final r-factor (work) = 0.2730          |
| start r-factor (free) = 0.3612      final r-factor (free) = 0.3404          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3371 = 0.71 * 1.00 * 6.0667 + 1.00 * 0.0294                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2368 = 0.71 * 1.00 * 5.9410 + 1.00 * 0.0182                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.27  19.57    None  None   None       |
|    all(noH): 2823   0      0.00    114.27  19.57    None  None   None       |
|    Sol.    : 438    0      0.00    114.27  40.42    None  None   None       |
|    Mac.    : 2385   0      0.00    95.74   15.74    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:     0.000 -  11.427: 1076   |   5:    57.136 -  68.564:   61        |
|      1:    11.427 -  22.855:  911   |   6:    68.564 -  79.991:   34        |
|      2:    22.855 -  34.282:  383   |   7:    79.991 -  91.418:   11        |
|      3:    34.282 -  45.709:  237   |   8:    91.418 - 102.846:    3        |
|      4:    45.709 -  57.136:  106   |   9:   102.846 - 114.273:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2730 r_free = 0.3404             target_work(ml) = 5.917         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2730 r_free = 0.3404             target_work(ml) = 5.917         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2730   r_free= 0.3404   ksol= 0.29   Bsol= 28.17   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.11,1.29,2.13,0.00,0.00,0.00); trace/3= 0.77                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.917209                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2725   r_free= 0.3392   ksol= 0.32   Bsol= 57.65   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,0.26,1.03,0.00,0.00,0.00); trace/3= -0.22                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.916244                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.389430              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.283   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.486127              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 102.980  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2725      final r-factor (work) = 0.2212          |
| start r-factor (free) = 0.3392      final r-factor (free) = 0.2804          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.1407 = 4.39 * 0.50 * 5.9412 + 1.00 * 0.1014                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.8953 = 4.39 * 0.50 * 5.8428 + 1.00 * 0.0721                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2212      final r-factor (work) = 0.2044          |
| start r-factor (free) = 0.2804      final r-factor (free) = 0.2717          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.6988 = 1.49 * 1.00 * 5.8428 + 1.00 * 0.0157                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4891 = 1.49 * 1.00 * 5.7001 + 1.00 * 0.0180                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.33  20.15    None  None   None       |
|    all(noH): 2823   0      0.00    111.33  20.15    None  None   None       |
|    Sol.    : 438    0      3.61    111.33  48.16    None  None   None       |
|    Mac.    : 2385   0      0.00    100.35  15.01    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.133: 1156   |   5:    55.667 -  66.800:   93        |
|      1:    11.133 -  22.267:  886   |   6:    66.800 -  77.934:   60        |
|      2:    22.267 -  33.400:  291   |   7:    77.934 -  89.067:   34        |
|      3:    33.400 -  44.534:  160   |   8:    89.067 - 100.201:   17        |
|      4:    44.534 -  55.667:  120   |   9:   100.201 - 111.334:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2044 r_free = 0.2717             target_work(ml) = 5.684         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2043 r_free = 0.2715             target_work(ml) = 5.684         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2043   r_free= 0.2715   ksol= 0.32   Bsol= 57.65   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,0.26,1.03,0.00,0.00,0.00); trace/3= -0.22                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.684143                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2044   r_free= 0.2718   ksol= 0.33   Bsol= 66.72   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,-0.67,0.11,-0.00,0.00,0.00); trace/3= -1.11                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.683984                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.248109              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.148   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.340014              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.879  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2044      final r-factor (work) = 0.1657          |
| start r-factor (free) = 0.2718      final r-factor (free) = 0.2267          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1869 = 4.25 * 0.50 * 5.7036 + 1.00 * 0.0721                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9781 = 4.25 * 0.50 * 5.6061 + 1.00 * 0.0705                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1657      final r-factor (work) = 0.1558          |
| start r-factor (free) = 0.2267      final r-factor (free) = 0.2103          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9239 = 0.34 * 1.00 * 5.6061 + 1.00 * 0.0178                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8740 = 0.34 * 1.00 * 5.4768 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.62  18.72    None  None   None       |
|    all(noH): 2823   0      0.00    105.62  18.72    None  None   None       |
|    Sol.    : 438    0      5.41    105.62  45.97    None  None   None       |
|    Mac.    : 2385   0      0.00    98.86   13.72    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 -  10.562: 1112   |   5:    52.810 -  63.372:   96        |
|      1:    10.562 -  21.124: 1052   |   6:    63.372 -  73.934:   57        |
|      2:    21.124 -  31.686:  207   |   7:    73.934 -  84.496:   26        |
|      3:    31.686 -  42.248:  139   |   8:    84.496 -  95.058:   15        |
|      4:    42.248 -  52.810:  112   |   9:    95.058 - 105.620:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1558 r_free = 0.2103             target_work(ml) = 5.440         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1556 r_free = 0.2099             target_work(ml) = 5.439         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1556   r_free= 0.2099   ksol= 0.33   Bsol= 66.72   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,-0.67,0.11,-0.00,0.00,0.00); trace/3= -1.11                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.438877                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1558   r_free= 0.2097   ksol= 0.33   Bsol= 66.72   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.22,-1.35,-0.35,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.439772                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.187088              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.903  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.568071              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.451  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1558      final r-factor (work) = 0.1421          |
| start r-factor (free) = 0.2097      final r-factor (free) = 0.1898          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0616 = 2.19 * 0.50 * 5.4786 + 1.00 * 0.0705                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9639 = 2.19 * 0.50 * 5.4021 + 1.00 * 0.0564                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1421      final r-factor (work) = 0.1378          |
| start r-factor (free) = 0.1898      final r-factor (free) = 0.1878          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0805 = 0.57 * 1.00 * 5.4021 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0471 = 0.57 * 1.00 * 5.3425 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.63    104.34  18.53    None  None   None       |
|    all(noH): 2823   0      0.63    104.34  18.53    None  None   None       |
|    Sol.    : 438    0      5.55    101.92  46.27    None  None   None       |
|    Mac.    : 2385   0      0.63    104.34  13.44    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.626 -  10.998: 1216   |   5:    52.485 -  62.857:   89        |
|      1:    10.998 -  21.370:  984   |   6:    62.857 -  73.229:   61        |
|      2:    21.370 -  31.742:  197   |   7:    73.229 -  83.600:   37        |
|      3:    31.742 -  42.113:  115   |   8:    83.600 -  93.972:   13        |
|      4:    42.113 -  52.485:  102   |   9:    93.972 - 104.344:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1378 r_free = 0.1878             target_work(ml) = 5.334         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1377 r_free = 0.1878             target_work(ml) = 5.334         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1377   r_free= 0.1878   ksol= 0.33   Bsol= 66.72   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.22,-1.35,-0.35,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.333896                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0116 -  4.6584 0.99   1483  162 0.1058 0.1473      5.4695      5.6909|
|  2:  4.6584 -  3.7160 0.99   1430  158 0.0946 0.1120      5.5317      5.6909|
|  3:  3.7160 -  3.2517 0.99   1401  163 0.1323 0.1734      5.6474      5.9369|
|  4:  3.2517 -  2.9569 0.98   1387  145 0.1601 0.2106       5.629      5.8404|
|  5:  2.9569 -  2.7463 0.99   1392  161 0.1719 0.2064      5.5506      5.7182|
|  6:  2.7463 -  2.5853 0.99   1378  154 0.1574 0.2455      5.4026      5.6092|
|  7:  2.5853 -  2.4564 0.98   1339  157 0.1542 0.1938      5.3467      5.4989|
|  8:  2.4564 -  2.3499 0.98   1388  150 0.1525 0.2369      5.2818      5.5719|
|  9:  2.3499 -  2.2597 0.99   1348  136 0.1425 0.2014      5.1947      5.3728|
| 10:  2.2597 -  2.1820 0.99   1378  152 0.1448 0.2143      5.1307      5.3334|
| 11:  2.1820 -  2.1139 0.97   1344  154 0.1440 0.2134      5.0763      5.4377|
| 12:  2.1139 -  2.0537 0.98   1346  156 0.1420 0.1835      5.0131       5.208|
| 13:  2.0537 -  1.9997 0.60    818   86 0.1322 0.2062      4.9203        5.15|
| 14:  1.9997 -  1.9511 0.14    198   25 0.1297 0.1940      4.8817      5.0161|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0116 -  4.6584  1483   162  0.93  10.50   0.96     0.93       8863.59|
|  2:  4.6584 -  3.7160  1430   158  0.94   9.36   1.02     1.00      11175.83|
|  3:  3.7160 -  3.2517  1401   163  0.92  13.89   1.03     1.03      13912.80|
|  4:  3.2517 -  2.9569  1387   145  0.88  18.66   1.02     1.00      14803.89|
|  5:  2.9569 -  2.7463  1392   161  0.86  21.01   1.01     1.00      13730.75|
|  6:  2.7463 -  2.5853  1378   154  0.86  20.34   0.98     0.94      10228.43|
|  7:  2.5853 -  2.4564  1339   157  0.86  20.34   1.00     0.97       9652.46|
|  8:  2.4564 -  2.3499  1388   150  0.86  20.88   1.01     0.94       8414.08|
|  9:  2.3499 -  2.2597  1348   136  0.86  20.32   0.99     0.93       7155.10|
| 10:  2.2597 -  2.1820  1378   152  0.87  19.73   1.00     0.96       6332.21|
| 11:  2.1820 -  2.1139  1344   154  0.87  20.07   0.99     0.94       5810.10|
| 12:  2.1139 -  2.0537  1346   156  0.87  19.81   0.99     0.99       5230.89|
| 13:  2.0537 -  1.9997   818    86  0.87  19.74   0.99     0.97       4486.45|
| 14:  1.9997 -  1.9511   198    25  0.89  16.74   0.96     0.91       3546.57|
|alpha:            min =        0.91 max =            1.03 mean =         0.97|
|beta:             min =     3546.57 max =        14803.89 mean =      9333.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.95 mean =        17.89|
|phase err.(test): min =        0.00 max =           89.66 mean =        17.33|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1377   r_free= 0.1878   ksol= 0.33   Bsol= 66.70   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.30,-1.56,-0.48,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.333892                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1377   r_free= 0.1878   ksol= 0.33   Bsol= 66.70   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.30,-1.56,-0.48,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.333892                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0116 -  4.6584 0.99   1483  162 0.1058 0.1472      5.4688      5.6901|
|  2:  4.6584 -  3.7160 0.99   1430  158 0.0945 0.1120      5.5315      5.6909|
|  3:  3.7160 -  3.2517 0.99   1401  163 0.1324 0.1735      5.6478      5.9371|
|  4:  3.2517 -  2.9569 0.98   1387  145 0.1601 0.2108      5.6291      5.8408|
|  5:  2.9569 -  2.7463 0.99   1392  161 0.1719 0.2062      5.5507      5.7178|
|  6:  2.7463 -  2.5853 0.99   1378  154 0.1573 0.2455      5.4023      5.6088|
|  7:  2.5853 -  2.4564 0.98   1339  157 0.1543 0.1939      5.3467      5.4992|
|  8:  2.4564 -  2.3499 0.98   1388  150 0.1525 0.2368      5.2817      5.5725|
|  9:  2.3499 -  2.2597 0.99   1348  136 0.1425 0.2016      5.1945      5.3729|
| 10:  2.2597 -  2.1820 0.99   1378  152 0.1447 0.2144      5.1308       5.334|
| 11:  2.1820 -  2.1139 0.97   1344  154 0.1439 0.2133      5.0762      5.4374|
| 12:  2.1139 -  2.0537 0.98   1346  156 0.1421 0.1835      5.0138      5.2086|
| 13:  2.0537 -  1.9997 0.60    818   86 0.1324 0.2062      4.9206      5.1493|
| 14:  1.9997 -  1.9511 0.14    198   25 0.1296 0.1939      4.8822      5.0177|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0116 -  4.6584  1483   162  0.93  10.49   0.96     0.93       8854.30|
|  2:  4.6584 -  3.7160  1430   158  0.94   9.35   1.01     1.00      11170.20|
|  3:  3.7160 -  3.2517  1401   163  0.92  13.89   1.03     1.02      13920.86|
|  4:  3.2517 -  2.9569  1387   145  0.88  18.66   1.01     0.99      14809.94|
|  5:  2.9569 -  2.7463  1392   161  0.86  21.00   1.00     0.99      13729.72|
|  6:  2.7463 -  2.5853  1378   154  0.86  20.34   0.98     0.93      10230.09|
|  7:  2.5853 -  2.4564  1339   157  0.86  20.34   0.99     0.96       9651.51|
|  8:  2.4564 -  2.3499  1388   150  0.86  20.88   1.00     0.94       8418.18|
|  9:  2.3499 -  2.2597  1348   136  0.86  20.33   0.99     0.92       7159.89|
| 10:  2.2597 -  2.1820  1378   152  0.87  19.73   0.99     0.95       6337.06|
| 11:  2.1820 -  2.1139  1344   154  0.87  20.07   0.98     0.93       5810.24|
| 12:  2.1139 -  2.0537  1346   156  0.87  19.81   0.98     0.98       5234.20|
| 13:  2.0537 -  1.9997   818    86  0.87  19.74   0.98     0.97       4485.33|
| 14:  1.9997 -  1.9511   198    25  0.89  16.75   0.96     0.90       3545.92|
|alpha:            min =        0.90 max =            1.02 mean =         0.96|
|beta:             min =     3545.92 max =        14809.94 mean =      9334.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.95 mean =        17.89|
|phase err.(test): min =        0.00 max =           89.66 mean =        17.33|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.61    104.32  18.51    None  None   None       |
|    all(noH): 2823   0      0.61    104.32  18.51    None  None   None       |
|    Sol.    : 438    0      5.53    101.90  46.25    None  None   None       |
|    Mac.    : 2385   0      0.61    104.32  13.42    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:     0.606 -  10.977: 1216   |   5:    52.465 -  62.836:   89        |
|      1:    10.977 -  21.349:  984   |   6:    62.836 -  73.208:   61        |
|      2:    21.349 -  31.721:  197   |   7:    73.208 -  83.580:   37        |
|      3:    31.721 -  42.093:  115   |   8:    83.580 -  93.952:   13        |
|      4:    42.093 -  52.465:  102   |   9:    93.952 - 104.323:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 330         
Filter by distance & map next to the model:
   mapped sites are within: 0.675 - 5.011
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 327 from: 330
   mapped sites are within: 0.729 - 5.011

peak=   10.875 closest distance to " O  BHOH Z  74 " =    1.508
peak=    9.305 closest distance to " O   HOH Z 203 " =    1.411
peak=    7.085 closest distance to " O   HOH Z 255 " =    1.436
peak=    6.668 closest distance to " O   HOH Z 117 " =    1.779
peak=    5.671 closest distance to " CZ3 TRP A 266 " =    1.120
peak=    5.415 closest distance to " O   HOH Z 248 " =    1.507
peak=    5.389 closest distance to " O   HOH Z 124 " =    1.348
peak=    5.356 closest distance to " O   HOH Z 404 " =    1.424
peak=    5.324 closest distance to " O   HOH Z  37 " =    1.145
peak=    5.150 closest distance to " CD2 TRP A 179 " =    1.344
peak=    5.090 closest distance to " O   HOH Z 264 " =    1.213
peak=    4.967 closest distance to " O   HOH Z 210 " =    1.374
peak=    4.929 closest distance to " O   HOH Z  97 " =    1.619
peak=    4.918 closest distance to " O   HOH Z 188 " =    2.653
peak=    4.871 closest distance to " O   HOH Z 264 " =    2.080
peak=    4.847 closest distance to " O   HOH Z  70 " =    1.171
peak=    4.826 closest distance to " O   GLN A  11 " =    0.969
peak=    4.812 closest distance to " O   HOH Z 112 " =    1.404
peak=    4.772 closest distance to " O   HOH Z 394 " =    1.788
peak=    4.735 closest distance to " O   HOH Z  49 " =    1.749
peak=    4.702 closest distance to " O   HOH Z 403 " =    2.242
peak=    4.685 closest distance to " O  BHOH Z 338 " =    1.460
peak=    4.654 closest distance to " O   HOH Z 102 " =    1.458
peak=    4.613 closest distance to " O   HOH Z 412 " =    3.722
peak=    4.592 closest distance to " CA  TYR A  30 " =    0.995
peak=    4.546 closest distance to " O   HOH Z 126 " =    1.610
peak=    4.535 closest distance to " CG  PRO A  54 " =    1.451
peak=    4.512 closest distance to " CA  ALA A 100 " =    1.113
peak=    4.488 closest distance to " O   HOH Z 277 " =    1.444
peak=    4.447 closest distance to " CB  ARG A 275 " =    0.871
peak=    4.442 closest distance to " O   HOH Z 113 " =    1.876
peak=    4.411 closest distance to " O   HOH Z 186 " =    1.834
peak=    4.366 closest distance to " O   HOH Z 402 " =    1.595
peak=    4.363 closest distance to " O   HOH Z 184 " =    1.516
peak=    4.340 closest distance to " CB  GLN A 223 " =    1.411
peak=    4.322 closest distance to " CA  ARG A  36 " =    1.089
peak=    4.297 closest distance to " O   GLY A  23 " =    2.812
peak=    4.290 closest distance to " O   HOH Z 287 " =    1.453
peak=    4.282 closest distance to " CB  SER A  62 " =    1.096
peak=    4.261 closest distance to " NH1AARG A 275 " =    1.445
peak=    4.231 closest distance to " O   HOH Z 417 " =    1.811
peak=    4.222 closest distance to " O   HOH Z 425 " =    1.517
peak=    4.216 closest distance to " CG  PRO A  90 " =    1.362
peak=    4.211 closest distance to " CZ  PHE A 218 " =    1.185
peak=    4.193 closest distance to " O   HOH Z 188 " =    1.554
peak=    4.164 closest distance to " O   HOH Z 193 " =    1.532
peak=    4.160 closest distance to " O   HOH Z 142 " =    2.567
peak=    4.157 closest distance to " O   HOH Z  67 " =    1.307
peak=    4.136 closest distance to " CA  GLN A  58 " =    0.811
peak=    4.129 closest distance to " O   HOH Z 414 " =    1.761
peak=    4.126 closest distance to " O   HOH Z 128 " =    1.612
peak=    4.123 closest distance to " O   HOH Z 214 " =    1.454
peak=    4.121 closest distance to " O   HOH Z 127 " =    1.171
peak=    4.119 closest distance to " O   HOH Z 147 " =    1.371
peak=    4.082 closest distance to " CG  PRO A 243 " =    1.098
peak=    4.049 closest distance to " CD  PRO A  54 " =    1.106
peak=    4.040 closest distance to " O   HOH Z 272 " =    1.468
peak=    4.020 closest distance to " CB  ASN A 148 " =    1.417
peak=    4.020 closest distance to " O   PRO A 198 " =    1.588
peak=    4.005 closest distance to " O   HOH Z  69 " =    1.255
peak=    4.003 closest distance to " CB  SER A  63 " =    1.188
peak=    3.993 closest distance to " O   THR A 220 " =    1.202
peak=    3.970 closest distance to " CG  GLN A  58 " =    1.212
peak=    3.964 closest distance to " CB  SER A  26 " =    1.768
peak=    3.963 closest distance to " CG2 VAL A 197 " =    1.205
peak=    3.923 closest distance to " O   HOH Z 251 " =    1.759
peak=    3.923 closest distance to " CG2AVAL A 121 " =    2.096
peak=    3.903 closest distance to " O   HOH Z 176 " =    1.762
peak=    3.901 closest distance to " O   HOH Z  63 " =    1.918
peak=    3.897 closest distance to " O   HOH Z  85 " =    1.607
peak=    3.894 closest distance to " ND2BASN A 224 " =    0.897
peak=    3.892 closest distance to " O   HOH Z 132 " =    2.726
peak=    3.889 closest distance to " CB  TRP A 179 " =    1.382
peak=    3.889 closest distance to " O   HOH Z  65 " =    1.056
peak=    3.881 closest distance to " CA  GLU A 152 " =    0.864
peak=    3.875 closest distance to " O   HOH Z 369 " =    1.203
peak=    3.872 closest distance to " CE  LYS A  76 " =    0.876
peak=    3.849 closest distance to " O   HOH Z  40 " =    2.099
peak=    3.846 closest distance to " O   HOH Z  63 " =    2.148
peak=    3.840 closest distance to " N   THR A  52 " =    1.162
peak=    3.834 closest distance to " CD  ARG A 195 " =    1.159
peak=    3.833 closest distance to " N   SER A 164 " =    0.999
peak=    3.829 closest distance to " O   HOH Z 406 " =    1.698
peak=    3.822 closest distance to " CA  GLN A  58 " =    1.178
peak=    3.820 closest distance to " O   HOH Z 134 " =    1.882
peak=    3.818 closest distance to " NZ  LYS A 117 " =    2.916
peak=    3.811 closest distance to " O   ALA A 165 " =    1.419
peak=    3.806 closest distance to " CB  SER A 273 " =    0.962
peak=    3.806 closest distance to " CD  LYS A  76 " =    1.901
peak=    3.800 closest distance to " CB  GLN A 183 " =    1.237
peak=    3.794 closest distance to " CB  ASN A 187 " =    1.315
peak=    3.790 closest distance to " O   SER A  87 " =    2.287
peak=    3.778 closest distance to " O   HOH Z  44 " =    1.451
peak=    3.773 closest distance to " CD  ARG A 139 " =    1.194
peak=    3.773 closest distance to " CG  GLN A  11 " =    1.391
peak=    3.770 closest distance to " O   HOH Z 433 " =    1.544
peak=    3.769 closest distance to " O   HOH Z 346 " =    1.623
peak=    3.758 closest distance to " OE1 GLN A  55 " =    1.482
peak=    3.754 closest distance to " O   HOH Z 426 " =    1.259
peak=    3.749 closest distance to " O   HOH Z 431 " =    1.267
peak=    3.743 closest distance to " CG1 ILE A  33 " =    1.225
peak=    3.741 closest distance to " OG BSER A 258 " =    2.830
peak=    3.736 closest distance to " CZ  PHE A  38 " =    1.008
peak=    3.733 closest distance to " CE1 TYR A  30 " =    1.137
peak=    3.730 closest distance to " CG2BVAL A  41 " =    0.842
peak=    3.726 closest distance to " CB  ALA A 248 " =    1.386
peak=    3.714 closest distance to " CG  PRO A 198 " =    1.344
peak=    3.707 closest distance to " CG AARG A 275 " =    1.334
peak=    3.705 closest distance to " CA  ARG A 156 " =    0.999
peak=    3.702 closest distance to " O   THR A 182 " =    1.519
peak=    3.700 closest distance to " O   VAL A  72 " =    1.243
peak=    3.696 closest distance to " O   HOH Z 343 " =    2.570
peak=    3.694 closest distance to " O   HOH Z 213 " =    1.920
peak=    3.692 closest distance to " O   HOH Z  88 " =    3.738
peak=    3.682 closest distance to " O   HOH Z 371 " =    2.363
peak=    3.678 closest distance to " O   HOH Z 299 " =    4.141
peak=    3.654 closest distance to " O   GLY A  23 " =    2.441
peak=    3.648 closest distance to " CD  ARG A 269 " =    0.955
peak=    3.632 closest distance to " CG  ARG A 138 " =    1.412
peak=    3.628 closest distance to " O   HOH Z 250 " =    2.544
peak=    3.627 closest distance to " O   HOH Z 340 " =    1.312
peak=    3.624 closest distance to " CB  ASP A 191 " =    1.265
peak=    3.623 closest distance to " O   HOH Z   4 " =    1.769
peak=    3.622 closest distance to " OE2 GLU A 152 " =    1.309
peak=    3.614 closest distance to " CA  ALA A  51 " =    1.049
peak=    3.611 closest distance to " O   HOH Z 306 " =    1.415
peak=    3.611 closest distance to " CB  ALA A 114 " =    0.817
peak=    3.609 closest distance to " O   HOH Z  21 " =    1.732
peak=    3.606 closest distance to " CB  ASN A 285 " =    0.946
peak=    3.604 closest distance to " CB  LEU A 300 " =    0.959
peak=    3.603 closest distance to " CB  ARG A 275 " =    1.078
peak=    3.601 closest distance to " O   HOH Z 234 " =    3.322
peak=    3.594 closest distance to " CD  ARG A  36 " =    1.049
peak=    3.593 closest distance to " O   HOH Z 144 " =    1.728
peak=    3.574 closest distance to " NE2 GLN A  11 " =    1.330
peak=    3.574 closest distance to " CG1AVAL A 121 " =    0.821
peak=    3.568 closest distance to " CD2 LEU A 297 " =    0.927
peak=    3.567 closest distance to " O   HOH Z 191 " =    1.155
peak=    3.566 closest distance to " O   HOH Z  80 " =    2.228
peak=    3.562 closest distance to " CB  ASN A 110 " =    0.999
peak=    3.561 closest distance to " CB  GLN A  55 " =    0.927
peak=    3.557 closest distance to " O   HOH Z 419 " =    1.657
peak=    3.554 closest distance to " NZ  LYS A 117 " =    0.895
peak=    3.554 closest distance to " CB  THR A  52 " =    0.802
peak=    3.548 closest distance to " O   HOH Z 130 " =    2.455
peak=    3.543 closest distance to " CG AARG A 102 " =    1.237
peak=    3.541 closest distance to " O   HOH Z  35 " =    2.263
peak=    3.536 closest distance to " O   HOH Z 361 " =    3.376
peak=    3.534 closest distance to " CD  ARG A 159 " =    0.824
peak=    3.534 closest distance to " CA  ARG A 195 " =    1.191
peak=    3.530 closest distance to " O   HOH Z 393 " =    3.473
peak=    3.526 closest distance to " CD  LYS A 166 " =    1.630
peak=    3.519 closest distance to " O   TYR A 116 " =    1.348
peak=    3.514 closest distance to " CG2 VAL A 268 " =    1.008
peak=    3.512 closest distance to " O   THR A 251 " =    1.229
peak=    3.510 closest distance to " O   HOH Z  76 " =    1.137
peak=    3.507 closest distance to " CB  PHE A 204 " =    0.729
peak=    3.507 closest distance to " O   HOH Z 207 " =    1.597
peak=    3.506 closest distance to " O   HOH Z 339 " =    1.537
peak=    3.504 closest distance to " O   GLU A   2 " =    1.727
peak=    3.502 closest distance to " NE2 GLN A  58 " =    2.960
peak=    3.499 closest distance to " O   HOH Z 368 " =    2.162
peak=    3.499 closest distance to " NE2 GLN A  77 " =    3.083
peak=    3.495 closest distance to " OD1 ASN A 301 " =    0.981
peak=    3.490 closest distance to " CB  LEU A  83 " =    0.782
peak=    3.488 closest distance to " CD2 LEU A  83 " =    1.613
peak=    3.488 closest distance to " OG1 THR A 264 " =    0.841
peak=    3.486 closest distance to " CB  GLN A  89 " =    1.379
peak=    3.482 closest distance to " CB  GLN A 194 " =    0.907
peak=    3.478 closest distance to " O   HOH Z  87 " =    1.642
peak=    3.473 closest distance to " CB  GLU A   2 " =    1.079
peak=    3.461 closest distance to " O   HOH Z 298 " =    4.278
peak=    3.460 closest distance to " CA  THR A 246 " =    1.110
peak=    3.456 closest distance to " NH1AARG A 102 " =    1.005
peak=    3.451 closest distance to " O   HOH Z 357 " =    2.134
peak=    3.451 closest distance to " CA  VAL A 112 " =    1.124
peak=    3.449 closest distance to " CA  SER A  12 " =    1.384
peak=    3.447 closest distance to " CB  MET A  40 " =    1.042
peak=    3.442 closest distance to " N   ALA A   1 " =    2.175
peak=    3.438 closest distance to " CB  TYR A  30 " =    1.106
peak=    3.435 closest distance to " CA  THR A 221 " =    0.997
peak=    3.434 closest distance to " CB  PHE A  16 " =    1.177
peak=    3.432 closest distance to " CB  VAL A 265 " =    1.129
peak=    3.428 closest distance to " O   HOH Z 345 " =    1.735
peak=    3.427 closest distance to " O   HOH Z 421 " =    2.090
peak=    3.425 closest distance to " CD2 LEU A 297 " =    1.034
peak=    3.425 closest distance to " NH2AARG A 145 " =    1.204
peak=    3.424 closest distance to " OE1 GLU A   2 " =    1.343
peak=    3.416 closest distance to " CB  ALA A   1 " =    1.232
peak=    3.416 closest distance to " CB  PRO A 198 " =    1.342
peak=    3.402 closest distance to " O   HOH Z  26 " =    1.128
peak=    3.401 closest distance to " O   HOH Z 298 " =    1.854
peak=    3.401 closest distance to " O   HOH Z 316 " =    3.096
peak=    3.390 closest distance to " O   HOH Z 365 " =    2.412
peak=    3.388 closest distance to " CB  PRO A  54 " =    1.038
peak=    3.383 closest distance to " CB  SER A  62 " =    3.838
peak=    3.381 closest distance to " CB  ARG A 190 " =    1.777
peak=    3.378 closest distance to " CB  ASN A  39 " =    0.730
peak=    3.375 closest distance to " O   HOH Z 132 " =    2.179
peak=    3.373 closest distance to " C   ALA A 299 " =    1.023
peak=    3.372 closest distance to " ND2 ASN A 249 " =    0.892
peak=    3.372 closest distance to " CB  LYS A 289 " =    1.128
peak=    3.371 closest distance to " NH2 ARG A  56 " =    1.187
peak=    3.365 closest distance to " O   HOH Z 359 " =    1.808
peak=    3.364 closest distance to " O   HOH Z  52 " =    1.376
peak=    3.359 closest distance to " CB  GLU A 277 " =    3.820
peak=    3.353 closest distance to " OG  SER A 245 " =    1.356
peak=    3.351 closest distance to " CB  PRO A  90 " =    0.989
peak=    3.346 closest distance to " CE1 TYR A 186 " =    1.213
peak=    3.336 closest distance to " CB  PRO A 243 " =    1.147
peak=    3.333 closest distance to " O   HOH Z 116 " =    1.847
peak=    3.319 closest distance to " CE  LYS A 119 " =    1.198
peak=    3.315 closest distance to " O   HOH Z 199 " =    1.354
peak=    3.315 closest distance to " O   HOH Z 163 " =    2.026
peak=    3.315 closest distance to " O   HOH Z 423 " =    1.834
peak=    3.312 closest distance to " O   HOH Z 368 " =    4.662
peak=    3.310 closest distance to " CB  ARG A 219 " =    1.322
peak=    3.302 closest distance to " CB  GLU A 128 " =    1.092
peak=    3.302 closest distance to " CG2 THR A  42 " =    1.020
peak=    3.302 closest distance to " CG  LEU A 237 " =    1.393
peak=    3.299 closest distance to " O   HOH Z 191 " =    1.237
peak=    3.296 closest distance to " O   HOH Z 331 " =    1.139
peak=    3.296 closest distance to " CE  MET A  40 " =    1.038
peak=    3.294 closest distance to " CG  LEU A 167 " =    1.085
peak=    3.294 closest distance to " CB  GLU A  46 " =    1.178
peak=    3.293 closest distance to " O   HOH Z 298 " =    1.798
peak=    3.292 closest distance to " O   HOH Z 371 " =    2.735
peak=    3.292 closest distance to " O   HOH Z  88 " =    1.605
peak=    3.290 closest distance to " O   HOH Z  54 " =    2.144
peak=    3.286 closest distance to " O   HOH Z  22 " =    2.392
peak=    3.278 closest distance to " O   HOH Z 435 " =    3.113
peak=    3.277 closest distance to " CG2 VAL A 257 " =    0.878
peak=    3.276 closest distance to " CA  SER A  62 " =    0.933
peak=    3.272 closest distance to " O   HOH Z 209 " =    1.947
peak=    3.270 closest distance to " CB  SER A 141 " =    1.216
peak=    3.268 closest distance to " CB  ASN A  45 " =    1.120
peak=    3.266 closest distance to " O   HOH Z  63 " =    2.328
peak=    3.265 closest distance to " CB  ALA A 154 " =    1.060
peak=    3.263 closest distance to " CA  ASN A  39 " =    0.941
peak=    3.258 closest distance to " OG  SER A 135 " =    1.304
peak=    3.256 closest distance to " NH1BARG A 145 " =    1.206
peak=    3.255 closest distance to " O   GLY A  91 " =    1.209
peak=    3.249 closest distance to " CB  ARG A  79 " =    0.878
peak=    3.249 closest distance to " O   HOH Z 369 " =    1.962
peak=    3.247 closest distance to " O   HOH Z  78 " =    1.740
peak=    3.247 closest distance to " ND1 HIS A  81 " =    1.169
peak=    3.247 closest distance to " O   HOH Z 191 " =    1.572
peak=    3.246 closest distance to " O   HOH Z   1 " =    2.460
peak=    3.239 closest distance to " CD1 ILE A 199 " =    1.396
peak=    3.239 closest distance to " CB  GLN A  88 " =    1.180
peak=    3.235 closest distance to " CA  ASP A 191 " =    0.906
peak=    3.232 closest distance to " O   HOH Z 258 " =    1.679
peak=    3.229 closest distance to " CG1 ILE A 120 " =    1.050
peak=    3.227 closest distance to " OG ASER A 258 " =    3.058
peak=    3.223 closest distance to " O   HOH Z 327 " =    2.479
peak=    3.223 closest distance to " CB  ASN A 209 " =    1.197
peak=    3.223 closest distance to " CD1 LEU A   5 " =    1.485
peak=    3.221 closest distance to " O   HOH Z  68 " =    1.816
peak=    3.220 closest distance to " O   HOH Z 219 " =    2.436
peak=    3.220 closest distance to " NE2 HIS A 108 " =    0.750
peak=    3.211 closest distance to " CB  ASN A 142 " =    1.068
peak=    3.210 closest distance to " O   HOH Z 141 " =    1.644
peak=    3.209 closest distance to " CG  MET A 185 " =    1.299
peak=    3.207 closest distance to " O   HOH Z 284 " =    3.033
peak=    3.202 closest distance to " CG2 THR A 220 " =    1.090
peak=    3.200 closest distance to " CG  ASP A  65 " =    1.011
peak=    3.200 closest distance to " O   HOH Z 407 " =    1.625
peak=    3.198 closest distance to " O   HOH Z  85 " =    1.402
peak=    3.197 closest distance to " CA  PHE A  59 " =    0.923
peak=    3.195 closest distance to " CA  ASP A 162 " =    1.120
peak=    3.195 closest distance to " CE3 TRP A 150 " =    1.204
peak=    3.190 closest distance to " CG  ARG A  56 " =    1.218
peak=    3.184 closest distance to " O   HOH Z 209 " =    1.129
peak=    3.184 closest distance to " O   PHE A  61 " =    1.419
peak=    3.175 closest distance to " O   HOH Z 437 " =    1.401
peak=    3.175 closest distance to " O   HOH Z 247 " =    1.337
peak=    3.175 closest distance to " CB  PHE A 225 " =    0.862
peak=    3.173 closest distance to " CB  ILE A 199 " =    1.229
peak=    3.171 closest distance to " O   HOH Z 227 " =    1.624
peak=    3.170 closest distance to " O   HOH Z 417 " =    1.864
peak=    3.166 closest distance to " OG BSER A  99 " =    2.877
peak=    3.165 closest distance to " OG BSER A 212 " =    2.460
peak=    3.162 closest distance to " CG1 VAL A 153 " =    1.107
peak=    3.159 closest distance to " O   THR A 157 " =    1.161
peak=    3.158 closest distance to " OE1 GLN A 223 " =    3.447
peak=    3.154 closest distance to " O   HOH Z 189 " =    2.535
peak=    3.150 closest distance to " CD2 TYR A  68 " =    0.820
peak=    3.149 closest distance to " CA  VAL A  41 " =    0.870
peak=    3.148 closest distance to " CB  ARG A 138 " =    0.977
peak=    3.146 closest distance to " CB  ASP A 124 " =    0.935
peak=    3.145 closest distance to " O   HOH Z 234 " =    1.803
peak=    3.141 closest distance to " O   HOH Z 313 " =    1.750
peak=    3.139 closest distance to " O   HOH Z  20 " =    1.619
peak=    3.138 closest distance to " CA  ALA A 129 " =    1.250
peak=    3.137 closest distance to " CG2 THR A 221 " =    1.102
peak=    3.136 closest distance to " CD  GLN A  58 " =    0.917
peak=    3.132 closest distance to " CG1 ILE A  20 " =    1.403
peak=    3.132 closest distance to " CB  LEU A   5 " =    1.142
peak=    3.131 closest distance to " O   HOH Z 191 " =    3.737
peak=    3.129 closest distance to " OD1 ASN A 217 " =    1.323
peak=    3.123 closest distance to " NH2AARG A 275 " =    2.667
peak=    3.122 closest distance to " CA  LEU A  83 " =    1.246
peak=    3.120 closest distance to " O   HOH Z 389 " =    1.856
peak=    3.119 closest distance to " CG2 THR A  31 " =    1.266
peak=    3.119 closest distance to " CA  ALA A   9 " =    0.988
peak=    3.117 closest distance to " O   HOH Z 213 " =    1.910
peak=    3.116 closest distance to " O   HOH Z 298 " =    2.175
peak=    3.116 closest distance to " O   HOH Z  41 " =    2.023
peak=    3.115 closest distance to " O   HOH Z 420 " =    5.011
peak=    3.115 closest distance to " O   HOH Z 303 " =    2.352
peak=    3.111 closest distance to " CD  PRO A 213 " =    1.614
peak=    3.110 closest distance to " OH  TYR A  68 " =    1.053
peak=    3.109 closest distance to " N   PHE A 130 " =    1.303
peak=    3.108 closest distance to " CB  ALA A 292 " =    0.865
peak=    3.095 closest distance to " NE2 HIS A  86 " =    1.445
peak=    3.087 closest distance to " O   HOH Z 250 " =    1.371
peak=    3.084 closest distance to " O   HOH Z 250 " =    1.357
peak=    3.078 closest distance to " O   HOH Z 236 " =    1.662
peak=    3.075 closest distance to " O   HOH Z 394 " =    3.449
peak=    3.069 closest distance to " CA  ASP A 149 " =    1.307
peak=    3.063 closest distance to " CA  SER A  26 " =    1.086
peak=    3.059 closest distance to " O   HOH Z  39 " =    1.438
peak=    3.059 closest distance to " N   HIS A 108 " =    1.752
peak=    3.049 closest distance to " O   HOH Z 195 " =    4.018
peak=    3.049 closest distance to " CA  SER A  32 " =    1.690
peak=    3.033 closest distance to " CA  GLY A 241 " =    1.084
peak=    3.014 closest distance to " CA  THR A 221 " =    1.385

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.474 - 5.740
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 201
   mapped sites are within: 0.730 - 5.740

peak=   -4.889 closest distance to " O   PRO A 198 " =    1.342
peak=   -4.863 closest distance to " CG2 ILE A  20 " =    2.864
peak=   -4.774 closest distance to " CD2 LEU A 237 " =    2.517
peak=   -4.459 closest distance to " O   HOH Z  37 " =    0.861
peak=   -4.380 closest distance to " O   HOH Z 422 " =    0.943
peak=   -4.331 closest distance to " CD  GLN A 223 " =    1.478
peak=   -4.312 closest distance to " CG  GLN A  58 " =    0.871
peak=   -4.274 closest distance to " O   ASP A 107 " =    1.799
peak=   -4.243 closest distance to " CZ2 TRP A  92 " =    2.844
peak=   -4.172 closest distance to " CG  GLN A  11 " =    1.272
peak=   -4.096 closest distance to " O   HOH Z 222 " =    1.028
peak=   -4.066 closest distance to " CD  ARG A  14 " =    3.268
peak=   -4.009 closest distance to " O   VAL A  67 " =    2.868
peak=   -4.000 closest distance to " CD2 TYR A 293 " =    1.838
peak=   -3.971 closest distance to " O   GLN A  11 " =    1.169
peak=   -3.970 closest distance to " O   HOH Z 166 " =    1.603
peak=   -3.955 closest distance to " NE2 GLN A  55 " =    1.832
peak=   -3.941 closest distance to " CG2 VAL A 189 " =    2.201
peak=   -3.920 closest distance to " N   ALA A  43 " =    2.610
peak=   -3.898 closest distance to " O  BHOH Z  74 " =    0.730
peak=   -3.857 closest distance to " CG  GLN A  58 " =    0.840
peak=   -3.851 closest distance to " CG  PRO A 243 " =    1.719
peak=   -3.827 closest distance to " O   HOH Z 150 " =    1.713
peak=   -3.824 closest distance to " O   HOH Z 221 " =    0.761
peak=   -3.813 closest distance to " CD2 TYR A  30 " =    2.687
peak=   -3.799 closest distance to " CA  ASP A  65 " =    1.259
peak=   -3.790 closest distance to " CE2 PHE A  61 " =    2.882
peak=   -3.788 closest distance to " O   HOH Z 203 " =    1.478
peak=   -3.787 closest distance to " O   HOH Z 345 " =    2.959
peak=   -3.769 closest distance to " OD2 ASP A 298 " =    1.005
peak=   -3.752 closest distance to " CD1 PHE A  59 " =    2.046
peak=   -3.751 closest distance to " O   HOH Z  52 " =    2.219
peak=   -3.733 closest distance to " OG BSER A 134 " =    1.389
peak=   -3.721 closest distance to " O   HOH Z 281 " =    2.561
peak=   -3.707 closest distance to " C   HIS A 108 " =    1.138
peak=   -3.691 closest distance to " O   SER A 146 " =    1.229
peak=   -3.687 closest distance to " O   GLU A 128 " =    1.025
peak=   -3.682 closest distance to " CB  PRO A 280 " =    2.146
peak=   -3.679 closest distance to " O   HOH Z 374 " =    2.054
peak=   -3.663 closest distance to " O   GLY A 241 " =    2.361
peak=   -3.652 closest distance to " O   HOH Z 205 " =    0.858
peak=   -3.634 closest distance to " CG  GLN A  58 " =    1.544
peak=   -3.612 closest distance to " O   HOH Z  67 " =    1.413
peak=   -3.612 closest distance to " O   HOH Z 278 " =    0.958
peak=   -3.609 closest distance to " O   HOH Z  41 " =    1.888
peak=   -3.606 closest distance to " ND2BASN A 224 " =    1.998
peak=   -3.606 closest distance to " CA  GLY A 133 " =    2.024
peak=   -3.594 closest distance to " O   HOH Z  70 " =    0.943
peak=   -3.582 closest distance to " CB  ALA A  43 " =    2.706
peak=   -3.575 closest distance to " CA  ASP A 298 " =    1.097
peak=   -3.572 closest distance to " SD  MET A 105 " =    1.029
peak=   -3.563 closest distance to " O   HOH Z 216 " =    0.968
peak=   -3.555 closest distance to " O   HOH Z 351 " =    1.666
peak=   -3.553 closest distance to " O   HOH Z 186 " =    2.478
peak=   -3.540 closest distance to " OD2 ASP A 171 " =    1.789
peak=   -3.518 closest distance to " CD2 PHE A  61 " =    2.138
peak=   -3.509 closest distance to " CD1 ILE A 109 " =    2.808
peak=   -3.508 closest distance to " CG1 VAL A 112 " =    2.699
peak=   -3.506 closest distance to " CB  ALA A 129 " =    2.536
peak=   -3.505 closest distance to " CZ  TYR A 172 " =    1.903
peak=   -3.495 closest distance to " C   ASN A 285 " =    2.187
peak=   -3.494 closest distance to " O   HOH Z 113 " =    1.579
peak=   -3.477 closest distance to " O   HOH Z 411 " =    5.573
peak=   -3.475 closest distance to " CG  GLU A  53 " =    1.310
peak=   -3.465 closest distance to " O   HOH Z 424 " =    3.298
peak=   -3.458 closest distance to " CG  ASP A 124 " =    0.866
peak=   -3.454 closest distance to " CZ  PHE A  38 " =    2.273
peak=   -3.449 closest distance to " OG  SER A  97 " =    1.668
peak=   -3.449 closest distance to " CD  LYS A 289 " =    2.389
peak=   -3.444 closest distance to " CB  ALA A 248 " =    2.156
peak=   -3.444 closest distance to " OG BSER A 134 " =    4.028
peak=   -3.441 closest distance to " N   SER A 134 " =    1.109
peak=   -3.441 closest distance to " CH2 TRP A 150 " =    1.222
peak=   -3.439 closest distance to " O   HOH Z 297 " =    2.597
peak=   -3.439 closest distance to " O   SER A   3 " =    0.965
peak=   -3.437 closest distance to " CG  TRP A 266 " =    1.874
peak=   -3.433 closest distance to " CD1 TRP A 179 " =    1.142
peak=   -3.430 closest distance to " O   HOH Z 340 " =    1.588
peak=   -3.429 closest distance to " CG1 VAL A 257 " =    2.407
peak=   -3.427 closest distance to " O   HOH Z 155 " =    2.066
peak=   -3.424 closest distance to " CD  GLU A 236 " =    1.144
peak=   -3.419 closest distance to " O   HOH Z 136 " =    1.274
peak=   -3.418 closest distance to " CE3 TRP A 150 " =    2.027
peak=   -3.416 closest distance to " O   HOH Z 214 " =    0.999
peak=   -3.411 closest distance to " CA  GLY A  57 " =    2.218
peak=   -3.410 closest distance to " O   HOH Z 434 " =    2.396
peak=   -3.406 closest distance to " CB  ASN A  45 " =    2.042
peak=   -3.404 closest distance to " N   ASP A 191 " =    1.403
peak=   -3.402 closest distance to " CE1 PHE A 218 " =    1.498
peak=   -3.396 closest distance to " CG  GLN A 103 " =    2.378
peak=   -3.392 closest distance to " N   LEU A 282 " =    2.243
peak=   -3.389 closest distance to " CG  LEU A  83 " =    2.322
peak=   -3.384 closest distance to " O   HOH Z 179 " =    2.058
peak=   -3.381 closest distance to " O   HOH Z 191 " =    5.740
peak=   -3.380 closest distance to " O   HOH Z  60 " =    1.610
peak=   -3.377 closest distance to " CA  TRP A 150 " =    1.351
peak=   -3.375 closest distance to " CD  ARG A 156 " =    2.069
peak=   -3.370 closest distance to " O   SER A 210 " =    1.727
peak=   -3.370 closest distance to " O   SER A 271 " =    1.747
peak=   -3.369 closest distance to " O   HOH Z  56 " =    1.074
peak=   -3.364 closest distance to " O   HOH Z 366 " =    1.356
peak=   -3.356 closest distance to " CD2 PHE A 225 " =    1.343
peak=   -3.354 closest distance to " O   HOH Z 428 " =    1.743
peak=   -3.353 closest distance to " CD  ARG A  56 " =    1.140
peak=   -3.352 closest distance to " O   HOH Z 145 " =    3.327
peak=   -3.342 closest distance to " O   HOH Z 171 " =    2.540
peak=   -3.334 closest distance to " O   HOH Z 111 " =    4.010
peak=   -3.331 closest distance to " O   VAL A 174 " =    2.167
peak=   -3.325 closest distance to " CD1 ILE A 106 " =    2.224
peak=   -3.318 closest distance to " CD  GLN A  73 " =    0.830
peak=   -3.310 closest distance to " O   HOH Z 250 " =    1.779
peak=   -3.305 closest distance to " O   HOH Z 397 " =    1.021
peak=   -3.304 closest distance to " O   HOH Z 154 " =    1.704
peak=   -3.301 closest distance to " CD1 LEU A 101 " =    2.449
peak=   -3.300 closest distance to " O   HOH Z   6 " =    1.909
peak=   -3.299 closest distance to " OG  SER A  97 " =    2.264
peak=   -3.297 closest distance to " O   HOH Z 423 " =    2.572
peak=   -3.293 closest distance to " O   HOH Z 152 " =    1.171
peak=   -3.293 closest distance to " O   HOH Z 435 " =    1.712
peak=   -3.291 closest distance to " O   HOH Z  17 " =    1.455
peak=   -3.291 closest distance to " CG2BVAL A 121 " =    1.393
peak=   -3.290 closest distance to " O   ILE A 106 " =    1.405
peak=   -3.287 closest distance to " O   HOH Z 418 " =    1.135
peak=   -3.286 closest distance to " OE2 GLU A 152 " =    1.365
peak=   -3.282 closest distance to " O   HOH Z 292 " =    2.859
peak=   -3.282 closest distance to " O   HOH Z 106 " =    1.966
peak=   -3.274 closest distance to " O   HOH Z 407 " =    2.976
peak=   -3.269 closest distance to " CB  PRO A 243 " =    2.885
peak=   -3.266 closest distance to " O   HOH Z 156 " =    3.470
peak=   -3.266 closest distance to " CA  ALA A 137 " =    2.538
peak=   -3.265 closest distance to " CD  GLN A  88 " =    0.971
peak=   -3.264 closest distance to " CB  ALA A 291 " =    2.397
peak=   -3.255 closest distance to " OXT GLY A 302 " =    3.054
peak=   -3.253 closest distance to " OE2 GLU A 128 " =    2.061
peak=   -3.250 closest distance to " CB  ALA A  10 " =    2.332
peak=   -3.247 closest distance to " CD  ARG A  36 " =    1.007
peak=   -3.245 closest distance to " O   HOH Z 215 " =    2.231
peak=   -3.242 closest distance to " OH  TYR A 172 " =    1.889
peak=   -3.237 closest distance to " CD1 ILE A 239 " =    2.379
peak=   -3.234 closest distance to " OG1 THR A  52 " =    2.613
peak=   -3.230 closest distance to " O   HOH Z  54 " =    1.968
peak=   -3.230 closest distance to " O   HOH Z 165 " =    1.625
peak=   -3.227 closest distance to " C   THR A 279 " =    1.112
peak=   -3.223 closest distance to " O   HOH Z 292 " =    1.588
peak=   -3.220 closest distance to " CG  ARG A 259 " =    2.330
peak=   -3.217 closest distance to " O   ASP A 171 " =    0.979
peak=   -3.215 closest distance to " CB  ASP A 162 " =    1.814
peak=   -3.215 closest distance to " CE1 HIS A 207 " =    1.991
peak=   -3.214 closest distance to " O   ASN A 110 " =    2.348
peak=   -3.212 closest distance to " CZ  TYR A 169 " =    1.963
peak=   -3.211 closest distance to " ND2 ASN A 301 " =    2.620
peak=   -3.209 closest distance to " CE3 TRP A 150 " =    1.331
peak=   -3.206 closest distance to " NE  ARG A  79 " =    1.305
peak=   -3.201 closest distance to " O   HOH Z 433 " =    0.902
peak=   -3.199 closest distance to " N   GLN A 223 " =    1.021
peak=   -3.198 closest distance to " SD  MET A 105 " =    2.401
peak=   -3.198 closest distance to " O   HOH Z 330 " =    1.162
peak=   -3.196 closest distance to " CA  GLY A 241 " =    3.324
peak=   -3.195 closest distance to " O   ARG A  56 " =    4.001
peak=   -3.195 closest distance to " O   PHE A 218 " =    1.430
peak=   -3.192 closest distance to " O   HOH Z   9 " =    0.896
peak=   -3.189 closest distance to " CB  ALA A  51 " =    1.874
peak=   -3.187 closest distance to " O   HOH Z 197 " =    1.626
peak=   -3.185 closest distance to " O   HOH Z 150 " =    1.321
peak=   -3.185 closest distance to " OE2 GLU A   2 " =    1.393
peak=   -3.177 closest distance to " CB  ALA A 100 " =    2.124
peak=   -3.165 closest distance to " O   ALA A 227 " =    1.106
peak=   -3.164 closest distance to " CA  GLN A  58 " =    1.041
peak=   -3.164 closest distance to " CA  HIS A  86 " =    1.202
peak=   -3.163 closest distance to " CA  ALA A 114 " =    0.954
peak=   -3.161 closest distance to " CE1 HIS A  81 " =    1.277
peak=   -3.156 closest distance to " CB  ASP A 286 " =    1.580
peak=   -3.154 closest distance to " O   HOH Z 231 " =    1.314
peak=   -3.153 closest distance to " CG1AVAL A  41 " =    2.425
peak=   -3.149 closest distance to " N   ALA A 226 " =    1.799
peak=   -3.147 closest distance to " O   SER A 273 " =    1.055
peak=   -3.144 closest distance to " CA  TYR A  68 " =    2.917
peak=   -3.140 closest distance to " NH2 ARG A  79 " =    1.413
peak=   -3.137 closest distance to " CE BMET A  47 " =    1.563
peak=   -3.131 closest distance to " O   HOH Z 116 " =    1.312
peak=   -3.123 closest distance to " CB  TRP A  85 " =    2.760
peak=   -3.120 closest distance to " O   HOH Z 274 " =    1.013
peak=   -3.119 closest distance to " CA  SER A 276 " =    1.530
peak=   -3.117 closest distance to " O   HOH Z  65 " =    1.718
peak=   -3.111 closest distance to " CA  GLY A  91 " =    2.153
peak=   -3.105 closest distance to " CA  TRP A 274 " =    1.118
peak=   -3.105 closest distance to " O   ARG A  79 " =    0.956
peak=   -3.100 closest distance to " NE2 GLN A 278 " =    1.120
peak=   -3.093 closest distance to " CD1 LEU A 167 " =    1.646
peak=   -3.093 closest distance to " O   HOH Z 141 " =    1.436
peak=   -3.080 closest distance to " CB  PRO A 163 " =    2.587
peak=   -3.080 closest distance to " O   HOH Z 314 " =    1.560
peak=   -3.076 closest distance to " O   HOH Z  60 " =    1.999
peak=   -3.073 closest distance to " O   HOH Z 285 " =    2.190
peak=   -3.064 closest distance to " CA  GLY A 203 " =    2.268
peak=   -3.062 closest distance to " CD2 TYR A 172 " =    2.086
peak=   -3.059 closest distance to " O   HOH Z 166 " =    1.713
peak=   -3.054 closest distance to " OD1 ASN A 301 " =    0.858
peak=   -3.044 closest distance to " O   HOH Z 393 " =    2.156

================= 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    :  0.5048 0.5119   6.306450e+00   6.306399e+00
   1_bss:  0.4994 0.5021   6.238030e+00   6.231870e+00
   1_xyz:  0.4027 0.4351   6.173316e+00   6.226002e+00
   1_adp:  0.3562 0.4414   6.128751e+00   6.236680e+00
   1_occ:  0.3559 0.4416   6.128807e+00   6.237849e+00
   2_bss:  0.3551 0.4399   6.126376e+00   6.235601e+00
   2_xyz:  0.2931 0.3612   5.960912e+00   6.115276e+00
   2_adp:  0.2730 0.3404   5.917471e+00   6.076655e+00
   2_occ:  0.2730 0.3404   5.917209e+00   6.076758e+00
   3_bss:  0.2725 0.3392   5.916244e+00   6.075271e+00
   3_xyz:  0.2212 0.2804   5.735530e+00   5.920667e+00
   3_adp:  0.2044 0.2717   5.684466e+00   5.891310e+00
   3_occ:  0.2043 0.2715   5.684143e+00   5.891071e+00
   4_bss:  0.2044 0.2718   5.683984e+00   5.890113e+00
   4_xyz:  0.1657 0.2267   5.496846e+00   5.726583e+00
   4_adp:  0.1558 0.2103   5.439549e+00   5.656534e+00
   4_occ:  0.1556 0.2099   5.438877e+00   5.655694e+00
   5_bss:  0.1558 0.2097   5.439772e+00   5.655731e+00
   5_xyz:  0.1421 0.1898   5.355286e+00   5.570223e+00
   5_adp:  0.1378 0.1878   5.334080e+00   5.553378e+00
   5_occ:  0.1377 0.1878   5.333896e+00   5.553214e+00
   5_bss:  0.1377 0.1878   5.333892e+00   5.553285e+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:  0.297  28.172  -1.680   1.768   2.763   0.000   0.000   0.000
   1_xyz:  0.297  28.172  -1.680   1.768   2.763   0.000   0.000   0.000
   1_adp:  0.297  28.172  -1.680   1.768   2.763   0.000   0.000   0.000
   1_occ:  0.297  28.172  -1.680   1.768   2.763   0.000   0.000   0.000
   2_bss:  0.288  28.172  -1.106   1.295   2.130   0.000   0.000   0.000
   2_xyz:  0.288  28.172  -1.106   1.295   2.130   0.000   0.000   0.000
   2_adp:  0.288  28.172  -1.106   1.295   2.130   0.000   0.000   0.000
   2_occ:  0.288  28.172  -1.106   1.295   2.130   0.000   0.000   0.000
   3_bss:  0.323  57.653  -1.938   0.255   1.028   0.000   0.000   0.000
   3_xyz:  0.323  57.653  -1.938   0.255   1.028   0.000   0.000   0.000
   3_adp:  0.323  57.653  -1.938   0.255   1.028   0.000   0.000   0.000
   3_occ:  0.323  57.653  -1.938   0.255   1.028   0.000   0.000   0.000
   4_bss:  0.325  66.722  -2.774  -0.671   0.112  -0.000   0.000   0.000
   4_xyz:  0.325  66.722  -2.774  -0.671   0.112  -0.000   0.000   0.000
   4_adp:  0.325  66.722  -2.774  -0.671   0.112  -0.000   0.000   0.000
   4_occ:  0.325  66.722  -2.774  -0.671   0.112  -0.000   0.000   0.000
   5_bss:  0.334  66.722  -3.217  -1.351  -0.353  -0.000  -0.000  -0.000
   5_xyz:  0.334  66.722  -3.217  -1.351  -0.353  -0.000  -0.000  -0.000
   5_adp:  0.334  66.722  -3.217  -1.351  -0.353  -0.000  -0.000  -0.000
   5_occ:  0.334  66.722  -3.217  -1.351  -0.353  -0.000  -0.000  -0.000
   5_bss:  0.334  66.701  -3.295  -1.565  -0.476  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  66.306 0.3108  0.4219    84510.499
   1_bss:  65.129 0.3254  0.4634    82756.466
   1_xyz:  50.484 0.5141  0.7195    57129.352
   1_adp:  51.478 0.5009  0.7119    59179.993
   1_occ:  51.547 0.5000  0.7098    59330.175
   2_bss:  51.233 0.5037  0.7116    58451.432
   2_xyz:  40.406 0.6361  0.8786    37971.872
   2_adp:  37.526 0.6711  0.8977    33853.510
   2_occ:  37.518 0.6711  0.8975    33835.679
   3_bss:  37.304 0.6737  0.8717    33628.734
   3_xyz:  29.331 0.7640  0.9621    21370.483
   3_adp:  27.950 0.7795  0.9645    19945.904
   3_occ:  27.938 0.7796  0.9645    19929.661
   4_bss:  27.855 0.7804  0.9358    19832.574
   4_xyz:  22.411 0.8370  0.9737    13251.152
   4_adp:  20.400 0.8578  0.9792    11634.659
   4_occ:  20.384 0.8580  0.9794    11616.470
   5_bss:  20.372 0.8581  0.9620    11621.363
   5_xyz:  18.277 0.8778  0.9718     9580.144
   5_adp:  17.841 0.8821  0.9679     9340.984
   5_occ:  17.838 0.8821  0.9678     9334.583
   5_bss:  17.836 0.8821  0.9627     9335.707
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   2.4262e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   2.4262e-01
   1_xyz:   1.839  0.014  0.112 16.344  0.007  4.098   1.8823e-01
   1_adp:   1.839  0.014  0.112 16.344  0.007  4.098   1.8823e-01
   1_occ:   1.839  0.014  0.112 16.344  0.007  4.098   1.8823e-01
   2_bss:   1.839  0.014  0.112 16.344  0.007  4.098   1.8823e-01
   2_xyz:   1.355  0.010  0.094 15.390  0.006  4.108   1.0144e-01
   2_adp:   1.355  0.010  0.094 15.390  0.006  4.108   1.0144e-01
   2_occ:   1.355  0.010  0.094 15.390  0.006  4.108   1.0144e-01
   3_bss:   1.355  0.010  0.094 15.390  0.006  4.108   1.0144e-01
   3_xyz:   1.082  0.008  0.070 14.760  0.004  4.122   7.2109e-02
   3_adp:   1.082  0.008  0.070 14.760  0.004  4.122   7.2109e-02
   3_occ:   1.082  0.008  0.070 14.760  0.004  4.122   7.2109e-02
   4_bss:   1.082  0.008  0.070 14.760  0.004  4.122   7.2109e-02
   4_xyz:   1.134  0.008  0.079 14.573  0.004  4.113   7.0501e-02
   4_adp:   1.134  0.008  0.079 14.573  0.004  4.113   7.0501e-02
   4_occ:   1.134  0.008  0.079 14.573  0.004  4.113   7.0501e-02
   5_bss:   1.134  0.008  0.079 14.573  0.004  4.113   7.0501e-02
   5_xyz:   1.002  0.007  0.071 14.428  0.004  4.120   5.6430e-02
   5_adp:   1.002  0.007  0.071 14.428  0.004  4.120   5.6430e-02
   5_occ:   1.002  0.007  0.071 14.428  0.004  4.120   5.6430e-02
   5_bss:   1.002  0.007  0.071 14.428  0.004  4.120   5.6430e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.011   2.4845e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.011   2.4845e-01
   1_xyz:   9.822  0.116  0.320 80.650  0.049  1.757   1.1611e-01
   1_adp:   9.822  0.116  0.320 80.650  0.049  1.757   1.1611e-01
   1_occ:   9.822  0.116  0.320 80.650  0.049  1.757   1.1611e-01
   2_bss:   9.822  0.116  0.320 80.650  0.049  1.757   1.1611e-01
   2_xyz:  10.211  0.056  0.378 83.946  0.033  2.108   1.1783e-01
   2_adp:  10.211  0.056  0.378 83.946  0.033  2.108   1.1783e-01
   2_occ:  10.211  0.056  0.378 83.946  0.033  2.108   1.1783e-01
   3_bss:  10.211  0.056  0.378 83.946  0.033  2.108   1.1783e-01
   3_xyz:   7.447  0.048  0.244 82.424  0.034  2.264   1.4376e-01
   3_adp:   7.447  0.048  0.244 82.424  0.034  2.264   1.4376e-01
   3_occ:   7.447  0.048  0.244 82.424  0.034  2.264   1.4376e-01
   4_bss:   7.447  0.048  0.244 82.424  0.034  2.264   1.4376e-01
   4_xyz:   8.107  0.045  0.244 79.771  0.043  2.323   5.4589e-02
   4_adp:   8.107  0.045  0.244 79.771  0.043  2.323   5.4589e-02
   4_occ:   8.107  0.045  0.244 79.771  0.043  2.323   5.4589e-02
   5_bss:   8.107  0.045  0.244 79.771  0.043  2.323   5.4589e-02
   5_xyz:   6.795  0.048  0.221 81.014  0.042  2.385   3.6632e-02
   5_adp:   6.795  0.048  0.221 81.014  0.042  2.385   3.6632e-02
   5_occ:   6.795  0.048  0.221 81.014  0.042  2.385   3.6632e-02
   5_bss:   6.795  0.048  0.221 81.014  0.042  2.385   3.6632e-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: 119.34   0.00  21.27 106.94   0.00  17.57 119.34   0.00  41.37
   1_occ: 119.34   0.00  21.27 106.94   0.00  17.57 119.34   0.00  41.37
   2_bss: 119.34   0.00  21.27 106.94   0.00  17.57 119.34   0.00  41.37
   2_xyz: 119.34   0.00  21.27 106.94   0.00  17.57 119.34   0.00  41.37
   2_adp: 114.27   0.00  19.57  95.74   0.00  15.74 114.27   0.00  40.42
   2_occ: 114.27   0.00  19.57  95.74   0.00  15.74 114.27   0.00  40.42
   3_bss: 114.27   0.00  19.57  95.74   0.00  15.74 114.27   0.00  40.42
   3_xyz: 114.27   0.00  19.57  95.74   0.00  15.74 114.27   0.00  40.42
   3_adp: 111.33   0.00  20.15 100.35   0.00  15.01 111.33   3.61  48.16
   3_occ: 111.33   0.00  20.15 100.35   0.00  15.01 111.33   3.61  48.16
   4_bss: 111.33   0.00  20.15 100.35   0.00  15.01 111.33   3.61  48.16
   4_xyz: 111.33   0.00  20.15 100.35   0.00  15.01 111.33   3.61  48.16
   4_adp: 105.62   0.00  18.72  98.86   0.00  13.72 105.62   5.41  45.97
   4_occ: 105.62   0.00  18.72  98.86   0.00  13.72 105.62   5.41  45.97
   5_bss: 105.62   0.00  18.72  98.86   0.00  13.72 105.62   5.41  45.97
   5_xyz: 105.62   0.00  18.72  98.86   0.00  13.72 105.62   5.41  45.97
   5_adp: 104.34   0.63  18.53 104.34   0.63  13.44 101.92   5.55  46.27
   5_occ: 104.34   0.63  18.53 104.34   0.63  13.44 101.92   5.55  46.27
   5_bss: 104.32   0.61  18.51 104.32   0.61  13.42 101.90   5.53  46.25
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    3.183    0.032    0.458
   1_adp:    3.183    0.032    0.458
   1_occ:    3.183    0.032    0.458
   2_bss:    3.183    0.032    0.458
   2_xyz:    3.020    0.042    0.628
   2_adp:    3.020    0.042    0.628
   2_occ:    3.020    0.042    0.628
   3_bss:    3.020    0.042    0.628
   3_xyz:    2.991    0.060    0.768
   3_adp:    2.991    0.060    0.768
   3_occ:    2.991    0.060    0.768
   4_bss:    2.991    0.060    0.768
   4_xyz:    2.974    0.056    0.856
   4_adp:    2.974    0.056    0.856
   4_occ:    2.974    0.056    0.856
   5_bss:    2.974    0.056    0.856
   5_xyz:    2.944    0.052    0.897
   5_adp:    2.944    0.052    0.897
   5_occ:    2.944    0.052    0.897
   5_bss:    2.944    0.052    0.897
------------------------------------------------------------------------

CPU time actual refinement: 345.34


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_109/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_109/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_109/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_109/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_109/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 345.18 
  Macro-tasks:
    bulk solvent and scale       = 38.68  
    individual site refinement   = 141.17 
    weights calculation          = 30.84  
    collect and process          = 6.49   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 217.31 
  Micro-tasks:
    mask                            = 2.49   
    f_calc                          = 111.90 
    alpha_beta                      = 8.39   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 120.31 
    fmodel                         = 6.42   
    r_factors                      = 0.25   
    phase_errors                   = 10.19  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 261.39 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.998 micro seconds
Total CPU time: 5.98 minutes
from_scatterers_fft:    625 calls, 111.55 s
gradients_fft:          570 calls, 107.93 s

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

# Date 2008-01-16 Time 04:02:24 PST -0800 (1200484944.78 s)
Start R-work = 0.5048, R-free = 0.5119 (no bulk solvent and anisotropic scale)
Final R-work = 0.1607, R-free = 0.2052 (no bulk solvent and anisotropic scale)

Start R-work = 0.4994, R-free = 0.5021
Final R-work = 0.1377, R-free = 0.1878