# Date 2008-01-16 Time 04:19:15 PST -0800 (1200485955.09 s)
#phil __OFF__

Command line arguments: "../263.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17923
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 263

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 45.9914, 88.5498, 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: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 45.9914, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9247 1.96247
Completeness in resolution range: 0.942096
Completeness with d_max=infinity: 0.93925

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9247
                             d_min =   1.9625

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 45.9914, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9247 1.96247
Completeness in resolution range: 0.942096
Completeness with d_max=infinity: 0.93925

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9251 -  4.1996 [2187/2211]  1965   222  10.2%
  bin  2:  4.1996 -  3.3457 [2099/2119]  1891   208   9.9%
  bin  3:  3.3457 -  2.9264 [2080/2099]  1877   203   9.8%
  bin  4:  2.9264 -  2.6605 [2034/2064]  1820   214  10.5%
  bin  5:  2.6605 -  2.4707 [2045/2064]  1841   204  10.0%
  bin  6:  2.4707 -  2.3256 [2039/2064]  1837   202   9.9%
  bin  7:  2.3256 -  2.2095 [2018/2046]  1819   199   9.9%
  bin  8:  2.2095 -  2.1136 [2007/2043]  1808   199   9.9%
  bin  9:  2.1136 -  2.0324 [1979/2049]  1787   192   9.7%
  bin 10:  2.0324 -  1.9625 [1101/2034]   985   116  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_263/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: 0.14 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:
        0.95 -     1.74: 7
        1.74 -     2.53: 71
        2.53 -     3.32: 3906
        3.32 -     4.11: 9483
        4.11 -     4.90: 15095
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  0.949 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.485 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.506 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.589 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  53 " - " O   HOH Z 102 "  1.616 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28557 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_263/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_263/model_refine_001.geo

CPU time processing inputs: 9.07


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 45.9914 88.54975 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: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4860   r_free= 0.4854   ksol= 0.00   Bsol= 0.00   scale= 0.882    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.292272                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9251 -  4.6841 0.99   1421  154 0.3837 0.3716       6.596       6.536|
|  2:  4.6841 -  3.7372 0.99   1367  155 0.4227 0.4493      6.8111       6.843|
|  3:  3.7372 -  3.2704 0.99   1332  150 0.4651 0.4401      6.7093      6.7061|
|  4:  3.2704 -  2.9740 0.99   1329  148 0.4874 0.5090      6.5483      6.5476|
|  5:  2.9740 -  2.7623 0.99   1327  144 0.5176 0.4693      6.3678      6.4018|
|  6:  2.7623 -  2.6003 0.99   1324  150 0.5259 0.5318      6.2936      6.1985|
|  7:  2.6003 -  2.4707 0.99   1294  150 0.5167 0.5375      6.2317      6.1514|
|  8:  2.4707 -  2.3636 0.98   1318  143 0.5384 0.5320      6.1897      6.2214|
|  9:  2.3636 -  2.2729 0.98   1293  138 0.5263 0.5280      6.1195      6.1905|
| 10:  2.2729 -  2.1947 1.00   1309  145 0.5337 0.5503      6.1068      6.1031|
| 11:  2.1947 -  2.1263 0.98   1281  147 0.5312 0.5029      6.0203        6.03|
| 12:  2.1263 -  2.0657 0.98   1297  140 0.5302 0.4979      5.9713      5.9624|
| 13:  2.0657 -  2.0114 0.90   1186  129 0.5204 0.5329       5.895      5.8348|
| 14:  2.0114 -  1.9625 0.43    552   66 0.5378 0.5308      5.8885      5.8057|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9251 -  4.6841  1421   154  0.71  33.66   0.81     0.77      72302.68|
|  2:  4.6841 -  3.7372  1367   155  0.65  39.32   0.90     0.76     127357.73|
|  3:  3.7372 -  3.2704  1332   150  0.52  50.36   0.90     0.70     138607.32|
|  4:  3.2704 -  2.9740  1329   148  0.40  59.61   0.89     0.58     129892.90|
|  5:  2.9740 -  2.7623  1327   144  0.37  61.99   0.86     0.54      88443.35|
|  6:  2.7623 -  2.6003  1324   150  0.35  63.87   0.89     0.50      75834.86|
|  7:  2.6003 -  2.4707  1294   150  0.35  63.95   0.89     0.48      65320.99|
|  8:  2.4707 -  2.3636  1318   143  0.31  66.57   0.89     0.45      61963.64|
|  9:  2.3636 -  2.2729  1293   138  0.32  66.12   0.91     0.47      56189.25|
| 10:  2.2729 -  2.1947  1309   145  0.34  64.90   0.91     0.50      50180.50|
| 11:  2.1947 -  2.1263  1281   147  0.32  66.15   0.92     0.51      49518.33|
| 12:  2.1263 -  2.0657  1297   140  0.31  67.23   0.93     0.50      44599.54|
| 13:  2.0657 -  2.0114  1186   129  0.31  67.22   0.94     0.50      38525.94|
| 14:  2.0114 -  1.9625   552    66  0.37  62.10   0.98     0.52      28723.56|
|alpha:            min =        0.45 max =            0.77 mean =         0.56|
|beta:             min =    28723.56 max =       138607.32 mean =     75962.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           90.00 mean =        59.08|
|phase err.(test): min =        0.00 max =           89.95 mean =        59.31|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.785524             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.802   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.135435              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.502   (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 |  0.949 -  1.344:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.344 -  1.739:        6 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.739 -  2.134:       22 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.134 -  2.530:       49 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.530 -  2.925:     1509 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.925 -  3.320:     2397 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.320 -  3.715:     3755 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.715 -  4.110:     5728 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.110 -  4.505:     6653 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.505 -  4.900:     8442 |
|-----------------------------------------------------------------------------|
|-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 |        0.203 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.107    4.900  0.949 |       0.791 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4860   r_free= 0.4854   ksol= 0.00   Bsol= 0.00   scale= 0.882    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.292272                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4775   r_free= 0.4756   ksol= 0.32   Bsol= 23.45   scale= 0.926   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,0.96,3.65,0.00,0.00,0.00); trace/3= 0.77                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.287562                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.106480             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.663   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.419965              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.182   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4775      final r-factor (work) = 0.3717          |
| start r-factor (free) = 0.4756      final r-factor (free) = 0.4109          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.5104 = 14.11 * 0.50 * 6.2819 + 1.00 * 0.2029                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.7509 = 14.11 * 0.50 * 6.1796 + 1.00 * 0.1648                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3717      final r-factor (work) = 0.3418          |
| start r-factor (free) = 0.4109      final r-factor (free) = 0.4185          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7812 = 1.42 * 1.00 * 6.1796 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7408 = 1.42 * 1.00 * 6.0850 + 1.00 * 0.1003                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    129.77  17.23    None  None   None       |
|    all(noH): 2823   0      0.00    129.77  17.23    None  None   None       |
|    Sol.    : 438    0      0.00    64.96   36.79    None  None   None       |
|    Mac.    : 2385   0      0.00    129.77  13.64    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 -  12.977: 1236   |   5:    64.885 -  77.861:    1        |
|      1:    12.977 -  25.954: 1038   |   6:    77.861 -  90.838:    0        |
|      2:    25.954 -  38.931:  321   |   7:    90.838 - 103.815:    0        |
|      3:    38.931 -  51.908:  172   |   8:   103.815 - 116.792:    0        |
|      4:    51.908 -  64.885:   54   |   9:   116.792 - 129.769:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3418 r_free = 0.4185             target_work(ml) = 6.091         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3416 r_free = 0.4193             target_work(ml) = 6.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3416   r_free= 0.4193   ksol= 0.32   Bsol= 23.45   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,0.96,3.65,0.00,0.00,0.00); trace/3= 0.77                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.090720                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3411   r_free= 0.4187   ksol= 0.35   Bsol= 66.25   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.03,0.63,2.77,0.00,0.00,0.00); trace/3= 0.79                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.092272                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.834345              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.681  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.254692              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.868   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3411      final r-factor (work) = 0.2668          |
| start r-factor (free) = 0.4187      final r-factor (free) = 0.3311          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.0497 = 8.83 * 0.50 * 6.0864 + 1.00 * 0.1651                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.6639 = 8.83 * 0.50 * 6.0144 + 1.00 * 0.0971                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2668      final r-factor (work) = 0.2421          |
| start r-factor (free) = 0.3311      final r-factor (free) = 0.3303          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 25.6175 = 4.25 * 1.00 * 6.0144 + 1.00 * 0.0279                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 24.9298 = 4.25 * 1.00 * 5.8532 + 1.00 * 0.0263                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    117.76  19.86    None  None   None       |
|    all(noH): 2823   0      0.00    117.76  19.86    None  None   None       |
|    Sol.    : 438    0      0.30    117.76  47.11    None  None   None       |
|    Mac.    : 2385   0      0.00    110.42  14.86    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 -  11.776: 1253   |   5:    58.880 -  70.655:   95        |
|      1:    11.776 -  23.552:  796   |   6:    70.655 -  82.431:   45        |
|      2:    23.552 -  35.328:  300   |   7:    82.431 -  94.207:   22        |
|      3:    35.328 -  47.104:  171   |   8:    94.207 - 105.983:    7        |
|      4:    47.104 -  58.880:  130   |   9:   105.983 - 117.759:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2421 r_free = 0.3303             target_work(ml) = 5.847         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2420 r_free = 0.3303             target_work(ml) = 5.847         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2420   r_free= 0.3303   ksol= 0.35   Bsol= 66.25   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.03,0.63,2.77,0.00,0.00,0.00); trace/3= 0.79                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.846700                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2423   r_free= 0.3303   ksol= 0.34   Bsol= 70.35   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.74,0.44,2.46,0.00,0.00,0.00); trace/3= 0.72                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.845016                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.275294              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.045  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.441415              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.986  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2423      final r-factor (work) = 0.1913          |
| start r-factor (free) = 0.3303      final r-factor (free) = 0.2641          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.3905 = 7.28 * 0.50 * 5.8536 + 1.00 * 0.0971                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.0264 = 7.28 * 0.50 * 5.7585 + 1.00 * 0.0788                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1913      final r-factor (work) = 0.1719          |
| start r-factor (free) = 0.2641      final r-factor (free) = 0.2331          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5679 = 0.44 * 1.00 * 5.7585 + 1.00 * 0.0260                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4806 = 0.44 * 1.00 * 5.5895 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.86  17.65    None  None   None       |
|    all(noH): 2823   0      0.00    110.86  17.65    None  None   None       |
|    Sol.    : 438    0      3.51    110.86  45.39    None  None   None       |
|    Mac.    : 2385   0      0.00    98.47   12.55    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 -  11.086: 1416   |   5:    55.430 -  66.516:   97        |
|      1:    11.086 -  22.172:  787   |   6:    66.516 -  77.602:   47        |
|      2:    22.172 -  33.258:  192   |   7:    77.602 -  88.688:   11        |
|      3:    33.258 -  44.344:  139   |   8:    88.688 -  99.774:   10        |
|      4:    44.344 -  55.430:  122   |   9:    99.774 - 110.860:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1719 r_free = 0.2331             target_work(ml) = 5.521         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1715 r_free = 0.2328             target_work(ml) = 5.520         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1715   r_free= 0.2328   ksol= 0.34   Bsol= 70.35   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.74,0.44,2.46,0.00,0.00,0.00); trace/3= 0.72                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.520215                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1712   r_free= 0.2324   ksol= 0.32   Bsol= 58.11   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.24,-0.67,1.47,-0.00,0.00,0.00); trace/3= -0.15                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.518981                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.342626              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.300  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.008782              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.716  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1712      final r-factor (work) = 0.1483          |
| start r-factor (free) = 0.2324      final r-factor (free) = 0.2003          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6283 = 2.34 * 0.50 * 5.5915 + 1.00 * 0.0788                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4542 = 2.34 * 0.50 * 5.4628 + 1.00 * 0.0556                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1483      final r-factor (work) = 0.1413          |
| start r-factor (free) = 0.2003      final r-factor (free) = 0.1943          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5240 = 1.01 * 1.00 * 5.4628 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4215 = 1.01 * 1.00 * 5.3604 + 1.00 * 0.0140                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.66  17.41    None  None   None       |
|    all(noH): 2823   0      0.00    108.66  17.41    None  None   None       |
|    Sol.    : 438    0      4.44    108.66  46.67    None  None   None       |
|    Mac.    : 2385   0      0.00    101.56  12.04    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 -  10.866: 1457   |   5:    54.329 -  65.195:   91        |
|      1:    10.866 -  21.732:  765   |   6:    65.195 -  76.060:   70        |
|      2:    21.732 -  32.597:  183   |   7:    76.060 -  86.926:   22        |
|      3:    32.597 -  43.463:  114   |   8:    86.926 -  97.792:    8        |
|      4:    43.463 -  54.329:  108   |   9:    97.792 - 108.658:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1413 r_free = 0.1943             target_work(ml) = 5.345         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1412 r_free = 0.1942             target_work(ml) = 5.345         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1412   r_free= 0.1942   ksol= 0.32   Bsol= 58.11   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.24,-0.67,1.47,-0.00,0.00,0.00); trace/3= -0.15                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.344535                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1414   r_free= 0.1945   ksol= 0.32   Bsol= 58.11   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.44,-0.94,1.24,-0.00,0.00,0.00); trace/3= -0.38                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.343933                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.665850              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.791  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.999111              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.007  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1414      final r-factor (work) = 0.1274          |
| start r-factor (free) = 0.1945      final r-factor (free) = 0.1788          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2013 = 2.67 * 0.50 * 5.3609 + 1.00 * 0.0556                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1292 = 2.67 * 0.50 * 5.3016 + 1.00 * 0.0625                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1274      final r-factor (work) = 0.1246          |
| start r-factor (free) = 0.1788      final r-factor (free) = 0.1766          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.2157 = 4.00 * 1.00 * 5.3016 + 1.00 * 0.0139                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 20.9964 = 4.00 * 1.00 * 5.2466 + 1.00 * 0.0147                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.45  17.23    None  None   None       |
|    all(noH): 2823   0      0.00    108.45  17.23    None  None   None       |
|    Sol.    : 438    0      4.00    108.45  46.84    None  None   None       |
|    Mac.    : 2385   0      0.00    107.38  11.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.845: 1500   |   5:    54.223 -  65.067:   75        |
|      1:    10.845 -  21.689:  747   |   6:    65.067 -  75.912:   70        |
|      2:    21.689 -  32.534:  174   |   7:    75.912 -  86.756:   36        |
|      3:    32.534 -  43.378:  107   |   8:    86.756 -  97.601:   13        |
|      4:    43.378 -  54.223:   93   |   9:    97.601 - 108.445:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1246 r_free = 0.1766             target_work(ml) = 5.240         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1246 r_free = 0.1767             target_work(ml) = 5.240         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1246   r_free= 0.1767   ksol= 0.32   Bsol= 58.11   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.44,-0.94,1.24,-0.00,0.00,0.00); trace/3= -0.38                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.240181                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9251 -  4.6841 0.99   1421  154 0.0978 0.1331      5.3991       5.602|
|  2:  4.6841 -  3.7372 0.99   1367  155 0.0859 0.1150      5.4681      5.6665|
|  3:  3.7372 -  3.2704 0.99   1332  150 0.1179 0.1655      5.5637      5.9162|
|  4:  3.2704 -  2.9740 0.99   1329  148 0.1436 0.1951      5.5696      5.7345|
|  5:  2.9740 -  2.7623 0.99   1327  144 0.1535 0.1810      5.4737      5.6496|
|  6:  2.7623 -  2.6003 0.99   1324  150 0.1435 0.2472      5.3411       5.645|
|  7:  2.6003 -  2.4707 0.99   1294  150 0.1502 0.1897      5.3134      5.4487|
|  8:  2.4707 -  2.3636 0.98   1318  143 0.1375 0.1953      5.2092      5.4794|
|  9:  2.3636 -  2.2729 0.98   1293  138 0.1338 0.1979      5.1381      5.4246|
| 10:  2.2729 -  2.1947 1.00   1309  145 0.1238 0.1792       5.034      5.2192|
| 11:  2.1947 -  2.1263 0.98   1281  147 0.1257 0.2026      5.0173      5.3619|
| 12:  2.1263 -  2.0657 0.98   1297  140 0.1290 0.1857      4.9598      5.2714|
| 13:  2.0657 -  2.0114 0.90   1186  129 0.1096 0.1733      4.7934       4.991|
| 14:  2.0114 -  1.9625 0.43    552   66 0.0977 0.1732      4.6557      4.9654|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9251 -  4.6841  1421   154  0.93  10.38   0.97     0.95       8422.30|
|  2:  4.6841 -  3.7372  1367   155  0.95   8.52   1.02     1.01      10002.01|
|  3:  3.7372 -  3.2704  1332   150  0.92  12.85   1.05     1.05      12193.22|
|  4:  3.2704 -  2.9740  1329   148  0.90  16.14   1.02     1.00      12823.15|
|  5:  2.9740 -  2.7623  1327   144  0.87  19.12   1.01     0.98      11817.07|
|  6:  2.7623 -  2.6003  1324   150  0.87  19.04   0.97     0.92       8985.49|
|  7:  2.6003 -  2.4707  1294   150  0.87  19.34   1.00     0.96       8666.08|
|  8:  2.4707 -  2.3636  1318   143  0.88  18.05   1.00     0.96       7156.56|
|  9:  2.3636 -  2.2729  1293   138  0.89  17.93   0.99     0.94       6172.18|
| 10:  2.2729 -  2.1947  1309   145  0.89  17.53   1.00     0.96       5231.80|
| 11:  2.1947 -  2.1263  1281   147  0.88  18.18   0.99     0.95       5255.07|
| 12:  2.1263 -  2.0657  1297   140  0.89  17.61   1.00     1.00       4580.91|
| 13:  2.0657 -  2.0114  1186   129  0.90  16.78   0.99     0.96       3504.98|
| 14:  2.0114 -  1.9625   552    66  0.93  12.59   0.98     0.96       2513.04|
|alpha:            min =        0.92 max =            1.05 mean =         0.97|
|beta:             min =     2513.04 max =        12823.15 mean =      7952.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        16.08|
|phase err.(test): min =        0.00 max =           89.35 mean =        15.60|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1245   r_free= 0.1766   ksol= 0.32   Bsol= 56.79   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.22,-0.84,1.39,-0.00,0.00,0.00); trace/3= -0.22                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.240240                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1245   r_free= 0.1766   ksol= 0.32   Bsol= 56.79   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.22,-0.84,1.39,-0.00,0.00,0.00); trace/3= -0.22                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.240240                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9251 -  4.6841 0.99   1421  154 0.0978 0.1332      5.3999      5.6033|
|  2:  4.6841 -  3.7372 0.99   1367  155 0.0859 0.1150      5.4684       5.666|
|  3:  3.7372 -  3.2704 0.99   1332  150 0.1179 0.1656      5.5636      5.9165|
|  4:  3.2704 -  2.9740 0.99   1329  148 0.1436 0.1952      5.5697      5.7348|
|  5:  2.9740 -  2.7623 0.99   1327  144 0.1534 0.1810      5.4738      5.6493|
|  6:  2.7623 -  2.6003 0.99   1324  150 0.1435 0.2472      5.3411      5.6451|
|  7:  2.6003 -  2.4707 0.99   1294  150 0.1502 0.1897      5.3136       5.449|
|  8:  2.4707 -  2.3636 0.98   1318  143 0.1375 0.1953      5.2094      5.4795|
|  9:  2.3636 -  2.2729 0.98   1293  138 0.1337 0.1979      5.1382      5.4247|
| 10:  2.2729 -  2.1947 1.00   1309  145 0.1237 0.1794       5.034      5.2203|
| 11:  2.1947 -  2.1263 0.98   1281  147 0.1256 0.2026      5.0173      5.3619|
| 12:  2.1263 -  2.0657 0.98   1297  140 0.1289 0.1854      4.9597      5.2705|
| 13:  2.0657 -  2.0114 0.90   1186  129 0.1096 0.1732      4.7929      4.9904|
| 14:  2.0114 -  1.9625 0.43    552   66 0.0977 0.1728      4.6548      4.9635|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9251 -  4.6841  1421   154  0.93  10.39   0.97     0.95       8441.10|
|  2:  4.6841 -  3.7372  1367   155  0.95   8.52   1.03     1.01      10011.21|
|  3:  3.7372 -  3.2704  1332   150  0.92  12.85   1.05     1.06      12197.15|
|  4:  3.2704 -  2.9740  1329   148  0.90  16.14   1.03     1.01      12825.01|
|  5:  2.9740 -  2.7623  1327   144  0.87  19.12   1.01     0.99      11819.95|
|  6:  2.7623 -  2.6003  1324   150  0.87  19.04   0.98     0.92       8984.84|
|  7:  2.6003 -  2.4707  1294   150  0.87  19.34   1.00     0.97       8669.36|
|  8:  2.4707 -  2.3636  1318   143  0.88  18.05   1.00     0.97       7156.78|
|  9:  2.3636 -  2.2729  1293   138  0.89  17.94   1.00     0.94       6175.59|
| 10:  2.2729 -  2.1947  1309   145  0.89  17.53   1.01     0.97       5232.13|
| 11:  2.1947 -  2.1263  1281   147  0.88  18.19   1.00     0.96       5256.95|
| 12:  2.1263 -  2.0657  1297   140  0.89  17.61   1.01     1.01       4581.24|
| 13:  2.0657 -  2.0114  1186   129  0.90  16.77   1.00     0.97       3498.57|
| 14:  2.0114 -  1.9625   552    66  0.93  12.57   0.99     0.97       2502.85|
|alpha:            min =        0.92 max =            1.06 mean =         0.98|
|beta:             min =     2502.85 max =        12825.01 mean =      7954.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        16.08|
|phase err.(test): min =        0.00 max =           89.36 mean =        15.61|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.45  17.23    None  None   None       |
|    all(noH): 2823   0      0.00    108.45  17.23    None  None   None       |
|    Sol.    : 438    0      4.00    108.45  46.84    None  None   None       |
|    Mac.    : 2385   0      0.00    107.38  11.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.848: 1500   |   5:    54.226 -  65.070:   75        |
|      1:    10.848 -  21.692:  747   |   6:    65.070 -  75.915:   70        |
|      2:    21.692 -  32.537:  174   |   7:    75.915 -  86.759:   36        |
|      3:    32.537 -  43.381:  107   |   8:    86.759 -  97.604:   13        |
|      4:    43.381 -  54.226:   93   |   9:    97.604 - 108.448:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 329         
Filter by distance & map next to the model:
   mapped sites are within: 0.394 - 4.861
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 323 from: 329
   mapped sites are within: 0.764 - 4.861

peak=   10.189 closest distance to " O   HOH Z 103 " =    1.539
peak=    6.794 closest distance to " O   HOH Z 178 " =    1.302
peak=    6.770 closest distance to " O   HOH Z 385 " =    1.423
peak=    6.644 closest distance to " O   HOH Z  41 " =    1.007
peak=    6.378 closest distance to " O   HOH Z 245 " =    1.160
peak=    5.659 closest distance to " O   HOH Z  70 " =    1.076
peak=    5.653 closest distance to " O   HOH Z 417 " =    2.511
peak=    5.638 closest distance to " O   HOH Z  65 " =    1.345
peak=    5.561 closest distance to " O   HOH Z 142 " =    1.907
peak=    5.537 closest distance to " O   HOH Z 117 " =    1.507
peak=    5.480 closest distance to " O   HOH Z 287 " =    2.016
peak=    5.429 closest distance to " NE2 GLN A  11 " =    1.200
peak=    5.415 closest distance to " O   HOH Z 105 " =    1.197
peak=    5.399 closest distance to " CG  PRO A  54 " =    1.441
peak=    5.398 closest distance to " O   HOH Z 422 " =    1.108
peak=    5.395 closest distance to " O   HOH Z 222 " =    1.183
peak=    5.375 closest distance to " O   HOH Z 423 " =    1.883
peak=    5.277 closest distance to " O   HOH Z  49 " =    1.407
peak=    5.265 closest distance to " O   HOH Z  83 " =    1.409
peak=    5.153 closest distance to " O   HOH Z  69 " =    1.657
peak=    5.116 closest distance to " O   HOH Z  63 " =    1.754
peak=    5.060 closest distance to " O   HOH Z 112 " =    1.266
peak=    5.037 closest distance to " O   HOH Z 403 " =    2.091
peak=    5.007 closest distance to " O   HOH Z 375 " =    1.198
peak=    4.975 closest distance to " O   HOH Z 126 " =    2.157
peak=    4.893 closest distance to " O   HOH Z   9 " =    2.272
peak=    4.855 closest distance to " O   HOH Z 427 " =    2.277
peak=    4.706 closest distance to " CG  GLN A  58 " =    1.186
peak=    4.694 closest distance to " O   HOH Z 278 " =    1.324
peak=    4.690 closest distance to " O   HOH Z 236 " =    1.476
peak=    4.666 closest distance to " O   HOH Z 132 " =    1.200
peak=    4.598 closest distance to " O   HOH Z   7 " =    1.483
peak=    4.550 closest distance to " O   HOH Z 403 " =    2.105
peak=    4.469 closest distance to " CB  PRO A  54 " =    1.082
peak=    4.453 closest distance to " O   HOH Z  39 " =    1.227
peak=    4.444 closest distance to " O   HOH Z 406 " =    1.723
peak=    4.442 closest distance to " CB  GLN A 223 " =    1.495
peak=    4.435 closest distance to " O   HOH Z 130 " =    1.080
peak=    4.423 closest distance to " O   HOH Z  76 " =    1.219
peak=    4.422 closest distance to " O   HOH Z  91 " =    2.409
peak=    4.411 closest distance to " O   HOH Z 427 " =    1.100
peak=    4.406 closest distance to " CB  ARG A 275 " =    1.053
peak=    4.400 closest distance to " O   HOH Z 425 " =    1.462
peak=    4.386 closest distance to " O   HOH Z 380 " =    1.922
peak=    4.332 closest distance to " CB  SER A  63 " =    1.306
peak=    4.325 closest distance to " O   HOH Z 243 " =    2.324
peak=    4.285 closest distance to " CB  PRO A 213 " =    1.286
peak=    4.248 closest distance to " O   HOH Z 303 " =    2.260
peak=    4.248 closest distance to " O   HOH Z 293 " =    1.412
peak=    4.230 closest distance to " O   HOH Z 394 " =    1.723
peak=    4.216 closest distance to " O   HOH Z 258 " =    1.086
peak=    4.200 closest distance to " CG  PRO A  90 " =    1.347
peak=    4.194 closest distance to " O   HOH Z 371 " =    2.000
peak=    4.184 closest distance to " O   HOH Z 327 " =    1.777
peak=    4.184 closest distance to " CD  ARG A  66 " =    2.446
peak=    4.181 closest distance to " CE  LYS A 119 " =    1.279
peak=    4.179 closest distance to " O   HOH Z 411 " =    3.937
peak=    4.178 closest distance to " O   HOH Z 232 " =    2.214
peak=    4.156 closest distance to " NH1AARG A 145 " =    1.199
peak=    4.149 closest distance to " O   HOH Z 139 " =    1.215
peak=    4.144 closest distance to " CB  ASN A 148 " =    1.412
peak=    4.134 closest distance to " O   PRO A 198 " =    1.373
peak=    4.130 closest distance to " NH2AARG A 190 " =    1.985
peak=    4.094 closest distance to " O   HOH Z 298 " =    1.891
peak=    4.058 closest distance to " CD2 TRP A 179 " =    1.277
peak=    4.053 closest distance to " CB  GLU A 277 " =    3.554
peak=    4.044 closest distance to " O   HOH Z  77 " =    1.240
peak=    4.043 closest distance to " O   HOH Z 145 " =    1.335
peak=    4.040 closest distance to " O   HOH Z 193 " =    1.274
peak=    4.016 closest distance to " O   HOH Z 103 " =    1.507
peak=    4.005 closest distance to " CA  TYR A  30 " =    1.036
peak=    4.004 closest distance to " CG2 VAL A 257 " =    0.900
peak=    4.004 closest distance to " O   HOH Z  59 " =    1.704
peak=    3.992 closest distance to " CA  VAL A 125 " =    1.128
peak=    3.978 closest distance to " NZ  LYS A 117 " =    2.828
peak=    3.971 closest distance to " O   HOH Z  26 " =    1.489
peak=    3.960 closest distance to " O   HOH Z 203 " =    1.530
peak=    3.958 closest distance to " NH2 ARG A  56 " =    2.080
peak=    3.952 closest distance to " O   HOH Z 218 " =    1.806
peak=    3.949 closest distance to " NZ  LYS A 119 " =    2.430
peak=    3.929 closest distance to " CB  SER A 216 " =    1.018
peak=    3.921 closest distance to " CB  ASP A 191 " =    1.223
peak=    3.902 closest distance to " O   HOH Z 234 " =    3.442
peak=    3.900 closest distance to " O   HOH Z 369 " =    1.771
peak=    3.893 closest distance to " CG AARG A 275 " =    1.303
peak=    3.892 closest distance to " O   HOH Z 425 " =    2.013
peak=    3.872 closest distance to " O   HOH Z 215 " =    1.529
peak=    3.868 closest distance to " O   HOH Z 402 " =    1.446
peak=    3.861 closest distance to " CB  SER A  62 " =    0.881
peak=    3.861 closest distance to " CG  LYS A  76 " =    1.805
peak=    3.854 closest distance to " CB  PRO A  90 " =    1.087
peak=    3.851 closest distance to " O   HOH Z 392 " =    1.179
peak=    3.851 closest distance to " NZ  LYS A 166 " =    1.025
peak=    3.850 closest distance to " CB  THR A  31 " =    1.597
peak=    3.844 closest distance to " CB  ARG A  79 " =    1.172
peak=    3.844 closest distance to " N   TYR A  15 " =    1.306
peak=    3.838 closest distance to " O   HOH Z 359 " =    1.542
peak=    3.831 closest distance to " CA  ASN A 127 " =    1.153
peak=    3.830 closest distance to " CZ3 TRP A 266 " =    1.147
peak=    3.808 closest distance to " CB  ALA A 114 " =    0.821
peak=    3.807 closest distance to " O   HOH Z 405 " =    1.650
peak=    3.802 closest distance to " CG  PRO A 243 " =    1.085
peak=    3.798 closest distance to " OG ASER A 258 " =    3.051
peak=    3.798 closest distance to " O   HOH Z 211 " =    0.898
peak=    3.797 closest distance to " O   HOH Z 185 " =    1.517
peak=    3.790 closest distance to " NE2 GLN A  58 " =    4.632
peak=    3.779 closest distance to " CD  GLN A  77 " =    1.233
peak=    3.775 closest distance to " CB  VAL A 265 " =    1.343
peak=    3.775 closest distance to " O   HOH Z  24 " =    2.058
peak=    3.774 closest distance to " O   HOH Z  71 " =    1.747
peak=    3.773 closest distance to " CB  SER A  99 " =    0.853
peak=    3.766 closest distance to " O   HOH Z 193 " =    1.198
peak=    3.766 closest distance to " O   HOH Z 365 " =    2.572
peak=    3.759 closest distance to " CB  ASN A 142 " =    1.001
peak=    3.757 closest distance to " CG  LEU A 167 " =    1.263
peak=    3.744 closest distance to " ND2 ASN A 249 " =    0.824
peak=    3.732 closest distance to " CB  VAL A 202 " =    1.660
peak=    3.730 closest distance to " O   HOH Z 434 " =    1.427
peak=    3.724 closest distance to " O   HOH Z 214 " =    2.514
peak=    3.723 closest distance to " O   HOH Z 126 " =    1.552
peak=    3.721 closest distance to " O   HOH Z 368 " =    3.619
peak=    3.708 closest distance to " CB  ARG A 190 " =    1.643
peak=    3.707 closest distance to " O   HOH Z  11 " =    1.020
peak=    3.703 closest distance to " O   HOH Z  61 " =    1.615
peak=    3.702 closest distance to " CB  LYS A 117 " =    1.281
peak=    3.692 closest distance to " O   HOH Z 414 " =    1.178
peak=    3.681 closest distance to " CA  ASN A 215 " =    1.075
peak=    3.680 closest distance to " CG  GLN A  11 " =    2.267
peak=    3.680 closest distance to " CA  ALA A 160 " =    1.068
peak=    3.672 closest distance to " CB  ASN A 110 " =    1.003
peak=    3.671 closest distance to " O   HOH Z 303 " =    2.582
peak=    3.666 closest distance to " CG2 VAL A 197 " =    1.217
peak=    3.665 closest distance to " CA  ALA A 129 " =    1.157
peak=    3.659 closest distance to " O   HOH Z  42 " =    1.327
peak=    3.658 closest distance to " CB  ASN A  39 " =    1.065
peak=    3.653 closest distance to " O   HOH Z 191 " =    3.015
peak=    3.650 closest distance to " N   GLU A   2 " =    1.454
peak=    3.650 closest distance to " CG  PRO A 198 " =    1.188
peak=    3.650 closest distance to " O   HOH Z   1 " =    1.546
peak=    3.648 closest distance to " O   HOH Z 143 " =    1.339
peak=    3.647 closest distance to " O   HOH Z 109 " =    1.253
peak=    3.640 closest distance to " O   HOH Z 272 " =    1.855
peak=    3.639 closest distance to " CA  ARG A 156 " =    1.063
peak=    3.638 closest distance to " O   HOH Z 362 " =    2.018
peak=    3.634 closest distance to " CB  ASN A 285 " =    1.092
peak=    3.628 closest distance to " CA  PHE A 283 " =    1.206
peak=    3.627 closest distance to " OG BSER A 164 " =    2.281
peak=    3.621 closest distance to " O   HOH Z 207 " =    2.466
peak=    3.614 closest distance to " CB  PHE A 130 " =    0.981
peak=    3.605 closest distance to " CA  ARG A 195 " =    1.339
peak=    3.601 closest distance to " O   HOH Z  78 " =    1.564
peak=    3.599 closest distance to " O   HOH Z  40 " =    1.620
peak=    3.597 closest distance to " O   HOH Z 365 " =    1.445
peak=    3.595 closest distance to " O   HOH Z 216 " =    3.980
peak=    3.593 closest distance to " O   HOH Z   1 " =    1.594
peak=    3.590 closest distance to " CG  GLN A  89 " =    1.521
peak=    3.590 closest distance to " O   HOH Z 437 " =    1.611
peak=    3.585 closest distance to " O   HOH Z 153 " =    3.698
peak=    3.582 closest distance to " O   HOH Z 201 " =    1.511
peak=    3.562 closest distance to " O   HOH Z 305 " =    3.580
peak=    3.553 closest distance to " CA  TYR A 116 " =    1.318
peak=    3.548 closest distance to " CA  ALA A  51 " =    1.073
peak=    3.545 closest distance to " OE1 GLU A   2 " =    1.427
peak=    3.544 closest distance to " CG2 ILE A 120 " =    0.945
peak=    3.538 closest distance to " O   HOH Z  67 " =    1.245
peak=    3.537 closest distance to " ND2BASN A 224 " =    0.868
peak=    3.535 closest distance to " O   HOH Z 261 " =    1.799
peak=    3.532 closest distance to " O   HOH Z 251 " =    1.299
peak=    3.525 closest distance to " CE3 TRP A 150 " =    1.128
peak=    3.524 closest distance to " O   HOH Z 368 " =    1.905
peak=    3.512 closest distance to " N   PHE A 130 " =    1.301
peak=    3.510 closest distance to " CA  ALA A 291 " =    0.865
peak=    3.509 closest distance to " CE  LYS A  76 " =    0.872
peak=    3.502 closest distance to " O   HOH Z 124 " =    1.304
peak=    3.502 closest distance to " CB  TRP A 266 " =    1.178
peak=    3.500 closest distance to " O   HOH Z  88 " =    3.824
peak=    3.500 closest distance to " O   HOH Z 280 " =    1.490
peak=    3.496 closest distance to " O   HOH Z  17 " =    1.710
peak=    3.495 closest distance to " O   HOH Z 213 " =    2.066
peak=    3.491 closest distance to " CB  TRP A 179 " =    1.404
peak=    3.490 closest distance to " O   HOH Z 290 " =    1.019
peak=    3.489 closest distance to " CG1 ILE A 120 " =    1.963
peak=    3.487 closest distance to " N   HIS A 108 " =    1.893
peak=    3.485 closest distance to " CB  LEU A 300 " =    0.948
peak=    3.481 closest distance to " CB  ASP A 124 " =    0.872
peak=    3.479 closest distance to " CB  SER A 276 " =    1.165
peak=    3.478 closest distance to " O   HOH Z 132 " =    2.135
peak=    3.475 closest distance to " CB  TYR A 116 " =    1.091
peak=    3.470 closest distance to " OE2 GLU A  53 " =    2.059
peak=    3.468 closest distance to " N   GLN A 278 " =    1.339
peak=    3.468 closest distance to " O   HOH Z 368 " =    4.251
peak=    3.465 closest distance to " O   HOH Z 173 " =    2.072
peak=    3.453 closest distance to " O   HOH Z 193 " =    1.687
peak=    3.448 closest distance to " O   HOH Z 431 " =    1.111
peak=    3.441 closest distance to " O   HOH Z  68 " =    1.956
peak=    3.439 closest distance to " CB  ASP A 107 " =    1.106
peak=    3.436 closest distance to " OG BSER A  99 " =    2.310
peak=    3.435 closest distance to " CB  GLU A 236 " =    1.361
peak=    3.430 closest distance to " O   HOH Z 423 " =    1.645
peak=    3.429 closest distance to " CB  ALA A   1 " =    1.068
peak=    3.428 closest distance to " O   HOH Z 357 " =    1.986
peak=    3.428 closest distance to " CA  MET A 105 " =    1.014
peak=    3.426 closest distance to " O   HOH Z 144 " =    1.721
peak=    3.422 closest distance to " O   HOH Z 352 " =    1.550
peak=    3.417 closest distance to " O  BHOH Z  74 " =    1.345
peak=    3.417 closest distance to " O   HOH Z  80 " =    1.617
peak=    3.410 closest distance to " CB  SER A  26 " =    1.778
peak=    3.409 closest distance to " O   HOH Z 128 " =    2.970
peak=    3.406 closest distance to " CB  ASP A 140 " =    1.068
peak=    3.400 closest distance to " O   HOH Z 119 " =    4.297
peak=    3.393 closest distance to " O   HOH Z 371 " =    3.095
peak=    3.393 closest distance to " O   HOH Z 296 " =    1.058
peak=    3.392 closest distance to " CB  ALA A 131 " =    1.783
peak=    3.386 closest distance to " O   HOH Z  60 " =    1.299
peak=    3.381 closest distance to " CB  HIS A 108 " =    0.902
peak=    3.381 closest distance to " CD  ARG A  66 " =    2.226
peak=    3.376 closest distance to " O   HOH Z  61 " =    1.653
peak=    3.375 closest distance to " O   HOH Z 378 " =    0.906
peak=    3.371 closest distance to " O   HOH Z 111 " =    1.516
peak=    3.368 closest distance to " CG  LEU A 101 " =    1.172
peak=    3.367 closest distance to " O   HOH Z 180 " =    2.305
peak=    3.367 closest distance to " CG2 VAL A 232 " =    0.980
peak=    3.364 closest distance to " O   HOH Z 244 " =    1.659
peak=    3.359 closest distance to " CA  GLN A  58 " =    1.031
peak=    3.358 closest distance to " CB  ASN A 215 " =    1.077
peak=    3.357 closest distance to " O   HOH Z  40 " =    2.142
peak=    3.348 closest distance to " CD  ARG A 195 " =    3.524
peak=    3.345 closest distance to " O   HOH Z 285 " =    2.341
peak=    3.344 closest distance to " CA  LEU A  83 " =    1.484
peak=    3.343 closest distance to " CA  ARG A 102 " =    1.149
peak=    3.341 closest distance to " NE1 TRP A 274 " =    0.951
peak=    3.340 closest distance to " CB  PHE A 204 " =    0.981
peak=    3.340 closest distance to " CG2 ILE A  20 " =    1.628
peak=    3.337 closest distance to " CZ  PHE A  38 " =    1.312
peak=    3.329 closest distance to " O   HOH Z 345 " =    1.838
peak=    3.327 closest distance to " CG2 ILE A 234 " =    0.952
peak=    3.323 closest distance to " N   ASN A 127 " =    1.434
peak=    3.318 closest distance to " N   VAL A 296 " =    1.906
peak=    3.314 closest distance to " O   HOH Z 295 " =    1.256
peak=    3.312 closest distance to " CB  GLN A 183 " =    1.219
peak=    3.308 closest distance to " O   HOH Z 246 " =    1.241
peak=    3.307 closest distance to " O   HOH Z 119 " =    1.512
peak=    3.304 closest distance to " CB  ARG A 219 " =    0.935
peak=    3.297 closest distance to " O   HOH Z  53 " =    2.382
peak=    3.295 closest distance to " N   GLY A 111 " =    1.373
peak=    3.295 closest distance to " O   HOH Z 222 " =    2.365
peak=    3.295 closest distance to " O   HOH Z 212 " =    1.795
peak=    3.289 closest distance to " OG  SER A  62 " =    3.035
peak=    3.289 closest distance to " N   PHE A  16 " =    1.492
peak=    3.285 closest distance to " CG1BVAL A  72 " =    1.203
peak=    3.282 closest distance to " CB  ARG A 156 " =    1.369
peak=    3.281 closest distance to " CD  ARG A 159 " =    0.786
peak=    3.278 closest distance to " CD1 ILE A 199 " =    1.310
peak=    3.277 closest distance to " CE  MET A  93 " =    1.281
peak=    3.277 closest distance to " CB  ASN A 148 " =    2.033
peak=    3.271 closest distance to " O   HOH Z  58 " =    1.835
peak=    3.267 closest distance to " O   HOH Z 331 " =    0.948
peak=    3.260 closest distance to " O   THR A 220 " =    1.326
peak=    3.257 closest distance to " O   HOH Z  44 " =    2.789
peak=    3.256 closest distance to " O   HOH Z   1 " =    1.927
peak=    3.253 closest distance to " N   ASN A 224 " =    1.791
peak=    3.238 closest distance to " O   HOH Z  90 " =    3.978
peak=    3.237 closest distance to " O   HOH Z 344 " =    3.251
peak=    3.232 closest distance to " CB  ASP A 272 " =    1.028
peak=    3.227 closest distance to " CB  ASP A 200 " =    0.835
peak=    3.224 closest distance to " O   HOH Z 248 " =    1.585
peak=    3.224 closest distance to " O   HOH Z 174 " =    2.147
peak=    3.216 closest distance to " CA  ALA A 154 " =    1.139
peak=    3.215 closest distance to " CD1 LEU A 167 " =    1.153
peak=    3.208 closest distance to " O   HOH Z 116 " =    2.938
peak=    3.206 closest distance to " CD2 LEU A   5 " =    1.290
peak=    3.206 closest distance to " O   HOH Z 422 " =    2.230
peak=    3.204 closest distance to " O   HOH Z 156 " =    2.547
peak=    3.202 closest distance to " NH2AARG A 145 " =    1.146
peak=    3.201 closest distance to " CB  GLN A  88 " =    1.314
peak=    3.199 closest distance to " CB  GLU A 152 " =    1.243
peak=    3.198 closest distance to " O   ALA A 242 " =    1.281
peak=    3.196 closest distance to " O   THR A 182 " =    1.574
peak=    3.195 closest distance to " CG2 ILE A  20 " =    1.308
peak=    3.191 closest distance to " CB  ASN A 176 " =    0.971
peak=    3.183 closest distance to " CG  ARG A 159 " =    0.764
peak=    3.177 closest distance to " NH1 ARG A  66 " =    1.636
peak=    3.169 closest distance to " CG  LYS A 166 " =    1.217
peak=    3.168 closest distance to " NH1BARG A 102 " =    1.031
peak=    3.168 closest distance to " O   HOH Z 329 " =    4.174
peak=    3.166 closest distance to " O   HOH Z  46 " =    0.998
peak=    3.165 closest distance to " CB  GLU A  46 " =    1.139
peak=    3.160 closest distance to " CA  VAL A 153 " =    1.140
peak=    3.159 closest distance to " CB  ALA A 233 " =    1.138
peak=    3.159 closest distance to " O   HOH Z  88 " =    3.065
peak=    3.158 closest distance to " O   HOH Z 122 " =    1.797
peak=    3.158 closest distance to " CA  GLY A 267 " =    1.137
peak=    3.157 closest distance to " CB  ALA A 114 " =    1.206
peak=    3.157 closest distance to " O   HOH Z 289 " =    1.481
peak=    3.157 closest distance to " CB  TYR A  30 " =    1.623
peak=    3.156 closest distance to " O   HOH Z 227 " =    1.944
peak=    3.152 closest distance to " O   HOH Z 371 " =    1.886
peak=    3.151 closest distance to " CA  TRP A 150 " =    1.115
peak=    3.149 closest distance to " CG1 VAL A 202 " =    1.755
peak=    3.139 closest distance to " CB  SER A  97 " =    0.795
peak=    3.134 closest distance to " OD1 ASN A  69 " =    2.422
peak=    3.127 closest distance to " O   HOH Z  32 " =    1.888
peak=    3.103 closest distance to " CG2 THR A 246 " =    1.441
peak=    3.103 closest distance to " CA  ALA A 100 " =    1.044
peak=    3.101 closest distance to " CG2 ILE A 239 " =    0.812
peak=    3.097 closest distance to " CB  ALA A  43 " =    0.844
peak=    3.096 closest distance to " N   SER A  97 " =    0.814
peak=    3.091 closest distance to " O   HOH Z 284 " =    1.420
peak=    3.087 closest distance to " O   HOH Z 381 " =    2.191
peak=    3.082 closest distance to " CB  MET A 105 " =    1.227
peak=    3.080 closest distance to " O   HOH Z 127 " =    1.130
peak=    3.080 closest distance to " O   HOH Z 199 " =    1.228
peak=    3.072 closest distance to " CG2 THR A 264 " =    1.230
peak=    3.072 closest distance to " O   HOH Z 432 " =    1.798
peak=    3.072 closest distance to " O   THR A 157 " =    1.466
peak=    3.065 closest distance to " N   ASP A 162 " =    1.008
peak=    3.053 closest distance to " CA  SER A  32 " =    1.697
peak=    3.049 closest distance to " O   HOH Z 172 " =    2.181
peak=    3.049 closest distance to " N   GLU A  44 " =    1.146
peak=    3.048 closest distance to " CA  ALA A 158 " =    1.230
peak=    3.042 closest distance to " O   HOH Z 374 " =    1.320
peak=    3.028 closest distance to " O   HOH Z 412 " =    4.861
peak=    3.026 closest distance to " O   HOH Z 323 " =    1.516

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.760 - 5.792
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 204
   mapped sites are within: 0.760 - 5.792

peak=   -5.030 closest distance to " CZ2 TRP A  92 " =    2.840
peak=   -4.534 closest distance to " O   PRO A 198 " =    1.243
peak=   -4.258 closest distance to " O   HOH Z  69 " =    1.725
peak=   -4.167 closest distance to " NE2 GLN A  55 " =    1.158
peak=   -4.128 closest distance to " OG BSER A 134 " =    1.440
peak=   -4.097 closest distance to " CD  ARG A  14 " =    3.228
peak=   -4.083 closest distance to " O   HOH Z 100 " =    0.993
peak=   -4.065 closest distance to " O   HOH Z  24 " =    1.053
peak=   -4.061 closest distance to " CG2 ILE A  20 " =    2.715
peak=   -4.058 closest distance to " CG  GLN A  55 " =    1.152
peak=   -3.979 closest distance to " O   GLU A 152 " =    1.426
peak=   -3.967 closest distance to " CE BMET A  47 " =    1.227
peak=   -3.966 closest distance to " O   HOH Z 276 " =    1.311
peak=   -3.960 closest distance to " CB  ASN A  45 " =    2.073
peak=   -3.954 closest distance to " O   HOH Z 131 " =    3.906
peak=   -3.940 closest distance to " O   HOH Z 348 " =    2.031
peak=   -3.933 closest distance to " CD2 TYR A 293 " =    1.794
peak=   -3.920 closest distance to " O   HOH Z 298 " =    2.577
peak=   -3.919 closest distance to " CD1 LEU A 101 " =    2.213
peak=   -3.870 closest distance to " CB  PRO A 243 " =    2.579
peak=   -3.863 closest distance to " SG BCYS A 201 " =    2.207
peak=   -3.861 closest distance to " O   HOH Z 385 " =    1.308
peak=   -3.859 closest distance to " CA  HIS A 207 " =    1.222
peak=   -3.849 closest distance to " O   SER A  22 " =    2.589
peak=   -3.840 closest distance to " O   HOH Z 266 " =    5.312
peak=   -3.805 closest distance to " O   HOH Z  70 " =    0.969
peak=   -3.792 closest distance to " OD2 ASP A 171 " =    2.124
peak=   -3.782 closest distance to " O   HOH Z  39 " =    1.123
peak=   -3.777 closest distance to " O   HOH Z 211 " =    1.032
peak=   -3.776 closest distance to " CB  ALA A  43 " =    2.440
peak=   -3.762 closest distance to " ND2 ASN A 285 " =    2.182
peak=   -3.755 closest distance to " O   HOH Z 377 " =    1.965
peak=   -3.735 closest distance to " O   HOH Z 242 " =    1.428
peak=   -3.733 closest distance to " CG  GLN A  58 " =    1.136
peak=   -3.730 closest distance to " O   HOH Z 107 " =    2.120
peak=   -3.729 closest distance to " CG1BVAL A  72 " =    2.284
peak=   -3.714 closest distance to " C   HIS A 108 " =    1.173
peak=   -3.699 closest distance to " NZ  LYS A 166 " =    1.452
peak=   -3.686 closest distance to " CE  MET A 105 " =    2.576
peak=   -3.681 closest distance to " CD1 LEU A 255 " =    2.905
peak=   -3.678 closest distance to " O   HOH Z  60 " =    1.984
peak=   -3.670 closest distance to " CD2 PHE A  61 " =    2.040
peak=   -3.669 closest distance to " O   HOH Z  41 " =    0.760
peak=   -3.667 closest distance to " CD  ARG A 156 " =    2.050
peak=   -3.663 closest distance to " CA  GLY A 241 " =    2.267
peak=   -3.662 closest distance to " CA  GLY A  98 " =    1.729
peak=   -3.658 closest distance to " CZ  PHE A  59 " =    1.557
peak=   -3.655 closest distance to " O   HOH Z 105 " =    1.937
peak=   -3.654 closest distance to " OG  SER A  63 " =    1.299
peak=   -3.653 closest distance to " O   ALA A  10 " =    1.546
peak=   -3.636 closest distance to " OG  SER A  87 " =    1.652
peak=   -3.635 closest distance to " NH2 ARG A 219 " =    1.681
peak=   -3.626 closest distance to " CD2 LEU A 237 " =    2.811
peak=   -3.607 closest distance to " O   HOH Z 165 " =    2.345
peak=   -3.606 closest distance to " CA  ASN A 127 " =    1.248
peak=   -3.606 closest distance to " O   HOH Z  71 " =    0.876
peak=   -3.604 closest distance to " O   HOH Z 123 " =    2.524
peak=   -3.601 closest distance to " N   GLN A  58 " =    1.185
peak=   -3.591 closest distance to " O   HOH Z 231 " =    1.021
peak=   -3.585 closest distance to " CB  GLN A  58 " =    1.307
peak=   -3.583 closest distance to " OE1 GLN A 223 " =    2.383
peak=   -3.582 closest distance to " CZ2 TRP A 274 " =    0.983
peak=   -3.580 closest distance to " O   HOH Z 231 " =    2.216
peak=   -3.579 closest distance to " O   HOH Z 427 " =    1.850
peak=   -3.559 closest distance to " O   HOH Z 151 " =    2.365
peak=   -3.559 closest distance to " O   HOH Z 313 " =    1.497
peak=   -3.548 closest distance to " O   HOH Z 185 " =    1.967
peak=   -3.539 closest distance to " O   HOH Z  28 " =    1.238
peak=   -3.537 closest distance to " O   HOH Z 102 " =    1.597
peak=   -3.533 closest distance to " O   PHE A 218 " =    1.506
peak=   -3.527 closest distance to " O   HOH Z 374 " =    1.932
peak=   -3.523 closest distance to " OE2 GLU A 152 " =    1.319
peak=   -3.522 closest distance to " CB  ALA A 291 " =    2.127
peak=   -3.521 closest distance to " O   HOH Z   5 " =    1.091
peak=   -3.520 closest distance to " OD1 ASP A 171 " =    1.568
peak=   -3.518 closest distance to " O   HOH Z  68 " =    1.429
peak=   -3.514 closest distance to " CG  MET A 105 " =    1.019
peak=   -3.498 closest distance to " O   HOH Z 426 " =    1.611
peak=   -3.495 closest distance to " O   HOH Z 105 " =    1.578
peak=   -3.494 closest distance to " O   HOH Z 201 " =    2.047
peak=   -3.491 closest distance to " N   THR A 157 " =    1.496
peak=   -3.490 closest distance to " O   HOH Z  37 " =    1.355
peak=   -3.488 closest distance to " CG1 VAL A 265 " =    2.611
peak=   -3.485 closest distance to " OD1 ASP A 191 " =    1.840
peak=   -3.484 closest distance to " CB  SER A 210 " =    1.172
peak=   -3.482 closest distance to " OD2 ASP A 270 " =    1.169
peak=   -3.478 closest distance to " O   HOH Z 111 " =    1.978
peak=   -3.467 closest distance to " O   HOH Z 143 " =    1.451
peak=   -3.459 closest distance to " OD1 ASN A 187 " =    1.709
peak=   -3.458 closest distance to " O   HOH Z 359 " =    3.251
peak=   -3.451 closest distance to " O   HOH Z 352 " =    1.214
peak=   -3.446 closest distance to " O   HOH Z 278 " =    1.110
peak=   -3.445 closest distance to " CA  GLY A 133 " =    1.879
peak=   -3.439 closest distance to " CG  PRO A 243 " =    1.829
peak=   -3.439 closest distance to " NE2 GLN A  11 " =    1.739
peak=   -3.426 closest distance to " O   HOH Z 351 " =    1.580
peak=   -3.421 closest distance to " O   HOH Z 132 " =    2.099
peak=   -3.417 closest distance to " CD2 PHE A  61 " =    2.293
peak=   -3.413 closest distance to " CG2 THR A  18 " =    2.807
peak=   -3.411 closest distance to " O   HOH Z 412 " =    3.697
peak=   -3.409 closest distance to " O   HOH Z 216 " =    1.516
peak=   -3.406 closest distance to " O   HOH Z 219 " =    4.572
peak=   -3.401 closest distance to " O   HOH Z 438 " =    0.964
peak=   -3.393 closest distance to " O   HOH Z 428 " =    2.823
peak=   -3.380 closest distance to " O   ARG A 145 " =    1.336
peak=   -3.379 closest distance to " C   ASP A 124 " =    2.019
peak=   -3.377 closest distance to " CZ  TYR A 169 " =    1.969
peak=   -3.376 closest distance to " O   HOH Z 147 " =    2.020
peak=   -3.375 closest distance to " CB  ASP A 132 " =    2.603
peak=   -3.375 closest distance to " O   HOH Z 238 " =    1.058
peak=   -3.367 closest distance to " NE2 GLN A 223 " =    1.786
peak=   -3.356 closest distance to " CB  ALA A 158 " =    1.649
peak=   -3.348 closest distance to " CD  PRO A 213 " =    2.094
peak=   -3.347 closest distance to " O   HOH Z 389 " =    1.260
peak=   -3.343 closest distance to " O   HOH Z 193 " =    0.848
peak=   -3.341 closest distance to " O   LYS A  76 " =    1.647
peak=   -3.338 closest distance to " NE  ARG A  36 " =    1.953
peak=   -3.333 closest distance to " O   HOH Z  11 " =    1.572
peak=   -3.329 closest distance to " CG  LEU A  83 " =    2.235
peak=   -3.327 closest distance to " O   HOH Z 217 " =    1.644
peak=   -3.326 closest distance to " CG  GLN A  88 " =    1.027
peak=   -3.322 closest distance to " CG1 VAL A 126 " =    2.494
peak=   -3.318 closest distance to " O   HOH Z 166 " =    1.730
peak=   -3.318 closest distance to " O   HOH Z  64 " =    1.169
peak=   -3.314 closest distance to " CD2 PHE A 225 " =    1.134
peak=   -3.313 closest distance to " OD2 ASP A 171 " =    1.620
peak=   -3.311 closest distance to " CD  GLU A 277 " =    1.236
peak=   -3.311 closest distance to " CD1 TRP A 179 " =    1.316
peak=   -3.311 closest distance to " O   HOH Z 198 " =    1.208
peak=   -3.308 closest distance to " OG  SER A  97 " =    2.203
peak=   -3.306 closest distance to " O   HOH Z 236 " =    1.461
peak=   -3.301 closest distance to " CD2 PHE A  61 " =    2.727
peak=   -3.297 closest distance to " O   HOH Z  77 " =    1.806
peak=   -3.291 closest distance to " C   GLN A  58 " =    1.957
peak=   -3.288 closest distance to " O   ILE A  49 " =    1.627
peak=   -3.284 closest distance to " O   HOH Z 263 " =    3.109
peak=   -3.281 closest distance to " O   HOH Z 412 " =    5.792
peak=   -3.278 closest distance to " O   GLY A  80 " =    2.609
peak=   -3.273 closest distance to " OD2 ASP A 191 " =    1.368
peak=   -3.269 closest distance to " O   HOH Z 359 " =    1.555
peak=   -3.268 closest distance to " O   HOH Z 179 " =    1.775
peak=   -3.265 closest distance to " O   HOH Z 134 " =    3.963
peak=   -3.262 closest distance to " OE1 GLU A 277 " =    1.975
peak=   -3.255 closest distance to " N   MET A 188 " =    1.949
peak=   -3.247 closest distance to " OD1 ASN A 173 " =    1.308
peak=   -3.237 closest distance to " CG  ARG A 269 " =    2.149
peak=   -3.234 closest distance to " O   ASN A 187 " =    1.435
peak=   -3.230 closest distance to " O   HOH Z 295 " =    2.174
peak=   -3.228 closest distance to " CG2BVAL A  72 " =    1.704
peak=   -3.228 closest distance to " OG  SER A 245 " =    1.618
peak=   -3.227 closest distance to " CZ3 TRP A 179 " =    1.384
peak=   -3.226 closest distance to " CA  GLY A 287 " =    1.186
peak=   -3.224 closest distance to " O   PRO A 163 " =    1.924
peak=   -3.222 closest distance to " CZ  PHE A  38 " =    2.444
peak=   -3.222 closest distance to " CB  TYR A  68 " =    1.060
peak=   -3.221 closest distance to " CG2 ILE A 263 " =    2.335
peak=   -3.219 closest distance to " O   HOH Z 292 " =    2.927
peak=   -3.218 closest distance to " O   HOH Z 116 " =    1.900
peak=   -3.216 closest distance to " O   HOH Z 407 " =    2.788
peak=   -3.215 closest distance to " O   ALA A  51 " =    1.197
peak=   -3.211 closest distance to " CG1 VAL A 112 " =    2.663
peak=   -3.211 closest distance to " O   HOH Z  26 " =    0.776
peak=   -3.208 closest distance to " C   SER A 276 " =    1.589
peak=   -3.198 closest distance to " ND2 ASN A 249 " =    2.106
peak=   -3.196 closest distance to " O   HOH Z 251 " =    2.093
peak=   -3.190 closest distance to " O   HOH Z 355 " =    1.918
peak=   -3.184 closest distance to " O   TRP A  70 " =    1.422
peak=   -3.182 closest distance to " O   HOH Z   1 " =    1.136
peak=   -3.179 closest distance to " O   HOH Z 256 " =    1.374
peak=   -3.158 closest distance to " CB  ASP A  27 " =    2.410
peak=   -3.156 closest distance to " CG2 THR A  52 " =    3.086
peak=   -3.153 closest distance to " O   HOH Z 383 " =    0.968
peak=   -3.151 closest distance to " O   HOH Z 129 " =    3.356
peak=   -3.147 closest distance to " N   ALA A  43 " =    2.544
peak=   -3.145 closest distance to " CB  ASP A 132 " =    2.483
peak=   -3.140 closest distance to " N   LYS A 166 " =    1.887
peak=   -3.139 closest distance to " ND2 ASN A  45 " =    2.373
peak=   -3.139 closest distance to " OE1 GLN A 223 " =    1.965
peak=   -3.137 closest distance to " CA  SER A  26 " =    0.960
peak=   -3.134 closest distance to " O   HOH Z 285 " =    1.746
peak=   -3.133 closest distance to " CD  GLU A 236 " =    1.158
peak=   -3.133 closest distance to " O   HOH Z 427 " =    1.461
peak=   -3.131 closest distance to " CG2 THR A 294 " =    3.081
peak=   -3.131 closest distance to " O   HOH Z  63 " =    2.618
peak=   -3.130 closest distance to " OE1 GLN A 183 " =    1.396
peak=   -3.129 closest distance to " NE2 GLN A 278 " =    1.421
peak=   -3.126 closest distance to " N   PRO A 163 " =    1.458
peak=   -3.126 closest distance to " N   ASP A 270 " =    1.263
peak=   -3.121 closest distance to " O   VAL A  67 " =    2.704
peak=   -3.114 closest distance to " CB  ASP A  50 " =    2.425
peak=   -3.110 closest distance to " O   HOH Z 109 " =    0.909
peak=   -3.109 closest distance to " O   HOH Z 281 " =    2.902
peak=   -3.097 closest distance to " O   HOH Z  64 " =    2.451
peak=   -3.096 closest distance to " CD1 ILE A 199 " =    2.421
peak=   -3.092 closest distance to " OG  SER A  97 " =    1.756
peak=   -3.091 closest distance to " CZ  PHE A 130 " =    1.072
peak=   -3.088 closest distance to " OD1 ASN A 148 " =    1.416
peak=   -3.078 closest distance to " OG  SER A  87 " =    1.063
peak=   -3.077 closest distance to " CG1 VAL A 265 " =    2.295
peak=   -3.071 closest distance to " CB  PHE A 155 " =    2.511
peak=   -3.059 closest distance to " O   ALA A  34 " =    2.629
peak=   -3.053 closest distance to " O   SER A 210 " =    1.924
peak=   -3.043 closest distance to " O   HOH Z 221 " =    2.124
peak=   -3.041 closest distance to " NH2 ARG A  79 " =    2.261

================= 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    :  0.4860 0.4854   6.292272e+00   6.279944e+00
   1_bss:  0.4775 0.4756   6.287562e+00   6.270827e+00
   1_xyz:  0.3717 0.4109   6.126183e+00   6.186718e+00
   1_adp:  0.3418 0.4185   6.090611e+00   6.194640e+00
   1_occ:  0.3416 0.4193   6.090720e+00   6.195622e+00
   2_bss:  0.3411 0.4187   6.092272e+00   6.197036e+00
   2_xyz:  0.2668 0.3311   5.895146e+00   6.047319e+00
   2_adp:  0.2421 0.3303   5.846922e+00   6.034320e+00
   2_occ:  0.2420 0.3303   5.846700e+00   6.034343e+00
   3_bss:  0.2423 0.3303   5.845016e+00   6.033441e+00
   3_xyz:  0.1913 0.2641   5.627608e+00   5.851593e+00
   3_adp:  0.1719 0.2331   5.521390e+00   5.740845e+00
   3_occ:  0.1715 0.2328   5.520215e+00   5.739380e+00
   4_bss:  0.1712 0.2324   5.518981e+00   5.737764e+00
   4_xyz:  0.1483 0.2003   5.382937e+00   5.603628e+00
   4_adp:  0.1413 0.1943   5.344616e+00   5.573436e+00
   4_occ:  0.1412 0.1942   5.344535e+00   5.573431e+00
   5_bss:  0.1414 0.1945   5.343933e+00   5.572847e+00
   5_xyz:  0.1274 0.1788   5.257023e+00   5.495200e+00
   5_adp:  0.1246 0.1766   5.240305e+00   5.483215e+00
   5_occ:  0.1246 0.1767   5.240181e+00   5.483131e+00
   5_bss:  0.1245 0.1766   5.240240e+00   5.483162e+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:  0.319  23.445  -2.300   0.957   3.646   0.000   0.000   0.000
   1_xyz:  0.319  23.445  -2.300   0.957   3.646   0.000   0.000   0.000
   1_adp:  0.319  23.445  -2.300   0.957   3.646   0.000   0.000   0.000
   1_occ:  0.319  23.445  -2.300   0.957   3.646   0.000   0.000   0.000
   2_bss:  0.348  66.248  -1.033   0.628   2.773   0.000   0.000   0.000
   2_xyz:  0.348  66.248  -1.033   0.628   2.773   0.000   0.000   0.000
   2_adp:  0.348  66.248  -1.033   0.628   2.773   0.000   0.000   0.000
   2_occ:  0.348  66.248  -1.033   0.628   2.773   0.000   0.000   0.000
   3_bss:  0.336  70.348  -0.739   0.439   2.462   0.000   0.000   0.000
   3_xyz:  0.336  70.348  -0.739   0.439   2.462   0.000   0.000   0.000
   3_adp:  0.336  70.348  -0.739   0.439   2.462   0.000   0.000   0.000
   3_occ:  0.336  70.348  -0.739   0.439   2.462   0.000   0.000   0.000
   4_bss:  0.323  58.105  -1.241  -0.665   1.466  -0.000   0.000   0.000
   4_xyz:  0.323  58.105  -1.241  -0.665   1.466  -0.000   0.000   0.000
   4_adp:  0.323  58.105  -1.241  -0.665   1.466  -0.000   0.000   0.000
   4_occ:  0.323  58.105  -1.241  -0.665   1.466  -0.000   0.000   0.000
   5_bss:  0.321  58.105  -1.441  -0.940   1.242  -0.000   0.000   0.000
   5_xyz:  0.321  58.105  -1.441  -0.940   1.242  -0.000   0.000   0.000
   5_adp:  0.321  58.105  -1.441  -0.940   1.242  -0.000   0.000   0.000
   5_occ:  0.321  58.105  -1.441  -0.940   1.242  -0.000   0.000   0.000
   5_bss:  0.319  56.795  -1.223  -0.837   1.392  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.103 0.4057  0.5606    75976.312
   1_bss:  57.653 0.4232  0.6019    72624.960
   1_xyz:  46.539 0.5628  0.7770    49960.944
   1_adp:  47.501 0.5503  0.7466    51474.779
   1_occ:  47.586 0.5492  0.7451    51617.831
   2_bss:  47.499 0.5504  0.7503    51637.348
   2_xyz:  35.507 0.6943  0.9153    30378.602
   2_adp:  34.572 0.7054  0.9065    29433.266
   2_occ:  34.577 0.7054  0.9063    29431.785
   3_bss:  34.486 0.7062  0.9042    29219.213
   3_xyz:  26.929 0.7895  0.9810    18151.554
   3_adp:  22.826 0.8333  0.9972    14047.406
   3_occ:  22.795 0.8336  0.9972    14000.488
   4_bss:  22.715 0.8343  0.9675    13922.883
   4_xyz:  19.014 0.8706  0.9854    10303.192
   4_adp:  18.128 0.8793  0.9785     9711.653
   4_occ:  18.126 0.8794  0.9783     9709.177
   5_bss:  18.106 0.8795  0.9703     9685.285
   5_xyz:  16.398 0.8945  0.9794     8169.849
   5_adp:  16.034 0.8980  0.9728     7958.749
   5_occ:  16.031 0.8980  0.9727     7952.624
   5_bss:  16.034 0.8980  0.9783     7955.396
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.107   2.0286e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.107   2.0286e-01
   1_xyz:   1.741  0.013  0.118 16.591  0.008  4.100   1.6482e-01
   1_adp:   1.741  0.013  0.118 16.591  0.008  4.100   1.6482e-01
   1_occ:   1.741  0.013  0.118 16.591  0.008  4.100   1.6482e-01
   2_bss:   1.741  0.013  0.118 16.591  0.008  4.100   1.6482e-01
   2_xyz:   1.364  0.009  0.099 15.792  0.005  4.123   9.7127e-02
   2_adp:   1.364  0.009  0.099 15.792  0.005  4.123   9.7127e-02
   2_occ:   1.364  0.009  0.099 15.792  0.005  4.123   9.7127e-02
   3_bss:   1.364  0.009  0.099 15.792  0.005  4.123   9.7127e-02
   3_xyz:   1.186  0.009  0.079 15.348  0.004  4.110   7.8843e-02
   3_adp:   1.186  0.009  0.079 15.348  0.004  4.110   7.8843e-02
   3_occ:   1.186  0.009  0.079 15.348  0.004  4.110   7.8843e-02
   4_bss:   1.186  0.009  0.079 15.348  0.004  4.110   7.8843e-02
   4_xyz:   0.946  0.006  0.068 14.729  0.004  4.117   5.5594e-02
   4_adp:   0.946  0.006  0.068 14.729  0.004  4.117   5.5594e-02
   4_occ:   0.946  0.006  0.068 14.729  0.004  4.117   5.5594e-02
   5_bss:   0.946  0.006  0.068 14.729  0.004  4.117   5.5594e-02
   5_xyz:   1.026  0.007  0.075 14.806  0.004  4.118   6.2499e-02
   5_adp:   1.026  0.007  0.075 14.806  0.004  4.118   6.2499e-02
   5_occ:   1.026  0.007  0.075 14.806  0.004  4.118   6.2499e-02
   5_bss:   1.026  0.007  0.075 14.806  0.004  4.118   6.2499e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  0.949   2.4208e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  0.949   2.4208e-01
   1_xyz:  11.411  0.080  0.355 88.548  0.054  1.844   1.0225e-01
   1_adp:  11.411  0.080  0.355 88.548  0.054  1.844   1.0225e-01
   1_occ:  11.411  0.080  0.355 88.548  0.054  1.844   1.0225e-01
   2_bss:  11.411  0.080  0.355 88.548  0.054  1.844   1.0225e-01
   2_xyz:   9.167  0.092  0.312 83.957  0.033  2.189   6.9178e-02
   2_adp:   9.167  0.092  0.312 83.957  0.033  2.189   6.9178e-02
   2_occ:   9.167  0.092  0.312 83.957  0.033  2.189   6.9178e-02
   3_bss:   9.167  0.092  0.312 83.957  0.033  2.189   6.9178e-02
   3_xyz:   9.576  0.055  0.260 87.466  0.037  2.290   7.9421e-02
   3_adp:   9.576  0.055  0.260 87.466  0.037  2.290   7.9421e-02
   3_occ:   9.576  0.055  0.260 87.466  0.037  2.290   7.9421e-02
   4_bss:   9.576  0.055  0.260 87.466  0.037  2.290   7.9421e-02
   4_xyz:   6.566  0.048  0.204 79.246  0.030  2.271   7.4264e-02
   4_adp:   6.566  0.048  0.204 79.246  0.030  2.271   7.4264e-02
   4_occ:   6.566  0.048  0.204 79.246  0.030  2.271   7.4264e-02
   5_bss:   6.566  0.048  0.204 79.246  0.030  2.271   7.4264e-02
   5_xyz:   6.746  0.043  0.236 81.517  0.039  2.178   4.3911e-02
   5_adp:   6.746  0.043  0.236 81.517  0.039  2.178   4.3911e-02
   5_occ:   6.746  0.043  0.236 81.517  0.039  2.178   4.3911e-02
   5_bss:   6.746  0.043  0.236 81.517  0.039  2.178   4.3911e-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: 129.77   0.00  17.23 129.77   0.00  13.64  64.96   0.00  36.79
   1_occ: 129.77   0.00  17.23 129.77   0.00  13.64  64.96   0.00  36.79
   2_bss: 129.77   0.00  17.23 129.77   0.00  13.64  64.96   0.00  36.79
   2_xyz: 129.77   0.00  17.23 129.77   0.00  13.64  64.96   0.00  36.79
   2_adp: 117.76   0.00  19.86 110.42   0.00  14.86 117.76   0.30  47.11
   2_occ: 117.76   0.00  19.86 110.42   0.00  14.86 117.76   0.30  47.11
   3_bss: 117.76   0.00  19.86 110.42   0.00  14.86 117.76   0.30  47.11
   3_xyz: 117.76   0.00  19.86 110.42   0.00  14.86 117.76   0.30  47.11
   3_adp: 110.86   0.00  17.65  98.47   0.00  12.55 110.86   3.51  45.39
   3_occ: 110.86   0.00  17.65  98.47   0.00  12.55 110.86   3.51  45.39
   4_bss: 110.86   0.00  17.65  98.47   0.00  12.55 110.86   3.51  45.39
   4_xyz: 110.86   0.00  17.65  98.47   0.00  12.55 110.86   3.51  45.39
   4_adp: 108.66   0.00  17.41 101.56   0.00  12.04 108.66   4.44  46.67
   4_occ: 108.66   0.00  17.41 101.56   0.00  12.04 108.66   4.44  46.67
   5_bss: 108.66   0.00  17.41 101.56   0.00  12.04 108.66   4.44  46.67
   5_xyz: 108.66   0.00  17.41 101.56   0.00  12.04 108.66   4.44  46.67
   5_adp: 108.45   0.00  17.23 107.38   0.00  11.79 108.45   4.00  46.84
   5_occ: 108.45   0.00  17.23 107.38   0.00  11.79 108.45   4.00  46.84
   5_bss: 108.45   0.00  17.23 107.38   0.00  11.79 108.45   4.00  46.84
------------------------------------------------------------------------
 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:    3.491    0.029    0.424
   1_adp:    3.491    0.029    0.424
   1_occ:    3.491    0.029    0.424
   2_bss:    3.491    0.029    0.424
   2_xyz:    2.643    0.026    0.609
   2_adp:    2.643    0.026    0.609
   2_occ:    2.643    0.026    0.609
   3_bss:    2.643    0.026    0.609
   3_xyz:    2.316    0.044    0.757
   3_adp:    2.316    0.044    0.757
   3_occ:    2.316    0.044    0.757
   4_bss:    2.316    0.044    0.757
   4_xyz:    2.211    0.080    0.802
   4_adp:    2.211    0.080    0.802
   4_occ:    2.211    0.080    0.802
   5_bss:    2.211    0.080    0.802
   5_xyz:    2.163    0.088    0.836
   5_adp:    2.163    0.088    0.836
   5_occ:    2.163    0.088    0.836
   5_bss:    2.163    0.088    0.836
------------------------------------------------------------------------

CPU time actual refinement: 325.38


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_263/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_263/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_263/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_263/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_263/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 325.24 
  Macro-tasks:
    bulk solvent and scale       = 43.14  
    individual site refinement   = 129.01 
    weights calculation          = 29.43  
    collect and process          = 6.43   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 208.10 
  Micro-tasks:
    mask                            = 2.42   
    f_calc                          = 101.20 
    alpha_beta                      = 8.63   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 109.01 
    fmodel                         = 7.13   
    r_factors                      = 0.26   
    phase_errors                   = 10.37  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 240.44 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.689 micro seconds
Total CPU time: 5.64 minutes
from_scatterers_fft:    623 calls, 100.93 s
gradients_fft:          568 calls,  96.39 s

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

# Date 2008-01-16 Time 04:24:53 PST -0800 (1200486293.57 s)
Start R-work = 0.4860, R-free = 0.4854 (no bulk solvent and anisotropic scale)
Final R-work = 0.1420, R-free = 0.1896 (no bulk solvent and anisotropic scale)

Start R-work = 0.4775, R-free = 0.4756
Final R-work = 0.1245, R-free = 0.1766