# Date 2008-01-16 Time 06:00:09 PST -0800 (1200492009.19 s)
#phil __OFF__

Command line arguments: "../969.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2965
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 969

-------------------------------------------------------------------------------
  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: (71.3037, 45.7567, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.32, per 1000 atoms: 1.18


================================== 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: (71.3037, 45.7567, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0711 1.95157
Completeness in resolution range: 0.944048
Completeness with d_max=infinity: 0.941326

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0711
                             d_min =   1.9516

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: (71.3037, 45.7567, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0711 1.95157
Completeness in resolution range: 0.944048
Completeness with d_max=infinity: 0.941326

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0715 -  4.1775 [2176/2203]  1962   214   9.8%
  bin  2:  4.1775 -  3.3275 [2090/2110]  1878   212  10.1%
  bin  3:  3.3275 -  2.9103 [2063/2082]  1856   207  10.0%
  bin  4:  2.9103 -  2.6458 [2039/2069]  1836   203  10.0%
  bin  5:  2.6458 -  2.4570 [2043/2062]  1843   200   9.8%
  bin  6:  2.4570 -  2.3127 [2025/2050]  1810   215  10.6%
  bin  7:  2.3127 -  2.1973 [2031/2059]  1832   199   9.8%
  bin  8:  2.1973 -  2.1019 [1987/2023]  1793   194   9.8%
  bin  9:  2.1019 -  2.0212 [1988/2043]  1793   195   9.8%
  bin 10:  2.0212 -  1.9516 [1147/2049]  1027   120  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_969/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: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.26 -     1.99: 14
        1.99 -     2.72: 234
        2.72 -     3.45: 4688
        3.45 -     4.17: 9525
        4.17 -     4.90: 14336
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.264 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.690 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.727 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  ... (remaining 28792 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_969/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_969/model_refine_001.geo

CPU time processing inputs: 9.92


============================ 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 = 71.30375 45.75675 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4933   r_free= 0.4943   ksol= 0.00   Bsol= 0.00   scale= 0.881    |
|                                                                             |
| 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:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.297963                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6601 0.99   1414  161 0.4065 0.4235      6.6049      6.6667|
|  2:  4.6601 -  3.7171 0.99   1357  146 0.4383 0.4424      6.8588      6.8274|
|  3:  3.7171 -  3.2527 0.99   1324  144 0.4739 0.4465      6.7151      6.7598|
|  4:  3.2527 -  2.9577 0.99   1345  158 0.4892 0.4841      6.5642       6.516|
|  5:  2.9577 -  2.7471 0.99   1313  144 0.5218 0.5298      6.3819      6.3933|
|  6:  2.7471 -  2.5860 0.99   1312  145 0.5311 0.5285      6.3001      6.2617|
|  7:  2.5860 -  2.4570 0.99   1310  138 0.5229 0.5162      6.2533      6.2136|
|  8:  2.4570 -  2.3505 0.98   1280  152 0.5319 0.5074      6.1743      6.1788|
|  9:  2.3505 -  2.2603 0.98   1304  145 0.5308 0.5613      6.1454      6.1565|
| 10:  2.2603 -  2.1826 1.00   1291  151 0.5310 0.5514      6.0878      6.1087|
| 11:  2.1826 -  2.1145 0.98   1299  133 0.5253 0.5583      6.0502      6.0663|
| 12:  2.1145 -  2.0542 0.98   1276  150 0.5293 0.5506      5.9597      5.9928|
| 13:  2.0542 -  2.0003 0.93   1214  127 0.5346 0.4958      5.8785      5.8249|
| 14:  2.0003 -  1.9516 0.45    591   65 0.5400 0.4603      5.8437       5.773|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0715 -  4.6601  1414   161  0.65  38.77   0.81     0.71      88256.69|
|  2:  4.6601 -  3.7171  1357   146  0.64  40.04   0.89     0.77     132665.70|
|  3:  3.7171 -  3.2527  1324   144  0.52  50.49   0.90     0.71     141138.16|
|  4:  3.2527 -  2.9577  1345   158  0.39  60.61   0.91     0.57     130274.46|
|  5:  2.9577 -  2.7471  1313   144  0.28  69.02   0.86     0.41     101117.93|
|  6:  2.7471 -  2.5860  1312   145  0.24  72.13   0.87     0.35      88668.13|
|  7:  2.5860 -  2.4570  1310   138  0.26  70.73   0.90     0.37      73947.14|
|  8:  2.4570 -  2.3505  1280   152  0.28  69.33   0.89     0.41      66036.34|
|  9:  2.3505 -  2.2603  1304   145  0.27  69.84   0.92     0.40      59468.76|
| 10:  2.2603 -  2.1826  1291   151  0.21  74.25   0.92     0.32      57347.36|
| 11:  2.1826 -  2.1145  1299   133  0.15  78.68   0.97     0.24      55880.96|
| 12:  2.1145 -  2.0542  1276   150  0.18  77.01   0.95     0.29      49834.24|
| 13:  2.0542 -  2.0003  1214   127  0.27  69.94   0.94     0.44      38888.94|
| 14:  2.0003 -  1.9516   591    65  0.43  57.62   0.96     0.67      26998.26|
|alpha:            min =        0.24 max =            0.77 mean =         0.47|
|beta:             min =    26998.26 max =       141138.16 mean =     82151.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.34|
|phase err.(work): min =        0.00 max =           90.00 mean =        64.12|
|phase err.(test): min =        0.00 max =           89.95 mean =        64.36|
|-----------------------------------------------------------------------------|

============================== 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 = 22.232212             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.344   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.232414              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.616   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.264 -  1.628:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.628 -  1.991:       13 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.991 -  2.355:       34 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.355 -  2.718:      200 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.718 -  3.082:     2343 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.082 -  3.446:     2345 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.446 -  3.809:     4209 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.809 -  4.173:     5316 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.173 -  4.536:     6422 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.536 -  4.900:     7914 |
|-----------------------------------------------------------------------------|
|-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 |        0.196 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.107    4.900  1.264 |       0.704 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.521)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4933   r_free= 0.4943   ksol= 0.00   Bsol= 0.00   scale= 0.881    |
|                                                                             |
| 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:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.297963                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4864   r_free= 0.4870   ksol= 0.34   Bsol= 28.47   scale= 0.906   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.50,1.13,0.33,0.00,0.00,0.00); trace/3= -0.01                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.296206                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.385603             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.359   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.882997              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.230   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4864      final r-factor (work) = 0.4001          |
| start r-factor (free) = 0.4870      final r-factor (free) = 0.4379          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 54.8945 = 17.39 * 0.50 * 6.2924 + 1.00 * 0.1956                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 54.2348 = 17.39 * 0.50 * 6.2200 + 1.00 * 0.1652                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4001      final r-factor (work) = 0.3653          |
| start r-factor (free) = 0.4379      final r-factor (free) = 0.4530          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.7183 = 1.88 * 1.00 * 6.2200 + 1.00 * 0.0060                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.5865 = 1.88 * 1.00 * 6.1403 + 1.00 * 0.0244                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.521)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.25  19.55    None  None   None       |
|    all(noH): 2823   0      0.00    103.25  19.55    None  None   None       |
|    Sol.    : 438    0      0.00    103.25  34.17    None  None   None       |
|    Mac.    : 2385   0      0.00    94.25   16.86    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 -  10.325:  904   |   5:    51.624 -  61.949:   75        |
|      1:    10.325 -  20.650:  843   |   6:    61.949 -  72.274:   35        |
|      2:    20.650 -  30.975:  559   |   7:    72.274 -  82.599:   10        |
|      3:    30.975 -  41.300:  245   |   8:    82.599 -  92.924:    8        |
|      4:    41.300 -  51.624:  140   |   9:    92.924 - 103.249:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3653 r_free = 0.4530             target_work(ml) = 6.149         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3647 r_free = 0.4516             target_work(ml) = 6.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3647   r_free= 0.4516   ksol= 0.34   Bsol= 28.47   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.50,1.13,0.33,0.00,0.00,0.00); trace/3= -0.01                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.147268                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3650   r_free= 0.4513   ksol= 0.37   Bsol= 64.64   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.32,0.46,0.52,0.00,0.00,0.00); trace/3= 0.22                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.149762                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.122423             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.320   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.697694              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.172  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3650      final r-factor (work) = 0.3205          |
| start r-factor (free) = 0.4513      final r-factor (free) = 0.4047          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.3258 = 11.12 * 0.50 * 6.1427 + 1.00 * 0.1652                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.0586 = 11.12 * 0.50 * 6.1088 + 1.00 * 0.0860                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3205      final r-factor (work) = 0.3114          |
| start r-factor (free) = 0.4047      final r-factor (free) = 0.3961          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2869 = 0.70 * 1.00 * 6.1088 + 1.00 * 0.0248                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2337 = 0.70 * 1.00 * 6.0461 + 1.00 * 0.0154                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.521)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.08  18.97    None  None   None       |
|    all(noH): 2823   0      0.00    102.08  18.97    None  None   None       |
|    Sol.    : 438    0      0.00    102.08  33.54    None  None   None       |
|    Mac.    : 2385   0      0.00    95.13   16.29    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.208:  862   |   5:    51.041 -  61.249:   70        |
|      1:    10.208 -  20.417:  946   |   6:    61.249 -  71.458:   21        |
|      2:    20.417 -  30.625:  550   |   7:    71.458 -  81.666:   11        |
|      3:    30.625 -  40.833:  242   |   8:    81.666 -  91.874:    5        |
|      4:    40.833 -  51.041:  112   |   9:    91.874 - 102.082:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3114 r_free = 0.3961             target_work(ml) = 6.037         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3114 r_free = 0.3961             target_work(ml) = 6.037         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3114   r_free= 0.3961   ksol= 0.37   Bsol= 64.64   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.32,0.46,0.52,0.00,0.00,0.00); trace/3= 0.22                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.036714                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3121   r_free= 0.3953   ksol= 0.36   Bsol= 70.99   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.01,-0.01,0.54,-0.00,0.00,0.00); trace/3= 0.17                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.035847                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.156779              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.932  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.598010              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.060  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3121      final r-factor (work) = 0.2609          |
| start r-factor (free) = 0.3953      final r-factor (free) = 0.3405          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.7238 = 7.16 * 0.50 * 6.0467 + 1.00 * 0.0864                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.4633 = 7.16 * 0.50 * 5.9742 + 1.00 * 0.0852                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2609      final r-factor (work) = 0.2432          |
| start r-factor (free) = 0.3405      final r-factor (free) = 0.3262          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5949 = 0.60 * 1.00 * 5.9742 + 1.00 * 0.0222                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5554 = 0.60 * 1.00 * 5.8596 + 1.00 * 0.0513                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.521)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.53  18.47    None  None   None       |
|    all(noH): 2823   0      0.00    101.53  18.47    None  None   None       |
|    Sol.    : 438    0      2.59    101.53  37.12    None  None   None       |
|    Mac.    : 2385   0      0.00    95.40   15.05    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 -  10.153:  943   |   5:    50.763 -  60.916:   64        |
|      1:    10.153 -  20.305:  942   |   6:    60.916 -  71.068:   25        |
|      2:    20.305 -  30.458:  440   |   7:    71.068 -  81.221:    6        |
|      3:    30.458 -  40.610:  260   |   8:    81.221 -  91.373:    6        |
|      4:    40.610 -  50.763:  133   |   9:    91.373 - 101.526:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2432 r_free = 0.3262             target_work(ml) = 5.836         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2429 r_free = 0.3260             target_work(ml) = 5.835         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2429   r_free= 0.3260   ksol= 0.36   Bsol= 70.99   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.01,-0.01,0.54,-0.00,0.00,0.00); trace/3= 0.17                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.835399                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2425   r_free= 0.3241   ksol= 0.35   Bsol= 64.26   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.79,-1.12,-0.45,-0.00,-0.00,-0.00); trace/3= -0.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.832983                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.275732              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.401  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.520971              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.444   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2425      final r-factor (work) = 0.2078          |
| start r-factor (free) = 0.3241      final r-factor (free) = 0.2802          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6826 = 3.28 * 0.50 * 5.8597 + 1.00 * 0.0852                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5094 = 3.28 * 0.50 * 5.7724 + 1.00 * 0.0549                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2078      final r-factor (work) = 0.1900          |
| start r-factor (free) = 0.2802      final r-factor (free) = 0.2612          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7986 = 1.52 * 1.00 * 5.7724 + 1.00 * 0.0189                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.6228 = 1.52 * 1.00 * 5.6589 + 1.00 * 0.0159                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.521)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.59  19.11    None  None   None       |
|    all(noH): 2823   0      0.00    107.59  19.11    None  None   None       |
|    Sol.    : 438    0      4.34    94.54   46.77    None  None   None       |
|    Mac.    : 2385   0      0.00    107.59  14.03    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 -  10.759: 1161   |   5:    53.795 -  64.554:   97        |
|      1:    10.759 -  21.518:  923   |   6:    64.554 -  75.313:   65        |
|      2:    21.518 -  32.277:  252   |   7:    75.313 -  86.073:   31        |
|      3:    32.277 -  43.036:  156   |   8:    86.073 -  96.832:    9        |
|      4:    43.036 -  53.795:  128   |   9:    96.832 - 107.591:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1900 r_free = 0.2612             target_work(ml) = 5.628         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1899 r_free = 0.2607             target_work(ml) = 5.627         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1899   r_free= 0.2607   ksol= 0.35   Bsol= 64.26   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.79,-1.12,-0.45,-0.00,-0.00,-0.00); trace/3= -0.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.627337                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1902   r_free= 0.2605   ksol= 0.33   Bsol= 57.29   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.94,-1.71,-0.56,-0.00,-0.00,-0.00); trace/3= -1.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.626720                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.127401              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.924  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.625720              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.303  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1902      final r-factor (work) = 0.1535          |
| start r-factor (free) = 0.2605      final r-factor (free) = 0.2169          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.5621 = 5.13 * 0.50 * 5.6587 + 1.00 * 0.0549                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.2676 = 5.13 * 0.50 * 5.5406 + 1.00 * 0.0632                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1535      final r-factor (work) = 0.1419          |
| start r-factor (free) = 0.2169      final r-factor (free) = 0.1984          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4826 = 0.63 * 1.00 * 5.5406 + 1.00 * 0.0157                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3925 = 0.63 * 1.00 * 5.4027 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.521)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.47  18.04    None  None   None       |
|    all(noH): 2823   0      0.00    109.47  18.04    None  None   None       |
|    Sol.    : 438    0      5.97    97.37   46.42    None  None   None       |
|    Mac.    : 2385   0      0.00    109.47  12.83    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 -  10.947: 1344   |   5:    54.733 -  65.680:  106        |
|      1:    10.947 -  21.893:  866   |   6:    65.680 -  76.626:   54        |
|      2:    21.893 -  32.840:  198   |   7:    76.626 -  87.573:   22        |
|      3:    32.840 -  43.786:  120   |   8:    87.573 -  98.519:    9        |
|      4:    43.786 -  54.733:  102   |   9:    98.519 - 109.466:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1419 r_free = 0.1984             target_work(ml) = 5.354         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1417 r_free = 0.1981             target_work(ml) = 5.353         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1417   r_free= 0.1981   ksol= 0.33   Bsol= 57.29   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.94,-1.71,-0.56,-0.00,-0.00,-0.00); trace/3= -1.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.353445                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6601 0.99   1414  161 0.1026 0.1442      5.4418      5.6863|
|  2:  4.6601 -  3.7171 0.99   1357  146 0.0970 0.1355      5.5774        5.84|
|  3:  3.7171 -  3.2527 0.99   1324  144 0.1344 0.1863      5.6698      6.0173|
|  4:  3.2527 -  2.9577 0.99   1345  158 0.1574 0.2166      5.6934      5.8705|
|  5:  2.9577 -  2.7471 0.99   1313  144 0.1690 0.2251      5.5384      5.7817|
|  6:  2.7471 -  2.5860 0.99   1312  145 0.1614 0.2194      5.4345      5.5982|
|  7:  2.5860 -  2.4570 0.99   1310  138 0.1618 0.2172      5.3599      5.5712|
|  8:  2.4570 -  2.3505 0.98   1280  152 0.1594 0.2300       5.302      5.5781|
|  9:  2.3505 -  2.2603 0.98   1304  145 0.1560 0.2285      5.2673      5.5002|
| 10:  2.2603 -  2.1826 1.00   1291  151 0.1483 0.2310      5.1826      5.4564|
| 11:  2.1826 -  2.1145 0.98   1299  133 0.1446 0.2213      5.1521      5.4716|
| 12:  2.1145 -  2.0542 0.98   1276  150 0.1431 0.2051      5.0745      5.3082|
| 13:  2.0542 -  2.0003 0.93   1214  127 0.1558 0.2329       5.021      5.2802|
| 14:  2.0003 -  1.9516 0.45    591   65 0.1571 0.1701      4.9428      5.0792|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0715 -  4.6601  1414   161  0.92  11.27   0.97     0.95       9398.85|
|  2:  4.6601 -  3.7171  1357   146  0.94  10.17   1.04     1.02      12499.83|
|  3:  3.7171 -  3.2527  1324   144  0.90  15.17   1.06     1.06      15605.24|
|  4:  3.2527 -  2.9577  1345   158  0.86  20.02   1.04     1.00      18098.50|
|  5:  2.9577 -  2.7471  1313   144  0.86  20.47   1.02     0.98      12862.92|
|  6:  2.7471 -  2.5860  1312   145  0.86  20.86   1.02     0.98      11209.67|
|  7:  2.5860 -  2.4570  1310   138  0.86  20.74   1.02     0.98       9588.40|
|  8:  2.4570 -  2.3505  1280   152  0.86  20.98   1.01     0.97       8655.27|
|  9:  2.3505 -  2.2603  1304   145  0.85  21.34   1.03     0.98       8241.03|
| 10:  2.2603 -  2.1826  1291   151  0.86  20.89   1.02     0.97       7144.20|
| 11:  2.1826 -  2.1145  1299   133  0.85  21.43   1.04     0.99       7027.87|
| 12:  2.1145 -  2.0542  1276   150  0.86  20.96   1.02     0.98       6238.62|
| 13:  2.0542 -  2.0003  1214   127  0.85  21.68   1.02     1.00       5351.34|
| 14:  2.0003 -  1.9516   591    65  0.87  19.79   1.01     0.98       4130.02|
|alpha:            min =        0.95 max =            1.06 mean =         0.99|
|beta:             min =     4130.02 max =        18098.50 mean =     10010.68|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.99 mean =        18.85|
|phase err.(test): min =        0.00 max =           89.18 mean =        18.06|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1422   r_free= 0.1977   ksol= 0.32   Bsol= 57.29   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.23,-2.11,-0.95,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.352910                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1422   r_free= 0.1977   ksol= 0.32   Bsol= 57.29   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.23,-2.11,-0.95,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.352910                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6601 0.99   1414  161 0.1029 0.1413      5.4349      5.6652|
|  2:  4.6601 -  3.7171 0.99   1357  146 0.0980 0.1356      5.5783      5.8463|
|  3:  3.7171 -  3.2527 0.99   1324  144 0.1352 0.1864      5.6723      6.0151|
|  4:  3.2527 -  2.9577 0.99   1345  158 0.1575 0.2170      5.6945       5.872|
|  5:  2.9577 -  2.7471 0.99   1313  144 0.1689 0.2245      5.5376      5.7829|
|  6:  2.7471 -  2.5860 0.99   1312  145 0.1614 0.2197      5.4342      5.5983|
|  7:  2.5860 -  2.4570 0.99   1310  138 0.1619 0.2175      5.3596      5.5726|
|  8:  2.4570 -  2.3505 0.98   1280  152 0.1592 0.2304      5.3017      5.5786|
|  9:  2.3505 -  2.2603 0.98   1304  145 0.1557 0.2283      5.2669      5.4996|
| 10:  2.2603 -  2.1826 1.00   1291  151 0.1485 0.2309      5.1822      5.4564|
| 11:  2.1826 -  2.1145 0.98   1299  133 0.1446 0.2208      5.1519      5.4712|
| 12:  2.1145 -  2.0542 0.98   1276  150 0.1430 0.2050      5.0737      5.3072|
| 13:  2.0542 -  2.0003 0.93   1214  127 0.1557 0.2328      5.0203      5.2803|
| 14:  2.0003 -  1.9516 0.45    591   65 0.1571 0.1697      4.9423      5.0776|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0715 -  4.6601  1414   161  0.92  11.00   0.97     0.95       9002.38|
|  2:  4.6601 -  3.7171  1357   146  0.94  10.03   1.04     1.02      12271.33|
|  3:  3.7171 -  3.2527  1324   144  0.90  15.14   1.06     1.05      15587.42|
|  4:  3.2527 -  2.9577  1345   158  0.86  20.03   1.03     1.00      18120.28|
|  5:  2.9577 -  2.7471  1313   144  0.86  20.43   1.01     0.97      12842.75|
|  6:  2.7471 -  2.5860  1312   145  0.86  20.85   1.00     0.97      11206.28|
|  7:  2.5860 -  2.4570  1310   138  0.86  20.73   1.01     0.97       9579.44|
|  8:  2.4570 -  2.3505  1280   152  0.86  20.99   1.00     0.96       8670.25|
|  9:  2.3505 -  2.2603  1304   145  0.85  21.34   1.01     0.96       8247.04|
| 10:  2.2603 -  2.1826  1291   151  0.86  20.89   1.00     0.95       7147.20|
| 11:  2.1826 -  2.1145  1299   133  0.85  21.42   1.02     0.97       7026.82|
| 12:  2.1145 -  2.0542  1276   150  0.86  20.93   0.99     0.96       6225.90|
| 13:  2.0542 -  2.0003  1214   127  0.85  21.65   1.00     0.98       5340.36|
| 14:  2.0003 -  1.9516   591    65  0.87  19.75   0.99     0.96       4119.39|
|alpha:            min =        0.95 max =            1.05 mean =         0.98|
|beta:             min =     4119.39 max =        18120.28 mean =      9958.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.95 mean =        18.81|
|phase err.(test): min =        0.00 max =           88.74 mean =        18.00|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.521)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.47  18.05    None  None   None       |
|    all(noH): 2823   0      0.00    109.47  18.05    None  None   None       |
|    Sol.    : 438    0      5.97    97.37   46.43    None  None   None       |
|    Mac.    : 2385   0      0.00    109.47  12.84    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 -  10.950: 1344   |   5:    54.736 -  65.683:  106        |
|      1:    10.950 -  21.896:  866   |   6:    65.683 -  76.629:   54        |
|      2:    21.896 -  32.843:  198   |   7:    76.629 -  87.576:   22        |
|      3:    32.843 -  43.789:  120   |   8:    87.576 -  98.522:    9        |
|      4:    43.789 -  54.736:  102   |   9:    98.522 - 109.469:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 345         
Filter by distance & map next to the model:
   mapped sites are within: 0.678 - 5.381
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 343 from: 345
   mapped sites are within: 0.727 - 5.381

peak=    8.430 closest distance to " O   HOH Z 138 " =    1.122
peak=    8.110 closest distance to " O   HOH Z 390 " =    1.426
peak=    8.051 closest distance to " O   HOH Z 399 " =    0.997
peak=    6.881 closest distance to " O   HOH Z 159 " =    1.166
peak=    6.865 closest distance to " O   HOH Z 289 " =    1.852
peak=    6.219 closest distance to " O   HOH Z 385 " =    1.693
peak=    6.063 closest distance to " O   HOH Z  61 " =    1.780
peak=    5.996 closest distance to " O   HOH Z 205 " =    1.209
peak=    5.841 closest distance to " O   HOH Z 350 " =    1.492
peak=    5.814 closest distance to " O   HOH Z  65 " =    1.768
peak=    5.791 closest distance to " O   HOH Z 120 " =    1.313
peak=    5.762 closest distance to " O   SER A  62 " =    0.978
peak=    5.659 closest distance to " O   HOH Z 431 " =    1.711
peak=    5.620 closest distance to " O   HOH Z 381 " =    1.225
peak=    5.399 closest distance to " O   HOH Z 130 " =    1.014
peak=    5.347 closest distance to " O   HOH Z 117 " =    1.446
peak=    5.228 closest distance to " CG  PRO A  90 " =    1.092
peak=    5.208 closest distance to " O   HOH Z   7 " =    1.995
peak=    5.206 closest distance to " O   HOH Z 222 " =    1.616
peak=    5.150 closest distance to " O   HOH Z 103 " =    1.088
peak=    5.096 closest distance to " O   HOH Z 214 " =    1.937
peak=    5.092 closest distance to " NE2 GLN A  11 " =    1.518
peak=    5.037 closest distance to " O   HOH Z  97 " =    1.645
peak=    5.026 closest distance to " O   HOH Z  78 " =    1.790
peak=    4.965 closest distance to " O   HOH Z 182 " =    1.475
peak=    4.963 closest distance to " O   HOH Z 278 " =    1.350
peak=    4.898 closest distance to " O   HOH Z 133 " =    1.615
peak=    4.808 closest distance to " O   HOH Z 403 " =    1.582
peak=    4.797 closest distance to " O   HOH Z 245 " =    1.357
peak=    4.731 closest distance to " NZ BLYS A 290 " =    1.237
peak=    4.671 closest distance to " O   HOH Z 427 " =    1.993
peak=    4.658 closest distance to " O   HOH Z 417 " =    1.749
peak=    4.642 closest distance to " O   HOH Z 415 " =    1.169
peak=    4.636 closest distance to " CG2 THR A 279 " =    1.310
peak=    4.612 closest distance to " O   HOH Z 427 " =    1.523
peak=    4.594 closest distance to " CB  PRO A  54 " =    1.108
peak=    4.585 closest distance to " O   HOH Z 258 " =    1.314
peak=    4.577 closest distance to " O   HOH Z 126 " =    2.058
peak=    4.556 closest distance to " O   HOH Z 414 " =    1.837
peak=    4.529 closest distance to " O   HOH Z  59 " =    1.409
peak=    4.490 closest distance to " O   HOH Z 363 " =    1.272
peak=    4.488 closest distance to " O   ASN A 285 " =    0.889
peak=    4.482 closest distance to " O   HOH Z 416 " =    1.455
peak=    4.463 closest distance to " O   PRO A 198 " =    1.326
peak=    4.451 closest distance to " N   SER A  63 " =    0.814
peak=    4.445 closest distance to " O   HOH Z 111 " =    1.745
peak=    4.444 closest distance to " O   HOH Z 316 " =    2.973
peak=    4.443 closest distance to " O   HOH Z 402 " =    1.417
peak=    4.441 closest distance to " O   HOH Z 144 " =    1.779
peak=    4.426 closest distance to " O   HOH Z 276 " =    1.578
peak=    4.404 closest distance to " O   HOH Z 358 " =    1.333
peak=    4.395 closest distance to " O   HOH Z 244 " =    1.486
peak=    4.387 closest distance to " OE1 GLN A  88 " =    1.043
peak=    4.366 closest distance to " ND2 ASN A 249 " =    1.867
peak=    4.334 closest distance to " N   GLU A   2 " =    1.339
peak=    4.323 closest distance to " CA  SER A  62 " =    1.132
peak=    4.322 closest distance to " OD1 ASP A  50 " =    1.119
peak=    4.318 closest distance to " O   HOH Z  49 " =    1.615
peak=    4.316 closest distance to " O   HOH Z 287 " =    1.917
peak=    4.273 closest distance to " O   HOH Z  69 " =    2.266
peak=    4.251 closest distance to " O   HOH Z 124 " =    1.249
peak=    4.245 closest distance to " CB  ASP A 124 " =    1.069
peak=    4.238 closest distance to " N   GLN A 278 " =    1.211
peak=    4.221 closest distance to " O   HOH Z  28 " =    1.722
peak=    4.206 closest distance to " O   HOH Z 424 " =    1.217
peak=    4.201 closest distance to " N   ARG A 156 " =    1.287
peak=    4.201 closest distance to " O   HOH Z  91 " =    2.165
peak=    4.198 closest distance to " CG  PRO A 213 " =    1.304
peak=    4.169 closest distance to " O   HOH Z 344 " =    1.235
peak=    4.160 closest distance to " O   HOH Z 139 " =    1.731
peak=    4.153 closest distance to " CE  MET A  93 " =    1.480
peak=    4.140 closest distance to " CG  PRO A  54 " =    1.311
peak=    4.139 closest distance to " NH2BARG A 102 " =    1.026
peak=    4.138 closest distance to " O   ASP A 286 " =    2.350
peak=    4.128 closest distance to " CG  LEU A 167 " =    1.288
peak=    4.121 closest distance to " CB  SER A 216 " =    1.016
peak=    4.116 closest distance to " O   HOH Z  63 " =    1.804
peak=    4.112 closest distance to " O   HOH Z  37 " =    1.252
peak=    4.100 closest distance to " O   HOH Z  29 " =    1.059
peak=    4.098 closest distance to " O   HOH Z 250 " =    2.126
peak=    4.087 closest distance to " O   HOH Z 374 " =    1.149
peak=    4.050 closest distance to " O   HOH Z 400 " =    0.793
peak=    4.046 closest distance to " O   ALA A 165 " =    1.218
peak=    4.044 closest distance to " CG  PRO A 198 " =    1.383
peak=    4.039 closest distance to " O   HOH Z 158 " =    1.472
peak=    4.033 closest distance to " O   HOH Z  54 " =    1.480
peak=    4.029 closest distance to " OG BSER A  12 " =    1.076
peak=    3.992 closest distance to " O   HOH Z 371 " =    2.101
peak=    3.983 closest distance to " O   HOH Z 132 " =    1.278
peak=    3.976 closest distance to " O   HOH Z 411 " =    3.176
peak=    3.962 closest distance to " O   HOH Z 217 " =    2.680
peak=    3.958 closest distance to " O   HOH Z 126 " =    1.654
peak=    3.955 closest distance to " NZ  LYS A 117 " =    1.172
peak=    3.953 closest distance to " CD1 PHE A 283 " =    1.020
peak=    3.941 closest distance to " O   HOH Z 261 " =    2.390
peak=    3.932 closest distance to " CB  ASN A 148 " =    1.433
peak=    3.925 closest distance to " O   HOH Z 134 " =    1.818
peak=    3.917 closest distance to " O   HOH Z 186 " =    1.386
peak=    3.914 closest distance to " CB  ARG A 275 " =    1.095
peak=    3.912 closest distance to " CG  GLN A  88 " =    1.009
peak=    3.912 closest distance to " CB  ASP A 132 " =    3.728
peak=    3.910 closest distance to " O   HOH Z 302 " =    1.600
peak=    3.899 closest distance to " O   HOH Z 246 " =    1.517
peak=    3.883 closest distance to " CA  TYR A  30 " =    1.069
peak=    3.873 closest distance to " O   HOH Z 311 " =    1.590
peak=    3.870 closest distance to " CG  PHE A  59 " =    1.080
peak=    3.860 closest distance to " O   HOH Z 282 " =    1.797
peak=    3.856 closest distance to " CB  GLN A 183 " =    1.082
peak=    3.835 closest distance to " O   HOH Z 183 " =    1.370
peak=    3.826 closest distance to " O   HOH Z  53 " =    2.371
peak=    3.812 closest distance to " CD  ARG A 138 " =    0.889
peak=    3.803 closest distance to " O   HOH Z 105 " =    1.358
peak=    3.801 closest distance to " O   HOH Z 431 " =    1.480
peak=    3.792 closest distance to " O   HOH Z 255 " =    0.941
peak=    3.792 closest distance to " CD BLYS A 290 " =    1.180
peak=    3.784 closest distance to " CG  PRO A 243 " =    1.145
peak=    3.774 closest distance to " O   HOH Z 128 " =    1.587
peak=    3.762 closest distance to " OD1 ASP A 286 " =    1.061
peak=    3.738 closest distance to " NE AARG A 275 " =    1.480
peak=    3.737 closest distance to " N   TYR A  15 " =    1.216
peak=    3.720 closest distance to " N   GLN A  73 " =    1.416
peak=    3.720 closest distance to " O   HOH Z 112 " =    1.122
peak=    3.719 closest distance to " O   HOH Z  32 " =    2.180
peak=    3.719 closest distance to " CA  LEU A 282 " =    1.039
peak=    3.700 closest distance to " O   HOH Z 259 " =    2.357
peak=    3.684 closest distance to " CB  ALA A 104 " =    1.314
peak=    3.684 closest distance to " O   HOH Z 272 " =    1.839
peak=    3.679 closest distance to " CD2 TRP A 179 " =    2.077
peak=    3.667 closest distance to " N   GLY A 287 " =    0.946
peak=    3.663 closest distance to " ND2 ASN A  60 " =    3.224
peak=    3.657 closest distance to " O   HOH Z 171 " =    2.359
peak=    3.653 closest distance to " O   HOH Z 145 " =    2.621
peak=    3.650 closest distance to " CB  SER A  63 " =    1.565
peak=    3.649 closest distance to " NH1AARG A 145 " =    1.119
peak=    3.641 closest distance to " CG2 THR A 251 " =    1.664
peak=    3.633 closest distance to " O   HOH Z   2 " =    1.855
peak=    3.630 closest distance to " CA  GLU A 152 " =    1.068
peak=    3.626 closest distance to " CB  VAL A 202 " =    1.592
peak=    3.626 closest distance to " O   HOH Z 193 " =    1.698
peak=    3.624 closest distance to " O   HOH Z 235 " =    1.198
peak=    3.623 closest distance to " O   HOH Z  11 " =    1.287
peak=    3.620 closest distance to " CB  PHE A 225 " =    1.543
peak=    3.613 closest distance to " OG BSER A 258 " =    1.096
peak=    3.608 closest distance to " O   HOH Z 233 " =    1.327
peak=    3.605 closest distance to " O   HOH Z 147 " =    1.665
peak=    3.605 closest distance to " O   HOH Z   6 " =    1.795
peak=    3.600 closest distance to " O   HOH Z 211 " =    1.620
peak=    3.598 closest distance to " O   HOH Z 380 " =    1.993
peak=    3.596 closest distance to " N   CYS A 260 " =    0.980
peak=    3.591 closest distance to " CB  TRP A 179 " =    1.561
peak=    3.585 closest distance to " CA  THR A 264 " =    0.801
peak=    3.583 closest distance to " NH2 ARG A 269 " =    0.828
peak=    3.582 closest distance to " O   HOH Z   5 " =    1.426
peak=    3.581 closest distance to " O   HOH Z 215 " =    1.670
peak=    3.581 closest distance to " NE1 TRP A 274 " =    1.121
peak=    3.576 closest distance to " CG2 THR A 221 " =    1.252
peak=    3.568 closest distance to " CB  ALA A   1 " =    1.051
peak=    3.565 closest distance to " CB  ALA A 233 " =    1.310
peak=    3.555 closest distance to " O   HOH Z 124 " =    1.025
peak=    3.547 closest distance to " O   HOH Z 369 " =    2.028
peak=    3.543 closest distance to " CA  ASN A 217 " =    1.212
peak=    3.537 closest distance to " CA  GLU A  46 " =    0.781
peak=    3.536 closest distance to " O   HOH Z 131 " =    1.098
peak=    3.536 closest distance to " CA  ARG A  36 " =    1.357
peak=    3.534 closest distance to " O   HOH Z 202 " =    1.547
peak=    3.529 closest distance to " CZ3 TRP A 274 " =    1.409
peak=    3.523 closest distance to " O   HOH Z 153 " =    3.515
peak=    3.523 closest distance to " CG1BVAL A 121 " =    1.765
peak=    3.522 closest distance to " CB  MET A 105 " =    1.235
peak=    3.513 closest distance to " NH2 ARG A 219 " =    1.628
peak=    3.511 closest distance to " O   HOH Z 383 " =    1.082
peak=    3.504 closest distance to " O   HOH Z 426 " =    1.191
peak=    3.503 closest distance to " OD2 ASP A 286 " =    2.558
peak=    3.502 closest distance to " O   HOH Z  44 " =    2.947
peak=    3.500 closest distance to " O   HOH Z 313 " =    2.205
peak=    3.497 closest distance to " N   ALA A   1 " =    1.483
peak=    3.492 closest distance to " O   HOH Z  88 " =    2.957
peak=    3.491 closest distance to " CB  GLU A 128 " =    0.996
peak=    3.489 closest distance to " O   HOH Z 352 " =    1.594
peak=    3.482 closest distance to " CA  ALA A 160 " =    0.794
peak=    3.479 closest distance to " O   HOH Z 179 " =    1.135
peak=    3.474 closest distance to " CB  MET A  47 " =    1.070
peak=    3.467 closest distance to " CB  LYS A 290 " =    0.918
peak=    3.466 closest distance to " CG2 ILE A 151 " =    1.277
peak=    3.457 closest distance to " NH2BARG A 190 " =    1.539
peak=    3.452 closest distance to " O   HOH Z 155 " =    2.231
peak=    3.443 closest distance to " OE1 GLN A  58 " =    5.381
peak=    3.442 closest distance to " O   HOH Z 207 " =    2.275
peak=    3.439 closest distance to " O   HOH Z 180 " =    2.120
peak=    3.437 closest distance to " O   HOH Z 405 " =    1.892
peak=    3.436 closest distance to " O   HOH Z 436 " =    2.242
peak=    3.434 closest distance to " CB  GLN A 223 " =    1.483
peak=    3.434 closest distance to " CG  ASP A 238 " =    0.899
peak=    3.418 closest distance to " O   HOH Z 193 " =    1.955
peak=    3.417 closest distance to " NE  ARG A 138 " =    1.095
peak=    3.414 closest distance to " O   HOH Z 393 " =    1.408
peak=    3.413 closest distance to " CB  GLU A 277 " =    1.167
peak=    3.411 closest distance to " CG  GLN A  55 " =    1.782
peak=    3.411 closest distance to " CB  ASP A 200 " =    0.904
peak=    3.409 closest distance to " CD  LYS A 166 " =    1.524
peak=    3.407 closest distance to " O   HOH Z 119 " =    1.397
peak=    3.403 closest distance to " CZ  PHE A  16 " =    0.868
peak=    3.399 closest distance to " OD1 ASN A  45 " =    1.206
peak=    3.397 closest distance to " O   HOH Z 298 " =    2.173
peak=    3.391 closest distance to " CG2BVAL A  41 " =    0.869
peak=    3.386 closest distance to " N   GLY A  98 " =    1.072
peak=    3.382 closest distance to " O   HOH Z  68 " =    1.852
peak=    3.379 closest distance to " O   HOH Z 222 " =    2.273
peak=    3.377 closest distance to " CD  GLN A 240 " =    2.000
peak=    3.376 closest distance to " CE AMET A  47 " =    1.302
peak=    3.376 closest distance to " O   HOH Z  22 " =    1.985
peak=    3.372 closest distance to " CZ  PHE A  38 " =    1.328
peak=    3.370 closest distance to " CG  LYS A 166 " =    1.430
peak=    3.366 closest distance to " O   HOH Z 258 " =    1.924
peak=    3.366 closest distance to " N   PHE A 130 " =    1.207
peak=    3.365 closest distance to " O   HOH Z 437 " =    2.583
peak=    3.364 closest distance to " O   HOH Z  77 " =    1.413
peak=    3.361 closest distance to " CB  ALA A  10 " =    1.116
peak=    3.354 closest distance to " O   HOH Z 191 " =    2.245
peak=    3.354 closest distance to " O   HOH Z 132 " =    2.286
peak=    3.352 closest distance to " O   HOH Z 384 " =    1.462
peak=    3.350 closest distance to " CD2 LEU A 300 " =    1.128
peak=    3.348 closest distance to " C   ASN A 209 " =    1.750
peak=    3.348 closest distance to " N   ASN A 285 " =    0.793
peak=    3.347 closest distance to " CZ3 TRP A 274 " =    2.152
peak=    3.347 closest distance to " O   HOH Z 166 " =    1.518
peak=    3.343 closest distance to " O   HOH Z 334 " =    1.555
peak=    3.342 closest distance to " CD2 LEU A 281 " =    1.006
peak=    3.340 closest distance to " O   HOH Z 151 " =    1.772
peak=    3.339 closest distance to " O   HOH Z 261 " =    1.967
peak=    3.337 closest distance to " CD1 LEU A 281 " =    1.570
peak=    3.337 closest distance to " O   HOH Z  47 " =    1.577
peak=    3.330 closest distance to " O   HOH Z 124 " =    2.279
peak=    3.322 closest distance to " O   HOH Z 110 " =    1.467
peak=    3.322 closest distance to " O   HOH Z  92 " =    1.196
peak=    3.319 closest distance to " O   HOH Z  15 " =    1.287
peak=    3.319 closest distance to " O   HOH Z  46 " =    1.098
peak=    3.301 closest distance to " O   HOH Z 361 " =    1.481
peak=    3.301 closest distance to " CE  LYS A  48 " =    0.945
peak=    3.299 closest distance to " CG1 VAL A 202 " =    2.075
peak=    3.291 closest distance to " CB  SER A   3 " =    1.431
peak=    3.290 closest distance to " O   HOH Z 293 " =    1.238
peak=    3.288 closest distance to " O   HOH Z 392 " =    1.295
peak=    3.287 closest distance to " O   HOH Z 369 " =    1.672
peak=    3.286 closest distance to " O   HOH Z 368 " =    1.624
peak=    3.283 closest distance to " CA  SER A  63 " =    0.915
peak=    3.280 closest distance to " CA  ALA A  21 " =    1.298
peak=    3.280 closest distance to " O   HOH Z  39 " =    1.101
peak=    3.279 closest distance to " O   HOH Z 364 " =    1.327
peak=    3.279 closest distance to " OG  SER A 276 " =    0.901
peak=    3.279 closest distance to " CA  ALA A 180 " =    1.156
peak=    3.273 closest distance to " CB  ARG A 102 " =    0.781
peak=    3.272 closest distance to " O   HOH Z 128 " =    2.185
peak=    3.263 closest distance to " O   HOH Z 108 " =    2.097
peak=    3.262 closest distance to " O   ASN A 301 " =    2.336
peak=    3.261 closest distance to " O   HOH Z 145 " =    2.007
peak=    3.259 closest distance to " O   HOH Z 130 " =    2.462
peak=    3.257 closest distance to " O   HOH Z 271 " =    2.197
peak=    3.255 closest distance to " CG  GLU A   2 " =    1.078
peak=    3.252 closest distance to " CA  PRO A  54 " =    0.952
peak=    3.251 closest distance to " O   HOH Z 189 " =    1.836
peak=    3.248 closest distance to " CB  GLU A 152 " =    1.222
peak=    3.246 closest distance to " CA  PRO A 280 " =    1.520
peak=    3.244 closest distance to " O   HOH Z  88 " =    3.819
peak=    3.244 closest distance to " O   HOH Z 365 " =    2.639
peak=    3.244 closest distance to " O   HOH Z  76 " =    1.037
peak=    3.244 closest distance to " O   HOH Z 383 " =    3.452
peak=    3.242 closest distance to " O   HOH Z 132 " =    1.936
peak=    3.242 closest distance to " CB  ASN A  60 " =    0.854
peak=    3.242 closest distance to " OE1 GLN A 278 " =    1.048
peak=    3.242 closest distance to " CG2 THR A 294 " =    1.071
peak=    3.241 closest distance to " OD1 ASN A 217 " =    1.662
peak=    3.239 closest distance to " O   THR A 220 " =    1.595
peak=    3.236 closest distance to " CG  ARG A 159 " =    0.727
peak=    3.235 closest distance to " O   HOH Z  48 " =    1.671
peak=    3.235 closest distance to " CZ3 TRP A 123 " =    1.287
peak=    3.234 closest distance to " O   HOH Z 220 " =    1.389
peak=    3.231 closest distance to " O   VAL A  72 " =    1.081
peak=    3.230 closest distance to " CB  TRP A 266 " =    0.977
peak=    3.227 closest distance to " O   HOH Z 407 " =    2.068
peak=    3.227 closest distance to " O   HOH Z 345 " =    1.992
peak=    3.225 closest distance to " O   HOH Z 325 " =    1.599
peak=    3.217 closest distance to " O   HOH Z 134 " =    1.393
peak=    3.217 closest distance to " C   ASN A 215 " =    1.345
peak=    3.215 closest distance to " CB  ILE A 263 " =    1.225
peak=    3.214 closest distance to " CB  ARG A  56 " =    1.212
peak=    3.212 closest distance to " O   HOH Z 368 " =    3.762
peak=    3.210 closest distance to " CD2 LEU A  25 " =    1.161
peak=    3.207 closest distance to " CA  SER A  12 " =    1.418
peak=    3.206 closest distance to " CB  ARG A  79 " =    0.959
peak=    3.206 closest distance to " O   HOH Z 410 " =    1.432
peak=    3.203 closest distance to " CG1 VAL A 232 " =    1.460
peak=    3.202 closest distance to " CB  ALA A  43 " =    1.036
peak=    3.197 closest distance to " N   SER A 210 " =    1.089
peak=    3.194 closest distance to " CB  ASP A 298 " =    1.064
peak=    3.191 closest distance to " O   HOH Z 139 " =    2.566
peak=    3.185 closest distance to " CB  THR A 235 " =    1.172
peak=    3.182 closest distance to " CB  GLN A  11 " =    1.487
peak=    3.180 closest distance to " CA  ILE A 234 " =    1.202
peak=    3.179 closest distance to " O   HOH Z 127 " =    0.943
peak=    3.178 closest distance to " CD  ARG A 195 " =    3.341
peak=    3.172 closest distance to " O   ALA A 233 " =    1.842
peak=    3.169 closest distance to " CE2 TRP A  70 " =    1.664
peak=    3.165 closest distance to " O   HOH Z  88 " =    2.632
peak=    3.162 closest distance to " CG AARG A 275 " =    1.112
peak=    3.159 closest distance to " O   HOH Z  25 " =    1.544
peak=    3.159 closest distance to " CG  GLN A  11 " =    1.972
peak=    3.151 closest distance to " CA  ASN A 284 " =    0.994
peak=    3.151 closest distance to " CA  ASN A  74 " =    1.240
peak=    3.149 closest distance to " CB  SER A 276 " =    1.206
peak=    3.147 closest distance to " O   HOH Z 266 " =    1.869
peak=    3.147 closest distance to " CB  TYR A 169 " =    0.741
peak=    3.140 closest distance to " CB  ASN A 285 " =    1.055
peak=    3.140 closest distance to " CB  TYR A 116 " =    1.107
peak=    3.138 closest distance to " O   HOH Z 279 " =    1.022
peak=    3.137 closest distance to " O   HOH Z 225 " =    1.942
peak=    3.133 closest distance to " N   ALA A 100 " =    0.827
peak=    3.133 closest distance to " O   HOH Z 334 " =    1.719
peak=    3.128 closest distance to " O   SER A 271 " =    1.283
peak=    3.127 closest distance to " CB  SER A 210 " =    0.976
peak=    3.126 closest distance to " O   HOH Z 319 " =    1.351
peak=    3.125 closest distance to " CA  ALA A 295 " =    0.983
peak=    3.115 closest distance to " O   HOH Z 303 " =    1.747
peak=    3.114 closest distance to " O   GLU A   2 " =    1.859
peak=    3.110 closest distance to " O   HOH Z 167 " =    1.606
peak=    3.109 closest distance to " CB  ASP A 140 " =    0.749
peak=    3.105 closest distance to " CB  PHE A  16 " =    1.048
peak=    3.101 closest distance to " C   SER A 135 " =    1.027
peak=    3.099 closest distance to " O   HOH Z  44 " =    2.362
peak=    3.095 closest distance to " OG1 THR A 246 " =    3.155
peak=    3.087 closest distance to " CG  GLN A  77 " =    2.163
peak=    3.086 closest distance to " O   HOH Z 343 " =    1.667
peak=    3.084 closest distance to " CB  ALA A 100 " =    1.211
peak=    3.082 closest distance to " O   HOH Z  44 " =    1.522
peak=    3.081 closest distance to " CA  ARG A 195 " =    1.329
peak=    3.080 closest distance to " N   ASN A 127 " =    1.578
peak=    3.079 closest distance to " NH1 ARG A  56 " =    1.333
peak=    3.077 closest distance to " CB  GLU A 236 " =    1.465
peak=    3.077 closest distance to " O   HOH Z 434 " =    1.436
peak=    3.076 closest distance to " O   HOH Z  65 " =    1.448
peak=    3.068 closest distance to " O   HOH Z 157 " =    3.032
peak=    3.060 closest distance to " O   HOH Z 274 " =    1.915
peak=    2.770 closest distance to " O   HOH Z 154 " =    2.037

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.665 - 5.744
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 209
   mapped sites are within: 0.721 - 5.744

peak=   -5.183 closest distance to " O   SER A  62 " =    1.093
peak=   -4.530 closest distance to " CA  GLY A 133 " =    1.976
peak=   -4.477 closest distance to " O   PRO A 198 " =    1.235
peak=   -4.441 closest distance to " CG  GLN A  88 " =    0.875
peak=   -4.401 closest distance to " OG  SER A  97 " =    2.169
peak=   -4.391 closest distance to " CD  ARG A  14 " =    2.991
peak=   -4.346 closest distance to " O   HOH Z 377 " =    1.640
peak=   -4.269 closest distance to " O   HOH Z  77 " =    1.634
peak=   -4.175 closest distance to " O   HOH Z 290 " =    1.178
peak=   -4.157 closest distance to " O   HOH Z 404 " =    0.918
peak=   -4.122 closest distance to " O   ASP A 191 " =    1.894
peak=   -4.084 closest distance to " CG  MET A 105 " =    0.924
peak=   -4.068 closest distance to " O   HOH Z 198 " =    2.462
peak=   -4.063 closest distance to " ND2 ASN A 209 " =    1.711
peak=   -4.062 closest distance to " O   HOH Z  39 " =    1.350
peak=   -4.041 closest distance to " CB  ASN A 285 " =    2.012
peak=   -4.012 closest distance to " CD1 TRP A 179 " =    1.137
peak=   -3.979 closest distance to " O   HOH Z 140 " =    4.366
peak=   -3.951 closest distance to " CB  ALA A 248 " =    1.822
peak=   -3.936 closest distance to " O   HOH Z  24 " =    1.201
peak=   -3.925 closest distance to " O   HOH Z  60 " =    1.871
peak=   -3.902 closest distance to " O   HOH Z 381 " =    1.063
peak=   -3.857 closest distance to " CG  PRO A 163 " =    2.482
peak=   -3.823 closest distance to " CB  ASP A  27 " =    2.465
peak=   -3.818 closest distance to " OG ASER A 134 " =    1.130
peak=   -3.792 closest distance to " O   HOH Z 409 " =    3.214
peak=   -3.774 closest distance to " N   GLN A  58 " =    1.242
peak=   -3.722 closest distance to " N   ASN A 127 " =    1.443
peak=   -3.722 closest distance to " CZ  PHE A  59 " =    1.439
peak=   -3.716 closest distance to " OG  SER A  63 " =    1.236
peak=   -3.712 closest distance to " O   SER A 146 " =    1.446
peak=   -3.709 closest distance to " O   HOH Z  14 " =    1.393
peak=   -3.705 closest distance to " CB  CYS A 201 " =    2.209
peak=   -3.700 closest distance to " CG  ASP A  50 " =    0.874
peak=   -3.685 closest distance to " O   HOH Z 266 " =    4.365
peak=   -3.683 closest distance to " C   SER A  63 " =    1.032
peak=   -3.662 closest distance to " NH2AARG A 275 " =    5.744
peak=   -3.659 closest distance to " O   HOH Z 415 " =    1.220
peak=   -3.657 closest distance to " O   HOH Z  51 " =    0.721
peak=   -3.649 closest distance to " O   HOH Z  52 " =    0.978
peak=   -3.642 closest distance to " CB  ALA A   8 " =    2.101
peak=   -3.642 closest distance to " O   SER A 135 " =    1.515
peak=   -3.637 closest distance to " O   HOH Z 185 " =    2.370
peak=   -3.633 closest distance to " O   ALA A   1 " =    1.117
peak=   -3.610 closest distance to " O   HOH Z 117 " =    0.751
peak=   -3.608 closest distance to " O   HOH Z 102 " =    2.125
peak=   -3.592 closest distance to " O   HOH Z 234 " =    4.708
peak=   -3.590 closest distance to " CG  GLU A 152 " =    2.649
peak=   -3.588 closest distance to " CA  LEU A 143 " =    1.236
peak=   -3.585 closest distance to " CG1BVAL A  72 " =    1.921
peak=   -3.583 closest distance to " C   VAL A  72 " =    0.987
peak=   -3.583 closest distance to " O   HOH Z 163 " =    1.595
peak=   -3.582 closest distance to " O   HOH Z 264 " =    1.153
peak=   -3.582 closest distance to " O   HOH Z 347 " =    0.976
peak=   -3.581 closest distance to " O   HOH Z  97 " =    1.070
peak=   -3.573 closest distance to " OD1 ASN A  60 " =    1.080
peak=   -3.570 closest distance to " N   GLN A  88 " =    1.752
peak=   -3.567 closest distance to " CG2BVAL A  41 " =    1.194
peak=   -3.563 closest distance to " OE1 GLN A  88 " =    0.913
peak=   -3.562 closest distance to " CE2 TYR A  30 " =    2.458
peak=   -3.560 closest distance to " O   HOH Z 399 " =    0.746
peak=   -3.559 closest distance to " O   HOH Z 410 " =    2.436
peak=   -3.557 closest distance to " O   HOH Z 417 " =    2.288
peak=   -3.557 closest distance to " O   ASN A 301 " =    1.530
peak=   -3.555 closest distance to " CD2 LEU A 237 " =    2.389
peak=   -3.550 closest distance to " CB  ALA A 227 " =    2.233
peak=   -3.546 closest distance to " O   LEU A 297 " =    0.804
peak=   -3.543 closest distance to " NH1 ARG A  56 " =    2.426
peak=   -3.537 closest distance to " O   HOH Z 425 " =    0.995
peak=   -3.533 closest distance to " CA  SER A  63 " =    1.210
peak=   -3.533 closest distance to " O   HOH Z 426 " =    1.528
peak=   -3.525 closest distance to " O   HOH Z 388 " =    1.952
peak=   -3.519 closest distance to " N   LYS A 166 " =    1.744
peak=   -3.519 closest distance to " CG1BVAL A  72 " =    4.604
peak=   -3.518 closest distance to " O   HOH Z   1 " =    3.829
peak=   -3.511 closest distance to " O   HOH Z 114 " =    4.588
peak=   -3.511 closest distance to " CG BLYS A 290 " =    0.883
peak=   -3.510 closest distance to " OD2 ASP A 140 " =    1.340
peak=   -3.504 closest distance to " CA  GLY A  98 " =    2.209
peak=   -3.494 closest distance to " O   HOH Z  13 " =    1.368
peak=   -3.488 closest distance to " O   HOH Z 221 " =    1.207
peak=   -3.480 closest distance to " N   HIS A 115 " =    1.909
peak=   -3.478 closest distance to " O   LYS A  76 " =    1.052
peak=   -3.470 closest distance to " O   HOH Z 385 " =    1.222
peak=   -3.470 closest distance to " O   HOH Z   4 " =    1.222
peak=   -3.452 closest distance to " O   HOH Z 109 " =    3.506
peak=   -3.450 closest distance to " N   LEU A 282 " =    2.316
peak=   -3.443 closest distance to " O   PHE A 208 " =    1.572
peak=   -3.441 closest distance to " O   HOH Z 399 " =    1.351
peak=   -3.440 closest distance to " CB  VAL A 125 " =    1.612
peak=   -3.437 closest distance to " NE2 GLN A  55 " =    0.758
peak=   -3.432 closest distance to " CE3 TRP A 179 " =    1.510
peak=   -3.423 closest distance to " O   HOH Z  65 " =    0.949
peak=   -3.423 closest distance to " O   HOH Z 166 " =    0.829
peak=   -3.422 closest distance to " O   HOH Z 148 " =    2.705
peak=   -3.422 closest distance to " OD2 ASP A 171 " =    2.034
peak=   -3.418 closest distance to " O   HOH Z  73 " =    1.424
peak=   -3.415 closest distance to " O   HOH Z 100 " =    1.398
peak=   -3.412 closest distance to " CZ3 TRP A 123 " =    1.774
peak=   -3.402 closest distance to " CB  PRO A 213 " =    1.675
peak=   -3.395 closest distance to " O   PRO A 243 " =    2.398
peak=   -3.394 closest distance to " CD2 TYR A 116 " =    2.226
peak=   -3.384 closest distance to " OG  SER A  63 " =    1.744
peak=   -3.380 closest distance to " NH1 ARG A 195 " =    0.965
peak=   -3.373 closest distance to " O   HOH Z  60 " =    1.282
peak=   -3.371 closest distance to " C   GLN A 205 " =    2.002
peak=   -3.369 closest distance to " O   HOH Z 197 " =    3.450
peak=   -3.368 closest distance to " N   THR A 157 " =    1.575
peak=   -3.367 closest distance to " CA  HIS A  86 " =    1.911
peak=   -3.365 closest distance to " O   ALA A  51 " =    1.226
peak=   -3.364 closest distance to " C   HIS A 108 " =    1.179
peak=   -3.363 closest distance to " CD2 TYR A 293 " =    1.932
peak=   -3.362 closest distance to " O   TYR A  30 " =    1.884
peak=   -3.361 closest distance to " CB  TRP A  85 " =    2.317
peak=   -3.354 closest distance to " CG1 VAL A 265 " =    2.351
peak=   -3.346 closest distance to " O   HOH Z 208 " =    0.890
peak=   -3.340 closest distance to " O   VAL A 189 " =    2.371
peak=   -3.338 closest distance to " O   HOH Z 138 " =    1.111
peak=   -3.329 closest distance to " O   HOH Z 231 " =    1.224
peak=   -3.315 closest distance to " OG BSER A 134 " =    1.683
peak=   -3.289 closest distance to " O   HOH Z  56 " =    0.906
peak=   -3.288 closest distance to " O   HOH Z 438 " =    0.998
peak=   -3.286 closest distance to " OE1 GLN A  58 " =    2.498
peak=   -3.280 closest distance to " N   ALA A  43 " =    2.428
peak=   -3.277 closest distance to " N   GLN A  58 " =    1.957
peak=   -3.276 closest distance to " O   HOH Z 143 " =    1.197
peak=   -3.272 closest distance to " O   HOH Z 139 " =    2.293
peak=   -3.271 closest distance to " O   HOH Z 231 " =    1.826
peak=   -3.268 closest distance to " CA  ASN A 148 " =    1.894
peak=   -3.262 closest distance to " O   ARG A  14 " =    2.246
peak=   -3.261 closest distance to " O   HOH Z  88 " =    1.831
peak=   -3.260 closest distance to " N   ASP A 171 " =    2.393
peak=   -3.259 closest distance to " CA  GLY A 211 " =    1.481
peak=   -3.259 closest distance to " CB  PRO A  90 " =    1.383
peak=   -3.252 closest distance to " O   HOH Z 292 " =    1.223
peak=   -3.246 closest distance to " N   SER A  12 " =    1.082
peak=   -3.243 closest distance to " O   HOH Z 359 " =    1.519
peak=   -3.234 closest distance to " O   GLN A 194 " =    1.166
peak=   -3.233 closest distance to " CG1 ILE A 234 " =    2.062
peak=   -3.230 closest distance to " O   HOH Z 300 " =    1.740
peak=   -3.225 closest distance to " N   ARG A 156 " =    1.038
peak=   -3.224 closest distance to " O   HOH Z  76 " =    1.086
peak=   -3.224 closest distance to " OE2 GLU A 152 " =    2.041
peak=   -3.224 closest distance to " O   SER A  62 " =    1.408
peak=   -3.223 closest distance to " O   HOH Z  95 " =    1.474
peak=   -3.223 closest distance to " OG1 THR A 294 " =    2.270
peak=   -3.220 closest distance to " O   HOH Z  68 " =    1.564
peak=   -3.216 closest distance to " OG1 THR A 178 " =    1.063
peak=   -3.213 closest distance to " OXT GLY A 302 " =    0.738
peak=   -3.207 closest distance to " CD1 LEU A  96 " =    2.144
peak=   -3.205 closest distance to " NH2 ARG A  79 " =    1.811
peak=   -3.203 closest distance to " CE1 PHE A 225 " =    1.653
peak=   -3.200 closest distance to " O   HOH Z 126 " =    1.818
peak=   -3.199 closest distance to " O   VAL A 174 " =    2.648
peak=   -3.198 closest distance to " O   TRP A  70 " =    1.468
peak=   -3.196 closest distance to " CG  GLN A  73 " =    1.251
peak=   -3.190 closest distance to " O   SER A 146 " =    1.001
peak=   -3.187 closest distance to " CB  TYR A  15 " =    2.090
peak=   -3.179 closest distance to " CA  GLY A  17 " =    1.483
peak=   -3.178 closest distance to " O   HOH Z 150 " =    2.954
peak=   -3.177 closest distance to " O   HOH Z  43 " =    1.313
peak=   -3.176 closest distance to " CD  GLN A  58 " =    1.186
peak=   -3.169 closest distance to " O   HOH Z  96 " =    1.287
peak=   -3.166 closest distance to " CG2 ILE A 151 " =    2.391
peak=   -3.163 closest distance to " O   HOH Z 220 " =    1.215
peak=   -3.162 closest distance to " CB  ALA A 291 " =    2.038
peak=   -3.162 closest distance to " CB  ALA A   9 " =    2.381
peak=   -3.159 closest distance to " O   HOH Z 168 " =    2.922
peak=   -3.156 closest distance to " O   HOH Z 308 " =    1.995
peak=   -3.156 closest distance to " CD  GLN A  77 " =    1.200
peak=   -3.149 closest distance to " CA  GLY A  98 " =    1.806
peak=   -3.146 closest distance to " C   GLY A  13 " =    1.121
peak=   -3.145 closest distance to " O   HOH Z  93 " =    2.057
peak=   -3.145 closest distance to " NH2 ARG A 159 " =    2.566
peak=   -3.141 closest distance to " O   HOH Z 102 " =    1.611
peak=   -3.137 closest distance to " O   TYR A 116 " =    2.177
peak=   -3.136 closest distance to " SG ACYS A 201 " =    1.758
peak=   -3.134 closest distance to " N   ALA A   1 " =    1.322
peak=   -3.134 closest distance to " O   GLY A  80 " =    2.625
peak=   -3.132 closest distance to " O   HOH Z 298 " =    1.154
peak=   -3.131 closest distance to " O   HOH Z 388 " =    2.092
peak=   -3.130 closest distance to " O   GLN A  77 " =    1.859
peak=   -3.125 closest distance to " O   SER A   3 " =    1.085
peak=   -3.124 closest distance to " CA  GLY A 287 " =    0.888
peak=   -3.122 closest distance to " O   SER A 216 " =    1.759
peak=   -3.121 closest distance to " CD  LYS A 289 " =    2.512
peak=   -3.110 closest distance to " CA  GLN A  55 " =    1.170
peak=   -3.105 closest distance to " O   THR A 235 " =    1.305
peak=   -3.105 closest distance to " O   HOH Z   2 " =    1.885
peak=   -3.101 closest distance to " OD1 ASP A  27 " =    1.939
peak=   -3.101 closest distance to " O   HOH Z 184 " =    2.606
peak=   -3.100 closest distance to " CD  LYS A 166 " =    2.470
peak=   -3.097 closest distance to " C   VAL A 265 " =    1.002
peak=   -3.082 closest distance to " CA  LYS A 290 " =    1.319
peak=   -3.076 closest distance to " OH  TYR A 247 " =    1.383
peak=   -3.075 closest distance to " O   HOH Z 124 " =    0.792
peak=   -3.075 closest distance to " CB  ALA A 244 " =    2.166
peak=   -3.065 closest distance to " CB  ASP A 286 " =    1.646
peak=   -3.061 closest distance to " O   HOH Z 138 " =    0.745
peak=   -3.060 closest distance to " O   VAL A  67 " =    2.881
peak=   -3.059 closest distance to " O   HOH Z 137 " =    1.367
peak=   -3.058 closest distance to " CE2 TYR A 186 " =    1.992
peak=   -3.057 closest distance to " O   THR A 221 " =    1.870
peak=   -3.050 closest distance to " CD1 TYR A 214 " =    1.420
peak=   -3.049 closest distance to " O   SER A 258 " =    2.570
peak=   -3.022 closest distance to " OG  SER A   3 " =    1.172

================= 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    :  0.4933 0.4943   6.297963e+00   6.296155e+00
   1_bss:  0.4864 0.4870   6.296206e+00   6.288604e+00
   1_xyz:  0.4001 0.4379   6.181909e+00   6.235738e+00
   1_adp:  0.3653 0.4530   6.148693e+00   6.245401e+00
   1_occ:  0.3647 0.4516   6.147268e+00   6.244509e+00
   2_bss:  0.3650 0.4513   6.149762e+00   6.243687e+00
   2_xyz:  0.3205 0.4047   6.051423e+00   6.191095e+00
   2_adp:  0.3114 0.3961   6.036825e+00   6.176118e+00
   2_occ:  0.3114 0.3961   6.036714e+00   6.176229e+00
   3_bss:  0.3121 0.3953   6.035847e+00   6.175806e+00
   3_xyz:  0.2609 0.3405   5.889924e+00   6.058169e+00
   3_adp:  0.2432 0.3262   5.836278e+00   6.021268e+00
   3_occ:  0.2429 0.3260   5.835399e+00   6.020360e+00
   4_bss:  0.2425 0.3241   5.832983e+00   6.017919e+00
   4_xyz:  0.2078 0.2802   5.697392e+00   5.900673e+00
   4_adp:  0.1900 0.2612   5.628280e+00   5.850621e+00
   4_occ:  0.1899 0.2607   5.627337e+00   5.849573e+00
   5_bss:  0.1902 0.2605   5.626720e+00   5.849355e+00
   5_xyz:  0.1535 0.2169   5.430143e+00   5.682949e+00
   5_adp:  0.1419 0.1984   5.354439e+00   5.600343e+00
   5_occ:  0.1417 0.1981   5.353445e+00   5.599426e+00
   5_bss:  0.1422 0.1977   5.352910e+00   5.598165e+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:  0.336  28.473  -1.502   1.131   0.330   0.000   0.000   0.000
   1_xyz:  0.336  28.473  -1.502   1.131   0.330   0.000   0.000   0.000
   1_adp:  0.336  28.473  -1.502   1.131   0.330   0.000   0.000   0.000
   1_occ:  0.336  28.473  -1.502   1.131   0.330   0.000   0.000   0.000
   2_bss:  0.365  64.642  -0.320   0.464   0.519   0.000   0.000   0.000
   2_xyz:  0.365  64.642  -0.320   0.464   0.519   0.000   0.000   0.000
   2_adp:  0.365  64.642  -0.320   0.464   0.519   0.000   0.000   0.000
   2_occ:  0.365  64.642  -0.320   0.464   0.519   0.000   0.000   0.000
   3_bss:  0.364  70.986  -0.007  -0.014   0.536  -0.000   0.000   0.000
   3_xyz:  0.364  70.986  -0.007  -0.014   0.536  -0.000   0.000   0.000
   3_adp:  0.364  70.986  -0.007  -0.014   0.536  -0.000   0.000   0.000
   3_occ:  0.364  70.986  -0.007  -0.014   0.536  -0.000   0.000   0.000
   4_bss:  0.350  64.259  -0.787  -1.122  -0.451  -0.000  -0.000  -0.000
   4_xyz:  0.350  64.259  -0.787  -1.122  -0.451  -0.000  -0.000  -0.000
   4_adp:  0.350  64.259  -0.787  -1.122  -0.451  -0.000  -0.000  -0.000
   4_occ:  0.350  64.259  -0.787  -1.122  -0.451  -0.000  -0.000  -0.000
   5_bss:  0.329  57.286  -0.941  -1.710  -0.565  -0.000  -0.000  -0.000
   5_xyz:  0.329  57.286  -0.941  -1.710  -0.565  -0.000  -0.000  -0.000
   5_adp:  0.329  57.286  -0.941  -1.710  -0.565  -0.000  -0.000  -0.000
   5_occ:  0.329  57.286  -0.941  -1.710  -0.565  -0.000  -0.000  -0.000
   5_bss:  0.325  57.289  -1.232  -2.110  -0.951  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  64.149 0.3396  0.4713    82156.474
   1_bss:  63.543 0.3461  0.4851    79497.780
   1_xyz:  52.140 0.4926  0.6759    59463.824
   1_adp:  54.141 0.4664  0.6438    61932.015
   1_occ:  54.038 0.4677  0.6442    61609.113
   2_bss:  54.011 0.4680  0.6522    61660.039
   2_xyz:  46.539 0.5612  0.7781    48110.927
   2_adp:  44.556 0.5864  0.8067    45966.885
   2_occ:  44.599 0.5858  0.8055    45964.257
   3_bss:  44.504 0.5867  0.8044    45639.287
   3_xyz:  35.821 0.6913  0.9273    31420.220
   3_adp:  33.330 0.7206  0.9463    28338.055
   3_occ:  33.292 0.7210  0.9462    28255.462
   4_bss:  33.133 0.7226  0.9158    27921.517
   4_xyz:  28.092 0.7777  0.9614    20291.203
   4_adp:  25.891 0.8019  0.9654    17829.202
   4_occ:  25.856 0.8022  0.9655    17774.127
   5_bss:  25.838 0.8023  0.9550    17720.532
   5_xyz:  21.053 0.8503  0.9882    11867.538
   5_adp:  18.811 0.8726  0.9899    10048.668
   5_occ:  18.775 0.8729  0.9899    10012.858
   5_bss:  18.729 0.8733  0.9774     9961.021
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.107   1.9563e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.107   1.9563e-01
   1_xyz:   1.766  0.013  0.120 16.644  0.006  4.101   1.6520e-01
   1_adp:   1.766  0.013  0.120 16.644  0.006  4.101   1.6520e-01
   1_occ:   1.766  0.013  0.120 16.644  0.006  4.101   1.6520e-01
   2_bss:   1.766  0.013  0.120 16.644  0.006  4.101   1.6520e-01
   2_xyz:   1.214  0.009  0.081 15.374  0.006  4.125   8.5972e-02
   2_adp:   1.214  0.009  0.081 15.374  0.006  4.125   8.5972e-02
   2_occ:   1.214  0.009  0.081 15.374  0.006  4.125   8.5972e-02
   3_bss:   1.214  0.009  0.081 15.374  0.006  4.125   8.5972e-02
   3_xyz:   1.196  0.010  0.078 14.739  0.005  4.112   8.5213e-02
   3_adp:   1.196  0.010  0.078 14.739  0.005  4.112   8.5213e-02
   3_occ:   1.196  0.010  0.078 14.739  0.005  4.112   8.5213e-02
   4_bss:   1.196  0.010  0.078 14.739  0.005  4.112   8.5213e-02
   4_xyz:   0.964  0.006  0.065 13.983  0.004  4.118   5.4931e-02
   4_adp:   0.964  0.006  0.065 13.983  0.004  4.118   5.4931e-02
   4_occ:   0.964  0.006  0.065 13.983  0.004  4.118   5.4931e-02
   5_bss:   0.964  0.006  0.065 13.983  0.004  4.118   5.4931e-02
   5_xyz:   1.034  0.007  0.070 14.269  0.004  4.109   6.3214e-02
   5_adp:   1.034  0.007  0.070 14.269  0.004  4.109   6.3214e-02
   5_occ:   1.034  0.007  0.070 14.269  0.004  4.109   6.3214e-02
   5_bss:   1.034  0.007  0.070 14.269  0.004  4.109   6.3214e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.264   2.3922e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.264   2.3922e-01
   1_xyz:  11.619  0.074  0.517 86.890  0.054  1.930   1.2902e-01
   1_adp:  11.619  0.074  0.517 86.890  0.054  1.930   1.2902e-01
   1_occ:  11.619  0.074  0.517 86.890  0.054  1.930   1.2902e-01
   2_bss:  11.619  0.074  0.517 86.890  0.054  1.930   1.2902e-01
   2_xyz:   8.332  0.050  0.309 84.126  0.072  2.193   7.7119e-02
   2_adp:   8.332  0.050  0.309 84.126  0.072  2.193   7.7119e-02
   2_occ:   8.332  0.050  0.309 84.126  0.072  2.193   7.7119e-02
   3_bss:   8.332  0.050  0.309 84.126  0.072  2.193   7.7119e-02
   3_xyz:   8.770  0.087  0.320 77.632  0.039  2.217   8.9897e-02
   3_adp:   8.770  0.087  0.320 77.632  0.039  2.217   8.9897e-02
   3_occ:   8.770  0.087  0.320 77.632  0.039  2.217   8.9897e-02
   4_bss:   8.770  0.087  0.320 77.632  0.039  2.217   8.9897e-02
   4_xyz:   6.622  0.042  0.202 75.813  0.047  2.307   3.9815e-02
   4_adp:   6.622  0.042  0.202 75.813  0.047  2.307   3.9815e-02
   4_occ:   6.622  0.042  0.202 75.813  0.047  2.307   3.9815e-02
   5_bss:   6.622  0.042  0.202 75.813  0.047  2.307   3.9815e-02
   5_xyz:   8.103  0.046  0.262 80.285  0.023  2.248   5.3339e-02
   5_adp:   8.103  0.046  0.262 80.285  0.023  2.248   5.3339e-02
   5_occ:   8.103  0.046  0.262 80.285  0.023  2.248   5.3339e-02
   5_bss:   8.103  0.046  0.262 80.285  0.023  2.248   5.3339e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp: 103.25   0.00  19.55  94.25   0.00  16.86 103.25   0.00  34.17
   1_occ: 103.25   0.00  19.55  94.25   0.00  16.86 103.25   0.00  34.17
   2_bss: 103.25   0.00  19.55  94.25   0.00  16.86 103.25   0.00  34.17
   2_xyz: 103.25   0.00  19.55  94.25   0.00  16.86 103.25   0.00  34.17
   2_adp: 102.08   0.00  18.97  95.13   0.00  16.29 102.08   0.00  33.54
   2_occ: 102.08   0.00  18.97  95.13   0.00  16.29 102.08   0.00  33.54
   3_bss: 102.08   0.00  18.97  95.13   0.00  16.29 102.08   0.00  33.54
   3_xyz: 102.08   0.00  18.97  95.13   0.00  16.29 102.08   0.00  33.54
   3_adp: 101.53   0.00  18.47  95.40   0.00  15.05 101.53   2.59  37.12
   3_occ: 101.53   0.00  18.47  95.40   0.00  15.05 101.53   2.59  37.12
   4_bss: 101.53   0.00  18.47  95.40   0.00  15.05 101.53   2.59  37.12
   4_xyz: 101.53   0.00  18.47  95.40   0.00  15.05 101.53   2.59  37.12
   4_adp: 107.59   0.00  19.11 107.59   0.00  14.03  94.54   4.34  46.77
   4_occ: 107.59   0.00  19.11 107.59   0.00  14.03  94.54   4.34  46.77
   5_bss: 107.59   0.00  19.11 107.59   0.00  14.03  94.54   4.34  46.77
   5_xyz: 107.59   0.00  19.11 107.59   0.00  14.03  94.54   4.34  46.77
   5_adp: 109.47   0.00  18.04 109.47   0.00  12.83  97.37   5.97  46.42
   5_occ: 109.47   0.00  18.04 109.47   0.00  12.83  97.37   5.97  46.42
   5_bss: 109.47   0.00  18.05 109.47   0.00  12.84  97.37   5.97  46.43
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    2.345    0.020    0.394
   1_adp:    2.345    0.020    0.394
   1_occ:    2.345    0.020    0.394
   2_bss:    2.345    0.020    0.394
   2_xyz:    1.778    0.059    0.523
   2_adp:    1.778    0.059    0.523
   2_occ:    1.778    0.059    0.523
   3_bss:    1.778    0.059    0.523
   3_xyz:    1.700    0.043    0.702
   3_adp:    1.700    0.043    0.702
   3_occ:    1.700    0.043    0.702
   4_bss:    1.700    0.043    0.702
   4_xyz:    1.717    0.046    0.779
   4_adp:    1.717    0.046    0.779
   4_occ:    1.717    0.046    0.779
   5_bss:    1.717    0.046    0.779
   5_xyz:    1.697    0.071    0.879
   5_adp:    1.697    0.071    0.879
   5_occ:    1.697    0.071    0.879
   5_bss:    1.697    0.071    0.879
------------------------------------------------------------------------

CPU time actual refinement: 376.36


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_969/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_969/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_969/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_969/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_969/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 376.21 
  Macro-tasks:
    bulk solvent and scale       = 39.30  
    individual site refinement   = 166.31 
    weights calculation          = 31.45  
    collect and process          = 6.41   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 243.60 
  Micro-tasks:
    mask                            = 3.17   
    f_calc                          = 126.70 
    alpha_beta                      = 8.37   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 135.98 
    fmodel                         = 6.50   
    r_factors                      = 0.18   
    phase_errors                   = 9.72   
    foms                           = 0.25   
    TOTAL for micro-tasks          = 292.04 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.284 micro seconds
Total CPU time: 6.51 minutes
from_scatterers_fft:    651 calls, 126.46 s
gradients_fft:          596 calls, 122.27 s

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

# Date 2008-01-16 Time 06:06:38 PST -0800 (1200492398.03 s)
Start R-work = 0.4933, R-free = 0.4943 (no bulk solvent and anisotropic scale)
Final R-work = 0.1596, R-free = 0.2133 (no bulk solvent and anisotropic scale)

Start R-work = 0.4864, R-free = 0.4870
Final R-work = 0.1422, R-free = 0.1977