# Date 2008-01-16 Time 05:45:04 PST -0800 (1200491104.79 s)
#phil __OFF__

Command line arguments: "../863.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27568
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 863

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 45.9914, 86.39, 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: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 45.9914, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1028 1.96347
Completeness in resolution range: 0.943503
Completeness with d_max=infinity: 0.940784

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1028
                             d_min =   1.9635

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 45.9914, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1028 1.96347
Completeness in resolution range: 0.943503
Completeness with d_max=infinity: 0.940784

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1033 -  4.2026 [2185/2212]  1965   220  10.1%
  bin  2:  4.2026 -  3.3477 [2096/2116]  1889   207   9.9%
  bin  3:  3.3477 -  2.9280 [2072/2091]  1863   209  10.1%
  bin  4:  2.9280 -  2.6619 [2047/2077]  1840   207  10.1%
  bin  5:  2.6619 -  2.4720 [2036/2055]  1841   195   9.6%
  bin  6:  2.4720 -  2.3268 [2024/2049]  1813   211  10.4%
  bin  7:  2.3268 -  2.2107 [2017/2045]  1818   199   9.9%
  bin  8:  2.2107 -  2.1147 [1999/2035]  1797   202  10.1%
  bin  9:  2.1147 -  2.0335 [2010/2052]  1816   194   9.7%
  bin 10:  2.0335 -  1.9635 [1103/2030]   988   115  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_863/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 32
        2.42 -     3.04: 2216
        3.04 -     3.66: 4730
        3.66 -     4.28: 9096
        4.28 -     4.90: 12334
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.830 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  2.019 3.120 x,y-1,z
  ... (remaining 28403 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_863/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_863/model_refine_001.geo

CPU time processing inputs: 9.51


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 45.9914 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4003   r_free= 0.3976   ksol= 0.00   Bsol= 0.00   scale= 0.932    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.211195                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1033 -  4.6880 0.99   1415  158 0.3380 0.3340      6.4819      6.4699|
|  2:  4.6880 -  3.7396 0.99   1356  152 0.3328 0.3168      6.6956      6.6165|
|  3:  3.7396 -  3.2724 0.99   1345  143 0.3540 0.3371      6.5585      6.5998|
|  4:  3.2724 -  2.9757 0.99   1333  155 0.3881 0.4055      6.4401      6.4693|
|  5:  2.9757 -  2.7638 0.99   1321  149 0.4262 0.3923      6.2928      6.2691|
|  6:  2.7638 -  2.6017 0.99   1307  143 0.4170 0.4482      6.2011      6.1687|
|  7:  2.6017 -  2.4720 0.99   1321  138 0.4318 0.4054      6.1807      6.1175|
|  8:  2.4720 -  2.3648 0.98   1291  147 0.4396 0.4396      6.1095      6.1464|
|  9:  2.3648 -  2.2741 0.98   1282  152 0.4331 0.4715      6.0654      6.0932|
| 10:  2.2741 -  2.1959 1.00   1313  142 0.4467 0.4396      6.0413      6.0121|
| 11:  2.1959 -  2.1274 0.98   1299  137 0.4380 0.4501      5.9869      6.0153|
| 12:  2.1274 -  2.0667 0.98   1283  146 0.4554 0.4574      5.9146      5.9748|
| 13:  2.0667 -  2.0125 0.98   1271  139 0.4548 0.4588      5.8306       5.775|
| 14:  2.0125 -  1.9635 0.38    493   58 0.5070 0.4750      5.8674       5.826|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1033 -  4.6880  1415   158  0.74  30.20   0.84     0.79      57749.79|
|  2:  4.6880 -  3.7396  1356   152  0.78  28.47   0.93     0.88      75454.53|
|  3:  3.7396 -  3.2724  1345   143  0.70  35.71   0.97     0.88      80751.59|
|  4:  3.2724 -  2.9757  1333   155  0.63  41.44   0.95     0.83      74554.19|
|  5:  2.9757 -  2.7638  1321   149  0.55  47.61   0.92     0.77      61512.70|
|  6:  2.7638 -  2.6017  1307   143  0.55  48.27   0.93     0.74      53647.97|
|  7:  2.6017 -  2.4720  1321   138  0.52  50.39   0.97     0.70      49998.69|
|  8:  2.4720 -  2.3648  1291   147  0.50  52.28   0.95     0.69      45755.34|
|  9:  2.3648 -  2.2741  1282   152  0.51  51.12   0.97     0.72      41302.43|
| 10:  2.2741 -  2.1959  1313   142  0.53  49.83   0.98     0.74      36173.82|
| 11:  2.1959 -  2.1274  1299   137  0.51  51.64   1.01     0.75      36334.33|
| 12:  2.1274 -  2.0667  1283   146  0.47  54.61   0.98     0.70      33881.37|
| 13:  2.0667 -  2.0125  1271   139  0.43  57.66   0.98     0.68      30798.01|
| 14:  2.0125 -  1.9635   493    58  0.49  52.82   0.99     0.69      24463.39|
|alpha:            min =        0.68 max =            0.88 mean =         0.76|
|beta:             min =    24463.39 max =        80751.59 mean =     51664.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.57|
|phase err.(work): min =        0.00 max =           89.97 mean =        46.06|
|phase err.(test): min =        0.00 max =           89.67 mean =        46.26|
|-----------------------------------------------------------------------------|

============================== 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 = 6.479857              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.208   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.518741              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.102   (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 |  1.806 -  2.115:       10 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       22 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      200 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2016 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1880 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2850 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4663 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4433 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5609 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6725 |
|-----------------------------------------------------------------------------|
|-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 |        0.171 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.806 |       0.315 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4003   r_free= 0.3976   ksol= 0.00   Bsol= 0.00   scale= 0.932    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.211195                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3879   r_free= 0.3882   ksol= 0.35   Bsol= 50.00   scale= 0.955   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.73,3.32,-1.87,0.00,-0.00,-0.00); trace/3= -0.09                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.196821                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.759463              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.308   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.787604              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.920   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3879      final r-factor (work) = 0.2940          |
| start r-factor (free) = 0.3882      final r-factor (free) = 0.3285          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.0170 = 5.76 * 0.50 * 6.1970 + 1.00 * 0.1713                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.5214 = 5.76 * 0.50 * 6.0498 + 1.00 * 0.0995                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2940      final r-factor (work) = 0.2686          |
| start r-factor (free) = 0.3285      final r-factor (free) = 0.3416          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7710 = 0.79 * 1.00 * 6.0498 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6786 = 0.79 * 1.00 * 5.9219 + 1.00 * 0.0145                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.92   17.95    None  None   None       |
|    all(noH): 2823   0      0.00    99.92   17.95    None  None   None       |
|    Sol.    : 438    0      2.67    99.92   37.83    None  None   None       |
|    Mac.    : 2385   0      0.00    61.72   14.30    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 -   9.993:  903   |   5:    49.962 -  59.955:   75        |
|      1:     9.993 -  19.985: 1046   |   6:    59.955 -  69.947:   29        |
|      2:    19.985 -  29.977:  413   |   7:    69.947 -  79.940:   14        |
|      3:    29.977 -  39.970:  210   |   8:    79.940 -  89.932:    0        |
|      4:    39.970 -  49.962:  132   |   9:    89.932 -  99.925:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2686 r_free = 0.3416             target_work(ml) = 5.934         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2683 r_free = 0.3418             target_work(ml) = 5.933         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2683   r_free= 0.3418   ksol= 0.35   Bsol= 50.00   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.73,3.32,-1.87,0.00,-0.00,-0.00); trace/3= -0.09                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.933015                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2673   r_free= 0.3388   ksol= 0.32   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.78,0.06,-1.25,0.00,-0.00,-0.00); trace/3= -0.99                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.929695                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.359780              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.960   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.334935              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.930  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2673      final r-factor (work) = 0.1967          |
| start r-factor (free) = 0.3388      final r-factor (free) = 0.2523          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.9683 = 5.36 * 0.50 * 5.9214 + 1.00 * 0.0995                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.6521 = 5.36 * 0.50 * 5.8055 + 1.00 * 0.0939                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1967      final r-factor (work) = 0.1803          |
| start r-factor (free) = 0.2523      final r-factor (free) = 0.2366          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9588 = 0.33 * 1.00 * 5.8055 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9014 = 0.33 * 1.00 * 5.5960 + 1.00 * 0.0271                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.43   17.72    None  None   None       |
|    all(noH): 2823   0      0.00    99.43   17.72    None  None   None       |
|    Sol.    : 438    0      4.74    99.43   39.06    None  None   None       |
|    Mac.    : 2385   0      0.00    65.03   13.80    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 -   9.943:  913   |   5:    49.714 -  59.657:   79        |
|      1:     9.943 -  19.886: 1139   |   6:    59.657 -  69.600:   27        |
|      2:    19.886 -  29.829:  306   |   7:    69.600 -  79.543:   12        |
|      3:    29.829 -  39.771:  202   |   8:    79.543 -  89.486:    0        |
|      4:    39.771 -  49.714:  144   |   9:    89.486 -  99.429:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1803 r_free = 0.2366             target_work(ml) = 5.565         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1801 r_free = 0.2360             target_work(ml) = 5.564         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1801   r_free= 0.2360   ksol= 0.32   Bsol= 50.00   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.78,0.06,-1.25,0.00,-0.00,-0.00); trace/3= -0.99                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.563653                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1794   r_free= 0.2341   ksol= 0.33   Bsol= 50.00   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.77,-1.41,-0.87,-0.00,-0.00,-0.00); trace/3= -1.35                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.559162                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.608417              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.239   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.335842              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.367   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1794      final r-factor (work) = 0.1405          |
| start r-factor (free) = 0.2341      final r-factor (free) = 0.1934          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.9853 = 4.61 * 0.50 * 5.5947 + 1.00 * 0.0939                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.6311 = 4.61 * 0.50 * 5.4545 + 1.00 * 0.0628                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1405      final r-factor (work) = 0.1286          |
| start r-factor (free) = 0.1934      final r-factor (free) = 0.1781          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9231 = 0.34 * 1.00 * 5.4545 + 1.00 * 0.0912                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7933 = 0.34 * 1.00 * 5.3145 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.63    96.79   17.18    None  None   None       |
|    all(noH): 2823   0      0.63    96.79   17.18    None  None   None       |
|    Sol.    : 438    0      7.18    96.79   40.26    None  None   None       |
|    Mac.    : 2385   0      0.63    72.47   12.94    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.632 -  10.248: 1067   |   5:    48.713 -  58.329:  102        |
|      1:    10.248 -  19.864: 1080   |   6:    58.329 -  67.945:   41        |
|      2:    19.864 -  29.480:  238   |   7:    67.945 -  77.561:   13        |
|      3:    29.480 -  39.097:  144   |   8:    77.561 -  87.177:    0        |
|      4:    39.097 -  48.713:  137   |   9:    87.177 -  96.794:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1286 r_free = 0.1781             target_work(ml) = 5.268         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1285 r_free = 0.1780             target_work(ml) = 5.267         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1285   r_free= 0.1780   ksol= 0.33   Bsol= 50.00   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.77,-1.41,-0.87,-0.00,-0.00,-0.00); trace/3= -1.35                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.267169                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1285   r_free= 0.1773   ksol= 0.33   Bsol= 50.00   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-2.34,-1.17,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.263941                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.781669              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.348  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.194201              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.743  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1285      final r-factor (work) = 0.1175          |
| start r-factor (free) = 0.1773      final r-factor (free) = 0.1649          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4582 = 2.78 * 0.50 * 5.3172 + 1.00 * 0.0628                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3308 = 2.78 * 0.50 * 5.2285 + 1.00 * 0.0588                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1175      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1649      final r-factor (free) = 0.1629          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2523 = 1.19 * 1.00 * 5.2285 + 1.00 * 0.0084                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1893 = 1.19 * 1.00 * 5.1745 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.79   17.36    None  None   None       |
|    all(noH): 2823   0      0.00    97.79   17.36    None  None   None       |
|    Sol.    : 438    0      6.14    97.79   41.92    None  None   None       |
|    Mac.    : 2385   0      0.00    89.32   12.85    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 -   9.779: 1024   |   5:    48.895 -  58.674:  105        |
|      1:     9.779 -  19.558: 1133   |   6:    58.674 -  68.454:   48        |
|      2:    19.558 -  29.337:  234   |   7:    68.454 -  78.233:   30        |
|      3:    29.337 -  39.116:  120   |   8:    78.233 -  88.012:    5        |
|      4:    39.116 -  48.895:  122   |   9:    88.012 -  97.791:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1138 r_free = 0.1629             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1137 r_free = 0.1628             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1628   ksol= 0.33   Bsol= 50.00   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-2.34,-1.17,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.167330                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1627   ksol= 0.32   Bsol= 50.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,-2.43,-1.07,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.166622                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.754538              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.529  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.748132              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.961  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1137      final r-factor (work) = 0.1099          |
| start r-factor (free) = 0.1627      final r-factor (free) = 0.1589          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1849 = 2.75 * 0.50 * 5.1741 + 1.00 * 0.0588                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1588 = 2.75 * 0.50 * 5.1524 + 1.00 * 0.0626                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1099      final r-factor (work) = 0.1091          |
| start r-factor (free) = 0.1589      final r-factor (free) = 0.1586          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.0169 = 1.75 * 1.00 * 5.1524 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.9936 = 1.75 * 1.00 * 5.1388 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.75   17.22    None  None   None       |
|    all(noH): 2823   0      0.00    97.75   17.22    None  None   None       |
|    Sol.    : 438    0      5.94    97.75   41.71    None  None   None       |
|    Mac.    : 2385   0      0.00    94.32   12.72    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.775: 1054   |   5:    48.875 -  58.650:   90        |
|      1:     9.775 -  19.550: 1112   |   6:    58.650 -  68.425:   53        |
|      2:    19.550 -  29.325:  226   |   7:    68.425 -  78.200:   30        |
|      3:    29.325 -  39.100:  129   |   8:    78.200 -  87.975:   10        |
|      4:    39.100 -  48.875:  116   |   9:    87.975 -  97.750:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1091 r_free = 0.1586             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1091 r_free = 0.1586             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1586   ksol= 0.32   Bsol= 50.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,-2.43,-1.07,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.139119                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1033 -  4.6880 0.99   1415  158 0.0914 0.1277      5.3316      5.5622|
|  2:  4.6880 -  3.7396 0.99   1356  152 0.0813 0.1081      5.4088      5.5963|
|  3:  3.7396 -  3.2724 0.99   1345  143 0.1058 0.1560      5.4662      5.8405|
|  4:  3.2724 -  2.9757 0.99   1333  155 0.1211 0.1677       5.443      5.6081|
|  5:  2.9757 -  2.7638 0.99   1321  149 0.1300 0.1767      5.3054       5.565|
|  6:  2.7638 -  2.6017 0.99   1307  143 0.1167 0.1875      5.1844       5.468|
|  7:  2.6017 -  2.4720 0.99   1321  138 0.1220 0.1546      5.1545      5.3032|
|  8:  2.4720 -  2.3648 0.98   1291  147 0.1138 0.1734      5.0542      5.3539|
|  9:  2.3648 -  2.2741 0.98   1282  152 0.1172 0.1775      5.0405      5.3187|
| 10:  2.2741 -  2.1959 1.00   1313  142 0.1082 0.1708      4.9358      5.1976|
| 11:  2.1959 -  2.1274 0.98   1299  137 0.1099 0.1849      4.9434      5.3364|
| 12:  2.1274 -  2.0667 0.98   1283  146 0.1107 0.1642      4.8667      5.1134|
| 13:  2.0667 -  2.0125 0.98   1271  139 0.1126 0.1745      4.7876       5.043|
| 14:  2.0125 -  1.9635 0.38    493   58 0.0988 0.1529      4.6752      4.8683|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1033 -  4.6880  1415   158  0.94   8.67   0.98     0.95       6666.01|
|  2:  4.6880 -  3.7396  1356   152  0.95   7.75   1.02     1.01       8899.33|
|  3:  3.7396 -  3.2724  1345   143  0.93  11.25   1.03     1.03      10249.94|
|  4:  3.2724 -  2.9757  1333   155  0.92  13.99   1.01     0.99      10292.25|
|  5:  2.9757 -  2.7638  1321   149  0.90  15.82   1.00     0.98       8145.02|
|  6:  2.7638 -  2.6017  1307   143  0.90  16.05   0.99     0.97       6967.83|
|  7:  2.6017 -  2.4720  1321   138  0.91  15.41   0.99     0.96       6196.30|
|  8:  2.4720 -  2.3648  1291   147  0.90  15.73   0.98     0.95       5319.15|
|  9:  2.3648 -  2.2741  1282   152  0.90  15.84   0.99     0.96       5168.92|
| 10:  2.2741 -  2.1959  1313   142  0.90  15.90   0.99     0.96       4387.82|
| 11:  2.1959 -  2.1274  1299   137  0.90  16.03   0.98     0.93       4378.18|
| 12:  2.1274 -  2.0667  1283   146  0.91  15.85   1.01     1.01       4004.69|
| 13:  2.0667 -  2.0125  1271   139  0.90  16.75   0.99     0.97       3454.11|
| 14:  2.0125 -  1.9635   493    58  0.91  14.72   0.97     0.95       2759.18|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     2759.18 max =        10292.25 mean =      6403.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.18|
|phase err.(test): min =        0.00 max =           88.79 mean =        13.71|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1586   ksol= 0.32   Bsol= 50.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-2.33,-0.88,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.139084                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1586   ksol= 0.32   Bsol= 50.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-2.33,-0.88,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.139084                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1033 -  4.6880 0.99   1415  158 0.0914 0.1279      5.3319      5.5637|
|  2:  4.6880 -  3.7396 0.99   1356  152 0.0814 0.1082      5.4094      5.5967|
|  3:  3.7396 -  3.2724 0.99   1345  143 0.1059 0.1560      5.4664      5.8406|
|  4:  3.2724 -  2.9757 0.99   1333  155 0.1211 0.1677       5.443       5.608|
|  5:  2.9757 -  2.7638 0.99   1321  149 0.1300 0.1767      5.3051      5.5646|
|  6:  2.7638 -  2.6017 0.99   1307  143 0.1166 0.1873       5.184      5.4672|
|  7:  2.6017 -  2.4720 0.99   1321  138 0.1221 0.1547      5.1544      5.3032|
|  8:  2.4720 -  2.3648 0.98   1291  147 0.1138 0.1734      5.0541      5.3537|
|  9:  2.3648 -  2.2741 0.98   1282  152 0.1173 0.1771      5.0405      5.3181|
| 10:  2.2741 -  2.1959 1.00   1313  142 0.1082 0.1711       4.936      5.1992|
| 11:  2.1959 -  2.1274 0.98   1299  137 0.1098 0.1849      4.9438      5.3364|
| 12:  2.1274 -  2.0667 0.98   1283  146 0.1106 0.1642      4.8664      5.1136|
| 13:  2.0667 -  2.0125 0.98   1271  139 0.1126 0.1742      4.7871      5.0417|
| 14:  2.0125 -  1.9635 0.38    493   58 0.0988 0.1528       4.674      4.8673|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1033 -  4.6880  1415   158  0.94   8.68   0.98     0.95       6672.75|
|  2:  4.6880 -  3.7396  1356   152  0.95   7.76   1.02     1.01       8908.58|
|  3:  3.7396 -  3.2724  1345   143  0.93  11.25   1.04     1.03      10255.45|
|  4:  3.2724 -  2.9757  1333   155  0.92  13.99   1.02     0.99      10290.10|
|  5:  2.9757 -  2.7638  1321   149  0.90  15.81   1.00     0.99       8137.72|
|  6:  2.7638 -  2.6017  1307   143  0.90  16.05   1.00     0.98       6961.48|
|  7:  2.6017 -  2.4720  1321   138  0.91  15.40   1.00     0.97       6193.10|
|  8:  2.4720 -  2.3648  1291   147  0.90  15.73   0.99     0.96       5314.35|
|  9:  2.3648 -  2.2741  1282   152  0.90  15.83   1.00     0.96       5166.59|
| 10:  2.2741 -  2.1959  1313   142  0.90  15.91   1.00     0.97       4392.22|
| 11:  2.1959 -  2.1274  1299   137  0.90  16.05   0.99     0.94       4385.26|
| 12:  2.1274 -  2.0667  1283   146  0.91  15.85   1.02     1.02       4005.99|
| 13:  2.0667 -  2.0125  1271   139  0.90  16.74   1.00     0.98       3449.73|
| 14:  2.0125 -  1.9635   493    58  0.91  14.67   0.98     0.96       2751.77|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2751.77 max =        10290.10 mean =      6403.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.18|
|phase err.(test): min =        0.00 max =           88.79 mean =        13.72|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.75   17.22    None  None   None       |
|    all(noH): 2823   0      0.00    97.75   17.22    None  None   None       |
|    Sol.    : 438    0      5.94    97.75   41.71    None  None   None       |
|    Mac.    : 2385   0      0.00    94.32   12.72    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.778: 1054   |   5:    48.878 -  58.653:   90        |
|      1:     9.778 -  19.553: 1112   |   6:    58.653 -  68.428:   53        |
|      2:    19.553 -  29.328:  226   |   7:    68.428 -  78.203:   30        |
|      3:    29.328 -  39.103:  129   |   8:    78.203 -  87.978:   10        |
|      4:    39.103 -  48.878:  116   |   9:    87.978 -  97.753:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 302         
Filter by distance & map next to the model:
   mapped sites are within: 0.582 - 4.663
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 297 from: 302
   mapped sites are within: 0.776 - 4.663

peak=    6.596 closest distance to " NE2 GLN A  11 " =    1.343
peak=    5.557 closest distance to " NH2 ARG A  56 " =    2.083
peak=    5.492 closest distance to " CG  PRO A  54 " =    1.239
peak=    5.288 closest distance to " O   HOH Z 126 " =    2.198
peak=    5.219 closest distance to " O   HOH Z 427 " =    2.543
peak=    5.137 closest distance to " O   HOH Z 144 " =    1.752
peak=    5.074 closest distance to " O   HOH Z 232 " =    2.287
peak=    5.050 closest distance to " O   HOH Z 417 " =    1.674
peak=    4.997 closest distance to " CB  GLN A 223 " =    1.537
peak=    4.956 closest distance to " O   HOH Z  63 " =    1.689
peak=    4.880 closest distance to " O   HOH Z 287 " =    2.044
peak=    4.880 closest distance to " CB  SER A  63 " =    1.266
peak=    4.750 closest distance to " O   HOH Z 298 " =    1.978
peak=    4.746 closest distance to " O   HOH Z 423 " =    1.846
peak=    4.696 closest distance to " O   HOH Z   7 " =    1.395
peak=    4.633 closest distance to " CG  PRO A 213 " =    1.273
peak=    4.588 closest distance to " O   HOH Z 369 " =    2.122
peak=    4.573 closest distance to " ND2 ASN A 187 " =    1.522
peak=    4.565 closest distance to " CB  GLN A 183 " =    1.230
peak=    4.538 closest distance to " CB  ASN A 148 " =    1.406
peak=    4.505 closest distance to " C   PRO A 198 " =    1.500
peak=    4.483 closest distance to " CB  PRO A  54 " =    0.952
peak=    4.441 closest distance to " O   HOH Z   2 " =    1.626
peak=    4.410 closest distance to " O   HOH Z 425 " =    1.375
peak=    4.408 closest distance to " CA  TYR A  30 " =    0.978
peak=    4.395 closest distance to " O   HOH Z   1 " =    1.844
peak=    4.390 closest distance to " O   HOH Z 214 " =    2.114
peak=    4.361 closest distance to " O   HOH Z 380 " =    1.747
peak=    4.357 closest distance to " O   HOH Z  78 " =    1.698
peak=    4.356 closest distance to " O   HOH Z   1 " =    1.732
peak=    4.328 closest distance to " CG  PRO A 198 " =    1.229
peak=    4.328 closest distance to " CB  ARG A 275 " =    0.920
peak=    4.219 closest distance to " CB  LEU A 228 " =    1.135
peak=    4.193 closest distance to " O   HOH Z 193 " =    1.786
peak=    4.175 closest distance to " CB  ARG A 190 " =    1.739
peak=    4.168 closest distance to " CG  PRO A  90 " =    1.185
peak=    4.126 closest distance to " CD  ARG A 159 " =    0.821
peak=    4.116 closest distance to " CB  GLU A 128 " =    1.036
peak=    4.110 closest distance to " CD  ARG A  66 " =    2.171
peak=    4.108 closest distance to " O   HOH Z 133 " =    2.435
peak=    4.087 closest distance to " O   HOH Z 419 " =    2.278
peak=    4.049 closest distance to " O   HOH Z 217 " =    2.896
peak=    4.033 closest distance to " O   HOH Z 261 " =    1.861
peak=    4.033 closest distance to " O   HOH Z 316 " =    3.109
peak=    4.029 closest distance to " CG  LEU A 167 " =    1.286
peak=    3.996 closest distance to " O   HOH Z 394 " =    1.685
peak=    3.991 closest distance to " CB  ASN A 187 " =    1.123
peak=    3.983 closest distance to " O   HOH Z 371 " =    1.976
peak=    3.978 closest distance to " O   HOH Z 209 " =    2.326
peak=    3.966 closest distance to " O   HOH Z   9 " =    2.007
peak=    3.965 closest distance to " O   HOH Z 171 " =    2.868
peak=    3.948 closest distance to " O   SER A  87 " =    2.285
peak=    3.947 closest distance to " CG  TRP A 179 " =    2.204
peak=    3.944 closest distance to " CB  GLU A 152 " =    1.379
peak=    3.942 closest distance to " OD1 ASN A  69 " =    2.653
peak=    3.933 closest distance to " ND1 HIS A  86 " =    1.793
peak=    3.929 closest distance to " O   HOH Z 392 " =    1.216
peak=    3.926 closest distance to " O   HOH Z 132 " =    2.421
peak=    3.925 closest distance to " CG2 THR A 221 " =    1.038
peak=    3.925 closest distance to " CB  SER A   3 " =    1.454
peak=    3.923 closest distance to " O   HOH Z 272 " =    1.777
peak=    3.922 closest distance to " O   HOH Z  10 " =    1.752
peak=    3.921 closest distance to " O   HOH Z  40 " =    2.243
peak=    3.917 closest distance to " O   HOH Z 389 " =    1.950
peak=    3.915 closest distance to " O   HOH Z  78 " =    2.256
peak=    3.911 closest distance to " O   HOH Z 368 " =    3.678
peak=    3.904 closest distance to " O   HOH Z 250 " =    1.454
peak=    3.892 closest distance to " CB  ARG A  79 " =    1.481
peak=    3.870 closest distance to " CB  TRP A 266 " =    1.057
peak=    3.867 closest distance to " O   HOH Z   3 " =    2.022
peak=    3.847 closest distance to " O   HOH Z 437 " =    1.800
peak=    3.833 closest distance to " CG1 ILE A  33 " =    1.191
peak=    3.812 closest distance to " N   PHE A 130 " =    1.221
peak=    3.794 closest distance to " O   HOH Z  88 " =    3.909
peak=    3.782 closest distance to " CA  GLY A 241 " =    3.819
peak=    3.781 closest distance to " O   HOH Z 193 " =    1.641
peak=    3.777 closest distance to " O   HOH Z 426 " =    1.845
peak=    3.777 closest distance to " CB  VAL A 265 " =    1.304
peak=    3.759 closest distance to " O   HOH Z  61 " =    1.577
peak=    3.751 closest distance to " O   HOH Z 234 " =    3.763
peak=    3.750 closest distance to " O   HOH Z 116 " =    2.946
peak=    3.747 closest distance to " O   HOH Z   9 " =    1.230
peak=    3.741 closest distance to " O   HOH Z 236 " =    1.456
peak=    3.737 closest distance to " CA  TYR A 116 " =    1.303
peak=    3.737 closest distance to " CG2 VAL A 257 " =    0.922
peak=    3.733 closest distance to " CB  GLU A 277 " =    3.587
peak=    3.725 closest distance to " O   HOH Z 352 " =    1.752
peak=    3.712 closest distance to " CZ  PHE A 218 " =    1.051
peak=    3.701 closest distance to " O   HOH Z 126 " =    1.442
peak=    3.697 closest distance to " CG  PRO A 243 " =    1.091
peak=    3.691 closest distance to " O   HOH Z 158 " =    2.803
peak=    3.671 closest distance to " CD2 LEU A 255 " =    1.604
peak=    3.670 closest distance to " CB  SER A 216 " =    0.862
peak=    3.666 closest distance to " O   HOH Z 327 " =    1.620
peak=    3.661 closest distance to " O   HOH Z 371 " =    2.818
peak=    3.661 closest distance to " O   HOH Z 144 " =    2.351
peak=    3.653 closest distance to " O   HOH Z 180 " =    2.114
peak=    3.649 closest distance to " CD BLYS A 290 " =    1.022
peak=    3.643 closest distance to " O   HOH Z  44 " =    2.779
peak=    3.642 closest distance to " CB  THR A 157 " =    1.157
peak=    3.637 closest distance to " O   HOH Z 386 " =    3.039
peak=    3.632 closest distance to " CD1 LEU A 300 " =    1.163
peak=    3.630 closest distance to " O   HOH Z  17 " =    1.757
peak=    3.630 closest distance to " CB  LYS A 117 " =    1.234
peak=    3.618 closest distance to " O   HOH Z 345 " =    1.764
peak=    3.611 closest distance to " CD2 TRP A 179 " =    1.242
peak=    3.611 closest distance to " O   HOH Z 365 " =    2.703
peak=    3.606 closest distance to " O   HOH Z 405 " =    1.410
peak=    3.601 closest distance to " O   HOH Z 286 " =    2.464
peak=    3.599 closest distance to " OD2 ASP A 286 " =    2.748
peak=    3.595 closest distance to " O   HOH Z 289 " =    1.646
peak=    3.593 closest distance to " O   HOH Z 258 " =    2.157
peak=    3.582 closest distance to " CB  ARG A 139 " =    1.017
peak=    3.575 closest distance to " O   HOH Z 195 " =    1.249
peak=    3.569 closest distance to " CE  LYS A  76 " =    0.833
peak=    3.561 closest distance to " O   ASN A 209 " =    1.390
peak=    3.558 closest distance to " NH1AARG A 145 " =    1.179
peak=    3.552 closest distance to " N   ALA A   1 " =    2.129
peak=    3.551 closest distance to " N   GLN A 278 " =    1.255
peak=    3.549 closest distance to " CG1 ILE A 151 " =    1.066
peak=    3.548 closest distance to " O   HOH Z 135 " =    1.688
peak=    3.547 closest distance to " N   ASN A 127 " =    1.378
peak=    3.541 closest distance to " CD2 LEU A 297 " =    1.006
peak=    3.530 closest distance to " CB  TYR A 169 " =    0.838
peak=    3.527 closest distance to " CB  TRP A 179 " =    1.434
peak=    3.527 closest distance to " O   HOH Z 147 " =    1.769
peak=    3.523 closest distance to " CA  ASN A 215 " =    1.197
peak=    3.521 closest distance to " CA  ALA A 299 " =    0.850
peak=    3.520 closest distance to " O   HOH Z 193 " =    2.081
peak=    3.519 closest distance to " OG BSER A  99 " =    2.240
peak=    3.518 closest distance to " O   HOH Z 175 " =    2.114
peak=    3.516 closest distance to " O   MET A 105 " =    1.795
peak=    3.514 closest distance to " O   HOH Z 146 " =    1.700
peak=    3.512 closest distance to " CD  PRO A 243 " =    1.699
peak=    3.511 closest distance to " CB  LEU A 143 " =    1.113
peak=    3.508 closest distance to " CB  ASP A 124 " =    0.911
peak=    3.507 closest distance to " CA  ALA A 233 " =    1.034
peak=    3.506 closest distance to " O   HOH Z  21 " =    1.692
peak=    3.506 closest distance to " CA  ARG A 195 " =    1.281
peak=    3.502 closest distance to " O   HOH Z  44 " =    1.590
peak=    3.500 closest distance to " CB  ILE A 120 " =    1.360
peak=    3.497 closest distance to " CB  SER A  62 " =    1.206
peak=    3.488 closest distance to " O   HOH Z 286 " =    2.205
peak=    3.487 closest distance to " O   HOH Z 305 " =    3.651
peak=    3.486 closest distance to " O   HOH Z 425 " =    1.884
peak=    3.486 closest distance to " NE2 GLN A  73 " =    3.750
peak=    3.485 closest distance to " O   HOH Z 119 " =    4.237
peak=    3.484 closest distance to " O   HOH Z  61 " =    1.502
peak=    3.478 closest distance to " O   HOH Z 219 " =    2.143
peak=    3.478 closest distance to " NH2BARG A 145 " =    2.138
peak=    3.469 closest distance to " CB  ALA A  34 " =    1.161
peak=    3.463 closest distance to " N   SER A  97 " =    0.834
peak=    3.459 closest distance to " N   SER A 134 " =    1.375
peak=    3.457 closest distance to " O   HOH Z 422 " =    2.724
peak=    3.453 closest distance to " O   TYR A 116 " =    1.359
peak=    3.451 closest distance to " CG  MET A 113 " =    1.365
peak=    3.446 closest distance to " O   HOH Z 362 " =    2.040
peak=    3.445 closest distance to " OG  SER A  62 " =    2.997
peak=    3.442 closest distance to " O   HOH Z 403 " =    1.618
peak=    3.442 closest distance to " CB  ALA A   1 " =    4.663
peak=    3.440 closest distance to " CA  ILE A 234 " =    1.057
peak=    3.439 closest distance to " O   HOH Z 423 " =    1.949
peak=    3.436 closest distance to " O   HOH Z 406 " =    1.615
peak=    3.429 closest distance to " OG BSER A 164 " =    2.197
peak=    3.423 closest distance to " O   HOH Z 172 " =    2.705
peak=    3.421 closest distance to " CB  VAL A 202 " =    1.712
peak=    3.416 closest distance to " NE2 GLN A  58 " =    3.847
peak=    3.411 closest distance to " CB  THR A  31 " =    1.748
peak=    3.411 closest distance to " O   HOH Z  59 " =    1.493
peak=    3.409 closest distance to " OG  SER A  62 " =    3.042
peak=    3.405 closest distance to " CB  TYR A 116 " =    0.869
peak=    3.404 closest distance to " O   HOH Z  64 " =    2.084
peak=    3.403 closest distance to " O   HOH Z 122 " =    1.550
peak=    3.400 closest distance to " NE AARG A 275 " =    1.415
peak=    3.398 closest distance to " CD  ARG A 138 " =    0.784
peak=    3.397 closest distance to " OD1BASN A 224 " =    2.315
peak=    3.396 closest distance to " OG  SER A  22 " =    2.831
peak=    3.396 closest distance to " CB  ALA A 114 " =    1.456
peak=    3.393 closest distance to " O   HOH Z  58 " =    1.567
peak=    3.390 closest distance to " CB  THR A  82 " =    1.336
peak=    3.389 closest distance to " CE1 TYR A 186 " =    1.360
peak=    3.387 closest distance to " O   HOH Z  68 " =    2.011
peak=    3.382 closest distance to " CB  GLN A  88 " =    1.282
peak=    3.381 closest distance to " O   HOH Z  97 " =    2.006
peak=    3.380 closest distance to " CG1BVAL A  72 " =    1.392
peak=    3.377 closest distance to " NH1BARG A 145 " =    1.308
peak=    3.372 closest distance to " O   HOH Z 359 " =    1.348
peak=    3.368 closest distance to " CB  SER A 212 " =    1.101
peak=    3.368 closest distance to " O   HOH Z  88 " =    3.085
peak=    3.366 closest distance to " O   HOH Z 345 " =    3.338
peak=    3.362 closest distance to " O   HOH Z 271 " =    2.556
peak=    3.362 closest distance to " CA  MET A 105 " =    0.936
peak=    3.362 closest distance to " O   HOH Z 225 " =    1.402
peak=    3.357 closest distance to " CA  ALA A 291 " =    0.891
peak=    3.353 closest distance to " CA  THR A 264 " =    0.880
peak=    3.352 closest distance to " O   HOH Z 371 " =    3.233
peak=    3.352 closest distance to " O   HOH Z 128 " =    2.209
peak=    3.352 closest distance to " OE2 GLU A  53 " =    2.041
peak=    3.351 closest distance to " O   HOH Z 357 " =    1.987
peak=    3.348 closest distance to " O   HOH Z 109 " =    2.524
peak=    3.346 closest distance to " O   HOH Z 329 " =    3.835
peak=    3.340 closest distance to " O   HOH Z  50 " =    1.690
peak=    3.336 closest distance to " O   HOH Z 284 " =    3.066
peak=    3.335 closest distance to " CA  SER A  87 " =    1.052
peak=    3.333 closest distance to " O   HOH Z 108 " =    2.162
peak=    3.329 closest distance to " CB  ASN A  39 " =    0.904
peak=    3.328 closest distance to " CA  SER A  95 " =    1.032
peak=    3.324 closest distance to " O   HOH Z 115 " =    1.676
peak=    3.323 closest distance to " O   HOH Z 139 " =    2.531
peak=    3.322 closest distance to " CB  ASN A 142 " =    0.924
peak=    3.318 closest distance to " CA  LEU A 101 " =    1.650
peak=    3.315 closest distance to " CA  GLY A 267 " =    1.229
peak=    3.314 closest distance to " O   HOH Z  55 " =    2.065
peak=    3.310 closest distance to " O   HOH Z 207 " =    2.150
peak=    3.309 closest distance to " CB  ASN A 215 " =    1.124
peak=    3.305 closest distance to " N   CYS A 260 " =    0.776
peak=    3.303 closest distance to " O   HOH Z 344 " =    3.292
peak=    3.303 closest distance to " O   HOH Z  20 " =    1.647
peak=    3.301 closest distance to " O   ASN A  74 " =    1.593
peak=    3.300 closest distance to " O   HOH Z 133 " =    1.594
peak=    3.294 closest distance to " CB  TYR A 169 " =    0.834
peak=    3.293 closest distance to " O   HOH Z 298 " =    2.632
peak=    3.289 closest distance to " O   HOH Z 282 " =    2.086
peak=    3.286 closest distance to " O   HOH Z 313 " =    1.626
peak=    3.285 closest distance to " O   HOH Z 374 " =    2.675
peak=    3.281 closest distance to " O   HOH Z 430 " =    1.592
peak=    3.278 closest distance to " O   HOH Z 266 " =    3.338
peak=    3.275 closest distance to " O   HOH Z 213 " =    2.213
peak=    3.263 closest distance to " N   TYR A  15 " =    0.908
peak=    3.262 closest distance to " ND1 HIS A  81 " =    1.642
peak=    3.260 closest distance to " CA  ALA A  21 " =    1.236
peak=    3.258 closest distance to " O   HOH Z 273 " =    2.804
peak=    3.255 closest distance to " CD1 ILE A 263 " =    1.378
peak=    3.254 closest distance to " O   HOH Z 368 " =    2.009
peak=    3.249 closest distance to " O   HOH Z 130 " =    3.743
peak=    3.249 closest distance to " O   HOH Z 325 " =    3.690
peak=    3.245 closest distance to " O   HOH Z  30 " =    1.714
peak=    3.242 closest distance to " CA  ARG A 102 " =    1.168
peak=    3.238 closest distance to " O   HOH Z 409 " =    2.185
peak=    3.236 closest distance to " CA  GLU A  46 " =    0.793
peak=    3.232 closest distance to " CA  ALA A 154 " =    0.942
peak=    3.226 closest distance to " O   HOH Z 291 " =    2.003
peak=    3.222 closest distance to " O   HOH Z  59 " =    2.464
peak=    3.222 closest distance to " CB  ASP A 140 " =    0.926
peak=    3.219 closest distance to " O   HOH Z 373 " =    1.436
peak=    3.218 closest distance to " O   HOH Z 119 " =    1.582
peak=    3.213 closest distance to " O   THR A 220 " =    1.465
peak=    3.212 closest distance to " CB  VAL A 265 " =    2.084
peak=    3.211 closest distance to " N   SER A 146 " =    1.675
peak=    3.211 closest distance to " O   HOH Z  59 " =    2.038
peak=    3.207 closest distance to " O   HOH Z 402 " =    1.403
peak=    3.207 closest distance to " CD  LYS A 166 " =    1.350
peak=    3.206 closest distance to " NE2 GLN A 278 " =    3.620
peak=    3.205 closest distance to " NH2 ARG A 219 " =    1.845
peak=    3.201 closest distance to " CD1 LEU A 167 " =    1.147
peak=    3.196 closest distance to " CG1 VAL A 189 " =    1.894
peak=    3.195 closest distance to " CB  SER A 276 " =    1.135
peak=    3.195 closest distance to " O   HOH Z 284 " =    1.411
peak=    3.194 closest distance to " CB  MET A  47 " =    1.141
peak=    3.192 closest distance to " O   HOH Z 130 " =    2.068
peak=    3.191 closest distance to " CB  ALA A  21 " =    1.873
peak=    3.190 closest distance to " CA  ASN A  74 " =    1.300
peak=    3.186 closest distance to " CG2 VAL A 197 " =    1.025
peak=    3.184 closest distance to " O   HOH Z 291 " =    1.486
peak=    3.175 closest distance to " O   HOH Z  88 " =    2.692
peak=    3.172 closest distance to " CB  GLU A  46 " =    1.046
peak=    3.169 closest distance to " CB  ASN A 110 " =    1.114
peak=    3.161 closest distance to " CE3 TRP A 274 " =    1.233
peak=    3.160 closest distance to " CD1 ILE A 106 " =    0.806
peak=    3.155 closest distance to " O   HOH Z 184 " =    1.665
peak=    3.151 closest distance to " O   HOH Z 116 " =    1.645
peak=    3.148 closest distance to " CG  GLU A 277 " =    4.392
peak=    3.144 closest distance to " O   HOH Z 218 " =    2.009
peak=    3.142 closest distance to " CB  ALA A  10 " =    0.848
peak=    3.140 closest distance to " O   HOH Z 145 " =    2.204
peak=    3.137 closest distance to " O   HOH Z 386 " =    2.683
peak=    3.134 closest distance to " CB  ASP A 171 " =    0.874
peak=    3.129 closest distance to " OD1 ASN A 217 " =    1.568
peak=    3.125 closest distance to " O   HOH Z  66 " =    2.156
peak=    3.123 closest distance to " NZ  LYS A 117 " =    1.337
peak=    3.117 closest distance to " O  BHOH Z 338 " =    2.453
peak=    3.116 closest distance to " CG  GLU A 277 " =    1.872
peak=    3.115 closest distance to " CG BARG A 275 " =    1.383
peak=    3.109 closest distance to " O   HOH Z 183 " =    1.374
peak=    3.107 closest distance to " N   VAL A 296 " =    1.727
peak=    3.104 closest distance to " O   PRO A 213 " =    1.580
peak=    3.093 closest distance to " O   HOH Z 302 " =    1.636
peak=    3.090 closest distance to " O   HOH Z  85 " =    2.124
peak=    3.085 closest distance to " O   HOH Z 213 " =    1.951
peak=    3.084 closest distance to " O   HOH Z 152 " =    1.815
peak=    3.082 closest distance to " O   HOH Z 211 " =    2.641
peak=    3.073 closest distance to " O   HOH Z 189 " =    2.191
peak=    3.071 closest distance to " CB  ARG A 138 " =    0.909
peak=    3.058 closest distance to " CB  GLU A 236 " =    1.278
peak=    3.047 closest distance to " CB  PRO A 243 " =    1.062
peak=    3.044 closest distance to " O   HOH Z  43 " =    2.180
peak=    3.038 closest distance to " O   HOH Z 238 " =    3.681

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.704 - 5.706
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 206
   mapped sites are within: 0.704 - 5.706

peak=   -4.819 closest distance to " O   HOH Z 377 " =    1.885
peak=   -4.607 closest distance to " CB  PRO A 243 " =    2.523
peak=   -4.239 closest distance to " O   PRO A 198 " =    1.329
peak=   -4.238 closest distance to " O   HOH Z 266 " =    4.808
peak=   -4.233 closest distance to " OG BSER A 134 " =    1.348
peak=   -4.227 closest distance to " CD  ARG A  14 " =    3.396
peak=   -4.220 closest distance to " O   HOH Z 407 " =    3.197
peak=   -4.210 closest distance to " O   HOH Z  52 " =    1.272
peak=   -4.204 closest distance to " CD1 LEU A 255 " =    2.985
peak=   -4.087 closest distance to " O   SER A 135 " =    1.477
peak=   -4.034 closest distance to " O   HOH Z 231 " =    2.107
peak=   -4.025 closest distance to " CD  ARG A 156 " =    2.128
peak=   -4.004 closest distance to " C   HIS A 108 " =    1.162
peak=   -3.942 closest distance to " N   THR A 157 " =    1.505
peak=   -3.929 closest distance to " O   HOH Z 351 " =    1.625
peak=   -3.919 closest distance to " O   HOH Z 185 " =    1.982
peak=   -3.867 closest distance to " ND2 ASN A 249 " =    2.349
peak=   -3.863 closest distance to " O   VAL A  67 " =    2.701
peak=   -3.852 closest distance to " O   HOH Z 389 " =    1.948
peak=   -3.850 closest distance to " CA  GLY A  98 " =    1.875
peak=   -3.845 closest distance to " N   ALA A  43 " =    2.568
peak=   -3.831 closest distance to " O   PRO A 198 " =    1.333
peak=   -3.830 closest distance to " O   HOH Z  38 " =    1.519
peak=   -3.828 closest distance to " CG1 VAL A 112 " =    2.952
peak=   -3.827 closest distance to " O   HOH Z 313 " =    1.737
peak=   -3.815 closest distance to " O   HOH Z 316 " =    1.923
peak=   -3.806 closest distance to " CG  GLN A 223 " =    2.086
peak=   -3.800 closest distance to " CE2 PHE A 218 " =    2.444
peak=   -3.780 closest distance to " CB  ASP A  27 " =    2.360
peak=   -3.758 closest distance to " O   HOH Z 152 " =    4.890
peak=   -3.757 closest distance to " O   HOH Z  60 " =    2.346
peak=   -3.751 closest distance to " CZ3 TRP A 179 " =    1.145
peak=   -3.736 closest distance to " O   HOH Z  13 " =    1.712
peak=   -3.735 closest distance to " CB  TRP A  85 " =    2.380
peak=   -3.718 closest distance to " CA  GLY A 203 " =    2.291
peak=   -3.708 closest distance to " CB  ALA A  43 " =    2.459
peak=   -3.686 closest distance to " O   PRO A 243 " =    2.297
peak=   -3.678 closest distance to " O   HOH Z 198 " =    1.965
peak=   -3.640 closest distance to " O   TYR A 247 " =    2.843
peak=   -3.640 closest distance to " ND2 ASN A  45 " =    1.952
peak=   -3.623 closest distance to " CB  CYS A 254 " =    2.107
peak=   -3.619 closest distance to " OG  SER A  87 " =    1.324
peak=   -3.614 closest distance to " O   ARG A 145 " =    1.439
peak=   -3.614 closest distance to " OD1 ASN A 148 " =    1.681
peak=   -3.612 closest distance to " ND2 ASN A  45 " =    1.182
peak=   -3.596 closest distance to " CZ  PHE A  59 " =    1.550
peak=   -3.596 closest distance to " CG2 THR A  18 " =    2.818
peak=   -3.595 closest distance to " O   HOH Z 131 " =    4.097
peak=   -3.580 closest distance to " OG  SER A  97 " =    2.224
peak=   -3.572 closest distance to " CB  PRO A  54 " =    2.391
peak=   -3.566 closest distance to " O   HOH Z 281 " =    2.845
peak=   -3.550 closest distance to " CD2 TYR A 293 " =    1.892
peak=   -3.548 closest distance to " NH1AARG A 275 " =    1.879
peak=   -3.547 closest distance to " CB  ALA A 248 " =    2.373
peak=   -3.547 closest distance to " OD2 ASP A 191 " =    1.481
peak=   -3.545 closest distance to " CD1 PHE A  59 " =    2.021
peak=   -3.540 closest distance to " CG  GLN A  58 " =    1.248
peak=   -3.537 closest distance to " CB  ALA A 291 " =    2.179
peak=   -3.536 closest distance to " O   HOH Z 317 " =    1.536
peak=   -3.532 closest distance to " O   VAL A 197 " =    1.803
peak=   -3.530 closest distance to " O   HOH Z 191 " =    5.502
peak=   -3.526 closest distance to " O   HOH Z 384 " =    2.700
peak=   -3.522 closest distance to " CE2 TYR A  30 " =    2.573
peak=   -3.518 closest distance to " C   ALA A 158 " =    1.489
peak=   -3.517 closest distance to " O   HOH Z  73 " =    2.209
peak=   -3.507 closest distance to " O   HOH Z 111 " =    1.917
peak=   -3.506 closest distance to " OG BSER A 134 " =    1.596
peak=   -3.500 closest distance to " ND2 ASN A 285 " =    2.041
peak=   -3.493 closest distance to " O   HOH Z 290 " =    1.186
peak=   -3.492 closest distance to " O   HOH Z  65 " =    1.270
peak=   -3.479 closest distance to " O   HOH Z 352 " =    2.168
peak=   -3.472 closest distance to " O   HOH Z 359 " =    3.216
peak=   -3.468 closest distance to " OD1 ASN A 187 " =    1.667
peak=   -3.467 closest distance to " CG  ASN A  39 " =    1.677
peak=   -3.466 closest distance to " CE3 TRP A 123 " =    1.471
peak=   -3.466 closest distance to " CA  GLY A 241 " =    2.217
peak=   -3.457 closest distance to " CB  ASN A  39 " =    2.366
peak=   -3.456 closest distance to " NH2 ARG A  79 " =    1.981
peak=   -3.454 closest distance to " O   HOH Z  43 " =    1.804
peak=   -3.453 closest distance to " CG1 VAL A 197 " =    2.185
peak=   -3.445 closest distance to " O   PHE A 218 " =    1.426
peak=   -3.438 closest distance to " CA  GLY A 133 " =    2.048
peak=   -3.436 closest distance to " CB  ALA A 248 " =    1.966
peak=   -3.430 closest distance to " O   HOH Z 198 " =    1.731
peak=   -3.430 closest distance to " O   HOH Z 298 " =    2.480
peak=   -3.428 closest distance to " CB  ALA A   9 " =    2.383
peak=   -3.428 closest distance to " NE  ARG A  36 " =    1.952
peak=   -3.420 closest distance to " OE1 GLN A  88 " =    1.176
peak=   -3.410 closest distance to " O   HOH Z 166 " =    1.310
peak=   -3.405 closest distance to " O   VAL A 189 " =    2.455
peak=   -3.404 closest distance to " O   HOH Z 211 " =    1.553
peak=   -3.394 closest distance to " O   SER A  22 " =    2.509
peak=   -3.392 closest distance to " ND2 ASN A 252 " =    1.863
peak=   -3.391 closest distance to " CG  GLN A 240 " =    2.405
peak=   -3.390 closest distance to " C   LEU A 222 " =    0.704
peak=   -3.390 closest distance to " CE  MET A 105 " =    2.426
peak=   -3.385 closest distance to " O   HOH Z  90 " =    2.604
peak=   -3.383 closest distance to " C   ALA A 114 " =    2.136
peak=   -3.381 closest distance to " CG2 ILE A  49 " =    2.666
peak=   -3.381 closest distance to " CD  ARG A 139 " =    1.580
peak=   -3.381 closest distance to " CG  PRO A 163 " =    2.537
peak=   -3.380 closest distance to " CB  PHE A 192 " =    1.914
peak=   -3.379 closest distance to " O   HOH Z 102 " =    1.617
peak=   -3.376 closest distance to " OD2 ASP A 171 " =    1.833
peak=   -3.376 closest distance to " ND2 ASN A 249 " =    2.042
peak=   -3.368 closest distance to " O   HOH Z 231 " =    1.339
peak=   -3.368 closest distance to " CE3 TRP A 274 " =    2.426
peak=   -3.362 closest distance to " CG  MET A 105 " =    0.957
peak=   -3.357 closest distance to " OD1 ASP A 171 " =    1.592
peak=   -3.354 closest distance to " O   HOH Z 253 " =    3.862
peak=   -3.353 closest distance to " CG  PHE A 283 " =    2.608
peak=   -3.353 closest distance to " C   LEU A 143 " =    1.285
peak=   -3.353 closest distance to " CA  GLY A  57 " =    2.147
peak=   -3.350 closest distance to " O   HOH Z 372 " =    2.406
peak=   -3.348 closest distance to " CE  MET A  93 " =    1.246
peak=   -3.348 closest distance to " CD2 PHE A 225 " =    1.186
peak=   -3.347 closest distance to " O   GLN A 240 " =    1.637
peak=   -3.343 closest distance to " O   HOH Z 385 " =    2.034
peak=   -3.343 closest distance to " CE  LYS A  76 " =    2.874
peak=   -3.342 closest distance to " O   HOH Z  60 " =    2.144
peak=   -3.338 closest distance to " ND2 ASN A 187 " =    1.465
peak=   -3.338 closest distance to " O   HOH Z 114 " =    2.917
peak=   -3.332 closest distance to " O   VAL A  67 " =    2.842
peak=   -3.332 closest distance to " O   ASP A 162 " =    2.221
peak=   -3.327 closest distance to " O   HOH Z   1 " =    1.507
peak=   -3.325 closest distance to " ND2BASN A 224 " =    1.679
peak=   -3.324 closest distance to " O   PRO A 163 " =    1.951
peak=   -3.321 closest distance to " O   HOH Z 348 " =    1.758
peak=   -3.319 closest distance to " CB  TYR A  15 " =    2.130
peak=   -3.316 closest distance to " O   HOH Z  11 " =    1.852
peak=   -3.312 closest distance to " O   ALA A 180 " =    1.239
peak=   -3.310 closest distance to " NH2AARG A 275 " =    5.370
peak=   -3.307 closest distance to " NH2BARG A 275 " =    1.613
peak=   -3.304 closest distance to " O   HOH Z 393 " =    3.130
peak=   -3.303 closest distance to " CZ2 TRP A 274 " =    0.955
peak=   -3.302 closest distance to " N   GLN A  58 " =    1.630
peak=   -3.297 closest distance to " NE2 GLN A 278 " =    1.802
peak=   -3.294 closest distance to " O   HOH Z 292 " =    1.440
peak=   -3.280 closest distance to " CB  ALA A 100 " =    2.093
peak=   -3.279 closest distance to " O   HOH Z 218 " =    3.423
peak=   -3.274 closest distance to " O   HOH Z 410 " =    2.302
peak=   -3.272 closest distance to " CE2 PHE A  61 " =    2.738
peak=   -3.271 closest distance to " CG  ARG A 269 " =    2.531
peak=   -3.264 closest distance to " O   HOH Z 323 " =    1.635
peak=   -3.263 closest distance to " O   VAL A 153 " =    2.347
peak=   -3.262 closest distance to " CD2 PHE A  61 " =    1.958
peak=   -3.259 closest distance to " O   HOH Z 337 " =    1.519
peak=   -3.258 closest distance to " CG  ASP A 231 " =    0.814
peak=   -3.257 closest distance to " CZ  TYR A 169 " =    1.600
peak=   -3.252 closest distance to " O   HOH Z 114 " =    0.816
peak=   -3.248 closest distance to " O   HOH Z 168 " =    1.797
peak=   -3.242 closest distance to " CG2 THR A 178 " =    2.155
peak=   -3.237 closest distance to " OXT GLY A 302 " =    3.158
peak=   -3.237 closest distance to " O   VAL A 174 " =    2.357
peak=   -3.235 closest distance to " O   HOH Z 140 " =    1.614
peak=   -3.231 closest distance to " N   ASP A 171 " =    2.405
peak=   -3.224 closest distance to " O   SER A   3 " =    1.158
peak=   -3.222 closest distance to " CA  ASP A 298 " =    1.000
peak=   -3.214 closest distance to " CB  PRO A 163 " =    2.436
peak=   -3.210 closest distance to " NE  ARG A 156 " =    1.923
peak=   -3.204 closest distance to " C   ALA A   8 " =    1.659
peak=   -3.200 closest distance to " SD  MET A 188 " =    2.434
peak=   -3.195 closest distance to " O   ILE A  49 " =    1.735
peak=   -3.195 closest distance to " N   ARG A  14 " =    1.087
peak=   -3.191 closest distance to " O   HOH Z 409 " =    5.706
peak=   -3.189 closest distance to " O   HOH Z 126 " =    1.896
peak=   -3.188 closest distance to " O   HOH Z 345 " =    2.195
peak=   -3.186 closest distance to " O   HOH Z 189 " =    1.819
peak=   -3.185 closest distance to " OG1 THR A 178 " =    1.291
peak=   -3.183 closest distance to " OE1 GLN A 223 " =    2.238
peak=   -3.181 closest distance to " C   LYS A  76 " =    1.516
peak=   -3.180 closest distance to " CB  ASP A 132 " =    2.345
peak=   -3.174 closest distance to " O   SER A   3 " =    1.278
peak=   -3.168 closest distance to " CE  LYS A  76 " =    2.788
peak=   -3.160 closest distance to " CB  ALA A 131 " =    1.946
peak=   -3.158 closest distance to " OH  TYR A 214 " =    1.257
peak=   -3.157 closest distance to " O   HOH Z 174 " =    2.541
peak=   -3.154 closest distance to " O   HOH Z 111 " =    1.162
peak=   -3.147 closest distance to " O   HOH Z 318 " =    1.703
peak=   -3.145 closest distance to " OD2 ASP A 171 " =    1.918
peak=   -3.145 closest distance to " O   TRP A  70 " =    1.479
peak=   -3.141 closest distance to " O   HOH Z  10 " =    1.342
peak=   -3.139 closest distance to " O   HOH Z   9 " =    1.645
peak=   -3.136 closest distance to " CE BMET A  47 " =    1.419
peak=   -3.132 closest distance to " O   HOH Z 263 " =    3.147
peak=   -3.132 closest distance to " O   HOH Z 350 " =    1.928
peak=   -3.131 closest distance to " N   SER A 276 " =    1.210
peak=   -3.130 closest distance to " CB  ALA A 291 " =    2.344
peak=   -3.124 closest distance to " C   GLU A 236 " =    0.797
peak=   -3.122 closest distance to " O   HOH Z 256 " =    1.469
peak=   -3.116 closest distance to " CG1 VAL A  78 " =    2.551
peak=   -3.115 closest distance to " O   ALA A 161 " =    1.682
peak=   -3.114 closest distance to " O   ALA A  84 " =    1.649
peak=   -3.104 closest distance to " OG ASER A 216 " =    0.974
peak=   -3.104 closest distance to " CG2 VAL A 189 " =    1.910
peak=   -3.103 closest distance to " O   HOH Z 252 " =    4.355
peak=   -3.101 closest distance to " CD  LYS A 289 " =    2.336
peak=   -3.100 closest distance to " O   LYS A 289 " =    3.161
peak=   -3.090 closest distance to " O   HOH Z 417 " =    2.192
peak=   -3.079 closest distance to " CD  PRO A 198 " =    1.735
peak=   -3.076 closest distance to " CG  GLN A  88 " =    0.832
peak=   -3.066 closest distance to " CB  ALA A 291 " =    2.001
peak=   -3.054 closest distance to " O   HOH Z 346 " =    1.620
peak=   -3.045 closest distance to " O   GLY A  80 " =    2.358
peak=   -3.030 closest distance to " O   HOH Z 177 " =    1.927
peak=   -3.029 closest distance to " CG  TRP A 266 " =    1.709

================= 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    :  0.4003 0.3976   6.211195e+00   6.204877e+00
   1_bss:  0.3879 0.3882   6.196821e+00   6.189087e+00
   1_xyz:  0.2940 0.3285   5.981575e+00   6.045228e+00
   1_adp:  0.2686 0.3416   5.933800e+00   6.068717e+00
   1_occ:  0.2683 0.3418   5.933015e+00   6.068440e+00
   2_bss:  0.2673 0.3388   5.929695e+00   6.063881e+00
   2_xyz:  0.1967 0.2523   5.642163e+00   5.816587e+00
   2_adp:  0.1803 0.2366   5.564780e+00   5.761300e+00
   2_occ:  0.1801 0.2360   5.563653e+00   5.760618e+00
   3_bss:  0.1794 0.2341   5.559162e+00   5.754943e+00
   3_xyz:  0.1405 0.1934   5.351348e+00   5.582720e+00
   3_adp:  0.1286 0.1781   5.267620e+00   5.501374e+00
   3_occ:  0.1285 0.1780   5.267169e+00   5.500662e+00
   4_bss:  0.1285 0.1773   5.263941e+00   5.496492e+00
   4_xyz:  0.1175 0.1649   5.187284e+00   5.427819e+00
   4_adp:  0.1138 0.1629   5.167621e+00   5.414378e+00
   4_occ:  0.1137 0.1628   5.167330e+00   5.414040e+00
   5_bss:  0.1137 0.1627   5.166622e+00   5.413650e+00
   5_xyz:  0.1099 0.1589   5.142179e+00   5.396656e+00
   5_adp:  0.1091 0.1586   5.139337e+00   5.396551e+00
   5_occ:  0.1091 0.1586   5.139119e+00   5.396318e+00
   5_bss:  0.1090 0.1586   5.139084e+00   5.396312e+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:  0.353  50.000  -1.728   3.318  -1.875   0.000  -0.000  -0.000
   1_xyz:  0.353  50.000  -1.728   3.318  -1.875   0.000  -0.000  -0.000
   1_adp:  0.353  50.000  -1.728   3.318  -1.875   0.000  -0.000  -0.000
   1_occ:  0.353  50.000  -1.728   3.318  -1.875   0.000  -0.000  -0.000
   2_bss:  0.321  50.000  -1.779   0.062  -1.254   0.000  -0.000  -0.000
   2_xyz:  0.321  50.000  -1.779   0.062  -1.254   0.000  -0.000  -0.000
   2_adp:  0.321  50.000  -1.779   0.062  -1.254   0.000  -0.000  -0.000
   2_occ:  0.321  50.000  -1.779   0.062  -1.254   0.000  -0.000  -0.000
   3_bss:  0.327  50.000  -1.766  -1.414  -0.869  -0.000  -0.000  -0.000
   3_xyz:  0.327  50.000  -1.766  -1.414  -0.869  -0.000  -0.000  -0.000
   3_adp:  0.327  50.000  -1.766  -1.414  -0.869  -0.000  -0.000  -0.000
   3_occ:  0.327  50.000  -1.766  -1.414  -0.869  -0.000  -0.000  -0.000
   4_bss:  0.327  50.000  -2.165  -2.343  -1.166  -0.000  -0.000  -0.000
   4_xyz:  0.327  50.000  -2.165  -2.343  -1.166  -0.000  -0.000  -0.000
   4_adp:  0.327  50.000  -2.165  -2.343  -1.166  -0.000  -0.000  -0.000
   4_occ:  0.327  50.000  -2.165  -2.343  -1.166  -0.000  -0.000  -0.000
   5_bss:  0.318  50.000  -2.086  -2.427  -1.070  -0.000  -0.000  -0.000
   5_xyz:  0.318  50.000  -2.086  -2.427  -1.070  -0.000  -0.000  -0.000
   5_adp:  0.318  50.000  -2.086  -2.427  -1.070  -0.000  -0.000  -0.000
   5_occ:  0.318  50.000  -2.086  -2.427  -1.070  -0.000  -0.000  -0.000
   5_bss:  0.317  50.003  -1.899  -2.335  -0.875  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.082 0.5708  0.7596    51663.486
   1_bss:  45.489 0.5765  0.7664    49248.443
   1_xyz:  34.722 0.7055  0.9009    30549.169
   1_adp:  36.486 0.6838  0.8812    32730.691
   1_occ:  36.503 0.6836  0.8807    32729.756
   2_bss:  35.898 0.6906  0.8635    31924.124
   2_xyz:  25.386 0.8063  0.9714    16396.463
   2_adp:  23.182 0.8299  0.9813    14245.583
   2_occ:  23.149 0.8302  0.9810    14203.242
   3_bss:  22.922 0.8323  0.9706    13959.318
   3_xyz:  18.586 0.8743  0.9945     9517.185
   3_adp:  16.618 0.8926  0.9952     8141.717
   3_occ:  16.606 0.8927  0.9951     8125.753
   4_bss:  16.505 0.8934  0.9767     8013.773
   4_xyz:  14.958 0.9067  0.9832     6870.448
   4_adp:  14.586 0.9101  0.9785     6669.936
   4_occ:  14.579 0.9102  0.9785     6664.757
   5_bss:  14.567 0.9103  0.9796     6654.662
   5_xyz:  14.171 0.9136  0.9804     6426.022
   5_adp:  14.137 0.9140  0.9741     6405.698
   5_occ:  14.131 0.9140  0.9742     6403.356
   5_bss:  14.132 0.9140  0.9798     6403.503
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.7126e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.7126e-01
   1_xyz:   1.342  0.010  0.091 15.409  0.006  4.106   9.9469e-02
   1_adp:   1.342  0.010  0.091 15.409  0.006  4.106   9.9469e-02
   1_occ:   1.342  0.010  0.091 15.409  0.006  4.106   9.9469e-02
   2_bss:   1.342  0.010  0.091 15.409  0.006  4.106   9.9469e-02
   2_xyz:   1.194  0.010  0.079 14.685  0.004  4.108   9.3913e-02
   2_adp:   1.194  0.010  0.079 14.685  0.004  4.108   9.3913e-02
   2_occ:   1.194  0.010  0.079 14.685  0.004  4.108   9.3913e-02
   3_bss:   1.194  0.010  0.079 14.685  0.004  4.108   9.3913e-02
   3_xyz:   1.034  0.007  0.074 14.598  0.004  4.112   6.2807e-02
   3_adp:   1.034  0.007  0.074 14.598  0.004  4.112   6.2807e-02
   3_occ:   1.034  0.007  0.074 14.598  0.004  4.112   6.2807e-02
   4_bss:   1.034  0.007  0.074 14.598  0.004  4.112   6.2807e-02
   4_xyz:   0.991  0.007  0.074 14.455  0.004  4.108   5.8834e-02
   4_adp:   0.991  0.007  0.074 14.455  0.004  4.108   5.8834e-02
   4_occ:   0.991  0.007  0.074 14.455  0.004  4.108   5.8834e-02
   5_bss:   0.991  0.007  0.074 14.455  0.004  4.108   5.8834e-02
   5_xyz:   1.029  0.007  0.076 14.599  0.004  4.110   6.2621e-02
   5_adp:   1.029  0.007  0.076 14.599  0.004  4.110   6.2621e-02
   5_occ:   1.029  0.007  0.076 14.599  0.004  4.110   6.2621e-02
   5_bss:   1.029  0.007  0.076 14.599  0.004  4.110   6.2621e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4042e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4042e-01
   1_xyz:   8.573  0.061  0.326 86.163  0.047  2.122   9.3875e-02
   1_adp:   8.573  0.061  0.326 86.163  0.047  2.122   9.3875e-02
   1_occ:   8.573  0.061  0.326 86.163  0.047  2.122   9.3875e-02
   2_bss:   8.573  0.061  0.326 86.163  0.047  2.122   9.3875e-02
   2_xyz:   7.225  0.082  0.264 82.573  0.027  2.168   2.5457e-01
   2_adp:   7.225  0.082  0.264 82.573  0.027  2.168   2.5457e-01
   2_occ:   7.225  0.082  0.264 82.573  0.027  2.168   2.5457e-01
   3_bss:   7.225  0.082  0.264 82.573  0.027  2.168   2.5457e-01
   3_xyz:   7.066  0.042  0.228 83.400  0.022  2.244   5.3056e-02
   3_adp:   7.066  0.042  0.228 83.400  0.022  2.244   5.3056e-02
   3_occ:   7.066  0.042  0.228 83.400  0.022  2.244   5.3056e-02
   4_bss:   7.066  0.042  0.228 83.400  0.022  2.244   5.3056e-02
   4_xyz:   7.227  0.043  0.243 84.297  0.030  2.319   4.4200e-02
   4_adp:   7.227  0.043  0.243 84.297  0.030  2.319   4.4200e-02
   4_occ:   7.227  0.043  0.243 84.297  0.030  2.319   4.4200e-02
   5_bss:   7.227  0.043  0.243 84.297  0.030  2.319   4.4200e-02
   5_xyz:   7.403  0.037  0.243 84.884  0.032  2.267   4.7645e-02
   5_adp:   7.403  0.037  0.243 84.884  0.032  2.267   4.7645e-02
   5_occ:   7.403  0.037  0.243 84.884  0.032  2.267   4.7645e-02
   5_bss:   7.403  0.037  0.243 84.884  0.032  2.267   4.7645e-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:  99.92   0.00  17.95  61.72   0.00  14.30  99.92   2.67  37.83
   1_occ:  99.92   0.00  17.95  61.72   0.00  14.30  99.92   2.67  37.83
   2_bss:  99.92   0.00  17.95  61.72   0.00  14.30  99.92   2.67  37.83
   2_xyz:  99.92   0.00  17.95  61.72   0.00  14.30  99.92   2.67  37.83
   2_adp:  99.43   0.00  17.72  65.03   0.00  13.80  99.43   4.74  39.06
   2_occ:  99.43   0.00  17.72  65.03   0.00  13.80  99.43   4.74  39.06
   3_bss:  99.43   0.00  17.72  65.03   0.00  13.80  99.43   4.74  39.06
   3_xyz:  99.43   0.00  17.72  65.03   0.00  13.80  99.43   4.74  39.06
   3_adp:  96.79   0.63  17.18  72.47   0.63  12.94  96.79   7.18  40.26
   3_occ:  96.79   0.63  17.18  72.47   0.63  12.94  96.79   7.18  40.26
   4_bss:  96.79   0.63  17.18  72.47   0.63  12.94  96.79   7.18  40.26
   4_xyz:  96.79   0.63  17.18  72.47   0.63  12.94  96.79   7.18  40.26
   4_adp:  97.79   0.00  17.36  89.32   0.00  12.85  97.79   6.14  41.92
   4_occ:  97.79   0.00  17.36  89.32   0.00  12.85  97.79   6.14  41.92
   5_bss:  97.79   0.00  17.36  89.32   0.00  12.85  97.79   6.14  41.92
   5_xyz:  97.79   0.00  17.36  89.32   0.00  12.85  97.79   6.14  41.92
   5_adp:  97.75   0.00  17.22  94.32   0.00  12.72  97.75   5.94  41.71
   5_occ:  97.75   0.00  17.22  94.32   0.00  12.72  97.75   5.94  41.71
   5_bss:  97.75   0.00  17.22  94.32   0.00  12.72  97.75   5.94  41.71
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.591    0.017    0.305
   1_adp:    1.591    0.017    0.305
   1_occ:    1.591    0.017    0.305
   2_bss:    1.591    0.017    0.305
   2_xyz:    1.430    0.031    0.506
   2_adp:    1.430    0.031    0.506
   2_occ:    1.430    0.031    0.506
   3_bss:    1.430    0.031    0.506
   3_xyz:    1.245    0.050    0.595
   3_adp:    1.245    0.050    0.595
   3_occ:    1.245    0.050    0.595
   4_bss:    1.245    0.050    0.595
   4_xyz:    1.298    0.053    0.622
   4_adp:    1.298    0.053    0.622
   4_occ:    1.298    0.053    0.622
   5_bss:    1.298    0.053    0.622
   5_xyz:    1.428    0.068    0.638
   5_adp:    1.428    0.068    0.638
   5_occ:    1.428    0.068    0.638
   5_bss:    1.428    0.068    0.638
------------------------------------------------------------------------

CPU time actual refinement: 356.54


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_863/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_863/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_863/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_863/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_863/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 356.39 
  Macro-tasks:
    bulk solvent and scale       = 35.84  
    individual site refinement   = 148.69 
    weights calculation          = 30.03  
    collect and process          = 6.53   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 221.20 
  Micro-tasks:
    mask                            = 1.88   
    f_calc                          = 119.94 
    alpha_beta                      = 8.39   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 127.74 
    fmodel                         = 6.47   
    r_factors                      = 0.19   
    phase_errors                   = 10.55  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 276.55 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 5.031 micro seconds
Total CPU time: 6.17 minutes
from_scatterers_fft:    670 calls, 119.58 s
gradients_fft:          615 calls, 113.99 s

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

# Date 2008-01-16 Time 05:51:13 PST -0800 (1200491473.41 s)
Start R-work = 0.4003, R-free = 0.3976 (no bulk solvent and anisotropic scale)
Final R-work = 0.1320, R-free = 0.1765 (no bulk solvent and anisotropic scale)

Start R-work = 0.3879, R-free = 0.3882
Final R-work = 0.1090, R-free = 0.1586