# Date 2008-01-16 Time 05:18:49 PST -0800 (1200489529.46 s)
#phil __OFF__

Command line arguments: "../681.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18954
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 681

-------------------------------------------------------------------------------
  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: (70.25, 47.1647, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.76, per 1000 atoms: 0.98


================================== 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: (70.25, 47.1647, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 2.00072
Completeness in resolution range: 0.958085
Completeness with d_max=infinity: 0.955095

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0929
                             d_min =   2.0007

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: (70.25, 47.1647, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 2.00072
Completeness in resolution range: 0.958085
Completeness with d_max=infinity: 0.955095

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0933 -  4.2807 [2151/2175]  1932   219  10.2%
  bin  2:  4.2807 -  3.4106 [2060/2079]  1857   203   9.9%
  bin  3:  3.4106 -  2.9833 [2036/2055]  1834   202   9.9%
  bin  4:  2.9833 -  2.7122 [2010/2040]  1806   204  10.1%
  bin  5:  2.7122 -  2.5188 [2011/2030]  1810   201  10.0%
  bin  6:  2.5188 -  2.3709 [2000/2025]  1799   201  10.1%
  bin  7:  2.3709 -  2.2526 [1991/2019]  1796   195   9.8%
  bin  8:  2.2526 -  2.1548 [1973/2009]  1770   203  10.3%
  bin  9:  2.1548 -  2.0720 [1966/2008]  1777   189   9.6%
  bin 10:  2.0720 -  2.0007 [1391/2006]  1249   142  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_681/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: 0.11 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:
        1.41 -     2.11: 7
        2.11 -     2.81: 764
        2.81 -     3.51: 4381
        3.51 -     4.20: 9182
        4.20 -     4.90: 13559
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.414 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.666 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.666 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.669 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.775 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27888 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_681/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_681/model_refine_001.geo

CPU time processing inputs: 8.03


============================ 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 = 70.25 47.16465 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3728   r_free= 0.3640   ksol= 0.00   Bsol= 0.00   scale= 0.931    |
|                                                                             |
| 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:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.161100                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7743 0.99   1397  153 0.3102 0.3007      6.4347      6.3311|
|  2:  4.7743 -  3.8096 0.99   1339  153 0.2955 0.3137      6.5991      6.7079|
|  3:  3.8096 -  3.3339 0.99   1312  146 0.3460 0.2946      6.5431      6.4331|
|  4:  3.3339 -  3.0318 0.99   1308  139 0.3495 0.3653      6.3771      6.3777|
|  5:  3.0318 -  2.8160 0.99   1304  146 0.3887 0.3280       6.244      6.1916|
|  6:  2.8160 -  2.6509 0.99   1291  148 0.3859 0.4447      6.1381      6.1352|
|  7:  2.6509 -  2.5188 0.99   1288  144 0.3902 0.3667      6.1125      6.0462|
|  8:  2.5188 -  2.4096 0.98   1284  138 0.4246 0.3779      6.1043      6.0595|
|  9:  2.4096 -  2.3172 0.98   1274  147 0.4012 0.4202      5.9989      6.0617|
| 10:  2.3172 -  2.2375 0.99   1274  137 0.4376 0.4061      6.0413      5.9753|
| 11:  2.2375 -  2.1677 0.98   1269  140 0.4438 0.4283      5.9726      5.9741|
| 12:  2.1677 -  2.1059 0.97   1256  142 0.4257 0.4096        5.89      5.9658|
| 13:  2.1059 -  2.0506 1.00   1277  141 0.4227 0.4670      5.8079      5.8002|
| 14:  2.0506 -  2.0007 0.58    757   85 0.3877 0.3532      5.7578      5.6577|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7743  1397   153  0.78  26.76   0.84     0.80      45447.45|
|  2:  4.7743 -  3.8096  1339   153  0.81  25.50   0.94     0.88      62299.03|
|  3:  3.8096 -  3.3339  1312   146  0.75  31.10   0.93     0.88      62731.70|
|  4:  3.3339 -  3.0318  1308   139  0.70  35.44   0.95     0.83      55153.64|
|  5:  3.0318 -  2.8160  1304   146  0.64  40.19   0.96     0.79      44017.53|
|  6:  2.8160 -  2.6509  1291   148  0.61  43.08   0.94     0.76      41938.25|
|  7:  2.6509 -  2.5188  1288   144  0.61  43.44   0.97     0.77      38117.93|
|  8:  2.5188 -  2.4096  1284   138  0.61  43.33   0.94     0.78      34678.12|
|  9:  2.4096 -  2.3172  1274   147  0.61  43.60   0.98     0.80      31623.91|
| 10:  2.3172 -  2.2375  1274   137  0.59  44.76   0.99     0.79      29714.46|
| 11:  2.2375 -  2.1677  1269   140  0.57  46.73   0.96     0.79      30533.92|
| 12:  2.1677 -  2.1059  1256   142  0.56  47.36   0.98     0.79      28262.80|
| 13:  2.1059 -  2.0506  1277   141  0.54  49.08   0.97     0.76      25424.91|
| 14:  2.0506 -  2.0007   757    85  0.56  47.64   1.02     0.71      20707.31|
|alpha:            min =        0.71 max =            0.88 mean =         0.80|
|beta:             min =    20707.31 max =        62731.70 mean =     40104.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.64|
|phase err.(work): min =        0.00 max =           89.98 mean =        40.18|
|phase err.(test): min =        0.00 max =           89.93 mean =        40.06|
|-----------------------------------------------------------------------------|

============================== 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 = 6.262288              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.314   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.964749              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.345   (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 |  1.414 -  1.762:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.762 -  2.111:        3 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.111 -  2.460:       14 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.460 -  2.808:      750 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.808 -  3.157:     2040 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.157 -  3.506:     2341 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.506 -  3.854:     4505 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.854 -  4.203:     4677 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.203 -  4.551:     6115 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.551 -  4.900:     7444 |
|-----------------------------------------------------------------------------|
|-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 |   4.114    4.900  1.414 |       0.273 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.194)------------------------------------------|
|    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: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3728   r_free= 0.3640   ksol= 0.00   Bsol= 0.00   scale= 0.931    |
|                                                                             |
| 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:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.161100                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3552   r_free= 0.3473   ksol= 0.31   Bsol= 58.31   scale= 0.960   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.43,-2.21,6.12,-0.00,0.00,0.00); trace/3= 0.16                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.135581                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.477770              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.046   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.533742              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.968   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3552      final r-factor (work) = 0.2360          |
| start r-factor (free) = 0.3473      final r-factor (free) = 0.2608          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.9740 = 5.48 * 0.50 * 6.1350 + 1.00 * 0.1709                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.2532 = 5.48 * 0.50 * 5.9006 + 1.00 * 0.0922                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2360      final r-factor (work) = 0.2168          |
| start r-factor (free) = 0.2608      final r-factor (free) = 0.2650          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1557 = 0.53 * 1.00 * 5.9006 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0817 = 0.53 * 1.00 * 5.7029 + 1.00 * 0.0378                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.194)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    64.04   16.78    None  None   None       |
|    all(noH): 2823   0      0.00    64.04   16.78    None  None   None       |
|    Sol.    : 438    0      4.30    64.04   38.09    None  None   None       |
|    Mac.    : 2385   0      0.00    64.02   12.87    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 -   6.404:  355   |   5:    32.019 -  38.423:  100        |
|      1:     6.404 -  12.808: 1066   |   6:    38.423 -  44.827:  102        |
|      2:    12.808 -  19.211:  651   |   7:    44.827 -  51.230:   91        |
|      3:    19.211 -  25.615:  273   |   8:    51.230 -  57.634:   51        |
|      4:    25.615 -  32.019:  114   |   9:    57.634 -  64.038:   20        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2168 r_free = 0.2650             target_work(ml) = 5.707         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2165 r_free = 0.2653             target_work(ml) = 5.708         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2165   r_free= 0.2653   ksol= 0.31   Bsol= 58.31   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.43,-2.21,6.12,-0.00,0.00,0.00); trace/3= 0.16                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.707515                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2121   r_free= 0.2618   ksol= 0.34   Bsol= 73.52   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.14,-2.27,1.42,-0.00,0.00,0.00); trace/3= -1.33                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.694623                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.350136              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.195   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.418413              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.893   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2121      final r-factor (work) = 0.1541          |
| start r-factor (free) = 0.2618      final r-factor (free) = 0.1946          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6431 = 3.35 * 0.50 * 5.7018 + 1.00 * 0.0922                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3799 = 3.35 * 0.50 * 5.5592 + 1.00 * 0.0679                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1541      final r-factor (work) = 0.1410          |
| start r-factor (free) = 0.1946      final r-factor (free) = 0.1850          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3672 = 0.42 * 1.00 * 5.5592 + 1.00 * 0.0411                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2499 = 0.42 * 1.00 * 5.3534 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.194)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.37    75.64   17.22    None  None   None       |
|    all(noH): 2823   0      0.37    75.64   17.22    None  None   None       |
|    Sol.    : 438    0      5.21    75.64   40.76    None  None   None       |
|    Mac.    : 2385   0      0.37    68.91   12.90    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:     0.366 -   7.894:  579   |   5:    38.004 -  45.531:   90        |
|      1:     7.894 -  15.421: 1277   |   6:    45.531 -  53.059:  102        |
|      2:    15.421 -  22.949:  405   |   7:    53.059 -  60.586:   87        |
|      3:    22.949 -  30.476:  144   |   8:    60.586 -  68.114:   31        |
|      4:    30.476 -  38.004:   96   |   9:    68.114 -  75.641:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1410 r_free = 0.1850             target_work(ml) = 5.332         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1409 r_free = 0.1849             target_work(ml) = 5.331         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1409   r_free= 0.1849   ksol= 0.34   Bsol= 73.52   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.14,-2.27,1.42,-0.00,0.00,0.00); trace/3= -1.33                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.331154                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1405   r_free= 0.1838   ksol= 0.34   Bsol= 74.67   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.82,-2.10,0.30,-0.00,0.00,0.00); trace/3= -1.54                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.326978                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.065719              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.279  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.039599              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.689  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1405      final r-factor (work) = 0.1259          |
| start r-factor (free) = 0.1838      final r-factor (free) = 0.1695          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5960 = 2.07 * 0.50 * 5.3523 + 1.00 * 0.0679                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5126 = 2.07 * 0.50 * 5.2792 + 1.00 * 0.0600                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1259      final r-factor (work) = 0.1225          |
| start r-factor (free) = 0.1695      final r-factor (free) = 0.1685          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4982 = 1.04 * 1.00 * 5.2792 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4409 = 1.04 * 1.00 * 5.2226 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.194)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.71   17.40    None  None   None       |
|    all(noH): 2823   0      0.00    88.71   17.40    None  None   None       |
|    Sol.    : 438    0      3.29    88.71   42.43    None  None   None       |
|    Mac.    : 2385   0      0.00    84.40   12.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.871:  845   |   5:    44.357 -  53.228:   97        |
|      1:     8.871 -  17.743: 1227   |   6:    53.228 -  62.100:   83        |
|      2:    17.743 -  26.614:  269   |   7:    62.100 -  70.971:   42        |
|      3:    26.614 -  35.486:  129   |   8:    70.971 -  79.843:   26        |
|      4:    35.486 -  44.357:   98   |   9:    79.843 -  88.714:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1225 r_free = 0.1685             target_work(ml) = 5.220         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1224 r_free = 0.1685             target_work(ml) = 5.220         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1224   r_free= 0.1685   ksol= 0.34   Bsol= 74.67   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.82,-2.10,0.30,-0.00,0.00,0.00); trace/3= -1.54                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.220029                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1222   r_free= 0.1683   ksol= 0.33   Bsol= 74.67   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-1.89,0.08,-0.00,0.00,0.00); trace/3= -1.42                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.219434                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.554194              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 138.584  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.143870              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.617  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1222      final r-factor (work) = 0.1159          |
| start r-factor (free) = 0.1683      final r-factor (free) = 0.1646          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7295 = 2.55 * 0.50 * 5.2224 + 1.00 * 0.0600                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7058 = 2.55 * 0.50 * 5.1956 + 1.00 * 0.0705                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1159      final r-factor (work) = 0.1173          |
| start r-factor (free) = 0.1646      final r-factor (free) = 0.1610          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7588 = 0.14 * 1.00 * 5.1956 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7544 = 0.14 * 1.00 * 5.1886 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.194)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.96    85.15   16.37    None  None   None       |
|    all(noH): 2823   0      0.96    85.15   16.37    None  None   None       |
|    Sol.    : 438    0      0.96    85.15   38.14    None  None   None       |
|    Mac.    : 2385   0      2.26    78.99   12.38    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:     0.964 -   9.383:  975   |   5:    43.058 -  51.477:   90        |
|      1:     9.383 -  17.802: 1139   |   6:    51.477 -  59.896:   60        |
|      2:    17.802 -  26.221:  256   |   7:    59.896 -  68.315:   36        |
|      3:    26.221 -  34.640:  127   |   8:    68.315 -  76.734:    7        |
|      4:    34.640 -  43.058:  128   |   9:    76.734 -  85.152:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1173 r_free = 0.1610             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1170 r_free = 0.1608             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1608   ksol= 0.33   Bsol= 74.67   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-1.89,0.08,-0.00,0.00,0.00); trace/3= -1.42                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.178216                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1603   ksol= 0.34   Bsol= 74.67   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.36,-1.85,-0.04,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.176441                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.573183              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.502  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.769892              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.904  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1170      final r-factor (work) = 0.1178          |
| start r-factor (free) = 0.1603      final r-factor (free) = 0.1616          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1510 = 1.57 * 0.50 * 5.1876 + 1.00 * 0.0705                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1340 = 1.57 * 0.50 * 5.1802 + 1.00 * 0.0592                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1178      final r-factor (work) = 0.1164          |
| start r-factor (free) = 0.1616      final r-factor (free) = 0.1627          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9961 = 0.77 * 1.00 * 5.1802 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9954 = 0.77 * 1.00 * 5.1764 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.194)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.66   16.67    None  None   None       |
|    all(noH): 2823   0      0.00    89.66   16.67    None  None   None       |
|    Sol.    : 438    0      0.00    89.66   40.13    None  None   None       |
|    Mac.    : 2385   0      0.00    86.30   12.36    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.966:  942   |   5:    44.832 -  53.799:   98        |
|      1:     8.966 -  17.933: 1176   |   6:    53.799 -  62.765:   70        |
|      2:    17.933 -  26.899:  244   |   7:    62.765 -  71.731:   35        |
|      3:    26.899 -  35.866:  129   |   8:    71.731 -  80.698:   14        |
|      4:    35.866 -  44.832:  110   |   9:    80.698 -  89.664:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1164 r_free = 0.1627             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1163 r_free = 0.1627             target_work(ml) = 5.182         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1627   ksol= 0.34   Bsol= 74.67   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.36,-1.85,-0.04,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.181528                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7743 0.99   1397  153 0.1022 0.1299      5.4175       5.526|
|  2:  4.7743 -  3.8096 0.99   1339  153 0.0882 0.1130      5.4576      5.6577|
|  3:  3.8096 -  3.3339 0.99   1312  146 0.1089 0.1508      5.4936      5.8419|
|  4:  3.3339 -  3.0318 0.99   1308  139 0.1247 0.1626      5.4754      5.6231|
|  5:  3.0318 -  2.8160 0.99   1304  146 0.1396 0.1692      5.3652      5.5669|
|  6:  2.8160 -  2.6509 0.99   1291  148 0.1291 0.2084      5.2561      5.5397|
|  7:  2.6509 -  2.5188 0.99   1288  144 0.1340 0.1715        5.22      5.3792|
|  8:  2.5188 -  2.4096 0.98   1284  138 0.1214 0.1743      5.1274      5.3882|
|  9:  2.4096 -  2.3172 0.98   1274  147 0.1239 0.1941      5.0811      5.3677|
| 10:  2.3172 -  2.2375 0.99   1274  137 0.1187 0.1659       4.986      5.1742|
| 11:  2.2375 -  2.1677 0.98   1269  140 0.1190 0.1794      4.9702      5.2295|
| 12:  2.1677 -  2.1059 0.97   1256  142 0.1204 0.1839      4.9254      5.3223|
| 13:  2.1059 -  2.0506 1.00   1277  141 0.1133 0.1831      4.8254      5.0561|
| 14:  2.0506 -  2.0007 0.58    757   85 0.0968 0.1723      4.6697       4.964|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7743  1397   153  0.94   9.55   0.96     0.94       7745.78|
|  2:  4.7743 -  3.8096  1339   153  0.95   7.99   1.00     0.98       9172.97|
|  3:  3.8096 -  3.3339  1312   146  0.93  11.31   1.01     1.01      10410.22|
|  4:  3.3339 -  3.0318  1308   139  0.92  13.88   1.00     0.98      10600.42|
|  5:  3.0318 -  2.8160  1304   146  0.90  16.15   0.99     0.96       8744.09|
|  6:  2.8160 -  2.6509  1291   148  0.89  16.97   0.97     0.95       7705.94|
|  7:  2.6509 -  2.5188  1288   144  0.90  16.55   0.98     0.94       6894.64|
|  8:  2.5188 -  2.4096  1284   138  0.90  16.04   0.98     0.95       6034.23|
|  9:  2.4096 -  2.3172  1274   147  0.90  16.33   0.99     0.95       5572.42|
| 10:  2.3172 -  2.2375  1274   137  0.90  16.31   0.98     0.94       4573.44|
| 11:  2.2375 -  2.1677  1269   140  0.90  16.58   0.97     0.93       4603.41|
| 12:  2.1677 -  2.1059  1256   142  0.90  16.50   0.98     0.97       4314.02|
| 13:  2.1059 -  2.0506  1277   141  0.90  16.71   0.97     0.94       3695.24|
| 14:  2.0506 -  2.0007   757    85  0.92  14.49   0.94     0.90       2621.54|
|alpha:            min =        0.90 max =            1.01 mean =         0.95|
|beta:             min =     2621.54 max =        10600.42 mean =      6777.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.88 mean =        14.61|
|phase err.(test): min =        0.00 max =           89.07 mean =        14.05|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1162   r_free= 0.1625   ksol= 0.32   Bsol= 64.11   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-1.62,0.15,-0.00,0.00,0.00); trace/3= -1.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.181413                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1162   r_free= 0.1625   ksol= 0.32   Bsol= 64.11   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-1.62,0.15,-0.00,0.00,0.00); trace/3= -1.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.181413                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7743 0.99   1397  153 0.1016 0.1294      5.4114      5.5218|
|  2:  4.7743 -  3.8096 0.99   1339  153 0.0878 0.1124      5.4539      5.6521|
|  3:  3.8096 -  3.3339 0.99   1312  146 0.1086 0.1510      5.4917      5.8421|
|  4:  3.3339 -  3.0318 0.99   1308  139 0.1250 0.1631      5.4774      5.6253|
|  5:  3.0318 -  2.8160 0.99   1304  146 0.1399 0.1696      5.3679      5.5692|
|  6:  2.8160 -  2.6509 0.99   1291  148 0.1292 0.2090      5.2579      5.5424|
|  7:  2.6509 -  2.5188 0.99   1288  144 0.1341 0.1718      5.2219      5.3813|
|  8:  2.5188 -  2.4096 0.98   1284  138 0.1216 0.1743      5.1284      5.3878|
|  9:  2.4096 -  2.3172 0.98   1274  147 0.1239 0.1940      5.0814      5.3676|
| 10:  2.3172 -  2.2375 0.99   1274  137 0.1188 0.1662      4.9862      5.1752|
| 11:  2.2375 -  2.1677 0.98   1269  140 0.1190 0.1793      4.9704      5.2292|
| 12:  2.1677 -  2.1059 0.97   1256  142 0.1204 0.1839      4.9255      5.3221|
| 13:  2.1059 -  2.0506 1.00   1277  141 0.1133 0.1835      4.8257      5.0569|
| 14:  2.0506 -  2.0007 0.58    757   85 0.0968 0.1723      4.6705      4.9643|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7743  1397   153  0.94   9.52   0.96     0.94       7667.35|
|  2:  4.7743 -  3.8096  1339   153  0.95   7.95   1.00     0.99       9100.99|
|  3:  3.8096 -  3.3339  1312   146  0.93  11.27   1.01     1.01      10367.57|
|  4:  3.3339 -  3.0318  1308   139  0.92  13.90   1.00     0.99      10630.99|
|  5:  3.0318 -  2.8160  1304   146  0.90  16.19   0.99     0.97       8794.46|
|  6:  2.8160 -  2.6509  1291   148  0.89  17.01   0.98     0.95       7741.11|
|  7:  2.6509 -  2.5188  1288   144  0.90  16.59   0.98     0.95       6925.92|
|  8:  2.5188 -  2.4096  1284   138  0.90  16.06   0.99     0.96       6045.14|
|  9:  2.4096 -  2.3172  1274   147  0.90  16.35   1.00     0.96       5580.39|
| 10:  2.3172 -  2.2375  1274   137  0.90  16.30   0.99     0.94       4570.33|
| 11:  2.2375 -  2.1677  1269   140  0.90  16.57   0.98     0.94       4603.12|
| 12:  2.1677 -  2.1059  1256   142  0.90  16.50   1.00     0.98       4314.12|
| 13:  2.1059 -  2.0506  1277   141  0.90  16.72   0.98     0.95       3698.23|
| 14:  2.0506 -  2.0007   757    85  0.92  14.49   0.96     0.92       2624.42|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2624.42 max =        10630.99 mean =      6775.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.61|
|phase err.(test): min =        0.00 max =           89.09 mean =        14.06|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.194)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.67   16.67    None  None   None       |
|    all(noH): 2823   0      0.00    89.67   16.67    None  None   None       |
|    Sol.    : 438    0      0.00    89.67   40.13    None  None   None       |
|    Mac.    : 2385   0      0.00    86.30   12.37    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 -   8.969:  942   |   5:    44.835 -  53.801:   98        |
|      1:     8.969 -  17.936: 1176   |   6:    53.801 -  62.768:   70        |
|      2:    17.936 -  26.902:  244   |   7:    62.768 -  71.734:   35        |
|      3:    26.902 -  35.869:  129   |   8:    71.734 -  80.701:   14        |
|      4:    35.869 -  44.835:  110   |   9:    80.701 -  89.667:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 298         
Filter by distance & map next to the model:
   mapped sites are within: 0.515 - 4.944
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 292 from: 298
   mapped sites are within: 0.707 - 4.944

peak=    5.333 closest distance to " CB  GLN A 223 " =    1.452
peak=    5.188 closest distance to " CG  PRO A  54 " =    1.434
peak=    5.155 closest distance to " O   HOH Z 113 " =    2.111
peak=    5.154 closest distance to " CZ  PHE A 218 " =    1.135
peak=    4.816 closest distance to " CB  ARG A 190 " =    1.565
peak=    4.782 closest distance to " CB  PRO A  54 " =    0.996
peak=    4.626 closest distance to " CG  PRO A 198 " =    1.356
peak=    4.596 closest distance to " CB  ARG A 275 " =    0.921
peak=    4.570 closest distance to " O   HOH Z 298 " =    1.973
peak=    4.567 closest distance to " NE2 GLN A  11 " =    1.090
peak=    4.549 closest distance to " CA  TYR A  30 " =    0.972
peak=    4.460 closest distance to " O   HOH Z 188 " =    2.897
peak=    4.450 closest distance to " CB  GLN A 183 " =    1.259
peak=    4.427 closest distance to " O   HOH Z 142 " =    1.714
peak=    4.413 closest distance to " CB  SER A  63 " =    1.167
peak=    4.394 closest distance to " O   HOH Z  19 " =    2.408
peak=    4.394 closest distance to " O   HOH Z 369 " =    2.219
peak=    4.391 closest distance to " CB  ARG A  79 " =    1.296
peak=    4.390 closest distance to " O   HOH Z 232 " =    2.315
peak=    4.389 closest distance to " CZ3 TRP A 266 " =    1.105
peak=    4.365 closest distance to " O  BHOH Z  74 " =    1.192
peak=    4.362 closest distance to " CG  PRO A 213 " =    1.202
peak=    4.354 closest distance to " CB  ASN A 148 " =    1.492
peak=    4.308 closest distance to " CB  GLU A 277 " =    3.761
peak=    4.279 closest distance to " CG2 VAL A 257 " =    0.838
peak=    4.247 closest distance to " ND2 ASN A 187 " =    1.504
peak=    4.234 closest distance to " CG  PRO A 243 " =    1.078
peak=    4.207 closest distance to " CB  VAL A 265 " =    1.273
peak=    4.203 closest distance to " CE  LYS A  76 " =    0.901
peak=    4.203 closest distance to " CE1 PHE A  38 " =    1.254
peak=    4.203 closest distance to " O   HOH Z 126 " =    1.861
peak=    4.148 closest distance to " CB  TYR A 169 " =    0.754
peak=    4.103 closest distance to " O   HOH Z 214 " =    2.250
peak=    4.061 closest distance to " CA  ALA A  51 " =    0.923
peak=    4.031 closest distance to " O   HOH Z 265 " =    2.138
peak=    4.028 closest distance to " O   HOH Z 406 " =    1.717
peak=    4.023 closest distance to " CB  PRO A  90 " =    1.123
peak=    4.022 closest distance to " CB  LEU A 228 " =    1.067
peak=    4.019 closest distance to " O   HOH Z  78 " =    1.604
peak=    4.019 closest distance to " O   HOH Z  43 " =    2.073
peak=    4.018 closest distance to " CB  ASN A  39 " =    0.888
peak=    4.012 closest distance to " O   HOH Z 303 " =    2.166
peak=    4.011 closest distance to " CG  MET A 185 " =    1.207
peak=    4.003 closest distance to " O   SER A  87 " =    2.331
peak=    4.000 closest distance to " OE1 GLN A  55 " =    1.559
peak=    3.999 closest distance to " CD  ARG A 269 " =    0.958
peak=    3.993 closest distance to " CA  ARG A 195 " =    1.261
peak=    3.977 closest distance to " C   PRO A 198 " =    1.527
peak=    3.971 closest distance to " ND2 ASN A 249 " =    0.878
peak=    3.965 closest distance to " CB  VAL A 202 " =    1.520
peak=    3.951 closest distance to " NH1AARG A 145 " =    1.370
peak=    3.943 closest distance to " CD2 TRP A 179 " =    1.302
peak=    3.939 closest distance to " O   HOH Z 368 " =    2.170
peak=    3.937 closest distance to " O   HOH Z 183 " =    1.518
peak=    3.922 closest distance to " CB  TRP A 266 " =    1.035
peak=    3.911 closest distance to " CB  ASP A 124 " =    0.762
peak=    3.906 closest distance to " O   HOH Z  63 " =    1.921
peak=    3.898 closest distance to " CA  ARG A  36 " =    1.082
peak=    3.895 closest distance to " O   HOH Z 427 " =    3.113
peak=    3.881 closest distance to " CB  LEU A  83 " =    0.747
peak=    3.870 closest distance to " O   HOH Z 261 " =    2.075
peak=    3.859 closest distance to " CB  ASN A 142 " =    0.997
peak=    3.851 closest distance to " O  BHOH Z 338 " =    2.288
peak=    3.849 closest distance to " O   HOH Z  15 " =    2.118
peak=    3.843 closest distance to " O   ASN A  74 " =    1.388
peak=    3.836 closest distance to " CB  GLU A 152 " =    1.233
peak=    3.835 closest distance to " O   HOH Z  40 " =    1.929
peak=    3.823 closest distance to " O   HOH Z 346 " =    1.740
peak=    3.822 closest distance to " CD1 LEU A  96 " =    0.724
peak=    3.816 closest distance to " CB  GLU A 128 " =    0.954
peak=    3.807 closest distance to " NZ  LYS A 117 " =    3.195
peak=    3.775 closest distance to " O   THR A 220 " =    1.190
peak=    3.767 closest distance to " O   HOH Z 158 " =    3.079
peak=    3.767 closest distance to " CD  LYS A 166 " =    1.262
peak=    3.755 closest distance to " CB  SER A 210 " =    0.809
peak=    3.753 closest distance to " CG  LEU A 167 " =    1.241
peak=    3.753 closest distance to " CD  ARG A 159 " =    0.748
peak=    3.749 closest distance to " CD1 LEU A 300 " =    1.147
peak=    3.741 closest distance to " O   HOH Z 203 " =    1.707
peak=    3.739 closest distance to " CA  ASN A 215 " =    1.045
peak=    3.729 closest distance to " O   HOH Z 133 " =    2.917
peak=    3.728 closest distance to " O   HOH Z 313 " =    1.991
peak=    3.722 closest distance to " CG2 ILE A 120 " =    1.180
peak=    3.721 closest distance to " O   HOH Z 172 " =    3.665
peak=    3.715 closest distance to " CB  GLU A  46 " =    0.991
peak=    3.699 closest distance to " O   HOH Z 250 " =    1.439
peak=    3.697 closest distance to " O   HOH Z 287 " =    2.025
peak=    3.697 closest distance to " CB  ASN A 110 " =    1.101
peak=    3.697 closest distance to " O   HOH Z 234 " =    3.825
peak=    3.696 closest distance to " O   HOH Z 248 " =    1.565
peak=    3.695 closest distance to " O   HOH Z 316 " =    3.154
peak=    3.694 closest distance to " O   THR A 182 " =    1.380
peak=    3.680 closest distance to " O   HOH Z  21 " =    1.808
peak=    3.674 closest distance to " CA  ALA A 160 " =    1.001
peak=    3.668 closest distance to " CG  ARG A  66 " =    2.499
peak=    3.655 closest distance to " CB  ASN A 187 " =    1.365
peak=    3.655 closest distance to " O   HOH Z 353 " =    2.601
peak=    3.655 closest distance to " O   ASN A  74 " =    2.076
peak=    3.653 closest distance to " CB  ALA A 104 " =    0.726
peak=    3.650 closest distance to " O   HOH Z 148 " =    3.493
peak=    3.632 closest distance to " CA  THR A 264 " =    0.919
peak=    3.629 closest distance to " CA  SER A  87 " =    1.070
peak=    3.609 closest distance to " O   HOH Z 280 " =    2.914
peak=    3.601 closest distance to " O   HOH Z 423 " =    1.909
peak=    3.601 closest distance to " O   HOH Z 294 " =    1.538
peak=    3.600 closest distance to " CA  MET A 105 " =    1.022
peak=    3.593 closest distance to " CG  GLU A  37 " =    0.936
peak=    3.591 closest distance to " O   HOH Z 251 " =    1.663
peak=    3.588 closest distance to " O   HOH Z 412 " =    3.973
peak=    3.588 closest distance to " O   HOH Z 392 " =    2.718
peak=    3.586 closest distance to " O   HOH Z  62 " =    2.195
peak=    3.585 closest distance to " N   ASN A  39 " =    1.262
peak=    3.582 closest distance to " O   HOH Z 193 " =    1.862
peak=    3.579 closest distance to " CA  GLN A  94 " =    0.780
peak=    3.567 closest distance to " OG BSER A 164 " =    2.333
peak=    3.565 closest distance to " CA  ALA A 154 " =    1.066
peak=    3.554 closest distance to " CA  ILE A 234 " =    0.977
peak=    3.550 closest distance to " O   HOH Z 285 " =    2.258
peak=    3.550 closest distance to " O   HOH Z 359 " =    1.581
peak=    3.549 closest distance to " CA  ALA A 100 " =    0.907
peak=    3.548 closest distance to " NE2 HIS A 207 " =    1.080
peak=    3.546 closest distance to " CB  SER A   3 " =    1.339
peak=    3.545 closest distance to " O   HOH Z 402 " =    1.385
peak=    3.533 closest distance to " CA  ASN A 127 " =    1.211
peak=    3.532 closest distance to " CG  GLN A  11 " =    1.679
peak=    3.530 closest distance to " O   HOH Z 180 " =    2.197
peak=    3.528 closest distance to " O   HOH Z 368 " =    3.582
peak=    3.528 closest distance to " OG BSER A 134 " =    2.826
peak=    3.524 closest distance to " CA  ASP A 162 " =    0.998
peak=    3.515 closest distance to " CB  LYS A 117 " =    1.215
peak=    3.514 closest distance to " CB  ALA A 291 " =    1.153
peak=    3.514 closest distance to " CB  ASP A 140 " =    1.125
peak=    3.508 closest distance to " O   HOH Z 394 " =    4.039
peak=    3.508 closest distance to " CB  MET A  40 " =    0.778
peak=    3.505 closest distance to " CA  VAL A 125 " =    1.195
peak=    3.502 closest distance to " O   HOH Z 199 " =    1.591
peak=    3.502 closest distance to " CG2AVAL A 121 " =    2.285
peak=    3.493 closest distance to " CH2 TRP A  70 " =    0.880
peak=    3.485 closest distance to " CG AARG A 275 " =    1.176
peak=    3.483 closest distance to " CB  ASN A 215 " =    1.161
peak=    3.480 closest distance to " CB  THR A  31 " =    1.584
peak=    3.478 closest distance to " CG2AVAL A  72 " =    1.774
peak=    3.478 closest distance to " CG1 VAL A 153 " =    1.016
peak=    3.478 closest distance to " O   HOH Z 209 " =    2.263
peak=    3.461 closest distance to " N   ARG A 156 " =    1.417
peak=    3.454 closest distance to " O   HOH Z 383 " =    2.109
peak=    3.449 closest distance to " ND2 ASN A 249 " =    1.901
peak=    3.439 closest distance to " CB  ILE A 120 " =    1.238
peak=    3.438 closest distance to " O   HOH Z 337 " =    3.592
peak=    3.434 closest distance to " CD  ARG A  66 " =    2.484
peak=    3.432 closest distance to " O   HOH Z 213 " =    1.989
peak=    3.427 closest distance to " O   ALA A 165 " =    1.537
peak=    3.426 closest distance to " OD1 ASN A  69 " =    2.547
peak=    3.421 closest distance to " O   HOH Z 272 " =    1.842
peak=    3.415 closest distance to " CD1 ILE A 199 " =    0.915
peak=    3.406 closest distance to " CB  PHE A 204 " =    0.778
peak=    3.406 closest distance to " CA  TYR A 116 " =    1.409
peak=    3.399 closest distance to " O   HOH Z 290 " =    1.028
peak=    3.395 closest distance to " O   HOH Z  88 " =    1.857
peak=    3.392 closest distance to " N   TYR A 116 " =    1.515
peak=    3.387 closest distance to " OE2 GLU A  53 " =    1.354
peak=    3.385 closest distance to " CB  GLN A  89 " =    1.323
peak=    3.383 closest distance to " O   HOH Z 365 " =    2.856
peak=    3.380 closest distance to " CA  ASN A 217 " =    1.241
peak=    3.379 closest distance to " CA  ARG A 139 " =    1.024
peak=    3.379 closest distance to " O   HOH Z 166 " =    4.043
peak=    3.378 closest distance to " CB  SER A  62 " =    0.767
peak=    3.375 closest distance to " O   HOH Z  48 " =    1.588
peak=    3.374 closest distance to " O   HOH Z 128 " =    2.223
peak=    3.372 closest distance to " O   SER A 164 " =    1.444
peak=    3.370 closest distance to " O   HOH Z  10 " =    1.734
peak=    3.365 closest distance to " O   HOH Z 419 " =    2.077
peak=    3.364 closest distance to " O   PHE A  61 " =    1.382
peak=    3.359 closest distance to " O   HOH Z   1 " =    2.289
peak=    3.358 closest distance to " O   HOH Z 163 " =    1.988
peak=    3.355 closest distance to " CG  PHE A 204 " =    1.005
peak=    3.354 closest distance to " O   HOH Z 126 " =    1.617
peak=    3.352 closest distance to " O   HOH Z 305 " =    3.694
peak=    3.350 closest distance to " O   HOH Z 325 " =    2.436
peak=    3.346 closest distance to " CG2 ILE A  20 " =    1.288
peak=    3.344 closest distance to " CE1 TYR A 186 " =    1.399
peak=    3.340 closest distance to " O   HOH Z 371 " =    3.038
peak=    3.340 closest distance to " CB  PRO A 198 " =    1.159
peak=    3.332 closest distance to " CB  SER A 141 " =    1.069
peak=    3.329 closest distance to " CB  TYR A 116 " =    0.755
peak=    3.324 closest distance to " CD2 LEU A 297 " =    0.898
peak=    3.318 closest distance to " NE2 GLN A  77 " =    3.396
peak=    3.315 closest distance to " C   ILE A 106 " =    1.914
peak=    3.315 closest distance to " CB  ALA A 114 " =    0.812
peak=    3.314 closest distance to " O   HOH Z  94 " =    2.498
peak=    3.313 closest distance to " CB  THR A  52 " =    0.713
peak=    3.310 closest distance to " O   HOH Z 421 " =    1.950
peak=    3.309 closest distance to " CB  GLN A  88 " =    1.199
peak=    3.309 closest distance to " N   PHE A 130 " =    1.187
peak=    3.307 closest distance to " CA  GLY A 211 " =    1.369
peak=    3.306 closest distance to " O   ASP A 191 " =    1.479
peak=    3.303 closest distance to " CA  ALA A 233 " =    1.541
peak=    3.302 closest distance to " OH  TYR A 116 " =    1.077
peak=    3.300 closest distance to " CA  GLU A 152 " =    0.875
peak=    3.299 closest distance to " CA  HIS A  86 " =    0.707
peak=    3.298 closest distance to " CG  ARG A 138 " =    1.316
peak=    3.295 closest distance to " OG  SER A  28 " =    1.487
peak=    3.291 closest distance to " O   HOH Z 340 " =    2.093
peak=    3.284 closest distance to " CB  LEU A  96 " =    1.363
peak=    3.280 closest distance to " CB  GLN A 205 " =    1.123
peak=    3.278 closest distance to " CB  ALA A 299 " =    0.967
peak=    3.275 closest distance to " CB  MET A  47 " =    0.967
peak=    3.273 closest distance to " O   HOH Z 291 " =    1.517
peak=    3.271 closest distance to " CG2 VAL A 197 " =    1.032
peak=    3.264 closest distance to " CG1 ILE A 151 " =    0.990
peak=    3.264 closest distance to " O   HOH Z  88 " =    2.643
peak=    3.262 closest distance to " OG  SER A  22 " =    2.688
peak=    3.261 closest distance to " CD BLYS A 290 " =    0.925
peak=    3.257 closest distance to " O   THR A 251 " =    1.102
peak=    3.254 closest distance to " O   HOH Z 227 " =    1.402
peak=    3.253 closest distance to " O   HOH Z  61 " =    1.688
peak=    3.252 closest distance to " O   HOH Z 147 " =    1.889
peak=    3.245 closest distance to " CB  ALA A  43 " =    0.810
peak=    3.245 closest distance to " CB  SER A 273 " =    0.875
peak=    3.245 closest distance to " CB  PRO A 243 " =    1.425
peak=    3.243 closest distance to " O   PRO A 213 " =    1.478
peak=    3.242 closest distance to " CB  ARG A 156 " =    1.180
peak=    3.239 closest distance to " CG2 THR A 220 " =    0.895
peak=    3.239 closest distance to " CA  THR A 221 " =    1.033
peak=    3.238 closest distance to " O   HOH Z 417 " =    3.351
peak=    3.238 closest distance to " CG1 ILE A  49 " =    1.576
peak=    3.237 closest distance to " O   HOH Z 128 " =    2.171
peak=    3.232 closest distance to " CA  ALA A 295 " =    1.085
peak=    3.230 closest distance to " O   GLY A  91 " =    1.374
peak=    3.230 closest distance to " CE3 TRP A 150 " =    1.127
peak=    3.229 closest distance to " O   HOH Z  59 " =    2.004
peak=    3.228 closest distance to " CG BARG A 102 " =    1.858
peak=    3.228 closest distance to " O   HOH Z 425 " =    1.272
peak=    3.226 closest distance to " OG  SER A 245 " =    1.716
peak=    3.225 closest distance to " O   HOH Z 298 " =    2.546
peak=    3.225 closest distance to " OD1 ASP A 171 " =    1.169
peak=    3.222 closest distance to " N   ALA A 256 " =    1.161
peak=    3.220 closest distance to " CB  ASP A 191 " =    1.249
peak=    3.216 closest distance to " CB  GLU A  37 " =    0.897
peak=    3.216 closest distance to " CG2 THR A 221 " =    1.087
peak=    3.215 closest distance to " N   ASN A 127 " =    1.256
peak=    3.212 closest distance to " O   HOH Z  68 " =    2.192
peak=    3.212 closest distance to " O   TYR A 116 " =    1.341
peak=    3.210 closest distance to " O   HOH Z 116 " =    1.806
peak=    3.203 closest distance to " O   HOH Z 299 " =    4.475
peak=    3.195 closest distance to " CG  MET A 185 " =    0.974
peak=    3.193 closest distance to " CB  ALA A 242 " =    0.828
peak=    3.190 closest distance to " O   PHE A 192 " =    1.423
peak=    3.190 closest distance to " CB  ASP A 298 " =    1.163
peak=    3.182 closest distance to " CB  SER A  26 " =    1.892
peak=    3.181 closest distance to " O   HOH Z  80 " =    1.718
peak=    3.181 closest distance to " CB  ARG A 145 " =    0.867
peak=    3.177 closest distance to " O   HOH Z 171 " =    4.061
peak=    3.175 closest distance to " O   HOH Z 422 " =    2.682
peak=    3.172 closest distance to " CD1 ILE A  33 " =    1.782
peak=    3.171 closest distance to " CB  ASN A 173 " =    1.134
peak=    3.171 closest distance to " CB  PHE A 283 " =    0.760
peak=    3.167 closest distance to " CB  TRP A 179 " =    1.437
peak=    3.165 closest distance to " OD2 ASP A 286 " =    3.298
peak=    3.158 closest distance to " O   LEU A 228 " =    1.888
peak=    3.157 closest distance to " NZ  LYS A  48 " =    1.212
peak=    3.155 closest distance to " CG BARG A 275 " =    1.423
peak=    3.153 closest distance to " CB  ARG A 102 " =    0.732
peak=    3.150 closest distance to " CA  ALA A 129 " =    1.267
peak=    3.148 closest distance to " O   ASP A 124 " =    1.091
peak=    3.147 closest distance to " O   ALA A 158 " =    1.239
peak=    3.145 closest distance to " CA  GLU A  46 " =    1.061
peak=    3.139 closest distance to " CB  ARG A 138 " =    0.969
peak=    3.138 closest distance to " CD1 LEU A 281 " =    0.995
peak=    3.135 closest distance to " CA  ASP A 140 " =    1.338
peak=    3.135 closest distance to " O   HOH Z 327 " =    1.847
peak=    3.129 closest distance to " O   HOH Z 391 " =    2.975
peak=    3.125 closest distance to " O   HOH Z 258 " =    1.674
peak=    3.120 closest distance to " CA  ILE A 106 " =    0.802
peak=    3.117 closest distance to " CB  SER A  62 " =    1.070
peak=    3.114 closest distance to " O   HOH Z  97 " =    2.414
peak=    3.113 closest distance to " CA  ARG A 102 " =    1.138
peak=    3.101 closest distance to " O   HOH Z 216 " =    4.944
peak=    3.090 closest distance to " CD1 LEU A 261 " =    1.282
peak=    3.087 closest distance to " CA  ALA A 248 " =    1.192
peak=    3.087 closest distance to " CG2 ILE A 234 " =    0.895
peak=    3.083 closest distance to " O   HOH Z 152 " =    2.030
peak=    3.076 closest distance to " O   HOH Z 384 " =    3.072
peak=    3.075 closest distance to " CG  MET A 188 " =    0.886
peak=    3.068 closest distance to " CB  ALA A 248 " =    1.622
peak=    3.068 closest distance to " CG1 ILE A  33 " =    1.256
peak=    3.067 closest distance to " O   HOH Z 106 " =    4.171
peak=    3.067 closest distance to " O   HOH Z 421 " =    2.973
peak=    3.065 closest distance to " CE2 PHE A  16 " =    0.902
peak=    3.058 closest distance to " NE  ARG A  79 " =    0.930
peak=    3.045 closest distance to " O   HOH Z 120 " =    3.467
peak=    3.026 closest distance to " O   HOH Z 213 " =    2.453

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 190         
Filter by distance & map next to the model:
   mapped sites are within: 0.933 - 5.843
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 190 from: 190
   mapped sites are within: 0.933 - 5.843

peak=   -4.904 closest distance to " CD  ARG A  14 " =    3.454
peak=   -4.745 closest distance to " CD  GLN A  58 " =    0.937
peak=   -4.631 closest distance to " CG1 VAL A 112 " =    2.638
peak=   -4.372 closest distance to " O   PRO A 198 " =    1.283
peak=   -4.366 closest distance to " C   HIS A 108 " =    1.096
peak=   -4.269 closest distance to " CD  ARG A 156 " =    2.086
peak=   -4.240 closest distance to " O   HOH Z 231 " =    2.277
peak=   -4.222 closest distance to " O   HOH Z 211 " =    1.171
peak=   -4.200 closest distance to " CD2 TYR A 293 " =    2.010
peak=   -4.172 closest distance to " CG1 VAL A 112 " =    2.863
peak=   -4.166 closest distance to " O   VAL A  67 " =    2.685
peak=   -4.153 closest distance to " O   HOH Z 377 " =    2.126
peak=   -4.126 closest distance to " O   HOH Z 196 " =    2.104
peak=   -4.123 closest distance to " CA  VAL A  67 " =    3.026
peak=   -4.070 closest distance to " O   HOH Z 198 " =    1.749
peak=   -4.070 closest distance to " CE2 PHE A  61 " =    2.672
peak=   -4.040 closest distance to " CZ3 TRP A 179 " =    1.203
peak=   -4.028 closest distance to " CB  PRO A 243 " =    2.716
peak=   -3.985 closest distance to " N   ALA A  43 " =    2.602
peak=   -3.977 closest distance to " OG BSER A 134 " =    1.336
peak=   -3.940 closest distance to " O   HOH Z 266 " =    5.711
peak=   -3.937 closest distance to " O   HOH Z  73 " =    2.413
peak=   -3.935 closest distance to " CG1 VAL A 250 " =    2.705
peak=   -3.918 closest distance to " CA  ASP A 298 " =    1.100
peak=   -3.915 closest distance to " OD1 ASN A 148 " =    1.417
peak=   -3.907 closest distance to " O   HOH Z 394 " =    1.520
peak=   -3.866 closest distance to " CA  GLY A 241 " =    2.393
peak=   -3.854 closest distance to " CA  GLY A 241 " =    3.368
peak=   -3.847 closest distance to " CG  GLN A  11 " =    1.717
peak=   -3.815 closest distance to " CG2 ILE A  49 " =    2.871
peak=   -3.804 closest distance to " CB  ALA A  43 " =    2.644
peak=   -3.794 closest distance to " O   HOH Z 290 " =    1.179
peak=   -3.786 closest distance to " CB  PHE A 192 " =    1.996
peak=   -3.781 closest distance to " CG  GLN A 223 " =    2.088
peak=   -3.776 closest distance to " CE3 TRP A 150 " =    2.305
peak=   -3.771 closest distance to " OG  SER A  97 " =    2.336
peak=   -3.737 closest distance to " CE BMET A  47 " =    1.515
peak=   -3.723 closest distance to " O   HOH Z 128 " =    2.634
peak=   -3.719 closest distance to " CD1 LEU A 101 " =    2.399
peak=   -3.715 closest distance to " O   SER A 210 " =    1.993
peak=   -3.710 closest distance to " OD1 ASP A 171 " =    1.603
peak=   -3.702 closest distance to " CE  MET A 105 " =    2.390
peak=   -3.699 closest distance to " CE2 TYR A  30 " =    2.723
peak=   -3.698 closest distance to " CG  GLU A 277 " =    1.192
peak=   -3.677 closest distance to " O   ALA A  10 " =    1.648
peak=   -3.664 closest distance to " CB  ALA A 161 " =    2.641
peak=   -3.664 closest distance to " CG  ARG A 269 " =    2.494
peak=   -3.662 closest distance to " O   HOH Z 102 " =    1.568
peak=   -3.636 closest distance to " CB  ASN A  39 " =    2.297
peak=   -3.618 closest distance to " O   HOH Z 216 " =    1.132
peak=   -3.613 closest distance to " OXT GLY A 302 " =    3.002
peak=   -3.612 closest distance to " CB  HIS A  86 " =    1.161
peak=   -3.590 closest distance to " CG  PRO A 198 " =    1.867
peak=   -3.586 closest distance to " O   HOH Z 185 " =    2.275
peak=   -3.584 closest distance to " O   HOH Z 166 " =    1.906
peak=   -3.578 closest distance to " CG  MET A 105 " =    1.024
peak=   -3.577 closest distance to " CB  ALA A   7 " =    2.330
peak=   -3.571 closest distance to " O   HOH Z  37 " =    1.827
peak=   -3.535 closest distance to " C   MET A 188 " =    1.335
peak=   -3.528 closest distance to " CB  ALA A 129 " =    2.479
peak=   -3.523 closest distance to " NH2AARG A 275 " =    5.405
peak=   -3.517 closest distance to " ND2 ASN A 249 " =    2.426
peak=   -3.515 closest distance to " O   HOH Z 372 " =    2.342
peak=   -3.514 closest distance to " CZ  PHE A 155 " =    1.214
peak=   -3.512 closest distance to " O   HOH Z 278 " =    1.155
peak=   -3.510 closest distance to " NH2 ARG A  79 " =    1.536
peak=   -3.496 closest distance to " O   TYR A 247 " =    2.864
peak=   -3.485 closest distance to " O   HOH Z 174 " =    3.787
peak=   -3.481 closest distance to " CB  TRP A  85 " =    2.592
peak=   -3.466 closest distance to " CA  GLY A 203 " =    2.482
peak=   -3.463 closest distance to " O   HOH Z  10 " =    1.514
peak=   -3.462 closest distance to " O   HOH Z 149 " =    2.179
peak=   -3.462 closest distance to " N   THR A  52 " =    1.622
peak=   -3.461 closest distance to " O   ILE A 106 " =    1.888
peak=   -3.457 closest distance to " O   HOH Z  38 " =    1.564
peak=   -3.446 closest distance to " NE2 GLN A 194 " =    1.967
peak=   -3.443 closest distance to " CG  PHE A 283 " =    2.647
peak=   -3.443 closest distance to " CG  ASP A 132 " =    2.339
peak=   -3.442 closest distance to " CG1 VAL A 125 " =    1.809
peak=   -3.424 closest distance to " O   HOH Z  64 " =    1.423
peak=   -3.424 closest distance to " CG2 ILE A 263 " =    2.369
peak=   -3.423 closest distance to " O   ALA A  34 " =    2.544
peak=   -3.420 closest distance to " CB  ALA A 291 " =    2.308
peak=   -3.416 closest distance to " O   HOH Z 295 " =    1.734
peak=   -3.409 closest distance to " ND2 ASN A  60 " =    1.313
peak=   -3.408 closest distance to " CD1 LEU A 255 " =    2.912
peak=   -3.407 closest distance to " O   VAL A 189 " =    1.626
peak=   -3.407 closest distance to " O   HOH Z 174 " =    2.652
peak=   -3.407 closest distance to " O   HOH Z 232 " =    1.787
peak=   -3.403 closest distance to " CB  ALA A 291 " =    2.279
peak=   -3.400 closest distance to " CG  GLU A  53 " =    1.570
peak=   -3.398 closest distance to " O   HOH Z 193 " =    1.410
peak=   -3.390 closest distance to " NE2 GLN A 278 " =    1.612
peak=   -3.390 closest distance to " O   HOH Z 133 " =    1.250
peak=   -3.387 closest distance to " CB  ALA A  10 " =    2.256
peak=   -3.380 closest distance to " CB  ALA A 248 " =    2.354
peak=   -3.378 closest distance to " O   TYR A 186 " =    1.727
peak=   -3.377 closest distance to " N   ALA A 248 " =    1.705
peak=   -3.377 closest distance to " O   PHE A 218 " =    1.494
peak=   -3.368 closest distance to " O   HOH Z 134 " =    3.232
peak=   -3.359 closest distance to " C   ASN A 285 " =    2.391
peak=   -3.356 closest distance to " O   HOH Z 348 " =    2.196
peak=   -3.354 closest distance to " O   HOH Z 421 " =    3.260
peak=   -3.349 closest distance to " O   HOH Z 359 " =    2.957
peak=   -3.338 closest distance to " CD  ARG A  79 " =    1.189
peak=   -3.334 closest distance to " CB  PHE A  16 " =    2.465
peak=   -3.331 closest distance to " O   VAL A 189 " =    2.638
peak=   -3.325 closest distance to " O   HOH Z 368 " =    1.812
peak=   -3.325 closest distance to " O   HOH Z 407 " =    3.116
peak=   -3.323 closest distance to " CG1BVAL A  41 " =    2.773
peak=   -3.321 closest distance to " O   HOH Z 275 " =    1.527
peak=   -3.319 closest distance to " O   TRP A  70 " =    1.544
peak=   -3.319 closest distance to " O   GLN A  94 " =    2.203
peak=   -3.315 closest distance to " C   LEU A 143 " =    1.072
peak=   -3.313 closest distance to " ND2 ASN A  45 " =    1.974
peak=   -3.313 closest distance to " CD  GLU A 236 " =    1.121
peak=   -3.312 closest distance to " O   HOH Z 351 " =    1.554
peak=   -3.310 closest distance to " CD  PRO A 243 " =    2.158
peak=   -3.309 closest distance to " OD2 ASP A 191 " =    1.483
peak=   -3.304 closest distance to " O   HOH Z   9 " =    1.881
peak=   -3.304 closest distance to " O   HOH Z  52 " =    1.790
peak=   -3.296 closest distance to " CA  GLY A 133 " =    2.303
peak=   -3.290 closest distance to " CG  LEU A  83 " =    2.022
peak=   -3.290 closest distance to " C   SER A 206 " =    1.478
peak=   -3.285 closest distance to " OH  TYR A 247 " =    2.188
peak=   -3.283 closest distance to " CD2 PHE A  61 " =    2.127
peak=   -3.275 closest distance to " ND2 ASN A  45 " =    1.139
peak=   -3.269 closest distance to " CA  GLY A 241 " =    2.878
peak=   -3.269 closest distance to " NE2 GLN A  88 " =    1.950
peak=   -3.265 closest distance to " O   HOH Z 311 " =    3.754
peak=   -3.256 closest distance to " O   HOH Z 171 " =    2.040
peak=   -3.256 closest distance to " CD  ARG A 195 " =    5.123
peak=   -3.254 closest distance to " O   PRO A 163 " =    1.990
peak=   -3.248 closest distance to " O   HOH Z  60 " =    2.194
peak=   -3.248 closest distance to " O   HOH Z 393 " =    1.319
peak=   -3.245 closest distance to " CZ  PHE A  38 " =    2.072
peak=   -3.243 closest distance to " CG2 VAL A 189 " =    2.173
peak=   -3.240 closest distance to " CG  PRO A 243 " =    1.710
peak=   -3.239 closest distance to " CG  TRP A 266 " =    1.824
peak=   -3.237 closest distance to " O   GLY A  17 " =    1.142
peak=   -3.231 closest distance to " O   SER A 135 " =    1.468
peak=   -3.229 closest distance to " O   HOH Z  51 " =    1.798
peak=   -3.225 closest distance to " O   HOH Z 429 " =    1.900
peak=   -3.224 closest distance to " CE3 TRP A 274 " =    2.491
peak=   -3.217 closest distance to " O   HOH Z 313 " =    1.809
peak=   -3.215 closest distance to " CD1 PHE A  59 " =    2.021
peak=   -3.214 closest distance to " O   HOH Z 114 " =    3.126
peak=   -3.213 closest distance to " O   ALA A 180 " =    1.396
peak=   -3.211 closest distance to " CA  GLY A 287 " =    1.666
peak=   -3.210 closest distance to " O   HOH Z 345 " =    2.199
peak=   -3.210 closest distance to " CZ  ARG A 259 " =    0.957
peak=   -3.209 closest distance to " CD1 LEU A   5 " =    2.518
peak=   -3.209 closest distance to " O   HOH Z 357 " =    2.186
peak=   -3.208 closest distance to " CG1AVAL A  41 " =    2.729
peak=   -3.206 closest distance to " CB  PRO A 163 " =    2.462
peak=   -3.205 closest distance to " CG  GLN A 103 " =    2.446
peak=   -3.202 closest distance to " O   HOH Z 252 " =    3.909
peak=   -3.201 closest distance to " OD2 ASP A 171 " =    1.824
peak=   -3.199 closest distance to " CD1 TRP A  70 " =    1.096
peak=   -3.194 closest distance to " CD1 ILE A 239 " =    2.287
peak=   -3.192 closest distance to " CB  ASP A 286 " =    2.157
peak=   -3.189 closest distance to " OE1 GLN A  88 " =    1.039
peak=   -3.183 closest distance to " O   HOH Z 351 " =    1.501
peak=   -3.164 closest distance to " C   GLY A 262 " =    2.041
peak=   -3.164 closest distance to " O   HOH Z 281 " =    2.596
peak=   -3.164 closest distance to " O   ALA A 227 " =    1.561
peak=   -3.161 closest distance to " O   HOH Z 285 " =    1.769
peak=   -3.161 closest distance to " O   HOH Z   6 " =    1.392
peak=   -3.159 closest distance to " CG  ARG A  66 " =    2.387
peak=   -3.155 closest distance to " O   HOH Z 298 " =    2.537
peak=   -3.154 closest distance to " OD1 ASN A 187 " =    1.672
peak=   -3.153 closest distance to " O   HOH Z 156 " =    3.491
peak=   -3.150 closest distance to " NE2 GLN A  88 " =    1.159
peak=   -3.141 closest distance to " CA  SER A 135 " =    1.258
peak=   -3.138 closest distance to " CB  ALA A 100 " =    2.194
peak=   -3.130 closest distance to " O   SER A  95 " =    1.805
peak=   -3.129 closest distance to " O   HOH Z  63 " =    1.745
peak=   -3.127 closest distance to " N   ALA A 226 " =    2.078
peak=   -3.126 closest distance to " C   ALA A 158 " =    1.469
peak=   -3.119 closest distance to " O   GLU A 152 " =    1.358
peak=   -3.118 closest distance to " O   HOH Z 191 " =    5.843
peak=   -3.116 closest distance to " O   HOH Z  71 " =    2.597
peak=   -3.103 closest distance to " N   GLN A 223 " =    0.988
peak=   -3.100 closest distance to " O   GLY A 211 " =    1.336
peak=   -3.079 closest distance to " O   SER A  62 " =    2.174
peak=   -3.072 closest distance to " OG  SER A  28 " =    2.143
peak=   -3.062 closest distance to " OD1 ASN A 173 " =    1.355
peak=   -3.060 closest distance to " CD  GLN A  73 " =    0.933
peak=   -3.049 closest distance to " O   HOH Z 236 " =    1.506
peak=   -3.020 closest distance to " OG BSER A 134 " =    1.949

================= 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    :  0.3728 0.3640   6.161100e+00   6.141648e+00
   1_bss:  0.3552 0.3473   6.135581e+00   6.114991e+00
   1_xyz:  0.2360 0.2608   5.758340e+00   5.839609e+00
   1_adp:  0.2168 0.2650   5.707418e+00   5.851863e+00
   1_occ:  0.2165 0.2653   5.707515e+00   5.853667e+00
   2_bss:  0.2121 0.2618   5.694623e+00   5.846401e+00
   2_xyz:  0.1541 0.1946   5.399226e+00   5.579082e+00
   2_adp:  0.1410 0.1850   5.332228e+00   5.537233e+00
   2_occ:  0.1409 0.1849   5.331154e+00   5.536177e+00
   3_bss:  0.1405 0.1838   5.326978e+00   5.530744e+00
   3_xyz:  0.1259 0.1695   5.236109e+00   5.454870e+00
   3_adp:  0.1225 0.1685   5.220305e+00   5.448298e+00
   3_occ:  0.1224 0.1685   5.220029e+00   5.448131e+00
   4_bss:  0.1222 0.1683   5.219434e+00   5.447988e+00
   4_xyz:  0.1159 0.1646   5.180892e+00   5.423038e+00
   4_adp:  0.1173 0.1610   5.179335e+00   5.407947e+00
   4_occ:  0.1170 0.1608   5.178216e+00   5.407465e+00
   5_bss:  0.1170 0.1603   5.176441e+00   5.404495e+00
   5_xyz:  0.1178 0.1616   5.185120e+00   5.413264e+00
   5_adp:  0.1164 0.1627   5.181284e+00   5.419182e+00
   5_occ:  0.1163 0.1627   5.181528e+00   5.419655e+00
   5_bss:  0.1162 0.1625   5.181413e+00   5.419674e+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:  0.314  58.313  -3.427  -2.212   6.125  -0.000   0.000   0.000
   1_xyz:  0.314  58.313  -3.427  -2.212   6.125  -0.000   0.000   0.000
   1_adp:  0.314  58.313  -3.427  -2.212   6.125  -0.000   0.000   0.000
   1_occ:  0.314  58.313  -3.427  -2.212   6.125  -0.000   0.000   0.000
   2_bss:  0.339  73.517  -3.135  -2.267   1.423  -0.000   0.000   0.000
   2_xyz:  0.339  73.517  -3.135  -2.267   1.423  -0.000   0.000   0.000
   2_adp:  0.339  73.517  -3.135  -2.267   1.423  -0.000   0.000   0.000
   2_occ:  0.339  73.517  -3.135  -2.267   1.423  -0.000   0.000   0.000
   3_bss:  0.338  74.669  -2.824  -2.099   0.295  -0.000   0.000   0.000
   3_xyz:  0.338  74.669  -2.824  -2.099   0.295  -0.000   0.000   0.000
   3_adp:  0.338  74.669  -2.824  -2.099   0.295  -0.000   0.000   0.000
   3_occ:  0.338  74.669  -2.824  -2.099   0.295  -0.000   0.000   0.000
   4_bss:  0.333  74.669  -2.442  -1.890   0.084  -0.000   0.000   0.000
   4_xyz:  0.333  74.669  -2.442  -1.890   0.084  -0.000   0.000   0.000
   4_adp:  0.333  74.669  -2.442  -1.890   0.084  -0.000   0.000   0.000
   4_occ:  0.333  74.669  -2.442  -1.890   0.084  -0.000   0.000   0.000
   5_bss:  0.337  74.669  -2.360  -1.855  -0.040  -0.000  -0.000  -0.000
   5_xyz:  0.337  74.669  -2.360  -1.855  -0.040  -0.000  -0.000  -0.000
   5_adp:  0.337  74.669  -2.360  -1.855  -0.040  -0.000  -0.000  -0.000
   5_occ:  0.337  74.669  -2.360  -1.855  -0.040  -0.000  -0.000  -0.000
   5_bss:  0.322  64.112  -2.099  -1.623   0.148  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  40.169 0.6432  0.7981    40105.262
   1_bss:  38.769 0.6584  0.8225    36699.596
   1_xyz:  26.077 0.8010  0.9669    17720.201
   1_adp:  26.584 0.7951  0.9635    18277.854
   1_occ:  26.675 0.7941  0.9623    18362.924
   2_bss:  25.934 0.8025  0.9258    17896.908
   2_xyz:  18.519 0.8755  0.9689     9616.107
   2_adp:  17.362 0.8863  0.9640     8805.540
   2_occ:  17.337 0.8865  0.9641     8781.337
   3_bss:  17.184 0.8879  0.9582     8663.515
   3_xyz:  15.472 0.9027  0.9674     7359.473
   3_adp:  15.235 0.9051  0.9585     7253.092
   3_occ:  15.231 0.9052  0.9584     7250.435
   4_bss:  15.216 0.9053  0.9630     7250.112
   4_xyz:  14.703 0.9095  0.9664     6870.218
   4_adp:  14.339 0.9126  0.9621     6706.981
   4_occ:  14.329 0.9127  0.9620     6695.288
   5_bss:  14.287 0.9130  0.9623     6632.228
   5_xyz:  14.416 0.9121  0.9618     6740.816
   5_adp:  14.548 0.9110  0.9541     6773.035
   5_occ:  14.554 0.9110  0.9539     6777.602
   5_bss:  14.560 0.9109  0.9616     6775.068
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.7087e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.7087e-01
   1_xyz:   1.289  0.010  0.085 15.461  0.005  4.115   9.2222e-02
   1_adp:   1.289  0.010  0.085 15.461  0.005  4.115   9.2222e-02
   1_occ:   1.289  0.010  0.085 15.461  0.005  4.115   9.2222e-02
   2_bss:   1.289  0.010  0.085 15.461  0.005  4.115   9.2222e-02
   2_xyz:   1.100  0.008  0.080 15.132  0.004  4.114   6.7891e-02
   2_adp:   1.100  0.008  0.080 15.132  0.004  4.114   6.7891e-02
   2_occ:   1.100  0.008  0.080 15.132  0.004  4.114   6.7891e-02
   3_bss:   1.100  0.008  0.080 15.132  0.004  4.114   6.7891e-02
   3_xyz:   1.000  0.008  0.074 14.811  0.003  4.123   5.9955e-02
   3_adp:   1.000  0.008  0.074 14.811  0.003  4.123   5.9955e-02
   3_occ:   1.000  0.008  0.074 14.811  0.003  4.123   5.9955e-02
   4_bss:   1.000  0.008  0.074 14.811  0.003  4.123   5.9955e-02
   4_xyz:   1.083  0.010  0.082 14.867  0.004  4.116   7.0500e-02
   4_adp:   1.083  0.010  0.082 14.867  0.004  4.116   7.0500e-02
   4_occ:   1.083  0.010  0.082 14.867  0.004  4.116   7.0500e-02
   5_bss:   1.083  0.010  0.082 14.867  0.004  4.116   7.0500e-02
   5_xyz:   0.987  0.008  0.076 14.647  0.003  4.116   5.9246e-02
   5_adp:   0.987  0.008  0.076 14.647  0.003  4.116   5.9246e-02
   5_occ:   0.987  0.008  0.076 14.647  0.003  4.116   5.9246e-02
   5_bss:   0.987  0.008  0.076 14.647  0.003  4.116   5.9246e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.414   2.4413e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.414   2.4413e-01
   1_xyz:   9.411  0.051  0.378 82.730  0.047  2.125   8.6696e-02
   1_adp:   9.411  0.051  0.378 82.730  0.047  2.125   8.6696e-02
   1_occ:   9.411  0.051  0.378 82.730  0.047  2.125   8.6696e-02
   2_bss:   9.411  0.051  0.378 82.730  0.047  2.125   8.6696e-02
   2_xyz:   7.078  0.045  0.256 86.167  0.054  2.330   5.4736e-02
   2_adp:   7.078  0.045  0.256 86.167  0.054  2.330   5.4736e-02
   2_occ:   7.078  0.045  0.256 86.167  0.054  2.330   5.4736e-02
   3_bss:   7.078  0.045  0.256 86.167  0.054  2.330   5.4736e-02
   3_xyz:   7.037  0.044  0.218 82.011  0.036  2.369   3.9773e-02
   3_adp:   7.037  0.044  0.218 82.011  0.036  2.369   3.9773e-02
   3_occ:   7.037  0.044  0.218 82.011  0.036  2.369   3.9773e-02
   4_bss:   7.037  0.044  0.218 82.011  0.036  2.369   3.9773e-02
   4_xyz:   7.416  0.056  0.278 83.736  0.038  2.354   4.8337e-02
   4_adp:   7.416  0.056  0.278 83.736  0.038  2.354   4.8337e-02
   4_occ:   7.416  0.056  0.278 83.736  0.038  2.354   4.8337e-02
   5_bss:   7.416  0.056  0.278 83.736  0.038  2.354   4.8337e-02
   5_xyz:   6.864  0.046  0.236 82.004  0.033  2.396   3.9721e-02
   5_adp:   6.864  0.046  0.236 82.004  0.033  2.396   3.9721e-02
   5_occ:   6.864  0.046  0.236 82.004  0.033  2.396   3.9721e-02
   5_bss:   6.864  0.046  0.236 82.004  0.033  2.396   3.9721e-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:  64.04   0.00  16.78  64.02   0.00  12.87  64.04   4.30  38.09
   1_occ:  64.04   0.00  16.78  64.02   0.00  12.87  64.04   4.30  38.09
   2_bss:  64.04   0.00  16.78  64.02   0.00  12.87  64.04   4.30  38.09
   2_xyz:  64.04   0.00  16.78  64.02   0.00  12.87  64.04   4.30  38.09
   2_adp:  75.64   0.37  17.22  68.91   0.37  12.90  75.64   5.21  40.76
   2_occ:  75.64   0.37  17.22  68.91   0.37  12.90  75.64   5.21  40.76
   3_bss:  75.64   0.37  17.22  68.91   0.37  12.90  75.64   5.21  40.76
   3_xyz:  75.64   0.37  17.22  68.91   0.37  12.90  75.64   5.21  40.76
   3_adp:  88.71   0.00  17.40  84.40   0.00  12.81  88.71   3.29  42.43
   3_occ:  88.71   0.00  17.40  84.40   0.00  12.81  88.71   3.29  42.43
   4_bss:  88.71   0.00  17.40  84.40   0.00  12.81  88.71   3.29  42.43
   4_xyz:  88.71   0.00  17.40  84.40   0.00  12.81  88.71   3.29  42.43
   4_adp:  85.15   0.96  16.37  78.99   2.26  12.38  85.15   0.96  38.14
   4_occ:  85.15   0.96  16.37  78.99   2.26  12.38  85.15   0.96  38.14
   5_bss:  85.15   0.96  16.37  78.99   2.26  12.38  85.15   0.96  38.14
   5_xyz:  85.15   0.96  16.37  78.99   2.26  12.38  85.15   0.96  38.14
   5_adp:  89.66   0.00  16.67  86.30   0.00  12.36  89.66   0.00  40.13
   5_occ:  89.66   0.00  16.67  86.30   0.00  12.36  89.66   0.00  40.13
   5_bss:  89.67   0.00  16.67  86.30   0.00  12.37  89.67   0.00  40.13
------------------------------------------------------------------------
 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:    1.739    0.015    0.376
   1_adp:    1.739    0.015    0.376
   1_occ:    1.739    0.015    0.376
   2_bss:    1.739    0.015    0.376
   2_xyz:    1.583    0.043    0.454
   2_adp:    1.583    0.043    0.454
   2_occ:    1.583    0.043    0.454
   3_bss:    1.583    0.043    0.454
   3_xyz:    1.458    0.057    0.497
   3_adp:    1.458    0.057    0.497
   3_occ:    1.458    0.057    0.497
   4_bss:    1.458    0.057    0.497
   4_xyz:    1.347    0.040    0.513
   4_adp:    1.347    0.040    0.513
   4_occ:    1.347    0.040    0.513
   5_bss:    1.347    0.040    0.513
   5_xyz:    1.384    0.050    0.520
   5_adp:    1.384    0.050    0.520
   5_occ:    1.384    0.050    0.520
   5_bss:    1.384    0.050    0.520
------------------------------------------------------------------------

CPU time actual refinement: 262.71


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_681/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_681/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_681/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_681/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_681/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 262.58 
  Macro-tasks:
    bulk solvent and scale       = 31.91  
    individual site refinement   = 105.67 
    weights calculation          = 24.01  
    collect and process          = 5.43   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 167.10 
  Micro-tasks:
    mask                            = 1.49   
    f_calc                          = 82.33  
    alpha_beta                      = 6.87   
    target                          = 1.01   
    gradients_wrt_atomic_parameters = 89.39  
    fmodel                         = 5.08   
    r_factors                      = 0.16   
    phase_errors                   = 9.07   
    foms                           = 0.26   
    TOTAL for micro-tasks          = 195.66 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 3.787 micro seconds
Total CPU time: 4.57 minutes
from_scatterers_fft:    624 calls, 82.06 s
gradients_fft:          569 calls, 78.42 s

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

# Date 2008-01-16 Time 05:23:22 PST -0800 (1200489802.48 s)
Start R-work = 0.3728, R-free = 0.3640 (no bulk solvent and anisotropic scale)
Final R-work = 0.1366, R-free = 0.1793 (no bulk solvent and anisotropic scale)

Start R-work = 0.3552, R-free = 0.3473
Final R-work = 0.1162, R-free = 0.1625