# Date 2008-01-16 Time 05:37:22 PST -0800 (1200490642.61 s)
#phil __OFF__

Command line arguments: "../813.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 23362
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 813

-------------------------------------------------------------------------------
  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: (70.6012, 47.3993, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.3993, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1485 2.01067
Completeness in resolution range: 0.963362
Completeness with d_max=infinity: 0.960339

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1485
                             d_min =   2.0107

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: (70.6012, 47.3993, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1485 2.01067
Completeness in resolution range: 0.963362
Completeness with d_max=infinity: 0.960339

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1489 -  4.3019 [2144/2168]  1926   218  10.2%
  bin  2:  4.3019 -  3.4275 [2045/2064]  1845   200   9.8%
  bin  3:  3.4275 -  2.9981 [2028/2047]  1824   204  10.1%
  bin  4:  2.9981 -  2.7257 [1999/2029]  1794   205  10.3%
  bin  5:  2.7257 -  2.5313 [2006/2025]  1809   197   9.8%
  bin  6:  2.5313 -  2.3827 [1979/2004]  1781   198  10.0%
  bin  7:  2.3827 -  2.2638 [1976/2004]  1781   195   9.9%
  bin  8:  2.2638 -  2.1655 [1976/2012]  1777   199  10.1%
  bin  9:  2.1655 -  2.0824 [1942/1984]  1748   194  10.0%
  bin 10:  2.0824 -  2.0107 [1494/1997]  1345   149  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_813/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.54 -     2.21: 8
        2.21 -     2.88: 1241
        2.88 -     3.55: 4337
        3.55 -     4.23: 9023
        4.23 -     4.90: 13135
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.536 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.713 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.713 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.845 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27739 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_813/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_813/model_refine_001.geo

CPU time processing inputs: 9.24


============================ 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 = 70.60125 47.3993 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: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4097   r_free= 0.4049   ksol= 0.00   Bsol= 0.00   scale= 0.910    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.211398                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7979 0.99   1394  153 0.3275 0.3204      6.4616       6.371|
|  2:  4.7979 -  3.8285 0.99   1326  152 0.3310 0.3540      6.6858      6.7723|
|  3:  3.8285 -  3.3505 0.99   1309  145 0.3746 0.3344      6.5868      6.5252|
|  4:  3.3505 -  3.0469 0.99   1302  139 0.3948 0.4042      6.4481      6.4118|
|  5:  3.0469 -  2.8300 0.99   1291  144 0.4257 0.3697      6.2974      6.2577|
|  6:  2.8300 -  2.6641 0.99   1293  149 0.4261 0.4762      6.2004      6.1687|
|  7:  2.6641 -  2.5313 0.99   1283  142 0.4335 0.4265      6.1708      6.1149|
|  8:  2.5313 -  2.4216 0.98   1280  137 0.4626 0.4301      6.1446       6.119|
|  9:  2.4216 -  2.3287 0.98   1260  145 0.4477 0.4480      6.0526      6.0781|
| 10:  2.3287 -  2.2486 0.99   1281  142 0.4789 0.4576      6.0877      6.0631|
| 11:  2.2486 -  2.1785 0.98   1259  136 0.4781 0.4877      6.0003        6.03|
| 12:  2.1785 -  2.1164 0.97   1247  139 0.4738 0.4731      5.9426      6.0392|
| 13:  2.1164 -  2.0608 1.00   1267  139 0.4764 0.4896      5.8659      5.8046|
| 14:  2.0608 -  2.0107 0.65    838   97 0.4484 0.4573       5.806      5.7369|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1489 -  4.7979  1394   153  0.77  28.19   0.84     0.79      50018.15|
|  2:  4.7979 -  3.8285  1326   152  0.79  27.60   0.93     0.85      72010.63|
|  3:  3.8285 -  3.3505  1309   145  0.71  34.38   0.92     0.85      74544.66|
|  4:  3.3505 -  3.0469  1302   139  0.65  40.01   0.92     0.78      67563.36|
|  5:  3.0469 -  2.8300  1291   144  0.58  45.54   0.94     0.72      54604.38|
|  6:  2.8300 -  2.6641  1293   149  0.54  49.10   0.91     0.68      52140.74|
|  7:  2.6641 -  2.5313  1283   142  0.53  49.73   0.94     0.68      47648.47|
|  8:  2.5313 -  2.4216  1280   137  0.53  50.02   0.91     0.70      43675.92|
|  9:  2.4216 -  2.3287  1260   145  0.53  49.97   0.94     0.72      39613.75|
| 10:  2.3287 -  2.2486  1281   142  0.51  51.11   0.95     0.70      36979.83|
| 11:  2.2486 -  2.1785  1259   136  0.47  54.44   0.93     0.67      37644.49|
| 12:  2.1785 -  2.1164  1247   139  0.46  55.64   0.94     0.65      35372.58|
| 13:  2.1164 -  2.0608  1267   139  0.45  56.58   0.92     0.64      31236.22|
| 14:  2.0608 -  2.0107   838    97  0.49  53.35   0.97     0.64      24246.44|
|alpha:            min =        0.64 max =            0.85 mean =         0.72|
|beta:             min =    24246.44 max =        74544.66 mean =     48462.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.57|
|phase err.(work): min =        0.00 max =           90.00 mean =        45.71|
|phase err.(test): min =        0.00 max =           89.94 mean =        45.85|
|-----------------------------------------------------------------------------|

============================== 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 = 5.677682              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.410   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.334498              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.586   (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 |  1.536 -  1.872:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.872 -  2.209:        3 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.209 -  2.545:       19 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.545 -  2.881:     1222 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.881 -  3.218:     1872 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.218 -  3.554:     2465 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.554 -  3.891:     4566 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.891 -  4.227:     4457 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.227 -  4.564:     5985 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.564 -  4.900:     7150 |
|-----------------------------------------------------------------------------|
|-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 |        0.168 |
| 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  1.536 |       0.222 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.329)------------------------------------------|
|    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: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4097   r_free= 0.4049   ksol= 0.00   Bsol= 0.00   scale= 0.910    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.211398                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3969   r_free= 0.3938   ksol= 0.31   Bsol= 59.89   scale= 0.947   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.30,-0.43,5.35,-0.00,0.00,0.00); trace/3= 0.54                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.195314                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.926650              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.118   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.747316              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.267   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3969      final r-factor (work) = 0.2899          |
| start r-factor (free) = 0.3938      final r-factor (free) = 0.3113          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.4264 = 4.93 * 0.50 * 6.1942 + 1.00 * 0.1681                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.9309 = 4.93 * 0.50 * 6.0203 + 1.00 * 0.1010                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2899      final r-factor (work) = 0.2630          |
| start r-factor (free) = 0.3113      final r-factor (free) = 0.3197          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5051 = 0.75 * 1.00 * 6.0203 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4035 = 0.75 * 1.00 * 5.8725 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.329)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.75   17.98    None  None   None       |
|    all(noH): 2823   0      0.00    95.75   17.98    None  None   None       |
|    Sol.    : 438    0      1.24    95.75   40.35    None  None   None       |
|    Mac.    : 2385   0      0.00    81.52   13.87    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 -   9.575:  956   |   5:    47.875 -  57.450:   77        |
|      1:     9.575 -  19.150:  986   |   6:    57.450 -  67.025:   48        |
|      2:    19.150 -  28.725:  382   |   7:    67.025 -  76.600:   33        |
|      3:    28.725 -  38.300:  197   |   8:    76.600 -  86.175:   10        |
|      4:    38.300 -  47.875:  131   |   9:    86.175 -  95.750:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2630 r_free = 0.3197             target_work(ml) = 5.878         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2628 r_free = 0.3199             target_work(ml) = 5.878         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2628   r_free= 0.3199   ksol= 0.31   Bsol= 59.89   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.30,-0.43,5.35,-0.00,0.00,0.00); trace/3= 0.54                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.878088                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2614   r_free= 0.3185   ksol= 0.33   Bsol= 75.72   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-0.63,2.32,-0.00,0.00,0.00); trace/3= -0.16                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.876794                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.191571              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.091   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.303856              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.909  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2614      final r-factor (work) = 0.1839          |
| start r-factor (free) = 0.3185      final r-factor (free) = 0.2369          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.3425 = 5.19 * 0.50 * 5.8717 + 1.00 * 0.1010                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.9772 = 5.19 * 0.50 * 5.7404 + 1.00 * 0.0763                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1839      final r-factor (work) = 0.1666          |
| start r-factor (free) = 0.2369      final r-factor (free) = 0.2131          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7591 = 0.30 * 1.00 * 5.7404 + 1.00 * 0.0149                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6876 = 0.30 * 1.00 * 5.5210 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.329)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.09    96.28   17.06    None  None   None       |
|    all(noH): 2823   0      1.09    96.28   17.06    None  None   None       |
|    Sol.    : 438    0      4.28    96.28   40.70    None  None   None       |
|    Mac.    : 2385   0      1.09    78.43   12.72    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.092 -  10.611: 1229   |   5:    48.688 -  58.207:  102        |
|      1:    10.611 -  20.130:  930   |   6:    58.207 -  67.726:   46        |
|      2:    20.130 -  29.649:  241   |   7:    67.726 -  77.245:   20        |
|      3:    29.649 -  39.168:  130   |   8:    77.245 -  86.764:    6        |
|      4:    39.168 -  48.688:  117   |   9:    86.764 -  96.284:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1666 r_free = 0.2131             target_work(ml) = 5.475         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1663 r_free = 0.2131             target_work(ml) = 5.474         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1663   r_free= 0.2131   ksol= 0.33   Bsol= 75.72   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-0.63,2.32,-0.00,0.00,0.00); trace/3= -0.16                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.474309                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1664   r_free= 0.2114   ksol= 0.34   Bsol= 79.61   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-1.16,0.88,-0.00,0.00,0.00); trace/3= -0.77                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.471120                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.173104              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.791  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.387994              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.837  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1664      final r-factor (work) = 0.1321          |
| start r-factor (free) = 0.2114      final r-factor (free) = 0.1757          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6000 = 4.17 * 0.50 * 5.5227 + 1.00 * 0.0766                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2884 = 4.17 * 0.50 * 5.3725 + 1.00 * 0.0784                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1321      final r-factor (work) = 0.1255          |
| start r-factor (free) = 0.1757      final r-factor (free) = 0.1717          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0945 = 0.39 * 1.00 * 5.3725 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0481 = 0.39 * 1.00 * 5.2521 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.329)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.53    95.53   16.75    None  None   None       |
|    all(noH): 2823   0      0.53    95.53   16.75    None  None   None       |
|    Sol.    : 438    0      3.34    95.53   40.98    None  None   None       |
|    Mac.    : 2385   0      0.53    78.71   12.31    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:     0.533 -  10.033: 1177   |   5:    48.032 -  57.532:  113        |
|      1:    10.033 -  19.533:  999   |   6:    57.532 -  67.032:   53        |
|      2:    19.533 -  29.032:  214   |   7:    67.032 -  76.532:   22        |
|      3:    29.032 -  38.532:  130   |   8:    76.532 -  86.032:    7        |
|      4:    38.532 -  48.032:  105   |   9:    86.032 -  95.532:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1255 r_free = 0.1717             target_work(ml) = 5.240         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1253 r_free = 0.1717             target_work(ml) = 5.239         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1253   r_free= 0.1717   ksol= 0.34   Bsol= 79.61   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-1.16,0.88,-0.00,0.00,0.00); trace/3= -0.77                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.239137                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1254   r_free= 0.1713   ksol= 0.33   Bsol= 74.53   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.95,-1.31,0.39,-0.00,0.00,0.00); trace/3= -0.96                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.237532                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.982855              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.405  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.462987              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.320  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1254      final r-factor (work) = 0.1223          |
| start r-factor (free) = 0.1713      final r-factor (free) = 0.1667          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2853 = 1.98 * 0.50 * 5.2520 + 1.00 * 0.0784                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2451 = 1.98 * 0.50 * 5.2275 + 1.00 * 0.0625                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1223      final r-factor (work) = 0.1209          |
| start r-factor (free) = 0.1667      final r-factor (free) = 0.1684          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 23.3404 = 4.46 * 1.00 * 5.2275 + 1.00 * 0.0102                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 23.2530 = 4.46 * 1.00 * 5.2074 + 1.00 * 0.0126                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.329)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.48  16.92    None  None   None       |
|    all(noH): 2823   0      0.00    104.48  16.92    None  None   None       |
|    Sol.    : 438    0      0.00    104.48  42.40    None  None   None       |
|    Mac.    : 2385   0      0.00    85.25   12.24    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.448: 1293   |   5:    52.238 -  62.686:   99        |
|      1:    10.448 -  20.895:  921   |   6:    62.686 -  73.134:   45        |
|      2:    20.895 -  31.343:  203   |   7:    73.134 -  83.581:   23        |
|      3:    31.343 -  41.791:  134   |   8:    83.581 -  94.029:    7        |
|      4:    41.791 -  52.238:   97   |   9:    94.029 - 104.477:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1209 r_free = 0.1684             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1208 r_free = 0.1682             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1682   ksol= 0.33   Bsol= 74.53   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.95,-1.31,0.39,-0.00,0.00,0.00); trace/3= -0.96                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.211295                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1680   ksol= 0.33   Bsol= 74.53   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.62,-1.07,0.51,-0.00,0.00,0.00); trace/3= -0.73                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.211216                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.733874              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.363  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 8.418009              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.533   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1206      final r-factor (work) = 0.1158          |
| start r-factor (free) = 0.1680      final r-factor (free) = 0.1667          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1810 = 2.73 * 0.50 * 5.2076 + 1.00 * 0.0625                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1721 = 2.73 * 0.50 * 5.1930 + 1.00 * 0.0736                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1158      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1667      final r-factor (free) = 0.1661          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 43.7273 = 8.42 * 1.00 * 5.1930 + 1.00 * 0.0125                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 43.6555 = 8.42 * 1.00 * 5.1844 + 1.00 * 0.0130                              |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.329)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.73  16.68    None  None   None       |
|    all(noH): 2823   0      0.00    106.73  16.68    None  None   None       |
|    Sol.    : 438    0      0.72    106.73  42.27    None  None   None       |
|    Mac.    : 2385   0      0.00    87.60   11.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.673: 1393   |   5:    53.363 -  64.036:   94        |
|      1:    10.673 -  21.345:  842   |   6:    64.036 -  74.709:   44        |
|      2:    21.345 -  32.018:  197   |   7:    74.709 -  85.381:   17        |
|      3:    32.018 -  42.691:  129   |   8:    85.381 -  96.054:    8        |
|      4:    42.691 -  53.363:   98   |   9:    96.054 - 106.727:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1154 r_free = 0.1661             target_work(ml) = 5.184         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1154 r_free = 0.1661             target_work(ml) = 5.184         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1661   ksol= 0.33   Bsol= 74.53   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.62,-1.07,0.51,-0.00,0.00,0.00); trace/3= -0.73                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.183897                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7979 0.99   1394  153 0.0960 0.1281      5.3785      5.5302|
|  2:  4.7979 -  3.8285 0.99   1326  152 0.0822 0.1116      5.4186      5.6403|
|  3:  3.8285 -  3.3505 0.99   1309  145 0.1057 0.1520      5.4796      5.8557|
|  4:  3.3505 -  3.0469 0.99   1302  139 0.1231 0.1685       5.478      5.6463|
|  5:  3.0469 -  2.8300 0.99   1291  144 0.1409 0.1778      5.3822      5.5811|
|  6:  2.8300 -  2.6641 0.99   1293  149 0.1298 0.2155      5.2764      5.5861|
|  7:  2.6641 -  2.5313 0.99   1283  142 0.1334 0.1690      5.2195      5.3609|
|  8:  2.5313 -  2.4216 0.98   1280  137 0.1223 0.1761      5.1371      5.4154|
|  9:  2.4216 -  2.3287 0.98   1260  145 0.1225 0.1951      5.0789      5.3564|
| 10:  2.3287 -  2.2486 0.99   1281  142 0.1165 0.1774      5.0062      5.2418|
| 11:  2.2486 -  2.1785 0.98   1259  136 0.1216 0.1878      4.9977      5.2711|
| 12:  2.1785 -  2.1164 0.97   1247  139 0.1202 0.1888      4.9514      5.3313|
| 13:  2.1164 -  2.0608 1.00   1267  139 0.1175 0.1880      4.8473      5.0873|
| 14:  2.0608 -  2.0107 0.65    838   97 0.1043 0.1816      4.7031      4.9948|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1489 -  4.7979  1394   153  0.94   9.36   0.96     0.93       7542.08|
|  2:  4.7979 -  3.8285  1326   152  0.95   8.00   1.00     0.98       9098.84|
|  3:  3.8285 -  3.3505  1309   145  0.94  11.16   1.02     1.01      10454.59|
|  4:  3.3505 -  3.0469  1302   139  0.92  14.13   1.00     0.98      10915.72|
|  5:  3.0469 -  2.8300  1291   144  0.89  16.68   1.00     0.97       9224.17|
|  6:  2.8300 -  2.6641  1293   149  0.89  17.58   0.97     0.95       8248.44|
|  7:  2.6641 -  2.5313  1283   142  0.89  16.88   0.98     0.94       7066.69|
|  8:  2.5313 -  2.4216  1280   137  0.90  16.18   0.98     0.95       6144.20|
|  9:  2.4216 -  2.3287  1260   145  0.90  16.24   0.99     0.95       5612.02|
| 10:  2.3287 -  2.2486  1281   142  0.89  16.91   0.97     0.93       4904.58|
| 11:  2.2486 -  2.1785  1259   136  0.89  17.25   0.97     0.93       4967.54|
| 12:  2.1785 -  2.1164  1247   139  0.89  17.19   0.98     0.97       4684.26|
| 13:  2.1164 -  2.0608  1267   139  0.89  17.20   0.96     0.93       3848.63|
| 14:  2.0608 -  2.0107   838    97  0.91  14.88   0.93     0.89       2742.26|
|alpha:            min =        0.89 max =            1.01 mean =         0.95|
|beta:             min =     2742.26 max =        10915.72 mean =      6954.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.91|
|phase err.(test): min =        0.00 max =           88.72 mean =        14.30|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1659   ksol= 0.33   Bsol= 74.54   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.27,-0.78,0.75,-0.00,0.00,0.00); trace/3= -0.43                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.184065                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1659   ksol= 0.33   Bsol= 74.54   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.27,-0.78,0.75,-0.00,0.00,0.00); trace/3= -0.43                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.184065                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7979 0.99   1394  153 0.0960 0.1282      5.3793      5.5318|
|  2:  4.7979 -  3.8285 0.99   1326  152 0.0822 0.1116      5.4194      5.6403|
|  3:  3.8285 -  3.3505 0.99   1309  145 0.1057 0.1521      5.4798      5.8565|
|  4:  3.3505 -  3.0469 0.99   1302  139 0.1231 0.1685      5.4781      5.6465|
|  5:  3.0469 -  2.8300 0.99   1291  144 0.1409 0.1776       5.382      5.5808|
|  6:  2.8300 -  2.6641 0.99   1293  149 0.1298 0.2156      5.2763      5.5863|
|  7:  2.6641 -  2.5313 0.99   1283  142 0.1334 0.1690      5.2196       5.361|
|  8:  2.5313 -  2.4216 0.98   1280  137 0.1223 0.1761      5.1375      5.4154|
|  9:  2.4216 -  2.3287 0.98   1260  145 0.1224 0.1950      5.0789      5.3562|
| 10:  2.3287 -  2.2486 0.99   1281  142 0.1165 0.1773      5.0061      5.2417|
| 11:  2.2486 -  2.1785 0.98   1259  136 0.1216 0.1875      4.9975      5.2701|
| 12:  2.1785 -  2.1164 0.97   1247  139 0.1202 0.1885      4.9511      5.3301|
| 13:  2.1164 -  2.0608 1.00   1267  139 0.1175 0.1883      4.8473      5.0883|
| 14:  2.0608 -  2.0107 0.65    838   97 0.1044 0.1814      4.7038      4.9941|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1489 -  4.7979  1394   153  0.94   9.38   0.96     0.94       7563.16|
|  2:  4.7979 -  3.8285  1326   152  0.95   8.01   1.00     0.99       9115.06|
|  3:  3.8285 -  3.3505  1309   145  0.94  11.17   1.02     1.02      10463.01|
|  4:  3.3505 -  3.0469  1302   139  0.92  14.14   1.01     0.99      10917.90|
|  5:  3.0469 -  2.8300  1291   144  0.89  16.68   1.00     0.98       9225.03|
|  6:  2.8300 -  2.6641  1293   149  0.89  17.58   0.98     0.96       8246.43|
|  7:  2.6641 -  2.5313  1283   142  0.89  16.88   0.99     0.95       7068.61|
|  8:  2.5313 -  2.4216  1280   137  0.90  16.19   0.99     0.96       6145.61|
|  9:  2.4216 -  2.3287  1260   145  0.90  16.24   1.00     0.96       5615.14|
| 10:  2.3287 -  2.2486  1281   142  0.89  16.90   0.99     0.94       4900.17|
| 11:  2.2486 -  2.1785  1259   136  0.89  17.24   0.98     0.94       4962.55|
| 12:  2.1785 -  2.1164  1247   139  0.89  17.19   1.00     0.98       4680.72|
| 13:  2.1164 -  2.0608  1267   139  0.89  17.20   0.98     0.95       3848.90|
| 14:  2.0608 -  2.0107   838    97  0.91  14.88   0.95     0.91       2744.39|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     2744.39 max =        10917.90 mean =      6957.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.91|
|phase err.(test): min =        0.00 max =           88.72 mean =        14.31|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.329)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.73  16.69    None  None   None       |
|    all(noH): 2823   0      0.00    106.73  16.69    None  None   None       |
|    Sol.    : 438    0      0.73    106.73  42.27    None  None   None       |
|    Mac.    : 2385   0      0.00    87.61   11.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.676: 1393   |   5:    53.366 -  64.039:   94        |
|      1:    10.676 -  21.348:  842   |   6:    64.039 -  74.712:   44        |
|      2:    21.348 -  32.021:  197   |   7:    74.712 -  85.384:   17        |
|      3:    32.021 -  42.694:  129   |   8:    85.384 -  96.057:    8        |
|      4:    42.694 -  53.366:   98   |   9:    96.057 - 106.730:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 300         
Filter by distance & map next to the model:
   mapped sites are within: 0.637 - 4.948
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 297 from: 300
   mapped sites are within: 0.755 - 4.948

peak=    5.440 closest distance to " CB  GLN A 223 " =    1.485
peak=    5.031 closest distance to " CG  PRO A  54 " =    1.360
peak=    5.014 closest distance to " CB  ARG A 190 " =    1.575
peak=    5.009 closest distance to " O   HOH Z 113 " =    2.001
peak=    4.875 closest distance to " CZ  PHE A 218 " =    1.134
peak=    4.745 closest distance to " O   HOH Z 369 " =    2.151
peak=    4.691 closest distance to " NE2 GLN A  11 " =    1.062
peak=    4.615 closest distance to " CB  GLN A 183 " =    1.268
peak=    4.511 closest distance to " CB  SER A  63 " =    1.177
peak=    4.506 closest distance to " CG  PRO A 280 " =    0.845
peak=    4.467 closest distance to " CA  TYR A  30 " =    0.975
peak=    4.455 closest distance to " O   HOH Z 232 " =    2.340
peak=    4.434 closest distance to " CG  PRO A 213 " =    1.153
peak=    4.425 closest distance to " O   HOH Z  19 " =    2.298
peak=    4.422 closest distance to " O   HOH Z 188 " =    2.888
peak=    4.383 closest distance to " CB  ARG A 275 " =    0.988
peak=    4.366 closest distance to " CZ3 TRP A 266 " =    1.113
peak=    4.327 closest distance to " CB  GLU A 277 " =    3.826
peak=    4.319 closest distance to " CB  ARG A  79 " =    1.468
peak=    4.293 closest distance to " O   HOH Z 142 " =    1.645
peak=    4.230 closest distance to " CG  PRO A 198 " =    1.267
peak=    4.206 closest distance to " CD  ARG A 269 " =    0.943
peak=    4.191 closest distance to " CB  PRO A  54 " =    0.952
peak=    4.177 closest distance to " ND2 ASN A 187 " =    1.494
peak=    4.170 closest distance to " CE  LYS A  76 " =    0.874
peak=    4.160 closest distance to " CB  VAL A 202 " =    1.563
peak=    4.135 closest distance to " O   HOH Z 287 " =    1.917
peak=    4.129 closest distance to " O   HOH Z 427 " =    3.172
peak=    4.114 closest distance to " CB  ASN A 148 " =    1.497
peak=    4.109 closest distance to " CD2 TRP A 179 " =    1.304
peak=    4.095 closest distance to " O   HOH Z 234 " =    3.838
peak=    4.066 closest distance to " O   HOH Z 368 " =    2.223
peak=    4.065 closest distance to " O   HOH Z 298 " =    2.023
peak=    4.062 closest distance to " CD  ARG A 159 " =    0.811
peak=    4.059 closest distance to " CA  ALA A  51 " =    0.925
peak=    4.052 closest distance to " O   HOH Z 406 " =    1.656
peak=    4.051 closest distance to " C   PRO A 198 " =    1.553
peak=    4.010 closest distance to " CA  ARG A  36 " =    1.141
peak=    3.998 closest distance to " O   HOH Z 265 " =    2.168
peak=    3.996 closest distance to " CB  VAL A 265 " =    1.271
peak=    3.990 closest distance to " O   HOH Z  15 " =    2.230
peak=    3.970 closest distance to " CB  LEU A 228 " =    1.106
peak=    3.939 closest distance to " CB  TYR A 169 " =    0.807
peak=    3.938 closest distance to " O   HOH Z 412 " =    3.826
peak=    3.932 closest distance to " CA  ALA A 160 " =    0.977
peak=    3.920 closest distance to " CA  ARG A 195 " =    1.263
peak=    3.912 closest distance to " O   SER A  87 " =    2.284
peak=    3.908 closest distance to " CB  ASP A 124 " =    0.762
peak=    3.902 closest distance to " CB  GLU A 128 " =    1.043
peak=    3.888 closest distance to " CD1 LEU A  96 " =    0.777
peak=    3.886 closest distance to " O  BHOH Z 338 " =    2.229
peak=    3.873 closest distance to " O   HOH Z 214 " =    2.474
peak=    3.873 closest distance to " OE1 GLN A  55 " =    1.523
peak=    3.866 closest distance to " CG  PRO A 243 " =    1.086
peak=    3.866 closest distance to " NZ  LYS A 117 " =    3.055
peak=    3.849 closest distance to " NH1AARG A 145 " =    1.353
peak=    3.842 closest distance to " O   HOH Z 359 " =    1.705
peak=    3.841 closest distance to " CG  MET A 185 " =    1.242
peak=    3.840 closest distance to " CB  ASP A 140 " =    1.162
peak=    3.839 closest distance to " O   HOH Z 126 " =    1.906
peak=    3.838 closest distance to " O   HOH Z 133 " =    2.869
peak=    3.836 closest distance to " CD  ARG A  66 " =    2.465
peak=    3.816 closest distance to " CA  ALA A 154 " =    1.024
peak=    3.812 closest distance to " N   HIS A 108 " =    1.912
peak=    3.808 closest distance to " O   HOH Z 158 " =    3.034
peak=    3.806 closest distance to " CB  PRO A  90 " =    1.214
peak=    3.804 closest distance to " CB  ASN A  39 " =    0.905
peak=    3.801 closest distance to " CB  TRP A 266 " =    1.084
peak=    3.800 closest distance to " O   HOH Z 346 " =    1.605
peak=    3.792 closest distance to " O   HOH Z  78 " =    1.588
peak=    3.792 closest distance to " O   HOH Z 303 " =    2.218
peak=    3.792 closest distance to " CB  GLU A 152 " =    1.232
peak=    3.787 closest distance to " CG  ARG A 138 " =    1.302
peak=    3.778 closest distance to " ND2 ASN A 249 " =    0.834
peak=    3.776 closest distance to " O   HOH Z 361 " =    3.722
peak=    3.773 closest distance to " O   HOH Z  63 " =    1.946
peak=    3.772 closest distance to " O   HOH Z 126 " =    1.636
peak=    3.766 closest distance to " O   HOH Z 261 " =    2.051
peak=    3.760 closest distance to " CA  MET A 105 " =    1.077
peak=    3.752 closest distance to " CA  VAL A 125 " =    1.195
peak=    3.745 closest distance to " O   HOH Z 392 " =    2.643
peak=    3.743 closest distance to " O   HOH Z 180 " =    2.172
peak=    3.739 closest distance to " O   HOH Z 248 " =    1.532
peak=    3.737 closest distance to " O   HOH Z 172 " =    3.864
peak=    3.727 closest distance to " CB  LEU A  83 " =    0.819
peak=    3.715 closest distance to " O   HOH Z  49 " =    0.938
peak=    3.707 closest distance to " O   HOH Z   1 " =    2.274
peak=    3.701 closest distance to " O   HOH Z  43 " =    2.038
peak=    3.701 closest distance to " O   HOH Z 353 " =    2.684
peak=    3.699 closest distance to " O   HOH Z 280 " =    2.921
peak=    3.698 closest distance to " O   ASN A  74 " =    1.505
peak=    3.691 closest distance to " CD  LYS A 166 " =    1.337
peak=    3.686 closest distance to " CZ  PHE A  38 " =    1.217
peak=    3.677 closest distance to " O   HOH Z  80 " =    1.787
peak=    3.676 closest distance to " CG  GLU A  37 " =    1.004
peak=    3.674 closest distance to " CA  ALA A 295 " =    1.125
peak=    3.672 closest distance to " O   THR A 182 " =    1.422
peak=    3.672 closest distance to " OG BSER A 134 " =    2.841
peak=    3.670 closest distance to " CG2 VAL A 257 " =    0.755
peak=    3.665 closest distance to " NE2 GLN A  77 " =    3.384
peak=    3.661 closest distance to " O   HOH Z 203 " =    1.710
peak=    3.659 closest distance to " O   HOH Z 313 " =    1.831
peak=    3.623 closest distance to " CG  LEU A 167 " =    1.232
peak=    3.616 closest distance to " CA  TYR A  30 " =    1.064
peak=    3.615 closest distance to " CD1 LEU A 300 " =    1.109
peak=    3.604 closest distance to " CB  THR A  31 " =    1.613
peak=    3.596 closest distance to " O   HOH Z  40 " =    1.843
peak=    3.595 closest distance to " O   HOH Z 423 " =    1.908
peak=    3.592 closest distance to " O   HOH Z 299 " =    4.398
peak=    3.591 closest distance to " NH2AARG A 275 " =    3.497
peak=    3.583 closest distance to " CB  ASN A 142 " =    1.091
peak=    3.582 closest distance to " O   ASP A 124 " =    1.200
peak=    3.581 closest distance to " O   HOH Z 271 " =    2.492
peak=    3.575 closest distance to " O   HOH Z 316 " =    3.132
peak=    3.566 closest distance to " O   HOH Z 199 " =    1.590
peak=    3.563 closest distance to " OD1 ASN A  69 " =    2.530
peak=    3.561 closest distance to " O   HOH Z  21 " =    1.846
peak=    3.551 closest distance to " O   ASN A  74 " =    2.100
peak=    3.551 closest distance to " CB  ASN A 215 " =    1.192
peak=    3.544 closest distance to " O   HOH Z 290 " =    1.018
peak=    3.542 closest distance to " CB  SER A 141 " =    1.095
peak=    3.539 closest distance to " N   ASN A  39 " =    1.321
peak=    3.535 closest distance to " CB  ASN A 148 " =    2.006
peak=    3.534 closest distance to " O   HOH Z 148 " =    3.492
peak=    3.527 closest distance to " CG2 ILE A 120 " =    1.098
peak=    3.525 closest distance to " CD2 LEU A 255 " =    1.745
peak=    3.522 closest distance to " NZ  LYS A  48 " =    1.284
peak=    3.520 closest distance to " O   HOH Z 383 " =    2.218
peak=    3.517 closest distance to " O   HOH Z 183 " =    1.533
peak=    3.508 closest distance to " CG  PHE A 204 " =    0.815
peak=    3.496 closest distance to " OG  SER A 245 " =    1.730
peak=    3.496 closest distance to " O   HOH Z  59 " =    2.316
peak=    3.495 closest distance to " CB  LYS A 117 " =    1.177
peak=    3.490 closest distance to " O   HOH Z 193 " =    1.868
peak=    3.484 closest distance to " OG BSER A 164 " =    2.363
peak=    3.484 closest distance to " CA  ASN A 215 " =    1.100
peak=    3.473 closest distance to " CG  GLN A  11 " =    1.648
peak=    3.470 closest distance to " O   HOH Z 325 " =    2.353
peak=    3.469 closest distance to " O   HOH Z 425 " =    1.307
peak=    3.469 closest distance to " CA  ALA A 100 " =    0.960
peak=    3.466 closest distance to " ND2 ASN A 249 " =    1.934
peak=    3.463 closest distance to " CG2AVAL A 121 " =    2.321
peak=    3.462 closest distance to " CB  ASP A 298 " =    1.183
peak=    3.459 closest distance to " OG  SER A  22 " =    2.739
peak=    3.458 closest distance to " O   HOH Z 285 " =    2.260
peak=    3.458 closest distance to " CG2 THR A 221 " =    1.088
peak=    3.457 closest distance to " CA  ALA A 158 " =    1.283
peak=    3.453 closest distance to " CA  ASP A 140 " =    1.642
peak=    3.452 closest distance to " OH  TYR A 116 " =    1.104
peak=    3.445 closest distance to " CE1 PHE A 218 " =    1.230
peak=    3.443 closest distance to " O   THR A 220 " =    1.158
peak=    3.437 closest distance to " CB  GLN A  89 " =    1.324
peak=    3.436 closest distance to " CA  GLN A  94 " =    0.769
peak=    3.434 closest distance to " O   HOH Z 192 " =    1.823
peak=    3.431 closest distance to " O   TYR A 116 " =    1.333
peak=    3.429 closest distance to " O   THR A 251 " =    1.061
peak=    3.427 closest distance to " O   HOH Z 250 " =    1.335
peak=    3.423 closest distance to " CB  GLU A  46 " =    0.968
peak=    3.416 closest distance to " O   HOH Z 251 " =    1.657
peak=    3.414 closest distance to " O   HOH Z 305 " =    3.679
peak=    3.410 closest distance to " O   HOH Z  90 " =    2.289
peak=    3.410 closest distance to " CB  SER A  62 " =    0.772
peak=    3.408 closest distance to " O   HOH Z 361 " =    3.780
peak=    3.407 closest distance to " CA  ALA A 233 " =    1.605
peak=    3.405 closest distance to " NE  ARG A  79 " =    1.016
peak=    3.403 closest distance to " O   HOH Z 294 " =    1.523
peak=    3.403 closest distance to " CA  ASN A 127 " =    1.197
peak=    3.400 closest distance to " OE1 GLN A  11 " =    2.061
peak=    3.388 closest distance to " CD2 LEU A 297 " =    0.929
peak=    3.388 closest distance to " OE2 GLU A  53 " =    1.968
peak=    3.378 closest distance to " O   HOH Z  97 " =    1.942
peak=    3.378 closest distance to " O   HOH Z 285 " =    2.125
peak=    3.376 closest distance to " CB  ALA A 104 " =    0.756
peak=    3.373 closest distance to " O   HOH Z 393 " =    3.092
peak=    3.372 closest distance to " CB  LEU A  96 " =    1.348
peak=    3.371 closest distance to " CB  ARG A 138 " =    1.014
peak=    3.370 closest distance to " O   HOH Z 417 " =    3.156
peak=    3.365 closest distance to " CB  GLU A  37 " =    0.822
peak=    3.363 closest distance to " O   HOH Z 402 " =    1.378
peak=    3.363 closest distance to " O   HOH Z 371 " =    3.098
peak=    3.360 closest distance to " CA  GLY A 241 " =    0.912
peak=    3.359 closest distance to " CA  GLU A  46 " =    0.848
peak=    3.354 closest distance to " O   HOH Z 130 " =    2.959
peak=    3.353 closest distance to " CG2 ILE A 234 " =    0.894
peak=    3.352 closest distance to " O   ALA A 158 " =    1.168
peak=    3.352 closest distance to " CD  GLU A 152 " =    0.814
peak=    3.346 closest distance to " O   ALA A 165 " =    1.443
peak=    3.344 closest distance to " CG AARG A 275 " =    1.182
peak=    3.343 closest distance to " O   HOH Z  48 " =    1.646
peak=    3.342 closest distance to " O   HOH Z 391 " =    2.981
peak=    3.335 closest distance to " O   HOH Z 214 " =    1.546
peak=    3.334 closest distance to " O   HOH Z 174 " =    2.556
peak=    3.334 closest distance to " CA  ASP A 162 " =    1.012
peak=    3.331 closest distance to " CB  GLN A  88 " =    1.248
peak=    3.325 closest distance to " O   HOH Z 422 " =    2.639
peak=    3.325 closest distance to " CB  TYR A 116 " =    0.825
peak=    3.322 closest distance to " CB  ALA A  43 " =    0.810
peak=    3.316 closest distance to " CA  GLU A 152 " =    0.876
peak=    3.315 closest distance to " O   HOH Z 380 " =    2.046
peak=    3.311 closest distance to " CA  TYR A 116 " =    1.343
peak=    3.306 closest distance to " CG1 ILE A  49 " =    1.553
peak=    3.304 closest distance to " O   HOH Z 272 " =    1.834
peak=    3.303 closest distance to " O   HOH Z 213 " =    1.957
peak=    3.303 closest distance to " O   ASP A 191 " =    1.496
peak=    3.296 closest distance to " CG2AVAL A  72 " =    1.938
peak=    3.287 closest distance to " CA  THR A 221 " =    1.093
peak=    3.284 closest distance to " O   HOH Z  44 " =    2.268
peak=    3.278 closest distance to " O   HOH Z  62 " =    2.211
peak=    3.277 closest distance to " O   HOH Z 106 " =    4.137
peak=    3.276 closest distance to " O   HOH Z 357 " =    2.147
peak=    3.275 closest distance to " CA  SER A  87 " =    1.096
peak=    3.274 closest distance to " CE1 TYR A 186 " =    1.326
peak=    3.271 closest distance to " O   HOH Z 185 " =    1.866
peak=    3.270 closest distance to " CB  SER A  22 " =    0.986
peak=    3.268 closest distance to " NE2 HIS A 207 " =    1.123
peak=    3.264 closest distance to " CH2 TRP A  70 " =    0.890
peak=    3.261 closest distance to " CB  ASN A 110 " =    1.159
peak=    3.259 closest distance to " CD1 ILE A 199 " =    1.123
peak=    3.259 closest distance to " O   HOH Z  88 " =    1.856
peak=    3.257 closest distance to " CB  ALA A 299 " =    0.897
peak=    3.255 closest distance to " CB  TRP A 179 " =    1.415
peak=    3.254 closest distance to " O   HOH Z 258 " =    1.977
peak=    3.252 closest distance to " OD1 ASN A 217 " =    1.611
peak=    3.252 closest distance to " N   CYS A 260 " =    0.815
peak=    3.250 closest distance to " CB  ALA A 291 " =    1.058
peak=    3.248 closest distance to " CA  ILE A 106 " =    0.865
peak=    3.247 closest distance to " O   HOH Z  44 " =    2.728
peak=    3.242 closest distance to " O   HOH Z 279 " =    2.265
peak=    3.240 closest distance to " O   HOH Z 298 " =    2.515
peak=    3.239 closest distance to " CB  ALA A   1 " =    4.948
peak=    3.234 closest distance to " NH2 ARG A 156 " =    1.153
peak=    3.232 closest distance to " N   ASN A 127 " =    1.315
peak=    3.231 closest distance to " O   HOH Z  10 " =    1.758
peak=    3.230 closest distance to " O   HOH Z 147 " =    1.836
peak=    3.227 closest distance to " CD BLYS A 290 " =    0.967
peak=    3.224 closest distance to " OD2 ASP A  50 " =    2.990
peak=    3.224 closest distance to " CB  PHE A 204 " =    0.874
peak=    3.223 closest distance to " CA  ASN A 252 " =    1.989
peak=    3.222 closest distance to " CB  PRO A 243 " =    1.751
peak=    3.220 closest distance to " O   PRO A 213 " =    1.521
peak=    3.207 closest distance to " CG2 VAL A 197 " =    1.114
peak=    3.205 closest distance to " CE1 HIS A  81 " =    1.698
peak=    3.204 closest distance to " O   HOH Z 116 " =    3.297
peak=    3.203 closest distance to " CB  ALA A   9 " =    1.657
peak=    3.200 closest distance to " CG1 ILE A  33 " =    1.196
peak=    3.196 closest distance to " O   HOH Z 248 " =    1.737
peak=    3.196 closest distance to " CD1 ILE A  33 " =    1.790
peak=    3.195 closest distance to " O   HOH Z 120 " =    3.380
peak=    3.192 closest distance to " N   VAL A 265 " =    1.319
peak=    3.190 closest distance to " O   HOH Z 128 " =    2.142
peak=    3.189 closest distance to " CD  ARG A  66 " =    2.310
peak=    3.189 closest distance to " CB  ALA A 248 " =    1.392
peak=    3.188 closest distance to " NH2BARG A 145 " =    2.276
peak=    3.184 closest distance to " CD2 LEU A  83 " =    1.442
peak=    3.183 closest distance to " CD  ARG A 195 " =    3.424
peak=    3.182 closest distance to " CB  ASN A 187 " =    1.291
peak=    3.181 closest distance to " O   HOH Z 394 " =    3.982
peak=    3.179 closest distance to " O   HOH Z 313 " =    1.412
peak=    3.175 closest distance to " CA  ARG A 139 " =    1.109
peak=    3.175 closest distance to " CB  ASN A 285 " =    0.978
peak=    3.170 closest distance to " CA  ARG A 156 " =    1.139
peak=    3.163 closest distance to " CG1 ILE A  20 " =    1.316
peak=    3.160 closest distance to " CB  ALA A 248 " =    0.981
peak=    3.156 closest distance to " CA  ARG A 102 " =    1.100
peak=    3.156 closest distance to " CG  MET A 185 " =    1.031
peak=    3.155 closest distance to " CA  THR A 264 " =    0.968
peak=    3.153 closest distance to " CB  SER A   3 " =    1.488
peak=    3.152 closest distance to " O   HOH Z 425 " =    1.992
peak=    3.151 closest distance to " CB  THR A  52 " =    0.757
peak=    3.150 closest distance to " O   HOH Z 419 " =    1.955
peak=    3.144 closest distance to " O   HOH Z 258 " =    1.582
peak=    3.143 closest distance to " O   HOH Z 171 " =    4.012
peak=    3.143 closest distance to " O   HOH Z 365 " =    2.834
peak=    3.141 closest distance to " N   TYR A 116 " =    1.630
peak=    3.138 closest distance to " CE3 TRP A 150 " =    1.112
peak=    3.136 closest distance to " OE2 GLU A  53 " =    1.510
peak=    3.132 closest distance to " NE2 GLN A  58 " =    4.396
peak=    3.123 closest distance to " O   HOH Z  88 " =    3.763
peak=    3.123 closest distance to " CG BARG A 275 " =    1.448
peak=    3.122 closest distance to " CB  MET A  47 " =    0.943
peak=    3.121 closest distance to " O   HOH Z 128 " =    2.351
peak=    3.115 closest distance to " OG BSER A 134 " =    3.116
peak=    3.113 closest distance to " O   HOH Z  88 " =    2.679
peak=    3.113 closest distance to " CB  ASN A 173 " =    1.223
peak=    3.110 closest distance to " CG2 THR A  29 " =    1.362
peak=    3.109 closest distance to " CA  ASP A 191 " =    1.269
peak=    3.099 closest distance to " CD  PRO A  54 " =    1.079
peak=    3.092 closest distance to " OG BSER A  99 " =    2.283
peak=    3.085 closest distance to " CB  ALA A 227 " =    1.109
peak=    3.084 closest distance to " CA  GLY A 211 " =    1.361
peak=    3.082 closest distance to " O   HOH Z 193 " =    2.139
peak=    3.073 closest distance to " CE1 HIS A 115 " =    0.976
peak=    3.071 closest distance to " CD  LYS A 193 " =    2.107
peak=    3.054 closest distance to " CG2 ILE A  20 " =    1.346
peak=    3.052 closest distance to " OG  SER A  62 " =    2.962
peak=    3.049 closest distance to " O   HOH Z  40 " =    1.557
peak=    3.030 closest distance to " N   PHE A 130 " =    1.267

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.877 - 5.924
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 205
   mapped sites are within: 0.877 - 5.924

peak=   -4.666 closest distance to " CD  ARG A  14 " =    3.421
peak=   -4.499 closest distance to " CB  PRO A 243 " =    2.705
peak=   -4.490 closest distance to " CD  GLN A  58 " =    0.971
peak=   -4.419 closest distance to " CG1 VAL A 250 " =    2.701
peak=   -4.379 closest distance to " CD  ARG A 156 " =    2.147
peak=   -4.379 closest distance to " O   HOH Z 267 " =    5.658
peak=   -4.325 closest distance to " O   HOH Z 196 " =    2.187
peak=   -4.292 closest distance to " O   HOH Z  10 " =    1.550
peak=   -4.277 closest distance to " CD2 TYR A 293 " =    1.964
peak=   -4.268 closest distance to " O   HOH Z  73 " =    2.525
peak=   -4.259 closest distance to " N   ALA A  43 " =    2.658
peak=   -4.242 closest distance to " C   HIS A 108 " =    1.108
peak=   -4.195 closest distance to " CE2 PHE A  61 " =    2.666
peak=   -4.166 closest distance to " CG1 VAL A 112 " =    2.609
peak=   -4.153 closest distance to " CA  ASP A 298 " =    1.062
peak=   -4.144 closest distance to " O   HOH Z 377 " =    2.075
peak=   -4.119 closest distance to " O   PRO A 198 " =    1.328
peak=   -4.104 closest distance to " O   VAL A  67 " =    2.754
peak=   -4.096 closest distance to " CG1 VAL A  67 " =    3.039
peak=   -4.059 closest distance to " O   HOH Z 231 " =    2.403
peak=   -4.028 closest distance to " CZ3 TRP A 179 " =    1.193
peak=   -4.014 closest distance to " O   HOH Z 211 " =    1.235
peak=   -3.983 closest distance to " OG BSER A 134 " =    1.352
peak=   -3.959 closest distance to " OD1 ASN A 148 " =    1.430
peak=   -3.903 closest distance to " OE1 GLN A 223 " =    2.169
peak=   -3.870 closest distance to " O   HOH Z 198 " =    1.970
peak=   -3.845 closest distance to " O   HOH Z 394 " =    1.545
peak=   -3.812 closest distance to " CE3 TRP A 150 " =    2.247
peak=   -3.809 closest distance to " OG  SER A  97 " =    2.302
peak=   -3.805 closest distance to " CD1 LEU A 101 " =    2.427
peak=   -3.804 closest distance to " O   HOH Z 166 " =    1.780
peak=   -3.793 closest distance to " O   HOH Z 128 " =    2.677
peak=   -3.781 closest distance to " O   HOH Z 438 " =    3.088
peak=   -3.778 closest distance to " CG  GLN A  11 " =    1.700
peak=   -3.777 closest distance to " CE2 TYR A  30 " =    2.676
peak=   -3.770 closest distance to " O   HOH Z 193 " =    1.429
peak=   -3.768 closest distance to " CG  ARG A 269 " =    2.396
peak=   -3.759 closest distance to " CD  GLN A 223 " =    1.357
peak=   -3.754 closest distance to " CA  GLY A 241 " =    3.366
peak=   -3.733 closest distance to " CE BMET A  47 " =    1.904
peak=   -3.732 closest distance to " CB  ALA A 161 " =    2.611
peak=   -3.730 closest distance to " O   HOH Z   6 " =    2.245
peak=   -3.719 closest distance to " NE2 GLN A 194 " =    2.026
peak=   -3.719 closest distance to " CG2 ILE A  49 " =    2.842
peak=   -3.715 closest distance to " O   HOH Z 185 " =    2.323
peak=   -3.678 closest distance to " CA  GLY A 241 " =    2.378
peak=   -3.673 closest distance to " O   HOH Z 348 " =    2.216
peak=   -3.650 closest distance to " CD1 ILE A 151 " =    2.475
peak=   -3.646 closest distance to " O   HOH Z  38 " =    1.521
peak=   -3.623 closest distance to " CB  ALA A 291 " =    2.490
peak=   -3.619 closest distance to " CB  ALA A  43 " =    2.683
peak=   -3.615 closest distance to " O   HOH Z 216 " =    0.943
peak=   -3.614 closest distance to " CB  HIS A  86 " =    1.150
peak=   -3.611 closest distance to " ND2 ASN A  45 " =    2.020
peak=   -3.584 closest distance to " CG  MET A 105 " =    1.042
peak=   -3.584 closest distance to " O   SER A 210 " =    1.863
peak=   -3.583 closest distance to " O   HOH Z 421 " =    3.455
peak=   -3.579 closest distance to " O   HOH Z 357 " =    2.197
peak=   -3.576 closest distance to " CG1 VAL A 112 " =    2.875
peak=   -3.572 closest distance to " O   ALA A  34 " =    2.488
peak=   -3.570 closest distance to " O   HOH Z 368 " =    1.818
peak=   -3.564 closest distance to " CG1 VAL A 125 " =    1.922
peak=   -3.559 closest distance to " CG  PRO A 243 " =    1.745
peak=   -3.554 closest distance to " CB  ASN A  39 " =    2.399
peak=   -3.542 closest distance to " O   HOH Z 174 " =    2.519
peak=   -3.538 closest distance to " O   HOH Z 393 " =    1.305
peak=   -3.538 closest distance to " CB  PHE A 192 " =    1.996
peak=   -3.536 closest distance to " O   GLN A 240 " =    2.598
peak=   -3.534 closest distance to " O   VAL A 189 " =    1.739
peak=   -3.528 closest distance to " CD1 PHE A  59 " =    2.066
peak=   -3.528 closest distance to " O   HOH Z 295 " =    1.742
peak=   -3.527 closest distance to " O   ALA A  10 " =    1.705
peak=   -3.525 closest distance to " CZ  PHE A 155 " =    1.234
peak=   -3.525 closest distance to " O   TYR A 186 " =    1.775
peak=   -3.518 closest distance to " CB  TRP A  85 " =    2.605
peak=   -3.515 closest distance to " NH2AARG A 275 " =    5.435
peak=   -3.515 closest distance to " N   THR A  52 " =    1.615
peak=   -3.508 closest distance to " O   HOH Z 106 " =    2.000
peak=   -3.508 closest distance to " O   HOH Z 275 " =    1.576
peak=   -3.505 closest distance to " O   HOH Z 290 " =    1.234
peak=   -3.501 closest distance to " O   HOH Z 111 " =    1.656
peak=   -3.492 closest distance to " O   HOH Z   6 " =    1.351
peak=   -3.490 closest distance to " O   HOH Z 102 " =    1.518
peak=   -3.488 closest distance to " CA  GLY A 203 " =    2.458
peak=   -3.474 closest distance to " CG  GLU A 277 " =    1.199
peak=   -3.468 closest distance to " O   HOH Z 265 " =    2.518
peak=   -3.466 closest distance to " O   SER A 276 " =    1.703
peak=   -3.466 closest distance to " O   HOH Z 264 " =    1.809
peak=   -3.462 closest distance to " O   HOH Z 171 " =    2.172
peak=   -3.458 closest distance to " O   HOH Z 149 " =    2.198
peak=   -3.452 closest distance to " O   HOH Z  71 " =    2.550
peak=   -3.449 closest distance to " CE  MET A 105 " =    2.490
peak=   -3.448 closest distance to " C   THR A 264 " =    1.399
peak=   -3.441 closest distance to " O   HOH Z 191 " =    5.924
peak=   -3.434 closest distance to " O   HOH Z  68 " =    1.749
peak=   -3.430 closest distance to " O   HOH Z 351 " =    1.676
peak=   -3.430 closest distance to " CB  ALA A 291 " =    2.203
peak=   -3.429 closest distance to " OH  TYR A 247 " =    2.295
peak=   -3.426 closest distance to " O   HOH Z 174 " =    3.740
peak=   -3.425 closest distance to " O   HOH Z 407 " =    3.245
peak=   -3.421 closest distance to " CB  PHE A  16 " =    2.443
peak=   -3.420 closest distance to " O   HOH Z 133 " =    1.352
peak=   -3.413 closest distance to " OD1 ASP A 171 " =    1.572
peak=   -3.406 closest distance to " CG2 VAL A 189 " =    2.195
peak=   -3.395 closest distance to " CE3 TRP A  70 " =    1.830
peak=   -3.390 closest distance to " OE1 GLN A  88 " =    1.035
peak=   -3.386 closest distance to " CG  GLU A  53 " =    1.614
peak=   -3.386 closest distance to " O   GLY A  17 " =    1.179
peak=   -3.386 closest distance to " CG  LYS A 193 " =    2.678
peak=   -3.385 closest distance to " CD  ARG A  79 " =    1.248
peak=   -3.383 closest distance to " OD2 ASP A 171 " =    1.793
peak=   -3.376 closest distance to " CB  ALA A  10 " =    2.256
peak=   -3.375 closest distance to " CG  ARG A  66 " =    2.395
peak=   -3.369 closest distance to " O   PHE A 218 " =    1.491
peak=   -3.365 closest distance to " CG1BVAL A  72 " =    2.461
peak=   -3.363 closest distance to " O   HOH Z  64 " =    1.375
peak=   -3.359 closest distance to " O   HOH Z 154 " =    1.642
peak=   -3.357 closest distance to " ND2 ASN A 249 " =    2.488
peak=   -3.356 closest distance to " CD2 PHE A  61 " =    2.135
peak=   -3.355 closest distance to " O   HOH Z  78 " =    1.954
peak=   -3.354 closest distance to " NH2 ARG A  79 " =    1.571
peak=   -3.350 closest distance to " CZ3 TRP A 274 " =    2.414
peak=   -3.346 closest distance to " CG1 VAL A 265 " =    2.285
peak=   -3.344 closest distance to " ND2 ASN A  45 " =    1.308
peak=   -3.330 closest distance to " O   HOH Z  37 " =    1.834
peak=   -3.326 closest distance to " O   HOH Z 236 " =    1.519
peak=   -3.324 closest distance to " O   HOH Z 156 " =    3.602
peak=   -3.322 closest distance to " O   SER A 271 " =    2.102
peak=   -3.319 closest distance to " OD1 ASN A 173 " =    1.297
peak=   -3.315 closest distance to " CA  GLY A 241 " =    2.916
peak=   -3.311 closest distance to " CD  GLN A  88 " =    0.877
peak=   -3.303 closest distance to " O   HOH Z 292 " =    4.801
peak=   -3.300 closest distance to " O   HOH Z 359 " =    2.966
peak=   -3.297 closest distance to " CG1AVAL A  41 " =    2.609
peak=   -3.295 closest distance to " CB  ASP A 132 " =    2.365
peak=   -3.295 closest distance to " O   HOH Z 285 " =    1.784
peak=   -3.294 closest distance to " O   HOH Z 234 " =    4.479
peak=   -3.290 closest distance to " CZ  PHE A  38 " =    2.052
peak=   -3.288 closest distance to " O   HOH Z  51 " =    1.885
peak=   -3.287 closest distance to " O   HOH Z 232 " =    1.759
peak=   -3.284 closest distance to " O   HOH Z 278 " =    1.292
peak=   -3.281 closest distance to " O   HOH Z  71 " =    1.687
peak=   -3.279 closest distance to " CD1 TRP A  70 " =    1.108
peak=   -3.278 closest distance to " OD2 ASP A 270 " =    1.177
peak=   -3.273 closest distance to " CB  ALA A 248 " =    2.330
peak=   -3.272 closest distance to " O   HOH Z 177 " =    1.782
peak=   -3.269 closest distance to " CA  GLY A 133 " =    2.347
peak=   -3.268 closest distance to " O   HOH Z 114 " =    3.311
peak=   -3.268 closest distance to " O   SER A 135 " =    1.494
peak=   -3.266 closest distance to " O   GLN A  94 " =    2.208
peak=   -3.262 closest distance to " O   HOH Z 251 " =    5.150
peak=   -3.258 closest distance to " O   HOH Z 166 " =    1.779
peak=   -3.251 closest distance to " N   SER A 276 " =    1.408
peak=   -3.251 closest distance to " O   HOH Z 259 " =    4.172
peak=   -3.250 closest distance to " O   HOH Z 197 " =    2.170
peak=   -3.247 closest distance to " O   HOH Z 326 " =    5.092
peak=   -3.243 closest distance to " O   HOH Z 396 " =    1.801
peak=   -3.238 closest distance to " CG  LEU A  83 " =    2.135
peak=   -3.236 closest distance to " O   HOH Z   9 " =    2.003
peak=   -3.235 closest distance to " SG BCYS A 201 " =    1.178
peak=   -3.225 closest distance to " CD2 LEU A 237 " =    2.937
peak=   -3.223 closest distance to " N   ALA A 226 " =    2.007
peak=   -3.223 closest distance to " CD1 LEU A   5 " =    2.516
peak=   -3.223 closest distance to " O   HOH Z  52 " =    1.628
peak=   -3.216 closest distance to " O   HOH Z 353 " =    2.360
peak=   -3.216 closest distance to " CD2 HIS A 207 " =    2.245
peak=   -3.216 closest distance to " CD  GLU A 236 " =    1.157
peak=   -3.212 closest distance to " O   HOH Z   9 " =    2.531
peak=   -3.203 closest distance to " O   HOH Z  13 " =    1.856
peak=   -3.195 closest distance to " O   PRO A 163 " =    2.051
peak=   -3.194 closest distance to " CH2 TRP A 150 " =    1.153
peak=   -3.193 closest distance to " O   HOH Z 145 " =    1.391
peak=   -3.183 closest distance to " CG  PRO A 163 " =    2.137
peak=   -3.178 closest distance to " CG1BVAL A  41 " =    2.714
peak=   -3.166 closest distance to " O   HOH Z 340 " =    1.848
peak=   -3.165 closest distance to " O   TRP A  70 " =    1.583
peak=   -3.165 closest distance to " O   HOH Z 114 " =    1.419
peak=   -3.164 closest distance to " ND2 ASN A  60 " =    1.291
peak=   -3.160 closest distance to " OE1 GLN A 183 " =    1.663
peak=   -3.152 closest distance to " CG  TRP A 266 " =    1.863
peak=   -3.151 closest distance to " C   LEU A 143 " =    1.172
peak=   -3.151 closest distance to " CG  PHE A 283 " =    2.626
peak=   -3.146 closest distance to " O   GLU A 152 " =    1.390
peak=   -3.133 closest distance to " O   HOH Z  85 " =    2.223
peak=   -3.132 closest distance to " CZ  TYR A 169 " =    1.836
peak=   -3.132 closest distance to " O   HOH Z 116 " =    1.554
peak=   -3.128 closest distance to " O   HOH Z 252 " =    3.854
peak=   -3.127 closest distance to " O   HOH Z 111 " =    1.921
peak=   -3.122 closest distance to " O   HOH Z 189 " =    1.995
peak=   -3.120 closest distance to " CE  MET A  93 " =    1.888
peak=   -3.117 closest distance to " N   ALA A 248 " =    1.809
peak=   -3.116 closest distance to " OD1 ASP A 191 " =    1.516
peak=   -3.114 closest distance to " C   SER A 206 " =    1.388
peak=   -3.108 closest distance to " O   ILE A 106 " =    1.943
peak=   -3.102 closest distance to " O   HOH Z  55 " =    1.926
peak=   -3.101 closest distance to " C   ARG A  79 " =    2.660
peak=   -3.101 closest distance to " OH  TYR A 247 " =    1.817
peak=   -3.099 closest distance to " CA  HIS A  86 " =    2.284
peak=   -3.096 closest distance to " CG  ARG A 219 " =    2.834
peak=   -3.092 closest distance to " CD2 LEU A 222 " =    2.188
peak=   -3.084 closest distance to " O   HOH Z 198 " =    1.528
peak=   -3.068 closest distance to " CZ  ARG A 156 " =    2.875
peak=   -3.055 closest distance to " CB  TYR A  15 " =    2.233
peak=   -3.041 closest distance to " NH2 ARG A  66 " =    2.280
peak=   -3.014 closest distance to " O   HOH Z 318 " =    1.984

================= 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    :  0.4097 0.4049   6.211398e+00   6.193745e+00
   1_bss:  0.3969 0.3938   6.195314e+00   6.177046e+00
   1_xyz:  0.2899 0.3113   5.935446e+00   5.999729e+00
   1_adp:  0.2630 0.3197   5.877886e+00   6.011491e+00
   1_occ:  0.2628 0.3199   5.878088e+00   6.012856e+00
   2_bss:  0.2614 0.3185   5.876794e+00   6.012716e+00
   2_xyz:  0.1839 0.2369   5.562884e+00   5.750584e+00
   2_adp:  0.1666 0.2131   5.474966e+00   5.663292e+00
   2_occ:  0.1663 0.2131   5.474309e+00   5.663229e+00
   3_bss:  0.1664 0.2114   5.471120e+00   5.657532e+00
   3_xyz:  0.1321 0.1757   5.276599e+00   5.493504e+00
   3_adp:  0.1255 0.1717   5.239510e+00   5.467590e+00
   3_occ:  0.1253 0.1717   5.239137e+00   5.467455e+00
   4_bss:  0.1254 0.1713   5.237532e+00   5.465225e+00
   4_xyz:  0.1223 0.1667   5.215777e+00   5.441960e+00
   4_adp:  0.1209 0.1684   5.211723e+00   5.446822e+00
   4_occ:  0.1208 0.1682   5.211295e+00   5.446710e+00
   5_bss:  0.1206 0.1680   5.211216e+00   5.446722e+00
   5_xyz:  0.1158 0.1667   5.187423e+00   5.437186e+00
   5_adp:  0.1154 0.1661   5.183923e+00   5.434767e+00
   5_occ:  0.1154 0.1661   5.183897e+00   5.434950e+00
   5_bss:  0.1152 0.1659   5.184065e+00   5.435022e+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:  0.308  59.891  -3.302  -0.425   5.351  -0.000   0.000   0.000
   1_xyz:  0.308  59.891  -3.302  -0.425   5.351  -0.000   0.000   0.000
   1_adp:  0.308  59.891  -3.302  -0.425   5.351  -0.000   0.000   0.000
   1_occ:  0.308  59.891  -3.302  -0.425   5.351  -0.000   0.000   0.000
   2_bss:  0.329  75.722  -2.179  -0.627   2.319  -0.000   0.000   0.000
   2_xyz:  0.329  75.722  -2.179  -0.627   2.319  -0.000   0.000   0.000
   2_adp:  0.329  75.722  -2.179  -0.627   2.319  -0.000   0.000   0.000
   2_occ:  0.329  75.722  -2.179  -0.627   2.319  -0.000   0.000   0.000
   3_bss:  0.338  79.613  -2.015  -1.164   0.881  -0.000   0.000   0.000
   3_xyz:  0.338  79.613  -2.015  -1.164   0.881  -0.000   0.000   0.000
   3_adp:  0.338  79.613  -2.015  -1.164   0.881  -0.000   0.000   0.000
   3_occ:  0.338  79.613  -2.015  -1.164   0.881  -0.000   0.000   0.000
   4_bss:  0.332  74.533  -1.955  -1.312   0.386  -0.000   0.000   0.000
   4_xyz:  0.332  74.533  -1.955  -1.312   0.386  -0.000   0.000   0.000
   4_adp:  0.332  74.533  -1.955  -1.312   0.386  -0.000   0.000   0.000
   4_occ:  0.332  74.533  -1.955  -1.312   0.386  -0.000   0.000   0.000
   5_bss:  0.326  74.533  -1.624  -1.073   0.508  -0.000   0.000   0.000
   5_xyz:  0.326  74.533  -1.624  -1.073   0.508  -0.000   0.000   0.000
   5_adp:  0.326  74.533  -1.624  -1.073   0.508  -0.000   0.000   0.000
   5_occ:  0.326  74.533  -1.624  -1.073   0.508  -0.000   0.000   0.000
   5_bss:  0.326  74.536  -1.268  -0.782   0.751  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  45.725 0.5747  0.7222    48460.730
   1_bss:  44.626 0.5869  0.7546    45663.211
   1_xyz:  33.053 0.7240  0.9026    26650.152
   1_adp:  33.735 0.7156  0.8863    27692.117
   1_occ:  33.838 0.7144  0.8848    27825.924
   2_bss:  33.441 0.7194  0.8724    27708.186
   2_xyz:  23.431 0.8269  0.9636    14152.461
   2_adp:  20.422 0.8580  0.9697    11614.127
   2_occ:  20.416 0.8581  0.9695    11604.925
   3_bss:  20.183 0.8601  0.9513    11396.443
   3_xyz:  16.348 0.8950  0.9726     7947.523
   3_adp:  15.648 0.9014  0.9651     7556.277
   3_occ:  15.639 0.9015  0.9651     7548.503
   4_bss:  15.598 0.9018  0.9590     7498.808
   4_xyz:  15.004 0.9071  0.9616     7068.356
   4_adp:  15.090 0.9066  0.9514     7115.894
   4_occ:  15.082 0.9066  0.9513     7113.230
   5_bss:  15.081 0.9066  0.9591     7115.211
   5_xyz:  14.915 0.9079  0.9614     6997.231
   5_adp:  14.848 0.9085  0.9523     6954.716
   5_occ:  14.847 0.9085  0.9522     6953.643
   5_bss:  14.851 0.9085  0.9623     6956.891
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6809e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6809e-01
   1_xyz:   1.427  0.010  0.086 15.362  0.006  4.113   1.0096e-01
   1_adp:   1.427  0.010  0.086 15.362  0.006  4.113   1.0096e-01
   1_occ:   1.427  0.010  0.086 15.362  0.006  4.113   1.0096e-01
   2_bss:   1.427  0.010  0.086 15.362  0.006  4.113   1.0096e-01
   2_xyz:   1.176  0.009  0.082 14.996  0.004  4.134   7.6265e-02
   2_adp:   1.176  0.009  0.082 14.996  0.004  4.134   7.6265e-02
   2_occ:   1.176  0.009  0.082 14.996  0.004  4.134   7.6265e-02
   3_bss:   1.176  0.009  0.082 14.996  0.004  4.134   7.6265e-02
   3_xyz:   1.162  0.011  0.085 14.900  0.004  4.138   7.8384e-02
   3_adp:   1.162  0.011  0.085 14.900  0.004  4.138   7.8384e-02
   3_occ:   1.162  0.011  0.085 14.900  0.004  4.138   7.8384e-02
   4_bss:   1.162  0.011  0.085 14.900  0.004  4.138   7.8384e-02
   4_xyz:   1.024  0.009  0.077 14.557  0.003  4.117   6.2463e-02
   4_adp:   1.024  0.009  0.077 14.557  0.003  4.117   6.2463e-02
   4_occ:   1.024  0.009  0.077 14.557  0.003  4.117   6.2463e-02
   5_bss:   1.024  0.009  0.077 14.557  0.003  4.117   6.2463e-02
   5_xyz:   1.105  0.011  0.083 14.697  0.003  4.121   7.3550e-02
   5_adp:   1.105  0.011  0.083 14.697  0.003  4.121   7.3550e-02
   5_occ:   1.105  0.011  0.083 14.697  0.003  4.121   7.3550e-02
   5_bss:   1.105  0.011  0.083 14.697  0.003  4.121   7.3550e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.536   2.4494e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.536   2.4494e-01
   1_xyz:   8.734  0.055  0.338 83.662  0.058  2.111   8.9084e-02
   1_adp:   8.734  0.055  0.338 83.662  0.058  2.111   8.9084e-02
   1_occ:   8.734  0.055  0.338 83.662  0.058  2.111   8.9084e-02
   2_bss:   8.734  0.055  0.338 83.662  0.058  2.111   8.9084e-02
   2_xyz:   7.341  0.057  0.271 81.008  0.043  2.236   6.0080e-02
   2_adp:   7.341  0.057  0.271 81.008  0.043  2.236   6.0080e-02
   2_occ:   7.341  0.057  0.271 81.008  0.043  2.236   6.0080e-02
   3_bss:   7.341  0.057  0.271 81.008  0.043  2.236   6.0080e-02
   3_xyz:   7.895  0.063  0.275 86.131  0.028  2.339   6.4381e-02
   3_adp:   7.895  0.063  0.275 86.131  0.028  2.339   6.4381e-02
   3_occ:   7.895  0.063  0.275 86.131  0.028  2.339   6.4381e-02
   4_bss:   7.895  0.063  0.275 86.131  0.028  2.339   6.4381e-02
   4_xyz:   6.951  0.048  0.251 81.907  0.026  2.421   3.9326e-02
   4_adp:   6.951  0.048  0.251 81.907  0.026  2.421   3.9326e-02
   4_occ:   6.951  0.048  0.251 81.907  0.026  2.421   3.9326e-02
   5_bss:   6.951  0.048  0.251 81.907  0.026  2.421   3.9326e-02
   5_xyz:   7.780  0.057  0.284 83.211  0.025  2.367   5.0270e-02
   5_adp:   7.780  0.057  0.284 83.211  0.025  2.367   5.0270e-02
   5_occ:   7.780  0.057  0.284 83.211  0.025  2.367   5.0270e-02
   5_bss:   7.780  0.057  0.284 83.211  0.025  2.367   5.0270e-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:  95.75   0.00  17.98  81.52   0.00  13.87  95.75   1.24  40.35
   1_occ:  95.75   0.00  17.98  81.52   0.00  13.87  95.75   1.24  40.35
   2_bss:  95.75   0.00  17.98  81.52   0.00  13.87  95.75   1.24  40.35
   2_xyz:  95.75   0.00  17.98  81.52   0.00  13.87  95.75   1.24  40.35
   2_adp:  96.28   1.09  17.06  78.43   1.09  12.72  96.28   4.28  40.70
   2_occ:  96.28   1.09  17.06  78.43   1.09  12.72  96.28   4.28  40.70
   3_bss:  96.28   1.09  17.06  78.43   1.09  12.72  96.28   4.28  40.70
   3_xyz:  96.28   1.09  17.06  78.43   1.09  12.72  96.28   4.28  40.70
   3_adp:  95.53   0.53  16.75  78.71   0.53  12.31  95.53   3.34  40.98
   3_occ:  95.53   0.53  16.75  78.71   0.53  12.31  95.53   3.34  40.98
   4_bss:  95.53   0.53  16.75  78.71   0.53  12.31  95.53   3.34  40.98
   4_xyz:  95.53   0.53  16.75  78.71   0.53  12.31  95.53   3.34  40.98
   4_adp: 104.48   0.00  16.92  85.25   0.00  12.24 104.48   0.00  42.40
   4_occ: 104.48   0.00  16.92  85.25   0.00  12.24 104.48   0.00  42.40
   5_bss: 104.48   0.00  16.92  85.25   0.00  12.24 104.48   0.00  42.40
   5_xyz: 104.48   0.00  16.92  85.25   0.00  12.24 104.48   0.00  42.40
   5_adp: 106.73   0.00  16.68  87.60   0.00  11.99 106.73   0.72  42.27
   5_occ: 106.73   0.00  16.68  87.60   0.00  11.99 106.73   0.72  42.27
   5_bss: 106.73   0.00  16.69  87.61   0.00  11.99 106.73   0.73  42.27
------------------------------------------------------------------------
 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:    1.726    0.031    0.322
   1_adp:    1.726    0.031    0.322
   1_occ:    1.726    0.031    0.322
   2_bss:    1.726    0.031    0.322
   2_xyz:    1.369    0.039    0.491
   2_adp:    1.369    0.039    0.491
   2_occ:    1.369    0.039    0.491
   3_bss:    1.369    0.039    0.491
   3_xyz:    1.292    0.034    0.576
   3_adp:    1.292    0.034    0.576
   3_occ:    1.292    0.034    0.576
   4_bss:    1.292    0.034    0.576
   4_xyz:    1.248    0.040    0.591
   4_adp:    1.248    0.040    0.591
   4_occ:    1.248    0.040    0.591
   5_bss:    1.248    0.040    0.591
   5_xyz:    1.314    0.052    0.606
   5_adp:    1.314    0.052    0.606
   5_occ:    1.314    0.052    0.606
   5_bss:    1.314    0.052    0.606
------------------------------------------------------------------------

CPU time actual refinement: 324.97


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_813/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_813/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_813/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_813/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_813/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 324.82 
  Macro-tasks:
    bulk solvent and scale       = 51.33  
    individual site refinement   = 124.94 
    weights calculation          = 29.31  
    collect and process          = 6.52   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 212.20 
  Micro-tasks:
    mask                            = 1.84   
    f_calc                          = 97.49  
    alpha_beta                      = 8.27   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 105.66 
    fmodel                         = 7.59   
    r_factors                      = 0.32   
    phase_errors                   = 10.75  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 233.32 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.663 micro seconds
Total CPU time: 5.64 minutes
from_scatterers_fft:    616 calls, 97.05 s
gradients_fft:          561 calls, 92.86 s

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

# Date 2008-01-16 Time 05:42:59 PST -0800 (1200490979.61 s)
Start R-work = 0.4097, R-free = 0.4049 (no bulk solvent and anisotropic scale)
Final R-work = 0.1326, R-free = 0.1799 (no bulk solvent and anisotropic scale)

Start R-work = 0.3969, R-free = 0.3938
Final R-work = 0.1152, R-free = 0.1659