# Date 2008-01-16 Time 05:13:58 PST -0800 (1200489238.29 s)
#phil __OFF__

Command line arguments: "../650.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17377
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 650

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.6953, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.6953, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9109 1.96116
Completeness in resolution range: 0.954304
Completeness with d_max=infinity: 0.951384

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9109
                             d_min =   1.9612

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.6953, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9109 1.96116
Completeness in resolution range: 0.954304
Completeness with d_max=infinity: 0.951384

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9113 -  4.1967 [2153/2181]  1941   212   9.8%
  bin  2:  4.1967 -  3.3434 [2062/2078]  1853   209  10.1%
  bin  3:  3.3434 -  2.9244 [2047/2066]  1842   205  10.0%
  bin  4:  2.9244 -  2.6587 [2036/2066]  1836   200   9.8%
  bin  5:  2.6587 -  2.4690 [2020/2039]  1820   200   9.9%
  bin  6:  2.4690 -  2.3240 [2007/2043]  1799   208  10.4%
  bin  7:  2.3240 -  2.2080 [1972/2005]  1774   198  10.0%
  bin  8:  2.2080 -  2.1122 [1996/2030]  1799   197   9.9%
  bin  9:  2.1122 -  2.0311 [1974/2002]  1775   199  10.1%
  bin 10:  2.0311 -  1.9612 [1322/2017]  1191   131   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_650/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.11 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 34
        2.42 -     3.04: 2234
        3.04 -     3.66: 4765
        3.66 -     4.28: 9110
        4.28 -     4.90: 12523
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.833 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.853 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.932 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.999 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28661 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_650/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_650/model_refine_001.geo

CPU time processing inputs: 8.07


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.69535 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3426   r_free= 0.3422   ksol= 0.00   Bsol= 0.00   scale= 0.971    |
|                                                                             |
| 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:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.093779                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9113 -  4.6810 0.99   1390  155 0.2990 0.2961      6.3898      6.3691|
|  2:  4.6810 -  3.7346 0.99   1362  147 0.2757 0.2576      6.5036      6.4612|
|  3:  3.7346 -  3.2682 0.99   1316  151 0.3024 0.3214      6.4036      6.5606|
|  4:  3.2682 -  2.9720 0.99   1316  148 0.3038 0.3129      6.2714       6.267|
|  5:  2.9720 -  2.7604 0.99   1311  143 0.3451 0.3114      6.1581      6.1025|
|  6:  2.7604 -  2.5986 0.99   1285  145 0.3646 0.3744      6.0894      6.1188|
|  7:  2.5986 -  2.4690 0.99   1312  137 0.3605 0.3333      6.0563      6.0318|
|  8:  2.4690 -  2.3620 0.98   1272  151 0.3738 0.3691      6.0225      6.0157|
|  9:  2.3620 -  2.2714 0.98   1280  144 0.3730 0.3737      5.9741      5.9248|
| 10:  2.2714 -  2.1933 0.98   1287  132 0.3848 0.4314      5.9425      6.0384|
| 11:  2.1933 -  2.1249 1.00   1275  146 0.3960 0.4180      5.9144      5.9876|
| 12:  2.1249 -  2.0643 0.97   1267  140 0.3889 0.3760      5.8401      5.8677|
| 13:  2.0643 -  2.0101 0.98   1272  140 0.3964 0.4045      5.7551      5.7267|
| 14:  2.0101 -  1.9612 0.53    685   80 0.4487 0.4176      5.7712      5.6459|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9113 -  4.6810  1390   155  0.78  27.13   0.87     0.80      45481.42|
|  2:  4.6810 -  3.7346  1362   147  0.82  24.27   0.97     0.91      54768.40|
|  3:  3.7346 -  3.2682  1316   151  0.77  28.94   0.99     0.95      55327.68|
|  4:  3.2682 -  2.9720  1316   148  0.74  32.36   1.01     0.93      48838.00|
|  5:  2.9720 -  2.7604  1311   143  0.68  37.05   0.97     0.89      40774.54|
|  6:  2.7604 -  2.5986  1285   145  0.66  38.65   0.98     0.87      36474.13|
|  7:  2.5986 -  2.4690  1312   137  0.67  38.25   1.00     0.88      33200.63|
|  8:  2.4690 -  2.3620  1272   151  0.65  39.71   0.99     0.88      30715.48|
|  9:  2.3620 -  2.2714  1280   144  0.65  40.06   1.03     0.87      28084.97|
| 10:  2.2714 -  2.1933  1287   132  0.62  42.84   1.04     0.86      28277.09|
| 11:  2.1933 -  2.1249  1275   146  0.61  43.58   1.05     0.85      27061.64|
| 12:  2.1249 -  2.0643  1267   140  0.61  43.86   1.06     0.89      25673.99|
| 13:  2.0643 -  2.0101  1272   140  0.59  45.18   1.04     0.85      21687.98|
| 14:  2.0101 -  1.9612   685    80  0.58  45.67   1.01     0.76      18374.75|
|alpha:            min =        0.76 max =            0.95 mean =         0.87|
|beta:             min =    18374.75 max =        55327.68 mean =     36154.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.68|
|phase err.(work): min =        0.00 max =           89.99 mean =        37.25|
|phase err.(test): min =        0.00 max =           89.95 mean =        37.45|
|-----------------------------------------------------------------------------|

============================== 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 = 3.440835              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.374   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.840092              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.562   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:       11 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       23 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      210 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2024 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1890 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2875 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4690 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4420 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5719 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6804 |
|-----------------------------------------------------------------------------|
|-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 |        0.167 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.275 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.630)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3426   r_free= 0.3422   ksol= 0.00   Bsol= 0.00   scale= 0.971    |
|                                                                             |
| 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:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.093779                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3258   r_free= 0.3225   ksol= 0.32   Bsol= 30.65   scale= 0.977   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-2.22,2.68,-0.00,0.00,0.00); trace/3= -0.88                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.075968                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.780371              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.384   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.414918              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.567   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3258      final r-factor (work) = 0.2201          |
| start r-factor (free) = 0.3225      final r-factor (free) = 0.2458          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6148 = 2.78 * 0.50 * 6.0765 + 1.00 * 0.1674                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1913 = 2.78 * 0.50 * 5.8411 + 1.00 * 0.0712                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2201      final r-factor (work) = 0.2047          |
| start r-factor (free) = 0.2458      final r-factor (free) = 0.2529          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4297 = 0.41 * 1.00 * 5.8411 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3715 = 0.41 * 1.00 * 5.6577 + 1.00 * 0.0240                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.630)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.51   16.87    None  None   None       |
|    all(noH): 2823   0      0.00    62.51   16.87    None  None   None       |
|    Sol.    : 438    0      4.46    62.51   37.77    None  None   None       |
|    Mac.    : 2385   0      0.00    60.95   13.04    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.251:  292   |   5:    31.254 -  37.505:  117        |
|      1:     6.251 -  12.502: 1086   |   6:    37.505 -  43.756:  109        |
|      2:    12.502 -  18.753:  657   |   7:    43.756 -  50.007:   79        |
|      3:    18.753 -  25.004:  267   |   8:    50.007 -  56.258:   64        |
|      4:    25.004 -  31.254:  126   |   9:    56.258 -  62.509:   26        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2047 r_free = 0.2529             target_work(ml) = 5.670         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2043 r_free = 0.2531             target_work(ml) = 5.669         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2043   r_free= 0.2531   ksol= 0.32   Bsol= 30.65   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-2.22,2.68,-0.00,0.00,0.00); trace/3= -0.88                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.669073                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2025   r_free= 0.2509   ksol= 0.31   Bsol= 37.49   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.89,-2.59,-0.49,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.661248                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.894362              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.595   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.238972              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.862   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2025      final r-factor (work) = 0.1403          |
| start r-factor (free) = 0.2509      final r-factor (free) = 0.1827          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0885 = 3.89 * 0.50 * 5.6581 + 1.00 * 0.0712                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7969 = 3.89 * 0.50 * 5.5155 + 1.00 * 0.0572                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1403      final r-factor (work) = 0.1274          |
| start r-factor (free) = 0.1827      final r-factor (free) = 0.1687          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3352 = 0.24 * 1.00 * 5.5155 + 1.00 * 0.0172                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2682 = 0.24 * 1.00 * 5.2764 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.630)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.36    69.74   16.94    None  None   None       |
|    all(noH): 2823   0      1.36    69.74   16.94    None  None   None       |
|    Sol.    : 438    0      5.62    69.74   38.42    None  None   None       |
|    Mac.    : 2385   0      1.36    67.90   12.99    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:     1.359 -   8.197:  526   |   5:    35.548 -  42.386:  100        |
|      1:     8.197 -  15.035: 1317   |   6:    42.386 -  49.224:  104        |
|      2:    15.035 -  21.872:  406   |   7:    49.224 -  56.061:   75        |
|      3:    21.872 -  28.710:  138   |   8:    56.061 -  62.899:   36        |
|      4:    28.710 -  35.548:  111   |   9:    62.899 -  69.737:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1274 r_free = 0.1687             target_work(ml) = 5.235         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1272 r_free = 0.1685             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1272   r_free= 0.1685   ksol= 0.31   Bsol= 37.49   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.89,-2.59,-0.49,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.233884                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1271   r_free= 0.1676   ksol= 0.32   Bsol= 39.12   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-2.51,-1.48,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.230168                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.323740              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.567  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.383794              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.961  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1271      final r-factor (work) = 0.1181          |
| start r-factor (free) = 0.1676      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5487 = 1.32 * 0.50 * 5.2752 + 1.00 * 0.0572                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4865 = 1.32 * 0.50 * 5.1983 + 1.00 * 0.0459                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1181      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1574      final r-factor (free) = 0.1570          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0024 = 0.38 * 1.00 * 5.1983 + 1.00 * 0.0073                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9877 = 0.38 * 1.00 * 5.1579 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.630)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.39    82.85   17.11    None  None   None       |
|    all(noH): 2823   0      1.39    82.85   17.11    None  None   None       |
|    Sol.    : 438    0      3.12    75.47   39.46    None  None   None       |
|    Mac.    : 2385   0      1.39    82.85   13.01    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:     1.389 -   9.535:  870   |   5:    42.120 -  50.267:  120        |
|      1:     9.535 -  17.681: 1191   |   6:    50.267 -  58.413:   73        |
|      2:    17.681 -  25.828:  273   |   7:    58.413 -  66.559:   40        |
|      3:    25.828 -  33.974:  131   |   8:    66.559 -  74.706:   13        |
|      4:    33.974 -  42.120:  108   |   9:    74.706 -  82.852:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1154 r_free = 0.1570             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1153 r_free = 0.1568             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1153   r_free= 0.1568   ksol= 0.32   Bsol= 39.12   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-2.51,-1.48,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.154953                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1153   r_free= 0.1567   ksol= 0.32   Bsol= 39.38   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-2.49,-1.76,-0.00,-0.00,-0.00); trace/3= -2.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.154490                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.868771              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.487  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.266262              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.532  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1153      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1525          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8647 = 1.87 * 0.50 * 5.1575 + 1.00 * 0.0456                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8466 = 1.87 * 0.50 * 5.1277 + 1.00 * 0.0554                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1083          |
| start r-factor (free) = 0.1525      final r-factor (free) = 0.1526          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3734 = 0.27 * 1.00 * 5.1277 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3690 = 0.27 * 1.00 * 5.1125 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.630)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.60    85.35   16.87    None  None   None       |
|    all(noH): 2823   0      1.60    85.35   16.87    None  None   None       |
|    Sol.    : 438    0      4.50    76.76   38.59    None  None   None       |
|    Mac.    : 2385   0      1.60    85.35   12.88    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:     1.600 -   9.975: 1009   |   5:    43.474 -  51.849:  111        |
|      1:     9.975 -  18.350: 1111   |   6:    51.849 -  60.224:   50        |
|      2:    18.350 -  26.725:  234   |   7:    60.224 -  68.599:   30        |
|      3:    26.725 -  35.099:  135   |   8:    68.599 -  76.974:    8        |
|      4:    35.099 -  43.474:  131   |   9:    76.974 -  85.348:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1083 r_free = 0.1526             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1082 r_free = 0.1525             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1082   r_free= 0.1525   ksol= 0.32   Bsol= 39.38   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-2.49,-1.76,-0.00,-0.00,-0.00); trace/3= -2.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.111593                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1526   ksol= 0.32   Bsol= 39.59   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-2.34,-1.69,-0.00,-0.00,-0.00); trace/3= -2.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.111686                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.262425              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.638  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.253113              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.923  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1081      final r-factor (work) = 0.1096          |
| start r-factor (free) = 0.1526      final r-factor (free) = 0.1534          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.2826 = 1.26 * 0.50 * 5.1128 + 1.00 * 0.0554                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.2780 = 1.26 * 0.50 * 5.1186 + 1.00 * 0.0471                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1096      final r-factor (work) = 0.1096          |
| start r-factor (free) = 0.1534      final r-factor (free) = 0.1534          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3033 = 0.25 * 1.00 * 5.1186 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3044 = 0.25 * 1.00 * 5.1231 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.630)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.54    86.00   16.74    None  None   None       |
|    all(noH): 2823   0      1.54    86.00   16.74    None  None   None       |
|    Sol.    : 438    0      6.22    76.88   38.30    None  None   None       |
|    Mac.    : 2385   0      1.54    86.00   12.78    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:     1.545 -   9.990: 1028   |   5:    43.772 -  52.218:  109        |
|      1:     9.990 -  18.436: 1101   |   6:    52.218 -  60.663:   47        |
|      2:    18.436 -  26.881:  234   |   7:    60.663 -  69.109:   27        |
|      3:    26.881 -  35.327:  135   |   8:    69.109 -  77.554:    8        |
|      4:    35.327 -  43.772:  130   |   9:    77.554 -  86.000:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1096 r_free = 0.1534             target_work(ml) = 5.124         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1096 r_free = 0.1534             target_work(ml) = 5.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1096   r_free= 0.1534   ksol= 0.32   Bsol= 39.59   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-2.34,-1.69,-0.00,-0.00,-0.00); trace/3= -2.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.123839                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9113 -  4.6810 0.99   1390  155 0.0999 0.1216      5.3723      5.4966|
|  2:  4.6810 -  3.7346 0.99   1362  147 0.0858 0.1109      5.4261      5.6223|
|  3:  3.7346 -  3.2682 0.99   1316  151 0.1055 0.1494      5.4595      5.8317|
|  4:  3.2682 -  2.9720 0.99   1316  148 0.1187 0.1502      5.4385       5.567|
|  5:  2.9720 -  2.7604 0.99   1311  143 0.1263 0.1702      5.2909      5.5011|
|  6:  2.7604 -  2.5986 0.99   1285  145 0.1170 0.1689      5.1659      5.4036|
|  7:  2.5986 -  2.4690 0.99   1312  137 0.1209 0.1534      5.1266      5.3274|
|  8:  2.4690 -  2.3620 0.98   1272  151 0.1121 0.1691      5.0238      5.2848|
|  9:  2.3620 -  2.2714 0.98   1280  144 0.1157 0.1841      5.0119      5.3121|
| 10:  2.2714 -  2.1933 0.98   1287  132 0.1098 0.1678      4.9381      5.1842|
| 11:  2.1933 -  2.1249 1.00   1275  146 0.1134 0.1710      4.9287      5.2709|
| 12:  2.1249 -  2.0643 0.97   1267  140 0.1054 0.1601      4.8395      5.0691|
| 13:  2.0643 -  2.0101 0.98   1272  140 0.1130 0.1713      4.7696      5.0409|
| 14:  2.0101 -  1.9612 0.53    685   80 0.1037 0.1611      4.6561      4.8891|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9113 -  4.6810  1390   155  0.95   8.36   0.98     0.96       6342.01|
|  2:  4.6810 -  3.7346  1362   147  0.96   7.52   1.02     1.01       8401.54|
|  3:  3.7346 -  3.2682  1316   151  0.93  11.20   1.03     1.02      10028.98|
|  4:  3.2682 -  2.9720  1316   148  0.92  13.26   1.01     0.99       9985.80|
|  5:  2.9720 -  2.7604  1311   143  0.90  15.25   0.99     0.97       7677.70|
|  6:  2.7604 -  2.5986  1285   145  0.91  15.09   0.99     0.96       6445.33|
|  7:  2.5986 -  2.4690  1312   137  0.91  14.61   0.99     0.96       5600.53|
|  8:  2.4690 -  2.3620  1272   151  0.92  14.45   1.00     0.98       4854.65|
|  9:  2.3620 -  2.2714  1280   144  0.92  14.52   1.01     0.99       4688.40|
| 10:  2.2714 -  2.1933  1287   132  0.91  15.10   1.00     0.96       4136.69|
| 11:  2.1933 -  2.1249  1275   146  0.90  15.93   1.00     0.97       4226.53|
| 12:  2.1249 -  2.0643  1267   140  0.92  14.26   1.01     0.99       3691.13|
| 13:  2.0643 -  2.0101  1272   140  0.90  16.06   1.01     1.00       3192.72|
| 14:  2.0101 -  1.9612   685    80  0.92  14.43   0.99     0.96       2490.08|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2490.08 max =        10028.98 mean =      5991.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.48|
|phase err.(test): min =        0.00 max =           89.94 mean =        13.07|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1534   ksol= 0.32   Bsol= 39.53   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-2.19,-1.56,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.123886                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1534   ksol= 0.32   Bsol= 39.53   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-2.19,-1.56,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.123886                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9113 -  4.6810 0.99   1390  155 0.1000 0.1217      5.3728      5.4973|
|  2:  4.6810 -  3.7346 0.99   1362  147 0.0858 0.1109      5.4262      5.6221|
|  3:  3.7346 -  3.2682 0.99   1316  151 0.1055 0.1494      5.4594      5.8318|
|  4:  3.2682 -  2.9720 0.99   1316  148 0.1187 0.1502      5.4384       5.567|
|  5:  2.9720 -  2.7604 0.99   1311  143 0.1263 0.1702      5.2909      5.5009|
|  6:  2.7604 -  2.5986 0.99   1285  145 0.1170 0.1689       5.166      5.4038|
|  7:  2.5986 -  2.4690 0.99   1312  137 0.1209 0.1534      5.1268      5.3276|
|  8:  2.4690 -  2.3620 0.98   1272  151 0.1121 0.1691      5.0238      5.2848|
|  9:  2.3620 -  2.2714 0.98   1280  144 0.1157 0.1841      5.0119      5.3122|
| 10:  2.2714 -  2.1933 0.98   1287  132 0.1098 0.1678      4.9382      5.1839|
| 11:  2.1933 -  2.1249 1.00   1275  146 0.1134 0.1709      4.9287      5.2708|
| 12:  2.1249 -  2.0643 0.97   1267  140 0.1054 0.1601      4.8393      5.0691|
| 13:  2.0643 -  2.0101 0.98   1272  140 0.1130 0.1712      4.7695      5.0405|
| 14:  2.0101 -  1.9612 0.53    685   80 0.1037 0.1611      4.6562      4.8894|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9113 -  4.6810  1390   155  0.95   8.37   0.98     0.96       6349.63|
|  2:  4.6810 -  3.7346  1362   147  0.96   7.53   1.02     1.01       8406.25|
|  3:  3.7346 -  3.2682  1316   151  0.93  11.20   1.03     1.03      10028.31|
|  4:  3.2682 -  2.9720  1316   148  0.92  13.26   1.01     1.00       9984.74|
|  5:  2.9720 -  2.7604  1311   143  0.90  15.25   1.00     0.97       7678.59|
|  6:  2.7604 -  2.5986  1285   145  0.91  15.09   0.99     0.97       6446.15|
|  7:  2.5986 -  2.4690  1312   137  0.91  14.61   0.99     0.96       5602.02|
|  8:  2.4690 -  2.3620  1272   151  0.92  14.45   1.00     0.98       4855.18|
|  9:  2.3620 -  2.2714  1280   144  0.92  14.52   1.01     0.99       4688.77|
| 10:  2.2714 -  2.1933  1287   132  0.91  15.09   1.00     0.97       4136.67|
| 11:  2.1933 -  2.1249  1275   146  0.90  15.93   1.01     0.98       4225.81|
| 12:  2.1249 -  2.0643  1267   140  0.92  14.26   1.01     1.00       3689.39|
| 13:  2.0643 -  2.0101  1272   140  0.90  16.05   1.01     1.01       3191.96|
| 14:  2.0101 -  1.9612   685    80  0.92  14.44   1.00     0.97       2490.58|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2490.58 max =        10028.31 mean =      5992.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.48|
|phase err.(test): min =        0.00 max =           89.94 mean =        13.07|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.630)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.49    85.94   16.68    None  None   None       |
|    all(noH): 2823   0      1.49    85.94   16.68    None  None   None       |
|    Sol.    : 438    0      6.16    76.82   38.24    None  None   None       |
|    Mac.    : 2385   0      1.49    85.94   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:     1.490 -   9.935: 1028   |   5:    43.717 -  52.163:  109        |
|      1:     9.935 -  18.381: 1101   |   6:    52.163 -  60.608:   47        |
|      2:    18.381 -  26.826:  234   |   7:    60.608 -  69.054:   27        |
|      3:    26.826 -  35.272:  135   |   8:    69.054 -  77.499:    8        |
|      4:    35.272 -  43.717:  130   |   9:    77.499 -  85.945:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 307         
Filter by distance & map next to the model:
   mapped sites are within: 0.437 - 4.473
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 303 from: 307
   mapped sites are within: 0.748 - 4.473

peak=    5.828 closest distance to " O   HOH Z 126 " =    1.976
peak=    5.772 closest distance to " NH2 ARG A  56 " =    2.160
peak=    5.560 closest distance to " NE2 GLN A  11 " =    1.148
peak=    5.548 closest distance to " CG  PRO A  54 " =    1.257
peak=    5.459 closest distance to " CB  ARG A 275 " =    0.915
peak=    5.379 closest distance to " CB  GLN A 223 " =    1.451
peak=    5.260 closest distance to " CB  SER A  63 " =    1.211
peak=    5.230 closest distance to " CG  PRO A  90 " =    1.159
peak=    5.199 closest distance to " O   HOH Z 144 " =    1.756
peak=    5.184 closest distance to " CG  PRO A 213 " =    1.255
peak=    4.859 closest distance to " CB  GLN A 183 " =    1.234
peak=    4.841 closest distance to " CB  PRO A  54 " =    0.970
peak=    4.735 closest distance to " O   HOH Z 193 " =    1.869
peak=    4.713 closest distance to " O   HOH Z 232 " =    2.275
peak=    4.697 closest distance to " CB  GLU A 128 " =    1.046
peak=    4.583 closest distance to " C   PRO A 198 " =    1.544
peak=    4.582 closest distance to " O   HOH Z 298 " =    1.904
peak=    4.567 closest distance to " O   HOH Z  78 " =    1.781
peak=    4.526 closest distance to " O   HOH Z 236 " =    2.034
peak=    4.512 closest distance to " CB  GLU A 152 " =    1.226
peak=    4.498 closest distance to " CB  ASN A 148 " =    1.394
peak=    4.490 closest distance to " O   HOH Z 427 " =    2.781
peak=    4.478 closest distance to " OD1 ASN A  69 " =    2.623
peak=    4.439 closest distance to " CB  SER A   3 " =    1.340
peak=    4.432 closest distance to " CG  PRO A 198 " =    1.262
peak=    4.421 closest distance to " CB  TYR A 169 " =    0.782
peak=    4.413 closest distance to " O   HOH Z 234 " =    3.685
peak=    4.397 closest distance to " ND2 ASN A 187 " =    1.532
peak=    4.386 closest distance to " CB  LEU A 228 " =    1.081
peak=    4.313 closest distance to " O   HOH Z 316 " =    3.000
peak=    4.301 closest distance to " O   HOH Z   9 " =    2.290
peak=    4.291 closest distance to " CA  TYR A  30 " =    0.970
peak=    4.268 closest distance to " CG2 VAL A 257 " =    0.964
peak=    4.233 closest distance to " CG  PRO A 243 " =    1.099
peak=    4.213 closest distance to " CA  ALA A  21 " =    1.142
peak=    4.202 closest distance to " OD2 ASP A 286 " =    2.790
peak=    4.113 closest distance to " CB  VAL A 265 " =    1.229
peak=    4.109 closest distance to " O   HOH Z  59 " =    1.935
peak=    4.098 closest distance to " O   HOH Z 344 " =    3.067
peak=    4.088 closest distance to " CG  PRO A 280 " =    0.753
peak=    4.078 closest distance to " O   HOH Z 128 " =    2.091
peak=    4.056 closest distance to " O   HOH Z  97 " =    1.969
peak=    4.054 closest distance to " CB  TRP A 179 " =    1.268
peak=    4.048 closest distance to " O   HOH Z 368 " =    1.883
peak=    4.047 closest distance to " O   HOH Z 369 " =    1.990
peak=    4.022 closest distance to " O   HOH Z 132 " =    2.364
peak=    4.006 closest distance to " NZ  LYS A 117 " =    3.210
peak=    4.001 closest distance to " CA  THR A 264 " =    0.849
peak=    3.988 closest distance to " CA  ASN A 215 " =    1.168
peak=    3.987 closest distance to " CG1 ILE A  33 " =    1.277
peak=    3.982 closest distance to " O   HOH Z 272 " =    1.846
peak=    3.958 closest distance to " O   HOH Z 189 " =    1.892
peak=    3.948 closest distance to " O   HOH Z 108 " =    1.288
peak=    3.946 closest distance to " O   HOH Z 207 " =    1.779
peak=    3.942 closest distance to " O   HOH Z  66 " =    2.101
peak=    3.938 closest distance to " O   HOH Z 389 " =    1.810
peak=    3.927 closest distance to " O   HOH Z  10 " =    1.852
peak=    3.912 closest distance to " O   HOH Z  44 " =    1.852
peak=    3.910 closest distance to " O   HOH Z  54 " =    1.665
peak=    3.899 closest distance to " O   HOH Z  21 " =    1.685
peak=    3.885 closest distance to " O   HOH Z 371 " =    3.194
peak=    3.877 closest distance to " O   HOH Z   9 " =    2.033
peak=    3.865 closest distance to " O   HOH Z 263 " =    2.257
peak=    3.858 closest distance to " CB  SER A 216 " =    0.748
peak=    3.856 closest distance to " NH1AARG A 145 " =    1.081
peak=    3.856 closest distance to " O   HOH Z 407 " =    2.407
peak=    3.854 closest distance to " NH1BARG A 145 " =    1.319
peak=    3.848 closest distance to " OG BSER A 164 " =    2.388
peak=    3.837 closest distance to " CA  THR A 221 " =    0.944
peak=    3.836 closest distance to " O   HOH Z 346 " =    1.710
peak=    3.834 closest distance to " O   SER A  87 " =    2.283
peak=    3.822 closest distance to " O   HOH Z 368 " =    3.622
peak=    3.816 closest distance to " CB  ARG A  79 " =    1.365
peak=    3.800 closest distance to " CB  TRP A 266 " =    0.988
peak=    3.785 closest distance to " O   HOH Z 352 " =    1.844
peak=    3.777 closest distance to " O   HOH Z 303 " =    2.072
peak=    3.738 closest distance to " O   HOH Z 144 " =    2.270
peak=    3.737 closest distance to " O   HOH Z 134 " =    1.326
peak=    3.736 closest distance to " O   HOH Z 295 " =    1.500
peak=    3.736 closest distance to " O   HOH Z  61 " =    1.604
peak=    3.732 closest distance to " O   HOH Z  88 " =    3.082
peak=    3.723 closest distance to " O   HOH Z  40 " =    1.542
peak=    3.723 closest distance to " O   HOH Z  93 " =    2.293
peak=    3.700 closest distance to " CG2 ILE A 120 " =    1.202
peak=    3.698 closest distance to " O   HOH Z 250 " =    1.380
peak=    3.697 closest distance to " CD BLYS A 290 " =    1.195
peak=    3.692 closest distance to " CB  ARG A 139 " =    0.920
peak=    3.690 closest distance to " O   HOH Z  61 " =    1.656
peak=    3.687 closest distance to " CE  LYS A  76 " =    0.909
peak=    3.678 closest distance to " O   MET A 105 " =    1.772
peak=    3.677 closest distance to " O   HOH Z 158 " =    2.922
peak=    3.670 closest distance to " O   HOH Z 402 " =    1.421
peak=    3.668 closest distance to " N   ASN A  39 " =    1.193
peak=    3.664 closest distance to " NH2BARG A 145 " =    2.041
peak=    3.663 closest distance to " CG1BVAL A  72 " =    1.474
peak=    3.660 closest distance to " CG  LEU A 167 " =    1.156
peak=    3.647 closest distance to " OE1 GLU A   2 " =    2.204
peak=    3.644 closest distance to " CA  GLY A 241 " =    3.805
peak=    3.640 closest distance to " CG  ARG A  66 " =    2.460
peak=    3.631 closest distance to " O   HOH Z 173 " =    1.881
peak=    3.626 closest distance to " O   HOH Z 353 " =    2.624
peak=    3.617 closest distance to " O   HOH Z 284 " =    2.950
peak=    3.616 closest distance to " O   HOH Z  43 " =    1.942
peak=    3.615 closest distance to " CB  ALA A 291 " =    1.345
peak=    3.615 closest distance to " O  BHOH Z  74 " =    1.468
peak=    3.603 closest distance to " O   HOH Z 425 " =    1.963
peak=    3.602 closest distance to " CB  ARG A 190 " =    1.735
peak=    3.600 closest distance to " O   HOH Z 425 " =    1.293
peak=    3.596 closest distance to " O   HOH Z 124 " =    1.340
peak=    3.581 closest distance to " O   HOH Z   1 " =    1.782
peak=    3.578 closest distance to " CD1 LEU A 300 " =    1.249
peak=    3.571 closest distance to " CD2 LEU A 297 " =    0.935
peak=    3.553 closest distance to " O   HOH Z 219 " =    2.127
peak=    3.551 closest distance to " N   ARG A 156 " =    1.256
peak=    3.551 closest distance to " O   HOH Z 366 " =    3.111
peak=    3.550 closest distance to " O   HOH Z 108 " =    2.059
peak=    3.547 closest distance to " O   HOH Z 209 " =    2.304
peak=    3.546 closest distance to " O   HOH Z 273 " =    2.713
peak=    3.541 closest distance to " CB  SER A 141 " =    1.071
peak=    3.531 closest distance to " O   HOH Z 236 " =    1.457
peak=    3.530 closest distance to " O   HOH Z  73 " =    1.534
peak=    3.530 closest distance to " O   HOH Z 163 " =    1.786
peak=    3.523 closest distance to " CB  VAL A 202 " =    1.622
peak=    3.514 closest distance to " O   HOH Z 193 " =    1.981
peak=    3.509 closest distance to " O   HOH Z   3 " =    1.799
peak=    3.509 closest distance to " CB  LEU A 143 " =    1.102
peak=    3.507 closest distance to " O   HOH Z 227 " =    2.177
peak=    3.499 closest distance to " O   HOH Z 163 " =    1.988
peak=    3.497 closest distance to " O   HOH Z 245 " =    1.303
peak=    3.493 closest distance to " O   HOH Z 125 " =    2.204
peak=    3.490 closest distance to " O   HOH Z 261 " =    1.511
peak=    3.489 closest distance to " O   HOH Z 374 " =    2.488
peak=    3.483 closest distance to " O   HOH Z 426 " =    1.560
peak=    3.480 closest distance to " CB  PRO A 198 " =    0.997
peak=    3.471 closest distance to " CA  MET A  40 " =    1.088
peak=    3.468 closest distance to " O   HOH Z 392 " =    3.117
peak=    3.466 closest distance to " CG  GLU A 277 " =    2.140
peak=    3.460 closest distance to " CD2 LEU A 255 " =    1.320
peak=    3.456 closest distance to " O   HOH Z 247 " =    1.233
peak=    3.452 closest distance to " CD2 TRP A 179 " =    1.359
peak=    3.448 closest distance to " CD  ARG A 159 " =    0.750
peak=    3.439 closest distance to " O   HOH Z  40 " =    1.929
peak=    3.438 closest distance to " O   HOH Z 214 " =    2.055
peak=    3.436 closest distance to " O   HOH Z 265 " =    2.368
peak=    3.432 closest distance to " O   HOH Z 261 " =    1.931
peak=    3.421 closest distance to " O   HOH Z 227 " =    1.546
peak=    3.416 closest distance to " CA  GLY A  80 " =    0.768
peak=    3.406 closest distance to " O   HOH Z 227 " =    1.681
peak=    3.401 closest distance to " O   HOH Z 234 " =    1.790
peak=    3.399 closest distance to " CG2BVAL A  41 " =    0.902
peak=    3.391 closest distance to " CA  ALA A 233 " =    1.299
peak=    3.390 closest distance to " O   HOH Z 260 " =    1.213
peak=    3.390 closest distance to " O   HOH Z 281 " =    4.473
peak=    3.388 closest distance to " O   HOH Z 409 " =    2.829
peak=    3.388 closest distance to " O   HOH Z  63 " =    2.049
peak=    3.383 closest distance to " O   HOH Z 183 " =    1.424
peak=    3.383 closest distance to " O   HOH Z  48 " =    1.336
peak=    3.383 closest distance to " CZ  PHE A 218 " =    1.019
peak=    3.379 closest distance to " O   HOH Z 337 " =    3.723
peak=    3.375 closest distance to " O   HOH Z 135 " =    1.629
peak=    3.375 closest distance to " CZ2 TRP A 179 " =    1.708
peak=    3.375 closest distance to " CD  ARG A 269 " =    0.992
peak=    3.372 closest distance to " N   GLN A 278 " =    1.008
peak=    3.368 closest distance to " CD1 ILE A 106 " =    0.917
peak=    3.368 closest distance to " O   HOH Z 172 " =    3.483
peak=    3.368 closest distance to " CB  SER A  62 " =    1.299
peak=    3.367 closest distance to " CB  ASN A 215 " =    1.066
peak=    3.364 closest distance to " O   HOH Z 433 " =    1.822
peak=    3.362 closest distance to " O   HOH Z 423 " =    1.872
peak=    3.362 closest distance to " O   ALA A   1 " =    1.654
peak=    3.359 closest distance to " O   HOH Z 271 " =    2.156
peak=    3.358 closest distance to " O   HOH Z   1 " =    1.669
peak=    3.357 closest distance to " NH2AARG A 190 " =    1.311
peak=    3.357 closest distance to " O   HOH Z 329 " =    3.580
peak=    3.355 closest distance to " CA  VAL A  41 " =    0.904
peak=    3.348 closest distance to " O   HOH Z 211 " =    2.505
peak=    3.346 closest distance to " O   ALA A   1 " =    1.450
peak=    3.344 closest distance to " CA  ALA A  51 " =    0.938
peak=    3.344 closest distance to " CB  ASN A  39 " =    0.882
peak=    3.342 closest distance to " CB  SER A  26 " =    1.567
peak=    3.340 closest distance to " NZ  LYS A 119 " =    1.324
peak=    3.337 closest distance to " O   HOH Z 214 " =    2.430
peak=    3.335 closest distance to " CG AARG A 275 " =    1.021
peak=    3.331 closest distance to " O   HOH Z 180 " =    2.158
peak=    3.331 closest distance to " OG  SER A  22 " =    2.684
peak=    3.318 closest distance to " CA  ASP A 140 " =    1.108
peak=    3.312 closest distance to " CA  ILE A 234 " =    0.926
peak=    3.311 closest distance to " O   HOH Z 291 " =    1.498
peak=    3.311 closest distance to " O   SER A  26 " =    1.662
peak=    3.310 closest distance to " NH2 ARG A 156 " =    1.210
peak=    3.309 closest distance to " O   HOH Z 419 " =    1.973
peak=    3.305 closest distance to " CG  MET A 113 " =    1.118
peak=    3.303 closest distance to " CG  MET A 185 " =    1.194
peak=    3.294 closest distance to " C   TYR A 214 " =    1.459
peak=    3.293 closest distance to " O   HOH Z 286 " =    2.451
peak=    3.291 closest distance to " N   PHE A 130 " =    1.342
peak=    3.290 closest distance to " O   HOH Z 299 " =    4.305
peak=    3.288 closest distance to " ND1 HIS A  86 " =    1.661
peak=    3.283 closest distance to " OD1BASN A 224 " =    2.271
peak=    3.281 closest distance to " CB  GLN A  88 " =    1.202
peak=    3.281 closest distance to " CD  LYS A 166 " =    1.247
peak=    3.270 closest distance to " CB  GLU A 277 " =    3.507
peak=    3.268 closest distance to " O   HOH Z 280 " =    1.838
peak=    3.266 closest distance to " CG  GLN A  89 " =    1.477
peak=    3.265 closest distance to " O   HOH Z 147 " =    1.674
peak=    3.265 closest distance to " OG  SER A 206 " =    1.296
peak=    3.265 closest distance to " O   HOH Z 193 " =    1.617
peak=    3.264 closest distance to " O   HOH Z 403 " =    1.673
peak=    3.261 closest distance to " O   HOH Z 336 " =    1.831
peak=    3.261 closest distance to " O   HOH Z 437 " =    1.641
peak=    3.254 closest distance to " CB  MET A  47 " =    1.051
peak=    3.252 closest distance to " CG  GLN A  77 " =    2.038
peak=    3.251 closest distance to " O   HOH Z 287 " =    1.871
peak=    3.251 closest distance to " CG2 THR A 221 " =    1.144
peak=    3.250 closest distance to " O   HOH Z 216 " =    2.430
peak=    3.249 closest distance to " O   HOH Z 128 " =    2.073
peak=    3.247 closest distance to " O   HOH Z 339 " =    2.166
peak=    3.240 closest distance to " O   HOH Z 133 " =    1.435
peak=    3.240 closest distance to " CE AMET A  47 " =    1.265
peak=    3.237 closest distance to " CB  GLU A  46 " =    1.056
peak=    3.237 closest distance to " O   HOH Z 327 " =    1.960
peak=    3.236 closest distance to " O   HOH Z 279 " =    2.103
peak=    3.235 closest distance to " O   HOH Z 286 " =    2.253
peak=    3.234 closest distance to " CB  ARG A  79 " =    0.842
peak=    3.233 closest distance to " O   HOH Z 345 " =    3.391
peak=    3.233 closest distance to " CD  PRO A 243 " =    1.545
peak=    3.231 closest distance to " O   HOH Z 357 " =    1.783
peak=    3.229 closest distance to " O   HOH Z  40 " =    2.513
peak=    3.226 closest distance to " OD1 ASP A 231 " =    1.871
peak=    3.223 closest distance to " CA  ARG A  36 " =    1.077
peak=    3.222 closest distance to " CB  ILE A 120 " =    1.276
peak=    3.221 closest distance to " O   HOH Z 148 " =    3.168
peak=    3.220 closest distance to " CG  MET A 185 " =    1.087
peak=    3.216 closest distance to " CG1 ILE A 151 " =    0.919
peak=    3.216 closest distance to " O   HOH Z 287 " =    2.086
peak=    3.209 closest distance to " O   HOH Z  59 " =    2.256
peak=    3.208 closest distance to " CA  ALA A 291 " =    0.946
peak=    3.207 closest distance to " O   HOH Z 261 " =    1.961
peak=    3.206 closest distance to " O   HOH Z  71 " =    1.077
peak=    3.203 closest distance to " O   GLY A 229 " =    1.491
peak=    3.203 closest distance to " O   HOH Z 334 " =    1.498
peak=    3.202 closest distance to " CG2 VAL A  67 " =    1.071
peak=    3.202 closest distance to " CA  SER A  87 " =    0.941
peak=    3.201 closest distance to " CA  VAL A 126 " =    1.128
peak=    3.201 closest distance to " CB  THR A 157 " =    1.018
peak=    3.199 closest distance to " NZ  LYS A  76 " =    1.249
peak=    3.199 closest distance to " O   HOH Z 411 " =    1.746
peak=    3.198 closest distance to " CG2 VAL A  78 " =    0.904
peak=    3.197 closest distance to " CB  ASP A 140 " =    0.802
peak=    3.195 closest distance to " OD1 ASP A 238 " =    1.043
peak=    3.195 closest distance to " CB  VAL A 268 " =    0.813
peak=    3.195 closest distance to " CB  LEU A 255 " =    0.780
peak=    3.194 closest distance to " O   HOH Z 128 " =    2.135
peak=    3.185 closest distance to " O   HOH Z 106 " =    2.317
peak=    3.180 closest distance to " CB  ASP A 171 " =    0.849
peak=    3.176 closest distance to " N   ASN A 127 " =    1.237
peak=    3.175 closest distance to " CA  ASN A 176 " =    1.144
peak=    3.172 closest distance to " CB  TYR A 116 " =    0.839
peak=    3.160 closest distance to " O   HOH Z 427 " =    2.998
peak=    3.158 closest distance to " O   HOH Z 291 " =    1.839
peak=    3.157 closest distance to " CB  GLU A 152 " =    1.377
peak=    3.156 closest distance to " CB  ARG A 102 " =    0.755
peak=    3.156 closest distance to " OG  SER A  62 " =    2.963
peak=    3.155 closest distance to " O   HOH Z 263 " =    1.565
peak=    3.153 closest distance to " CA  ALA A 158 " =    1.137
peak=    3.148 closest distance to " CB  ALA A 114 " =    1.162
peak=    3.147 closest distance to " CB  LYS A 117 " =    1.143
peak=    3.146 closest distance to " O   HOH Z 285 " =    1.495
peak=    3.143 closest distance to " O   TRP A 274 " =    1.772
peak=    3.143 closest distance to " O   HOH Z 269 " =    3.647
peak=    3.142 closest distance to " O   HOH Z  71 " =    1.871
peak=    3.142 closest distance to " CG BARG A 102 " =    1.838
peak=    3.142 closest distance to " CA  LEU A 282 " =    1.111
peak=    3.141 closest distance to " NE2 GLN A  73 " =    3.622
peak=    3.139 closest distance to " CG  LYS A  76 " =    1.034
peak=    3.135 closest distance to " CB  ALA A  71 " =    1.426
peak=    3.134 closest distance to " O   HOH Z 298 " =    2.585
peak=    3.132 closest distance to " O   HOH Z 175 " =    2.085
peak=    3.131 closest distance to " O   HOH Z 188 " =    2.002
peak=    3.131 closest distance to " CB  THR A  31 " =    1.692
peak=    3.128 closest distance to " O   HOH Z 305 " =    3.669
peak=    3.124 closest distance to " CG2 ILE A  20 " =    1.512
peak=    3.122 closest distance to " CA  LYS A 290 " =    1.251
peak=    3.119 closest distance to " CA  ALA A 248 " =    1.260
peak=    3.117 closest distance to " O   HOH Z 192 " =    1.910
peak=    3.116 closest distance to " CA  ALA A  43 " =    1.181
peak=    3.112 closest distance to " O   HOH Z 403 " =    1.329
peak=    3.112 closest distance to " O   GLY A 147 " =    1.296
peak=    3.110 closest distance to " N   CYS A 260 " =    0.763
peak=    3.108 closest distance to " CB  ASN A 110 " =    1.068
peak=    3.105 closest distance to " O   HOH Z  83 " =    1.929
peak=    3.104 closest distance to " O   HOH Z  49 " =    2.052
peak=    3.099 closest distance to " O   HOH Z 250 " =    1.889
peak=    3.097 closest distance to " O   HOH Z 313 " =    1.629
peak=    3.087 closest distance to " O   HOH Z 112 " =    2.678
peak=    3.082 closest distance to " CB  GLN A 103 " =    0.805
peak=    3.080 closest distance to " CD2 HIS A  81 " =    1.187
peak=    3.076 closest distance to " OE2 GLU A  53 " =    2.102
peak=    3.075 closest distance to " O   HOH Z  49 " =    2.274
peak=    3.074 closest distance to " CG  GLN A  88 " =    1.011
peak=    3.064 closest distance to " CD1AILE A 234 " =    1.034
peak=    3.041 closest distance to " ND1 HIS A  81 " =    1.559
peak=    3.036 closest distance to " OG1 THR A 246 " =    3.178

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 184         
Filter by distance & map next to the model:
   mapped sites are within: 0.769 - 5.260
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 183 from: 184
   mapped sites are within: 0.769 - 5.260

peak=   -4.614 closest distance to " O   HOH Z 266 " =    4.388
peak=   -4.464 closest distance to " O   HOH Z 290 " =    1.028
peak=   -4.424 closest distance to " CB  PRO A 243 " =    2.584
peak=   -4.216 closest distance to " O   HOH Z 377 " =    1.938
peak=   -4.206 closest distance to " O   HOH Z 372 " =    2.416
peak=   -4.192 closest distance to " CD  ARG A 156 " =    1.934
peak=   -4.190 closest distance to " O   ILE A 109 " =    2.578
peak=   -4.179 closest distance to " O   HOH Z 198 " =    2.008
peak=   -4.148 closest distance to " O   PRO A 198 " =    1.251
peak=   -4.075 closest distance to " CG  GLN A 223 " =    1.827
peak=   -4.069 closest distance to " C   HIS A 108 " =    1.076
peak=   -4.041 closest distance to " O   VAL A  67 " =    2.684
peak=   -4.034 closest distance to " ND2 ASN A  45 " =    1.017
peak=   -4.030 closest distance to " SG  CYS A 254 " =    3.208
peak=   -3.982 closest distance to " C   ALA A 158 " =    1.239
peak=   -3.978 closest distance to " O   VAL A 153 " =    2.330
peak=   -3.973 closest distance to " O   HOH Z  43 " =    1.622
peak=   -3.973 closest distance to " CZ  PHE A  59 " =    1.528
peak=   -3.955 closest distance to " CE2 TYR A  30 " =    2.877
peak=   -3.955 closest distance to " O   HOH Z 185 " =    2.177
peak=   -3.947 closest distance to " N   GLN A  58 " =    1.798
peak=   -3.943 closest distance to " O   HOH Z  13 " =    1.361
peak=   -3.927 closest distance to " O   HOH Z 353 " =    2.174
peak=   -3.923 closest distance to " O   HOH Z 435 " =    2.719
peak=   -3.895 closest distance to " CG1 VAL A 112 " =    2.864
peak=   -3.888 closest distance to " CB  PHE A 283 " =    2.716
peak=   -3.887 closest distance to " CE2 PHE A 218 " =    2.527
peak=   -3.886 closest distance to " OXT GLY A 302 " =    2.707
peak=   -3.882 closest distance to " CZ3 TRP A 179 " =    1.246
peak=   -3.877 closest distance to " CZ  TYR A 169 " =    1.684
peak=   -3.853 closest distance to " O   HOH Z 351 " =    1.467
peak=   -3.849 closest distance to " CE  MET A 105 " =    2.182
peak=   -3.842 closest distance to " CG  ASP A 231 " =    0.769
peak=   -3.841 closest distance to " O   PRO A 163 " =    1.923
peak=   -3.828 closest distance to " CA  GLY A  98 " =    1.925
peak=   -3.803 closest distance to " CB  CYS A 201 " =    2.589
peak=   -3.788 closest distance to " O   ALA A 161 " =    1.536
peak=   -3.771 closest distance to " CA  VAL A  67 " =    2.707
peak=   -3.769 closest distance to " CB  TYR A  15 " =    2.189
peak=   -3.740 closest distance to " O   HOH Z 118 " =    3.005
peak=   -3.734 closest distance to " O   HOH Z 407 " =    3.091
peak=   -3.729 closest distance to " OD1 ASN A 187 " =    1.672
peak=   -3.722 closest distance to " OG BSER A 134 " =    1.170
peak=   -3.716 closest distance to " O   HOH Z  47 " =    1.530
peak=   -3.713 closest distance to " O   HOH Z 388 " =    2.029
peak=   -3.709 closest distance to " OG  SER A  97 " =    2.053
peak=   -3.708 closest distance to " NH1 ARG A 195 " =    2.540
peak=   -3.706 closest distance to " O   HOH Z 389 " =    1.849
peak=   -3.687 closest distance to " CB  ASN A  39 " =    2.146
peak=   -3.676 closest distance to " CD  ARG A 139 " =    1.507
peak=   -3.665 closest distance to " O   HOH Z 313 " =    2.010
peak=   -3.660 closest distance to " CD1 PHE A  59 " =    1.860
peak=   -3.651 closest distance to " O   HOH Z 126 " =    1.815
peak=   -3.649 closest distance to " O   HOH Z 395 " =    5.076
peak=   -3.649 closest distance to " CB  ALA A 291 " =    2.222
peak=   -3.640 closest distance to " O   HOH Z 102 " =    1.697
peak=   -3.639 closest distance to " CB  ALA A 248 " =    1.983
peak=   -3.639 closest distance to " O   HOH Z 231 " =    1.940
peak=   -3.625 closest distance to " O   HOH Z  52 " =    1.395
peak=   -3.623 closest distance to " OE1 GLN A  88 " =    1.103
peak=   -3.621 closest distance to " N   ASP A 286 " =    2.408
peak=   -3.610 closest distance to " N   SER A 212 " =    1.937
peak=   -3.583 closest distance to " O   SER A 135 " =    1.507
peak=   -3.561 closest distance to " CA  GLY A 203 " =    2.265
peak=   -3.559 closest distance to " CD2 LEU A 300 " =    2.870
peak=   -3.547 closest distance to " CD1 LEU A 228 " =    2.206
peak=   -3.546 closest distance to " CD1 LEU A 101 " =    2.394
peak=   -3.514 closest distance to " N   ALA A 248 " =    1.589
peak=   -3.513 closest distance to " N   ALA A  43 " =    2.312
peak=   -3.505 closest distance to " CB  ASP A 132 " =    2.290
peak=   -3.502 closest distance to " OD1 ASP A 191 " =    1.697
peak=   -3.502 closest distance to " O   HOH Z 385 " =    2.021
peak=   -3.497 closest distance to " NH2AARG A 275 " =    5.260
peak=   -3.496 closest distance to " OD2 ASP A 171 " =    2.324
peak=   -3.495 closest distance to " O   HOH Z  11 " =    1.814
peak=   -3.492 closest distance to " O   HOH Z 298 " =    1.178
peak=   -3.490 closest distance to " O   HOH Z 210 " =    1.045
peak=   -3.488 closest distance to " CA  SER A 146 " =    2.344
peak=   -3.487 closest distance to " CG  MET A 105 " =    0.930
peak=   -3.481 closest distance to " OXT GLY A 302 " =    3.456
peak=   -3.478 closest distance to " O   HOH Z  93 " =    1.720
peak=   -3.475 closest distance to " SG ACYS A 201 " =    2.043
peak=   -3.462 closest distance to " O   VAL A 174 " =    1.971
peak=   -3.445 closest distance to " CA  TRP A  70 " =    2.447
peak=   -3.442 closest distance to " O   HOH Z  24 " =    1.430
peak=   -3.437 closest distance to " CB  ALA A 291 " =    2.419
peak=   -3.437 closest distance to " CB  PRO A 163 " =    2.555
peak=   -3.414 closest distance to " O   MET A  40 " =    2.692
peak=   -3.414 closest distance to " N   HIS A 115 " =    1.922
peak=   -3.389 closest distance to " O   HOH Z 198 " =    1.409
peak=   -3.389 closest distance to " CE3 TRP A 123 " =    1.342
peak=   -3.387 closest distance to " CD  GLU A 152 " =    2.649
peak=   -3.381 closest distance to " CA  TRP A 274 " =    1.522
peak=   -3.381 closest distance to " CE3 TRP A 274 " =    2.390
peak=   -3.375 closest distance to " O   HOH Z 166 " =    1.408
peak=   -3.367 closest distance to " O   HOH Z 417 " =    2.428
peak=   -3.361 closest distance to " OG BSER A 134 " =    1.691
peak=   -3.361 closest distance to " NH2 ARG A  79 " =    1.856
peak=   -3.358 closest distance to " CB  ASP A 132 " =    2.175
peak=   -3.354 closest distance to " CD2 LEU A 237 " =    2.799
peak=   -3.354 closest distance to " O   GLY A 196 " =    0.994
peak=   -3.352 closest distance to " CD1 ILE A 239 " =    2.512
peak=   -3.344 closest distance to " O   HOH Z 211 " =    1.680
peak=   -3.341 closest distance to " O   HOH Z 385 " =    1.974
peak=   -3.340 closest distance to " C   LEU A 143 " =    1.152
peak=   -3.336 closest distance to " O   HOH Z  11 " =    2.011
peak=   -3.334 closest distance to " O   HOH Z 250 " =    1.446
peak=   -3.328 closest distance to " O   HOH Z  63 " =    1.443
peak=   -3.326 closest distance to " N   GLN A 122 " =    1.457
peak=   -3.326 closest distance to " O   ALA A  51 " =    1.400
peak=   -3.323 closest distance to " OD1 ASP A 191 " =    1.426
peak=   -3.320 closest distance to " O   ASN A  45 " =    1.908
peak=   -3.319 closest distance to " N   ALA A 226 " =    2.043
peak=   -3.314 closest distance to " O   SER A 146 " =    1.001
peak=   -3.312 closest distance to " CE3 TRP A 150 " =    1.977
peak=   -3.310 closest distance to " O   HOH Z   3 " =    1.902
peak=   -3.302 closest distance to " CG2 ILE A 263 " =    2.266
peak=   -3.299 closest distance to " OD1 ASN A 148 " =    1.625
peak=   -3.297 closest distance to " N   THR A 157 " =    1.522
peak=   -3.288 closest distance to " CD  GLN A  88 " =    0.811
peak=   -3.284 closest distance to " O   HOH Z 311 " =    3.552
peak=   -3.278 closest distance to " O   TRP A  92 " =    1.602
peak=   -3.272 closest distance to " O   HOH Z  88 " =    2.506
peak=   -3.266 closest distance to " ND2 ASN A 187 " =    1.494
peak=   -3.266 closest distance to " CD2 PHE A 192 " =    2.059
peak=   -3.264 closest distance to " CA  GLY A 133 " =    1.928
peak=   -3.264 closest distance to " C   GLN A 205 " =    1.970
peak=   -3.262 closest distance to " O   HOH Z 281 " =    2.753
peak=   -3.259 closest distance to " O   GLY A 211 " =    1.391
peak=   -3.254 closest distance to " CD1 ILE A 239 " =    2.039
peak=   -3.254 closest distance to " OH  TYR A 214 " =    1.197
peak=   -3.245 closest distance to " C   MET A 188 " =    1.563
peak=   -3.245 closest distance to " CG  GLU A 277 " =    1.194
peak=   -3.240 closest distance to " N   THR A 235 " =    1.311
peak=   -3.232 closest distance to " O   ALA A  34 " =    2.461
peak=   -3.230 closest distance to " O   HOH Z 148 " =    3.311
peak=   -3.228 closest distance to " O   HOH Z 298 " =    2.469
peak=   -3.226 closest distance to " CB  CYS A 254 " =    2.291
peak=   -3.225 closest distance to " CB  ASP A 149 " =    2.045
peak=   -3.221 closest distance to " CE  MET A  93 " =    1.130
peak=   -3.220 closest distance to " CB  ALA A  43 " =    2.357
peak=   -3.217 closest distance to " O   HOH Z  15 " =    1.641
peak=   -3.214 closest distance to " O   HOH Z 423 " =    1.126
peak=   -3.214 closest distance to " O   ASN A 249 " =    1.496
peak=   -3.206 closest distance to " O   SER A  22 " =    2.357
peak=   -3.202 closest distance to " CA  ARG A 139 " =    1.055
peak=   -3.201 closest distance to " O   HOH Z 263 " =    2.837
peak=   -3.193 closest distance to " CA  ASP A  27 " =    2.352
peak=   -3.192 closest distance to " CD2 LEU A 300 " =    2.835
peak=   -3.186 closest distance to " O   PRO A 198 " =    1.232
peak=   -3.184 closest distance to " N   SER A 276 " =    1.144
peak=   -3.184 closest distance to " OG1 THR A 246 " =    1.459
peak=   -3.176 closest distance to " CD2 TYR A 293 " =    2.012
peak=   -3.174 closest distance to " O   HOH Z  90 " =    2.734
peak=   -3.168 closest distance to " O   HOH Z  88 " =    2.093
peak=   -3.167 closest distance to " CD  GLN A  88 " =    1.969
peak=   -3.166 closest distance to " O   HOH Z 317 " =    2.541
peak=   -3.161 closest distance to " O   HOH Z  10 " =    1.417
peak=   -3.155 closest distance to " O   HOH Z 222 " =    1.107
peak=   -3.153 closest distance to " CD2 LEU A 237 " =    2.634
peak=   -3.145 closest distance to " O   HOH Z 322 " =    1.575
peak=   -3.142 closest distance to " CB  ASP A 286 " =    2.242
peak=   -3.141 closest distance to " O   HOH Z 377 " =    0.801
peak=   -3.131 closest distance to " CD  ARG A  36 " =    1.930
peak=   -3.118 closest distance to " OG  SER A 206 " =    1.722
peak=   -3.116 closest distance to " CB  TRP A  85 " =    2.483
peak=   -3.112 closest distance to " CG  ARG A 269 " =    2.555
peak=   -3.109 closest distance to " O   HOH Z 193 " =    2.015
peak=   -3.108 closest distance to " CB  ILE A  33 " =    2.916
peak=   -3.107 closest distance to " O   HOH Z 377 " =    1.306
peak=   -3.107 closest distance to " CA  GLY A 241 " =    3.167
peak=   -3.099 closest distance to " O   HOH Z  97 " =    1.659
peak=   -3.094 closest distance to " NH1 ARG A  36 " =    2.025
peak=   -3.094 closest distance to " C   PHE A 218 " =    1.613
peak=   -3.094 closest distance to " NE2 GLN A  58 " =    1.248
peak=   -3.092 closest distance to " NH2 ARG A  66 " =    4.815
peak=   -3.091 closest distance to " CG  TRP A 266 " =    1.812
peak=   -3.089 closest distance to " CZ  PHE A 130 " =    0.841
peak=   -3.085 closest distance to " CG1 VAL A 197 " =    2.215
peak=   -3.074 closest distance to " CG  GLU A 152 " =    0.856
peak=   -3.061 closest distance to " CA  TYR A  68 " =    2.879
peak=   -3.051 closest distance to " O   ASP A 231 " =    2.389
peak=   -3.026 closest distance to " O   HOH Z 348 " =    2.215

================= 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    :  0.3426 0.3422   6.093779e+00   6.099597e+00
   1_bss:  0.3258 0.3225   6.075968e+00   6.061821e+00
   1_xyz:  0.2201 0.2458   5.710778e+00   5.806610e+00
   1_adp:  0.2047 0.2529   5.670346e+00   5.834022e+00
   1_occ:  0.2043 0.2531   5.669073e+00   5.833758e+00
   2_bss:  0.2025 0.2509   5.661248e+00   5.827581e+00
   2_xyz:  0.1403 0.1827   5.321028e+00   5.524526e+00
   2_adp:  0.1274 0.1687   5.234910e+00   5.445179e+00
   2_occ:  0.1272 0.1685   5.233884e+00   5.444077e+00
   3_bss:  0.1271 0.1676   5.230168e+00   5.439803e+00
   3_xyz:  0.1181 0.1574   5.169000e+00   5.384924e+00
   3_adp:  0.1154 0.1570   5.155378e+00   5.378825e+00
   3_occ:  0.1153 0.1568   5.154953e+00   5.378393e+00
   4_bss:  0.1153 0.1567   5.154490e+00   5.378171e+00
   4_xyz:  0.1088 0.1525   5.114334e+00   5.354768e+00
   4_adp:  0.1083 0.1526   5.111917e+00   5.353238e+00
   4_occ:  0.1082 0.1525   5.111593e+00   5.353059e+00
   5_bss:  0.1081 0.1526   5.111686e+00   5.353144e+00
   5_xyz:  0.1096 0.1534   5.123475e+00   5.361866e+00
   5_adp:  0.1096 0.1534   5.124007e+00   5.363214e+00
   5_occ:  0.1096 0.1534   5.123839e+00   5.363100e+00
   5_bss:  0.1095 0.1534   5.123886e+00   5.363132e+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:  0.325  30.652  -3.103  -2.221   2.684  -0.000   0.000   0.000
   1_xyz:  0.325  30.652  -3.103  -2.221   2.684  -0.000   0.000   0.000
   1_adp:  0.325  30.652  -3.103  -2.221   2.684  -0.000   0.000   0.000
   1_occ:  0.325  30.652  -3.103  -2.221   2.684  -0.000   0.000   0.000
   2_bss:  0.312  37.488  -2.891  -2.585  -0.492  -0.000  -0.000  -0.000
   2_xyz:  0.312  37.488  -2.891  -2.585  -0.492  -0.000  -0.000  -0.000
   2_adp:  0.312  37.488  -2.891  -2.585  -0.492  -0.000  -0.000  -0.000
   2_occ:  0.312  37.488  -2.891  -2.585  -0.492  -0.000  -0.000  -0.000
   3_bss:  0.319  39.115  -2.678  -2.512  -1.477  -0.000  -0.000  -0.000
   3_xyz:  0.319  39.115  -2.678  -2.512  -1.477  -0.000  -0.000  -0.000
   3_adp:  0.319  39.115  -2.678  -2.512  -1.477  -0.000  -0.000  -0.000
   3_occ:  0.319  39.115  -2.678  -2.512  -1.477  -0.000  -0.000  -0.000
   4_bss:  0.318  39.382  -2.660  -2.492  -1.762  -0.000  -0.000  -0.000
   4_xyz:  0.318  39.382  -2.660  -2.492  -1.762  -0.000  -0.000  -0.000
   4_adp:  0.318  39.382  -2.660  -2.492  -1.762  -0.000  -0.000  -0.000
   4_occ:  0.318  39.382  -2.660  -2.492  -1.762  -0.000  -0.000  -0.000
   5_bss:  0.321  39.588  -2.505  -2.345  -1.693  -0.000  -0.000  -0.000
   5_xyz:  0.321  39.588  -2.505  -2.345  -1.693  -0.000  -0.000  -0.000
   5_adp:  0.321  39.588  -2.505  -2.345  -1.693  -0.000  -0.000  -0.000
   5_occ:  0.321  39.588  -2.505  -2.345  -1.693  -0.000  -0.000  -0.000
   5_bss:  0.321  39.534  -2.353  -2.192  -1.563  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  37.266 0.6778  0.8745    36153.713
   1_bss:  35.429 0.6968  0.8714    31536.695
   1_xyz:  24.365 0.8191  0.9784    15984.274
   1_adp:  25.624 0.8049  0.9689    17068.291
   1_occ:  25.629 0.8048  0.9688    17059.186
   2_bss:  25.207 0.8092  0.9363    16686.614
   2_xyz:  17.170 0.8874  0.9892     8385.464
   2_adp:  15.325 0.9037  0.9955     7219.272
   2_occ:  15.306 0.9039  0.9954     7200.652
   3_bss:  15.205 0.9047  0.9874     7138.698
   3_xyz:  13.959 0.9152  0.9902     6275.513
   3_adp:  13.792 0.9168  0.9869     6203.740
   3_occ:  13.782 0.9168  0.9868     6197.572
   4_bss:  13.775 0.9169  0.9838     6196.583
   4_xyz:  13.376 0.9198  0.9849     5889.136
   4_adp:  13.308 0.9205  0.9815     5879.268
   4_occ:  13.302 0.9205  0.9814     5876.593
   5_bss:  13.306 0.9205  0.9858     5880.557
   5_xyz:  13.429 0.9197  0.9850     5978.815
   5_adp:  13.443 0.9196  0.9814     5992.798
   5_occ:  13.440 0.9196  0.9813     5991.638
   5_bss:  13.441 0.9196  0.9845     5992.560
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6736e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6736e-01
   1_xyz:   1.108  0.008  0.068 15.140  0.004  4.107   7.1157e-02
   1_adp:   1.108  0.008  0.068 15.140  0.004  4.107   7.1157e-02
   1_occ:   1.108  0.008  0.068 15.140  0.004  4.107   7.1157e-02
   2_bss:   1.108  0.008  0.068 15.140  0.004  4.107   7.1157e-02
   2_xyz:   1.008  0.006  0.071 14.401  0.004  4.112   5.7197e-02
   2_adp:   1.008  0.006  0.071 14.401  0.004  4.112   5.7197e-02
   2_occ:   1.008  0.006  0.071 14.401  0.004  4.112   5.7197e-02
   3_bss:   1.008  0.006  0.071 14.401  0.004  4.112   5.7197e-02
   3_xyz:   0.844  0.005  0.063 14.209  0.003  4.111   4.5877e-02
   3_adp:   0.844  0.005  0.063 14.209  0.003  4.111   4.5877e-02
   3_occ:   0.844  0.005  0.063 14.209  0.003  4.111   4.5877e-02
   4_bss:   0.844  0.005  0.063 14.209  0.003  4.111   4.5877e-02
   4_xyz:   0.969  0.006  0.071 14.498  0.004  4.111   5.5358e-02
   4_adp:   0.969  0.006  0.071 14.498  0.004  4.111   5.5358e-02
   4_occ:   0.969  0.006  0.071 14.498  0.004  4.111   5.5358e-02
   5_bss:   0.969  0.006  0.071 14.498  0.004  4.111   5.5358e-02
   5_xyz:   0.871  0.005  0.066 14.216  0.003  4.111   4.7086e-02
   5_adp:   0.871  0.005  0.066 14.216  0.003  4.111   4.7086e-02
   5_occ:   0.871  0.005  0.066 14.216  0.003  4.111   4.7086e-02
   5_bss:   0.871  0.005  0.066 14.216  0.003  4.111   4.7086e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3869e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3869e-01
   1_xyz:   8.685  0.045  0.293 84.862  0.034  2.273   6.6244e-02
   1_adp:   8.685  0.045  0.293 84.862  0.034  2.273   6.6244e-02
   1_occ:   8.685  0.045  0.293 84.862  0.034  2.273   6.6244e-02
   2_bss:   8.685  0.045  0.293 84.862  0.034  2.273   6.6244e-02
   2_xyz:   7.036  0.035  0.256 81.797  0.037  2.336   4.3342e-02
   2_adp:   7.036  0.035  0.256 81.797  0.037  2.336   4.3342e-02
   2_occ:   7.036  0.035  0.256 81.797  0.037  2.336   4.3342e-02
   3_bss:   7.036  0.035  0.256 81.797  0.037  2.336   4.3342e-02
   3_xyz:   6.585  0.047  0.197 83.992  0.034  2.376   3.3891e-02
   3_adp:   6.585  0.047  0.197 83.992  0.034  2.376   3.3891e-02
   3_occ:   6.585  0.047  0.197 83.992  0.034  2.376   3.3891e-02
   4_bss:   6.585  0.047  0.197 83.992  0.034  2.376   3.3891e-02
   4_xyz:   6.392  0.033  0.222 83.123  0.037  2.310   4.8102e-02
   4_adp:   6.392  0.033  0.222 83.123  0.037  2.310   4.8102e-02
   4_occ:   6.392  0.033  0.222 83.123  0.037  2.310   4.8102e-02
   5_bss:   6.392  0.033  0.222 83.123  0.037  2.310   4.8102e-02
   5_xyz:   6.313  0.038  0.211 83.318  0.034  2.366   2.6888e-02
   5_adp:   6.313  0.038  0.211 83.318  0.034  2.366   2.6888e-02
   5_occ:   6.313  0.038  0.211 83.318  0.034  2.366   2.6888e-02
   5_bss:   6.313  0.038  0.211 83.318  0.034  2.366   2.6888e-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:  62.51   0.00  16.87  60.95   0.00  13.04  62.51   4.46  37.77
   1_occ:  62.51   0.00  16.87  60.95   0.00  13.04  62.51   4.46  37.77
   2_bss:  62.51   0.00  16.87  60.95   0.00  13.04  62.51   4.46  37.77
   2_xyz:  62.51   0.00  16.87  60.95   0.00  13.04  62.51   4.46  37.77
   2_adp:  69.74   1.36  16.94  67.90   1.36  12.99  69.74   5.62  38.42
   2_occ:  69.74   1.36  16.94  67.90   1.36  12.99  69.74   5.62  38.42
   3_bss:  69.74   1.36  16.94  67.90   1.36  12.99  69.74   5.62  38.42
   3_xyz:  69.74   1.36  16.94  67.90   1.36  12.99  69.74   5.62  38.42
   3_adp:  82.85   1.39  17.11  82.85   1.39  13.01  75.47   3.12  39.46
   3_occ:  82.85   1.39  17.11  82.85   1.39  13.01  75.47   3.12  39.46
   4_bss:  82.85   1.39  17.11  82.85   1.39  13.01  75.47   3.12  39.46
   4_xyz:  82.85   1.39  17.11  82.85   1.39  13.01  75.47   3.12  39.46
   4_adp:  85.35   1.60  16.87  85.35   1.60  12.88  76.76   4.50  38.59
   4_occ:  85.35   1.60  16.87  85.35   1.60  12.88  76.76   4.50  38.59
   5_bss:  85.35   1.60  16.87  85.35   1.60  12.88  76.76   4.50  38.59
   5_xyz:  85.35   1.60  16.87  85.35   1.60  12.88  76.76   4.50  38.59
   5_adp:  86.00   1.54  16.74  86.00   1.54  12.78  76.88   6.22  38.30
   5_occ:  86.00   1.54  16.74  86.00   1.54  12.78  76.88   6.22  38.30
   5_bss:  85.94   1.49  16.68  85.94   1.49  12.72  76.82   6.16  38.24
------------------------------------------------------------------------
 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:    1.686    0.014    0.268
   1_adp:    1.686    0.014    0.268
   1_occ:    1.686    0.014    0.268
   2_bss:    1.686    0.014    0.268
   2_xyz:    0.980    0.019    0.393
   2_adp:    0.980    0.019    0.393
   2_occ:    0.980    0.019    0.393
   3_bss:    0.980    0.019    0.393
   3_xyz:    1.130    0.028    0.409
   3_adp:    1.130    0.028    0.409
   3_occ:    1.130    0.028    0.409
   4_bss:    1.130    0.028    0.409
   4_xyz:    1.131    0.034    0.430
   4_adp:    1.131    0.034    0.430
   4_occ:    1.131    0.034    0.430
   5_bss:    1.131    0.034    0.430
   5_xyz:    1.192    0.037    0.433
   5_adp:    1.192    0.037    0.433
   5_occ:    1.192    0.037    0.433
   5_bss:    1.192    0.037    0.433
------------------------------------------------------------------------

CPU time actual refinement: 274.90


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_650/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_650/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_650/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_650/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_650/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 274.78 
  Macro-tasks:
    bulk solvent and scale       = 30.43  
    individual site refinement   = 112.93 
    weights calculation          = 24.99  
    collect and process          = 5.54   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 173.99 
  Micro-tasks:
    mask                            = 0.99   
    f_calc                          = 88.18  
    alpha_beta                      = 7.04   
    target                          = 1.02   
    gradients_wrt_atomic_parameters = 96.03  
    fmodel                         = 5.50   
    r_factors                      = 0.19   
    phase_errors                   = 9.05   
    foms                           = 0.17   
    TOTAL for micro-tasks          = 208.17 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 3.902 micro seconds
Total CPU time: 4.77 minutes
from_scatterers_fft:    655 calls, 87.89 s
gradients_fft:          600 calls, 84.36 s

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

# Date 2008-01-16 Time 05:18:43 PST -0800 (1200489523.69 s)
Start R-work = 0.3426, R-free = 0.3422 (no bulk solvent and anisotropic scale)
Final R-work = 0.1350, R-free = 0.1747 (no bulk solvent and anisotropic scale)

Start R-work = 0.3258, R-free = 0.3225
Final R-work = 0.1095, R-free = 0.1534