# Date 2008-01-16 Time 05:05:19 PST -0800 (1200488719.45 s)
#phil __OFF__

Command line arguments: "../586.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17008
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 586

-------------------------------------------------------------------------------
  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: (69.8988, 47.8686, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.33, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.8686, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9494 1.98135
Completeness in resolution range: 0.954537
Completeness with d_max=infinity: 0.951569

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9494
                             d_min =   1.9814

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: (69.8988, 47.8686, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9494 1.98135
Completeness in resolution range: 0.954537
Completeness with d_max=infinity: 0.951569

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9498 -  4.2393 [2158/2186]  1942   216  10.0%
  bin  2:  4.2393 -  3.3776 [2059/2082]  1853   206  10.0%
  bin  3:  3.3776 -  2.9544 [2046/2071]  1840   206  10.1%
  bin  4:  2.9544 -  2.6860 [2031/2047]  1830   201   9.9%
  bin  5:  2.6860 -  2.4944 [1999/2036]  1796   203  10.2%
  bin  6:  2.4944 -  2.3479 [1995/2029]  1804   191   9.6%
  bin  7:  2.3479 -  2.2307 [1978/2015]  1777   201  10.2%
  bin  8:  2.2307 -  2.1339 [1988/2030]  1784   204  10.3%
  bin  9:  2.1339 -  2.0520 [1977/2012]  1785   192   9.7%
  bin 10:  2.0520 -  1.9813 [1358/2014]  1219   139  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_586/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: 0.13 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: 27
        2.42 -     3.04: 2199
        3.04 -     3.66: 4678
        3.66 -     4.28: 8964
        4.28 -     4.90: 12408
  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 206 " - " O   HOH Z 342 "  1.865 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.868 3.040 -x+1/2,-y+1,z-1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.881 3.040 -x+1/2,-y+1,z+1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.982 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28271 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_586/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_586/model_refine_001.geo

CPU time processing inputs: 9.01


============================ 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 = 69.89875 47.8686 85.5261 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: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4028   r_free= 0.3916   ksol= 0.00   Bsol= 0.00   scale= 0.928    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.209226                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9498 -  4.7281 0.99   1396  158 0.3281 0.3531      6.4689      6.4909|
|  2:  4.7281 -  3.7727 0.99   1353  145 0.3425 0.3384      6.7046      6.6742|
|  3:  3.7727 -  3.3017 0.99   1314  152 0.3576 0.3448      6.5604      6.5513|
|  4:  3.3017 -  3.0025 0.99   1323  141 0.3762 0.3454      6.4194      6.3244|
|  5:  3.0025 -  2.7887 0.98   1286  145 0.4135 0.3708      6.2982      6.2418|
|  6:  2.7887 -  2.6253 0.99   1296  144 0.4374 0.3899      6.2296      6.0669|
|  7:  2.6253 -  2.4944 0.99   1293  147 0.4305 0.3680      6.1846      6.0573|
|  8:  2.4944 -  2.3863 0.99   1296  138 0.4400 0.4806      6.1173      6.1596|
|  9:  2.3863 -  2.2948 0.99   1281  142 0.4653 0.4447      6.0798       6.133|
| 10:  2.2948 -  2.2158 0.97   1261  142 0.4540 0.4509      6.0611      6.0447|
| 11:  2.2158 -  2.1467 0.98   1270  147 0.4613 0.4281      6.0005      5.9759|
| 12:  2.1467 -  2.0855 1.00   1270  136 0.4423 0.4767      5.9211      5.9768|
| 13:  2.0855 -  2.0308 0.96   1261  137 0.4681 0.4400      5.8338      5.8343|
| 14:  2.0308 -  1.9813 0.56    730   85 0.4473 0.4668      5.7914      5.7062|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9498 -  4.7281  1396   158  0.72  32.57   0.85     0.75      64525.44|
|  2:  4.7281 -  3.7727  1353   145  0.77  29.05   0.94     0.85      73991.12|
|  3:  3.7727 -  3.3017  1314   152  0.72  33.32   0.95     0.88      72513.10|
|  4:  3.3017 -  3.0025  1323   141  0.69  36.64   0.95     0.87      60012.84|
|  5:  3.0025 -  2.7887  1286   145  0.64  40.28   0.93     0.84      48444.28|
|  6:  2.7887 -  2.6253  1296   144  0.63  41.54   0.93     0.82      40814.73|
|  7:  2.6253 -  2.4944  1293   147  0.62  42.35   0.96     0.80      39048.56|
|  8:  2.4944 -  2.3863  1296   138  0.55  48.20   0.95     0.75      41197.17|
|  9:  2.3863 -  2.2948  1281   142  0.51  51.30   0.94     0.71      40298.16|
| 10:  2.2948 -  2.2158  1261   142  0.50  51.88   0.98     0.70      38669.27|
| 11:  2.2158 -  2.1467  1270   147  0.51  51.05   0.97     0.74      34256.70|
| 12:  2.1467 -  2.0855  1270   136  0.52  50.86   1.00     0.75      32029.59|
| 13:  2.0855 -  2.0308  1261   137  0.49  53.44   0.96     0.71      27728.11|
| 14:  2.0308 -  1.9813   730    85  0.48  54.00   1.01     0.65      24429.12|
|alpha:            min =        0.65 max =            0.88 mean =         0.78|
|beta:             min =    24429.12 max =        73991.12 mean =     46585.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.60|
|phase err.(work): min =        0.00 max =           89.99 mean =        43.52|
|phase err.(test): min =        0.00 max =           90.00 mean =        43.60|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.845782              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.981   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.263758              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.240   (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:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       20 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      192 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2007 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1864 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2814 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4620 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4344 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5659 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6749 |
|-----------------------------------------------------------------------------|
|-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 |   4.113    4.900  1.806 |       0.250 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    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: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4028   r_free= 0.3916   ksol= 0.00   Bsol= 0.00   scale= 0.928    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.209226                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3895   r_free= 0.3773   ksol= 0.30   Bsol= 26.35   scale= 0.956   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.33,5.08,-0.81,0.00,-0.00,-0.00); trace/3= 0.31                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.192593                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.349621              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.684   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.678300              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.015   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3895      final r-factor (work) = 0.2893          |
| start r-factor (free) = 0.3773      final r-factor (free) = 0.3121          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.7340 = 5.35 * 0.50 * 6.1935 + 1.00 * 0.1675                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.1773 = 5.35 * 0.50 * 6.0110 + 1.00 * 0.0990                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2893      final r-factor (work) = 0.2637          |
| start r-factor (free) = 0.3121      final r-factor (free) = 0.3248          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0832 = 0.68 * 1.00 * 6.0110 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0099 = 0.68 * 1.00 * 5.8920 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.06   17.48    None  None   None       |
|    all(noH): 2823   0      0.00    90.06   17.48    None  None   None       |
|    Sol.    : 438    0      2.25    90.06   36.58    None  None   None       |
|    Mac.    : 2385   0      0.00    84.53   13.97    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.006:  866   |   5:    45.031 -  54.038:   81        |
|      1:     9.006 -  18.013: 1011   |   6:    54.038 -  63.044:   49        |
|      2:    18.013 -  27.019:  421   |   7:    63.044 -  72.050:   29        |
|      3:    27.019 -  36.025:  217   |   8:    72.050 -  81.057:   14        |
|      4:    36.025 -  45.031:  131   |   9:    81.057 -  90.063:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2637 r_free = 0.3248             target_work(ml) = 5.902         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2634 r_free = 0.3246             target_work(ml) = 5.902         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2634   r_free= 0.3246   ksol= 0.30   Bsol= 26.35   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.33,5.08,-0.81,0.00,-0.00,-0.00); trace/3= 0.31                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.901739                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2620   r_free= 0.3225   ksol= 0.31   Bsol= 49.61   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,2.17,-0.72,0.00,-0.00,-0.00); trace/3= -0.30                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.899449                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.548989              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.007   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.286731              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.326  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2620      final r-factor (work) = 0.1898          |
| start r-factor (free) = 0.3225      final r-factor (free) = 0.2361          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.3906 = 6.55 * 0.50 * 5.8915 + 1.00 * 0.0990                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.9800 = 6.55 * 0.50 * 5.7712 + 1.00 * 0.0821                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1898      final r-factor (work) = 0.1717          |
| start r-factor (free) = 0.2361      final r-factor (free) = 0.2181          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6682 = 0.29 * 1.00 * 5.7712 + 1.00 * 0.0134                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5981 = 0.29 * 1.00 * 5.5412 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.54   16.96    None  None   None       |
|    all(noH): 2823   0      0.00    87.54   16.96    None  None   None       |
|    Sol.    : 438    0      4.55    87.54   37.93    None  None   None       |
|    Mac.    : 2385   0      0.00    80.53   13.11    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.754:  877   |   5:    43.768 -  52.522:   94        |
|      1:     8.754 -  17.507: 1117   |   6:    52.522 -  61.276:   48        |
|      2:    17.507 -  26.261:  311   |   7:    61.276 -  70.030:   27        |
|      3:    26.261 -  35.015:  179   |   8:    70.030 -  78.783:   18        |
|      4:    35.015 -  43.768:  148   |   9:    78.783 -  87.537:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1717 r_free = 0.2181             target_work(ml) = 5.509         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1716 r_free = 0.2182             target_work(ml) = 5.508         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1716   r_free= 0.2182   ksol= 0.31   Bsol= 49.61   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,2.17,-0.72,0.00,-0.00,-0.00); trace/3= -0.30                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.508434                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1710   r_free= 0.2174   ksol= 0.32   Bsol= 54.37   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,0.17,-0.91,0.00,-0.00,-0.00); trace/3= -0.97                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.505718                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.237432              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.998  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.895827              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.315  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1710      final r-factor (work) = 0.1322          |
| start r-factor (free) = 0.2174      final r-factor (free) = 0.1763          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.5935 = 5.24 * 0.50 * 5.5414 + 1.00 * 0.0821                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.2005 = 5.24 * 0.50 * 5.3927 + 1.00 * 0.0786                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1322      final r-factor (work) = 0.1206          |
| start r-factor (free) = 0.1763      final r-factor (free) = 0.1680          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 26.4109 = 4.90 * 1.00 * 5.3927 + 1.00 * 0.0093                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 25.6338 = 4.90 * 1.00 * 5.2335 + 1.00 * 0.0115                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.40    95.27   17.24    None  None   None       |
|    all(noH): 2823   0      0.40    95.27   17.24    None  None   None       |
|    Sol.    : 438    0      5.30    95.27   42.09    None  None   None       |
|    Mac.    : 2385   0      0.40    94.39   12.68    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:     0.397 -   9.885: 1136   |   5:    47.836 -  57.324:   96        |
|      1:     9.885 -  19.373: 1026   |   6:    57.324 -  66.812:   72        |
|      2:    19.373 -  28.861:  212   |   7:    66.812 -  76.299:   35        |
|      3:    28.861 -  38.348:  125   |   8:    76.299 -  85.787:   10        |
|      4:    38.348 -  47.836:  104   |   9:    85.787 -  95.275:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1206 r_free = 0.1680             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1206 r_free = 0.1679             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1679   ksol= 0.32   Bsol= 54.37   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,0.17,-0.91,0.00,-0.00,-0.00); trace/3= -0.97                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.207236                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1210   r_free= 0.1677   ksol= 0.33   Bsol= 60.24   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-0.55,-0.92,-0.00,-0.00,-0.00); trace/3= -1.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.207414                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.897309              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.436  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.915697              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 103.349  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1210      final r-factor (work) = 0.1174          |
| start r-factor (free) = 0.1677      final r-factor (free) = 0.1634          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0449 = 1.90 * 0.50 * 5.2351 + 1.00 * 0.0786                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9885 = 1.90 * 0.50 * 5.1981 + 1.00 * 0.0573                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1174      final r-factor (work) = 0.1163          |
| start r-factor (free) = 0.1634      final r-factor (free) = 0.1625          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7713 = 0.92 * 1.00 * 5.1981 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7578 = 0.92 * 1.00 * 5.1835 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.75   16.92    None  None   None       |
|    all(noH): 2823   0      0.00    99.75   16.92    None  None   None       |
|    Sol.    : 438    0      5.12    94.85   41.61    None  None   None       |
|    Mac.    : 2385   0      0.00    99.75   12.39    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.975: 1203   |   5:    49.875 -  59.850:   92        |
|      1:     9.975 -  19.950: 1009   |   6:    59.850 -  69.825:   55        |
|      2:    19.950 -  29.925:  187   |   7:    69.825 -  79.800:   25        |
|      3:    29.925 -  39.900:  131   |   8:    79.800 -  89.775:    8        |
|      4:    39.900 -  49.875:  108   |   9:    89.775 -  99.749:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1163 r_free = 0.1625             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1163 r_free = 0.1626             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1626   ksol= 0.33   Bsol= 60.24   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-0.55,-0.92,-0.00,-0.00,-0.00); trace/3= -1.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.179448                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1162   r_free= 0.1626   ksol= 0.33   Bsol= 60.24   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.93,-0.60,-0.73,-0.00,-0.00,-0.00); trace/3= -1.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.179511                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.515211              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.552  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.995410              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.074  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1162      final r-factor (work) = 0.1110          |
| start r-factor (free) = 0.1626      final r-factor (free) = 0.1601          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5764 = 2.52 * 0.50 * 5.1837 + 1.00 * 0.0573                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5576 = 2.52 * 0.50 * 5.1609 + 1.00 * 0.0672                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1110      final r-factor (work) = 0.1103          |
| start r-factor (free) = 0.1601      final r-factor (free) = 0.1593          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1483 = 1.00 * 1.00 * 5.1609 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1332 = 1.00 * 1.00 * 5.1459 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.01  16.55    None  None   None       |
|    all(noH): 2823   0      0.00    108.01  16.55    None  None   None       |
|    Sol.    : 438    0      4.85    93.12   40.60    None  None   None       |
|    Mac.    : 2385   0      0.00    108.01  12.13    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.801: 1420   |   5:    54.005 -  64.806:   82        |
|      1:    10.801 -  21.602:  841   |   6:    64.806 -  75.607:   30        |
|      2:    21.602 -  32.403:  189   |   7:    75.607 -  86.408:   12        |
|      3:    32.403 -  43.204:  126   |   8:    86.408 -  97.209:    6        |
|      4:    43.204 -  54.005:  115   |   9:    97.209 - 108.010:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1103 r_free = 0.1593             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1103 r_free = 0.1594             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1594   ksol= 0.33   Bsol= 60.24   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.93,-0.60,-0.73,-0.00,-0.00,-0.00); trace/3= -1.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.144310                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9498 -  4.7281 0.99   1396  158 0.0950 0.1266      5.3492      5.5267|
|  2:  4.7281 -  3.7727 0.99   1353  145 0.0817 0.1077      5.3979      5.6108|
|  3:  3.7727 -  3.3017 0.99   1314  152 0.1014 0.1477       5.444      5.8376|
|  4:  3.3017 -  3.0025 0.99   1323  141 0.1229 0.1602       5.459      5.6296|
|  5:  3.0025 -  2.7887 0.98   1286  145 0.1323 0.1751      5.3422       5.523|
|  6:  2.7887 -  2.6253 0.99   1296  144 0.1274 0.2033      5.2456      5.4815|
|  7:  2.6253 -  2.4944 0.99   1293  147 0.1203 0.1701      5.1513      5.4019|
|  8:  2.4944 -  2.3863 0.99   1296  138 0.1165 0.1708      5.0823       5.319|
|  9:  2.3863 -  2.2948 0.99   1281  142 0.1158 0.1832      5.0229      5.3523|
| 10:  2.2948 -  2.2158 0.97   1261  142 0.1108 0.1811      4.9829      5.1991|
| 11:  2.2158 -  2.1467 0.98   1270  147 0.1146 0.1807      4.9296      5.2602|
| 12:  2.1467 -  2.0855 1.00   1270  136 0.1076 0.1667      4.8666      5.1349|
| 13:  2.0855 -  2.0308 0.96   1261  137 0.1114 0.1717      4.7861       5.077|
| 14:  2.0308 -  1.9813 0.56    730   85 0.1088 0.1754      4.7096      4.9285|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9498 -  4.7281  1396   158  0.94   8.94   0.97     0.95       6938.44|
|  2:  4.7281 -  3.7727  1353   145  0.95   7.83   1.01     1.00       8581.66|
|  3:  3.7727 -  3.3017  1314   152  0.94  10.79   1.03     1.02       9891.04|
|  4:  3.3017 -  3.0025  1323   141  0.92  14.06   1.01     0.98      10490.16|
|  5:  3.0025 -  2.7887  1286   145  0.90  16.35   1.00     0.97       8677.14|
|  6:  2.7887 -  2.6253  1296   144  0.89  17.03   0.98     0.95       7643.68|
|  7:  2.6253 -  2.4944  1293   147  0.91  15.35   0.99     0.96       6180.71|
|  8:  2.4944 -  2.3863  1296   138  0.91  15.58   0.99     0.96       5627.00|
|  9:  2.3863 -  2.2948  1281   142  0.90  15.86   0.99     0.95       4975.64|
| 10:  2.2948 -  2.2158  1261   142  0.90  16.04   0.99     0.95       4751.92|
| 11:  2.2158 -  2.1467  1270   147  0.90  16.08   0.98     0.94       4254.18|
| 12:  2.1467 -  2.0855  1270   136  0.91  14.98   0.99     0.98       3892.62|
| 13:  2.0855 -  2.0308  1261   137  0.90  16.54   0.98     0.98       3425.06|
| 14:  2.0308 -  1.9813   730    85  0.91  15.35   0.96     0.93       2797.25|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2797.25 max =        10490.16 mean =      6443.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.83 mean =        14.24|
|phase err.(test): min =        0.00 max =           89.47 mean =        13.75|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1102   r_free= 0.1593   ksol= 0.32   Bsol= 56.16   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,-0.52,-0.49,-0.00,-0.00,-0.00); trace/3= -0.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.144489                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1102   r_free= 0.1593   ksol= 0.32   Bsol= 56.16   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,-0.52,-0.49,-0.00,-0.00,-0.00); trace/3= -0.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.144489                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9498 -  4.7281 0.99   1396  158 0.0949 0.1266      5.3498      5.5269|
|  2:  4.7281 -  3.7727 0.99   1353  145 0.0814 0.1074      5.3958      5.6077|
|  3:  3.7727 -  3.3017 0.99   1314  152 0.1013 0.1476      5.4428      5.8378|
|  4:  3.3017 -  3.0025 0.99   1323  141 0.1231 0.1603      5.4597        5.63|
|  5:  3.0025 -  2.7887 0.98   1286  145 0.1325 0.1750       5.343      5.5232|
|  6:  2.7887 -  2.6253 0.99   1296  144 0.1275 0.2031      5.2457      5.4812|
|  7:  2.6253 -  2.4944 0.99   1293  147 0.1204 0.1703      5.1518      5.4023|
|  8:  2.4944 -  2.3863 0.99   1296  138 0.1165 0.1711      5.0831      5.3202|
|  9:  2.3863 -  2.2948 0.99   1281  142 0.1158 0.1831      5.0234      5.3529|
| 10:  2.2948 -  2.2158 0.97   1261  142 0.1109 0.1813      4.9838      5.2006|
| 11:  2.2158 -  2.1467 0.98   1270  147 0.1147 0.1805        4.93      5.2601|
| 12:  2.1467 -  2.0855 1.00   1270  136 0.1075 0.1668      4.8667      5.1358|
| 13:  2.0855 -  2.0308 0.96   1261  137 0.1114 0.1717      4.7863      5.0768|
| 14:  2.0308 -  1.9813 0.56    730   85 0.1088 0.1753      4.7098      4.9286|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9498 -  4.7281  1396   158  0.94   8.94   0.97     0.95       6948.80|
|  2:  4.7281 -  3.7727  1353   145  0.95   7.82   1.01     1.00       8554.02|
|  3:  3.7727 -  3.3017  1314   152  0.94  10.76   1.03     1.02       9849.01|
|  4:  3.3017 -  3.0025  1323   141  0.92  14.07   1.01     0.99      10498.04|
|  5:  3.0025 -  2.7887  1286   145  0.90  16.35   1.00     0.97       8675.52|
|  6:  2.7887 -  2.6253  1296   144  0.89  17.02   0.99     0.96       7642.58|
|  7:  2.6253 -  2.4944  1293   147  0.91  15.35   0.99     0.97       6185.92|
|  8:  2.4944 -  2.3863  1296   138  0.91  15.60   1.00     0.97       5636.97|
|  9:  2.3863 -  2.2948  1281   142  0.90  15.88   1.00     0.96       4989.72|
| 10:  2.2948 -  2.2158  1261   142  0.90  16.06   1.00     0.96       4761.83|
| 11:  2.2158 -  2.1467  1270   147  0.90  16.09   0.99     0.95       4259.34|
| 12:  2.1467 -  2.0855  1270   136  0.91  14.99   1.00     0.99       3896.79|
| 13:  2.0855 -  2.0308  1261   137  0.90  16.54   1.00     0.99       3424.24|
| 14:  2.0308 -  1.9813   730    85  0.91  15.35   0.98     0.94       2795.08|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2795.08 max =        10498.04 mean =      6442.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.24|
|phase err.(test): min =        0.00 max =           89.62 mean =        13.75|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.01  16.55    None  None   None       |
|    all(noH): 2823   0      0.00    108.01  16.55    None  None   None       |
|    Sol.    : 438    0      4.86    93.12   40.61    None  None   None       |
|    Mac.    : 2385   0      0.00    108.01  12.14    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.804: 1420   |   5:    54.008 -  64.809:   82        |
|      1:    10.804 -  21.605:  841   |   6:    64.809 -  75.610:   30        |
|      2:    21.605 -  32.406:  189   |   7:    75.610 -  86.411:   12        |
|      3:    32.406 -  43.207:  126   |   8:    86.411 -  97.212:    6        |
|      4:    43.207 -  54.008:  115   |   9:    97.212 - 108.013:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 293         
Filter by distance & map next to the model:
   mapped sites are within: 0.581 - 4.582
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 288 from: 293
   mapped sites are within: 0.707 - 4.582

peak=    5.841 closest distance to " O   HOH Z 113 " =    2.388
peak=    5.267 closest distance to " CB  GLN A 223 " =    1.395
peak=    5.208 closest distance to " CB  SER A  63 " =    1.146
peak=    4.888 closest distance to " CB  ARG A 275 " =    0.914
peak=    4.846 closest distance to " CG  PRO A 213 " =    1.219
peak=    4.842 closest distance to " CB  GLN A 183 " =    1.305
peak=    4.792 closest distance to " C   PRO A 198 " =    1.474
peak=    4.778 closest distance to " CA  TYR A  30 " =    0.921
peak=    4.727 closest distance to " O   HOH Z 232 " =    2.329
peak=    4.719 closest distance to " O   HOH Z  15 " =    2.114
peak=    4.603 closest distance to " O   HOH Z 403 " =    1.800
peak=    4.581 closest distance to " O   HOH Z 209 " =    2.350
peak=    4.533 closest distance to " O   HOH Z  59 " =    2.381
peak=    4.507 closest distance to " O   HOH Z 134 " =    1.589
peak=    4.491 closest distance to " O   HOH Z 234 " =    3.714
peak=    4.484 closest distance to " CB  GLU A 152 " =    1.132
peak=    4.384 closest distance to " O   HOH Z 402 " =    1.557
peak=    4.384 closest distance to " CA  ALA A  21 " =    1.372
peak=    4.376 closest distance to " CB  ARG A 190 " =    1.721
peak=    4.333 closest distance to " CB  ARG A  79 " =    1.439
peak=    4.322 closest distance to " O   HOH Z  97 " =    1.893
peak=    4.321 closest distance to " O   HOH Z  80 " =    1.670
peak=    4.290 closest distance to " CG1 ILE A  33 " =    1.215
peak=    4.278 closest distance to " O   SER A  87 " =    2.195
peak=    4.268 closest distance to " O   HOH Z 210 " =    0.969
peak=    4.262 closest distance to " O   HOH Z 352 " =    1.831
peak=    4.250 closest distance to " CB  TYR A 169 " =    0.875
peak=    4.243 closest distance to " CG  ARG A  66 " =    2.720
peak=    4.202 closest distance to " NH2BARG A 145 " =    2.129
peak=    4.182 closest distance to " CG  PRO A  90 " =    1.111
peak=    4.174 closest distance to " O   HOH Z  43 " =    2.223
peak=    4.172 closest distance to " O   HOH Z  20 " =    1.507
peak=    4.162 closest distance to " O   HOH Z 279 " =    2.144
peak=    4.160 closest distance to " CB  GLU A 128 " =    1.175
peak=    4.148 closest distance to " CB  GLU A 277 " =    3.604
peak=    4.146 closest distance to " CG  PRO A 198 " =    1.145
peak=    4.144 closest distance to " O   HOH Z  63 " =    1.955
peak=    4.126 closest distance to " NE2 GLN A  11 " =    1.018
peak=    4.125 closest distance to " O   HOH Z 298 " =    1.871
peak=    4.123 closest distance to " O   HOH Z  44 " =    1.969
peak=    4.093 closest distance to " NH2 ARG A 156 " =    1.175
peak=    4.067 closest distance to " O   HOH Z 368 " =    2.100
peak=    4.047 closest distance to " CB  SER A   3 " =    1.265
peak=    4.047 closest distance to " O   HOH Z 126 " =    1.613
peak=    4.036 closest distance to " OD1 ASN A  69 " =    2.544
peak=    4.033 closest distance to " O   HOH Z 142 " =    1.544
peak=    4.027 closest distance to " CA  ASN A 176 " =    1.260
peak=    4.007 closest distance to " CA  ARG A 195 " =    1.271
peak=    4.006 closest distance to " O   HOH Z 284 " =    2.917
peak=    4.001 closest distance to " O   HOH Z 423 " =    1.945
peak=    4.000 closest distance to " O   HOH Z 193 " =    1.810
peak=    3.999 closest distance to " O   HOH Z  78 " =    1.715
peak=    3.991 closest distance to " O   HOH Z 369 " =    2.413
peak=    3.990 closest distance to " CD  ARG A 269 " =    0.974
peak=    3.984 closest distance to " O   HOH Z 345 " =    1.657
peak=    3.980 closest distance to " O   HOH Z 124 " =    1.289
peak=    3.976 closest distance to " O   HOH Z  68 " =    2.080
peak=    3.968 closest distance to " NZ  LYS A 117 " =    3.083
peak=    3.946 closest distance to " CG  GLN A  58 " =    2.606
peak=    3.942 closest distance to " CB  SER A 141 " =    1.014
peak=    3.940 closest distance to " CD2 TRP A 179 " =    1.421
peak=    3.938 closest distance to " O   HOH Z 357 " =    2.049
peak=    3.937 closest distance to " O   HOH Z 411 " =    3.591
peak=    3.934 closest distance to " O   HOH Z 374 " =    2.731
peak=    3.933 closest distance to " O   HOH Z 389 " =    2.005
peak=    3.920 closest distance to " O   HOH Z 316 " =    2.994
peak=    3.913 closest distance to " CG2 THR A 221 " =    1.157
peak=    3.894 closest distance to " CB  TRP A 179 " =    1.300
peak=    3.889 closest distance to " O   HOH Z  61 " =    1.533
peak=    3.888 closest distance to " O   HOH Z 421 " =    1.706
peak=    3.881 closest distance to " O   HOH Z 406 " =    1.565
peak=    3.872 closest distance to " O   HOH Z 108 " =    2.687
peak=    3.872 closest distance to " CA  ALA A  51 " =    0.957
peak=    3.870 closest distance to " O   HOH Z 154 " =    1.325
peak=    3.846 closest distance to " OD2 ASP A 286 " =    2.827
peak=    3.840 closest distance to " O   HOH Z  40 " =    1.808
peak=    3.836 closest distance to " O   HOH Z  21 " =    1.786
peak=    3.836 closest distance to " O   HOH Z   6 " =    2.199
peak=    3.834 closest distance to " O   HOH Z 189 " =    2.196
peak=    3.829 closest distance to " O   HOH Z 132 " =    2.685
peak=    3.823 closest distance to " OG BSER A 164 " =    2.408
peak=    3.818 closest distance to " O   HOH Z 383 " =    2.086
peak=    3.815 closest distance to " O   HOH Z 132 " =    2.467
peak=    3.813 closest distance to " O   HOH Z 419 " =    1.643
peak=    3.805 closest distance to " O   HOH Z 128 " =    2.082
peak=    3.801 closest distance to " O   HOH Z 272 " =    1.873
peak=    3.796 closest distance to " CB  LEU A 228 " =    1.149
peak=    3.796 closest distance to " CB  VAL A 202 " =    1.501
peak=    3.791 closest distance to " CB  ASN A 148 " =    1.341
peak=    3.784 closest distance to " CG2 VAL A 197 " =    1.110
peak=    3.778 closest distance to " O   HOH Z 158 " =    2.931
peak=    3.775 closest distance to " O   HOH Z  54 " =    1.670
peak=    3.769 closest distance to " O   HOH Z 214 " =    2.560
peak=    3.768 closest distance to " O   HOH Z 418 " =    1.416
peak=    3.760 closest distance to " O   HOH Z 227 " =    1.681
peak=    3.758 closest distance to " NH2AARG A 145 " =    2.324
peak=    3.755 closest distance to " O   HOH Z 250 " =    1.420
peak=    3.755 closest distance to " CD1 LEU A 300 " =    1.183
peak=    3.754 closest distance to " OG  SER A  62 " =    2.914
peak=    3.746 closest distance to " CD  LYS A 166 " =    1.386
peak=    3.742 closest distance to " O   HOH Z 245 " =    1.387
peak=    3.738 closest distance to " CA  ARG A  36 " =    1.081
peak=    3.730 closest distance to " O   HOH Z 344 " =    3.114
peak=    3.714 closest distance to " CZ  PHE A 218 " =    1.112
peak=    3.708 closest distance to " O   HOH Z 426 " =    1.473
peak=    3.707 closest distance to " O   HOH Z 365 " =    2.822
peak=    3.702 closest distance to " O   HOH Z 346 " =    1.483
peak=    3.698 closest distance to " O   HOH Z 163 " =    1.496
peak=    3.696 closest distance to " CG  PRO A 243 " =    1.176
peak=    3.695 closest distance to " O   HOH Z 327 " =    1.690
peak=    3.689 closest distance to " O   HOH Z 361 " =    3.403
peak=    3.676 closest distance to " O   HOH Z 345 " =    2.873
peak=    3.670 closest distance to " O   ALA A 165 " =    1.359
peak=    3.663 closest distance to " O   HOH Z 147 " =    1.801
peak=    3.658 closest distance to " OD2 ASP A 298 " =    3.973
peak=    3.653 closest distance to " CA  LYS A 117 " =    1.257
peak=    3.652 closest distance to " O   HOH Z 287 " =    1.982
peak=    3.648 closest distance to " CA  ALA A 160 " =    0.834
peak=    3.641 closest distance to " O   HOH Z 247 " =    1.361
peak=    3.635 closest distance to " C   ILE A 106 " =    1.875
peak=    3.629 closest distance to " O   HOH Z 416 " =    2.956
peak=    3.624 closest distance to " O   HOH Z  35 " =    2.333
peak=    3.620 closest distance to " O   HOH Z 334 " =    1.370
peak=    3.619 closest distance to " CA  THR A 221 " =    0.951
peak=    3.615 closest distance to " ND2 ASN A 187 " =    1.548
peak=    3.608 closest distance to " CD2 LEU A 297 " =    0.829
peak=    3.605 closest distance to " O   HOH Z 130 " =    2.307
peak=    3.596 closest distance to " OG1 THR A 294 " =    2.377
peak=    3.594 closest distance to " CG  ARG A  66 " =    0.982
peak=    3.593 closest distance to " O   HOH Z 126 " =    1.974
peak=    3.590 closest distance to " N   ASN A  39 " =    1.321
peak=    3.587 closest distance to " O   HOH Z 386 " =    2.310
peak=    3.585 closest distance to " NZ  LYS A 117 " =    1.930
peak=    3.580 closest distance to " O   HOH Z 250 " =    1.748
peak=    3.571 closest distance to " O   HOH Z 427 " =    2.846
peak=    3.570 closest distance to " O   HOH Z 417 " =    3.065
peak=    3.570 closest distance to " CG2 ILE A 120 " =    1.047
peak=    3.567 closest distance to " O   HOH Z 156 " =    3.461
peak=    3.567 closest distance to " O   HOH Z 155 " =    3.217
peak=    3.559 closest distance to " O   HOH Z 313 " =    1.885
peak=    3.552 closest distance to " CB  ASP A 140 " =    0.898
peak=    3.547 closest distance to " CG2 ILE A  20 " =    1.387
peak=    3.528 closest distance to " O   HOH Z  30 " =    1.104
peak=    3.526 closest distance to " CB  ARG A 139 " =    0.875
peak=    3.526 closest distance to " O   HOH Z 102 " =    1.201
peak=    3.524 closest distance to " CB  ASN A  39 " =    0.832
peak=    3.518 closest distance to " CB  SER A  62 " =    0.739
peak=    3.514 closest distance to " OG  SER A 245 " =    1.593
peak=    3.513 closest distance to " CG1BVAL A  72 " =    1.711
peak=    3.512 closest distance to " CB  ALA A 248 " =    1.326
peak=    3.506 closest distance to " O   ALA A 158 " =    1.188
peak=    3.503 closest distance to " CZ  PHE A  38 " =    1.393
peak=    3.502 closest distance to " O   HOH Z 291 " =    1.546
peak=    3.500 closest distance to " O   GLY A  57 " =    2.651
peak=    3.495 closest distance to " CA  ASP A 191 " =    0.965
peak=    3.493 closest distance to " CD  ARG A 159 " =    0.820
peak=    3.489 closest distance to " O   HOH Z  49 " =    1.834
peak=    3.486 closest distance to " CB  MET A  40 " =    0.881
peak=    3.483 closest distance to " CA  ASP A 162 " =    1.180
peak=    3.477 closest distance to " O   HOH Z  64 " =    2.161
peak=    3.477 closest distance to " O   HOH Z 265 " =    2.244
peak=    3.477 closest distance to " CE  LYS A 119 " =    1.133
peak=    3.473 closest distance to " O   HOH Z 173 " =    2.205
peak=    3.467 closest distance to " O   HOH Z 258 " =    2.262
peak=    3.461 closest distance to " O   HOH Z 183 " =    1.510
peak=    3.445 closest distance to " O   ASN A  74 " =    1.624
peak=    3.444 closest distance to " O   HOH Z 281 " =    4.582
peak=    3.443 closest distance to " O   HOH Z 336 " =    1.632
peak=    3.442 closest distance to " CA  ASP A 140 " =    1.157
peak=    3.439 closest distance to " O   HOH Z  97 " =    2.535
peak=    3.437 closest distance to " O   HOH Z 303 " =    2.135
peak=    3.435 closest distance to " O   HOH Z 435 " =    2.923
peak=    3.435 closest distance to " O   HOH Z 427 " =    3.020
peak=    3.435 closest distance to " O   HOH Z  66 " =    2.131
peak=    3.434 closest distance to " CB  ALA A 291 " =    1.342
peak=    3.433 closest distance to " O   HOH Z 380 " =    1.837
peak=    3.430 closest distance to " CE1 HIS A 115 " =    3.737
peak=    3.430 closest distance to " O   HOH Z 299 " =    4.401
peak=    3.425 closest distance to " CE  LYS A  76 " =    0.840
peak=    3.424 closest distance to " NZ  LYS A 166 " =    2.981
peak=    3.423 closest distance to " O   HOH Z 261 " =    1.790
peak=    3.419 closest distance to " O   HOH Z 185 " =    1.701
peak=    3.417 closest distance to " C   SER A  32 " =    1.053
peak=    3.410 closest distance to " O   HOH Z  39 " =    0.895
peak=    3.408 closest distance to " CB  TRP A 266 " =    0.943
peak=    3.400 closest distance to " O   HOH Z 128 " =    2.166
peak=    3.398 closest distance to " CA  THR A 221 " =    1.310
peak=    3.396 closest distance to " O   HOH Z 408 " =    1.518
peak=    3.391 closest distance to " O   THR A 251 " =    1.189
peak=    3.385 closest distance to " CG2BVAL A  41 " =    0.854
peak=    3.384 closest distance to " O   HOH Z 123 " =    2.110
peak=    3.383 closest distance to " NH2AARG A 275 " =    3.617
peak=    3.375 closest distance to " CD1 LEU A  96 " =    0.718
peak=    3.371 closest distance to " CA  LEU A  83 " =    1.291
peak=    3.369 closest distance to " CB  ALA A 100 " =    1.258
peak=    3.368 closest distance to " O   HOH Z 295 " =    1.560
peak=    3.364 closest distance to " CD1 ILE A 106 " =    0.884
peak=    3.363 closest distance to " CA  ALA A 291 " =    0.879
peak=    3.362 closest distance to " O   HOH Z 358 " =    1.988
peak=    3.358 closest distance to " CA  ALA A  84 " =    1.192
peak=    3.355 closest distance to " O   HOH Z 261 " =    1.642
peak=    3.353 closest distance to " ND1 HIS A  81 " =    1.550
peak=    3.352 closest distance to " O   HOH Z  88 " =    3.255
peak=    3.351 closest distance to " O   HOH Z 145 " =    2.346
peak=    3.346 closest distance to " O   HOH Z 286 " =    2.152
peak=    3.345 closest distance to " OH  TYR A 116 " =    1.139
peak=    3.339 closest distance to " O   HOH Z 197 " =    2.129
peak=    3.336 closest distance to " O   HOH Z 282 " =    2.126
peak=    3.330 closest distance to " O   HOH Z 437 " =    1.455
peak=    3.321 closest distance to " CB  TYR A 116 " =    1.010
peak=    3.318 closest distance to " OE1 GLN A  11 " =    1.999
peak=    3.314 closest distance to " CA  ALA A 295 " =    1.158
peak=    3.312 closest distance to " CB  ASN A 187 " =    1.251
peak=    3.312 closest distance to " O   HOH Z 109 " =    2.394
peak=    3.302 closest distance to " O   ASP A 124 " =    1.600
peak=    3.301 closest distance to " O   HOH Z 305 " =    3.650
peak=    3.299 closest distance to " O   HOH Z 197 " =    2.431
peak=    3.297 closest distance to " CB  TYR A 169 " =    0.886
peak=    3.290 closest distance to " CA  LYS A 166 " =    1.338
peak=    3.289 closest distance to " O   HOH Z  19 " =    1.685
peak=    3.285 closest distance to " CB  ASN A 148 " =    1.983
peak=    3.284 closest distance to " OG BSER A 134 " =    2.897
peak=    3.283 closest distance to " CA  VAL A  41 " =    0.898
peak=    3.280 closest distance to " O   HOH Z 255 " =    1.704
peak=    3.278 closest distance to " O   HOH Z 162 " =    1.672
peak=    3.270 closest distance to " O   HOH Z 150 " =    1.552
peak=    3.268 closest distance to " O   HOH Z 214 " =    1.518
peak=    3.268 closest distance to " CB  THR A 157 " =    1.012
peak=    3.268 closest distance to " O   TRP A 274 " =    1.973
peak=    3.261 closest distance to " CB  ALA A  71 " =    1.279
peak=    3.259 closest distance to " CG  MET A 185 " =    1.151
peak=    3.252 closest distance to " O   HOH Z 411 " =    1.697
peak=    3.250 closest distance to " O   HOH Z 409 " =    3.201
peak=    3.244 closest distance to " O   HOH Z  19 " =    1.378
peak=    3.243 closest distance to " NZ  LYS A  48 " =    1.283
peak=    3.242 closest distance to " O   SER A  26 " =    1.599
peak=    3.241 closest distance to " O   HOH Z 438 " =    2.223
peak=    3.238 closest distance to " CG2 VAL A  78 " =    0.930
peak=    3.236 closest distance to " CG AARG A 275 " =    1.108
peak=    3.229 closest distance to " O   HOH Z 359 " =    1.388
peak=    3.229 closest distance to " O   HOH Z 189 " =    2.746
peak=    3.225 closest distance to " NH1AARG A 145 " =    1.236
peak=    3.221 closest distance to " CD  ARG A 195 " =    0.889
peak=    3.212 closest distance to " CG2 THR A 220 " =    0.769
peak=    3.208 closest distance to " CD2 TYR A  30 " =    0.924
peak=    3.203 closest distance to " CA  ARG A  66 " =    0.947
peak=    3.199 closest distance to " CB  ASN A 215 " =    1.159
peak=    3.198 closest distance to " CD BLYS A 290 " =    1.057
peak=    3.195 closest distance to " CA  TYR A 116 " =    1.321
peak=    3.193 closest distance to " O   HOH Z  88 " =    3.090
peak=    3.192 closest distance to " O   HOH Z 425 " =    2.091
peak=    3.192 closest distance to " CB  MET A 105 " =    1.102
peak=    3.191 closest distance to " CB  ASN A 285 " =    0.915
peak=    3.183 closest distance to " O   HOH Z 394 " =    1.702
peak=    3.180 closest distance to " CA  VAL A 125 " =    1.249
peak=    3.178 closest distance to " CG  PRO A  54 " =    1.227
peak=    3.175 closest distance to " CB  VAL A 265 " =    1.260
peak=    3.170 closest distance to " CB  ILE A 120 " =    1.257
peak=    3.169 closest distance to " O   HOH Z 325 " =    1.994
peak=    3.169 closest distance to " CG2 VAL A 257 " =    0.757
peak=    3.167 closest distance to " O   HOH Z   1 " =    2.528
peak=    3.165 closest distance to " CG1 VAL A 174 " =    1.275
peak=    3.163 closest distance to " O   HOH Z  89 " =    2.131
peak=    3.159 closest distance to " CG BARG A 102 " =    1.835
peak=    3.156 closest distance to " CD2 HIS A  81 " =    1.109
peak=    3.149 closest distance to " O   HOH Z 393 " =    3.376
peak=    3.148 closest distance to " CB  THR A  52 " =    0.933
peak=    3.134 closest distance to " O   HOH Z  73 " =    2.048
peak=    3.133 closest distance to " CG  LYS A  76 " =    1.098
peak=    3.124 closest distance to " CA  GLY A 241 " =    0.861
peak=    3.121 closest distance to " O   HOH Z 423 " =    3.338
peak=    3.117 closest distance to " N   CYS A 260 " =    0.783
peak=    3.116 closest distance to " CB  SER A  26 " =    1.678
peak=    3.115 closest distance to " CA  ASP A 124 " =    0.707
peak=    3.102 closest distance to " CA  ASN A 215 " =    1.146
peak=    3.098 closest distance to " CD  GLN A 240 " =    1.371
peak=    3.082 closest distance to " CB  ALA A   9 " =    1.547
peak=    3.078 closest distance to " CA  GLY A  80 " =    0.864
peak=    3.076 closest distance to " O   HOH Z 425 " =    1.207
peak=    3.074 closest distance to " O   HOH Z 128 " =    1.753
peak=    3.074 closest distance to " O   HOH Z  61 " =    1.514
peak=    3.067 closest distance to " CA  MET A 105 " =    1.115
peak=    3.064 closest distance to " O   HOH Z  63 " =    2.202
peak=    3.063 closest distance to " O   HOH Z 414 " =    1.664
peak=    3.053 closest distance to " O   HOH Z  10 " =    1.766
peak=    3.050 closest distance to " OG BSER A 258 " =    3.465
peak=    3.036 closest distance to " O   HOH Z  47 " =    2.244
peak=    3.028 closest distance to " O   HOH Z 387 " =    2.510

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 223         
Filter by distance & map next to the model:
   mapped sites are within: 0.885 - 5.900
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 221 from: 223
   mapped sites are within: 0.885 - 5.900

peak=   -5.089 closest distance to " O   HOH Z 266 " =    4.626
peak=   -4.478 closest distance to " CD  ARG A 156 " =    2.044
peak=   -4.425 closest distance to " OXT GLY A 302 " =    2.776
peak=   -4.341 closest distance to " O   PRO A 163 " =    2.144
peak=   -4.334 closest distance to " O   HOH Z  13 " =    1.661
peak=   -4.214 closest distance to " CD1 LEU A 101 " =    2.479
peak=   -4.131 closest distance to " O   HOH Z 165 " =    1.999
peak=   -4.119 closest distance to " N   ALA A  43 " =    2.814
peak=   -4.113 closest distance to " O   VAL A  67 " =    2.737
peak=   -4.090 closest distance to " O   HOH Z 292 " =    4.614
peak=   -4.048 closest distance to " C   HIS A 108 " =    1.126
peak=   -4.013 closest distance to " O   HOH Z   5 " =    1.585
peak=   -3.999 closest distance to " O   VAL A  67 " =    2.858
peak=   -3.986 closest distance to " O   HOH Z 210 " =    0.885
peak=   -3.985 closest distance to " CE2 TYR A  30 " =    2.685
peak=   -3.975 closest distance to " OG  SER A  97 " =    2.101
peak=   -3.931 closest distance to " SG  CYS A 254 " =    3.393
peak=   -3.919 closest distance to " CD  GLN A  58 " =    1.165
peak=   -3.917 closest distance to " O   HOH Z 377 " =    2.107
peak=   -3.885 closest distance to " CB  PRO A 243 " =    2.666
peak=   -3.876 closest distance to " CG  ASP A 132 " =    2.386
peak=   -3.876 closest distance to " O   HOH Z 407 " =    3.287
peak=   -3.856 closest distance to " CA  ASP A 298 " =    1.038
peak=   -3.833 closest distance to " CD1 PHE A 130 " =    2.354
peak=   -3.820 closest distance to " O   HOH Z 394 " =    1.520
peak=   -3.819 closest distance to " O   HOH Z 166 " =    1.847
peak=   -3.807 closest distance to " OG  SER A  62 " =    1.550
peak=   -3.781 closest distance to " O   HOH Z 353 " =    2.271
peak=   -3.778 closest distance to " O   PRO A 198 " =    1.342
peak=   -3.776 closest distance to " O   TRP A  92 " =    1.898
peak=   -3.750 closest distance to " O   HOH Z 372 " =    2.475
peak=   -3.726 closest distance to " N   SER A 276 " =    1.484
peak=   -3.719 closest distance to " CB  ALA A 291 " =    2.334
peak=   -3.707 closest distance to " O   HOH Z 150 " =    2.254
peak=   -3.705 closest distance to " OG BSER A 210 " =    2.235
peak=   -3.699 closest distance to " CD1 PHE A  59 " =    1.951
peak=   -3.693 closest distance to " C   SER A 206 " =    1.557
peak=   -3.690 closest distance to " O   ALA A   1 " =    1.993
peak=   -3.685 closest distance to " O   HOH Z 234 " =    4.163
peak=   -3.669 closest distance to " OE1 GLN A 223 " =    2.243
peak=   -3.666 closest distance to " CG2 ILE A 263 " =    2.260
peak=   -3.657 closest distance to " CD  GLN A 223 " =    1.372
peak=   -3.652 closest distance to " CH2 TRP A 179 " =    1.243
peak=   -3.652 closest distance to " O   SER A 210 " =    1.893
peak=   -3.652 closest distance to " NH2 ARG A  66 " =    1.665
peak=   -3.646 closest distance to " ND2 ASN A 187 " =    1.505
peak=   -3.641 closest distance to " CD2 LEU A 237 " =    2.611
peak=   -3.638 closest distance to " CD1 LEU A  25 " =    2.461
peak=   -3.625 closest distance to " O   PHE A 218 " =    1.512
peak=   -3.624 closest distance to " O   HOH Z 196 " =    2.043
peak=   -3.622 closest distance to " CD1 LEU A 228 " =    2.228
peak=   -3.616 closest distance to " O   HOH Z  71 " =    1.757
peak=   -3.611 closest distance to " O   HOH Z 126 " =    1.997
peak=   -3.603 closest distance to " O   ILE A 109 " =    2.619
peak=   -3.595 closest distance to " O   HOH Z 283 " =    2.054
peak=   -3.595 closest distance to " OD1 ASN A  39 " =    2.235
peak=   -3.591 closest distance to " OD1 ASN A 148 " =    1.598
peak=   -3.587 closest distance to " CD2 LEU A 300 " =    2.888
peak=   -3.582 closest distance to " C   THR A 279 " =    1.172
peak=   -3.579 closest distance to " CG2 VAL A 189 " =    2.201
peak=   -3.565 closest distance to " CB  PHE A 208 " =    2.308
peak=   -3.555 closest distance to " CG  ASP A 231 " =    0.905
peak=   -3.554 closest distance to " O   HOH Z 377 " =    1.394
peak=   -3.538 closest distance to " ND2 ASN A  45 " =    1.751
peak=   -3.529 closest distance to " C   ASN A 285 " =    2.374
peak=   -3.528 closest distance to " OG  SER A   3 " =    1.756
peak=   -3.524 closest distance to " O   HOH Z 166 " =    1.913
peak=   -3.521 closest distance to " OD1 ASP A 191 " =    1.716
peak=   -3.518 closest distance to " O   GLY A 196 " =    1.018
peak=   -3.518 closest distance to " CD  ARG A 139 " =    1.627
peak=   -3.506 closest distance to " CB  ASP A 286 " =    2.060
peak=   -3.504 closest distance to " N   THR A  52 " =    1.699
peak=   -3.500 closest distance to " N   ALA A 248 " =    1.750
peak=   -3.500 closest distance to " N   GLN A  58 " =    1.553
peak=   -3.498 closest distance to " CG  GLU A  53 " =    1.444
peak=   -3.492 closest distance to " O   VAL A 125 " =    2.184
peak=   -3.490 closest distance to " CA  GLY A 133 " =    2.351
peak=   -3.490 closest distance to " ND2 ASN A  45 " =    1.070
peak=   -3.482 closest distance to " O   ASN A 187 " =    1.534
peak=   -3.479 closest distance to " OG BSER A 134 " =    1.262
peak=   -3.477 closest distance to " C   LEU A 143 " =    1.078
peak=   -3.471 closest distance to " NH2 ARG A  66 " =    5.464
peak=   -3.468 closest distance to " OH  TYR A 169 " =    1.006
peak=   -3.458 closest distance to " O   HOH Z 118 " =    3.587
peak=   -3.457 closest distance to " ND2 ASN A 249 " =    2.334
peak=   -3.451 closest distance to " N   THR A 235 " =    1.349
peak=   -3.441 closest distance to " O   HOH Z 290 " =    1.082
peak=   -3.438 closest distance to " O   HOH Z  52 " =    1.647
peak=   -3.433 closest distance to " O   HOH Z  90 " =    3.093
peak=   -3.423 closest distance to " C   GLY A  80 " =    2.538
peak=   -3.423 closest distance to " CG1 VAL A 112 " =    2.587
peak=   -3.421 closest distance to " O   HOH Z   6 " =    1.707
peak=   -3.418 closest distance to " CB  PHE A 192 " =    1.921
peak=   -3.417 closest distance to " O   HOH Z  15 " =    1.467
peak=   -3.408 closest distance to " OG BSER A 210 " =    1.274
peak=   -3.406 closest distance to " OE2 GLU A   2 " =    1.608
peak=   -3.398 closest distance to " O   VAL A 189 " =    2.603
peak=   -3.395 closest distance to " CD2 LEU A 167 " =    1.740
peak=   -3.391 closest distance to " CD1 TRP A 179 " =    1.165
peak=   -3.388 closest distance to " CZ  PHE A  38 " =    1.934
peak=   -3.386 closest distance to " NH1 ARG A 195 " =    2.592
peak=   -3.383 closest distance to " CB  ALA A  43 " =    2.468
peak=   -3.379 closest distance to " O   HOH Z 198 " =    2.112
peak=   -3.378 closest distance to " O   ALA A  34 " =    2.324
peak=   -3.377 closest distance to " O   HOH Z 171 " =    2.137
peak=   -3.377 closest distance to " C   ALA A 158 " =    1.330
peak=   -3.372 closest distance to " O   HOH Z 197 " =    2.042
peak=   -3.368 closest distance to " O   HOH Z  93 " =    1.684
peak=   -3.361 closest distance to " ND2 ASN A  69 " =    1.629
peak=   -3.359 closest distance to " O   ALA A 160 " =    1.430
peak=   -3.354 closest distance to " CG  PRO A 243 " =    1.709
peak=   -3.351 closest distance to " O   HOH Z 145 " =    1.998
peak=   -3.348 closest distance to " N   ALA A 248 " =    2.108
peak=   -3.346 closest distance to " CG  LYS A 119 " =    2.932
peak=   -3.345 closest distance to " CG1 VAL A 112 " =    2.773
peak=   -3.343 closest distance to " O   HOH Z 111 " =    1.727
peak=   -3.341 closest distance to " O   HOH Z  11 " =    1.888
peak=   -3.336 closest distance to " NE2 GLN A  88 " =    1.832
peak=   -3.333 closest distance to " O   VAL A 174 " =    2.200
peak=   -3.329 closest distance to " O   HOH Z 311 " =    3.632
peak=   -3.328 closest distance to " OG  SER A  26 " =    1.418
peak=   -3.327 closest distance to " CD  ARG A 195 " =    5.063
peak=   -3.325 closest distance to " O   HOH Z 185 " =    2.447
peak=   -3.321 closest distance to " CD  LYS A 289 " =    2.352
peak=   -3.313 closest distance to " O   HOH Z 393 " =    1.586
peak=   -3.308 closest distance to " O   HOH Z 150 " =    1.962
peak=   -3.305 closest distance to " CZ  TYR A 169 " =    1.857
peak=   -3.302 closest distance to " O   HOH Z  90 " =    2.091
peak=   -3.298 closest distance to " CZ3 TRP A 274 " =    2.424
peak=   -3.298 closest distance to " O   HOH Z 414 " =    1.750
peak=   -3.291 closest distance to " O   HOH Z 396 " =    1.707
peak=   -3.284 closest distance to " CD2 PHE A 225 " =    1.282
peak=   -3.281 closest distance to " O   HOH Z  41 " =    2.307
peak=   -3.275 closest distance to " O   HOH Z 418 " =    1.386
peak=   -3.275 closest distance to " CB  ALA A 248 " =    2.185
peak=   -3.274 closest distance to " O   PRO A 198 " =    1.332
peak=   -3.273 closest distance to " NH2 ARG A 159 " =    2.394
peak=   -3.269 closest distance to " CA  GLY A  98 " =    2.158
peak=   -3.265 closest distance to " OD2 ASP A 171 " =    2.295
peak=   -3.263 closest distance to " N   ALA A 226 " =    2.024
peak=   -3.262 closest distance to " CE  MET A  93 " =    1.212
peak=   -3.261 closest distance to " CD1 LEU A 167 " =    2.160
peak=   -3.260 closest distance to " N   LEU A 281 " =    1.762
peak=   -3.259 closest distance to " CD  PRO A 213 " =    2.203
peak=   -3.258 closest distance to " O   SER A 135 " =    1.595
peak=   -3.256 closest distance to " O   HOH Z  17 " =    1.364
peak=   -3.253 closest distance to " O   ALA A  10 " =    1.776
peak=   -3.250 closest distance to " O   HOH Z 252 " =    3.467
peak=   -3.249 closest distance to " NH2 ARG A  79 " =    2.025
peak=   -3.244 closest distance to " CD  ARG A  36 " =    1.866
peak=   -3.243 closest distance to " O   HOH Z 350 " =    2.127
peak=   -3.242 closest distance to " CB  ALA A  10 " =    2.170
peak=   -3.240 closest distance to " CE BMET A  47 " =    2.125
peak=   -3.236 closest distance to " O   HOH Z  43 " =    1.573
peak=   -3.229 closest distance to " O   LEU A 167 " =    1.573
peak=   -3.225 closest distance to " CA  GLY A 203 " =    2.252
peak=   -3.221 closest distance to " CB  SER A 245 " =    2.025
peak=   -3.220 closest distance to " O   HOH Z  97 " =    1.574
peak=   -3.218 closest distance to " O   HOH Z 417 " =    2.715
peak=   -3.212 closest distance to " O   HOH Z 252 " =    4.053
peak=   -3.211 closest distance to " NH2 ARG A  66 " =    5.699
peak=   -3.210 closest distance to " O   HOH Z 426 " =    1.726
peak=   -3.209 closest distance to " OG BSER A 134 " =    1.846
peak=   -3.205 closest distance to " CE  MET A 105 " =    2.126
peak=   -3.202 closest distance to " ND2 ASN A  60 " =    1.594
peak=   -3.195 closest distance to " CD2 LEU A 237 " =    2.680
peak=   -3.187 closest distance to " O   HOH Z 351 " =    1.474
peak=   -3.186 closest distance to " NE2 GLN A  58 " =    1.095
peak=   -3.182 closest distance to " N   VAL A 189 " =    1.736
peak=   -3.182 closest distance to " CE3 TRP A 150 " =    2.146
peak=   -3.182 closest distance to " O   HOH Z 265 " =    2.191
peak=   -3.181 closest distance to " O   HOH Z  78 " =    1.747
peak=   -3.176 closest distance to " CG  GLN A  58 " =    1.107
peak=   -3.174 closest distance to " CB  TRP A  85 " =    2.399
peak=   -3.170 closest distance to " OD2 ASP A 171 " =    1.868
peak=   -3.167 closest distance to " OG ASER A 134 " =    1.237
peak=   -3.164 closest distance to " O   ALA A  34 " =    2.046
peak=   -3.163 closest distance to " OD1 ASP A 171 " =    1.610
peak=   -3.160 closest distance to " O   HOH Z 361 " =    3.412
peak=   -3.154 closest distance to " NE2 GLN A 194 " =    1.778
peak=   -3.154 closest distance to " CA  GLY A 133 " =    2.040
peak=   -3.153 closest distance to " CD2 HIS A 207 " =    2.430
peak=   -3.152 closest distance to " O   GLY A 118 " =    2.406
peak=   -3.150 closest distance to " CG1 VAL A  78 " =    2.617
peak=   -3.148 closest distance to " O   ASN A 301 " =    1.281
peak=   -3.148 closest distance to " O   SER A  26 " =    1.352
peak=   -3.148 closest distance to " CD2 HIS A 115 " =    1.092
peak=   -3.148 closest distance to " CA  VAL A 197 " =    0.952
peak=   -3.146 closest distance to " CB  ALA A   9 " =    2.542
peak=   -3.146 closest distance to " O   MET A  40 " =    2.723
peak=   -3.145 closest distance to " O   HOH Z 123 " =    2.298
peak=   -3.140 closest distance to " NH1 ARG A  66 " =    3.561
peak=   -3.136 closest distance to " CG  PRO A 163 " =    2.665
peak=   -3.134 closest distance to " O   HOH Z  37 " =    1.830
peak=   -3.131 closest distance to " CB  CYS A 254 " =    2.537
peak=   -3.128 closest distance to " O   HOH Z 191 " =    5.900
peak=   -3.127 closest distance to " O   HOH Z 384 " =    2.158
peak=   -3.126 closest distance to " CE  MET A 105 " =    1.906
peak=   -3.124 closest distance to " ND2 ASN A  60 " =    1.609
peak=   -3.122 closest distance to " O   SER A   3 " =    1.179
peak=   -3.121 closest distance to " CB  PRO A 163 " =    2.700
peak=   -3.118 closest distance to " O   HOH Z 149 " =    1.884
peak=   -3.116 closest distance to " O   HOH Z 174 " =    2.169
peak=   -3.104 closest distance to " O   HOH Z 298 " =    2.778
peak=   -3.102 closest distance to " CE3 TRP A  92 " =    2.617
peak=   -3.095 closest distance to " NE2 GLN A 223 " =    1.345
peak=   -3.091 closest distance to " C   ALA A 242 " =    1.958
peak=   -3.088 closest distance to " O   HOH Z 128 " =    2.542
peak=   -3.087 closest distance to " O   ILE A 234 " =    1.309
peak=   -3.085 closest distance to " ND2 ASN A 209 " =    1.538
peak=   -3.078 closest distance to " O   HOH Z 193 " =    1.989
peak=   -3.078 closest distance to " O   HOH Z 280 " =    2.424
peak=   -3.077 closest distance to " NE1 TRP A 266 " =    2.288
peak=   -3.074 closest distance to " CG  ASN A 301 " =    2.026
peak=   -3.073 closest distance to " O   GLY A  80 " =    2.511
peak=   -3.070 closest distance to " O   HOH Z  61 " =    1.609
peak=   -3.067 closest distance to " O   SER A 276 " =    1.672
peak=   -3.065 closest distance to " O   HOH Z 193 " =    1.702
peak=   -3.065 closest distance to " O   HOH Z  91 " =    2.107
peak=   -3.054 closest distance to " O   ALA A  51 " =    1.436
peak=   -3.047 closest distance to " O   HOH Z  77 " =    1.998

================= 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    :  0.4028 0.3916   6.209226e+00   6.179109e+00
   1_bss:  0.3895 0.3773   6.192593e+00   6.155607e+00
   1_xyz:  0.2893 0.3121   5.953191e+00   6.015988e+00
   1_adp:  0.2637 0.3248   5.902338e+00   6.037765e+00
   1_occ:  0.2634 0.3246   5.901739e+00   6.037870e+00
   2_bss:  0.2620 0.3225   5.899449e+00   6.035111e+00
   2_xyz:  0.1898 0.2361   5.589182e+00   5.759596e+00
   2_adp:  0.1717 0.2181   5.509113e+00   5.692191e+00
   2_occ:  0.1716 0.2182   5.508434e+00   5.691812e+00
   3_bss:  0.1710 0.2174   5.505718e+00   5.688153e+00
   3_xyz:  0.1322 0.1763   5.276118e+00   5.494230e+00
   3_adp:  0.1206 0.1680   5.207616e+00   5.445281e+00
   3_occ:  0.1206 0.1679   5.207236e+00   5.444907e+00
   4_bss:  0.1210 0.1677   5.207414e+00   5.443295e+00
   4_xyz:  0.1174 0.1634   5.188772e+00   5.426358e+00
   4_adp:  0.1163 0.1625   5.179572e+00   5.418235e+00
   4_occ:  0.1163 0.1626   5.179448e+00   5.418269e+00
   5_bss:  0.1162 0.1626   5.179511e+00   5.418422e+00
   5_xyz:  0.1110 0.1601   5.148914e+00   5.399375e+00
   5_adp:  0.1103 0.1593   5.144319e+00   5.395661e+00
   5_occ:  0.1103 0.1594   5.144310e+00   5.395884e+00
   5_bss:  0.1102 0.1593   5.144489e+00   5.396006e+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:  0.298  26.349  -3.335   5.080  -0.813   0.000  -0.000  -0.000
   1_xyz:  0.298  26.349  -3.335   5.080  -0.813   0.000  -0.000  -0.000
   1_adp:  0.298  26.349  -3.335   5.080  -0.813   0.000  -0.000  -0.000
   1_occ:  0.298  26.349  -3.335   5.080  -0.813   0.000  -0.000  -0.000
   2_bss:  0.312  49.611  -2.332   2.167  -0.724   0.000  -0.000  -0.000
   2_xyz:  0.312  49.611  -2.332   2.167  -0.724   0.000  -0.000  -0.000
   2_adp:  0.312  49.611  -2.332   2.167  -0.724   0.000  -0.000  -0.000
   2_occ:  0.312  49.611  -2.332   2.167  -0.724   0.000  -0.000  -0.000
   3_bss:  0.318  54.371  -2.155   0.168  -0.910   0.000  -0.000  -0.000
   3_xyz:  0.318  54.371  -2.155   0.168  -0.910   0.000  -0.000  -0.000
   3_adp:  0.318  54.371  -2.155   0.168  -0.910   0.000  -0.000  -0.000
   3_occ:  0.318  54.371  -2.155   0.168  -0.910   0.000  -0.000  -0.000
   4_bss:  0.326  60.236  -2.111  -0.546  -0.920  -0.000  -0.000  -0.000
   4_xyz:  0.326  60.236  -2.111  -0.546  -0.920  -0.000  -0.000  -0.000
   4_adp:  0.326  60.236  -2.111  -0.546  -0.920  -0.000  -0.000  -0.000
   4_occ:  0.326  60.236  -2.111  -0.546  -0.920  -0.000  -0.000  -0.000
   5_bss:  0.326  60.236  -1.928  -0.604  -0.729  -0.000  -0.000  -0.000
   5_xyz:  0.326  60.236  -1.928  -0.604  -0.729  -0.000  -0.000  -0.000
   5_adp:  0.326  60.236  -1.928  -0.604  -0.729  -0.000  -0.000  -0.000
   5_occ:  0.326  60.236  -1.928  -0.604  -0.729  -0.000  -0.000  -0.000
   5_bss:  0.325  56.158  -1.683  -0.516  -0.485  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.528 0.6027  0.7778    46583.497
   1_bss:  42.314 0.6156  0.7970    42490.313
   1_xyz:  33.882 0.7145  0.8979    27872.312
   1_adp:  35.156 0.6992  0.8682    29605.027
   1_occ:  35.176 0.6989  0.8674    29613.603
   2_bss:  34.685 0.7048  0.8618    29158.562
   2_xyz:  23.678 0.8241  0.9714    14259.916
   2_adp:  21.325 0.8487  0.9799    12234.991
   2_occ:  21.316 0.8488  0.9800    12225.811
   3_bss:  21.138 0.8505  0.9603    12071.829
   3_xyz:  16.498 0.8934  0.9859     7889.000
   3_adp:  15.375 0.9035  0.9823     7171.533
   3_occ:  15.364 0.9036  0.9822     7165.902
   4_bss:  15.321 0.9039  0.9750     7122.958
   4_xyz:  14.864 0.9080  0.9748     6832.583
   4_adp:  14.673 0.9097  0.9674     6755.861
   4_occ:  14.670 0.9097  0.9673     6755.976
   5_bss:  14.670 0.9097  0.9713     6757.486
   5_xyz:  14.291 0.9127  0.9740     6482.862
   5_adp:  14.189 0.9136  0.9669     6439.025
   5_occ:  14.191 0.9136  0.9669     6442.658
   5_bss:  14.193 0.9136  0.9738     6441.979
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6749e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6749e-01
   1_xyz:   1.386  0.011  0.084 15.567  0.005  4.112   9.9046e-02
   1_adp:   1.386  0.011  0.084 15.567  0.005  4.112   9.9046e-02
   1_occ:   1.386  0.011  0.084 15.567  0.005  4.112   9.9046e-02
   2_bss:   1.386  0.011  0.084 15.567  0.005  4.112   9.9046e-02
   2_xyz:   1.254  0.009  0.080 15.056  0.005  4.112   8.2119e-02
   2_adp:   1.254  0.009  0.080 15.056  0.005  4.112   8.2119e-02
   2_occ:   1.254  0.009  0.080 15.056  0.005  4.112   8.2119e-02
   3_bss:   1.254  0.009  0.080 15.056  0.005  4.112   8.2119e-02
   3_xyz:   1.169  0.010  0.080 15.177  0.005  4.123   7.8590e-02
   3_adp:   1.169  0.010  0.080 15.177  0.005  4.123   7.8590e-02
   3_occ:   1.169  0.010  0.080 15.177  0.005  4.123   7.8590e-02
   4_bss:   1.169  0.010  0.080 15.177  0.005  4.123   7.8590e-02
   4_xyz:   0.983  0.007  0.072 14.806  0.004  4.125   5.7310e-02
   4_adp:   0.983  0.007  0.072 14.806  0.004  4.125   5.7310e-02
   4_occ:   0.983  0.007  0.072 14.806  0.004  4.125   5.7310e-02
   5_bss:   0.983  0.007  0.072 14.806  0.004  4.125   5.7310e-02
   5_xyz:   1.070  0.008  0.079 15.014  0.004  4.111   6.7168e-02
   5_adp:   1.070  0.008  0.079 15.014  0.004  4.111   6.7168e-02
   5_occ:   1.070  0.008  0.079 15.014  0.004  4.111   6.7168e-02
   5_bss:   1.070  0.008  0.079 15.014  0.004  4.111   6.7168e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4131e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4131e-01
   1_xyz:   9.299  0.074  0.459 86.440  0.034  2.249   9.7319e-02
   1_adp:   9.299  0.074  0.459 86.440  0.034  2.249   9.7319e-02
   1_occ:   9.299  0.074  0.459 86.440  0.034  2.249   9.7319e-02
   2_bss:   9.299  0.074  0.459 86.440  0.034  2.249   9.7319e-02
   2_xyz:   7.463  0.058  0.261 89.319  0.048  2.208   8.7876e-02
   2_adp:   7.463  0.058  0.261 89.319  0.048  2.208   8.7876e-02
   2_occ:   7.463  0.058  0.261 89.319  0.048  2.208   8.7876e-02
   3_bss:   7.463  0.058  0.261 89.319  0.048  2.208   8.7876e-02
   3_xyz:   8.628  0.068  0.264 82.627  0.034  2.303   6.9973e-02
   3_adp:   8.628  0.068  0.264 82.627  0.034  2.303   6.9973e-02
   3_occ:   8.628  0.068  0.264 82.627  0.034  2.303   6.9973e-02
   4_bss:   8.628  0.068  0.264 82.627  0.034  2.303   6.9973e-02
   4_xyz:   6.934  0.036  0.231 82.510  0.035  2.381   3.7228e-02
   4_adp:   6.934  0.036  0.231 82.510  0.035  2.381   3.7228e-02
   4_occ:   6.934  0.036  0.231 82.510  0.035  2.381   3.7228e-02
   5_bss:   6.934  0.036  0.231 82.510  0.035  2.381   3.7228e-02
   5_xyz:   8.206  0.044  0.260 81.650  0.033  2.308   4.8195e-02
   5_adp:   8.206  0.044  0.260 81.650  0.033  2.308   4.8195e-02
   5_occ:   8.206  0.044  0.260 81.650  0.033  2.308   4.8195e-02
   5_bss:   8.206  0.044  0.260 81.650  0.033  2.308   4.8195e-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:  90.06   0.00  17.48  84.53   0.00  13.97  90.06   2.25  36.58
   1_occ:  90.06   0.00  17.48  84.53   0.00  13.97  90.06   2.25  36.58
   2_bss:  90.06   0.00  17.48  84.53   0.00  13.97  90.06   2.25  36.58
   2_xyz:  90.06   0.00  17.48  84.53   0.00  13.97  90.06   2.25  36.58
   2_adp:  87.54   0.00  16.96  80.53   0.00  13.11  87.54   4.55  37.93
   2_occ:  87.54   0.00  16.96  80.53   0.00  13.11  87.54   4.55  37.93
   3_bss:  87.54   0.00  16.96  80.53   0.00  13.11  87.54   4.55  37.93
   3_xyz:  87.54   0.00  16.96  80.53   0.00  13.11  87.54   4.55  37.93
   3_adp:  95.27   0.40  17.24  94.39   0.40  12.68  95.27   5.30  42.09
   3_occ:  95.27   0.40  17.24  94.39   0.40  12.68  95.27   5.30  42.09
   4_bss:  95.27   0.40  17.24  94.39   0.40  12.68  95.27   5.30  42.09
   4_xyz:  95.27   0.40  17.24  94.39   0.40  12.68  95.27   5.30  42.09
   4_adp:  99.75   0.00  16.92  99.75   0.00  12.39  94.85   5.12  41.61
   4_occ:  99.75   0.00  16.92  99.75   0.00  12.39  94.85   5.12  41.61
   5_bss:  99.75   0.00  16.92  99.75   0.00  12.39  94.85   5.12  41.61
   5_xyz:  99.75   0.00  16.92  99.75   0.00  12.39  94.85   5.12  41.61
   5_adp: 108.01   0.00  16.55 108.01   0.00  12.13  93.12   4.85  40.60
   5_occ: 108.01   0.00  16.55 108.01   0.00  12.13  93.12   4.85  40.60
   5_bss: 108.01   0.00  16.55 108.01   0.00  12.14  93.12   4.86  40.61
------------------------------------------------------------------------
 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:    1.789    0.005    0.323
   1_adp:    1.789    0.005    0.323
   1_occ:    1.789    0.005    0.323
   2_bss:    1.789    0.005    0.323
   2_xyz:    1.233    0.042    0.516
   2_adp:    1.233    0.042    0.516
   2_occ:    1.233    0.042    0.516
   3_bss:    1.233    0.042    0.516
   3_xyz:    1.291    0.075    0.621
   3_adp:    1.291    0.075    0.621
   3_occ:    1.291    0.075    0.621
   4_bss:    1.291    0.075    0.621
   4_xyz:    1.285    0.026    0.634
   4_adp:    1.285    0.026    0.634
   4_occ:    1.285    0.026    0.634
   5_bss:    1.285    0.026    0.634
   5_xyz:    1.308    0.076    0.654
   5_adp:    1.308    0.076    0.654
   5_occ:    1.308    0.076    0.654
   5_bss:    1.308    0.076    0.654
------------------------------------------------------------------------

CPU time actual refinement: 345.08


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_586/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_586/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_586/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_586/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_586/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 344.95 
  Macro-tasks:
    bulk solvent and scale       = 41.11  
    individual site refinement   = 150.37 
    weights calculation          = 29.17  
    collect and process          = 6.57   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 227.31 
  Micro-tasks:
    mask                            = 1.72   
    f_calc                          = 111.91 
    alpha_beta                      = 8.15   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 117.76 
    fmodel                         = 7.10   
    r_factors                      = 0.15   
    phase_errors                   = 11.62  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 259.81 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.782 micro seconds
Total CPU time: 5.97 minutes
from_scatterers_fft:    658 calls, 111.40 s
gradients_fft:          603 calls, 105.32 s

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

# Date 2008-01-16 Time 05:11:18 PST -0800 (1200489078.11 s)
Start R-work = 0.4028, R-free = 0.3916 (no bulk solvent and anisotropic scale)
Final R-work = 0.1293, R-free = 0.1758 (no bulk solvent and anisotropic scale)

Start R-work = 0.3895, R-free = 0.3773
Final R-work = 0.1102, R-free = 0.1593